#!/bin/bash ########################################################################################### ########################################################################################### ########################################################################################### allcrystals="alphaquartz anatase aucu bcc bcc_c bct betaquartz betatin cdi2 cristobalite cscl cubiclaves cuprite dhcp diamond diamond_c fcc fcc_c fluorite graphite hcp hexagonallaves molybdenite nacl nickeline pyrite rutile sc tridymite wurtzite x2o3 x2o5 xo3 zincblende" allcrystals_supercells="sup_alphaquartz sup_anatase sup_aucu sup_bcc sup_bcc_c sup_bct sup_betaquartz sup_betatin sup_cdi2 sup_cristobalite sup_cscl sup_cubiclaves sup_cuprite sup_dhcp sup_diamond sup_diamond_c sup_fcc sup_fcc_c sup_fluorite sup_graphite sup_hcp sup_hexagonallaves sup_molybdenite sup_nacl sup_nickeline sup_pyrite sup_rutile sup_sc sup_tridymite sup_wurtzite sup_x2o3 sup_x2o5 sup_xo3 sup_zincblende" allsurfaces="bcc_100 bcc_110 bcc_111 diamond_100 fcc_100 fcc_110 fcc_111 hcp_001 hcp_100" allsurfaces_supercells="sup_bcc_100 sup_bcc_110 sup_bcc_111 sup_diamond_100 sup_fcc_100 sup_fcc_110 sup_fcc_111 sup_hcp_001 sup_hcp_100" allmolecules="bent_mol diatomic_mol linear_mol monatomic_mol" allmolecules_supercells="" TOTALTIME=0 ANERROROCCURED=false ALLPOTCARS=/home/ws2006/potcars ########################################################################################### ########################################################################################### ########################################################################################### alphaquartz () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=9 ATOMS_PER_SUBCELL=9 NUMBER_OF_SHIFTS=4 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="3 6" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_alphaquartz=1.10009 SHIFT_alphaquartz_1=0.46990 SHIFT_alphaquartz_2=0.41410 SHIFT_alphaquartz_3=0.26810 SHIFT_alphaquartz_4=0.78540 } EOF if [ -z $C_A_RATIO_alphaquartz ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_alphaquartz \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_alphaquartz_1 | bc -l` s2=`echo -$SHIFT_alphaquartz_1 | bc -l` s3=`echo $SHIFT_alphaquartz_2 | bc -l` s4=`echo $SHIFT_alphaquartz_3 | bc -l` s5=`echo $SHIFT_alphaquartz_4 | bc -l` s6=`echo -$SHIFT_alphaquartz_2 | bc -l` s7=`echo -$SHIFT_alphaquartz_3 | bc -l` s8=`echo -$SHIFT_alphaquartz_4 | bc -l` s9=`echo $SHIFT_alphaquartz_2 - $SHIFT_alphaquartz_3 | bc -l` s10=`echo $SHIFT_alphaquartz_3 - $SHIFT_alphaquartz_2 | bc -l` s11=`echo 0.6666666666666666666666 + $SHIFT_alphaquartz_4 | bc -l` s12=`echo 0.3333333333333333333333 + $SHIFT_alphaquartz_4 | bc -l` s13=`echo 0.6666666666666666666666 - $SHIFT_alphaquartz_4 | bc -l` s14=`echo 0.3333333333333333333333 - $SHIFT_alphaquartz_4 | bc -l` cat > POSCAR << EOF alphaquartz crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_alphaquartz $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.6666666666666666666666 | bc -l` x2=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.3333333333333333333333 | bc -l` x3=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x4=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s5 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s7 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s9 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s11 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s10 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s6 | bc -l` z6=`echo $d \* $nz - $d + $d \* $s12 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z7=`echo $d \* $nz - $d + $d \* $s8 | bc -l` x8=`echo $d \* $nx - $d + $d \* $s6 | bc -l` y8=`echo $d \* $ny - $d + $d \* $s10 | bc -l` z8=`echo $d \* $nz - $d + $d \* $s13 | bc -l` x9=`echo $d \* $nx - $d + $d \* $s9 | bc -l` y9=`echo $d \* $ny - $d + $d \* $s7 | bc -l` z9=`echo $d \* $nz - $d + $d \* $s14 | bc -l` echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '9p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_alphaquartz_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_alphaquartz_1=$shift_alphaquartz_1 fi row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_alphaquartz_2=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_alphaquartz_2=$shift_alphaquartz_2 fi row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[1]} shift_alphaquartz_3=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_alphaquartz_3=$shift_alphaquartz_3 fi row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_alphaquartz_4=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_alphaquartz_4=$shift_alphaquartz_4 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### anatase () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_anatase=2.51430 SHIFT_anatase_1=0.08310 } EOF if [ -z $C_A_RATIO_anatase ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_anatase \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_anatase_1 | bc -l` s2=`echo 0.5 + $SHIFT_anatase_1 | bc -l` s3=`echo 0.5 - $SHIFT_anatase_1 | bc -l` s4=`echo 0.25 + $SHIFT_anatase_1 | bc -l` s5=`echo 0.25 - $SHIFT_anatase_1 | bc -l` s6=`echo 0.5 + 2 \* $SHIFT_anatase_1 | bc -l` s7=`echo 0.5 - 2 \* $SHIFT_anatase_1 | bc -l` s8=`echo 1 - 2 \* $SHIFT_anatase_1 | bc -l` s9=`echo 2 \* $SHIFT_anatase_1 | bc -l` cat > POSCAR << EOF anatase crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 $C_A_RATIO_anatase $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.625 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.375 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s5 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s9 | bc -l` x4=`echo $d \* $nx - $d + $d \* -$s4 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s6 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y5=`echo $d \* $ny - $d + $d \* -$s5 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s8 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z6=`echo $d \* $nz - $d + $d \* $s7 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '13p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_anatase_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_anatase_1=$shift_anatase_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### aucu () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_aucu=0.92632 } EOF if [ -z $C_A_RATIO_aucu ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_aucu \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF aucu crystal $SUPERCELL_FACTOR -$v 0.5 -0.5 0 0.5 0.5 0 0 0 $C_A_RATIO_aucu $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### bcc () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_bcc \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF bcc crystal $SUPERCELL_FACTOR -$v -0.5 0.5 0.5 0.5 -0.5 0.5 0.5 0.5 -0.5 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### bcc_c () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_bcc_c \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF bcc_c crystal -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### bct () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_bct=1.41421 } EOF if [ -z $C_A_RATIO_bct ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_bct \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` c=`echo 0.5 \* $C_A_RATIO_bct | bc -l` cat > POSCAR << EOF bct crystal -$v 1 0 0 0 1 0 0.5 0.5 $c $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### betaquartz () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=9 ATOMS_PER_SUBCELL=9 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="3 6" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_betaquartz=1.10020 SHIFT_betaquartz_1=0.42020 } EOF if [ -z $C_A_RATIO_betaquartz ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_betaquartz \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_betaquartz_1 | bc -l` s2=`echo 2 \* $SHIFT_betaquartz_1 | bc -l` s3=`echo -2 \* $SHIFT_betaquartz_1 | bc -l` s4=`echo - $SHIFT_betaquartz_1 | bc -l` cat > POSCAR << EOF betaquartz crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_betaquartz $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.6666666666666666666666 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.3333333333333333333333 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x4=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.1666666666666666666666 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.833333333333333333333 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x8=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y8=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.1666666666666666666666 | bc -l` x9=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y9=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z9=`echo $d \* $nz - $d + $d \* 0.833333333333333333333 | bc -l` echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_betaquartz_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_betaquartz_1=$shift_betaquartz_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### betatin () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_betatin=0.54547 } EOF if [ -z $C_A_RATIO_betatin ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_betatin \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` c=`echo 0.5 \* $C_A_RATIO_betatin | bc -l` cat > POSCAR << EOF betatin crystal -$v 1 0 0 0 1 0 0.5 0.5 $c $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* -0.375 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.375 | bc -l` z2=`echo $d \* $nz - $d + $d \* -0.25 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### cdi2 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=3 ATOMS_PER_SUBCELL=3 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_cdi2=2.44949 SHIFT_cdi2_1=0.16667 } EOF if [ -z $C_A_RATIO_cdi2 ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_cdi2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo 0.5 - $SHIFT_cdi2_1 | bc -l` s2=`echo 0.5 + $SHIFT_cdi2_1 | bc -l` cat > POSCAR << EOF cdi2 crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_cdi2 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z2=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s2 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_cdi2_1=`echo $column \* $SUPERCELL_FACTOR - 0.5 \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_cdi2_1=$shift_cdi2_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### cristobalite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=24 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_cristobalite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF cristobalite crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.125 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.125 | bc -l` x2=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* -0.125 | bc -l` z2=`echo $d \* $nz - $d + $d \* -0.125 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### cscl () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_cscl \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF cscl crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### cubiclaves () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=24 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_cubiclaves \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF cubiclaves crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.125 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.125 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.875 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.875 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.875 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### cuprite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=6 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_cuprite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF cuprite crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### dhcp () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_dhcp=3.26598 } EOF if [ -z $C_A_RATIO_dhcp ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_dhcp \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF dhcp crystal -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_dhcp $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### diamond () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_diamond \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF diamond crystal -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* -0.125 | bc -l` z1=`echo $d \* $nz - $d + $d \* -0.125 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.125 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.125 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### diamond_c () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=8 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="8" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_diamond_c \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF diamond_c crystal -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x7=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y7=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x8=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y8=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### fcc () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_fcc \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF fcc crystal -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### fcc_c () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_fcc_c \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF fcc_c crystal -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### fluorite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=3 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_fluorite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF fluorite crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x3=`echo $d \* $nx - $d + $d \* -0.25 | bc -l` y3=`echo $d \* $ny - $d + $d \* -0.25 | bc -l` z3=`echo $d \* $nz - $d + $d \* -0.25 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### graphite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_graphite=2.00000 } EOF if [ -z $C_A_RATIO_graphite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_graphite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF graphite crystal -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_graphite $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### hcp () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_hcp=1.63299 } EOF if [ -z $C_A_RATIO_hcp ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_hcp \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF hcp crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_hcp $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### hexagonallaves () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=12 NUMBER_OF_SHIFTS=2 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="8 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_hexagonallaves=1.64479 SHIFT_hexagonallaves_1=-0.16988 SHIFT_hexagonallaves_2=0.06681 } EOF if [ -z $C_A_RATIO_hexagonallaves ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_hexagonallaves \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_hexagonallaves_1 | bc -l` s2=`echo 2 \* $SHIFT_hexagonallaves_1 | bc -l` s3=`echo -2 \* $SHIFT_hexagonallaves_1 | bc -l` s4=`echo 0.0 - $SHIFT_hexagonallaves_1 | bc -l` s5=`echo $SHIFT_hexagonallaves_2 | bc -l` s6=`echo -$SHIFT_hexagonallaves_2 | bc -l` s7=`echo 0.5 + $SHIFT_hexagonallaves_2 | bc -l` s8=`echo 0.5 - $SHIFT_hexagonallaves_2 | bc -l` cat > POSCAR << EOF hexagonallaves crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_hexagonallaves $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x8=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y8=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x9=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y9=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z9=`echo $d \* $nz - $d + $d \* $s5 | bc -l` x10=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y10=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z10=`echo $d \* $nz - $d + $d \* $s6 | bc -l` x11=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y11=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z11=`echo $d \* $nz - $d + $d \* $s7 | bc -l` x12=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y12=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z12=`echo $d \* $nz - $d + $d \* $s8 | bc -l` echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_hexagonallaves_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` row=$(sed -n '17p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_hexagonallaves_2=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_hexagonallaves_1=$shift_hexagonallaves_1 SHIFT_hexagonallaves_2=$shift_hexagonallaves_2 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### molybdenite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_molybdenite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=6 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_molybdenite=3.88924 SHIFT_molybdenite_1=0.62000 } EOF if [ -z $C_A_RATIO_molybdenite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_molybdenite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_molybdenite_1 | bc -l` s2=`echo 0.5 + $SHIFT_molybdenite_1 | bc -l` s3=`echo 0.5 - $SHIFT_molybdenite_1 | bc -l` s4=`echo - $SHIFT_molybdenite_1 | bc -l` cat > POSCAR << EOF molybdenite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_molybdenite $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s2 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s3 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z6=`echo $d \* $nz - $d + $d \* $s4 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_molybdenite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_molybdenite_1=$shift_molybdenite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### nacl () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_nacl \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF nacl crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### nickeline () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_nickeline=1.63299 } EOF if [ -z $C_A_RATIO_nickeline ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_nickeline \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF nickeline crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_nickeline $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### pyrite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=12 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 8" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { SHIFT_pyrite_1=0.38600 } EOF if [ -z $SHIFT_pyrite_1 ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_pyrite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_pyrite_1 | bc -l` s2=`echo 0.5 + $SHIFT_pyrite_1 | bc -l` s3=`echo 0.5 - $SHIFT_pyrite_1 | bc -l` cat > POSCAR << EOF pyrite crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x6=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y6=`echo $d \* $ny - $d + $d \* -$s1 | bc -l` z6=`echo $d \* $nz - $d + $d \* -$s1 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z7=`echo $d \* $nz - $d + $d \* -$s1 | bc -l` x8=`echo $d \* $nx - $d + $d \* -$s2 | bc -l` y8=`echo $d \* $ny - $d + $d \* -$s3 | bc -l` z8=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x9=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y9=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z9=`echo $d \* $nz - $d + $d \* $s3 | bc -l` x10=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y10=`echo $d \* $ny - $d + $d \* -$s2 | bc -l` z10=`echo $d \* $nz - $d + $d \* -$s3 | bc -l` x11=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y11=`echo $d \* $ny - $d + $d \* -$s1 | bc -l` z11=`echo $d \* $nz - $d + $d \* $s2 | bc -l` x12=`echo $d \* $nx - $d + $d \* -$s3 | bc -l` y12=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z12=`echo $d \* $nz - $d + $d \* -$s2 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '13p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_pyrite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_pyrite_1=$shift_pyrite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### rutile () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=6 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_rutile=0.64395 SHIFT_rutile_1=0.30530 } EOF if [ -z $C_A_RATIO_rutile ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_rutile \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_rutile_1 | bc -l` s2=`echo 0.5 + $SHIFT_rutile_1 | bc -l` s3=`echo 0.5 - $SHIFT_rutile_1 | bc -l` cat > POSCAR << EOF rutile crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 $C_A_RATIO_rutile $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x4=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y4=`echo $d \* $ny - $d + $d \* -$s1 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_rutile_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_rutile_1=$shift_rutile_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sc () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=1 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sc \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sc crystal -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### tridymite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=12 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 8" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_tridymite=1.63698 SHIFT_tridymite_1=0.06200 } EOF if [ -z $C_A_RATIO_tridymite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_tridymite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_tridymite_1 | bc -l` s2=`echo -$SHIFT_tridymite_1 | bc -l` s3=`echo 0.5 + $SHIFT_tridymite_1 | bc -l` s4=`echo 0.5 - $SHIFT_tridymite_1 | bc -l` cat > POSCAR << EOF tridymite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_tridymite $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* $s2 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s3 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s4 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x7=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y7=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x8=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y8=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x9=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y9=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z9=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x10=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y10=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z10=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x11=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y11=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z11=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x12=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y12=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z12=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '9p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_tridymite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_tridymite_1=$shift_tridymite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### wurtzite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_wurtzite=1.63299 SHIFT_wurtzite_1=0.37480 } EOF if [ -z $C_A_RATIO_wurtzite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_wurtzite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_wurtzite_1 | bc -l` s2=`echo 0.5 + $SHIFT_wurtzite_1 | bc -l` cat > POSCAR << EOF wurtzite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_wurtzite $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s2 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_wurtzite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_wurtzite_1=$shift_wurtzite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### x2o3 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=10 ATOMS_PER_SUBCELL=10 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 6" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_x2o3 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF x2o3 crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### x2o5 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=14 ATOMS_PER_SUBCELL=14 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 10" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_x2o5 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF x2o5 crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x7=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y7=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x8=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y8=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x9=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y9=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z9=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x10=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y10=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z10=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x11=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y11=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z11=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x12=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y12=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z12=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x13=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y13=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z13=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x14=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y14=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z14=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR echo $x13 " " $y13 " " $z13 >> POSCAR echo $x14 " " $y14 " " $z14 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### xo3 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 3" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_xo3 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF xo3 crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### zincblende () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_zincblende \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF zincblende crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_alphaquartz () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_alphaquartz STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=9 ATOMS_PER_SUBCELL=9 NUMBER_OF_SHIFTS=4 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="3 6" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_alphaquartz=1.10009 SHIFT_sup_alphaquartz_1=0.46990 SHIFT_sup_alphaquartz_2=0.41410 SHIFT_sup_alphaquartz_3=0.26810 SHIFT_sup_alphaquartz_4=0.78540 } EOF if [ -z $C_A_RATIO_sup_alphaquartz ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_alphaquartz \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_alphaquartz_1 | bc -l` s2=`echo -$SHIFT_sup_alphaquartz_1 | bc -l` s3=`echo $SHIFT_sup_alphaquartz_2 | bc -l` s4=`echo $SHIFT_sup_alphaquartz_3 | bc -l` s5=`echo $SHIFT_sup_alphaquartz_4 | bc -l` s6=`echo -$SHIFT_sup_alphaquartz_2 | bc -l` s7=`echo -$SHIFT_sup_alphaquartz_3 | bc -l` s8=`echo -$SHIFT_sup_alphaquartz_4 | bc -l` s9=`echo $SHIFT_sup_alphaquartz_2 - $SHIFT_sup_alphaquartz_3 | bc -l` s10=`echo $SHIFT_sup_alphaquartz_3 - $SHIFT_sup_alphaquartz_2 | bc -l` s11=`echo 0.6666666666666666666666 + $SHIFT_sup_alphaquartz_4 | bc -l` s12=`echo 0.3333333333333333333333 + $SHIFT_sup_alphaquartz_4 | bc -l` s13=`echo 0.6666666666666666666666 - $SHIFT_sup_alphaquartz_4 | bc -l` s14=`echo 0.3333333333333333333333 - $SHIFT_sup_alphaquartz_4 | bc -l` cat > POSCAR << EOF sup_alphaquartz crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_alphaquartz $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.6666666666666666666666 | bc -l` x2=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.3333333333333333333333 | bc -l` x3=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x4=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s5 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s7 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s9 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s11 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s10 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s6 | bc -l` z6=`echo $d \* $nz - $d + $d \* $s12 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z7=`echo $d \* $nz - $d + $d \* $s8 | bc -l` x8=`echo $d \* $nx - $d + $d \* $s6 | bc -l` y8=`echo $d \* $ny - $d + $d \* $s10 | bc -l` z8=`echo $d \* $nz - $d + $d \* $s13 | bc -l` x9=`echo $d \* $nx - $d + $d \* $s9 | bc -l` y9=`echo $d \* $ny - $d + $d \* $s7 | bc -l` z9=`echo $d \* $nz - $d + $d \* $s14 | bc -l` echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '9p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_sup_alphaquartz_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_alphaquartz_1=$shift_sup_alphaquartz_1 fi row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_sup_alphaquartz_2=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_alphaquartz_2=$shift_sup_alphaquartz_2 fi row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[1]} shift_sup_alphaquartz_3=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_alphaquartz_3=$shift_sup_alphaquartz_3 fi row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_alphaquartz_4=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_alphaquartz_4=$shift_sup_alphaquartz_4 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_anatase () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_anatase STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_anatase=2.51430 SHIFT_sup_anatase_1=0.08310 } EOF if [ -z $C_A_RATIO_sup_anatase ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_anatase \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_anatase_1 | bc -l` s2=`echo 0.5 + $SHIFT_sup_anatase_1 | bc -l` s3=`echo 0.5 - $SHIFT_sup_anatase_1 | bc -l` s4=`echo 0.25 + $SHIFT_sup_anatase_1 | bc -l` s5=`echo 0.25 - $SHIFT_sup_anatase_1 | bc -l` s6=`echo 0.5 + 2 \* $SHIFT_sup_anatase_1 | bc -l` s7=`echo 0.5 - 2 \* $SHIFT_sup_anatase_1 | bc -l` s8=`echo 1 - 2 \* $SHIFT_sup_anatase_1 | bc -l` s9=`echo 2 \* $SHIFT_sup_anatase_1 | bc -l` cat > POSCAR << EOF sup_anatase crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 $C_A_RATIO_sup_anatase $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.625 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.375 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s5 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s9 | bc -l` x4=`echo $d \* $nx - $d + $d \* -$s4 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s6 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y5=`echo $d \* $ny - $d + $d \* -$s5 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s8 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z6=`echo $d \* $nz - $d + $d \* $s7 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '13p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_sup_anatase_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_anatase_1=$shift_sup_anatase_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_aucu () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_aucu STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_aucu=0.92632 } EOF if [ -z $C_A_RATIO_sup_aucu ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_aucu \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_aucu crystal $SUPERCELL_FACTOR -$v 0.5 -0.5 0 0.5 0.5 0 0 0 $C_A_RATIO_sup_aucu $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_bcc () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_bcc STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_bcc \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_bcc crystal $SUPERCELL_FACTOR -$v -0.5 0.5 0.5 0.5 -0.5 0.5 0.5 0.5 -0.5 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_bcc_c () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_bcc_c STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_bcc_c \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_bcc_c crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_bct () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_bct STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_bct=1.41421 } EOF if [ -z $C_A_RATIO_sup_bct ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_bct \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` c=`echo 0.5 \* $C_A_RATIO_sup_bct | bc -l` cat > POSCAR << EOF sup_bct crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0.5 0.5 $c $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_betaquartz () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_betaquartz STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=9 ATOMS_PER_SUBCELL=9 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="3 6" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_betaquartz=1.10020 SHIFT_sup_betaquartz_1=0.42020 } EOF if [ -z $C_A_RATIO_sup_betaquartz ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_betaquartz \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_betaquartz_1 | bc -l` s2=`echo 2 \* $SHIFT_sup_betaquartz_1 | bc -l` s3=`echo -2 \* $SHIFT_sup_betaquartz_1 | bc -l` s4=`echo - $SHIFT_sup_betaquartz_1 | bc -l` cat > POSCAR << EOF sup_betaquartz crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_betaquartz $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.6666666666666666666666 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.3333333333333333333333 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x4=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.1666666666666666666666 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.833333333333333333333 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x8=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y8=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.1666666666666666666666 | bc -l` x9=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y9=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z9=`echo $d \* $nz - $d + $d \* 0.833333333333333333333 | bc -l` echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '12p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_sup_betaquartz_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_betaquartz_1=$shift_sup_betaquartz_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_betatin () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_betatin STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_betatin=0.54547 } EOF if [ -z $C_A_RATIO_sup_betatin ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_betatin \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` c=`echo 0.5 \* $C_A_RATIO_sup_betatin | bc -l` cat > POSCAR << EOF sup_betatin crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0.5 0.5 $c $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* -0.375 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.375 | bc -l` z2=`echo $d \* $nz - $d + $d \* -0.25 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_cdi2 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_cdi2 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=3 ATOMS_PER_SUBCELL=3 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_cdi2=2.44949 SHIFT_sup_cdi2_1=0.16667 } EOF if [ -z $C_A_RATIO_sup_cdi2 ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_cdi2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo 0.5 - $SHIFT_sup_cdi2_1 | bc -l` s2=`echo 0.5 + $SHIFT_sup_cdi2_1 | bc -l` cat > POSCAR << EOF sup_cdi2 crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_cdi2 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z2=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s2 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_cdi2_1=`echo $column \* $SUPERCELL_FACTOR - 0.5 \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_cdi2_1=$shift_sup_cdi2_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_cristobalite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_cristobalite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=24 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_cristobalite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_cristobalite crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.125 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.125 | bc -l` x2=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* -0.125 | bc -l` z2=`echo $d \* $nz - $d + $d \* -0.125 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_cscl () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_cscl STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_cscl \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_cscl crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_cubiclaves () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_cubiclaves STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=24 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_cubiclaves \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_cubiclaves crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.125 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.125 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.875 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.875 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.875 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_cuprite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_cuprite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=6 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_cuprite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_cuprite crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_dhcp () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_dhcp STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_dhcp=3.26598 } EOF if [ -z $C_A_RATIO_sup_dhcp ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_dhcp \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_dhcp crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_dhcp $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_diamond () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_diamond STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_diamond \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_diamond crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* -0.125 | bc -l` y1=`echo $d \* $ny - $d + $d \* -0.125 | bc -l` z1=`echo $d \* $nz - $d + $d \* -0.125 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.125 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.125 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.125 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_diamond_c () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_diamond_c STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=8 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="8" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_diamond_c \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_diamond_c crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x7=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y7=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x8=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y8=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_fcc () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_fcc STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_fcc \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_fcc crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_fcc_c () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_fcc_c STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_fcc_c \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_fcc_c crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_fluorite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_fluorite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=3 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_fluorite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_fluorite crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x3=`echo $d \* $nx - $d + $d \* -0.25 | bc -l` y3=`echo $d \* $ny - $d + $d \* -0.25 | bc -l` z3=`echo $d \* $nz - $d + $d \* -0.25 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_graphite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_graphite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_graphite=2.00000 } EOF if [ -z $C_A_RATIO_sup_graphite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_graphite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_graphite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_graphite $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_hcp () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_hcp STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_hcp=1.63299 } EOF if [ -z $C_A_RATIO_sup_hcp ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_hcp \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_hcp crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_hcp $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_hexagonallaves () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_hexagonallaves STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=12 NUMBER_OF_SHIFTS=2 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="8 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_hexagonallaves=1.64479 SHIFT_sup_hexagonallaves_1=-0.16988 SHIFT_sup_hexagonallaves_2=0.06681 } EOF if [ -z $C_A_RATIO_sup_hexagonallaves ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_hexagonallaves \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_hexagonallaves_1 | bc -l` s2=`echo 2 \* $SHIFT_sup_hexagonallaves_1 | bc -l` s3=`echo -2 \* $SHIFT_sup_hexagonallaves_1 | bc -l` s4=`echo 0.0 - $SHIFT_sup_hexagonallaves_1 | bc -l` s5=`echo $SHIFT_sup_hexagonallaves_2 | bc -l` s6=`echo -$SHIFT_sup_hexagonallaves_2 | bc -l` s7=`echo 0.5 + $SHIFT_sup_hexagonallaves_2 | bc -l` s8=`echo 0.5 - $SHIFT_sup_hexagonallaves_2 | bc -l` cat > POSCAR << EOF sup_hexagonallaves crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_hexagonallaves $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y4=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s4 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x8=`echo $d \* $nx - $d + $d \* $s4 | bc -l` y8=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x9=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y9=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z9=`echo $d \* $nz - $d + $d \* $s5 | bc -l` x10=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y10=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z10=`echo $d \* $nz - $d + $d \* $s6 | bc -l` x11=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y11=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z11=`echo $d \* $nz - $d + $d \* $s7 | bc -l` x12=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y12=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z12=`echo $d \* $nz - $d + $d \* $s8 | bc -l` echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_sup_hexagonallaves_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` row=$(sed -n '17p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_hexagonallaves_2=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_hexagonallaves_1=$shift_sup_hexagonallaves_1 SHIFT_sup_hexagonallaves_2=$shift_sup_hexagonallaves_2 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_molybdenite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_molybdenite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=6 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_molybdenite=3.88924 SHIFT_sup_molybdenite_1=0.62000 } EOF if [ -z $C_A_RATIO_sup_molybdenite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_molybdenite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_molybdenite_1 | bc -l` s2=`echo 0.5 + $SHIFT_sup_molybdenite_1 | bc -l` s3=`echo 0.5 - $SHIFT_sup_molybdenite_1 | bc -l` s4=`echo - $SHIFT_sup_molybdenite_1 | bc -l` cat > POSCAR << EOF sup_molybdenite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_molybdenite $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s2 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s3 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z6=`echo $d \* $nz - $d + $d \* $s4 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_molybdenite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_molybdenite_1=$shift_sup_molybdenite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_nacl () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_nacl STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_nacl \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_nacl crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_nickeline () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_nickeline STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_nickeline=1.63299 } EOF if [ -z $C_A_RATIO_sup_nickeline ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_nickeline \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_nickeline crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_nickeline $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_pyrite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_pyrite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=12 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 8" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { SHIFT_sup_pyrite_1=0.38600 } EOF if [ -z $SHIFT_sup_pyrite_1 ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_pyrite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_pyrite_1 | bc -l` s2=`echo 0.5 + $SHIFT_sup_pyrite_1 | bc -l` s3=`echo 0.5 - $SHIFT_sup_pyrite_1 | bc -l` cat > POSCAR << EOF sup_pyrite crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z5=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x6=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y6=`echo $d \* $ny - $d + $d \* -$s1 | bc -l` z6=`echo $d \* $nz - $d + $d \* -$s1 | bc -l` x7=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y7=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z7=`echo $d \* $nz - $d + $d \* -$s1 | bc -l` x8=`echo $d \* $nx - $d + $d \* -$s2 | bc -l` y8=`echo $d \* $ny - $d + $d \* -$s3 | bc -l` z8=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x9=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y9=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z9=`echo $d \* $nz - $d + $d \* $s3 | bc -l` x10=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y10=`echo $d \* $ny - $d + $d \* -$s2 | bc -l` z10=`echo $d \* $nz - $d + $d \* -$s3 | bc -l` x11=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y11=`echo $d \* $ny - $d + $d \* -$s1 | bc -l` z11=`echo $d \* $nz - $d + $d \* $s2 | bc -l` x12=`echo $d \* $nx - $d + $d \* -$s3 | bc -l` y12=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z12=`echo $d \* $nz - $d + $d \* -$s2 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '13p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_pyrite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_pyrite_1=$shift_sup_pyrite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_rutile () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_rutile STRUCTURE_TYPE=crystal LATTICE_SYSTEM=tetragonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=6 ATOMS_PER_SUBCELL=6 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 4" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_rutile=0.64395 SHIFT_sup_rutile_1=0.30530 } EOF if [ -z $C_A_RATIO_sup_rutile ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_rutile \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_rutile_1 | bc -l` s2=`echo 0.5 + $SHIFT_sup_rutile_1 | bc -l` s3=`echo 0.5 - $SHIFT_sup_rutile_1 | bc -l` cat > POSCAR << EOF sup_rutile crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 $C_A_RATIO_sup_rutile $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* $s1 | bc -l` y3=`echo $d \* $ny - $d + $d \* $s1 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x4=`echo $d \* $nx - $d + $d \* -$s1 | bc -l` y4=`echo $d \* $ny - $d + $d \* -$s1 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x5=`echo $d \* $nx - $d + $d \* $s2 | bc -l` y5=`echo $d \* $ny - $d + $d \* $s3 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x6=`echo $d \* $nx - $d + $d \* $s3 | bc -l` y6=`echo $d \* $ny - $d + $d \* $s2 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[0]} shift_sup_rutile_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_rutile_1=$shift_sup_rutile_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_sc () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_sc STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=1 ATOMS_PER_SUBCELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_sc \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_sc crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_tridymite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_tridymite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=12 ATOMS_PER_SUBCELL=12 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 8" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_tridymite=1.63698 SHIFT_sup_tridymite_1=0.06200 } EOF if [ -z $C_A_RATIO_sup_tridymite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_tridymite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_tridymite_1 | bc -l` s2=`echo -$SHIFT_sup_tridymite_1 | bc -l` s3=`echo 0.5 + $SHIFT_sup_tridymite_1 | bc -l` s4=`echo 0.5 - $SHIFT_sup_tridymite_1 | bc -l` cat > POSCAR << EOF sup_tridymite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_tridymite $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* $s2 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s3 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s4 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x7=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y7=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x8=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y8=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x9=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y9=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z9=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x10=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y10=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z10=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x11=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y11=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z11=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x12=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y12=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z12=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '9p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_tridymite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_tridymite_1=$shift_sup_tridymite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_wurtzite () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_wurtzite STRUCTURE_TYPE=crystal LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=1 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="2 2" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_wurtzite=1.63299 SHIFT_sup_wurtzite_1=0.37480 } EOF if [ -z $C_A_RATIO_sup_wurtzite ] ; then source defaultshiftsandratios defaultshiftsandratios fi v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_wurtzite \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` s1=`echo $SHIFT_sup_wurtzite_1 | bc -l` s2=`echo 0.5 + $SHIFT_sup_wurtzite_1 | bc -l` cat > POSCAR << EOF sup_wurtzite crystal $SUPERCELL_FACTOR -$v 0.5 -0.86602540378443864676372317075294 0 0.5 0.86602540378443864676372317075294 0 0 0 $C_A_RATIO_sup_wurtzite $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x3=`echo $d \* $nx - $d + $d \* 0.3333333333333333333333 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.6666666666666666666666 | bc -l` z3=`echo $d \* $nz - $d + $d \* $s1 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.6666666666666666666666 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.3333333333333333333333 | bc -l` z4=`echo $d \* $nz - $d + $d \* $s2 | bc -l` echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { row=$(sed -n '11p' < CONTCAR) # nth atom + 8 column=${row[2]} shift_sup_wurtzite_1=`echo $column \* $SUPERCELL_FACTOR | bc -l` if [ "$UPDATEVARIABLES" = true ]; then SHIFT_sup_wurtzite_1=$shift_sup_wurtzite_1 fi } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_x2o3 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_x2o3 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=10 ATOMS_PER_SUBCELL=10 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 6" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_x2o3 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_x2o3 crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x5=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_x2o5 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_x2o5 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=14 ATOMS_PER_SUBCELL=14 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="4 10" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_x2o5 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_x2o5 crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x5=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y5=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z5=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x6=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y6=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z6=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x7=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y7=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z7=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x8=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y8=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z8=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` x9=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y9=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z9=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x10=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y10=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z10=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x11=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y11=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z11=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` x12=`echo $d \* $nx - $d + $d \* 0.75 | bc -l` y12=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z12=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x13=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y13=`echo $d \* $ny - $d + $d \* 0.75 | bc -l` z13=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` x14=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y14=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z14=`echo $d \* $nz - $d + $d \* 0.75 | bc -l` echo $x5 " " $y5 " " $z5 >> POSCAR echo $x6 " " $y6 " " $z6 >> POSCAR echo $x7 " " $y7 " " $z7 >> POSCAR echo $x8 " " $y8 " " $z8 >> POSCAR echo $x9 " " $y9 " " $z9 >> POSCAR echo $x10 " " $y10 " " $z10 >> POSCAR echo $x11 " " $y11 " " $z11 >> POSCAR echo $x12 " " $y12 " " $z12 >> POSCAR echo $x13 " " $y13 " " $z13 >> POSCAR echo $x14 " " $y14 " " $z14 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_xo3 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_xo3 STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=4 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 3" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_xo3 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_xo3 crystal $SUPERCELL_FACTOR -$v 1 0 0 0 1 0 0 0 1 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.5 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x3=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y3=`echo $d \* $ny - $d + $d \* 0.5 | bc -l` z3=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` x4=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y4=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z4=`echo $d \* $nz - $d + $d \* 0.5 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR echo $x3 " " $y3 " " $z3 >> POSCAR echo $x4 " " $y4 " " $z4 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### sup_zincblende () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_zincblende STRUCTURE_TYPE=crystal LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=2 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=2 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1 1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF v=`echo $ATOMS_PER_SUBCELL \* $VOLUME_sup_zincblende \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms2=${array[1]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` natoms2=`echo $natoms2 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` cat > POSCAR << EOF sup_zincblende crystal $SUPERCELL_FACTOR -$v 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0 $POTCAR $natoms1 $natoms2 Direct EOF d=`echo 1.0 / $SUPERCELL_FACTOR | bc -l` for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo $d \* $nx - $d + $d \* 0.0 | bc -l` y1=`echo $d \* $ny - $d + $d \* 0.0 | bc -l` z1=`echo $d \* $nz - $d + $d \* 0.0 | bc -l` echo $x1 " " $y1 " " $z1 >> POSCAR done done done for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do x2=`echo $d \* $nx - $d + $d \* 0.25 | bc -l` y2=`echo $d \* $ny - $d + $d \* 0.25 | bc -l` z2=`echo $d \* $nz - $d + $d \* 0.25 | bc -l` echo $x2 " " $y2 " " $z2 >> POSCAR done done done if [ "$READSHIFTS" = true ]; then cat > readshifts << EOF readshifts () { x=x } EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### addadsorbate () { name="ADSORPTION_DISTANCE_${1}" adsdist=`echo ${!name}` h=`echo 9 + $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS \* $NUMBER_OF_ATOMS_PER_LAYER_PER_CELL | bc -l` harray=($(sed -n "$h"'p' < POSCAR)) hight=${harray[2]} vector1=($(sed -n '3p' < POSCAR)) vector2=($(sed -n '4p' < POSCAR)) vector11=${vector1[0]} vector12=${vector1[1]} vector21=${vector2[0]} vector22=${vector2[1]} vector11=`echo $vector11 / $SUPERCELL_FACTOR | bc -l` vector12=`echo $vector12 / $SUPERCELL_FACTOR | bc -l` vector21=`echo $vector21 / $SUPERCELL_FACTOR | bc -l` vector22=`echo $vector22 / $SUPERCELL_FACTOR | bc -l` array1=($2) adir=${array1[0]} bdir=${array1[1]} array2=($3) asup=${array2[0]} bsup=${array2[1]} let asup=$asup-1 let bsup=$bsup-1 mkdir teemp cd teemp $1 cd .. rm -r teemp setpotcar $POTCAR $4 sed -i "/surface/{n;n;n;n;n;s/.*/$POTCAR/}" POSCAR buildpotcar for irrr in $(seq 1 1 $ATOMS_PER_SUBCELL) ; do fjhvbu=$(sed -n '7p' < POSCAR) fjhvbu=$fjhvbu" 1" sed -i "/surface/{n;n;n;n;n;n;s/.*/$fjhvbu/}" POSCAR name="POSITION_ATOM_${irrr}_${1}" poss=`echo ${!name}` pos=($poss) value1=${pos[0]} value2=${pos[1]} value3=${pos[2]} let h2=$h+$irrr+$numberofatomsthatwereaddedbefore-1 value1=`echo $asup \* $vector11 + $bsup \* $vector21 + $adir \* $vector11 + $bdir \* $vector21 + $value1 | bc -l` value2=`echo $asup \* $vector12 + $bsup \* $vector22 + $adir \* $vector12 + $bdir \* $vector22 + $value2 | bc -l` value3=`echo $hight + $adsdist + $value3 | bc -l` btbeb=" $value1 $value2 $value3 T T T" sed -i "$h2""a $btbeb" POSCAR done let numberofatomsthatwereaddedbefore=$numberofatomsthatwereaddedbefore+$ATOMS_PER_SUBCELL source poscardescription poscardescription } ########################################################################################### ########################################################################################### ########################################################################################### addsubstitution () { natpelarray=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) elemarray=($POTCAR) array=($3) a=${array[0]} b=${array[1]} c=${array[2]} for irrr in $(seq 0 1 8); do if [ "${elemarray[$irrr]}" = $1 ]; then jhct=($(sed -n '7p' < POSCAR)) jdcnj=${jhct[$irrr]} let fvvwknf=$jdcnj-1 jhct[$irrr]=$fvvwknf sdfvfkjvn=${jhct[@]} sed -i "/crystal/{n;n;n;n;n;n;s/.*/$sdfvfkjvn/}" POSCAR m=0 if [ "$NUMBER_OF_ELEMENTS" != 1 ]; then for jrrr in $(seq 1 1 $irrr); do let jrrr=$jrrr-1 echo "hello" for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do let m=$m+${natpelarray[$jrrr]} done done done done fi for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do let m=$m+${natpelarray[$irrr]} if [ "$nx $ny $nz" = "$a $b $c" ]; then break 3 fi done done done let m=8+$m+$2-${natpelarray[$irrr]} btbeb=$(sed -n "$m"'p' < POSCAR) sed -i "$m"'d' POSCAR setpotcar $POTCAR $4 sed -i "/crystal/{n;n;n;n;n;s/.*/$POTCAR/}" POSCAR buildpotcar fjhvbu=$(sed -n '7p' < POSCAR) fjhvbu=$fjhvbu" 1" sed -i "/crystal/{n;n;n;n;n;n;s/.*/$fjhvbu/}" POSCAR let M=7+$ATOMS_PER_SUBCELL*$SUPERCELL_FACTOR*$SUPERCELL_FACTOR*$SUPERCELL_FACTOR sed -i "$M""a $btbeb" POSCAR fi done } ########################################################################################### ########################################################################################### ########################################################################################### addvacancy () { natpelarray=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) elemarray=($POTCAR) array=($3) a=${array[0]} b=${array[1]} c=${array[2]} for irrr in $(seq 0 1 8); do if [ "${elemarray[$irrr]}" = $1 ]; then jhct=($(sed -n '7p' < POSCAR)) jdcnj=${jhct[$irrr]} let fvvwknf=$jdcnj-1 jhct[$irrr]=$fvvwknf sdfvfkjvn=${jhct[@]} sed -i "/crystal/{n;n;n;n;n;n;s/.*/$sdfvfkjvn/}" POSCAR m=0 if [ "$NUMBER_OF_ELEMENTS" != 1 ]; then for jrrr in $(seq 1 1 $irrr); do let jrrr=$jrrr-1 echo "hello" for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do let m=$m+${natpelarray[$jrrr]} done done done done fi for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do for nz in $(seq 1 1 $SUPERCELL_FACTOR); do let m=$m+${natpelarray[$irrr]} if [ "$nx $ny $nz" = "$a $b $c" ]; then break 3 fi done done done let m=8+$m+$2-${natpelarray[$irrr]} sed -i "$m"'d' POSCAR fi done } ########################################################################################### ########################################################################################### ########################################################################################### bent_mol () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=molecule ATOMS_PER_SUBCELL=3 } EOF source poscardescription poscardescription cat > defaultatomicpositions << EOF defaultatomicpositions () { POSITION_ATOM_1_bent_mol="0 0 0" POSITION_ATOM_2_bent_mol="0 1 0.5" POSITION_ATOM_3_bent_mol="0 -1 0.5" } EOF if [ -z $POSITION_ATOM_1_bent_mol ] ; then source defaultshiftsandratios defaultshiftsandratios fi xx=`echo $MOLECULE_CELL_SIZE_bent_mol \* $SUPERCELL_FACTOR - $MOLECULE_ASYMETRY_bent_mol | bc -l` yy=`echo $MOLECULE_CELL_SIZE_bent_mol \* $SUPERCELL_FACTOR | bc -l` zz=`echo $MOLECULE_CELL_SIZE_bent_mol \* $SUPERCELL_FACTOR + $MOLECULE_ASYMETRY_bent_mol | bc -l` cat > POSCAR << EOF bent_mol molecule 1.0 $xx 0 0 0 $yy 0 0 0 $zz $POTCAR 1 1 1 Cartesian $POSITION_ATOM_1_bent_mol $POSITION_ATOM_2_bent_mol $POSITION_ATOM_3_bent_mol EOF } ########################################################################################### ########################################################################################### ########################################################################################### diatomic_mol () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=molecule ATOMS_PER_SUBCELL=2 } EOF source poscardescription poscardescription cat > defaultatomicpositions << EOF defaultatomicpositions () { POSITION_ATOM_1_diatomic_mol="0 0 0" POSITION_ATOM_2_diatomic_mol="0 0 1" } EOF if [ -z $POSITION_ATOM_1_diatomic_mol ] ; then source defaultshiftsandratios defaultshiftsandratios fi xx=`echo $MOLECULE_CELL_SIZE_diatomic_mol \* $SUPERCELL_FACTOR - $MOLECULE_ASYMETRY_diatomic_mol | bc -l` yy=`echo $MOLECULE_CELL_SIZE_diatomic_mol \* $SUPERCELL_FACTOR | bc -l` zz=`echo $MOLECULE_CELL_SIZE_diatomic_mol \* $SUPERCELL_FACTOR + $MOLECULE_ASYMETRY_diatomic_mol | bc -l` cat > POSCAR << EOF diatomic_mol molecule 1.0 $xx 0 0 0 $yy 0 0 0 $zz $POTCAR 1 1 Cartesian $POSITION_ATOM_1_diatomic_mol $POSITION_ATOM_2_diatomic_mol EOF } ########################################################################################### ########################################################################################### ########################################################################################### linear_mol () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=molecule ATOMS_PER_SUBCELL=3 } EOF source poscardescription poscardescription cat > defaultatomicpositions << EOF defaultatomicpositions () { POSITION_ATOM_1_linear_mol="0 0 0" POSITION_ATOM_2_linear_mol="0 0 1" POSITION_ATOM_3_linear_mol="0 0 2" } EOF if [ -z $POSITION_ATOM_1_linear_mol ] ; then source defaultshiftsandratios defaultshiftsandratios fi xx=`echo $MOLECULE_CELL_SIZE_linear_mol \* $SUPERCELL_FACTOR - $MOLECULE_ASYMETRY_linear_mol | bc -l` yy=`echo $MOLECULE_CELL_SIZE_linear_mol \* $SUPERCELL_FACTOR | bc -l` zz=`echo $MOLECULE_CELL_SIZE_linear_mol \* $SUPERCELL_FACTOR + $MOLECULE_ASYMETRY_linear_mol | bc -l` cat > POSCAR << EOF linear_mol molecule 1.0 $xx 0 0 0 $yy 0 0 0 $zz $POTCAR 1 1 1 Cartesian $POSITION_ATOM_1_linear_mol $POSITION_ATOM_2_linear_mol $POSITION_ATOM_3_linear_mol EOF } ########################################################################################### ########################################################################################### ########################################################################################### monatomic_mol () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 STRUCTURE_TYPE=molecule ATOMS_PER_SUBCELL=1 } EOF source poscardescription poscardescription cat > defaultatomicpositions << EOF defaultatomicpositions () { POSITION_ATOM_1_monatomic_mol="0 0 0" } EOF if [ -z $POSITION_ATOM_1_monatomic_mol ] ; then source defaultshiftsandratios defaultshiftsandratios fi xx=`echo $MOLECULE_CELL_SIZE_monatomic_mol \* $SUPERCELL_FACTOR - $MOLECULE_ASYMETRY_monatomic_mol | bc -l` yy=`echo $MOLECULE_CELL_SIZE_monatomic_mol \* $SUPERCELL_FACTOR | bc -l` zz=`echo $MOLECULE_CELL_SIZE_monatomic_mol \* $SUPERCELL_FACTOR + $MOLECULE_ASYMETRY_monatomic_mol | bc -l` cat > POSCAR << EOF monatomic_mol molecule 1.0 $xx 0 0 0 $yy 0 0 0 $zz $POTCAR 1 Cartesian $POSITION_ATOM_1_monatomic_mol EOF } ########################################################################################### ########################################################################################### ########################################################################################### bcc_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_bcc_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_bcc_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` # c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.5 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_bcc_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF bcc_100 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_bcc_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_bcc_100" = "defaulthights" ]; then hight=`echo 0.5 \* $ig - 0.5 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_bcc_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_bcc_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_bcc_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### bcc_110 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_bcc_110 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_bcc_110 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` # c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.7071067811865475244008443621048 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_bcc_110 / $c | bc -l` xx=`echo 0.8660254037844386467637231707529 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.2886751345948128822545743902510 \* $c | bc -l` yy=`echo 0.8164965809277260327324280249020 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF bcc_110 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_bcc_110 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 0.8660254037844386467637231707529 \* $nx - 0.8660254037844386467637231707529 + 0.2886751345948128822545743902510 \* $ny - 0.2886751345948128822545743902510 + 0.57735026918962576450914878050196 | bc -l` y1=`echo 0 \* $nx - 0 + 0.8164965809277260327324280249020 \* $ny - 0.8164965809277260327324280249020 + 0.40824829046386301636621401245098 | bc -l` x2=`echo 0.8660254037844386467637231707529 \* $nx - 0.8660254037844386467637231707529 + 0.2886751345948128822545743902510 \* $ny - 0.2886751345948128822545743902510 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 0.8164965809277260327324280249020 \* $ny - 0.8164965809277260327324280249020 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_bcc_110" = "defaulthights" ]; then hight=`echo 0.7071067811865475244008443621048 \* $ig - 0.7071067811865475244008443621048 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_bcc_110) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_bcc_110 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_bcc_110" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### bcc_111 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_bcc_111 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=3 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_bcc_111 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` # c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.2886751345948128822545743902510 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_bcc_111 / $c | bc -l` xx=`echo 1.4142135623730950488016887242097 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.7071067811865475244008443621048 \* $c | bc -l` yy=`echo 1.2247448713915890490986420373529 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF bcc_111 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_bcc_111 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1.4142135623730950488016887242097 \* $nx - 1.4142135623730950488016887242097 + 0.7071067811865475244008443621048 \* $ny - 0.7071067811865475244008443621048 + 0.7071067811865475244008443621048 | bc -l` y1=`echo 0 \* $nx - 0 + 1.2247448713915890490986420373529 \* $ny - 1.2247448713915890490986420373529 + 0.40824829046386301636621401245098 | bc -l` x2=`echo 1.4142135623730950488016887242097 \* $nx - 1.4142135623730950488016887242097 + 0.7071067811865475244008443621048 \* $ny - 0.7071067811865475244008443621048 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1.2247448713915890490986420373529 \* $ny - 1.2247448713915890490986420373529 + 0.00000000000000000000000000000000 | bc -l` x3=`echo 1.4142135623730950488016887242097 \* $nx - 1.4142135623730950488016887242097 + 0.7071067811865475244008443621048 \* $ny - 0.7071067811865475244008443621048 + 1.4142135623730950488016887242097 | bc -l` y3=`echo 0 \* $nx - 0 + 1.2247448713915890490986420373529 \* $ny - 1.2247448713915890490986420373529 + 0.81649658092772603273242802490196 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_bcc_111" = "defaulthights" ]; then hight=`echo 0.2886751345948128822545743902510 \* $ig - 0.2886751345948128822545743902510 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_bcc_111) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_bcc_111 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_bcc_111" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### diamond_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_diamond_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=4 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_diamond_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.35355339664904762812604531564108 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_diamond_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF diamond_100 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_diamond_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x3=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x4=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y4=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` x4=`echo $c \* $x4 / $SUPERCELL_FACTOR | bc -l` y4=`echo $c \* $y4 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_diamond_100" = "defaulthights" ]; then hight=`echo 0.35355339664904762812604531564108 \* $ig - 0.35355339664904762812604531564108 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_diamond_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_diamond_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_diamond_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### fcc_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_fcc_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_fcc_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.70710678118654752440084436210485 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_fcc_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF fcc_100 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_fcc_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_fcc_100" = "defaulthights" ]; then hight=`echo 0.70710678118654752440084436210485 \* $ig - 0.70710678118654752440084436210485 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_fcc_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_fcc_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_fcc_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### fcc_110 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_fcc_110 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_fcc_110 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.5 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_fcc_110 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1.4142135623730950488016887242097 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF fcc_110 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_fcc_110 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1.4142135623730950488016887242097 \* $ny - 1.4142135623730950488016887242097 + 0.70710678118654752440084436210485 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1.4142135623730950488016887242097 \* $ny - 1.4142135623730950488016887242097 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_fcc_110" = "defaulthights" ]; then hight=`echo 0.5 \* $ig - 0.5 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_fcc_110) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_fcc_110 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_fcc_110" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### fcc_111 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_fcc_111 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=3 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_fcc_111 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.81649658092772603273242802490195 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_fcc_111 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.5 \* $c | bc -l` yy=`echo 0.86602540378443864676372317075294 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF fcc_111 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_fcc_111 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 1.00000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.57735026918962576450914878050196 | bc -l` x2=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.00000000000000000000000000000000 | bc -l` x3=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 0.50000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.28867513459481288225457439025098 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_fcc_111" = "defaulthights" ]; then hight=`echo 0.81649658092772603273242802490195 \* $ig - 0.81649658092772603273242802490195 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_fcc_111) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_fcc_111 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_fcc_111" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### hcp_001 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_hcp_001 STRUCTURE_TYPE=surface LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_hcp_001=1.63299 } EOF if [ -z $C_A_RATIO_hcp_001 ] ; then source defaultshiftsandratios defaultshiftsandratios fi array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_hcp_001 | bc -l` v=`echo 1.1547005383792515290182975610039 \* $v / $C_A_RATIO_hcp_001 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` h=`echo 0.5 \* $C_A_RATIO_hcp_001 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_hcp_001 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.5 \* $c | bc -l` yy=`echo 0.86602540378443864676372317075294 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF hcp_001 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_hcp_001 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 1.00000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.57735026918962576450914878050196 | bc -l` x2=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_hcp_001" = "defaulthights" ]; then hight=`echo 0.5 \* $C_A_RATIO_hcp_001 \* $ig - 0.5 \* $C_A_RATIO_hcp_001 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_hcp_001) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_hcp_001 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_hcp_001" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### hcp_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=false SUPERCELL_FACTOR=1 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_hcp_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=4 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_hcp_100=1.63299 } EOF if [ -z $C_A_RATIO_hcp_100 ] ; then source defaultshiftsandratios defaultshiftsandratios fi array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_hcp_100 | bc -l` v=`echo 1.1547005383792515290182975610039 \* $v / $C_A_RATIO_hcp_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` h=`echo 0.25 \* 1.73205080756887729352744634150587 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_hcp_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo $C_A_RATIO_hcp_100 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF hcp_100 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_hcp_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + $C_A_RATIO_hcp_100 \* $ny - $C_A_RATIO_hcp_100 + $C_A_RATIO_hcp_100 \* 0.25000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + $C_A_RATIO_hcp_100 \* $ny - $C_A_RATIO_hcp_100 + $C_A_RATIO_hcp_100 \* 0.75000000000000000000000000000000 | bc -l` x3=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + $C_A_RATIO_hcp_100 \* $ny - $C_A_RATIO_hcp_100 + $C_A_RATIO_hcp_100 \* 0.25000000000000000000000000000000 | bc -l` x4=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y4=`echo 0 \* $nx - 0 + $C_A_RATIO_hcp_100 \* $ny - $C_A_RATIO_hcp_100 + $C_A_RATIO_hcp_100 \* 0.75000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` x4=`echo $c \* $x4 / $SUPERCELL_FACTOR | bc -l` y4=`echo $c \* $y4 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_hcp_100" = "defaulthights" ]; then #different from rest of surfaces because layers not equally spaced res=$(($ig % $ATOMS_PER_SUBCELL)) if [ $(echo "$res == 0" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 1.00 \* 1.73205080756887729352744634150587 + 0.66666666666666666666666666666667 \* 1.73205080756887729352744634150587 | bc -l` fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 0.25 \* 1.73205080756887729352744634150587 | bc -l` fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 0.50 \* 1.73205080756887729352744634150587 + 0.16666666666666666666666666666667 \* 1.73205080756887729352744634150587 | bc -l` fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 0.75 \* 1.73205080756887729352744634150587 + 0.5 \* 1.73205080756887729352744634150587 | bc -l` fi hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_hcp_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_hcp_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_hcp_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_bcc_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_bcc_100 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_bcc_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_bcc_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` # c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.5 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_bcc_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_bcc_100 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_bcc_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_bcc_100" = "defaulthights" ]; then hight=`echo 0.5 \* $ig - 0.5 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_bcc_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_bcc_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_bcc_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_bcc_110 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_bcc_110 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_bcc_110 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_bcc_110 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` # c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.7071067811865475244008443621048 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_bcc_110 / $c | bc -l` xx=`echo 0.8660254037844386467637231707529 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.2886751345948128822545743902510 \* $c | bc -l` yy=`echo 0.8164965809277260327324280249020 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_bcc_110 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_bcc_110 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 0.8660254037844386467637231707529 \* $nx - 0.8660254037844386467637231707529 + 0.2886751345948128822545743902510 \* $ny - 0.2886751345948128822545743902510 + 0.57735026918962576450914878050196 | bc -l` y1=`echo 0 \* $nx - 0 + 0.8164965809277260327324280249020 \* $ny - 0.8164965809277260327324280249020 + 0.40824829046386301636621401245098 | bc -l` x2=`echo 0.8660254037844386467637231707529 \* $nx - 0.8660254037844386467637231707529 + 0.2886751345948128822545743902510 \* $ny - 0.2886751345948128822545743902510 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 0.8164965809277260327324280249020 \* $ny - 0.8164965809277260327324280249020 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_bcc_110" = "defaulthights" ]; then hight=`echo 0.7071067811865475244008443621048 \* $ig - 0.7071067811865475244008443621048 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_bcc_110) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_bcc_110 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_bcc_110" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_bcc_111 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_bcc_111 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_bcc_111 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=I ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=3 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_bcc_111 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` # c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.2886751345948128822545743902510 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_bcc_111 / $c | bc -l` xx=`echo 1.4142135623730950488016887242097 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.7071067811865475244008443621048 \* $c | bc -l` yy=`echo 1.2247448713915890490986420373529 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_bcc_111 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_bcc_111 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1.4142135623730950488016887242097 \* $nx - 1.4142135623730950488016887242097 + 0.7071067811865475244008443621048 \* $ny - 0.7071067811865475244008443621048 + 1.4142135623730950488016887242097 | bc -l` y1=`echo 0 \* $nx - 0 + 1.2247448713915890490986420373529 \* $ny - 1.2247448713915890490986420373529 + 0.81649658092772603273242802490196 | bc -l` x2=`echo 1.4142135623730950488016887242097 \* $nx - 1.4142135623730950488016887242097 + 0.7071067811865475244008443621048 \* $ny - 0.7071067811865475244008443621048 + 0.7071067811865475244008443621048 | bc -l` y2=`echo 0 \* $nx - 0 + 1.2247448713915890490986420373529 \* $ny - 1.2247448713915890490986420373529 + 0.40824829046386301636621401245098 | bc -l` x3=`echo 1.4142135623730950488016887242097 \* $nx - 1.4142135623730950488016887242097 + 0.7071067811865475244008443621048 \* $ny - 0.7071067811865475244008443621048 + 0.00000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + 1.2247448713915890490986420373529 \* $ny - 1.2247448713915890490986420373529 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_bcc_111" = "defaulthights" ]; then hight=`echo 0.2886751345948128822545743902510 \* $ig - 0.2886751345948128822545743902510 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_bcc_111) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_bcc_111 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_bcc_111" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_diamond_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_diamond_100 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_diamond_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=8 ATOMS_PER_SUBCELL=4 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_diamond_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.35355339664904762812604531564108 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_diamond_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_diamond_100 surface ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_diamond_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x3=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x4=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y4=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` x4=`echo $c \* $x4 / $SUPERCELL_FACTOR | bc -l` y4=`echo $c \* $y4 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_diamond_100" = "defaulthights" ]; then hight=`echo 0.35355339664904762812604531564108 \* $ig - 0.35355339664904762812604531564108 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_diamond_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_diamond_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_diamond_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_fcc_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_fcc_100 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_fcc_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_fcc_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.70710678118654752440084436210485 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_fcc_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_fcc_100 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_fcc_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.50000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1 \* $ny - 1 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_fcc_100" = "defaulthights" ]; then hight=`echo 0.70710678118654752440084436210485 \* $ig - 0.70710678118654752440084436210485 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_fcc_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_fcc_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_fcc_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_fcc_110 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_fcc_110 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_fcc_110 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_fcc_110 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.5 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_fcc_110 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo 1.4142135623730950488016887242097 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_fcc_110 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_fcc_110 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 1.4142135623730950488016887242097 \* $ny - 1.4142135623730950488016887242097 + 0.70710678118654752440084436210485 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 1.4142135623730950488016887242097 \* $ny - 1.4142135623730950488016887242097 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_fcc_100" = "defaulthights" ]; then hight=`echo 0.5 \* $ig - 0.5 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_fcc_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_fcc_110 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_fcc_110" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_fcc_111 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_fcc_111 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_fcc_111 STRUCTURE_TYPE=surface LATTICE_SYSTEM=cubic BRAVAIS_LATTICE=F ATOMS_PER_CONVENTIONAL_CELL=4 ATOMS_PER_SUBCELL=3 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { x=x } EOF array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_fcc_111 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR / 1.4142135623730950488016887242097 | bc -l` h=`echo 0.81649658092772603273242802490195 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_fcc_111 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.5 \* $c | bc -l` yy=`echo 0.86602540378443864676372317075294 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_fcc_111 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_fcc_111 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 1.00000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.57735026918962576450914878050196 | bc -l` x2=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.00000000000000000000000000000000 | bc -l` x3=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 0.50000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.28867513459481288225457439025098 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_fcc_111" = "defaulthights" ]; then hight=`echo 0.81649658092772603273242802490195 \* $ig - 0.81649658092772603273242802490195 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_fcc_111) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_fcc_111 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_fcc_111" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_hcp_001 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_hcp_001 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_hcp_001 STRUCTURE_TYPE=surface LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=2 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_hcp_001=1.63299 } EOF if [ -z $C_A_RATIO_sup_hcp_001 ] ; then source defaultshiftsandratios defaultshiftsandratios fi array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_hcp_001 | bc -l` v=`echo 1.1547005383792515290182975610039 \* $v / $C_A_RATIO_sup_hcp_001 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` h=`echo 0.5 \* $C_A_RATIO_sup_hcp_001 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_hcp_001 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0.5 \* $c | bc -l` yy=`echo 0.86602540378443864676372317075294 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_hcp_001 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_hcp_001 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 1.00000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.57735026918962576450914878050196 | bc -l` x2=`echo 1 \* $nx - 1 + 0.5 \* $ny - 0.5 + 0.00000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + 0.86602540378443864676372317075294 \* $ny - 0.86602540378443864676372317075294 + 0.00000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_hcp_001" = "defaulthights" ]; then hight=`echo 0.5 \* $C_A_RATIO_sup_hcp_001 \* $ig - 0.5 \* $C_A_RATIO_sup_hcp_001 | bc -l` hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_hcp_001) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_hcp_001 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_hcp_001" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### sup_hcp_100 () { cat > poscardescription << EOF poscardescription () { THISISSUPERCELL=true SUPERCELL_FACTOR=$SUPERCELL_FACTOR_sup_hcp_100 NUMBER_OF_LAYERS=$NUMBER_OF_LAYERS_sup_hcp_100 STRUCTURE_TYPE=surface LATTICE_SYSTEM=hexagonal BRAVAIS_LATTICE=P ATOMS_PER_CONVENTIONAL_CELL=2 ATOMS_PER_SUBCELL=4 NUMBER_OF_ATOMS_PER_LAYER_PER_CELL=1 NUMBER_OF_SHIFTS=0 NUMBER_OF_ELEMENTS=1 NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT="1" } EOF source poscardescription poscardescription cat > defaultshiftsandratios << EOF defaultshiftsandratios () { C_A_RATIO_sup_hcp_100=1.63299 } EOF if [ -z $C_A_RATIO_sup_hcp_100 ] ; then source defaultshiftsandratios defaultshiftsandratios fi array=($NUMBER_OF_ATOMS_PER_SUBCELL_PER_ELEMENT) natoms1=${array[0]} natoms1=`echo $natoms1 \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $NUMBER_OF_LAYERS | bc -l` v=`echo $ATOMS_PER_CONVENTIONAL_CELL \* $VOLUME_sup_hcp_100 | bc -l` v=`echo 1.1547005383792515290182975610039 \* $v / $C_A_RATIO_sup_hcp_100 | bc -l` c=`echo " e( l($v)/3 ) " | bc -l` c=`echo $c \* $SUPERCELL_FACTOR | bc -l` h=`echo 0.25 \* 1.73205080756887729352744634150587 \* $NUMBER_OF_LAYERS / $SUPERCELL_FACTOR + $VACUUM_SIZE_sup_hcp_100 / $c | bc -l` xx=`echo 1 \* $c | bc -l` xy=`echo 0 \* $c | bc -l` xz=`echo 0 \* $c | bc -l` yx=`echo 0 \* $c | bc -l` yy=`echo $C_A_RATIO_sup_hcp_100 \* $c | bc -l` yz=`echo 0 \* $c | bc -l` zx=`echo 0 \* $c | bc -l` zy=`echo 0 \* $c | bc -l` zz=`echo $h \* $c | bc -l` cat > POSCAR << EOF sup_hcp_100 surface $SUPERCELL_FACTOR ; layers: $NUMBER_OF_LAYERS ; vacuum: $VACUUM_SIZE_sup_hcp_100 1.0 $xx $xy $xz $yx $yy $yz $zx $zy $zz $POTCAR $natoms1 Selective dynamics Cartesian EOF for ig in $(seq 1 1 $NUMBER_OF_LAYERS); do for nx in $(seq 1 1 $SUPERCELL_FACTOR); do for ny in $(seq 1 1 $SUPERCELL_FACTOR); do x1=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y1=`echo 0 \* $nx - 0 + $C_A_RATIO_sup_hcp_100 \* $ny - $C_A_RATIO_sup_hcp_100 + $C_A_RATIO_sup_hcp_100 \* 0.25000000000000000000000000000000 | bc -l` x2=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.50000000000000000000000000000000 | bc -l` y2=`echo 0 \* $nx - 0 + $C_A_RATIO_sup_hcp_100 \* $ny - $C_A_RATIO_sup_hcp_100 + $C_A_RATIO_sup_hcp_100 \* 0.75000000000000000000000000000000 | bc -l` x3=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y3=`echo 0 \* $nx - 0 + $C_A_RATIO_sup_hcp_100 \* $ny - $C_A_RATIO_sup_hcp_100 + $C_A_RATIO_sup_hcp_100 \* 0.25000000000000000000000000000000 | bc -l` x4=`echo 1 \* $nx - 1 + 0 \* $ny - 0 + 0.00000000000000000000000000000000 | bc -l` y4=`echo 0 \* $nx - 0 + $C_A_RATIO_sup_hcp_100 \* $ny - $C_A_RATIO_sup_hcp_100 + $C_A_RATIO_sup_hcp_100 \* 0.75000000000000000000000000000000 | bc -l` x1=`echo $c \* $x1 / $SUPERCELL_FACTOR | bc -l` y1=`echo $c \* $y1 / $SUPERCELL_FACTOR | bc -l` x2=`echo $c \* $x2 / $SUPERCELL_FACTOR | bc -l` y2=`echo $c \* $y2 / $SUPERCELL_FACTOR | bc -l` x3=`echo $c \* $x3 / $SUPERCELL_FACTOR | bc -l` y3=`echo $c \* $y3 / $SUPERCELL_FACTOR | bc -l` x4=`echo $c \* $x4 / $SUPERCELL_FACTOR | bc -l` y4=`echo $c \* $y4 / $SUPERCELL_FACTOR | bc -l` if [ "$LAYER_HIGHTS_sup_hcp_100" = "defaulthights" ]; then #different from rest of surfaces because layers not equally spaced res=$(($ig % $ATOMS_PER_SUBCELL)) if [ $(echo "$res == 0" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 1.00 \* 1.73205080756887729352744634150587 + 0.66666666666666666666666666666667 \* 1.73205080756887729352744634150587 | bc -l` fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 0.25 \* 1.73205080756887729352744634150587 | bc -l` fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 0.50 \* 1.73205080756887729352744634150587 + 0.16666666666666666666666666666667 \* 1.73205080756887729352744634150587 | bc -l` fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then hight=`echo 0.25 \* 1.73205080756887729352744634150587 \* $ig - 0.75 \* 1.73205080756887729352744634150587 + 0.5 \* 1.73205080756887729352744634150587 | bc -l` fi hight=`echo $c \* $hight / $SUPERCELL_FACTOR | bc -l` else let iii=$ig-1 hightsarray=($LAYER_HIGHTS_sup_hcp_100) hight=${hightsarray[$iii]} fi res=$(($ig % $ATOMS_PER_SUBCELL)) seldynup=`echo $NUMBER_OF_LAYERS - $ig | bc -l` seldyndown=`echo $SELECTIVE_DYNAMICS_DEPTH_sup_hcp_100 + 1 | bc -l` if [ $(echo "$seldynup < $SELECTIVE_DYNAMICS_DEPTH_sup_hcp_100" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi elif [ $(echo "$ig < $seldyndown" | bc) -eq 1 ]; then if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " T T T " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " T T T " >> POSCAR fi else if [ $(echo "$res == 0" | bc) -eq 1 ]; then echo "$x1 $y1 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 1" | bc) -eq 1 ]; then echo "$x2 $y2 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 2" | bc) -eq 1 ]; then echo "$x3 $y3 " $hight " F F F " >> POSCAR fi if [ $(echo "$res == 3" | bc) -eq 1 ]; then echo "$x4 $y4 " $hight " F F F " >> POSCAR fi fi done done done numberofatomsthatwereaddedbefore=0 } ########################################################################################### ########################################################################################### ########################################################################################### gencutconvergence () { secsgencutconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: gencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " #gencutconvergence fcc "15 1 35 25" 0.001 autovar electronicmin fcc addvacancy $potcar 1 "1 1 1" v echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: gencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " #gencutconvergence fcc "15 1 35 25" 0.001 autovar electronicmin fcc addvacancy $potcar 1 "1 1 1" v echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi backupencut=$ENCUT mkdir gencutconvergence_${1} cd gencutconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ENCUT Result Difference" echo " " >> $MAINDIR/output.txt echo " ENCUT Result Difference" >> $MAINDIR/output.txt fi array=($(echo "$2")) value1=`echo ${array[0]} | bc -l` value2=`echo ${array[1]} | bc -l` value3=`echo ${array[2]} | bc -l` counterfff=0 for i in $(seq ${value1%.*} ${value2%.*} ${value3%.*}); do let counterfff=$counterfff+1 mkdir $i cd $i ENCUT=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done hhh=($(echo "$2")) hhhh=${hhh[3]} hhhhhh=${hhhh%.*} referencevaluedcarr=($(tail -n 1 data.dat | head -n 1)) referencevaluedc=${referencevaluedcarr[1]} secondreferencevaluedcarr=($(tail -n 2 data.dat | head -n 1)) secondreferencevaluedc=${secondreferencevaluedcarr[1]} diff=`echo $referencevaluedc - $secondreferencevaluedc | bc -l` notconverged=false if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi elif [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi fi if [ "$notconverged" = false ]; then for i in $(seq 2 1 $counterfff); do #let fhjvjnejv=$i+1 argkgvnjarr=($(tail -n $i data.dat | head -n 1)) argkgvnj=${argkgvnjarr[1]} isniin=${argkgvnjarr[0]} ENCUT=$isniin diff=`echo $referencevaluedc - $argkgvnj | bc -l` if [ $(echo "$isniin < $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at ENCUT = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at ENCUT = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at ENCUT = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at ENCUT = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin == $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin > $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER ENCUT = $hhhhhh (at ENCUT = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi done fi if [ "$UPDATEVARIABLES" = false ]; then ENCUT=$backupencut fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > gencutconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 ENCUT convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Cutoff energy (eV)" set ylabel "$ylabel" unset key set term png set output "gencutconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gencutconvergence_gnup_${1}_${METAGGA} fi else cat > gencutconvergence_gnup_${1}_${GGA} << EOF set title "$1 ENCUT convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Cutoff energy (eV)" set ylabel "$ylabel" unset key set term png set output "gencutconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gencutconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secsgencutconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### gkpointsconvergence () { secsgkpointsconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: gkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: gkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi name="KPOINTS_$1" backupkpts=`echo ${!name}` mkdir gkpointsconvergence_${1} cd gkpointsconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Number of kpoints Result Difference" echo " " >> $MAINDIR/output.txt echo " Number of kpoints Result Difference" >> $MAINDIR/output.txt fi jnvjskvnfkj=($2) arewvwt1=${jnvjskvnfkj[0]} arewvwt2=${jnvjskvnfkj[1]} arewvwt3=${jnvjskvnfkj[2]} counterfff=0 for i in $(seq $arewvwt1 $arewvwt2 $arewvwt3); do let counterfff=$counterfff+1 mkdir $i cd $i name="KPOINTS_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done hhh=($(echo "$2")) hhhh=${hhh[3]} hhhhhh=${hhhh%.*} referencevaluedcarr=($(tail -n 1 data.dat | head -n 1)) referencevaluedc=${referencevaluedcarr[1]} secondreferencevaluedcarr=($(tail -n 2 data.dat | head -n 1)) secondreferencevaluedc=${secondreferencevaluedcarr[1]} diff=`echo $referencevaluedc - $secondreferencevaluedc | bc -l` notconverged=false if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi elif [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi fi if [ "$notconverged" = false ]; then for i in $(seq 2 1 $counterfff); do #let fhjvjnejv=$i+1 argkgvnjarr=($(tail -n $i data.dat | head -n 1)) argkgvnj=${argkgvnjarr[1]} isniin=${argkgvnjarr[0]} name="KPOINTS_$1" eval $name=$isniin diff=`echo $referencevaluedc - $argkgvnj | bc -l` if [ $(echo "$isniin < $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at KPOINTS_$1 = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at KPOINTS_$1 = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at KPOINTS_$1 = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at KPOINTS_$1 = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin == $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin > $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER KPOINTS_$1 = $hhhhhh (at KPOINTS_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi done fi if [ "$UPDATEVARIABLES" = false ]; then name="KPOINTS_$1" eval $name=$backupkpts fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > gkpointsconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 kpoints convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of kpoints along x-, y-, z- direction" set ylabel "$ylabel" unset key set term png set output "gkpointsconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gkpointsconvergence_gnup_${1}_${METAGGA} fi else cat > gkpointsconvergence_gnup_${1}_${GGA} << EOF set title "$1 kpoints convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of kpoints along x-, y-, z- direction" set ylabel "$ylabel" unset key set term png set output "gkpointsconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gkpointsconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secsgkpointsconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### gnomegaconvergence () { secsgnomegaconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: gnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: gnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi backupnomega=$NOMEGA mkdir gnomegaconvergence_${1} cd gnomegaconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " NOMEGA Result Difference" echo " " >> $MAINDIR/output.txt echo " NOMEGA Result Difference" >> $MAINDIR/output.txt fi jnvjskvnfkj=($2) arewvwt1=${jnvjskvnfkj[0]} arewvwt2=${jnvjskvnfkj[1]} arewvwt3=${jnvjskvnfkj[2]} counterfff=0 for i in $(seq $arewvwt1 $arewvwt2 $arewvwt3); do let counterfff=$counterfff+1 mkdir $i cd $i NOMEGA=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done hhh=($(echo "$2")) hhhh=${hhh[3]} hhhhhh=${hhhh%.*} referencevaluedcarr=($(tail -n 1 data.dat | head -n 1)) referencevaluedc=${referencevaluedcarr[1]} secondreferencevaluedcarr=($(tail -n 2 data.dat | head -n 1)) secondreferencevaluedc=${secondreferencevaluedcarr[1]} diff=`echo $referencevaluedc - $secondreferencevaluedc | bc -l` notconverged=false if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi elif [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi fi if [ "$notconverged" = false ]; then for i in $(seq 2 1 $counterfff); do #let fhjvjnejv=$i+1 argkgvnjarr=($(tail -n $i data.dat | head -n 1)) argkgvnj=${argkgvnjarr[1]} isniin=${argkgvnjarr[0]} NOMEGA=$isniin diff=`echo $referencevaluedc - $argkgvnj | bc -l` if [ $(echo "$isniin < $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at NOMEGA = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at NOMEGA = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at NOMEGA = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at NOMEGA = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin == $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin > $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NOMEGA = $hhhhhh (at NOMEGA = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi done fi if [ "$UPDATEVARIABLES" = false ]; then NOMEGA=$backupnomega fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > gnomegaconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 NOMEGA convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of imaginary frequency and time points" set ylabel "$ylabel" unset key set term png set output "gnomegaconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gnomegaconvergence_gnup_${1}_${METAGGA} fi else cat > gnomegaconvergence_gnup_${1}_${GGA} << EOF set title "$1 NOMEGA convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of imaginary frequency and time points" set ylabel "$ylabel" unset key set term png set output "gnomegaconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gnomegaconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secsgnomegaconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### gnumberoflayersconvergence () { secsgnumberoflayersconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: gnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: gnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi name="NUMBER_OF_LAYERS_$i" backupnumberoflayers=`echo ${!name}` mkdir gnumberoflayersconvergence_${1} cd gnumberoflayersconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Number of layers Result Difference" echo " " >> $MAINDIR/output.txt echo " Number of layers Result Difference" >> $MAINDIR/output.txt fi jnvjskvnfkj=($2) arewvwt1=${jnvjskvnfkj[0]} arewvwt2=${jnvjskvnfkj[1]} arewvwt3=${jnvjskvnfkj[2]} counterfff=0 for i in $(seq $arewvwt1 $arewvwt2 $arewvwt3); do let counterfff=$counterfff+1 mkdir $i cd $i name="NUMBER_OF_LAYERS_$i" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done hhh=($(echo "$2")) hhhh=${hhh[3]} hhhhhh=${hhhh%.*} referencevaluedcarr=($(tail -n 1 data.dat | head -n 1)) referencevaluedc=${referencevaluedcarr[1]} secondreferencevaluedcarr=($(tail -n 2 data.dat | head -n 1)) secondreferencevaluedc=${secondreferencevaluedcarr[1]} diff=`echo $referencevaluedc - $secondreferencevaluedc | bc -l` notconverged=false if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi elif [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi fi if [ "$notconverged" = false ]; then for i in $(seq 2 1 $counterfff); do #let fhjvjnejv=$i+1 argkgvnjarr=($(tail -n $i data.dat | head -n 1)) argkgvnj=${argkgvnjarr[1]} isniin=${argkgvnjarr[0]} name="NUMBER_OF_LAYERS_$i" eval $name=$isniin diff=`echo $referencevaluedc - $argkgvnj | bc -l` if [ $(echo "$isniin < $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at NUMBER_OF_LAYERS_$i = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at NUMBER_OF_LAYERS_$i = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at NUMBER_OF_LAYERS_$i = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at NUMBER_OF_LAYERS_$i = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin == $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin > $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER NUMBER_OF_LAYERS_$i = $hhhhhh (at NUMBER_OF_LAYERS_$i = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$i has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi done fi if [ "$UPDATEVARIABLES" = false ]; then name="NUMBER_OF_LAYERS_$i" eval $name=$backupnumberoflayers fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > gnumberoflayersconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 number of layers convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of layers per surface slab" set ylabel "$ylabel" unset key set term png set output "gnumberoflayersconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gnumberoflayersconvergence_gnup_${1}_${METAGGA} fi else cat > gnumberoflayersconvergence_gnup_${1}_${GGA} << EOF set title "$1 number of layers convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of layers per surface slab" set ylabel "$ylabel" unset key set term png set output "gnumberoflayersconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gnumberoflayersconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secsgnumberoflayersconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### gsupercellconvergence () { secsgsupercellconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: gsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: gsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi name="SUPERCELL_FACTOR_$1" backupsupercell=`echo ${!name}` mkdir gsupercellconvergence_${1} cd gsupercellconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Supercell factor Result Difference" echo " " >> $MAINDIR/output.txt echo " Supercell factor Result Difference" >> $MAINDIR/output.txt fi jnvjskvnfkj=($2) arewvwt1=${jnvjskvnfkj[0]} arewvwt2=${jnvjskvnfkj[1]} arewvwt3=${jnvjskvnfkj[2]} counterfff=0 for i in $(seq $arewvwt1 $arewvwt2 $arewvwt3); do let counterfff=$counterfff+1 mkdir $i cd $i name="SUPERCELL_FACTOR_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done hhh=($(echo "$2")) hhhh=${hhh[3]} hhhhhh=${hhhh%.*} referencevaluedcarr=($(tail -n 1 data.dat | head -n 1)) referencevaluedc=${referencevaluedcarr[1]} secondreferencevaluedcarr=($(tail -n 2 data.dat | head -n 1)) secondreferencevaluedc=${secondreferencevaluedcarr[1]} diff=`echo $referencevaluedc - $secondreferencevaluedc | bc -l` notconverged=false if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi elif [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi fi if [ "$notconverged" = false ]; then for i in $(seq 2 1 $counterfff); do #let fhjvjnejv=$i+1 argkgvnjarr=($(tail -n $i data.dat | head -n 1)) argkgvnj=${argkgvnjarr[1]} isniin=${argkgvnjarr[0]} name="SUPERCELL_FACTOR_$1" eval $name=$isniin diff=`echo $referencevaluedc - $argkgvnj | bc -l` if [ $(echo "$isniin < $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at SUPERCELL_FACTOR_$1 = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at SUPERCELL_FACTOR_$1 = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at SUPERCELL_FACTOR_$1 = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at SUPERCELL_FACTOR_$1 = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin == $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin > $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER SUPERCELL_FACTOR_$1 = $hhhhhh (at SUPERCELL_FACTOR_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi done fi if [ "$UPDATEVARIABLES" = false ]; then name="SUPERCELL_FACTOR_$1" eval $name=$backupsupercell fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > gsupercellconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 supercell convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Supercell factor" set ylabel "$ylabel" unset key set term png set output "gsupercellconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gsupercellconvergence_gnup_${1}_${METAGGA} fi else cat > gsupercellconvergence_gnup_${1}_${GGA} << EOF set title "$1 supercell convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Supercell factor" set ylabel "$ylabel" unset key set term png set output "gsupercellconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gsupercellconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secsgsupercellconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### gvacuumsizeconvergence () { secsgvacuumsizeconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: gvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: gvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: gvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi name="VACUUM_SIZE_$1" backupvacuumsize=`echo ${!name}` mkdir gvacuumsizeconvergence_${1} cd gvacuumsizeconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Vacuum size Result Difference" echo " " >> $MAINDIR/output.txt echo " Vacuum size Result Difference" >> $MAINDIR/output.txt fi jnvjskvnfkj=($2) arewvwt1=${jnvjskvnfkj[0]} arewvwt2=${jnvjskvnfkj[1]} arewvwt3=${jnvjskvnfkj[2]} counterfff=0 for i in $(seq $arewvwt1 $arewvwt2 $arewvwt3); do let counterfff=$counterfff+1 mkdir $i cd $i name="VACUUM_SIZE_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done hhh=($(echo "$2")) hhhh=${hhh[3]} hhhhhh=${hhhh%.*} referencevaluedcarr=($(tail -n 1 data.dat | head -n 1)) referencevaluedc=${referencevaluedcarr[1]} secondreferencevaluedcarr=($(tail -n 2 data.dat | head -n 1)) secondreferencevaluedc=${secondreferencevaluedcarr[1]} diff=`echo $referencevaluedc - $secondreferencevaluedc | bc -l` notconverged=false if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi elif [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then notconverged=true if [ "$PRINTOUTPUT" = true ]; then echo " " echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " GLOBAL CONVERGENCE CRITERION OF " $3 " WAS NEVER REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi fi if [ "$notconverged" = false ]; then for i in $(seq 2 1 $counterfff); do #let fhjvjnejv=$i+1 argkgvnjarr=($(tail -n $i data.dat | head -n 1)) argkgvnj=${argkgvnjarr[1]} isniin=${argkgvnjarr[0]} name="VACUUM_SIZE_$1" eval $name=$isniin diff=`echo $referencevaluedc - $argkgvnj | bc -l` if [ $(echo "$isniin < $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at VACUUM_SIZE_$1 = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at VACUUM_SIZE_$1 = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was reached at VACUUM_SIZE_$1 = " $isniin if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was reached at VACUUM_SIZE_$1 = " $isniin >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin == $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi if [ $(echo "$isniin > $hhhhhh" | bc) -eq 1 ]; then if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 < $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "$diff < 0.0" | bc) -eq 1 ]; then if [ $(echo "-$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " global convergence criterion of " $3 " was only met AFTER VACUUM_SIZE_$1 = $hhhhhh (at VACUUM_SIZE_$1 = $isniin)" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi break fi fi fi done fi if [ "$UPDATEVARIABLES" = false ]; then name="VACUUM_SIZE_$1" eval $name=$backupvacuumsize fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > gvacuumsizeconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 vacuum size convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Vacuum size ({\305})" set ylabel "$ylabel" unset key set term png set output "gvacuumsizeconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gvacuumsizeconvergence_gnup_${1}_${METAGGA} fi else cat > gvacuumsizeconvergence_gnup_${1}_${GGA} << EOF set title "$1 vacuum size convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Vacuum size ({\305})" set ylabel "$ylabel" unset key set term png set output "gvacuumsizeconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT gvacuumsizeconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secsgvacuumsizeconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### lencutconvergence () { secslencutconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: lencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " #lencutconvergence fcc "15 1 25" 0.001 autovar electronicmin fcc addvacancy $potcar 1 "1 1 1" v echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: lencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " #lencutconvergence fcc "15 1 25" 0.001 autovar electronicmin fcc addvacancy $potcar 1 "1 1 1" v echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lencutconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi backupencut=$ENCUT mkdir lencutconvergence_${1} cd lencutconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ENCUT Result Difference" echo " " >> $MAINDIR/output.txt echo " ENCUT Result Difference" >> $MAINDIR/output.txt fi array=($(echo "$2")) value1=`echo ${array[0]} | bc -l` value2=`echo ${array[1]} | bc -l` value3=`echo ${array[2]} | bc -l` for i in $(seq ${value1%.*} ${value2%.*} ${value3%.*}); do mkdir $i cd $i ENCUT=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at ENCUT = " $i if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at ENCUT = " $i >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at ENCUT = " $i if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at ENCUT = " $i >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENCUT has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then ENCUT=$backupencut fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > lencutconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 ENCUT convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Cutoff energy (eV)" set ylabel "$ylabel" unset key set term png set output "lencutconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lencutconvergence_gnup_${1}_${METAGGA} fi else cat > lencutconvergence_gnup_${1}_${GGA} << EOF set title "$1 ENCUT convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Cutoff energy (eV)" set ylabel "$ylabel" unset key set term png set output "lencutconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lencutconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secslencutconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### lkpointsconvergence () { secslkpointsconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: lkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " echo " Number of kpoints Result Difference" echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Number of kpoints Result Difference" >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: lkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " echo " Number of kpoints Result Difference" echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lkpointsconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Number of kpoints Result Difference" >> $MAINDIR/output.txt fi fi fi mkdir lkpointsconvergence_${1} cd lkpointsconvergence_${1} VARIABLEFORCONVERGENCE_last=0 name="KPOINTS_$1" backupkpts=`echo ${!name}` for i in $(seq $2); do mkdir $i cd $i name="KPOINTS_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at " $i " kpoints." if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at " $i " kpoints." >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at " $i " kpoints." if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at " $i " kpoints." >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " KPOINTS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then name="KPOINTS_$i" eval $name=$backupkpts fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > lkpointsconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 kpoints convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of kpoints along x-, y-, z- direction" set ylabel "$ylabel" unset key set term png set output "lkpointsconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lkpointsconvergence_gnup_${1}_${METAGGA} fi else cat > lkpointsconvergence_gnup_${1}_${GGA} << EOF set title "$1 kpoints convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of kpoints along x-, y-, z- direction" set ylabel "$ylabel" unset key set term png set output "lkpointsconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lkpointsconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secslkpointsconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### lnomegaconvergence () { secslnomegaconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: lnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: lnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lnomegaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi backupnomega=$NOMEGA mkdir lnomegaconvergence_${1} cd lnomegaconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " NOMEGA Result Difference" echo " " >> $MAINDIR/output.txt echo " NOMEGA Result Difference" >> $MAINDIR/output.txt fi for i in $(seq $2); do mkdir $i cd $i NOMEGA=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $s $VARIABLEFORCONVERGENCE $diff" echo " $s $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at NOMEGA = " $i if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at NOMEGA = " $i >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at NOMEGA = " $i if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at NOMEGA = " $i >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NOMEGA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then NOMEGA=$backupnomega fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > lnomegaconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 NOMEGA convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of imaginary frequency and time points" set ylabel "$ylabel" unset key set term png set output "lnomegaconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lnomegaconvergence_gnup_${1}_${METAGGA} fi else cat > lnomegaconvergence_gnup_${1}_${GGA} << EOF set title "$1 NOMEGA convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of imaginary frequency and time points" set ylabel "$ylabel" unset key set term png set output "lnomegaconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lnomegaconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secslnomegaconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### lnumberoflayersconvergence () { secslnumberoflayersconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: lnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " echo " Number of layers Result Difference" echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Number of layers Result Difference" >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: lnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " echo " Number of layers Result Difference" echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lnumberoflayersconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Number of layers Result Difference" >> $MAINDIR/output.txt fi fi fi mkdir lnumberoflayersconvergence_${1} cd lnumberoflayersconvergence_${1} VARIABLEFORCONVERGENCE_last=0 name="NUMBER_OF_LAYERS_$1" backupnum=`echo ${!name}` for i in $(seq $2); do mkdir $i cd $i name="NUMBER_OF_LAYERS_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at " $i " layers." if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at " $i " layers." >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at " $i " layers." if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at " $i " layers." >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " NUMBER_OF_LAYERS_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then name="NUMBER_OF_LAYERS_$i" eval $name=$backupnum fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > lnumberoflayersconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 number of layers convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of layers per surface slab" set ylabel "$ylabel" unset key set term png set output "lnumberoflayersconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lnumberoflayersconvergence_gnup_${1}_${METAGGA} fi else cat > lnumberoflayersconvergence_gnup_${1}_${GGA} << EOF set title "$1 number of layers convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Number of layers per surface slab" set ylabel "$ylabel" unset key set term png set output "lnumberoflayersconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lnumberoflayersconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secslnumberoflayersconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### lsupercellconvergence () { secslsupercellconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: lsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: lsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lsupercellconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi name="SUPERCELL_FACTOR_$1" backupsup=`echo ${!name}` mkdir lsupercellconvergence_${1} cd lsupercellconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " supercell factor Result Difference" echo " " >> $MAINDIR/output.txt echo " supercell factor Result Difference" >> $MAINDIR/output.txt fi for i in $(seq $2); do mkdir $i cd $i name="SUPERCELL_FACTOR_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at a supercell factor of " $i if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at a supercell factor of " $i >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at a supercell factor of " $i if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at a supercell factor of " $i >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SUPERCELL_FACTOR_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then name="SUPERCELL_FACTOR_$i" eval $name=$backupsup fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > lsupercellconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 supercell size convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Supercell factor" set ylabel "$ylabel" unset key set term png set output "lsupercellconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lsupercellconvergence_gnup_${1}_${METAGGA} fi else cat > lsupercellconvergence_gnup_${1}_${GGA} << EOF set title "$1 supercell size convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Supercell factor" set ylabel "$ylabel" unset key set term png set output "lsupercellconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lsupercellconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secslsupercellconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### lvacuumsizeconvergence () { secslvacuumsizeconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: lvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " echo " Vacuum size Result Difference" echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Vacuum size Result Difference" >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: lvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " echo " Vacuum size Result Difference" echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: lvacuumsizeconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Vacuum size Result Difference" >> $MAINDIR/output.txt fi fi fi mkdir lvacuumsizeconvergence_${1} cd lvacuumsizeconvergence_${1} VARIABLEFORCONVERGENCE_last=0 name="VACUUM_SIZE_$1" backupvac=`echo ${!name}` for i in $(seq $2); do mkdir $i cd $i name="VACUUM_SIZE_$1" eval $name=$i PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $i $VARIABLEFORCONVERGENCE $diff" echo " $i $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at a vacuum size of " $i " Angstrom." if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at a vacuum size of " $i " Angstrom." >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at a vacuum size of " $i " Angstrom." if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at a vacuum size of " $i " Angstrom." >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VACUUM_SIZE_$1 has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then name="VACUUM_SIZE_$i" eval $name=$backupvac fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > lvacuumsizeconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 vacuum size convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Vacuum size ({\305})" set ylabel "$ylabel" unset key set term png set output "lvacuumsizeconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lvacuumsizeconvergence_gnup_${1}_${METAGGA} fi else cat > lvacuumsizeconvergence_gnup_${1}_${GGA} << EOF set title "$1 vacuum size convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Vacuum size ({\305})" set ylabel "$ylabel" unset key set term png set output "lvacuumsizeconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT lvacuumsizeconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secslvacuumsizeconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### sigmaconvergence () { secssigmaconvergence=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: sigmaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: sigmaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: sigmaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: sigmaconvergence $1 \"$2\" $3 $4 $5 $6 $7 $8 $9 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi backupsigma=$SIGMA mkdir sigmaconvergence_${1} cd sigmaconvergence_${1} VARIABLEFORCONVERGENCE_last=0 if [ "$PRINTOUTPUT" = true ]; then echo " " echo " SIGMA Result Difference" echo " " >> $MAINDIR/output.txt echo " SIGMA Result Difference" >> $MAINDIR/output.txt fi array=($(echo "$2")) value1=`echo ${array[0]} \* 10000 | bc -l` value2=`echo ${array[1]} \* 10000 | bc -l` value3=`echo ${array[2]} \* 10000 | bc -l` for i in $(seq ${value1%.*} ${value2%.*} ${value3%.*}); do s=`echo $i / 10000 | bc -l` mkdir $s cd $s SIGMA=$s PRINTOUTPUT=false "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" "${82}" "${83}" "${84}" "${85}" "${86}" PRINTOUTPUT=true cd .. if [ "$4" != "autovar" ]; then name="$4" VARIABLEFORCONVERGENCE=`echo ${!name}` fi echo " $i $VARIABLEFORCONVERGENCE " >> data.dat diff=`echo $VARIABLEFORCONVERGENCE - $VARIABLEFORCONVERGENCE_last | bc -l` echo " $s $VARIABLEFORCONVERGENCE $diff" echo " $s $VARIABLEFORCONVERGENCE $diff" >> $MAINDIR/output.txt if [ $(echo "$diff > 0.0" | bc) -eq 1 ]; then if [ $(echo "$3 > $diff" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at SIGMA = " $s if [ "$UPDATEVARIABLES" = true ]; then echo " SIGMA has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at SIGMA = " $s >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SIGMA has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi if [ $(echo "0.0 > $diff" | bc) -eq 1 ]; then if [ $(echo "$diff > -$3" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " convergence criterion of " $3 " was reached at SIGMA = " $s if [ "$UPDATEVARIABLES" = true ]; then echo " SIGMA has been updated to the optimized value " fi echo " " >> $MAINDIR/output.txt echo " convergence criterion of " $3 " was reached at SIGMA = " $s >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SIGMA has been updated to the optimized value " >> $MAINDIR/output.txt fi fi break fi fi hhh=($2) hhhhhh=${hhh[2]} if [ $(echo "$i == $hhhhhh" | bc) -eq 1 ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" if [ "$UPDATEVARIABLES" = true ]; then echo " SIGMA has been updated to $hhhhhh " fi echo " " >> $MAINDIR/output.txt echo " CONVERGENCE CRITERION OF " $3 " WAS NOT REACHED!!!" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " SIGMA has been updated to $hhhhhh " >> $MAINDIR/output.txt fi fi fi VARIABLEFORCONVERGENCE_last=$VARIABLEFORCONVERGENCE done if [ "$UPDATEVARIABLES" = false ]; then SIGMA=$backupsigma fi plotxydata data.dat if [ "$4" = "autovar" ]; then if [ "$5" = "electronicmin" ]; then ylabel="Total free energy per atom (eV)" fi if [ "$5" = "relaxation" ]; then ylabel="Volume per atom ({\305}^3)" fi fi if [ "$4" != "autovar" ]; then ylabel="$4" fi if [ -n "$METAGGA" ]; then cat > sigmaconvergence_gnup_${1}_${METAGGA} << EOF set title "$1 SIGMA convergence test ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Smearing width (eV)" set ylabel "$ylabel" unset key set term png set output "sigmaconvergence_${1}_${METAGGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT sigmaconvergence_gnup_${1}_${METAGGA} fi else cat > sigmaconvergence_gnup_${1}_${GGA} << EOF set title "$1 SIGMA convergence test ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Smearing width (eV)" set ylabel "$ylabel" unset key set term png set output "sigmaconvergence_${1}_${GGA}.png" p 'data.dat' u 1:2 w lp EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT sigmaconvergence_gnup_${1}_${GGA} fi fi let secs=$SECONDS-$secssigmaconvergence let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### densityofstates () { # $2 is for addpointdefect ... / addadsorbant ... secs=$SECONDS mkdir densityofstates_${1} cd densityofstates_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: densityofstates $1 $2 ; $ALGO $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: densityofstates $1 $2 ; $ALGO $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: densityofstates $1 $2 ; $ALGO $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: densityofstates $1 $2 ; $ALGO $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi $1 ; if [ -n "$2" ]; then $2 "$3" "$4" "$5" "$6" fi if [ -n "$7" ]; then $7 "$8" "$9" "${10}" "${11}" fi if [ -n "${12}" ]; then ${12} "${13}" "${14}" "${15}" "${16}" fi if [ -n "${17}" ]; then ${17} "${18}" "${19}" "${20}" "${21}" fi if [ -n "${22}" ]; then ${22} "${23}" "${24}" "${25}" "${26}" fi if [ -n "${27}" ]; then ${27} "${28}" "${29}" "${30}" "${31}" fi if [ -n "${32}" ]; then ${32} "${33}" "${34}" "${35}" "${36}" fi if [ -n "${37}" ]; then ${37} "${38}" "${39}" "${40}" "${41}" fi if [ -n "${42}" ]; then ${42} "${43}" "${44}" "${45}" "${46}" fi if [ -n "${47}" ]; then ${47} "${48}" "${49}" "${50}" "${51}" fi if [ -n "${52}" ]; then ${52} "${53}" "${54}" "${55}" "${56}" fi if [ -n "${57}" ]; then ${57} "${58}" "${59}" "${60}" "${61}" fi if [ -n "${62}" ]; then ${62} "${63}" "${64}" "${65}" "${66}" fi if [ -n "${67}" ]; then ${67} "${68}" "${69}" "${70}" "${71}" fi if [ -n "${72}" ]; then ${72} "${73}" "${74}" "${75}" "${76}" fi if [ -n "${77}" ]; then ${77} "${78}" "${79}" "${80}" "${81}" fi if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi buildkpoints $1 backupismear=$ISMEAR ISMEAR=-5 buildincar ISMEAR=$backupismear echo "#density of states:" >> INCAR echo "LORBIT = 11" >> INCAR echo "NEDOS = $NEDOS" >> INCAR echo "EMAX = $EMAX" >> INCAR echo "EMIN = $EMIN" >> INCAR echo " " >> INCAR buildpotcar $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST INCAR REPORT defaultshiftsandratios PROCAR XDATCAR KPOINTS CHGCAR poscardescription POSCAR CONTCAR WAVECAR minipotcar POTCAR EIGENVAL PCDAT CHG IBZKPT fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi awk 'BEGIN{i=1} /dos>/,\ /\/dos>/ \ {a[i]=$2 ; b[i]=$3 ; i=i+1} \ END{for (j=12;j dos.dat ef=`awk '/efermi/ {print $3}' vasprun.xml` if [ -n "$METAGGA" ]; then cat > densityofstates_gnup_${1}_${METAGGA} << EOF set title "$1 density of states ; METAGGA = $METAGGA, POTCAR = $POTCAR" set xlabel "Energy - Fermi energy (eV)" set ylabel "Density of States (states/eV)" unset key p "dos.dat" using (\$1-$ef):(\$2) w l set term png set output "densityofstates_${1}_${METAGGA}.png" p "dos.dat" using (\$1-$ef):(\$2) w l EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT densityofstates_gnup_${1}_${METAGGA} fi else cat > densityofstates_gnup_${1}_${GGA} << EOF set title "$1 density of states ; GGA = $GGA, POTCAR = $POTCAR" set xlabel "Energy - Fermi energy (eV)" set ylabel "Density of States (states/eV)" unset key p "dos.dat" using (\$1-$ef):(\$2) w l set term png set output "densityofstates_${1}_${GGA}.png" p "dos.dat" using (\$1-$ef):(\$2) w l EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT densityofstates_gnup_${1}_${GGA} fi fi echo " " echo " " >> $MAINDIR/output.txt lines=$NEDOS calculatebandgapwidth=false lineminone=( -1000000 0.0 ) for dkjnvgjnvg in $(seq 1 1 $lines) ; do line=($(sed -n "$dkjnvgjnvg"'p' < dos.dat)) if [ $(echo "${lineminone[0]} < $ef" | bc) -eq 1 ]; then x=x if [ $(echo "${line[0]} > $ef" | bc) -eq 1 ]; then if [ $(echo "${lineminone[1]} == 0.0000" | bc) -eq 1 ]; then x=x if [ $(echo "${line[1]} == 0.0000" | bc) -eq 1 ]; then echo " Fermi energy = $ef eV - lies within a band gap (insulator/semiconductor) " echo " Fermi energy = $ef eV - lies within a band gap (insulator/semiconductor) " >> $MAINDIR/output.txt calculatebandgapwidth=true fi fi if [ $(echo "${lineminone[1]} != 0.0000" | bc) -eq 1 ]; then x=x if [ $(echo "${line[1]} != 0.0000" | bc) -eq 1 ]; then echo " Fermi energy = $ef eV - lies within a band (metal/semimetal) " echo " Fermi energy = $ef eV - lies within a band (metal/semimetal) " >> $MAINDIR/output.txt fi fi if [ $(echo "${lineminone[1]} == 0.0000" | bc) -eq 1 ]; then x=x if [ $(echo "${line[1]} != 0.0000" | bc) -eq 1 ]; then echo " Fermi energy = $ef eV - lies at the upper band gap border (n-type insulator/semiconductor) " echo " Fermi energy = $ef eV - lies at the upper band gap border (n-type insulator/semiconductor) " >> $MAINDIR/output.txt calculatebandgapwidth=true fi fi if [ $(echo "${lineminone[1]} != 0.0000" | bc) -eq 1 ]; then x=x if [ $(echo "${line[1]} == 0.0000" | bc) -eq 1 ]; then echo " Fermi energy = $ef eV - lies at the lower band gap border (p-type insulator/semiconductor) " echo " Fermi energy = $ef eV - lies at the lower band gap border (p-type insulator/semiconductor) " >> $MAINDIR/output.txt calculatebandgapwidth=true fi fi fi fi lineminone=( "${line[@]}" ) done if [ "$calculatebandgapwidth" = true ]; then lineminone=( -1000000 0.0 ) for dkjnvgjnvg in $(seq 1 1 $lines) ; do line=($(sed -n "$dkjnvgjnvg"'p' < dos.dat)) if [ $(echo "${line[1]} == 0.0000" | bc) -eq 1 ]; then if [ $(echo "${lineminone[1]} != 0.0000" | bc) -eq 1 ]; then if [ $(echo "$ef > ${lineminone[0]}" | bc) -eq 1 ]; then band_gap_lower="${lineminone[0]}" fi fi fi lineminone=( "${line[@]}" ) done lineplusone=( 1000000 0.0 ) for dkjnvgjnvg in $(seq 1 1 $lines) ; do let antiline=$lines-$dkjnvgjnvg line=($(sed -n "$antiline"'p' < dos.dat)) if [ $(echo "${line[1]} == 0.0000" | bc) -eq 1 ]; then if [ $(echo "${lineplusone[1]} != 0.0000" | bc) -eq 1 ]; then if [ $(echo "$ef < ${lineplusone[0]}" | bc) -eq 1 ]; then band_gap_upper="${lineplusone[0]}" fi fi fi lineplusone=( "${line[@]}" ) done band_gap_width=`echo $band_gap_upper - $band_gap_lower | bc -l` lineminone=( -1000000 0.0 ) for dkjnvgjnvg in $(seq 1 1 $lines) ; do line=($(sed -n "$dkjnvgjnvg"'p' < dos.dat)) if [ $(echo "${line[1]} != 0.0000" | bc) -eq 1 ]; then if [ $(echo "${lineminone[1]} == 0.0000" | bc) -eq 1 ]; then if [ $(echo "$band_gap_lower > ${line[0]}" | bc) -eq 1 ]; then valence_band_lower="${line[0]}" fi fi fi lineminone=( "${line[@]}" ) done lineplusone=( 1000000 0.0 ) for dkjnvgjnvg in $(seq 1 1 $lines) ; do let antiline=$lines-$dkjnvgjnvg line=($(sed -n "$antiline"'p' < dos.dat)) if [ $(echo "${line[1]} != 0.0000" | bc) -eq 1 ]; then if [ $(echo "${lineplusone[1]} == 0.0000" | bc) -eq 1 ]; then if [ $(echo "$band_gap_upper < ${line[0]}" | bc) -eq 1 ]; then conduction_band_upper="${line[0]}" fi fi fi lineplusone=( "${line[@]}" ) done valence_band_width=`echo $band_gap_lower - $valence_band_lower | bc -l` conduction_band_width=`echo $conduction_band_upper - $band_gap_upper | bc -l` echo " conduction band: [$band_gap_upper, $conduction_band_upper] eV (width: $conduction_band_width eV)" echo " band gap: [$band_gap_lower, $band_gap_upper] eV (width: $band_gap_width eV)" echo " valence band: [$valence_band_lower, $band_gap_lower] eV (width: $valence_band_width eV)" echo " conduction band: [$band_gap_upper, $conduction_band_upper] eV (width: $conduction_band_width eV)" >> $MAINDIR/output.txt echo " band gap: [$band_gap_lower, $band_gap_upper] eV (width: $band_gap_width eV)" >> $MAINDIR/output.txt echo " valence band: [$valence_band_lower, $band_gap_lower] eV (width: $valence_band_width eV)" >> $MAINDIR/output.txt #echo " lower border of band gap: $band_gap_lower eV " #echo " upper border of band gap: $band_gap_upper eV " #echo " width of band gap: $width eV " #echo " lower border of band gap: $band_gap_lower eV " >> $MAINDIR/output.txt #echo " upper border of band gap: $band_gap_upper eV " >> $MAINDIR/output.txt #echo " width of band gap: $width eV " >> $MAINDIR/output.txt fi plotxydata+ dos.dat #echo " ^ " #echo " fermi energy = $ef eV" #echo " ^ " >> $MAINDIR/output.txt #echo " fermi energy = $ef eV" >> $MAINDIR/output.txt let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### electronicmin () { # $2 is for addpointdefect ... / addadsorbant ... secs=$SECONDS mkdir electronicmin_${1} cd electronicmin_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: electronicmin $1 $2 ; $ALGO $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: electronicmin $1 $2 ; $ALGO $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: electronicmin $1 $2 ; $ALGO $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: electronicmin $1 $2 ; $ALGO $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi $1 ; if [ -n "$2" ]; then $2 "$3" "$4" "$5" "$6" fi if [ -n "$7" ]; then $7 "$8" "$9" "${10}" "${11}" fi if [ -n "${12}" ]; then ${12} "${13}" "${14}" "${15}" "${16}" fi if [ -n "${17}" ]; then ${17} "${18}" "${19}" "${20}" "${21}" fi if [ -n "${22}" ]; then ${22} "${23}" "${24}" "${25}" "${26}" fi if [ -n "${27}" ]; then ${27} "${28}" "${29}" "${30}" "${31}" fi if [ -n "${32}" ]; then ${32} "${33}" "${34}" "${35}" "${36}" fi if [ -n "${37}" ]; then ${37} "${38}" "${39}" "${40}" "${41}" fi if [ -n "${42}" ]; then ${42} "${43}" "${44}" "${45}" "${46}" fi if [ -n "${47}" ]; then ${47} "${48}" "${49}" "${50}" "${51}" fi if [ -n "${52}" ]; then ${52} "${53}" "${54}" "${55}" "${56}" fi if [ -n "${57}" ]; then ${57} "${58}" "${59}" "${60}" "${61}" fi if [ -n "${62}" ]; then ${62} "${63}" "${64}" "${65}" "${66}" fi if [ -n "${67}" ]; then ${67} "${68}" "${69}" "${70}" "${71}" fi if [ -n "${72}" ]; then ${72} "${73}" "${74}" "${75}" "${76}" fi if [ -n "${77}" ]; then ${77} "${78}" "${79}" "${80}" "${81}" fi if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi buildkpoints $1 buildincar buildpotcar $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST INCAR REPORT defaultshiftsandratios XDATCAR KPOINTS CHGCAR poscardescription POSCAR CONTCAR DOSCAR vasprun.xml WAVECAR minipotcar POTCAR EIGENVAL PCDAT CHG IBZKPT fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi array1=($(grep 'number of ions' OUTCAR)) value1=${array1[11]} if [ "$ALGO" = RPAR ]; then array2=($(grep 'HF-free energy' OUTCAR)) array3=($(grep 'HF+RPA corr. energy' OUTCAR)) array4=($(grep 'HF+E_corr' OUTCAR)) array5=($(grep 'exchange ACFDT corr.' OUTCAR)) value2=${array2[4]} value3=${array2[5]} value4=${array2[2]} value5=${array2[4]} value2=`echo $value2 / $value1 | bc -l` value3=`echo $value3 / $value1 | bc -l` value4=`echo $value4 / $value1 | bc -l` value5=`echo $value5 / $value1 | bc -l` VARIABLEFORCONVERGENCE=$value3 cd .. if [ "$PRINTOUTPUT" = true ]; then echo " " echo " resulting HF-free energy per atom: $value2 eV" echo " resulting HF+RPA corr. energy per atom: $value3 eV" echo " resulting HF+E_corr(extrapolated) per atom: $value4 eV" echo " resulting exchange ACFDT corr. per atom: $value5 eV" echo " " >> $MAINDIR/output.txt echo " resulting HF-free energy per atom: $value2 eV" >> $MAINDIR/output.txt echo " resulting HF+RPA corr. energy per atom: $value3 eV" >> $MAINDIR/output.txt echo " resulting HF+E_corr(extrapolated) per atom: $value4 eV" >> $MAINDIR/output.txt echo " resulting exchange ACFDT corr. per atom: $value5 eV" >> $MAINDIR/output.txt fi else array2=($(grep 'free en' OUTCAR)) array3=($(grep 'energy without entropy' OUTCAR)) value2=${array2[4]} value3=${array3[4]} value4=${array3[7]} value2=`echo $value2 / $value1 | bc -l` value3=`echo $value3 / $value1 | bc -l` value4=`echo $value4 / $value1 | bc -l` if [ "$UPDATEVARIABLES" = true ]; then name="FREE_ENERGY_$1" eval $name=$value2 name="ENERGY_WITHOUT_ENTROPY_$1" eval $name=$value3 name="ENERGY_SIGMA_ZERO_$1" eval $name=$value4 if [ "$MAINENE" = 1 ]; then name="ENERGY_$1" eval $name=$value2 fi if [ "$MAINENE" = 2 ]; then name="ENERGY_$1" eval $name=$value3 fi if [ "$MAINENE" = 3 ]; then name="ENERGY_$1" eval $name=$value4 fi fi if [ "$MAINENE" = 1 ]; then mainene=$value2 fi if [ "$MAINENE" = 2 ]; then mainene=$value3 fi if [ "$MAINENE" = 3 ]; then mainene=$value4 fi VARIABLEFORCONVERGENCE=$mainene cd .. if [ "$PRINTOUTPUT" = true ]; then echo " " echo " resulting free energy per atom: $value2 eV " echo " resulting energy without entropy per atom: $value3 eV " echo " resulting energy(sigma->0) per atom: $value4 eV " if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 has been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " resulting free energy per atom: $value2 eV " >> $MAINDIR/output.txt echo " resulting energy without entropy per atom: $value3 eV " >> $MAINDIR/output.txt echo " resulting energy(sigma->0) per atom: $value4 eV " >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 has been updated accordingly " >> $MAINDIR/output.txt fi fi fi let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi } ########################################################################################### ########################################################################################### ########################################################################################### adsorptionenergy () { secsadsorptionenergy=$SECONDS mkdir adsorptionenergy_${1} cd adsorptionenergy_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: adsorptionenergy $1 $2 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: adsorptionenergy $1 $2 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: adsorptionenergy $1 $2 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: adsorptionenergy $1 $2 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi printoutputbackup=$PRINTOUTPUT mkdir clean_surface cd clean_surface updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false relaxation $1 PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup cd relaxation_${1} if [ "$MAINENE" = 1 ]; then array2=($(grep 'free en' OUTCAR | tail -1)) energy_clean_surface=${array2[4]} fi if [ "$MAINENE" = 2 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) energy_clean_surface=${array2[4]} fi if [ "$MAINENE" = 3 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) energy_clean_surface=${array2[7]} fi cd .. cd .. mkdir surface_with_adsorbate cd surface_with_adsorbate mkdir part1 cd part1 name="SELECTIVE_DYNAMICS_DEPTH_$1" backupseldyn=`echo ${!name}` name="SELECTIVE_DYNAMICS_DEPTH_$1" eval $name=0 backupediffg=$EDIFFG EDIFFG=0 backupnsw=$NSW NSW=16 backupnelm=$NELM NELM=60 updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false relaxation $1 $2 "$3" "$4" "$5" "$6" $7 "$8" "$9" "${10}" "${11}" ${12} "${13}" "${14}" "${15}" "${16}" ${17} "${18}" "${19}" "${20}" "${21}" ${22} "${23}" "${24}" "${25}" "${26}" ${27} "${28}" "${29}" "${30}" "${31}" ${32} "${33}" "${34}" "${35}" "${36}" ${37} "${38}" "${39}" "${40}" "${41}" ${42} "${43}" "${44}" "${45}" "${46}" ${47} "${48}" "${49}" "${50}" "${51}" ${52} "${53}" "${54}" "${55}" "${56}" ${57} "${58}" "${59}" "${60}" "${61}" ${62} "${63}" "${64}" "${65}" "${66}" ${67} "${68}" "${69}" "${70}" "${71}" ${72} "${73}" "${74}" "${75}" "${76}" ${77} "${78}" "${79}" "${80}" "${81}" PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup name="SELECTIVE_DYNAMICS_DEPTH_$1" eval $name=$backupseldyn EDIFFG=$backupediffg NSW=$backupnsw NELM=$backupnelm cd .. mkdir part2 cd part2 updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false buildincar echo "#ionic relaxation:" >> INCAR echo "IBRION = $IBRION" >> INCAR echo "EDIFFG = $EDIFFG" >> INCAR echo "NSW = $NSW" >> INCAR echo "POTIM = $POTIM" >> INCAR echo "ISIF = $ISIF" >> INCAR echo " " >> INCAR cp ../part1/relaxation_${1}/KPOINTS . cp ../part1/relaxation_${1}/POTCAR . cp ../part1/relaxation_${1}/minipotcar . cp ../part1/relaxation_${1}/defaultshiftsandratios . cp ../part1/relaxation_${1}/poscardescription . cp ../part1/relaxation_${1}/CONTCAR . linewuthint=$(sed -n "7p" CONTCAR) sumatoms=0 summolatoms=0 for word in $linewuthint; do let sumatoms=$sumatoms+$word if [ "$word" -eq "1" ]; then let summolatoms=$summolatoms+$word fi done let fvwfwvw=$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR\*$backupseldyn let shdfbv=$fvwfwvw+1+$sumatoms+$summolatoms tail -n $shdfbv CONTCAR | tr 'F' 'T' > temp_file2 head -n -$shdfbv CONTCAR > temp_file1 rm CONTCAR cat temp_file1 >> POSCAR cat temp_file2 >> POSCAR rm temp_file1 rm temp_file2 if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR XDATCAR fi sInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup if [ "$MAINENE" = 1 ]; then array2=($(grep 'free en' OUTCAR | tail -1)) energy_surface_with_adsorbate=${array2[4]} fi if [ "$MAINENE" = 2 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) energy_surface_with_adsorbate=${array2[4]} fi if [ "$MAINENE" = 3 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) energy_surface_with_adsorbate=${array2[7]} fi cd .. cd .. adsorption_energy=`echo - $energy_surface_with_adsorbate + $energy_clean_surface | bc -l` nummol=0 for i in $(seq 0 1 16) ; do let j=$i\*5+3 name="${j}" molecccc=`echo ${!name}` if [ -n "$molecccc" ]; then let nummol=$nummol+1 name="ENERGY_$molecccc" energy_molecule=`echo ${!name}` mkdir tpdir cd tpdir $molecccc cd .. rm -r tpdir adsorption_energy=`echo $adsorption_energy + $energy_molecule \* $ATOMS_PER_SUBCELL | bc -l` fi done adsorption_energy=`echo $adsorption_energy / $nummol | bc -l` PRINTOUTPUT=$printoutputbackup if [ "$PRINTOUTPUT" = true ]; then echo " " echo " resulting adsorption energy: $adsorption_energy eV " echo " " >> $MAINDIR/output.txt echo " resulting adsorption energy: $adsorption_energy eV " >> $MAINDIR/output.txt fi let secs=$SECONDS-$secsadsorptionenergy let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$adsorption_energy cd .. } ########################################################################################### ########################################################################################### ########################################################################################### surfaceenergy () { secssurfaceenergy=$SECONDS mkdir surfaceenergy_${1} cd surfaceenergy_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: surfaceenergy $1 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: surfaceenergy $1 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: surfaceenergy $1 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: surfaceenergy $1 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi printoutputbackup=$PRINTOUTPUT if [ "$RECALCSURFACE" = "true" ]; then mkdir surface cd surface updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false relaxation $1 PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup cd relaxation_${1} array1=($(grep 'number of ions' OUTCAR)) N=${array1[11]} if [ "$MAINENE" = 1 ]; then array2=($(grep 'free en' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 2 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 3 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[7]} fi energy_slab=`echo $value2 / $N | bc -l` cd .. cd .. else mkdir temppppp cd temppppp $1 cd .. rm -r temppppp name="ENERGY_$1" energy_slab=`echo ${!name}` fi if [ "$RECALCBULK" = "true" ]; then mkdir bulk cd bulk name="VACUUM_SIZE_$1" backupvacuum=`echo ${!name}` name="NUMBER_OF_LAYERS_$1" backuplayers=`echo ${!name}` let dif=$backuplayers%$ATOMS_PER_SUBCELL let newnumberoflayers=$backuplayers-$dif name="VACUUM_SIZE_$1" eval $name=0 name="NUMBER_OF_LAYERS_$1" eval $name=$newnumberoflayers name="LAYER_HIGHTS_$1" backuplayerhights=`echo ${!name}` name="LAYER_HIGHTS_$1" eval $name="defaulthights" updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false electronicmin $1 PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup name="LAYER_HIGHTS_$1" eval $name="$backuplayerhights" cd electronicmin_${1} array1=($(grep 'number of ions' OUTCAR)) N=${array1[11]} if [ "$MAINENE" = 1 ]; then array2=($(grep 'free en' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 2 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 3 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[7]} fi energy_bulk=`echo $value2 / $N | bc -l` cd .. name="VACUUM_SIZE_$1" eval $name=$backupvacuum name="NUMBER_OF_LAYERS_$1" eval $name=$backuplayers cd .. else name="NUMBER_OF_LAYERS_$1" backuplayers=`echo ${!name}` akjfvlakjb=`echo "$1" | sed 's/....$//'` name="ENERGY_$akjfvlakjb" energy_bulk=`echo ${!name}` fi surface_energy_per_surface_atom=`echo $energy_slab \* $backuplayers \* $NUMBER_OF_ATOMS_PER_LAYER_PER_CELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR - $energy_bulk \* $backuplayers \* $NUMBER_OF_ATOMS_PER_LAYER_PER_CELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` denom=`echo 2 \* $NUMBER_OF_ATOMS_PER_LAYER_PER_CELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` surface_energy_per_surface_atom=`echo $surface_energy_per_surface_atom / $denom | bc -l` if [ "$RECALCSURFACE" = "true" ]; then cd surface cd relaxation_${1} lattice_vectors=() count=0 while read line; do if [ $count -ge 2 ] && [ $count -le 4 ]; then lattice_vectors+=("$line") fi count=$((count + 1)) done < CONTCAR cd .. cd .. else mkdir temmmp cd temmmp $1 lattice_vectors=() count=0 while read line; do if [ $count -ge 2 ] && [ $count -le 4 ]; then lattice_vectors+=("$line") fi count=$((count + 1)) done < POSCAR cd .. rm -r temmmp fi lattice_vectors=( $(echo ${lattice_vectors[@]}) ) normal_vector_x=$(echo "${lattice_vectors[1]} * ${lattice_vectors[5]} - ${lattice_vectors[2]} * ${lattice_vectors[4]}" | bc -l) normal_vector_y=$(echo "${lattice_vectors[2]} * ${lattice_vectors[3]} - ${lattice_vectors[0]} * ${lattice_vectors[5]}" | bc -l) normal_vector_z=$(echo "${lattice_vectors[0]} * ${lattice_vectors[4]} - ${lattice_vectors[1]} * ${lattice_vectors[3]}" | bc -l) area=$(echo "sqrt(${normal_vector_x}^2 + ${normal_vector_y}^2 + ${normal_vector_z}^2)" | bc -l) surface_energy_per_surface_area=`echo $energy_slab \* $backuplayers \* $NUMBER_OF_ATOMS_PER_LAYER_PER_CELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR - $energy_bulk \* $backuplayers \* $NUMBER_OF_ATOMS_PER_LAYER_PER_CELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` denom=`echo 2 \* $area | bc -l` surface_energy_per_surface_area=`echo $surface_energy_per_surface_area / $denom | bc -l` PRINTOUTPUT=$printoutputbackup if [ "$PRINTOUTPUT" = true ]; then echo " " echo " resulting surface energy per surface atom: $surface_energy_per_surface_atom eV " echo " resulting surface energy per surface area: $surface_energy_per_surface_area eV / Angstrom^2 " if [ "$RECALCSURFACE" = "true" ]; then echo " energy of relaxed surface slab: $energy_slab eV " fi if [ "$RECALCBULK" = "true" ]; then echo " energy of surface slab without vacuum (# of layers addapted): $energy_bulk eV " fi echo " " >> $MAINDIR/output.txt echo " resulting surface energy per surface atom: $surface_energy_per_surface_atom eV " >> $MAINDIR/output.txt echo " resulting surface energy per surface area: $surface_energy_per_surface_area eV / Angstrom^2 " >> $MAINDIR/output.txt if [ "$RECALCSURFACE" = "true" ]; then echo " energy of relaxed surface slab: $energy_slab eV " >> $MAINDIR/output.txt fi if [ "$RECALCBULK" = "true" ]; then echo " energy of surface slab without vacuum (# of layers addapted): $energy_bulk eV " >> $MAINDIR/output.txt fi fi let secs=$SECONDS-$secssurfaceenergy let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$surface_energy_per_surface_atom cd .. } ########################################################################################### ########################################################################################### ########################################################################################### vacancyformationenergy () { secsvacancyformationenergy=$SECONDS mkdir vacancyformationenergy_${1} cd vacancyformationenergy_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: vacancyformationenergy $1 $2 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: vacancyformationenergy $1 $2 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: vacancyformationenergy $1 $2 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: vacancyformationenergy $1 $2 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi mkdir vacancy cd vacancy updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false relaxation $1 $2 "$3" "$4" "$5" "$6" $7 "$8" "$9" "${10}" "${11}" ${12} "${13}" "${14}" "${15}" "${16}" ${17} "${18}" "${19}" "${20}" "${21}" ${22} "${23}" "${24}" "${25}" "${26}" ${27} "${28}" "${29}" "${30}" "${31}" ${32} "${33}" "${34}" "${35}" "${36}" ${37} "${38}" "${39}" "${40}" "${41}" ${42} "${43}" "${44}" "${45}" "${46}" ${47} "${48}" "${49}" "${50}" "${51}" ${52} "${53}" "${54}" "${55}" "${56}" ${57} "${58}" "${59}" "${60}" "${61}" ${62} "${63}" "${64}" "${65}" "${66}" ${67} "${68}" "${69}" "${70}" "${71}" ${72} "${73}" "${74}" "${75}" "${76}" ${77} "${78}" "${79}" "${80}" "${81}" PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup cd relaxation_${1} array1=($(grep 'number of ions' OUTCAR)) N=${array1[11]} if [ "$MAINENE" = 1 ]; then array2=($(grep 'free en' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 2 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 3 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[7]} fi energy_defect=`echo $value2 / $N | bc -l` cd temp arraylatticeconst=($(grep 'ALAT' OUTCAR)) latticeconstt=${arraylatticeconst[2]} latticeconst=`echo $latticeconstt / $SUPERCELL_FACTOR | bc -l` if [ "$LATTICE_SYSTEM" = cubic ]; then volume_defect=`echo $latticeconst \* $latticeconst \* $latticeconst / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` volume_defect_gfcytc=$volume_defect volume_defect=`echo $volume_defect \* $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR / $N | bc -l` fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} volume_defect=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio \* 0.86602540378443864676372317075294 / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` volume_defect_gfcytc=$volume_defect volume_defect=`echo $volume_defect \* $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR / $N | bc -l` fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} volume_defect=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` volume_defect_gfcytc=$volume_defect volume_defect=`echo $volume_defect \* $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR / $N | bc -l` fi cd .. cd .. cd .. if [ "$RECALCBULK" = "true" ]; then mkdir bulk cd bulk updatevariablesbackup=$UPDATEVARIABLES printoutputbackup=$PRINTOUTPUT UPDATEVARIABLES=false PRINTOUTPUT=false relaxation $1 PRINTOUTPUT=$printoutputbackup UPDATEVARIABLES=$updatevariablesbackup cd relaxation_${1} if [ "$MAINENE" = 1 ]; then array2=($(grep 'free en' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 2 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[4]} fi if [ "$MAINENE" = 3 ]; then array2=($(grep 'energy without entropy' OUTCAR | tail -1)) value2=${array2[7]} fi array1=($(grep 'number of ions' OUTCAR)) M=${array1[11]} energy_perfect=`echo $value2 / $M | bc -l` cd temp arraylatticeconst=($(grep 'ALAT' OUTCAR)) latticeconstt=${arraylatticeconst[2]} latticeconst=`echo $latticeconstt / $SUPERCELL_FACTOR | bc -l` if [ "$LATTICE_SYSTEM" = cubic ]; then volume_perfect=`echo $latticeconst \* $latticeconst \* $latticeconst / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` volume_perfect_gfcytc=$volume_perfect volume_perfect=`echo $volume_perfect \* $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR / $M | bc -l` fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} volume_perfect=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio \* 0.86602540378443864676372317075294 / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` volume_perfect_gfcytc=$volume_perfect volume_perfect=`echo $volume_perfect \* $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR / $M | bc -l` fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} volume_perfect=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` volume_perfect_gfcytc=$volume_perfect volume_perfect=`echo $volume_perfect \* $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR / $M | bc -l` fi cd .. cd .. cd .. else name="ENERGY_$1" energy_perfect=`echo ${!name}` name="VOLUME_$1" volume_perfect=`echo ${!name}` fi #if [ "$1" = contcar ]; then #array=($(awk '{ if (NR==1) print $0 }' POSCAR)) #bfrv=${array[0]} #name="FREE_ENERGY_$bfrv" #energy_perfect=`echo ${!name}` #name="VOLUME_$bfrv" #volume_perfect=`echo ${!name}` #fi energy_formation=`echo $energy_defect \* $N - $energy_perfect \* $N | bc -l` volume_formation=`echo $volume_defect \* $N - $volume_perfect \* $N | bc -l` ratio_energy=`echo $energy_formation / $energy_perfect | bc -l` ratio_volume=`echo $volume_formation / $volume_perfect | bc -l` if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Energy per atom of structure with defect: $energy_defect eV" if [ "$RECALCBULK" = "true" ]; then echo " Energy per atom of structure without defect: $energy_perfect eV" fi echo " resulting vacancy formation energy: $energy_formation eV " echo " resulting vacancy formation volume: $volume_formation Angstrom^3 " echo " vacancy formation energy / bulk energy per atom: $ratio_energy " echo " vacancy formation volume / bulk volume per atom: $ratio_volume " echo " VOLUME_$1 for structure with defect: $volume_defect_gfcytc " echo " " >> $MAINDIR/output.txt echo " Energy per atom of structure with defect: $energy_defect eV" >> $MAINDIR/output.txt if [ "$RECALCBULK" = "true" ]; then echo " Energy per atom of structure without defect: $energy_perfect eV" >> $MAINDIR/output.txt fi echo " resulting vacancy formation energy: $energy_formation eV " >> $MAINDIR/output.txt echo " resulting vacancy formation volume: $volume_formation Angstrom^3 " >> $MAINDIR/output.txt echo " vacancy formation energy / bulk energy per atom: $ratio_energy " >> $MAINDIR/output.txt echo " vacancy formation volume / bulk volume per atom: $ratio_volume " >> $MAINDIR/output.txt echo " VOLUME_$1 for structure with defect: $volume_defect_gfcytc " >> $MAINDIR/output.txt fi let secs=$SECONDS-$secsvacancyformationenergy let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$energy_formation cd .. } ########################################################################################### ########################################################################################### ########################################################################################### applymlff () { # $2 is for addvacancy ... / addadsorbant ... secs=$SECONDS mkdir applymlff_${1}_${2}_${3} cd applymlff_${1}_${2}_${3} if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: applymlff $1 $2 $3 $4 $5 $6 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: applymlff $1 $2 $3 $4 $5 $6 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: applymlff $1 $2 $3 $4 $5 $6 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: applymlff $1 $2 $3 $4 $5 $6 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi backupbvotherincartags=$OTHERINCARTAGS OTHERINCARTAGS="$backupbvotherincartags ; ML_LMLFF = .TRUE. ; ML_ISTART = 2 ;" vjsnjsfnv=$(pwd) mkdir $MAINDIR/tempfjnjn cd $MAINDIR/tempfjnjn cp $MAINDIR/mlffs/$1/ML_FFN ML_FF backupbvotherinputfiles=$OTHERINPUTFILES OTHERINPUTFILES="$backupbvotherinputfiles $MAINDIR/tempfjnjn/ML_FF" cd $vjsnjsfnv backupbvencut=$ENCUT ENCUT=20 MLFFBEIGAPPLIED=true $2 "$3" "$4" "$5" "$6" "$7" "$8" "$9" "${10}" "${11}" "${12}" "${13}" "${14}" "${15}" "${16}" "${17}" "${18}" "${19}" "${20}" "${21}" "${22}" "${23}" "${24}" "${25}" "${26}" "${27}" "${28}" "${29}" "${30}" "${31}" "${32}" "${33}" "${34}" "${35}" "${36}" "${37}" "${38}" "${39}" "${40}" "${41}" "${42}" "${43}" "${44}" "${45}" "${46}" "${47}" "${48}" "${49}" "${50}" "${51}" "${52}" "${53}" "${54}" "${55}" "${56}" "${57}" "${58}" "${59}" "${60}" "${61}" "${62}" "${63}" "${64}" "${65}" "${66}" "${67}" "${68}" "${69}" "${70}" "${71}" "${72}" "${73}" "${74}" "${75}" "${76}" "${77}" "${78}" "${79}" "${80}" "${81}" MLFFBEIGAPPLIED=false OTHERINCARTAGS="$backupbvotherincartags" OTHERINPUTFILES="backupbvotherinputfiles" ENCUT=$backupbvencut rm -r $MAINDIR/tempfjnjn cd .. } ########################################################################################### ########################################################################################### ########################################################################################### elasticmoduli () { secs=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: elasticmoduli $1 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: elasticmoduli $1 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: elasticmoduli $1 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: elasticmoduli $1 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi mkdir elasticmoduli_${1} cd elasticmoduli_${1} if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi $1 buildkpoints $1 buildincar echo "#elastic mouduli calculation:" >> INCAR #echo "LPHON_DISPERSION = .TRUE." >> INCAR echo "IBRION = 6" >> INCAR echo "NSW = 1" >> INCAR echo "POTIM = 0.015" >> INCAR echo "ISIF = 3" >> INCAR echo " " >> INCAR buildpotcar $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST DYNMAT INCAR REPORT defaultshiftsandratios XDATCAR KPOINTS CHGCAR poscardescription POSCAR CONTCAR DOSCAR vasprun.xml WAVECAR minipotcar POTCAR EIGENVAL PCDAT CHG IBZKPT fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi if [ "$PRINTOUTPUT" = true ]; then echo " " echo " total elastic tensor (kBar):" sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; p }' OUTCAR sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; p }' OUTCAR sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; p }' OUTCAR sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; p }' OUTCAR sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; p }' OUTCAR sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; n; p }' OUTCAR sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; n; n; p }' OUTCAR echo " " >> $MAINDIR/output.txt echo " total elastic tensor (kBar):" >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; p }' OUTCAR >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; p }' OUTCAR >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; p }' OUTCAR >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; p }' OUTCAR >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; p }' OUTCAR >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; n; p }' OUTCAR >> $MAINDIR/output.txt sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; n; n; p }' OUTCAR >> $MAINDIR/output.txt fi array1=($(sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; p }' OUTCAR)) array2=($(sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; p }' OUTCAR)) array3=($(sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; p }' OUTCAR)) array4=($(sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; p }' OUTCAR)) array5=($(sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; n; p }' OUTCAR)) array6=($(sed -n '/TOTAL ELASTIC MODULI (kBar)/{ n; n; n; n; n; n; n; n; p }' OUTCAR)) const11=${array1[1]} const12=${array2[1]} const13=${array3[1]} const21=${array1[2]} const22=${array2[2]} const23=${array3[2]} const31=${array1[3]} const32=${array2[3]} const33=${array3[3]} const44=${array4[4]} const55=${array5[5]} const66=${array6[6]} #if [ "$LATTICE_SYSTEM" = cubic ]; then #bulkmodulus=`echo $const11 \* 0.3333333333333333 \* 0.1 + 2 \* $const12 \* 0.3333333333333333 \* 0.1 | bc -l` #shearmodulus=`echo $const44 \* 0.1 | bc -l` #youngsmodulus1=`echo $const11 \* 0.1 - $const12 \* 0.1 | bc -l` #youngsmodulus2=`echo $const11 \* 0.1 + 2 \* $const12 \* 0.1 | bc -l` #youngsmodulus3=`echo $const11 \* 0.1 + $const12 \* 0.1 | bc -l` #youngsmodulus=`echo $youngsmodulus1 \* $youngsmodulus2 / $youngsmodulus3 | bc -l` #poissonratio1=`echo $const11 + $const12 | bc -l` #poissonratio_100=`echo $const12 / $poissonratio1 | bc -l` #bgratio=`echo $bulkmodulus / $shearmodulus | bc -l` #poissonratio1=`echo 3 \* $bulkmodulus - 2 \* $shearmodulus | bc -l` #poissonratio2=`echo 6 \* $bulkmodulus + 2 \* $shearmodulus | bc -l` #poissonratio=`echo $poissonratio1 / $poissonratio2 | bc -l` #youngsmodulus=`echo 2 \* $shearmodulus \* 1 + 2 \* $shearmodulus \* poissonratio | bc -l` #fi #if [ "$LATTICE_SYSTEM" = hexagonal ]; then #bulkmodulus=`echo 2 \* $const11 \* 0.1111111111111111 \* 0.1 + 2 \* $const12 \* 0.1111111111111111 \* 0.1 + 4 \* $const13 \* 0.1111111111111111 \* 0.1 + $const33 \* 0.1111111111111111 \* 0.1 | bc -l` #shearmodulus=`echo 3.5 \* $const11 \* 0.0666666666666667 - 2.5 \* $const12 \* 0.0666666666666667 - 2 \* $const13 \* 0.0666666666666667 + $const33 \* 0.0666666666666667 + 6 \* $const44 \* 0.0666666666666667 | bc -l` #youngsmodulus1=`echo 3 \* 4.5 \* $const11 + 3 \* 2.5 \* $const12 + 3 \* 6 \* $const13 + 3 \* 2 \* $const23 + 3 \* 2 \* $const44 | bc -l` #youngsmodulus=`echo $shearmodulus \* 15 \* $bulkmodulus \* 9 / $youngsmodulus1 | bc -l` #poissonratio_100= #bgratio=`echo $bulkmodulus / $shearmodulus | bc -l` #fi bulkmodulus=`echo $const11 \* 0.1111111111111111 \* 0.1 + $const22 \* 0.1111111111111111 \* 0.1 + $const33 \* 0.1111111111111111 \* 0.1 + 2 \* $const12 \* 0.1111111111111111 \* 0.1 + 2 \* $const23 \* 0.1111111111111111 \* 0.1 + 2 \* $const31 \* 0.1111111111111111 \* 0.1 | bc -l` shearmodulus=`echo $const11 \* 0.0666666666666667 \* 0.1 + $const22 \* 0.0666666666666667 \* 0.1 + $const33 \* 0.0666666666666667 \* 0.1 - $const12 \* 0.0666666666666667 \* 0.1 - $const23 \* 0.0666666666666667 \* 0.1 - $const31 \* 0.0666666666666667 \* 0.1 + 3 \* $const44 \* 0.0666666666666667 \* 0.1 + 3 \* $const55 \* 0.0666666666666667 \* 0.1 + 3 \* $const66 \* 0.0666666666666667 \* 0.1 | bc -l` poissonratio1=`echo 3 \* $bulkmodulus - 2 \* $shearmodulus | bc -l` poissonratio2=`echo 6 \* $bulkmodulus + 2 \* $shearmodulus | bc -l` poissonratio=`echo $poissonratio1 / $poissonratio2 | bc -l` youngsmodulus=`echo 3 \* $bulkmodulus - 6 \* $bulkmodulus \* $poissonratio | bc -l` bgratio=`echo $bulkmodulus / $shearmodulus | bc -l` #bulkmodulus=`echo 2 \* $const11 \* 0.1111111111111111 \* 0.1 + 2 \* $const12 \* 0.1111111111111111 \* 0.1 + 4 \* $const13 \* 0.1111111111111111 \* 0.1 + $const33 \* 0.1111111111111111 \* 0.1 | bc -l` #shearmodulus=`echo 3.5 \* $const11 \* 0.0666666666666667 \* 0.1 - 2.5 \* $const12 \* 0.0666666666666667 \* 0.1 - 2 \* $const13 \* 0.0666666666666667 \* 0.1 + $const33 \* 0.0666666666666667 \* 0.1 + 6 \* $const44 \* 0.0666666666666667 \* 0.1 | bc -l` #youngsmodulus1=`echo 3 \* 4.5 \* $const11 \* 0.1 + 3 \* 2.5 \* $const12 \* 0.1 + 3 \* 6 \* $const13 \* 0.1 + 3 \* 2 \* $const23 \* 0.1 + 3 \* 2 \* $const44 \* 0.1 | bc -l` #youngsmodulus=`echo $shearmodulus \* 15 \* $bulkmodulus \* 9 / $youngsmodulus1 | bc -l` #poissonratio=`echo -1.0 + 0.5 \* $youngsmodulus / $shearmodulus | bc -l` #bgratio=`echo $bulkmodulus / $shearmodulus | bc -l` bulkmodinevangst=`echo $bulkmodulus \* 0.006242 | bc -l` shearmodinevangst=`echo $shearmodulus \* 0.006242 | bc -l` youngsmodinevangst=`echo $youngsmodulus \* 0.006242 | bc -l` if [ "$PRINTOUTPUT" = true ]; then echo " " echo " => bulk modulus =" $bulkmodulus "GPa =" $bulkmodinevangst "eV/Angstrom^3 " echo " shear modulus =" $shearmodulus "GPa =" $shearmodinevangst "eV/Angstrom^3 " echo " youngs modulus =" $youngsmodulus "GPa =" $youngsmodinevangst "eV/Angstrom^3 " echo " poisson ratio =" $poissonratio echo " bulk modulus / shear modulus =" $bgratio echo " " >> $MAINDIR/output.txt echo " => bulk modulus =" $bulkmodulus "GPa =" $bulkmodinevangst "eV/Angstrom^3 " >> $MAINDIR/output.txt echo " shear modulus =" $shearmodulus "GPa =" $shearmodinevangst "eV/Angstrom^3 " >> $MAINDIR/output.txt echo " youngs modulus =" $youngsmodulus "GPa =" $youngsmodinevangst "eV/Angstrom^3 " >> $MAINDIR/output.txt echo " poisson ratio =" $poissonratio >> $MAINDIR/output.txt echo " bulk modulus / shear modulus =" $bgratio >> $MAINDIR/output.txt fi let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$bulkmodulus cd .. } ########################################################################################### ########################################################################################### ########################################################################################### energyvolumecurves () { secsenergyvolumecurves=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: energyvolumecurves \"$1\" $2 $3 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: energyvolumecurves \"$1\" $2 $3 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: energyvolumecurves \"$1\" $2 $3 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: energyvolumecurves \"$1\" $2 $3 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi structure=() energy=() x=-1 for i in $1; do let x=x+1 name="ENERGY_$i" ener=`echo ${!name}` structure[$x]=$i energy[$x]=$ener done for ((i = 0; i<5; i++)) ; do for ((j = 0; j<5-i-1; j++)) ; do if [ "$(echo "${energy[$j]} > ${energy[$((j+1))]}" | bc)" -eq 1 ]; then temp=${energy[j]} energy[$j]=${energy[$((j+1))]} energy[$((j+1))]=$temp tempstr=${structure[j]} structure[$j]=${structure[$((j+1))]} structure[$((j+1))]=$tempstr fi done done if [ "$PRINTOUTPUT" = true ]; then echo " " echo " phase stability table (in order):" echo " phase energy per atom (eV) energy difference to the most stable phase (eV) " N=${#structure[@]} let NN=N-1 fffffffff=${energy[0]} for i in $(seq 0 1 $NN) ; do diff=`echo ${energy[$i]} - $fffffffff | bc -l` #fffffffff=${energy[$i]} echo " " ${structure[$i]} " " ${energy[$i]} " " $diff done echo " " >> $MAINDIR/output.txt echo " phase stability table (in order):" >> $MAINDIR/output.txt echo " phase energy per atom (eV) energy difference to the most stable phase (eV) " >> $MAINDIR/output.txt N=${#structure[@]} let NN=N-1 fffffffff=${energy[0]} for i in $(seq 0 1 $NN) ; do diff=`echo ${energy[$i]} - $fffffffff | bc -l` fffffffff=${energy[$i]} echo " " ${structure[$i]} " " ${energy[$i]} " " $diff >> $MAINDIR/output.txt done fi mkdir energyvolumecurves cd energyvolumecurves mkdir pldirs for i in $1; do cd pldirs mkdir pldir_${i} cd .. mkdir $i cd $i #if [ -n "$KSPACING" ]; then #mkdir tempforkpts #cd tempforkpts # #buildposcar $i #nelmbackup=$NELM #NELM=1 #buildincar #buildpotcar #$VASP #NELM=$nelmbackup # #generate k-points for: 8 8 8 # # #kspacingbackup=$KSPACING #KSPACING= # #cd .. #fi name="VOLUME_$i" backupvvvol=`echo ${!name}` name="ENERGY_$i" backupeeen=`echo ${!name}` if [ -n "$KSPACING" ]; then backupkspacing=$KSPACING fi for j in $(seq 1 1 $2); do mkdir $j cd $j jnlkfvjk=`echo $j - 0.5 - $2 / 2 | bc -l` afragrgw=`echo -0.5 + $2 / 2 | bc -l` jvwoejvnwojvnwe=`echo $3 \* $backupvvvol / 100 | bc -l` fnjfvkfn=`echo $jnlkfvjk \* $jvwoejvnwojvnwe / $afragrgw | bc -l` vvol=`echo $backupvvvol + $fnjfvkfn | bc -l` name="VOLUME_$i" eval $name=$vvol if [ -n "$KSPACING" ]; then backuplatccoonsst=`echo " e( l($backupvvvol)/3 ) " | bc -l` latccoonsst=`echo " e( l($vvol)/3 ) " | bc -l` KSPACING=`echo $backupkspacing \* $backuplatccoonsst / $latccoonsst | bc -l` fi isifbackup=$ISIF ISIF=4 PRINTOUTPUT=false relaxation $i PRINTOUTPUT=true ISIF=$isifbackup cd .. name="ENERGY_$i" enerryy=`echo ${!name}` echo $vvol " Angstrom^3 per atom " $enerryy " eV " >> energies.dat cd $j cd relaxation_${i} pprreea=($(grep 'external pressure' OUTCAR | tail -1)) pprree=${pprreea[3]} pprreeevan=`echo $pprree \* 0.0006242 | bc -l` eennttaallppppy=`echo $enerryy + $pprreeevan \* $vvol | bc -l` cd .. cd .. echo $vvol " Angstrom^3 per atom " $pprreeevan " eV/Angstrom^3 " >> pressures.dat echo $pprreeevan " eV/Angstrom^3 " $eennttaallppppy " eV " >> enthalpies.dat cd .. cd pldirs cd pldir_${i} echo $vvol " " $enerryy >> data.dat cd .. cd .. cd $i done name="VOLUME_$i" eval $name=$backupvvvol name="ENERGY_$i" eval $name=$backupeeen if [ -n "$KSPACING" ]; then KSPACING=$backupkspacing fi cd .. done #cd pldirs #for i in $1; do #cd pldir_${i} #eennee2=0 #vvooll2=0 #for j in $(seq 1 1 $2); do #akjrnvkjnv=($(sed -n "$j"'p' < data.dat)) #eennee1=${akjrnvkjnv[1]} #vvooll1=${akjrnvkjnv[0]} #delene=`echo $eennee2 - $eennee1 | bc -l` #delvol=`echo $vvooll2 - $vvooll1 | bc -l` #steig=`echo $delene / $delvol | bc -l` #hohe=`echo $eennee1 - $steig \* $vvooll1 | bc -l` #echo $vvooll1 " " $eennee1 " " $steig " " $hohe >> critpress.dat #eennee2=$eennee1 #vvooll2=$vvooll1 #done #cd .. #done #cd .. cd pldirs for i in $1; do cd pldir_${i} for j in $(seq 1 1 $2); do akjrnvkjnv=($(sed -n "$j"'p' < data.dat)) eennee=${akjrnvkjnv[1]} vvooll=${akjrnvkjnv[0]} cd .. cd .. cd $i cd $j cd relaxation_${i} pprreea=($(grep 'external pressure' OUTCAR | tail -1)) pprree=${pprreea[3]} pprreeevan=`echo $pprree \* 0.0006242 | bc -l` cd .. cd .. cd .. cd pldirs cd pldir_${i} hohe=`echo $eennee + $pprreeevan \* $vvooll | bc -l` echo $pprreeevan " " $hohe >> critpress.dat done cd .. done cd .. svfnjgvgergtbe="p " njeorjtgnejben="p " jnjnvwnjijwvtj="p " for i in $1; do svfnjgvgergtbe=$svfnjgvgergtbe"'"$i"/energies.dat' u 1:5 w l title '"$i"', " njeorjtgnejben=$njeorjtgnejben"'"$i"/pressures.dat' u 1:5 w l title '"$i"', " jnjnvwnjijwvtj=$jnjnvwnjijwvtj"'"$i"/enthalpies.dat' u 1:3 w l title '"$i"', " done if [ -n "$METAGGA" ]; then cat > energyvolumecurves_gnup_${METAGGA} << EOF set title "Energy-volume curves ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Energy per atom (eV)" set term png set output "energyvolumecurves_${METAGGA}.png" $svfnjgvgergtbe EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT energyvolumecurves_gnup_${METAGGA} fi cat > pressurevolumecurves_gnup_${METAGGA} << EOF set title "Pressure-volume curves ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Pressure (eV/{\305}^3)" set term png set output "pressurevolumecurves_${METAGGA}.png" $njeorjtgnejben EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT pressurevolumecurves_gnup_${METAGGA} fi cat > enthalpypressurecurves_gnup_${METAGGA} << EOF set title "Enthalpy-pressure curves ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Pressure (eV/{\305}^3)" set ylabel "Enthalpy (eV)" set term png set output "enthalpypressurecurves_${METAGGA}.png" $jnjnvwnjijwvtj EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT enthalpypressurecurves_gnup_${METAGGA} fi else cat > energyvolumecurves_gnup_${GGA} << EOF set title "Energy-volume curves ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Energy per atom (eV)" set term png set output "energyvolumecurves_${GGA}.png" $svfnjgvgergtbe EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT energyvolumecurves_gnup_${GGA} fi cat > pressurevolumecurves_gnup_${GGA} << EOF set title "Pressure-volume curves ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Pressure (eV/{\305}^3)" set term png set output "pressurevolumecurves_${GGA}.png" $njeorjtgnejben EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT pressurevolumecurves_gnup_${GGA} fi cat > enthalpypressurecurves_gnup_${GGA} << EOF set title "Enthalpy-pressure curves ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Pressure (eV/{\305}^3)" set ylabel "Enthalpy (eV)" set term png set output "enthalpypressurecurves_${GGA}.png" $jnjnvwnjijwvtj EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT enthalpypressurecurves_gnup_${GGA} fi fi cd pldirs plotxydata++ data.dat cd .. let secs=$SECONDS-$secsenergyvolumecurves let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### fitbirchmurnaghan () { secsfitbirchmurnaghan=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: fitbirchmurnaghan $1 $2 $3 $4 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: fitbirchmurnaghan $1 $2 $3 $4 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: fitbirchmurnaghan $1 $2 $3 $4 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: fitbirchmurnaghan $1 $2 $3 $4 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi mkdir fitbirchmurnaghan_${3} cd fitbirchmurnaghan_${3} name="ENERGY_$3" backupen=`echo ${!name}` name="VOLUME_$3" backupvol=`echo ${!name}` if [ -n "$KSPACING" ]; then backupkspacing=$KSPACING fi for j in $(seq 1 1 $1); do mkdir $j cd $j jnlkfvjk=`echo $j - 0.5 - $1 / 2 | bc -l` afragrgw=`echo -0.5 + $1 / 2 | bc -l` jvwoejvnwojvnwe=`echo $2 \* $backupvol / 100 | bc -l` fnjfvkfn=`echo $jnlkfvjk \* $jvwoejvnwojvnwe / $afragrgw | bc -l` vvol=`echo $backupvol + $fnjfvkfn | bc -l` name="VOLUME_$3" eval $name=$vvol if [ -n "$KSPACING" ]; then backuplatccoonsst=`echo " e( l($backupvol)/3 ) " | bc -l` latccoonsst=`echo " e( l($vvol)/3 ) " | bc -l` KSPACING=`echo $backupkspacing \* $backuplatccoonsst / $latccoonsst | bc -l` fi isifbackup=$ISIF ISIF=4 PRINTOUTPUT=false ###$2 $1 relaxation $3 $4 "$5" "$6" "$7" "$8" $9 "${10}" "${11}" "${12}" "${13}" ${14} "${15}" "${16}" "${17}" "${18}" ${19} "${20}" "${21}" "${22}" "${23}" ${24} "${25}" "${26}" "${27}" "${28}" ${29} "${30}" "${31}" "${32}" "${33}" ${34} "${35}" "${36}" "${37}" "${38}" ${39} "${40}" "${41}" "${42}" "${43}" ${44} "${45}" "${46}" "${47}" "${48}" ${49} "${50}" "${51}" "${52}" "${53}" ${54} "${55}" "${56}" "${56}" "${58}" ${59} "${60}" "${61}" "${62}" "${63}" ${64} "${65}" "${66}" "${67}" "${68}" ${69} "${70}" "${71}" "${72}" "${73}" ${74} "${75}" "${76}" "${77}" "${78}" ${79} "${80}" "${81}" "${82}" "${83}" PRINTOUTPUT=true ISIF=$isifbackup cd .. name="ENERGY_$3" viuyiuyguy=`echo ${!name}` echo $vvol " Angstrom^3 per atom " $viuyiuyguy " eV " >> energies.dat echo $vvol $viuyiuyguy >> data.dat done if [ -n "$KSPACING" ]; then KSPACING=$backupkspacing fi #name="VOLUME_$1" #eval $name=$backupvol #name="FREE_ENERGY_$1" #iusiunbb=`echo ${!name}` cat > eosfit_31_adapted.py << EOF # eosfit.py fits E(V) data to a Birch-Murnaghan equation of state. # Current version: 3.1 # # Copyright (C) 2012 Kurt Lejaeghere , Center for # Molecular Modeling (CMM), Ghent University, Ghent, Belgium # # eosfit.py is free software; you can redistribute it and/or modify it under # the terms of the GNU Lesser General Public License as published by the Free # Software Foundation; either version 2.1 of the License, or (at your option) # any later version. # # eosfit.py is distributed in the hope that it will be useful, but WITHOUT ANY # WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS # FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for # more details. # # You should have received a copy of the GNU Lesser General Public License # along with eosfit.py; if not, see . # The following code is based on the source code of eos.py from the Atomic # Simulation Environment (ASE) . # Python and numpy are required to use this script. import numpy as np echarge = 1.60217733e-19 def BM(energies): fitdata = np.polyfit(energies[:,0]**(-2./3.), energies[:,1], 3, full=True) ssr = fitdata[1] sst = np.sum((energies[:,1] - np.average(energies[:,1]))**2.) residuals0 = ssr/sst deriv0 = np.poly1d(fitdata[0]) deriv1 = np.polyder(deriv0, 1) deriv2 = np.polyder(deriv1, 1) deriv3 = np.polyder(deriv2, 1) volume0 = 0 x = 0 for x in np.roots(deriv1): # Last check: it's real, no imaginary part if x > 0 and deriv2(x) > 0 and abs(x.imag) < 1.e-8: volume0 = x**(-3./2.) break if volume0 == 0: raise ValueError('Error: No minimum could be found') # Get also the E0 and return it E0 = deriv0(x) derivV2 = 4./9. * x**5. * deriv2(x) derivV3 = (-20./9. * x**(13./2.) * deriv2(x) - 8./27. * x**(15./2.) * deriv3(x)) bulk_modulus0 = derivV2 / x**(3./2.) bulk_deriv0 = -1 - x**(-3./2.) * derivV3 / derivV2 return volume0, E0, bulk_modulus0, bulk_deriv0, residuals0 if __name__ == "__main__": from sys import argv usage = '''\ Use: python eosfit.py filename calculates the Birch-Murnaghan equation of state from a given file, containing in its columns the volumes in A^3/atom and energies in eV/atom, respectively output is printed in filename.eosout --help gives an overview of all options ''' if len(argv) != 2: print('Error: Wrong number of arguments') exit() else: if argv[1] == '--help': print(usage) exit() infile = argv[1] data = np.loadtxt(infile) volume, E, bulk_modulus, bulk_deriv, residuals = BM(data) outstr = '''\ Equation Of State parameters - least squares fit of a Birch Murnaghan curve %.8f \t %.8f \t %.8f \t %.8f V0 \t \t E0 \t \t B0 \t \t BP [A^3/at] \t [eV/at] \t [GPa] \t \t [--] 1-R^2: %.8f ''' % (volume, E, (bulk_modulus * echarge * 1.0e21), bulk_deriv, residuals[0]) outfile = open(infile+'.eosout', 'w') outfile.write(outstr) outfile.close() EOF $PYTHON eosfit_31_adapted.py data.dat array2=($(sed -n '3p' < data.dat.eosout)) name="ENERGY_$i" eval $name=$backupen name="VOLUME_$i" eval $name=$backupvol value22=${array2[1]} if [ "$UPDATEVARIABLES" = true ]; then name="ENERGY_$3" eval $name=$value22 fi value23=${array2[2]} value23=`echo $value23 / 160.2 | bc -l` if [ "$UPDATEVARIABLES" = true ]; then name="BULK_MODULUS_$3" eval $name=$value23 fi jveignjveijvn=`echo $value23 \* 160.2 | bc -l` value24=${array2[0]} if [ "$UPDATEVARIABLES" = true ]; then name="VOLUME_$3" eval $name=$value24 fi bulkmodulusderrivative=${array2[3]} if [ -n "$METAGGA" ]; then cat > fitbirchmurnaghan_gnup_${3}_${METAGGA} << EOF h = $value22 b = $value23 v = $value24 d = $bulkmodulusderrivative e(x) = h + (9.0/16.0)*b*v*( d*((v/x)**(2.0/3.0) - 1)**3 + (((v/x)**(2.0/3.0) - 1)**2)*(6 - 4*(v/x)**(2.0/3.0)) ) set title "$3 Birch-Murnaghan EOS fit ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Energy per atom (eV)" set term png set output "fitbirchmurnaghan_${3}_${METAGGA}.png" p 'energies.dat' u 1:5 w p title 'data points', e(x) title 'fitted EOS' EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT fitbirchmurnaghan_gnup_${3}_${METAGGA} fi else cat > fitbirchmurnaghan_gnup_${3}_${GGA} << EOF h = $value22 b = $value23 v = $value24 d = $bulkmodulusderrivative e(x) = h + (9.0/16.0)*b*v*( d*((v/x)**(2.0/3.0) - 1)**3 + (((v/x)**(2.0/3.0) - 1)**2)*(6 - 4*(v/x)**(2.0/3.0)) ) set title "$3 Birch-Murnaghan EOS fit ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Energy per atom (eV)" set term png set output "fitbirchmurnaghan_${3}_${GGA}.png" p 'energies.dat' u 1:5 w p title 'data points', e(x) title 'fitted EOS' EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT fitbirchmurnaghan_gnup_${3}_${GGA} fi fi if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Murnaghan equation of state has been fitted. Resulting parameters:" echo " volume per atom = " $value24 " Anstrom^3 per atom " echo " energy per atom = " $value22 " eV " echo " bulk modulus = " $value23 " eV/Angstrom^3 = " $jveignjveijvn " GPa " echo " derrivative of bulk modulus wrt pressure = " $bulkmodulusderrivative " eV/Angstrom^3 " if [ "$UPDATEVARIABLES" = true ]; then echo " VOLUME_$3, ENERGY_$3, and BULK_MODULUS_$3 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " Murnaghan equation of state has been fitted. Resulting parameters:" >> $MAINDIR/output.txt echo " volume per atom = " $value24 " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " energy per atom = " $value22 " eV " >> $MAINDIR/output.txt echo " bulk modulus = " $value23 " eV/Angstrom^3 = " $jveignjveijvn " GPa " >> $MAINDIR/output.txt echo " derrivative of bulk modulus wrt pressure = " $bulkmodulusderrivative " eV/Angstrom^3 " >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VOLUME_$3, ENERGY_$3, and BULK_MODULUS_$3 have been updated accordingly " >> $MAINDIR/output.txt fi fi let secs=$SECONDS-$secsfitbirchmurnaghan let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$value24 cd .. } ########################################################################################### ########################################################################################### ########################################################################################### fitmurnaghan () { secsfitmurnaghan=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: fitmurnaghan $1 $2 $3 $4 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: fitmurnaghan $1 $2 $3 $4 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: fitmurnaghan $1 $2 $3 $4 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: fitmurnaghan $1 $2 $3 $4 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi mkdir fitmurnaghan_${3} cd fitmurnaghan_${3} name="ENERGY_$3" backupen=`echo ${!name}` name="VOLUME_$3" backupvol=`echo ${!name}` if [ -n "$KSPACING" ]; then backupkspacing=$KSPACING fi for j in $(seq 1 1 $1); do mkdir $j cd $j jnlkfvjk=`echo $j - 0.5 - $1 / 2 | bc -l` afragrgw=`echo -0.5 + $1 / 2 | bc -l` jvwoejvnwojvnwe=`echo $2 \* $backupvol / 100 | bc -l` fnjfvkfn=`echo $jnlkfvjk \* $jvwoejvnwojvnwe / $afragrgw | bc -l` vvol=`echo $backupvol + $fnjfvkfn | bc -l` name="VOLUME_$3" eval $name=$vvol if [ -n "$KSPACING" ]; then backuplatccoonsst=`echo " e( l($backupvol)/3 ) " | bc -l` latccoonsst=`echo " e( l($vvol)/3 ) " | bc -l` KSPACING=`echo $backupkspacing \* $backuplatccoonsst / $latccoonsst | bc -l` fi isifbackup=$ISIF ISIF=4 PRINTOUTPUT=false ###$2 $1 relaxation $3 $4 "$5" "$6" "$7" "$8" $9 "${10}" "${11}" "${12}" "${13}" ${14} "${15}" "${16}" "${17}" "${18}" ${19} "${20}" "${21}" "${22}" "${23}" ${24} "${25}" "${26}" "${27}" "${28}" ${29} "${30}" "${31}" "${32}" "${33}" ${34} "${35}" "${36}" "${37}" "${38}" ${39} "${40}" "${41}" "${42}" "${43}" ${44} "${45}" "${46}" "${47}" "${48}" ${49} "${50}" "${51}" "${52}" "${53}" ${54} "${55}" "${56}" "${56}" "${58}" ${59} "${60}" "${61}" "${62}" "${63}" ${64} "${65}" "${66}" "${67}" "${68}" ${69} "${70}" "${71}" "${72}" "${73}" ${74} "${75}" "${76}" "${77}" "${78}" ${79} "${80}" "${81}" "${82}" "${83}" PRINTOUTPUT=true ISIF=$isifbackup cd .. name="ENERGY_$3" viuyiuyguy=`echo ${!name}` echo $vvol " Angstrom^3 per atom " $viuyiuyguy " eV " >> energies.dat done if [ -n "$KSPACING" ]; then KSPACING=$backupkspacing fi #name="VOLUME_$1" #eval $name=$backupvol #name="FREE_ENERGY_$1" #iusiunbb=`echo ${!name}` if [ -n "$METAGGA" ]; then cat > fitmurnaghan_gnup_${3}_${METAGGA} << EOF h = $backupen b = 1.25 v = $backupvol d = 3.5 e(x) = h + (b*x/d)*(((v/x)**d)/(d-1)+1) - b*v/(d-1) fit e(x) 'energies.dat' u 1:5 via h, b, v, d set title "$3 Murnaghan EOS fit ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Energy per atom (eV)" set term png set output "fitmurnaghan_${3}_${METAGGA}.png" p 'energies.dat' u 1:5 w p title 'data points', e(x) title 'fitted EOS' EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT fitmurnaghan_gnup_${3}_${METAGGA} fi else cat > fitmurnaghan_gnup_${3}_${GGA} << EOF h = $backupen b = 1.25 v = $backupvol d = 3.5 e(x) = h + (b*x/d)*(((v/x)**d)/(d-1)+1) - b*v/(d-1) fit e(x) 'energies.dat' u 1:5 via h, b, v, d set title "$3 Murnaghan EOS fit ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Volume per atom ({\305}^3)" set ylabel "Energy per atom (eV)" set term png set output "fitmurnaghan_${3}_${GGA}.png" p 'energies.dat' u 1:5 w p title 'data points', e(x) title 'fitted EOS' EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT fitmurnaghan_gnup_${3}_${GGA} fi fi name="ENERGY_$i" eval $name=$backupen name="VOLUME_$i" eval $name=$backupvol array2=($(grep 'h ' fit.log | tail -2 | head -1)) value22=${array2[2]} if [ "$UPDATEVARIABLES" = true ]; then name="ENERGY_$3" eval $name=$value22 fi array2=($(grep 'b ' fit.log | tail -2 | head -1)) value23=${array2[2]} if [ "$UPDATEVARIABLES" = true ]; then name="BULK_MODULUS_$3" eval $name=$value23 fi jveignjveijvn=`echo $value23 \* 160.2 | bc -l` array2=($(grep 'v ' fit.log | tail -2 | head -1)) value24=${array2[2]} if [ "$UPDATEVARIABLES" = true ]; then name="VOLUME_$3" eval $name=$value24 fi array2=($(grep 'd ' fit.log | tail -2 | head -1)) bulkmodulusderrivative=${array2[2]} if [ "$PRINTOUTPUT" = true ]; then echo " " echo " Murnaghan equation of state has been fitted. Resulting parameters:" echo " volume per atom = " $value24 " Anstrom^3 per atom " echo " energy per atom = " $value22 " eV " echo " bulk modulus = " $value23 " eV/Angstrom^3 = " $jveignjveijvn " GPa " echo " derrivative of bulk modulus wrt pressure = " $bulkmodulusderrivative " eV/Angstrom^3 " if [ "$UPDATEVARIABLES" = true ]; then echo " VOLUME_$3, ENERGY_$3, and BULK_MODULUS_$3 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " Murnaghan equation of state has been fitted. Resulting parameters:" >> $MAINDIR/output.txt echo " volume per atom = " $value24 " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " energy per atom = " $value22 " eV " >> $MAINDIR/output.txt echo " bulk modulus = " $value23 " eV/Angstrom^3 = " $jveignjveijvn " GPa " >> $MAINDIR/output.txt echo " derrivative of bulk modulus wrt pressure = " $bulkmodulusderrivative " eV/Angstrom^3 " >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " VOLUME_$3, ENERGY_$3, and BULK_MODULUS_$3 have been updated accordingly " >> $MAINDIR/output.txt fi fi let secs=$SECONDS-$secsfitmurnaghan let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$value24 cd .. } ########################################################################################### ########################################################################################### ########################################################################################### moleculardynamics () { # $2 is for addvacancy ... / addadsorbant ... secs=$SECONDS mkdir moleculardynamics_${1} cd moleculardynamics_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: moleculardynamics $1 $2 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: moleculardynamics $1 $2 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: moleculardynamics $1 $2 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: moleculardynamics $1 $2 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi $1 ; if [ -n "$2" ]; then $2 "$3" "$4" "$5" "$6" fi if [ -n "$7" ]; then $7 "$8" "$9" "${10}" "${11}" fi if [ -n "${12}" ]; then ${12} "${13}" "${14}" "${15}" "${16}" fi if [ -n "${17}" ]; then ${17} "${18}" "${19}" "${20}" "${21}" fi if [ -n "${22}" ]; then ${22} "${23}" "${24}" "${25}" "${26}" fi if [ -n "${27}" ]; then ${27} "${28}" "${29}" "${30}" "${31}" fi if [ -n "${32}" ]; then ${32} "${33}" "${34}" "${35}" "${36}" fi if [ -n "${37}" ]; then ${37} "${38}" "${39}" "${40}" "${41}" fi if [ -n "${42}" ]; then ${42} "${43}" "${44}" "${45}" "${46}" fi if [ -n "${47}" ]; then ${47} "${48}" "${49}" "${50}" "${51}" fi if [ -n "${52}" ]; then ${52} "${53}" "${54}" "${55}" "${56}" fi if [ -n "${57}" ]; then ${57} "${58}" "${59}" "${60}" "${61}" fi if [ -n "${62}" ]; then ${62} "${63}" "${64}" "${65}" "${66}" fi if [ -n "${67}" ]; then ${67} "${68}" "${69}" "${70}" "${71}" fi if [ -n "${72}" ]; then ${72} "${73}" "${74}" "${75}" "${76}" fi if [ -n "${77}" ]; then ${77} "${78}" "${79}" "${80}" "${81}" fi if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi buildkpoints $1 isymbackup=$ISYM nwritebackup=$NWRITE ISYM=0 NWRITE=1 buildincar ISYM=$isymbackup NWRITE=$nwritebackup echo "#molecular dynamics:" >> INCAR echo "IBRION = 0" >> INCAR echo "TEBEG = $TEBEG" >> INCAR echo "TEEND = $TEEND" >> INCAR echo "POTIM = $POTIM" >> INCAR echo "NSW = $NSW" >> INCAR echo " " >> INCAR echo "#thermostat & ensembles:" >> INCAR echo "ISIF = $ISIF" >> INCAR echo "MDALGO = $MDALGO" >> INCAR echo "LANGEVIN_GAMMA = $LANGEVIN_GAMMA" >> INCAR echo "LANGEVIN_GAMMA_L = $LANGEVIN_GAMMA_L" >> INCAR echo " " >> INCAR echo "#machine learned force fields:" >> INCAR echo "ML_LMLFF = $ML_LMLFF" >> INCAR echo "ML_ISTART = $ML_ISTART" >> INCAR echo "ML_CTIFOR = $ML_CTIFOR" >> INCAR echo "ML_ICRITERIA = $ML_ICRITERIA " >> INCAR echo "ML_RCUT1 = $ML_RCUT1" >> INCAR echo "ML_RCUT2 = $ML_RCUT2" >> INCAR echo " " >> INCAR buildpotcar $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi if [ "$ML_LMLFF" = .TRUE. ]; then grep "BEEF " ML_LOGFILE > beef.dat if [ -n "$METAGGA" ]; then cat > mlff_forceerrors_gnup_${1}_${METAGGA} << EOF set title "$1 MLFF Bayesian error estimates ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in force (max) (eV/{\305})" set term png set output "mlff_forceerrors_${1}_${METAGGA}.png" p 'beef.dat' u 2:4 w l title 'Estimated Bayesian error', 'beef.dat' u 2:6 w l title 'Threshold for Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_forceerrors_gnup_${1}_${METAGGA} fi else cat > mlff_forceerrors_gnup_${1}_${GGA} << EOF set title "$1 MLFF Bayesian error estimates ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in force (max) (eV/{\305})" set term png set output "mlff_forceerrors_${1}_${GGA}.png" p 'beef.dat' u 2:4 w l title 'Estimated Bayesian error', 'beef.dat' u 2:6 w l title 'Threshold for Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_forceerrors_gnup_${1}_${GGA} fi fi if [ -n "$METAGGA" ]; then cat > mlff_energyerrors_gnup_${1}_${METAGGA} << EOF set title "$1 MLFF Bayesian error estimates ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in energy (eV)" set term png set output "mlff_energyerrors_${1}_${METAGGA}.png" p 'beef.dat' u 2:3 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_energyerrors_gnup_${1}_${METAGGA} fi else cat > mlff_energyerrors_gnup_${1}_${GGA} << EOF set title "$1 MLFF Bayesian error estimates ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in energy (eV)" set term png set output "mlff_energyerrors_${1}_${GGA}.png" p 'beef.dat' u 2:3 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_energyerrors_gnup_${1}_${GGA} fi fi if [ -n "$METAGGA" ]; then cat > mlff_stresserrors_gnup_${1}_${METAGGA} << EOF set title "$1 MLFF Bayesian error estimates ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in stress (max) (kB)" set term png set output "mlff_stresserrors_${1}_${METAGGA}.png" p 'beef.dat' u 2:7 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_stresserrors_gnup_${1}_${METAGGA} fi else cat > mlff_stresserrors_gnup_${1}_${GGA} << EOF set title "$1 MLFF Bayesian error estimates ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in stress (max) (kB)" set term png set output "mlff_stresserrors_${1}_${GGA}.png" p 'beef.dat' u 2:7 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_stresserrors_gnup_${1}_${GGA} fi fi arrayconf=($(grep 'Configuration num.' ML_ABN | tail -1)) confnum=${arrayconf[2]} if [ "$ML_ISTART" = 0 ]; then if [ "$PRINTOUTPUT" = true ]; then if [ "$UPDATEVARIABLES" = true ]; then echo " " echo " A force field has been trained. " echo " Total number of configurations: $confnum " echo " " >> $MAINDIR/output.txt echo " A force field has been trained. " >> $MAINDIR/output.txt echo " Total number of configurations: $confnum " >> $MAINDIR/output.txt fi fi elif [ "$ML_ISTART" = 1 ]; then if [ "$PRINTOUTPUT" = true ]; then if [ "$UPDATEVARIABLES" = true ]; then echo " " echo " Force field training has been continued. " echo " Total number of configurations: $confnum " echo " " >> $MAINDIR/output.txt echo " Force field training has been continued. " >> $MAINDIR/output.txt echo " Total number of configurations: $confnum " >> $MAINDIR/output.txt fi fi fi fi let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### phonondispersion () { secs=$SECONDS if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: phonondispersion $1 \"$2\" ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: phonondispersion $1 \"$2\" ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: phonondispersion $1 \"$2\" ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: phonondispersion $1 \"$2\" ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi mkdir phonondispersion_${1} cd phonondispersion_${1} if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi $1 buildkpoints $1 buildqpoints $1 $2 buildincar echo "#phonon calculation:" >> INCAR echo "LPHON_DISPERSION = .TRUE." >> INCAR echo "IBRION = 6" >> INCAR echo "NSW = 1" >> INCAR echo "POTIM = 0.015" >> INCAR echo "ISIF = 2" >> INCAR echo " " >> INCAR buildpotcar $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST DYNMAT QPOINTS INCAR REPORT defaultshiftsandratios XDATCAR KPOINTS CHGCAR poscardescription POSCAR CONTCAR DOSCAR vasprun.xml WAVECAR minipotcar POTCAR EIGENVAL PCDAT CHG IBZKPT fi NATOMS=`awk '/ions per / {print $5}' OUTCAR` NCELL=`grep -m1 "primitive cells build up your supercell" OUTCAR | awk '{print $1}'` if [ -z $NCELL ] then NCELL=1 fi NBANDS=$((NATOMS/NCELL*3)) #NBANDS=6 NQ=`grep -A1 "q-point" OUTCAR |tail -1| awk '{print $1}'` echo found $NBANDS bands and $NQ frequencies #cut OUTCAR down awk '/Phonons/,0' OUTCAR > temp.dat for q_cur in `seq 0 $(($NQ-1))` do for b in `seq 0 $(($NBANDS-1))`; do line_q=$(($q_cur*($NBANDS+5)+3)) line_f=$(($line_q+$b+3)) #echo $line_q q=$(awk -v n=$line_q '/Phonons/ { for (i=1; i<=n ; i++) getline; print $5} ' temp.dat) q_x=$(awk -v n=$line_q '/Phonons/ { for (i=1; i<=n ; i++) getline; print $2} ' temp.dat) q_y=$(awk -v n=$line_q '/Phonons/ { for (i=1; i<=n ; i++) getline; print $3} ' temp.dat) q_z=$(awk -v n=$line_q '/Phonons/ { for (i=1; i<=n ; i++) getline; print $4} ' temp.dat) f[$b]=$(awk -v n=$line_f '/Phonons/ { for (i=1; i<=n ; i++) getline; print $2} ' temp.dat) done echo " l" $q " xyz" $q_x $q_y $q_z " f" ${f[*]} >> phonons.dat echo $q ${f[*]} >> phononsx.dat done rm temp.dat for value in $path ; do if [ "$LATTICE_SYSTEM" = cubic ]; then if [ "$BRAVAIS_LATTICE" = F ]; then if [ "$value" = G ]; then arrayghv=($(grep "xyz 0.000000 0.000000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " G : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = X ]; then arrayghv=($(grep "xyz 0.000000 0.500000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " X : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = U ]; then arrayghv=($(grep "xyz 0.250000 0.625000 0.625000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " U : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = K ]; then arrayghv=($(grep "xyz 0.375000 0.750000 0.375000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " K : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = L ]; then arrayghv=($(grep "xyz 0.500000 0.500000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " L : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = W ]; then arrayghv=($(grep "xyz 0.250000 0.750000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " W : " ${arrayghv[@]} >> tempvvfhb fi fi if [ "$BRAVAIS_LATTICE" = I ]; then if [ "$value" = G ]; then arrayghv=($(grep "xyz 0.000000 0.000000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " G : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = H ]; then arrayghv=($(grep "xyz -0.500000 0.500000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " H : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = P ]; then arrayghv=($(grep "xyz 0.250000 0.250000 0.250000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " P : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = N ]; then arrayghv=($(grep "xyz 0.000000 0.500000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " N : " ${arrayghv[@]} >> tempvvfhb fi fi if [ "$BRAVAIS_LATTICE" = P ]; then if [ "$value" = G ]; then arrayghv=($(grep "xyz 0.000000 0.000000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " G : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = R ]; then arrayghv=($(grep "xyz 0.500000 0.500000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " R : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = X ]; then arrayghv=($(grep "xyz 0.000000 0.500000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " X : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = M ]; then arrayghv=($(grep "xyz 0.500000 0.500000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " M : " ${arrayghv[@]} >> tempvvfhb fi fi fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then if [ "$BRAVAIS_LATTICE" = P ]; then if [ "$value" = G ]; then arrayghv=($(grep "xyz 0.000000 0.000000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " G : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = A ]; then arrayghv=($(grep "xyz 0.000000 0.000000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " A : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = K ]; then arrayghv=($(grep "xyz 0.666667 0.333333 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " K : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = H ]; then arrayghv=($(grep "xyz 0.666667 0.333333 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " H : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = M ]; then arrayghv=($(grep "xyz 0.500000 0.000000 0.000000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " M : " ${arrayghv[@]} >> tempvvfhb elif [ "$value" = L ]; then arrayghv=($(grep "xyz 0.500000 0.000000 0.500000" phonons.dat | tail -1)) arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") arrayghv=("${arrayghv[@]:1}") echo " L : " ${arrayghv[@]} >> tempvvfhb fi fi fi done if [ -n "$METAGGA" ]; then cat > phonondispersion_gnup_${1}_${METAGGA} << EOF set title "$1 phonon dispersion relation ; METAGGA = $METAGGA, POTCAR = $POTCAR" set xlabel "$path" set ylabel "Frequency (THz)" unset key set term png set output "phonondispersion_${1}_${METAGGA}.png" p 'phonons.dat' u 2:8 w l, 'phonons.dat' u 2:9 w l, 'phonons.dat' u 2:10 w l, 'phonons.dat' u 2:11 w l, 'phonons.dat' u 2:12 w l, 'phonons.dat' u 2:13 w l EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT phonondispersion_gnup_${1}_${METAGGA} fi else cat > phonondispersion_gnup_${1}_${GGA} << EOF set title "$1 phonon dispersion relation ; GGA = $GGA, POTCAR = $POTCAR" set xlabel "$path" set ylabel "Frequency (THz)" unset key set term png set output "phonondispersion_${1}_${GGA}.png" p 'phonons.dat' u 2:8 w l, 'phonons.dat' u 2:9 w l, 'phonons.dat' u 2:10 w l, 'phonons.dat' u 2:11 w l, 'phonons.dat' u 2:12 w l, 'phonons.dat' u 2:13 w l EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT phonondispersion_gnup_${1}_${GGA} fi fi numberofcolumns=$(awk '{print NF; exit}' phononsx.dat) local data=$(cat phononsx.dat) if [ "$numberofcolumns" = 2 ]; then local ymax=$(echo "$data" | awk '{print $2}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 3 ]; then local ymax=$(echo "$data" | awk '{print $2, $3}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 4 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 5 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 6 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 7 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 8 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 9 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8, $9}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 10 ]; then local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8, $9, $10}' | tr ' ' '\n'| sort -n | tail -1) fi hjbshbhrjbs=$ymax echo " " #echo " path: $path" echo " phonon frequencies (THz) at high symmetry points (ordered according to specified path): " cat tempvvfhb echo " maximum phonon frequency: $ymax THz" echo " " >> $MAINDIR/output.txt #echo " path: $path" >> $MAINDIR/output.txt echo " phonon frequencies (THz) at high symmetry points (ordered according to specified path): " >> $MAINDIR/output.txt cat tempvvfhb >> $MAINDIR/output.txt echo " maximum phonon frequency: $ymax THz" >> $MAINDIR/output.txt plotxydata+ phononsx.dat rm phononsx.dat rm tempvvfhb let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi VARIABLEFORCONVERGENCE=$hjbshbhrjbs cd .. } ########################################################################################### ########################################################################################### ########################################################################################### relaxation () { # $2 is for addvacancy ... / addadsorbant ... secs=$SECONDS mkdir relaxation_${1} cd relaxation_${1} if [ "$MLFFBEIGAPPLIED" = false ]; then if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: relaxation $1 $2 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: relaxation $1 $2 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: relaxation $1 $2 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: relaxation $1 $2 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi fi $1 ; if [ -n "$2" ]; then $2 "$3" "$4" "$5" "$6" fi if [ -n "$7" ]; then $7 "$8" "$9" "${10}" "${11}" fi if [ -n "${12}" ]; then ${12} "${13}" "${14}" "${15}" "${16}" fi if [ -n "${17}" ]; then ${17} "${18}" "${19}" "${20}" "${21}" fi if [ -n "${22}" ]; then ${22} "${23}" "${24}" "${25}" "${26}" fi if [ -n "${27}" ]; then ${27} "${28}" "${29}" "${30}" "${31}" fi if [ -n "${32}" ]; then ${32} "${33}" "${34}" "${35}" "${36}" fi if [ -n "${37}" ]; then ${37} "${38}" "${39}" "${40}" "${41}" fi if [ -n "${42}" ]; then ${42} "${43}" "${44}" "${45}" "${46}" fi if [ -n "${47}" ]; then ${47} "${48}" "${49}" "${50}" "${51}" fi if [ -n "${52}" ]; then ${52} "${53}" "${54}" "${55}" "${56}" fi if [ -n "${57}" ]; then ${57} "${58}" "${59}" "${60}" "${61}" fi if [ -n "${62}" ]; then ${62} "${63}" "${64}" "${65}" "${66}" fi if [ -n "${67}" ]; then ${67} "${68}" "${69}" "${70}" "${71}" fi if [ -n "${72}" ]; then ${72} "${73}" "${74}" "${75}" "${76}" fi if [ -n "${77}" ]; then ${77} "${78}" "${79}" "${80}" "${81}" fi if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi buildkpoints $1 buildincar echo "#ionic relaxation:" >> INCAR echo "IBRION = $IBRION" >> INCAR echo "EDIFFG = $EDIFFG" >> INCAR echo "NSW = $NSW" >> INCAR echo "POTIM = $POTIM" >> INCAR echo "ISIF = $ISIF" >> INCAR echo " " >> INCAR buildpotcar if [ "$RELREPETITIONS" = 0 ]; then $VASP if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR XDATCAR fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi cp CONTCAR CONTCAR_ cp OUTCAR OUTCAR_ else lwavebackup=$LWAVE lchargbackup=$LCHARG istartbackup=$ISTART ichargbackup=$ICHARG LWAVE=.TRUE. LCHARG=.TRUE. buildincar if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi echo "#ionic relaxation:" >> INCAR echo "IBRION = $IBRION" >> INCAR echo "EDIFFG = $EDIFFG" >> INCAR echo "NSW = $NSW" >> INCAR echo "POTIM = $POTIM" >> INCAR echo "ISIF = $ISIF" >> INCAR echo " " >> INCAR $VASP isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi ISTART=1 ICHARG=0 kjbnwkjtbnwkjtb=$(pwd) for qrgqek in $(seq 1 1 $RELREPETITIONS) ; do mkdir continuation_${qrgqek} cp KPOINTS continuation_${qrgqek} cp POTCAR continuation_${qrgqek} cp CONTCAR continuation_${qrgqek}/POSCAR cp WAVECAR continuation_${qrgqek} cp CHGCAR continuation_${qrgqek} cp CHG continuation_${qrgqek} cd continuation_${qrgqek} buildincar if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi echo "#ionic relaxation:" >> INCAR echo "IBRION = $IBRION" >> INCAR echo "EDIFFG = $EDIFFG" >> INCAR echo "NSW = $NSW" >> INCAR echo "POTIM = $POTIM" >> INCAR echo "ISIF = $ISIF" >> INCAR echo " " >> INCAR $VASP isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi cp CONTCAR $kjbnwkjtbnwkjtb/CONTCAR_ cp OUTCAR $kjbnwkjtbnwkjtb/OUTCAR_ done cd $kjbnwkjtbnwkjtb if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR XDATCAR fi for qrgqek in $(seq 1 1 $RELREPETITIONS) ; do cd continuation_${qrgqek} if [ "$lwavebackup" = ".FALSE." ]; then rm WAVECAR fi if [ "$lchargbackup" = ".FALSE." ]; then rm CHGCAR CHG fi if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR XDATCAR fi done cd $kjbnwkjtbnwkjtb LWAVE=$lwavebackup LCHARG=$lchargbackup ISTART=$istartbackup ICHARG=$ichargbackup fi arraynumberofions=($(grep 'number of ions' OUTCAR_)) valuenumberofions=${arraynumberofions[11]} array2=($(grep 'free en' OUTCAR_ | tail -1)) array3=($(grep 'energy without entropy' OUTCAR_ | tail -1)) value2=${array2[4]} value3=${array3[4]} value4=${array3[7]} value2=`echo $value2 / $valuenumberofions | bc -l` value3=`echo $value3 / $valuenumberofions | bc -l` value4=`echo $value4 / $valuenumberofions | bc -l` if [ "$UPDATEVARIABLES" = true ]; then name="FREE_ENERGY_$1" eval $name=$value2 name="ENERGY_WITHOUT_ENTROPY_$1" eval $name=$value3 name="ENERGY_SIGMA_ZERO_$1" eval $name=$value4 if [ "$MAINENE" = 1 ]; then name="ENERGY_$1" eval $name=$value2 fi if [ "$MAINENE" = 2 ]; then name="ENERGY_$1" eval $name=$value3 fi if [ "$MAINENE" = 3 ]; then name="ENERGY_$1" eval $name=$value4 fi fi if [ "$MAINENE" = 1 ]; then mainene=$value2 fi if [ "$MAINENE" = 2 ]; then mainene=$value3 fi if [ "$MAINENE" = 3 ]; then mainene=$value4 fi if [ "$MAINENE" = 1 ]; then arrayenbefrel=($(grep 'free en' OUTCAR | head -1)) enbefrell=${arrayenbefrel[4]} fi if [ "$MAINENE" = 2 ]; then array3=($(grep 'energy without entropy' OUTCAR | head -1)) enbefrell=${arrayenbefrel[4]} fi if [ "$MAINENE" = 3 ]; then array3=($(grep 'energy without entropy' OUTCAR | head -1)) enbefrell=${arrayenbefrel[7]} fi enbefrel=`echo $enbefrell / $valuenumberofions | bc -l` relen=`echo $enbefrel - $mainene | bc -l` if [ "$STRUCTURE_TYPE" = crystal ]; then mkdir temp cat CONTCAR_ > temp/POSCAR cd temp if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi isymbackup=$ISYM ISYM=2 buildkpoints 1 nelmbackup=$NELM NELM=1 buildincar buildpotcar $VASP NELM=$nelmbackup ISYM=$isymbackup arraylatticeconst=($(grep 'ALAT' OUTCAR)) latticeconstt=${arraylatticeconst[2]} latticeconst=`echo $latticeconstt / $SUPERCELL_FACTOR | bc -l` if [ "$LATTICE_SYSTEM" = cubic ]; then volume=`echo $latticeconst \* $latticeconst \* $latticeconst / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} if [ "$UPDATEVARIABLES" = true ]; then name="C_A_RATIO_$1" eval $name=$valuecaratio fi volume=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio \* 0.86602540378443864676372317075294 / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} if [ "$UPDATEVARIABLES" = true ]; then name="C_A_RATIO_$1" eval $name=$valuecaratio fi volume=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` fi if [ "$UPDATEVARIABLES" = true ]; then name="VOLUME_$1" eval $name=$volume fi if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR XDATCAR fi cd .. if [ "$PRINTOUTPUT" = true ]; then if [ "$LATTICE_SYSTEM" = cubic ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " volume per atom = " $volume " Anstrom^3 per atom " echo " lattice constant a = " $latticeconst " Angstrom " if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and VOLUME_$1 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " volume per atom = " $volume " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " lattice constant a = " $latticeconst " Angstrom " >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and VOLUME_$1 have been updated accordingly " >> $MAINDIR/output.txt fi fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " volume per atom = " $volume " Anstrom^3 per atom " echo " lattice constant a = " $latticeconst " Angstrom " hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` echo " lattice constant c = " $hjbsugbr " Angstrom " echo " c/a-ratio = " $valuecaratio if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " volume per atom = " $volume " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " lattice constant a = " $latticeconst " Angstrom " >> $MAINDIR/output.txt hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` >> $MAINDIR/output.txt echo " lattice constant c = " $hjbsugbr " Angstrom " >> $MAINDIR/output.txt echo " c/a-ratio = " $valuecaratio >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " >> $MAINDIR/output.txt fi fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " volume per atom = " $volume " Anstrom^3 per atom " echo " lattice constant a = " $latticeconst " Angstrom " hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` echo " lattice constant c = " $hjbsugbr " Angstrom " echo " c/a-ratio = " $valuecaratio if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " volume per atom = " $volume " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " lattice constant a = " $latticeconst " Angstrom " >> $MAINDIR/output.txt hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` >> $MAINDIR/output.txt echo " lattice constant c = " $hjbsugbr " Angstrom " >> $MAINDIR/output.txt echo " c/a-ratio = " $valuecaratio >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " >> $MAINDIR/output.txt fi fi fi fi if [ "$STRUCTURE_TYPE" = surface ]; then name="VACUUM_SIZE_$1" vacuumsize=`echo ${!name}` if [ "$vacuumsize" = 0 ]; then mkdir temp cat CONTCAR_ > temp/POSCAR cd temp if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi isymbackup=$ISYM ISYM=2 buildkpoints 1 nelmbackup=$NELM NELM=1 buildincar buildpotcar $VASP NELM=$nelmbackup ISYM=$isymbackup arraylatticeconst=($(grep 'ALAT' OUTCAR | tail -1)) latticeconstt=${arraylatticeconst[2]} latticeconst=`echo $latticeconstt / $SUPERCELL_FACTOR | bc -l` if [ "$LATTICE_SYSTEM" = cubic ]; then volume=`echo $latticeconst \* $latticeconst \* $latticeconst / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} if [ "$UPDATEVARIABLES" = true ]; then name="C_A_RATIO_$1" eval $name=$valuecaratio fi volume=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio \* 0.86602540378443864676372317075294 / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then arraycaratio=($(grep 'C/A-ratio' OUTCAR)) valuecaratio=${arraycaratio[2]} if [ "$UPDATEVARIABLES" = true ]; then name="C_A_RATIO_$1" eval $name=$valuecaratio fi volume=`echo $latticeconst \* $latticeconst \* $latticeconst \* $valuecaratio / $ATOMS_PER_CONVENTIONAL_CELL | bc -l` fi if [ "$UPDATEVARIABLES" = true ]; then name="VOLUME_$1" eval $name=$volume fi if [ "$RMFILES" = true ]; then rm -rf ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR XDATCAR fi cd .. if [ "$PRINTOUTPUT" = true ]; then if [ "$LATTICE_SYSTEM" = cubic ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " volume per atom = " $volume " Anstrom^3 per atom " echo " lattice constant a = " $latticeconst " Angstrom " if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and VOLUME_$1 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " volume per atom = " $volume " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " lattice constant a = " $latticeconst " Angstrom " >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and VOLUME_$1 have been updated accordingly " >> $MAINDIR/output.txt fi fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " volume per atom = " $volume " Anstrom^3 per atom " echo " lattice constant a = " $latticeconst " Angstrom " hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` echo " lattice constant c = " $hjbsugbr " Angstrom " echo " c/a-ratio = " $valuecaratio if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " volume per atom = " $volume " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " lattice constant a = " $latticeconst " Angstrom " >> $MAINDIR/output.txt hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` >> $MAINDIR/output.txt echo " lattice constant c = " $hjbsugbr " Angstrom " >> $MAINDIR/output.txt echo " c/a-ratio = " $valuecaratio >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " >> $MAINDIR/output.txt fi fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " volume per atom = " $volume " Anstrom^3 per atom " echo " lattice constant a = " $latticeconst " Angstrom " hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` echo " lattice constant c = " $hjbsugbr " Angstrom " echo " c/a-ratio = " $valuecaratio if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " volume per atom = " $volume " Anstrom^3 per atom " >> $MAINDIR/output.txt echo " lattice constant a = " $latticeconst " Angstrom " >> $MAINDIR/output.txt hjbsugbr=`echo $valuecaratio \* $latticeconst | bc -l` >> $MAINDIR/output.txt echo " lattice constant c = " $hjbsugbr " Angstrom " >> $MAINDIR/output.txt echo " c/a-ratio = " $valuecaratio >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 , VOLUME_$1 and C_A_RATIO_$1 have been updated accordingly " >> $MAINDIR/output.txt fi fi fi else cellhightt=($(sed -n '5p' < CONTCAR_)) cellhight=${cellhightt[2]} let num=1\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9 firstlayerr=($(sed -n "$num"'p' < CONTCAR_)) firstlayer=${firstlayerr[2]} if [ $(echo "$firstlayer > 0.8" | bc) -eq 1 ]; then # for when atom moves out of cell and vasp outputs it as on the other side of cell instead of outputing negative coordinates firstlayer=`echo $firstlayer - 1 | bc -l` fi firstlayer=`echo $firstlayer \* $cellhight | bc -l` let num=2\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9 secondlayerr=($(sed -n "$num"'p' < CONTCAR_)) secondlayer=${secondlayerr[2]} secondlayer=`echo $secondlayer \* $cellhight | bc -l` let num=3\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9 thirdlayerr=($(sed -n "$num"'p' < CONTCAR_)) thirdlayer=${thirdlayerr[2]} thirdlayer=`echo $thirdlayer \* $cellhight | bc -l` let num=4\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9 fourthlayerr=($(sed -n "$num"'p' < CONTCAR_)) fourthlayer=${fourthlayerr[2]} fourthlayer=`echo $fourthlayer \* $cellhight | bc -l` difffirstsecondlayer=`echo $secondlayer - $firstlayer | bc -l` diffsecondthirdlayer=`echo $thirdlayer - $secondlayer | bc -l` diffthirdfourthlayer=`echo $fourthlayer - $thirdlayer | bc -l` name="VACUUM_SIZE_$1" vacuumsize=`echo ${!name}` name="NUMBER_OF_LAYERS_$1" numberoflayers=`echo ${!name}` bulklayerdistance=`echo $cellhight - $vacuumsize | bc -l` bulklayerdistance=`echo $bulklayerdistance / $numberoflayers | bc -l` relchangefirstsecondlayer=`echo 100 \* $difffirstsecondlayer / $bulklayerdistance - 100 | bc -l` relchangesecondthirdlayer=`echo 100 \* $diffsecondthirdlayer / $bulklayerdistance - 100 | bc -l` relchangethirdfourthlayer=`echo 100 \* $diffthirdfourthlayer / $bulklayerdistance - 100 | bc -l` layerhights=" " for ifv in $(seq 1 1 $NUMBER_OF_LAYERS) ; do let num=$ifv\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9 hightt=($(sed -n "$num"'p' < CONTCAR_)) hight=${hightt[2]} hight=`echo $hight \* $cellhight | bc -l` layerhights=$layerhights" "$hight done if [ "$UPDATEVARIABLES" = true ]; then name="LAYER_HIGHTS_$1" eval $name='$layerhights' fi if [ "$PRINTOUTPUT" = true ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at: " echo " relaxation energy: $relen eV " echo " difference between first & second layer: " $difffirstsecondlayer " Angstrom" echo " difference between second & third layer: " $diffsecondthirdlayer " Angstrom" echo " difference between third & fourth layer: " $diffthirdfourthlayer " Angstrom" echo " for reference, layer distance in bulk structure: " $bulklayerdistance " Angstrom" echo " relative change in first & second layer distance: " $relchangefirstsecondlayer " %" echo " relative change in second & third layer distance: " $relchangesecondthirdlayer " %" echo " relative change in third & fourth layer distance: " $relchangethirdfourthlayer " %" if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and LAYER_HIGHTS_$1 has been updated accordingly. " fi echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at: " >> $MAINDIR/output.txt echo " relaxation energy: $relen eV " >> $MAINDIR/output.txt echo " difference between first & second layer: " $difffirstsecondlayer " Angstrom" >> $MAINDIR/output.txt echo " difference between second & third layer: " $diffsecondthirdlayer " Angstrom" >> $MAINDIR/output.txt echo " difference between third & fourth layer: " $diffthirdfourthlayer " Angstrom" >> $MAINDIR/output.txt echo " for reference, layer distance in bulk structure: " $bulklayerdistance " Angstrom" >> $MAINDIR/output.txt echo " relative change in first & second layer distance: " $relchangefirstsecondlayer " %" >> $MAINDIR/output.txt echo " relative change in second & third layer distance: " $relchangesecondthirdlayer " %" >> $MAINDIR/output.txt echo " relative change in third & fourth layer distance: " $relchangethirdfourthlayer " %" >> $MAINDIR/output.txt if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and LAYER_HIGHTS_$1 has been updated accordingly. " >> $MAINDIR/output.txt fi fi if [ "$2" = addadsorbate ]; then let num=$NUMBER_OF_LAYERS\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9 hightlastt=($(sed -n "$num"'p' < CONTCAR_)) hightlast=${hightlastt[2]} hightlast=`echo $hightlast \* $cellhight | bc -l` let num=$NUMBER_OF_LAYERS\*$SUPERCELL_FACTOR\*$SUPERCELL_FACTOR+9+1 hightmoll=($(sed -n "$num"'p' < CONTCAR_)) hightmol=${hightmoll[2]} hightmol=`echo $hightmol \* $cellhight | bc -l` adsdist=`echo $hightmol - $hightlast | bc -l` if [ "$UPDATEVARIABLES" = true ]; then name="ADSORPTION_DISTANCE_$3" eval $name=$adsdist fi if [ "$PRINTOUTPUT" = true ]; then echo " adsorption distance of first adsorbate: " $adsdist " Angstrom" if [ "$UPDATEVARIABLES" = true ]; then echo " ADSORPTION_DISTANCE_$3 has been updated accordingly. " fi fi fi fi fi if [ "$STRUCTURE_TYPE" = molecule ]; then if [ "$PRINTOUTPUT" = true ]; then echo " " echo " energy minimum of $mainene eV per atom was reached at these atomic positions: " echo " " >> $MAINDIR/output.txt echo " energy minimum of $mainene eV per atom was reached at these atomic positions: " >> $MAINDIR/output.txt fi for ifv in $(seq 1 1 $ATOMS_PER_SUBCELL) ; do let num=$ifv+8 positionss=($(sed -n "$num"'p' < CONTCAR_)) position1=${positionss[0]} position2=${positionss[1]} position3=${positionss[2]} name="MOLECULE_ASYMETRY_$1" asymetry=`echo ${!name}` name="MOLECULE_CELL_SIZE_$1" molcellsize=`echo ${!name}` position1=`echo $position1 \* $molcellsize \* $SUPERCELL_FACTOR - $position1 \* $asymetry | bc -l` position2=`echo $position2 \* $molcellsize \* $SUPERCELL_FACTOR | bc -l` position3=`echo $position3 \* $molcellsize \* $SUPERCELL_FACTOR + $position3 \* $asymetry | bc -l` positions="$position1 $position2 $position3" if [ "$UPDATEVARIABLES" = true ]; then name="POSITION_ATOM_${i}_$1" eval $name='$positions' fi if [ "$PRINTOUTPUT" = true ]; then echo " $positions" echo " $positions" >> $MAINDIR/output.txt fi done if [ "$PRINTOUTPUT" = true ]; then if [ "$UPDATEVARIABLES" = true ]; then echo " ENERGY_$1 and POSITION_ATOM_n_$1 for n=1,...,$ATOMS_PER_SUBCELL have been updated accordingly. " echo " ENERGY_$1 and POSITION_ATOM_n_$1 for n=1,...,$ATOMS_PER_SUBCELL have been updated accordingly. " >> $MAINDIR/output.txt fi fi fi let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi rm CONTCAR_ rm OUTCAR_ VARIABLEFORCONVERGENCE=$volume cd .. } ########################################################################################### ########################################################################################### ########################################################################################### trainmlff () { # $2 is for addvacancy ... / addadsorbant ... secs=$SECONDS if [ -f $MAINDIR/mlffs ] ; then x=x else mkdir $MAINDIR/mlffs fi mkdir $MAINDIR/mlffs/$2 mkdir trainmlff_${2} cd trainmlff_${2} if [ "$PRINTOUTPUT" = true ]; then if [ -n "$METAGGA" ]; then echo " " echo " ###########################################################################################" echo " " echo " Running now: trainmlff $1 $2 $3 $4 ; $METAGGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: trainmlff $1 $2 $3 $4 ; $METAGGA $POTCAR " >> $MAINDIR/output.txt else echo " " echo " ###########################################################################################" echo " " echo " Running now: trainmlff $1 $2 $3 $4 ; $GGA $POTCAR " echo " " >> $MAINDIR/output.txt echo " ###########################################################################################" >> $MAINDIR/output.txt echo " " >> $MAINDIR/output.txt echo " Running now: trainmlff $1 $2 $3 $4 ; $GGA $POTCAR " >> $MAINDIR/output.txt fi fi $3 ; if [ -n "$4" ]; then $4 "$5" "$6" "$7" "$8" fi if [ -n "$9" ]; then $9 "${10}" "${11}" "${12}" "${13}" fi if [ -n "${14}" ]; then ${14} "${15}" "${16}" "${17}" "${18}" fi if [ -n "${19}" ]; then ${19} "${20}" "${21}" "${22}" "${23}" fi if [ -n "${24}" ]; then ${24} "${25}" "${26}" "${27}" "${28}" fi if [ -n "${29}" ]; then ${29} "${30}" "${31}" "${32}" "${33}" fi if [ -n "${34}" ]; then ${34} "${35}" "${36}" "${37}" "${38}" fi if [ -n "${39}" ]; then ${39} "${40}" "${41}" "${42}" "${43}" fi if [ -n "${44}" ]; then ${44} "${45}" "${46}" "${47}" "${48}" fi if [ -n "${49}" ]; then ${49} "${50}" "${51}" "${52}" "${53}" fi if [ -n "${54}" ]; then ${54} "${55}" "${56}" "${57}" "${58}" fi if [ -n "${59}" ]; then ${59} "${60}" "${61}" "${62}" "${63}" fi if [ -n "${64}" ]; then ${64} "${65}" "${66}" "${67}" "${68}" fi if [ -n "${69}" ]; then ${69} "${70}" "${71}" "${72}" "${73}" fi if [ -n "${74}" ]; then ${74} "${75}" "${76}" "${77}" "${78}" fi if [ -n "${79}" ]; then ${79} "${80}" "${81}" "${82}" "${83}" fi if [ "$ADDASYMMETRY" = true ]; then last_row_number=$(tail -n 1 "POSCAR" | awk -v col=3 '{print $col}') new_number=$(echo "$last_row_number + 0.0001" | bc) sed -i "\$s/[^[:space:]]\+\$/ $new_number/" "POSCAR" fi if [ "$1" = "new" ]; then x=x else cp $MAINDIR/mlffs/$1/ML_ABN ML_AB fi if [ -n "$OTHERINPUTFILES" ]; then cp $OTHERINPUTFILES . fi buildkpoints $3 isymbackup=$ISYM nwritebackup=$NWRITE ISYM=0 NWRITE=1 buildincar ISYM=$isymbackup NWRITE=$nwritebackup echo "#molecular dynamics:" >> INCAR echo "IBRION = 0" >> INCAR echo "TEBEG = $TEBEG" >> INCAR echo "TEEND = $TEEND" >> INCAR echo "POTIM = $POTIM" >> INCAR echo "NSW = $NSW" >> INCAR echo " " >> INCAR echo "#thermostat & ensembles:" >> INCAR echo "ISIF = $ISIF" >> INCAR echo "MDALGO = $MDALGO" >> INCAR echo "LANGEVIN_GAMMA = $LANGEVIN_GAMMA" >> INCAR echo "LANGEVIN_GAMMA_L = $LANGEVIN_GAMMA_L" >> INCAR echo " " >> INCAR echo "#machine learned force fields:" >> INCAR echo "ML_LMLFF = .TRUE." >> INCAR if [ "$1" = "new" ]; then echo "ML_ISTART = 0" >> INCAR else echo "ML_ISTART = 1" >> INCAR fi echo "ML_CTIFOR = $ML_CTIFOR" >> INCAR echo "ML_ICRITERIA = $ML_ICRITERIA " >> INCAR echo "ML_MB = $ML_MB " >> INCAR echo "ML_MCONF = $ML_MCONF " >> INCAR echo "ML_RCUT1 = $ML_RCUT1" >> INCAR echo "ML_RCUT2 = $ML_RCUT2" >> INCAR echo " " >> INCAR buildpotcar $VASP if [ "$RMFILES" = true ]; then rm -rf defaultshiftsandratios poscardescription ML_REG ML_HIS HILLSPOT ICONST CHG CHGCAR DOSCAR EIGENVAL IBZKPT INCAR KPOINTS minipotcar PCDAT POSCAR POTCAR REPORT vasprun.xml WAVECAR fi isInFile=$(cat OUTCAR | grep -c "General timing and accounting information") if [ $isInFile -eq 0 ]; then ANERROROCCURED=true fi cp ML_ABN ML_FFN $MAINDIR/mlffs/$2 grep "BEEF " ML_LOGFILE > beef.dat if [ -n "$METAGGA" ]; then cat > mlff_forceerrors_gnup_${2}_${METAGGA} << EOF set title "$2 MLFF Bayesian error estimates ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in force (max) (eV/{\305})" set term png set output "mlff_forceerrors_${2}_${METAGGA}.png" p 'beef.dat' u 2:4 w l title 'Estimated Bayesian error', 'beef.dat' u 2:6 w l title 'Threshold for Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_forceerrors_gnup_${2}_${METAGGA} fi else cat > mlff_forceerrors_gnup_${2}_${GGA} << EOF set title "$2 MLFF Bayesian error estimates ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in force (max) (eV/{\305})" set term png set output "mlff_forceerrors_${2}_${GGA}.png" p 'beef.dat' u 2:4 w l title 'Estimated Bayesian error', 'beef.dat' u 2:6 w l title 'Threshold for Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_forceerrors_gnup_${2}_${GGA} fi fi if [ -n "$METAGGA" ]; then cat > mlff_energyerrors_gnup_${2}_${METAGGA} << EOF set title "$2 MLFF Bayesian error estimates ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in energy (eV)" set term png set output "mlff_energyerrors_${2}_${METAGGA}.png" p 'beef.dat' u 2:3 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_energyerrors_gnup_${2}_${METAGGA} fi else cat > mlff_energyerrors_gnup_${2}_${GGA} << EOF set title "$2 MLFF Bayesian error estimates ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in energy (eV)" set term png set output "mlff_energyerrors_${2}_${GGA}.png" p 'beef.dat' u 2:3 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_energyerrors_gnup_${2}_${GGA} fi fi if [ -n "$METAGGA" ]; then cat > mlff_stresserrors_gnup_${2}_${METAGGA} << EOF set title "$2 MLFF Bayesian error estimates ; METAGGA = $METAGGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in stress (max) (kB)" set term png set output "mlff_stresserrors_${2}_${METAGGA}.png" p 'beef.dat' u 2:7 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_stresserrors_gnup_${2}_${METAGGA} fi else cat > mlff_stresserrors_gnup_${2}_${GGA} << EOF set title "$2 MLFF Bayesian error estimates ; GGA = $GGA, POTCAR = $POTCAR" set encoding iso_8859_1 set xlabel "Molecular dynamics step" set ylabel "Error in stress (max) (kB)" set term png set output "mlff_stresserrors_${2}_${GGA}.png" p 'beef.dat' u 2:7 w l title 'Estimated Bayesian error', EOF if [ -n "$GNUPLOT" ]; then $GNUPLOT mlff_stresserrors_gnup_${2}_${GGA} fi fi arrayconf=($(grep 'Configuration num.' ML_ABN | tail -1)) confnum=${arrayconf[2]} #if [ "$1" = "new" ]; then #echo " $2 $3 $POTCAR $NSW $TEBEG - $TEEND $confnum ($4)" >> $MAINDIR/mlffs/$2/traininghistory #else #cp $MAINDIR/mlffs/$1/traininghistory $MAINDIR/mlffs/$2/traininghistory #oldconfnum=$(awk '{sum += $8} END {print sum}' $MAINDIR/mlffs/$1/traininghistory ) #let diffconfnum=$confnum-$oldconfnum #echo " $2 $3 $POTCAR $NSW $TEBEG - $TEEND $diffconfnum ($4)" >> $MAINDIR/mlffs/$2/traininghistory #fi # # #if [ "$PRINTOUTPUT" = true ]; then #if [ "$UPDATEVARIABLES" = true ]; then # echo " " # echo " Training run has concluded. New MLFF has been stored under the name $name2" # echo " Complete training history: " # echo " name structure POTCAR # MD steps temp. range (K) # added conf." #cat $MAINDIR/mlffs/$2/traininghistory # echo " Total number of configurations: $confnum " # # echo " " >> $MAINDIR/output.txt # echo " Training run has concluded. New MLFF has been stored under the name $name2" >> $MAINDIR/output.txt # echo " Complete training history: " >> $MAINDIR/output.txt # echo " name structure POTCAR # MD steps temp. range (K) # added conf." >> $MAINDIR/output.txt #cat $MAINDIR/mlffs/$2/traininghistory >> $MAINDIR/output.txt # echo " Total number of configurations: $confnum " >> $MAINDIR/output.txt #fi #fi if [ "$1" = "new" ]; then echo " $2 $NSW $TEBEG - $TEEND $confnum " >> $MAINDIR/mlffs/$2/traininghistory else cp $MAINDIR/mlffs/$1/traininghistory $MAINDIR/mlffs/$2/traininghistory oldconfnum=$(awk '{sum += $6} END {print sum}' $MAINDIR/mlffs/$1/traininghistory ) let diffconfnum=$confnum-$oldconfnum echo " $2 $NSW $TEBEG - $TEEND $diffconfnum " >> $MAINDIR/mlffs/$2/traininghistory fi if [ "$PRINTOUTPUT" = true ]; then if [ "$UPDATEVARIABLES" = true ]; then echo " " echo " Training run has concluded. New MLFF has been stored under the name $name2" echo " Complete training history: " echo " name # MD steps temp. range (K) # added conf." cat $MAINDIR/mlffs/$2/traininghistory echo " Total number of configurations: $confnum " echo " " >> $MAINDIR/output.txt echo " Training run has concluded. New MLFF has been stored under the name $name2" >> $MAINDIR/output.txt echo " Complete training history: " >> $MAINDIR/output.txt echo " name # MD steps temp. range (K) # added conf." >> $MAINDIR/output.txt cat $MAINDIR/mlffs/$2/traininghistory >> $MAINDIR/output.txt echo " Total number of configurations: $confnum " >> $MAINDIR/output.txt fi fi let secs=$SECONDS-$secs let TOTALTIME=$TOTALTIME+$secs hrs=$(( secs/3600 )); mins=$(( (secs-hrs*3600)/60 )); secs=$(( secs-hrs*3600-mins*60 )) if [ "$PRINTOUTPUT" = true ]; then echo " " echo " ellapsed time: $hrs h $mins min $secs s" echo " " >> $MAINDIR/output.txt echo " ellapsed time: $hrs h $mins min $secs s" >> $MAINDIR/output.txt fi if [ "$PRINTOUTPUT" = true ]; then if [ "$ANERROROCCURED" = true ]; then echo " " echo " An ERROR occured during this calculation - please check what happened!" echo " " >> $MAINDIR/output.txt echo " An ERROR occured during this calculation - please check what happened!" >> $MAINDIR/output.txt ANERROROCCURED=false fi fi cd .. } ########################################################################################### ########################################################################################### ########################################################################################### buildincar () { if [ -e INCAR ] ; then rm INCAR fi cat >> INCAR << EOF #starting parameters: ISTART = $ISTART ICHARG = $ICHARG #writing parameters: LWAVE = $LWAVE LCHARG = $LCHARG NWRITE = $NWRITE #electronic optimization: ALGO = $ALGO PREC = $PREC NELM = $NELM EDIFF = $EDIFF #NBANDS = $NBANDS LASPH = $LASPH EOF if [ -n "$METAGGA" ]; then cat >> INCAR << EOF METAGGA = $METAGGA EOF else cat >> INCAR << EOF GGA = $GGA EOF fi if [ "$ALGO" = RPAR ]; then cat >> INCAR << EOF NOMEGA = $NOMEGA EOF fi cat >> INCAR << EOF #kpoint sampling: ENCUT = $ENCUT ISMEAR = $ISMEAR SIGMA = $SIGMA ISYM = $ISYM KGAMMA = $KGAMMA EOF if [ -n "$KSPACING" ]; then cat >> INCAR << EOF KSPACING = $KSPACING EOF fi cat >> INCAR << EOF #magnetism: ISPIN = $ISPIN #MAGMOM = $MAGMOM #performance optimization: KPAR = $KPAR NCORE = $NCORE LREAL = $LREAL #other incar tags: EOF echo " " >> INCAR echo "$OTHERINCARTAGS" >> INCAR echo " " >> INCAR } ########################################################################################### ########################################################################################### ########################################################################################### buildkpoints () { if [ -e KPOINTS ] ; then rm KPOINTS fi if [ "$MLFFBEIGAPPLIED" = false ]; then if [ -n "$KSPACING" ]; then x=x else if [ -n "$1" ] && [ "$1" -eq "$1" ] 2>/dev/null; then cat >> KPOINTS << EOF Regular ${1}x${1}x${1} k-point mesh 0 EOF if [ "$KGAMMA" = .TRUE. ]; then cat >> KPOINTS << EOF Gamma EOF elif [ "$KGAMMA" = .FALSE. ]; then cat >> KPOINTS << EOF Monkhorst-Pack EOF fi cat >> KPOINTS << EOF $1 $1 $1 0 0 0 EOF else array=($1) a=${array[0]} b=${array[1]} c=${array[2]} if [ -n "$a" ] && [ "$a" -eq "$a" ] 2>/dev/null; then cat >> KPOINTS << EOF Regular ${a}x${b}x${c} k-point mesh 0 EOF if [ "$KGAMMA" = .TRUE. ]; then cat >> KPOINTS << EOF Gamma EOF elif [ "$KGAMMA" = .FALSE. ]; then cat >> KPOINTS << EOF Monkhorst-Pack EOF fi cat >> KPOINTS << EOF $a $b $c 0 0 0 EOF else mkdir temp_kdsj cd temp_kdsj $1 cd .. rm -r temp_kdsj name="KPOINTS_$1" kpts=`echo ${!name}` cat >> KPOINTS << EOF k-point mesh for $1 $STRUCTURE_TYPE 0 EOF if [ "$KGAMMA" = .TRUE. ]; then cat >> KPOINTS << EOF Gamma EOF elif [ "$KGAMMA" = .FALSE. ]; then cat >> KPOINTS << EOF Monkhorst-Pack EOF fi if [ "$STRUCTURE_TYPE" = molecule ]; then cat >> KPOINTS << EOF 1 1 1 0 0 0 EOF elif [ "$STRUCTURE_TYPE" = crystal ]; then cat >> KPOINTS << EOF $kpts $kpts $kpts 0 0 0 EOF elif [ "$STRUCTURE_TYPE" = surface ]; then name="VACUUM_SIZE_$1" vacusizzze=`echo ${!name}` if [ "$vacusizzze" = 0 ]; then name="NUMBER_OF_LAYERS_$1" nulayyyers=`echo ${!name}` if [ "$nulayyyers" = $ATOMS_PER_SUBCELL ]; then let zkpts=$kpts else let zkpts=1+$kpts*$SUPERCELL_FACTOR/$nulayyyers fi cat >> KPOINTS << EOF $kpts $kpts $zkpts 0 0 0 EOF else cat >> KPOINTS << EOF $kpts $kpts 1 0 0 0 EOF fi elif [ "$STRUCTURE_TYPE" = chain ]; then cat >> KPOINTS << EOF 1 1 $kpts 0 0 0 EOF fi fi fi fi else cat >> KPOINTS << EOF Minimal k-point mesh for MLFF 0 EOF if [ "$KGAMMA" = .TRUE. ]; then cat >> KPOINTS << EOF Gamma EOF elif [ "$KGAMMA" = .FALSE. ]; then cat >> KPOINTS << EOF Monkhorst-Pack EOF fi cat >> KPOINTS << EOF 1 1 1 0 0 0 EOF fi } ########################################################################################### ########################################################################################### ########################################################################################### buildpotcar () { potarray=($POTCAR) potential1=${potarray[0]} potential2=${potarray[1]} potential3=${potarray[2]} potential4=${potarray[3]} potential5=${potarray[4]} potential6=${potarray[5]} potential7=${potarray[6]} potential8=${potarray[7]} cat $ALLPOTCARS/$potential1/POTCAR $ALLPOTCARS/$potential2/POTCAR $ALLPOTCARS/$potential3/POTCAR $ALLPOTCARS/$potential4/POTCAR $ALLPOTCARS/$potential5/POTCAR $ALLPOTCARS/$potential6/POTCAR $ALLPOTCARS/$potential7/POTCAR $ALLPOTCARS/$potential8/POTCAR > POTCAR 2>&- echo $POTCAR >> minipotcar } ########################################################################################### ########################################################################################### ########################################################################################### buildqpoints () { if [ "$LATTICE_SYSTEM" = cubic ]; then if [ "$BRAVAIS_LATTICE" = F ]; then path=$2 if [ "$path" = defaultpath ]; then path="G X U , K G L W X" fi cat > QPOINTS << EOF k-points for bandstructure $path 251 line reciprocal EOF array=($(echo $path)) value=${array[0]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = X ]; then echo "0.000000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = U ]; then echo "0.250000 0.625000 0.625000 1" >> QPOINTS elif [ "$value" = K ]; then echo "0.375000 0.750000 0.375000 1" >> QPOINTS elif [ "$value" = L ]; then echo "0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = W ]; then echo "0.250000 0.750000 0.500000 1" >> QPOINTS fi total_number_of_characters=`echo $path |tr " " "\n" |wc -l` total_number_of_separation_character=`echo $path | tr -cd '-' | wc -c` let total_number_of_high_symmetry_points=$total_number_of_characters-$total_number_of_separation_character let k=$total_number_of_characters-2 for high_symmetry_point in $(seq 1 1 $k); do array=($(echo $path)) value=${array[$high_symmetry_point]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = X ]; then echo "0.000000 0.500000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = U ]; then echo "0.250000 0.625000 0.625000 1" >> QPOINTS echo " " >> QPOINTS echo "0.250000 0.625000 0.625000 1" >> QPOINTS elif [ "$value" = K ]; then echo "0.375000 0.750000 0.375000 1" >> QPOINTS echo " " >> QPOINTS echo "0.375000 0.750000 0.375000 1" >> QPOINTS elif [ "$value" = L ]; then echo "0.500000 0.500000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = W ]; then echo "0.250000 0.750000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.250000 0.750000 0.500000 1" >> QPOINTS fi done let k=$total_number_of_characters-1 array=($(echo $path)) value=${array[$k]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = X ]; then echo "0.000000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = U ]; then echo "0.250000 0.625000 0.625000 1" >> QPOINTS elif [ "$value" = K ]; then echo "0.375000 0.750000 0.375000 1" >> QPOINTS elif [ "$value" = L ]; then echo "0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = W ]; then echo "0.250000 0.750000 0.500000 1" >> QPOINTS fi for character in $(seq 0 1 $k); do array=($(echo $path)) value=${array[$character]} if [ "$value" = , ]; then let line1=3*$character+2 let line2=3*$character+3 let line3=3*$character+4 sed ${line3}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line2}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line1}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS fi done fi if [ "$BRAVAIS_LATTICE" = I ]; then path=$2 if [ "$path" = defaultpath ]; then path="G H P G N" fi cat > QPOINTS << EOF k-points for bandstructure $path 251 line reciprocal EOF array=($(echo $path)) value=${array[0]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = H ]; then echo "-0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = P ]; then echo "0.250000 0.250000 0.205000 1" >> QPOINTS elif [ "$value" = N ]; then echo "0.000000 0.500000 0.000000 1" >> QPOINTS fi total_number_of_characters=`echo $path |tr " " "\n" |wc -l` total_number_of_separation_character=`echo $path | tr -cd '-' | wc -c` let total_number_of_high_symmetry_points=$total_number_of_characters-$total_number_of_separation_character let k=$total_number_of_characters-2 for high_symmetry_point in $(seq 1 1 $k); do array=($(echo $path)) value=${array[$high_symmetry_point]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = H ]; then echo "-0.500000 0.500000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "-0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = P ]; then echo "0.250000 0.250000 0.250000 1" >> QPOINTS echo " " >> QPOINTS echo "0.250000 0.250000 0.250000 1" >> QPOINTS elif [ "$value" = N ]; then echo "0.000000 0.500000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.500000 0.000000 1" >> QPOINTS fi done let k=$total_number_of_characters-1 array=($(echo $path)) value=${array[$k]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = H ]; then echo "-0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = P ]; then echo "0.250000 0.250000 0.250000 1" >> QPOINTS elif [ "$value" = N ]; then echo "0.000000 0.500000 0.000000 1" >> QPOINTS fi for character in $(seq 0 1 $k); do array=($(echo $path)) value=${array[$character]} if [ "$value" = , ]; then let line1=3*$character+2 let line2=3*$character+3 let line3=3*$character+4 sed ${line3}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line2}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line1}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS fi done fi if [ "$BRAVAIS_LATTICE" = P ]; then path=$2 if [ "$path" = defaultpath ]; then path="G X M G R" fi cat > QPOINTS << EOF k-points for bandstructure $path 251 line reciprocal EOF array=($(echo $path)) value=${array[0]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = R ]; then echo "0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = X ]; then echo "0.000000 0.500000 0.000000 1" >> QPOINTS elif [ "$value" = M ]; then echo "0.500000 0.500000 0.000000 1" >> QPOINTS fi total_number_of_characters=`echo $path |tr " " "\n" |wc -l` total_number_of_separation_character=`echo $path | tr -cd '-' | wc -c` let total_number_of_high_symmetry_points=$total_number_of_characters-$total_number_of_separation_character let k=$total_number_of_characters-2 for high_symmetry_point in $(seq 1 1 $k); do array=($(echo $path)) value=${array[$high_symmetry_point]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = R ]; then echo "0.500000 0.500000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = X ]; then echo "0.000000 0.500000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.500000 0.000000 1" >> QPOINTS elif [ "$value" = M ]; then echo "0.500000 0.500000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.500000 0.500000 0.000000 1" >> QPOINTS fi done let k=$total_number_of_characters-1 array=($(echo $path)) value=${array[$k]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = R ]; then echo "0.500000 0.500000 0.500000 1" >> QPOINTS elif [ "$value" = X ]; then echo "0.000000 0.500000 0.000000 1" >> QPOINTS elif [ "$value" = M ]; then echo "0.500000 0.500000 0.000000 1" >> QPOINTS fi for character in $(seq 0 1 $k); do array=($(echo $path)) value=${array[$character]} if [ "$value" = , ]; then let line1=3*$character+2 let line2=3*$character+3 let line3=3*$character+4 sed ${line3}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line2}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line1}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS fi done fi fi if [ "$LATTICE_SYSTEM" = hexagonal ]; then if [ "$BRAVAIS_LATTICE" = P ]; then path=$2 if [ "$path" = defaultpath ]; then path="G K M G" fi cat > QPOINTS << EOF k-points for bandstructure $path 251 line reciprocal EOF array=($(echo $path)) value=${array[0]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = A ]; then echo "0.000000 0.000000 0.500000 1" >> QPOINTS elif [ "$value" = K ]; then echo "0.666667 0.333333 0.000000 1" >> QPOINTS elif [ "$value" = H ]; then echo "0.666667 0.333333 0.500000 1" >> QPOINTS elif [ "$value" = M ]; then echo "0.500000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = L ]; then echo "0.500000 0.000000 0.500000 1" >> QPOINTS fi total_number_of_characters=`echo $path |tr " " "\n" |wc -l` total_number_of_separation_character=`echo $path | tr -cd '-' | wc -c` let total_number_of_high_symmetry_points=$total_number_of_characters-$total_number_of_separation_character let k=$total_number_of_characters-2 for high_symmetry_point in $(seq 1 1 $k); do array=($(echo $path)) value=${array[$high_symmetry_point]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = A ]; then echo "0.000000 0.000000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.000000 0.000000 0.500000 1" >> QPOINTS elif [ "$value" = K ]; then echo "0.666667 0.333333 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.666667 0.333333 0.000000 1" >> QPOINTS elif [ "$value" = H ]; then echo "0.666667 0.333333 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.666667 0.333333 0.500000 1" >> QPOINTS elif [ "$value" = M ]; then echo "0.500000 0.000000 0.000000 1" >> QPOINTS echo " " >> QPOINTS echo "0.500000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = L ]; then echo "0.500000 0.000000 0.500000 1" >> QPOINTS echo " " >> QPOINTS echo "0.500000 0.000000 0.500000 1" >> QPOINTS fi done let k=$total_number_of_characters-1 array=($(echo $path)) value=${array[$k]} if [ "$value" = G ]; then echo "0.000000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = A ]; then echo "0.000000 0.000000 0.500000 1" >> QPOINTS elif [ "$value" = K ]; then echo "0.666667 0.333333 0.000000 1" >> QPOINTS elif [ "$value" = H ]; then echo "0.666667 0.333333 0.500000 1" >> QPOINTS elif [ "$value" = M ]; then echo "0.500000 0.000000 0.000000 1" >> QPOINTS elif [ "$value" = L ]; then echo "0.500000 0.000000 0.500000 1" >> QPOINTS fi for character in $(seq 0 1 $k); do array=($(echo $path)) value=${array[$character]} if [ "$value" = , ]; then let line1=3*$character+2 let line2=3*$character+3 let line3=3*$character+4 sed ${line3}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line2}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS sed ${line1}d QPOINTS >> temp rm QPOINTS mv temp QPOINTS fi done fi fi } ########################################################################################### ########################################################################################### ########################################################################################### readenmax () { mkdir temp cd temp buildpotcar arrayenmax1=($(grep -m1 ENMAX POTCAR |tail -1)) arrayenmax2=($(grep -m2 ENMAX POTCAR |tail -1)) arrayenmax3=($(grep -m3 ENMAX POTCAR |tail -1)) arrayenmax4=($(grep -m4 ENMAX POTCAR |tail -1)) arrayenmax5=($(grep -m5 ENMAX POTCAR |tail -1)) arrayenmax6=($(grep -m6 ENMAX POTCAR |tail -1)) arrayenmax7=($(grep -m7 ENMAX POTCAR |tail -1)) arrayenmax8=($(grep -m8 ENMAX POTCAR |tail -1)) ENMAXS=( ${arrayenmax1[2]%?} ${arrayenmax2[2]%?} ${arrayenmax3[2]%?} ${arrayenmax4[2]%?} ${arrayenmax5[2]%?} ${arrayenmax6[2]%?} ${arrayenmax7[2]%?} ${arrayenmax8[2]%?} ) ENMAX=${ENMAXS[0]} for j in ${ENMAXS[@]}; do if [ $(echo "$j > $ENCUT" | bc) -eq 1 ]; then ENMAX=$j fi done cd .. rm -r temp } ########################################################################################### ########################################################################################### ########################################################################################### setpotcar () { POTCAR="$1 $2 $3 $4 $5 $6 $7 $8" } ########################################################################################### ########################################################################################### ########################################################################################### plotxydata () { cat > graph.dat << EOF EOF local data=$(cat $1) local xmin=$(echo "$data" | awk '{print $1}' | sort -n | head -n 1) local xmax=$(echo "$data" | awk '{print $1}' | sort -n | tail -n 1) local ymin=$(echo "$data" | awk '{print $2}' | sort -n | head -n 1) local ymax=$(echo "$data" | awk '{print $2}' | sort -n | tail -n 1) local xscale=86 local yscale=8 data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($2-ymin)/(ymax-ymin))*yscale)}') while read -r line; do local x=$(echo "$line" | awk '{print $1}') local y=$(echo "$line" | awk '{print $2}') let yvjn=-$y+9 line=$(sed -n "${yvjn}p" graph.dat) newline=${line:0:x}x${line:x+1} sed -i "${yvjn}s/.*/$newline/" graph.dat done <<< "$data" let fvjndvj=$yscale+1 for ijknvf in $(seq 1 1 $fvjndvj) ; do line="$(sed -r -n "${ijknvf}p" graph.dat)" echo " |" "$line""|" >> graph.dattt done cp graph.dattt graph.dat rm graph.dattt echo " " >> graph.datt echo " ----------------------------------- preview graph: ----------------------------------------" >> graph.datt cat graph.dat >> graph.datt cp graph.datt graph.dat echo " -------------------------------------------------------------------------------------------" >> graph.dat if [ "$PRINTOUTPUT" = true ]; then cat graph.dat cat graph.dat >> $MAINDIR/output.txt fi rm graph.dat rm graph.datt } ########################################################################################### ########################################################################################### ########################################################################################### plotxydata+ () { cat > graph.dat << EOF EOF numberofcolumns=$(awk '{print NF; exit}' $1) xscale=86 yscale=16 local data=$(cat $1) local xmin=$(echo "$data" | awk '{print $1}' | sort -n | head -n 1) local xmax=$(echo "$data" | awk '{print $1}' | sort -n | tail -n 1) if [ "$numberofcolumns" = 2 ]; then local ymin=$(echo "$data" | awk '{print $2}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 3 ]; then local ymin=$(echo "$data" | awk '{print $2, $3}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 4 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 5 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4, $5}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 6 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4, $5, $6}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 7 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 8 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 9 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8, $9}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8, $9}' | tr ' ' '\n'| sort -n | tail -1) fi if [ "$numberofcolumns" = 10 ]; then local ymin=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8, $9, $10}' | tr ' ' '\n'| sort -n | head -1) local ymax=$(echo "$data" | awk '{print $2, $3, $4, $5, $6, $7, $8, $9, $10}' | tr ' ' '\n'| sort -n | tail -1) fi symbolarray=( x o u n c s z m w ) for column in $(seq 2 1 $numberofcolumns) ; do let vjnsjvfjvn=$column-2 symbol=${symbolarray[$vjnsjvfjvn]} local data=$(cat $1) if [ "$symbol" = x ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($2-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = o ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($3-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = u ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($4-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = n ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($5-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = c ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($6-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = s ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($7-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = z ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($8-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = m ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($9-ymin)/(ymax-ymin))*yscale)}') fi if [ "$symbol" = w ]; then data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($10-ymin)/(ymax-ymin))*yscale)}') fi while read -r line; do local x=$(echo "$line" | awk '{print $1}') local y=$(echo "$line" | awk '{print $2}') let yvjn=$yscale-$y+1 line=$(sed -n "${yvjn}p" graph.dat) newline=${line:0:x}$symbol${line:x+1} sed -i "${yvjn}s/.*/$newline/" graph.dat done <<< "$data" let fvjndvj=$yscale+1 for ijknvf in $(seq 1 1 $fvjndvj) ; do line="$(sed -r -n "${ijknvf}p" graph.dat)" if [ "$column" = $numberofcolumns ]; then echo " |" "$line""|" >> graph.dattt else echo "$line" >> graph.dattt fi done cp graph.dattt graph.dat rm graph.dattt done echo " " >> graph.datt echo " ----------------------------------- preview graph: ----------------------------------------" >> graph.datt cat graph.dat >> graph.datt cp graph.datt graph.dat echo " -------------------------------------------------------------------------------------------" >> graph.dat if [ "$PRINTOUTPUT" = true ]; then cat graph.dat cat graph.dat >> $MAINDIR/output.txt fi rm graph.dat rm graph.datt } ########################################################################################### ########################################################################################### ########################################################################################### plotxydata++ () { cat > graph.dat << EOF EOF jnvsgjns=0 for sfvnwvf in pldir_* ; do let jnvsgjns=$jnvsgjns+1 cd $sfvnwvf cat $1 >> ../datatemp cd .. done local data=$(cat datatemp) local xmin=$(echo "$data" | awk '{print $1}' | sort -n | head -n 1) local xmax=$(echo "$data" | awk '{print $1}' | sort -n | tail -n 1) local ymin=$(echo "$data" | awk '{print $2}' | sort -n | head -n 1) local ymax=$(echo "$data" | awk '{print $2}' | sort -n | tail -n 1) rm datatemp local xscale=86 local yscale=24 fvjhwjvghkb=0 for sfvnwvf in pldir_* ; do let fvjhwjvghkb=$fvjhwjvghkb+1 cd $sfvnwvf cp $1 .. cd .. if [ "$fvjhwjvghkb" = "1" ]; then symbol="x" fi if [ "$fvjhwjvghkb" = "2" ]; then symbol="o" fi if [ "$fvjhwjvghkb" = "3" ]; then symbol="u" fi if [ "$fvjhwjvghkb" = "4" ]; then symbol="n" fi if [ "$fvjhwjvghkb" = "5" ]; then symbol="c" fi if [ "$fvjhwjvghkb" = "6" ]; then symbol="s" fi if [ "$fvjhwjvghkb" = "7" ]; then symbol="z" fi if [ "$fvjhwjvghkb" = "8" ]; then symbol="m" fi if [ "$fvjhwjvghkb" = "9" ]; then symbol="w" fi local data=$(cat $1) data=$(echo "$data" | awk -v xmin=$xmin -v xmax=$xmax -v ymin=$ymin -v ymax=$ymax -v xscale=$xscale -v yscale=$yscale '{print int((($1-xmin)/(xmax-xmin))*xscale), int((($2-ymin)/(ymax-ymin))*yscale)}') while read -r line; do local x=$(echo "$line" | awk '{print $1}') local y=$(echo "$line" | awk '{print $2}') let yvjn=$yscale-$y+1 line=$(sed -n "${yvjn}p" graph.dat) newline=${line:0:x}$symbol${line:x+1} sed -i "${yvjn}s/.*/$newline/" graph.dat done <<< "$data" let fvjndvj=$yscale+1 for ijknvf in $(seq 1 1 $fvjndvj) ; do line="$(sed -r -n "${ijknvf}p" graph.dat)" if [ "$jnvsgjns" = $fvjhwjvghkb ]; then echo " |" "$line""|" >> graph.dattt else echo "$line" >> graph.dattt fi done cp graph.dattt graph.dat rm graph.dattt rm $1 done echo " " >> graph.datt echo " ----------------------------------- preview graph: ----------------------------------------" >> graph.datt cat graph.dat >> graph.datt cp graph.datt graph.dat echo " -------------------------------------------------------------------------------------------" >> graph.dat if [ "$PRINTOUTPUT" = true ]; then cat graph.dat cat graph.dat >> $MAINDIR/output.txt fi rm graph.dat rm graph.datt } ########################################################################################### ########################################################################################### ########################################################################################### readenergyvariables () { source $1 energyvariables } ########################################################################################### ########################################################################################### ########################################################################################### readincarvariables () { source $1 incarvariables } ########################################################################################### ########################################################################################### ########################################################################################### readkpointsvariables () { source $1 kpointsvariables } ########################################################################################### ########################################################################################### ########################################################################################### readstructuralvariables () { source $1 structuralvariables } ########################################################################################### ########################################################################################### ########################################################################################### readvariables () { source $1 incarvariables kpointsvariables structuralvariables readenergyvariables } ########################################################################################### ########################################################################################### ########################################################################################### setdefaults () { UPDATEVARIABLES=true PRINTOUTPUT=true RMFILES=false MAINENE=1 RELREPETITIONS=1 RECALCBULK=true RECALCSURFACE=true ADDASYMMETRY=true MLFFBEIGAPPLIED=false setincardefaults 2>&- setkpointsdefaults 2>&- setstructuraldefaults 2>&- setenergydefaults 2>&- } ########################################################################################### ########################################################################################### ########################################################################################### setenergydefaults () { for str in $allcrystals ; do str="${str##*/}" name="ENERGY_$str" eval $name=NaN done for str in $allcrystals_supercells ; do str="${str##*/}" name="ENERGY_$str" eval $name=NaN done for str in $allsurfaces ; do str="${str##*/}" name="ENERGY_$str" eval $name=NaN done for str in $allsurfaces_supercells ; do str="${str##*/}" name="ENERGY_$str" eval $name=NaN done for str in $allmolecules ; do str="${str##*/}" name="ENERGY_$str" eval $name=NaN done #for str in $allmolecules_supercells ; do #str="${str##*/}" #name="ENERGY_$str" #eval $name=NaN #done } ########################################################################################### ########################################################################################### ########################################################################################### setincardefaults () { natomsss=`echo $ATOMS_PER_SUBCELL \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR \* $SUPERCELL_FACTOR | bc -l` #starting parameters: ISTART=0 ICHARG=2 #writing parameters: LWAVE=".FALSE." LCHARG=".FALSE." NWRITE=2 #electronic optimization: ALGO="Normal" PREC="Normal" NELM=100 EDIFF="1E-06" NBANDS=48 GGA="PE" METAGGA="" LASPH=".TRUE." NOMEGA=12 #kpoint sampling: ENCUT=400 ISMEAR=1 SIGMA=0.2 ISYM=2 KGAMMA=".TRUE." #magnetism: ISPIN=1 MAGMOM="$natomsss*1.0" #performance optimization: KPAR=1 NCORE=1 LREAL=.FALSE. #defaults for relaxation: IBRION=2 EDIFFG=-0.001 #EDIFF="1E-05" NSW=100 POTIM=0.5 ISIF=3 #defaults for DOS: NEDOS=1001 EMAX= EMIN= #defaults for MD: TEBEG=100 TEEND=500 #defaults for thermostat & ensembles: MDALGO=3 LANGEVIN_GAMMA="1*5.0" LANGEVIN_GAMMA_L="1*5.0" #defaults for machine learned force fields: ML_LMLFF=".TRUE." ML_ISTART=0 ML_CTIFOR=0.002 ML_ICRITERIA=1 ML_MB=5000 ML_MCONF=5000 ML_RCUT1=8.0 ML_RCUT2=5.0 } ########################################################################################### ########################################################################################### ########################################################################################### setkpointsdefaults () { for str in $allcrystals ; do str="${str##*/}" name="KPOINTS_$str" eval $name=12 done for str in $allcrystals_supercells ; do str="${str##*/}" name="KPOINTS_$str" eval $name=6 done for str in $allsurfaces ; do str="${str##*/}" name="KPOINTS_$str" eval $name=12 done for str in $allsurfaces_supercells ; do str="${str##*/}" name="KPOINTS_$str" eval $name=6 done } ########################################################################################### ########################################################################################### ########################################################################################### setstructuraldefaults () { for str in $allcrystals ; do str="${str##*/}" name="VOLUME_$str" eval $name=15 #mkdir temppp #cd temppp #$str #source defaultshiftsandratios #defaultshiftsandratios #cd .. #rm -r temppp done for str in $allcrystals_supercells ; do str="${str##*/}" name="VOLUME_$str" eval $name=15 name="SUPERCELL_FACTOR_$str" eval $name=2 #mkdir temppp #cd temppp #$str #source defaultshiftsandratios #defaultshiftsandratios #cd .. #rm -r temppp done for str in $allsurfaces ; do str="${str##*/}" name="VOLUME_$str" eval $name=15 name="NUMBER_OF_LAYERS_$str" eval $name=6 name="VACUUM_SIZE_$str" eval $name=10 name="SELECTIVE_DYNAMICS_DEPTH_$str" eval $name=2 name="LAYER_HIGHTS_$str" eval $name=defaulthights #mkdir temppp #cd temppp #$str #source defaultshiftsandratios #defaultshiftsandratios #cd .. #rm -r temppp done for str in $allsurfaces_supercells ; do str="${str##*/}" name="VOLUME_$str" eval $name=15 name="SUPERCELL_FACTOR_$str" eval $name=2 name="NUMBER_OF_LAYERS_$str" eval $name=6 name="VACUUM_SIZE_$str" eval $name=10 name="SELECTIVE_DYNAMICS_DEPTH_$str" eval $name=2 name="LAYER_HIGHTS_$str" eval $name=defaulthights #mkdir temppp #cd temppp #$str #source defaultshiftsandratios #defaultshiftsandratios #cd .. #rm -r temppp done for str in $allmolecules ; do #str="${str##*/}" #mkdir temppp #cd temppp #$str #source defaultatomicpositions #defaultatomicpositions #cd .. #rm -r temppp name="MOLECULE_CELL_SIZE_$str" eval $name=10 name="MOLECULE_ASYMETRY_$str" eval $name=1 name="ADSORPTION_DISTANCE_$str" eval $name=2 done #for str in $allmolecules_supercells ; do #str="${str##*/}" #mkdir temppp #cd temppp #$str #source defaultatomicpositions #defaultatomicpositions #cd .. #rm -r temppp #name="MOLECULE_CELL_SIZE_$str" #eval $name=10 #name="MOLECULE_ASYMETRY_$str" #eval $name=1 #name="ADSORPTION_DISTANCE_$str" #eval $name=2 #name="SUPERCELL_FACTOR_$str" #eval $name=2 #done } ########################################################################################### ########################################################################################### ########################################################################################### storecontcar () { # storecontcar $directorywherecontisstored $name if [ -f $MAINDIR/contcars ] ; then x=x else mkdir $MAINDIR/contcars fi rm $MAINDIR/contcars/$2 touch $MAINDIR/contcars/$2 chmod +x $MAINDIR/contcars/$2 echo "$2 () {" >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "cat > poscardescription << EOF" >> $MAINDIR/contcars/$2 cat $1/poscardescription >> $MAINDIR/contcars/$2 echo "EOF" >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "source poscardescription " >> $MAINDIR/contcars/$2 echo "poscardescription " >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "cat > defaultshiftsandratios << EOF" >> $MAINDIR/contcars/$2 cat $1/defaultshiftsandratios >> $MAINDIR/contcars/$2 echo "EOF" >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "cat > POSCAR << EOF" >> $MAINDIR/contcars/$2 cat $1/CONTCAR >> $MAINDIR/contcars/$2 echo "EOF" >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "if [ \"\$READSHIFTS\" = true ]; then" >> $MAINDIR/contcars/$2 echo "cat > readshifts << EOF" >> $MAINDIR/contcars/$2 echo "readshifts () { " >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 cat $1/readshifts >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "x=x " >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "} " >> $MAINDIR/contcars/$2 echo "EOF" >> $MAINDIR/contcars/$2 echo "fi" >> $MAINDIR/contcars/$2 echo " " >> $MAINDIR/contcars/$2 echo "} " >> $MAINDIR/contcars/$2 source $MAINDIR/contcars/$2 } ########################################################################################### ########################################################################################### ########################################################################################### storeenergyvariables () { echo "energyvariables () {" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 echo "MAINENE=1" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals ; do str="${str##*/}" name="ENERGY_$str" ene=`echo ${!name}` echo "ENERGY_$str=$ene" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals_supercells ; do str="${str##*/}" name="ENERGY_$str" ene=`echo ${!name}` echo "ENERGY_$str=$ene" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" name="ENERGY_$str" ene=`echo ${!name}` echo "ENERGY_$str=$ene" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="ENERGY_$str" ene=`echo ${!name}` echo "ENERGY_$str=$ene" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 echo "}" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 } ########################################################################################### ########################################################################################### ########################################################################################### storeincarvariables () { cat > $MAINDIR/allvariables/$1 << EOF incarvariables () { ISTART=$ISTART ICHARG=$ICHARG LWAVE=$LWAVE LCHARG=$LCHARG NWRITE=$NWRITE PREC=$PREC ALGO=$ALGO NELM=$NELM EDIFF=$EDIFF GGA=$GGA METAGGA=$METAGGA LASPH=$LASPH NOMEGA=$NOMEGA ENCUT=$ENCUT ISMEAR=$ISMEAR SIGMA=$SIGMA ISYM=$ISYM KGAMMA=$KGAMMA ISPIN=$ISPIN MAGMOM=$MAGMOM KPAR=$KPAR NCORE=$NCORE LREAL=$LREAL #for relaxations: IBRION=$IBRION EDIFFG=$EDIFFG NSW=$NSW POTIM=$POTIM ISIF=$ISIF #for DOS: NEDOS=$NEDOS EMAX=$EMAX EMIN=$EMIN #for MD: TEBEG=$TEBEG TEEND=$TEEND #for thermostat & ensembles: MDALGO=$MDALGO LANGEVIN_GAMMA="$LANGEVIN_GAMMA" LANGEVIN_GAMMA_L="$LANGEVIN_GAMMA_L" #for machine learned force fields: ML_LMLFF=$ML_LMLFF ML_ISTART=$ML_ISTART ML_CTIFOR=$ML_CTIFOR ML_ICRITERIA=$ML_ICRITERIA ML_RCUT1=$ML_RCUT1 ML_RCUT2=$ML_RCUT2 KSPACING=$KSPACING } EOF } ########################################################################################### ########################################################################################### ########################################################################################### storekpointsvariables () { echo "kpointsvariables () {" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals ; do str="${str##*/}" name="KPOINTS_$str" kpts=`echo ${!name}` echo "KPOINTS_$str=$kpts" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals_supercells ; do str="${str##*/}" name="KPOINTS_$str" kpts=`echo ${!name}` echo "KPOINTS_$str=$kpts" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" name="KPOINTS_$str" kpts=`echo ${!name}` echo "KPOINTS_$str=$kpts" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="KPOINTS_$str" kpts=`echo ${!name}` echo "KPOINTS_$str=$kpts" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 echo "}" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 } ########################################################################################### ########################################################################################### ########################################################################################### storestructuralvariables () { echo "structuralvariables () {" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals ; do str="${str##*/}" name="VOLUME_$str" vol=`echo ${!name}` echo "VOLUME_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals_supercells ; do str="${str##*/}" name="VOLUME_$str" vol=`echo ${!name}` echo "VOLUME_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals_supercells ; do str="${str##*/}" name="SUPERCELL_FACTOR_$str" fact=`echo ${!name}` echo "SUPERCELL_FACTOR_$str=$fact" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals ; do str="${str##*/}" mkdir temppp cd temppp $str if [ "$LATTICE_SYSTEM" = hexagonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals_supercells ; do str="${str##*/}" mkdir temppp cd temppp $str if [ "$LATTICE_SYSTEM" = hexagonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals ; do str="${str##*/}" mkdir temppp cd temppp $str for i in $(seq 1 1 $NUMBER_OF_SHIFTS) ; do name="SHIFT_${str}_${i}" shift=`echo ${!name}` echo "SHIFT_${str}_${i}=$shift" >> $MAINDIR/allvariables/$1 done cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allcrystals_supercells ; do str="${str##*/}" mkdir temppp cd temppp $str for i in $(seq 1 1 $NUMBER_OF_SHIFTS) ; do name="SHIFT_${str}_${i}" shift=`echo ${!name}` echo "SHIFT_${str}_${i}=$shift" >> $MAINDIR/allvariables/$1 done cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" name="VOLUME_$str" vol=`echo ${!name}` echo "VOLUME_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" name="NUMBER_OF_LAYERS_$str" vol=`echo ${!name}` echo "NUMBER_OF_LAYERS_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" name="VACUUM_SIZE_$str" vol=`echo ${!name}` echo "VACUUM_SIZE_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" name="SELECTIVE_DYNAMICS_DEPTH_$str" vol=`echo ${!name}` echo "SELECTIVE_DYNAMICS_DEPTH_$str=$vol" >> $MAINDIR/allvariables/$1 done for str in $allsurfaces ; do str="${str##*/}" name="LAYER_HIGHTS_$str" vol=`echo ${!name}` echo "LAYER_HIGHTS_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="VOLUME_$str" vol=`echo ${!name}` echo "VOLUME_$str=$vol" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="SUPERCELL_FACTOR_$str" fact=`echo ${!name}` echo "SUPERCELL_FACTOR_$str=$fact" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="NUMBER_OF_LAYERS_$str" fact=`echo ${!name}` echo "NUMBER_OF_LAYERS_$str=$fact" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="VACUUM_SIZE_$str" fact=`echo ${!name}` echo "VACUUM_SIZE_$str=$fact" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="SELECTIVE_DYNAMICS_DEPTH_$str" fact=`echo ${!name}` echo "SELECTIVE_DYNAMICS_DEPTH_$str=$fact" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" name="LAYER_HIGHTS_$str" fact=`echo ${!name}` echo "LAYER_HIGHTS_$str=$fact" >> $MAINDIR/allvariables/$1 done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" mkdir temppp cd temppp $str if [ "$LATTICE_SYSTEM" = hexagonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" mkdir temppp cd temppp $str if [ "$LATTICE_SYSTEM" = hexagonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi if [ "$LATTICE_SYSTEM" = tetragonal ]; then name="C_A_RATIO_$str" ratio=`echo ${!name}` echo "C_A_RATIO_$str=$ratio" >> $MAINDIR/allvariables/$1 fi cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces ; do str="${str##*/}" mkdir temppp cd temppp $str for i in $(seq 1 1 $NUMBER_OF_SHIFTS) ; do name="SHIFT_${str}_${i}" shift=`echo ${!name}` echo "SHIFT_${str}_${i}=$shift" >> $MAINDIR/allvariables/$1 done cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 for str in $allsurfaces_supercells ; do str="${str##*/}" mkdir temppp cd temppp $str for i in $(seq 1 1 $NUMBER_OF_SHIFTS) ; do name="SHIFT_${str}_${i}" shift=`echo ${!name}` echo "SHIFT_${str}_${i}=$shift" >> $MAINDIR/allvariables/$1 done cd .. rm -r temppp done echo " " >> $MAINDIR/allvariables/$1 echo "}" >> $MAINDIR/allvariables/$1 echo " " >> $MAINDIR/allvariables/$1 } ########################################################################################### ########################################################################################### ########################################################################################### storevariables () { if [ -f $MAINDIR/allvariables ] ; then x=x else mkdir $MAINDIR/allvariables fi storeincarvariables $1 storekpointsvariables $1 storestructuralvariables $1 storeenergyvariables $1 } ########################################################################################### ########################################################################################### ########################################################################################### transfercontcars () { cp $1/contcars/* $MAINDIR/contcars for contc in $MAINDIR/contcars/* ; do source $contc contc="${contc##*/}" done } ########################################################################################### ########################################################################################### ###########################################################################################