#!/bin/bash ulimit -s unlimited case=`echo $PWD | awk -F "/" ' { split($0,pole,"/") ; print pole[NF] } ' ` echo "case = $case" parentCase=`echo $PWD | awk -F "/" ' { split($0,pole,"/") ; print pole[NF-1] } ' ` echo "parentCase = $parentCase" parentDirectory=${PWD%%/${case}} echo "parent directory: " echo $parentDirectory mySCRATCH=${parentDirectory} cd ${mySCRATCH}/${case} echo "in $PWD" echo "running in $PWD" # Czech ZDE means HERE ZDE=$PWD #ls printf "\n" test -d hiddenBox && rm -r hiddenBox mkdir hiddenBox if test -f BACKUPvol.struct then mv BACKUPvol.struct hiddenBox/ for i in A*.scf do test $i = ${case}.scf || mv $i hiddenBox/ done cd hiddenBox test -f A*B*.scf && rm A*B*.scf echo "Before running cellShapeOrtho hiddenBox now contains: " cd .. ls hiddenBox else echo "could not find the file BACKUPvol.struct" echo "you probably want to optimize only the orthorhombic cell shape" rmdir hiddenBox fi function Computing() { source compute.job } # function Computing #@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ case=`echo $ZDE | awk -F "/" ' { split($0,pole,"/") ; print pole[NF] } ' ` echo "case = $case" parentDirectory=${ZDE%%/${case}} echo "parent directory: " echo $parentDirectory export mySCRATCH=$parentDirectory cd ${mySCRATCH}/${case} echo "in $PWD" if test -f BACKUP.struct then echo "File BACKUP.struct already exists" echo "Probably a second run" echo "Therefore copying the structure backup BACKUP.struct to ${case}.struct" cp BACKUP.struct ${case}.struct else echo "Making backup of ${case}.struct to BACKUP.struct" cp ${case}.struct BACKUP.struct fi if test -f A0.0B0.0.scf then echo "file A0.0B0.0.scf already exists" echo "no computing this time ... probably second rund of this script " else test -f *.broyd* && rm *.broyd* test -f *.error* && rm *.error* Computing echo y | clean_lapw -s cp ${case}.scf A0.0B0.0.scf fi ENE=`grep :ENE A0.0B0.0.scf | tail -1 | awk ' { print $9 } '` echo "energy: $ENE " test -f ENE && mv ENE ENE.old for i in A0.0B0.0.scf do grep :LAT $i | tail -1 | awk ' { printf "%.6f \t %.6f \t %.6f \t", $5, $6, $7 } ' grep :ENE $i | tail -1 | awk ' { printf "%.6f \n", $9 } ' done > ENE test -f soubor.txt && rm soubor.txt awk ' { printf "%.7f \t %.7f \n", $3/$1, $2/$1 } ' ENE > soubor.txt ; rm ENE read cAOriginal bAOriginal < soubor.txt ; rm soubor.txt echo "cAOriginal je $cAOriginal" echo "bAOriginal je $bAOriginal" #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% initialHowMuchA=0.5 initialHowMuchB=0.5 howMuchA=$initialHowMuchA howMuchB=$initialHowMuchB function Compass() { compute="false" if test -z $1 then echo "usage: first argument is N, NE, E, SE, S, SW, W or NW " exit 1 fi case $1 in N) Aa=$A Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "Bb = $Bb" echo "position N is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy N is $newENE" printf "\n" ;; NE) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position NE is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy NE is $newENE " printf "\n" ;; E) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=$B echo "position E is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy E is $newENE" printf "\n" ;; SE) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position SE is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy SE is $newENE " printf "\n" ;; S) Aa=$A Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position S is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy S is $newENE" printf "\n" ;; SW) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position SW is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy SW is $newENE" printf "\n" ;; W) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=$B echo "position W is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy W is $newENE " printf "\n" ;; NW) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position NW is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy NW is $newENE" printf "\n" ;; *) echo "usage: first argument is N, NE, E, SE, S, SW, W or NW " exit 1 ;; esac #compute begin ------------------------------------------------ if test $compute == "true" then parentDirectory=${mySCRATCH} echo "parent directory: " echo $parentDirectory cd ${parentDirectory} test -d ${parentDirectory}/ariel${case}${1} && rm -rf ${parentDirectory}/ariel${case}${1} mkdir ${parentDirectory}/ariel${case}${1} cp -r $case ariel${case}${1}/ cd ${parentDirectory}/ariel${case}${1}/${case}/ echo "in $PWD" echo "erasing struct files except BACKUP.struct" for i in *\.struct do test $i = BACKUP.struct || rm $i done cp BACKUP.struct ${case}.struct cat > ariel${case}${1}.txt <<+ 3 1 $Aa + x optimize < ariel${case}${1}.txt ; rm ariel${case}${1}.txt mv ${case}_coa_*\.struct TEMPORARY.struct for i in *\.struct do if test $i = BACKUP.struct -o $i = TEMPORARY.struct then echo "not erasing $i" else rm $i fi done mv TEMPORARY.struct ${case}.struct cat > ariel${case}${1}.txt <<+ 4 1 $Bb + x optimize < ariel${case}${1}.txt ; rm ariel${case}${1}.txt mv ${case}_boa_*\.struct ${case}.struct test -f *.broyd* && rm *.broyd* test -f *.error* && rm *.error* Computing echo y | clean_lapw -s cd ${parentDirectory}/ariel${case}${1}/${case} echo "in $PWD" newENE=`grep :ENE ${case}.scf | tail -1 | awk ' { print $9 } '` echo "energy in $1 : $newENE " cp ${parentDirectory}/ariel${case}${1}/${case}/${case}.scf ${parentDirectory}/${case}/A${Aa}B${Bb}.scf fi #compute end -------------------------------------------------- } # function beforeCompass() { compute="false" if test -z $1 then echo "usage: first argument is N, NE, E, SE, S, SW, W or NW " exit 1 fi case $1 in P) Aa=$A Bb=$B echo "position P is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy P is $newENE" printf "\n" ;; N) Aa=$A Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "Bb = $Bb" echo "position N is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy N is $newENE" printf "\n" ;; NE) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position NE is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy NE is $newENE " printf "\n" ;; E) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=$B echo "position E is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy E is $newENE" printf "\n" ;; SE) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position SE is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy SE is $newENE " printf "\n" ;; S) Aa=$A Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position S is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy S is $newENE" printf "\n" ;; SW) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position SW is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy SW is $newENE" printf "\n" ;; W) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=$B echo "position W is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy W is $newENE " printf "\n" ;; NW) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position NW is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then cp ${parentDirectory}/${case}/A${Aa}B${Bb}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy NW is $newENE" printf "\n" ;; *) echo "usage: first argument is N, NE, E, SE, S, SW, W or NW " exit 1 ;; esac #compute begin ------------------------------------------------ if test $compute == "true" then parentDirectory=${mySCRATCH} echo "parent directory: " echo $parentDirectory printf "%s \t %s \t %s \n" $1 $howMuchA $howMuchB >> ${parentDirectory}/toDoList.txt echo "beforeCompass $1 says it will be computed soon" else echo "beforeCompass $1 says it has been already computed" fi #compute end -------------------------------------------------- rm -r ${parentDirectory}/ariel${case}* } function afterCompass() { compute="false" if test -z $1 then echo "usage: first argument is N, NE, E, SE, S, SW, W or NW " exit 1 fi case $1 in N) Aa=$A Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "Bb = $Bb" echo "position N is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy N is $newENE" printf "\n" ;; NE) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position NE is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy NE is $newENE " printf "\n" ;; E) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=$B echo "position E is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy E is $newENE" printf "\n" ;; SE) Aa=` echo "$A + $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position SE is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy SE is $newENE " printf "\n" ;; S) Aa=$A Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position S is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy S is $newENE" printf "\n" ;; SW) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B - $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position SW is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy SW is $newENE" printf "\n" ;; W) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=$B echo "position W is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy W is $newENE " printf "\n" ;; NW) Aa=` echo "$A - $howMuchA" | bc -l | awk ' { printf "%.1f", $1 } ' ` Bb=` echo "$B + $howMuchB" | bc -l | awk ' { printf "%.1f", $1 } ' ` echo "position NW is A = $Aa B = $Bb " if test -f ${parentDirectory}/${case}/A${Aa}B${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/A${Aa}B${Bb}.scf | tail -1 | awk ' { print $9 } '` elif test -f ${parentDirectory}/${case}/C${Aa}D${Bb}.scf then newENE=`grep :ENE ${parentDirectory}/${case}/C${Aa}D${Bb}.scf | tail -1 | awk ' { print $9 } '` else compute="true" fi echo "energy NW is $newENE" printf "\n" ;; *) echo "usage: first argument is N, NE, E, SE, S, SW, W or NW " exit 1 ;; esac #compute begin ------------------------------------------------ if test $compute == "true" then parentDirectory=${mySCRATCH} echo "parent directory: " echo $parentDirectory cd ${parentDirectory} test -d ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB} && rm -rf ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB} mkdir ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB} cp -r $case ariel${case}${1}${howMuchA}_${howMuchB}/ cd ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB}/${case}/ echo "in $PWD" echo "erasing struct files except BACKUP.struct" for i in *\.struct do test $i = BACKUP.struct || rm $i done cp BACKUP.struct ${case}.struct cat > ariel${case}${1}.txt <<+ 3 1 $Aa + x optimize < ariel${case}${1}.txt ; rm ariel${case}${1}.txt mv ${case}_coa_*\.struct TEMPORARY.struct for i in *\.struct do if test $i = BACKUP.struct -o $i = TEMPORARY.struct then echo "not erasing $i" else rm $i fi done mv TEMPORARY.struct ${case}.struct cat > ariel${case}${1}.txt <<+ 4 1 $Bb + x optimize < ariel${case}${1}.txt ; rm ariel${case}${1}.txt mv ${case}_boa_*\.struct ${case}.struct test -f chybovaHlaska.txt && rm chybovaHlaska.txt echo 2 | x nn | grep -A 2 ERROR > chybovaHlaska.txt if test -s chybovaHlaska.txt then echo "nn overlap" echo "skipping this computation" else test -f *.broyd* && rm *.broyd* test -f *.error* && rm *.error* Computing echo y | clean_lapw -s cd ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB}/${case} echo "in $PWD" newENE=`grep :ENE ${case}.scf | tail -1 | awk ' { print $9 } '` echo "energy in $1 : $newENE " # cp ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB}/${case}/${case}.scf ${parentDirectory}/${case}/A${Aa}B${Bb}.scf cp ${parentDirectory}/ariel${case}${1}${howMuchA}_${howMuchB}/${case}/${case}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf fi # no nn overlap cd ${parentDirectory} rm -rf ariel${case}${1}${howMuchA}_${howMuchB} fi # compute=true #compute end -------------------------------------------------- } #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% function Erase() { cd ${parentDirectory} sort -k2 -n nextStep.txt | sed -e "1d" | sed -e "/P/d" > erase.txt while test -s ${parentDirectory}/erase.txt do read point pointENE < ${parentDirectory}/erase.txt sed -e "1d" ${parentDirectory}/erase.txt > ${parentDirectory}/erase.new mv ${parentDirectory}/erase.new ${parentDirectory}/erase.txt if test -d ${parentDirectory}/ariel${case}${point} then echo "erasing directory ${parentDirectory}/ariel${case}${point}" rm -rf ${parentDirectory}/ariel${case}${point} fi done rm ${parentDirectory}/erase.txt } # searching negative energy gradient echo "searching negative energy gradient" cd ${parentDirectory}/${case} STOP="false" numberIterations=0 A=0.0 B=0.0 while test $STOP == "false" do test -f ${parentDirectory}/nextStep.txt && rm ${parentDirectory}/nextStep.txt printf "%s \t %.6f \n" "P" $ENE >> ${parentDirectory}/nextStep.txt test -f ${parentDirectory}/toDoList.txt && rm ${parentDirectory}/toDoList.txt beforeCompass N beforeCompass NE beforeCompass E beforeCompass SE beforeCompass S beforeCompass SW beforeCompass W beforeCompass NW test -f soubor.txt && rm soubor.txt wc -l ${parentDirectory}/toDoList.txt > soubor.txt read lines nic < soubor.txt ; rm soubor.txt echo "toDoList.txt contains $lines lines" cat ${parentDirectory}/toDoList.txt printf "\n" function DoingList() { while test -s ${parentDirectory}/toDoList.txt do read direction somePadding < ${parentDirectory}/toDoList.txt sed -i -e '1d' ${parentDirectory}/toDoList.txt (Compass $direction printf "%s \t %.6f \n" $direction $newENE >> ${parentDirectory}/nextStep.txt) & done wait Erase } # function DoingList if test $lines -le 5 then DoingList else echo "file toDoList contains more than 5 lines" split --lines=5 --suffix-length=1 ${parentDirectory}/toDoList.txt ${parentDirectory}/toDoList mv ${parentDirectory}/toDoLista ${parentDirectory}/toDoList.txt DoingList mv ${parentDirectory}/toDoListb ${parentDirectory}/toDoList.txt DoingList fi sort -k2 -n ${parentDirectory}/nextStep.txt > ${parentDirectory}/nextStep.new mv ${parentDirectory}/nextStep.new ${parentDirectory}/nextStep.txt cat ${parentDirectory}/nextStep.txt read nextStep lowestENE < ${parentDirectory}/nextStep.txt rm ${parentDirectory}/nextStep.txt printf "\n" echo "place with lowest energy: " printf "%s \t %.6f \n" $nextStep $lowestENE if test $nextStep == "P" then echo "reached minimum energy" STOP="true" echo "quit" break else echo "next step is $nextStep" fi cd ${parentDirectory} ENE=$lowestENE if test -d ${parentDirectory}/ariel${case}${nextStep}/${case} then cd ${parentDirectory}/${case} mv A*B*.scf ${parentDirectory}/ test -f ${parentDirectory}/${case}.scf && rm ${parentDirectory}/${case}.scf rm -rf ${parentDirectory}/${case} mv ${parentDirectory}/ariel${case}${nextStep}/${case} ${parentDirectory}/${case} cd ${parentDirectory} mv A*B*.scf ${parentDirectory}/${case}/ fi rm -rf ${parentDirectory}/ariel${case}* numberIterations=$((numberIterations + 1)) echo "where to go next time?" Compass $nextStep A=$Aa B=$Bb done AguessMin=$A; BguessMin=$B echo "AguessMin je $AguessMin" echo "BguessMin je $BguessMin" cd ${parentDirectory}/${case} echo y | clean_lapw cd ${parentDirectory} rm -rf ariel${case}* # making some vicinity of A, B for future fitting echo "making some vicinity around AguessMin, BguessMin for future fitting" cd ${parentDirectory}/${case} originalHowMuchA=$howMuchA originalHowMuchB=$howMuchB test -f ${parentDirectory}/toDoList.txt && rm ${parentDirectory}/toDoList.txt beforeCompass P for extentA in -4 -2 0 2 4 do for extentB in -4 -2 0 2 4 do howMuchA=` echo "$originalHowMuchA $initialHowMuchA $extentA" | awk ' { printf "%.1f", $1 + $2*$3 } ' ` echo "extentA is $extentA" echo "howMuchA is $howMuchA" howMuchB=` echo "$originalHowMuchB $initialHowMuchB $extentB" | awk ' { printf "%.1f", $1 + $2*$3 } ' ` echo "extentB is $extentB" echo "howMuchB is $howMuchB" beforeCompass NE done done if test ! -f ${parentDirectory}/toDoList.txt then echo "no toDoList.txt to do" echo "everything has been already computed" echo "no need to compute this vicinity" else #____________________________________________________ test -f soubor.txt && rm soubor.txt wc -l ${parentDirectory}/toDoList.txt > soubor.txt read lines nic < soubor.txt ; rm soubor.txt echo "toDoList.txt contains $lines lines" cat ${parentDirectory}/toDoList.txt printf "\n" function DoingListAgain() { while test -s ${parentDirectory}/toDoList.txt do read direction howMuchA howMuchB < ${parentDirectory}/toDoList.txt sed -i -e '1d' ${parentDirectory}/toDoList.txt ( afterCompass $direction ) & done wait } # function DoingListAgain if test $lines -le 5 then echo "file toDoList contains up to 5 lines" DoingListAgain else echo "file toDoList contains more than 5 lines" split --lines=5 --suffix-length=1 ${parentDirectory}/toDoList.txt ${parentDirectory}/toDoList for i in ${parentDirectory}/toDoList[a-z] do echo "computing batch of 5 processors $i" mv $i ${parentDirectory}/toDoList.txt DoingListAgain done fi #____________________________________________________ fi #test ! -f ${parentDirectory}/toDoList.txt A=$AguessMin; B=$BguessMin cd ${parentDirectory}/${case} echo "in directory $PWD we make file ENE and ENEpath" test -f ENEpath && mv ENE ENEpath.old for i in A*B*\.scf do grep :LAT $i | tail -1 | awk ' { printf "%.7f \t %.7f \t %.7f \t", $5, $6, $7 } ' grep :ENE $i | tail -1 | awk ' { printf "%.8f \n", $9 } ' done > ENEpath test -f ENE && mv ENE ENE.old for i in C*D*\.scf do grep :LAT $i | tail -1 | awk ' { printf "%.7f \t %.7f \t %.7f \t", $5, $6, $7 } ' grep :ENE $i | tail -1 | awk ' { printf "%.8f \n", $9 } ' done > ENE cat ENE level=` sort -k4 -n ENE | head -1 | awk ' { printf "%.8f", -$4 } ' ` echo "level is $level" test -f matrixATA.awk && rm matrixATA.awk cat > matrixATA.awk <<+ { x[NR] = 10.0*\$3/\$1; y[NR] = 10.0*\$2/\$1; sumA11 += (x[NR])^4 sumA12 += (x[NR])^2*(y[NR])^2 sumA13 += (x[NR])^3*(y[NR]) sumA14 += (x[NR])^3 sumA15 += (x[NR])^2*(y[NR]) sumA16 += (x[NR])^2 #sumA21 will be sumA12 sumA22 += (y[NR])^4 sumA23 += (x[NR])*(y[NR])^3 sumA24 += (x[NR])*(y[NR])^2 sumA25 += (y[NR])^3 sumA26 += (y[NR])^2 #sumA31 will be sumA13 #sumA32 will be sumA23 sumA33 += (x[NR])^2*(y[NR])^2 sumA34 += (x[NR])^2*(y[NR]) sumA35 += (x[NR])*(y[NR])^2 sumA36 += (x[NR])*(y[NR]) #sumA41 will be sumA14 #sumA42 will be sumA24 #sumA43 will be sumA34 sumA44 += (x[NR])^2 sumA45 += (x[NR])*(y[NR]) sumA46 += (x[NR]) #sumA51 will be sumA15 #sumA52 will be sumA25 #sumA53 will be sumA35 #sumA54 will be sumA45 sumA55 += (y[NR])^2 sumA56 += (y[NR]) #sumA61 will be sumA16 #sumA62 will be sumA26 #sumA63 will be sumA36 #sumA64 will be sumA46 #sumA65 will be sumA56 sumA66 += 1 } END { sumA21 = sumA12 ; sumA31 = sumA13; sumA41 = sumA14 ; sumA51 = sumA15; sumA61 = sumA16 sumA32 = sumA23; sumA42 = sumA24 ; sumA52 = sumA25; sumA62 = sumA26 sumA43 = sumA34 ; sumA53 = sumA35; sumA63 = sumA36 sumA54 = sumA45; sumA64 = sumA46 sumA65 = sumA56 printf "%.20f \t %.20f \t %.20f \t %.20f \t %.20f \t %.20f \n", sumA11, sumA12, sumA13, sumA14, sumA15, sumA16 printf "%.20f \t %.20f \t %.20f \t %.20f \t %.20f \t %.20f \n", sumA21, sumA22, sumA23, sumA24, sumA25, sumA26 printf "%.20f \t %.20f \t %.20f \t %.20f \t %.20f \t %.20f \n", sumA31, sumA32, sumA33, sumA34, sumA35, sumA36 printf "%.20f \t %.20f \t %.20f \t %.20f \t %.20f \t %.20f \n", sumA41, sumA42, sumA43, sumA44, sumA45, sumA46 printf "%.20f \t %.20f \t %.20f \t %.20f \t %.20f \t %.20f \n", sumA51, sumA52, sumA53, sumA54, sumA55, sumA56 printf "%.20f \t %.20f \t %.20f \t %.20f \t %.20f \t %.20f \n", sumA61, sumA62, sumA63, sumA64, sumA65, sumA66 } + test -f matrix0.txt && rm matrix0.txt awk -f matrixATA.awk ENE > matrix0.txt test -f matrixATB.awk && rm matrixATB.awk cat > matrixATB.awk <<+ { x[NR] = 10.0*\$3/\$1; y[NR] = 10.0*\$2/\$1; z[NR] = (\$4 + level)*13.6058 sumB1 += (x[NR])^2*(z[NR]) sumB2 += (y[NR])^2*(z[NR]) sumB3 += (x[NR])*(y[NR])*(z[NR]) sumB4 += (x[NR])*(z[NR]) sumB5 += (y[NR])*(z[NR]) sumB6 += (z[NR]) } END { printf "%.20f \n", sumB1 printf "%.20f \n", sumB2 printf "%.20f \n", sumB3 printf "%.20f \n", sumB4 printf "%.20f \n", sumB5 printf "%.20f \n", sumB6 } + test -f columnB.txt && rm columnB.txt awk -f matrixATB.awk -v level=$level ENE > columnB.txt test -f auxiliary.txt && rm auxiliary.txt cut -f 2,3,4,5,6 matrix0.txt > auxiliary.txt test -f matrix1.txt && rm matrix1.txt paste columnB.txt auxiliary.txt > matrix1.txt rm auxiliary.txt test -f auxiliary1.txt && rm auxiliary1.txt test -f auxiliary.txt && rm auxiliary.txt cut -f 1 matrix0.txt > auxiliary1.txt cut -f 3,4,5,6 matrix0.txt > auxiliary.txt test -f matrix2.txt && rm matrix2.txt paste auxiliary1.txt columnB.txt auxiliary.txt > matrix2.txt rm auxiliary1.txt auxiliary.txt test -f auxiliary1.txt && rm auxiliary1.txt test -f auxiliary.txt && rm auxiliary.txt cut -f 1,2 matrix0.txt > auxiliary1.txt cut -f 4,5,6 matrix0.txt > auxiliary.txt test -f matrix3.txt && rm matrix3.txt paste auxiliary1.txt columnB.txt auxiliary.txt > matrix3.txt rm auxiliary1.txt auxiliary.txt test -f auxiliary1.txt && rm auxiliary1.txt test -f auxiliary.txt && rm auxiliary.txt cut -f 1,2,3 matrix0.txt > auxiliary1.txt cut -f 5,6 matrix0.txt > auxiliary.txt test -f matrix4.txt && rm matrix4.txt paste auxiliary1.txt columnB.txt auxiliary.txt > matrix4.txt rm auxiliary1.txt auxiliary.txt test -f auxiliary1.txt && rm auxiliary1.txt test -f auxiliary.txt && rm auxiliary.txt cut -f 1,2,3,4 matrix0.txt > auxiliary1.txt cut -f 6 matrix0.txt > auxiliary.txt test -f matrix5.txt && rm matrix5.txt paste auxiliary1.txt columnB.txt auxiliary.txt > matrix5.txt rm auxiliary1.txt auxiliary.txt test -f auxiliary.txt && rm auxiliary.txt cut -f 1,2,3,4,5 matrix0.txt > auxiliary.txt test -f matrix6.txt && rm matrix6.txt paste auxiliary.txt columnB.txt > matrix6.txt rm auxiliary.txt cd $ZDE echo "in $PWD" echo "solving set of equations by Cramers rule" test -f listOfSequences.txt && rm listOfSequences.txt # begin listOfSequences cat > listOfSequences.txt <<+ 1 2 3 4 5 6 1 2 3 4 6 5 1 2 3 5 4 6 1 2 3 5 6 4 1 2 3 6 4 5 1 2 3 6 5 4 1 2 4 3 5 6 1 2 4 3 6 5 1 2 4 5 3 6 1 2 4 5 6 3 1 2 4 6 3 5 1 2 4 6 5 3 1 2 5 3 4 6 1 2 5 3 6 4 1 2 5 4 3 6 1 2 5 4 6 3 1 2 5 6 3 4 1 2 5 6 4 3 1 2 6 3 4 5 1 2 6 3 5 4 1 2 6 4 3 5 1 2 6 4 5 3 1 2 6 5 3 4 1 2 6 5 4 3 1 3 2 4 5 6 1 3 2 4 6 5 1 3 2 5 4 6 1 3 2 5 6 4 1 3 2 6 4 5 1 3 2 6 5 4 1 3 4 2 5 6 1 3 4 2 6 5 1 3 4 5 2 6 1 3 4 5 6 2 1 3 4 6 2 5 1 3 4 6 5 2 1 3 5 2 4 6 1 3 5 2 6 4 1 3 5 4 2 6 1 3 5 4 6 2 1 3 5 6 2 4 1 3 5 6 4 2 1 3 6 2 4 5 1 3 6 2 5 4 1 3 6 4 2 5 1 3 6 4 5 2 1 3 6 5 2 4 1 3 6 5 4 2 1 4 2 3 5 6 1 4 2 3 6 5 1 4 2 5 3 6 1 4 2 5 6 3 1 4 2 6 3 5 1 4 2 6 5 3 1 4 3 2 5 6 1 4 3 2 6 5 1 4 3 5 2 6 1 4 3 5 6 2 1 4 3 6 2 5 1 4 3 6 5 2 1 4 5 2 3 6 1 4 5 2 6 3 1 4 5 3 2 6 1 4 5 3 6 2 1 4 5 6 2 3 1 4 5 6 3 2 1 4 6 2 3 5 1 4 6 2 5 3 1 4 6 3 2 5 1 4 6 3 5 2 1 4 6 5 2 3 1 4 6 5 3 2 1 5 2 3 4 6 1 5 2 3 6 4 1 5 2 4 3 6 1 5 2 4 6 3 1 5 2 6 3 4 1 5 2 6 4 3 1 5 3 2 4 6 1 5 3 2 6 4 1 5 3 4 2 6 1 5 3 4 6 2 1 5 3 6 2 4 1 5 3 6 4 2 1 5 4 2 3 6 1 5 4 2 6 3 1 5 4 3 2 6 1 5 4 3 6 2 1 5 4 6 2 3 1 5 4 6 3 2 1 5 6 2 3 4 1 5 6 2 4 3 1 5 6 3 2 4 1 5 6 3 4 2 1 5 6 4 2 3 1 5 6 4 3 2 1 6 2 3 4 5 1 6 2 3 5 4 1 6 2 4 3 5 1 6 2 4 5 3 1 6 2 5 3 4 1 6 2 5 4 3 1 6 3 2 4 5 1 6 3 2 5 4 1 6 3 4 2 5 1 6 3 4 5 2 1 6 3 5 2 4 1 6 3 5 4 2 1 6 4 2 3 5 1 6 4 2 5 3 1 6 4 3 2 5 1 6 4 3 5 2 1 6 4 5 2 3 1 6 4 5 3 2 1 6 5 2 3 4 1 6 5 2 4 3 1 6 5 3 2 4 1 6 5 3 4 2 1 6 5 4 2 3 1 6 5 4 3 2 2 1 3 4 5 6 2 1 3 4 6 5 2 1 3 5 4 6 2 1 3 5 6 4 2 1 3 6 4 5 2 1 3 6 5 4 2 1 4 3 5 6 2 1 4 3 6 5 2 1 4 5 3 6 2 1 4 5 6 3 2 1 4 6 3 5 2 1 4 6 5 3 2 1 5 3 4 6 2 1 5 3 6 4 2 1 5 4 3 6 2 1 5 4 6 3 2 1 5 6 3 4 2 1 5 6 4 3 2 1 6 3 4 5 2 1 6 3 5 4 2 1 6 4 3 5 2 1 6 4 5 3 2 1 6 5 3 4 2 1 6 5 4 3 2 3 1 4 5 6 2 3 1 4 6 5 2 3 1 5 4 6 2 3 1 5 6 4 2 3 1 6 4 5 2 3 1 6 5 4 2 3 4 1 5 6 2 3 4 1 6 5 2 3 4 5 1 6 2 3 4 5 6 1 2 3 4 6 1 5 2 3 4 6 5 1 2 3 5 1 4 6 2 3 5 1 6 4 2 3 5 4 1 6 2 3 5 4 6 1 2 3 5 6 1 4 2 3 5 6 4 1 2 3 6 1 4 5 2 3 6 1 5 4 2 3 6 4 1 5 2 3 6 4 5 1 2 3 6 5 1 4 2 3 6 5 4 1 2 4 1 3 5 6 2 4 1 3 6 5 2 4 1 5 3 6 2 4 1 5 6 3 2 4 1 6 3 5 2 4 1 6 5 3 2 4 3 1 5 6 2 4 3 1 6 5 2 4 3 5 1 6 2 4 3 5 6 1 2 4 3 6 1 5 2 4 3 6 5 1 2 4 5 1 3 6 2 4 5 1 6 3 2 4 5 3 1 6 2 4 5 3 6 1 2 4 5 6 1 3 2 4 5 6 3 1 2 4 6 1 3 5 2 4 6 1 5 3 2 4 6 3 1 5 2 4 6 3 5 1 2 4 6 5 1 3 2 4 6 5 3 1 2 5 1 3 4 6 2 5 1 3 6 4 2 5 1 4 3 6 2 5 1 4 6 3 2 5 1 6 3 4 2 5 1 6 4 3 2 5 3 1 4 6 2 5 3 1 6 4 2 5 3 4 1 6 2 5 3 4 6 1 2 5 3 6 1 4 2 5 3 6 4 1 2 5 4 1 3 6 2 5 4 1 6 3 2 5 4 3 1 6 2 5 4 3 6 1 2 5 4 6 1 3 2 5 4 6 3 1 2 5 6 1 3 4 2 5 6 1 4 3 2 5 6 3 1 4 2 5 6 3 4 1 2 5 6 4 1 3 2 5 6 4 3 1 2 6 1 3 4 5 2 6 1 3 5 4 2 6 1 4 3 5 2 6 1 4 5 3 2 6 1 5 3 4 2 6 1 5 4 3 2 6 3 1 4 5 2 6 3 1 5 4 2 6 3 4 1 5 2 6 3 4 5 1 2 6 3 5 1 4 2 6 3 5 4 1 2 6 4 1 3 5 2 6 4 1 5 3 2 6 4 3 1 5 2 6 4 3 5 1 2 6 4 5 1 3 2 6 4 5 3 1 2 6 5 1 3 4 2 6 5 1 4 3 2 6 5 3 1 4 2 6 5 3 4 1 2 6 5 4 1 3 2 6 5 4 3 1 3 1 2 4 5 6 3 1 2 4 6 5 3 1 2 5 4 6 3 1 2 5 6 4 3 1 2 6 4 5 3 1 2 6 5 4 3 1 4 2 5 6 3 1 4 2 6 5 3 1 4 5 2 6 3 1 4 5 6 2 3 1 4 6 2 5 3 1 4 6 5 2 3 1 5 2 4 6 3 1 5 2 6 4 3 1 5 4 2 6 3 1 5 4 6 2 3 1 5 6 2 4 3 1 5 6 4 2 3 1 6 2 4 5 3 1 6 2 5 4 3 1 6 4 2 5 3 1 6 4 5 2 3 1 6 5 2 4 3 1 6 5 4 2 3 2 1 4 5 6 3 2 1 4 6 5 3 2 1 5 4 6 3 2 1 5 6 4 3 2 1 6 4 5 3 2 1 6 5 4 3 2 4 1 5 6 3 2 4 1 6 5 3 2 4 5 1 6 3 2 4 5 6 1 3 2 4 6 1 5 3 2 4 6 5 1 3 2 5 1 4 6 3 2 5 1 6 4 3 2 5 4 1 6 3 2 5 4 6 1 3 2 5 6 1 4 3 2 5 6 4 1 3 2 6 1 4 5 3 2 6 1 5 4 3 2 6 4 1 5 3 2 6 4 5 1 3 2 6 5 1 4 3 2 6 5 4 1 3 4 1 2 5 6 3 4 1 2 6 5 3 4 1 5 2 6 3 4 1 5 6 2 3 4 1 6 2 5 3 4 1 6 5 2 3 4 2 1 5 6 3 4 2 1 6 5 3 4 2 5 1 6 3 4 2 5 6 1 3 4 2 6 1 5 3 4 2 6 5 1 3 4 5 1 2 6 3 4 5 1 6 2 3 4 5 2 1 6 3 4 5 2 6 1 3 4 5 6 1 2 3 4 5 6 2 1 3 4 6 1 2 5 3 4 6 1 5 2 3 4 6 2 1 5 3 4 6 2 5 1 3 4 6 5 1 2 3 4 6 5 2 1 3 5 1 2 4 6 3 5 1 2 6 4 3 5 1 4 2 6 3 5 1 4 6 2 3 5 1 6 2 4 3 5 1 6 4 2 3 5 2 1 4 6 3 5 2 1 6 4 3 5 2 4 1 6 3 5 2 4 6 1 3 5 2 6 1 4 3 5 2 6 4 1 3 5 4 1 2 6 3 5 4 1 6 2 3 5 4 2 1 6 3 5 4 2 6 1 3 5 4 6 1 2 3 5 4 6 2 1 3 5 6 1 2 4 3 5 6 1 4 2 3 5 6 2 1 4 3 5 6 2 4 1 3 5 6 4 1 2 3 5 6 4 2 1 3 6 1 2 4 5 3 6 1 2 5 4 3 6 1 4 2 5 3 6 1 4 5 2 3 6 1 5 2 4 3 6 1 5 4 2 3 6 2 1 4 5 3 6 2 1 5 4 3 6 2 4 1 5 3 6 2 4 5 1 3 6 2 5 1 4 3 6 2 5 4 1 3 6 4 1 2 5 3 6 4 1 5 2 3 6 4 2 1 5 3 6 4 2 5 1 3 6 4 5 1 2 3 6 4 5 2 1 3 6 5 1 2 4 3 6 5 1 4 2 3 6 5 2 1 4 3 6 5 2 4 1 3 6 5 4 1 2 3 6 5 4 2 1 4 1 2 3 5 6 4 1 2 3 6 5 4 1 2 5 3 6 4 1 2 5 6 3 4 1 2 6 3 5 4 1 2 6 5 3 4 1 3 2 5 6 4 1 3 2 6 5 4 1 3 5 2 6 4 1 3 5 6 2 4 1 3 6 2 5 4 1 3 6 5 2 4 1 5 2 3 6 4 1 5 2 6 3 4 1 5 3 2 6 4 1 5 3 6 2 4 1 5 6 2 3 4 1 5 6 3 2 4 1 6 2 3 5 4 1 6 2 5 3 4 1 6 3 2 5 4 1 6 3 5 2 4 1 6 5 2 3 4 1 6 5 3 2 4 2 1 3 5 6 4 2 1 3 6 5 4 2 1 5 3 6 4 2 1 5 6 3 4 2 1 6 3 5 4 2 1 6 5 3 4 2 3 1 5 6 4 2 3 1 6 5 4 2 3 5 1 6 4 2 3 5 6 1 4 2 3 6 1 5 4 2 3 6 5 1 4 2 5 1 3 6 4 2 5 1 6 3 4 2 5 3 1 6 4 2 5 3 6 1 4 2 5 6 1 3 4 2 5 6 3 1 4 2 6 1 3 5 4 2 6 1 5 3 4 2 6 3 1 5 4 2 6 3 5 1 4 2 6 5 1 3 4 2 6 5 3 1 4 3 1 2 5 6 4 3 1 2 6 5 4 3 1 5 2 6 4 3 1 5 6 2 4 3 1 6 2 5 4 3 1 6 5 2 4 3 2 1 5 6 4 3 2 1 6 5 4 3 2 5 1 6 4 3 2 5 6 1 4 3 2 6 1 5 4 3 2 6 5 1 4 3 5 1 2 6 4 3 5 1 6 2 4 3 5 2 1 6 4 3 5 2 6 1 4 3 5 6 1 2 4 3 5 6 2 1 4 3 6 1 2 5 4 3 6 1 5 2 4 3 6 2 1 5 4 3 6 2 5 1 4 3 6 5 1 2 4 3 6 5 2 1 4 5 1 2 3 6 4 5 1 2 6 3 4 5 1 3 2 6 4 5 1 3 6 2 4 5 1 6 2 3 4 5 1 6 3 2 4 5 2 1 3 6 4 5 2 1 6 3 4 5 2 3 1 6 4 5 2 3 6 1 4 5 2 6 1 3 4 5 2 6 3 1 4 5 3 1 2 6 4 5 3 1 6 2 4 5 3 2 1 6 4 5 3 2 6 1 4 5 3 6 1 2 4 5 3 6 2 1 4 5 6 1 2 3 4 5 6 1 3 2 4 5 6 2 1 3 4 5 6 2 3 1 4 5 6 3 1 2 4 5 6 3 2 1 4 6 1 2 3 5 4 6 1 2 5 3 4 6 1 3 2 5 4 6 1 3 5 2 4 6 1 5 2 3 4 6 1 5 3 2 4 6 2 1 3 5 4 6 2 1 5 3 4 6 2 3 1 5 4 6 2 3 5 1 4 6 2 5 1 3 4 6 2 5 3 1 4 6 3 1 2 5 4 6 3 1 5 2 4 6 3 2 1 5 4 6 3 2 5 1 4 6 3 5 1 2 4 6 3 5 2 1 4 6 5 1 2 3 4 6 5 1 3 2 4 6 5 2 1 3 4 6 5 2 3 1 4 6 5 3 1 2 4 6 5 3 2 1 5 1 2 3 4 6 5 1 2 3 6 4 5 1 2 4 3 6 5 1 2 4 6 3 5 1 2 6 3 4 5 1 2 6 4 3 5 1 3 2 4 6 5 1 3 2 6 4 5 1 3 4 2 6 5 1 3 4 6 2 5 1 3 6 2 4 5 1 3 6 4 2 5 1 4 2 3 6 5 1 4 2 6 3 5 1 4 3 2 6 5 1 4 3 6 2 5 1 4 6 2 3 5 1 4 6 3 2 5 1 6 2 3 4 5 1 6 2 4 3 5 1 6 3 2 4 5 1 6 3 4 2 5 1 6 4 2 3 5 1 6 4 3 2 5 2 1 3 4 6 5 2 1 3 6 4 5 2 1 4 3 6 5 2 1 4 6 3 5 2 1 6 3 4 5 2 1 6 4 3 5 2 3 1 4 6 5 2 3 1 6 4 5 2 3 4 1 6 5 2 3 4 6 1 5 2 3 6 1 4 5 2 3 6 4 1 5 2 4 1 3 6 5 2 4 1 6 3 5 2 4 3 1 6 5 2 4 3 6 1 5 2 4 6 1 3 5 2 4 6 3 1 5 2 6 1 3 4 5 2 6 1 4 3 5 2 6 3 1 4 5 2 6 3 4 1 5 2 6 4 1 3 5 2 6 4 3 1 5 3 1 2 4 6 5 3 1 2 6 4 5 3 1 4 2 6 5 3 1 4 6 2 5 3 1 6 2 4 5 3 1 6 4 2 5 3 2 1 4 6 5 3 2 1 6 4 5 3 2 4 1 6 5 3 2 4 6 1 5 3 2 6 1 4 5 3 2 6 4 1 5 3 4 1 2 6 5 3 4 1 6 2 5 3 4 2 1 6 5 3 4 2 6 1 5 3 4 6 1 2 5 3 4 6 2 1 5 3 6 1 2 4 5 3 6 1 4 2 5 3 6 2 1 4 5 3 6 2 4 1 5 3 6 4 1 2 5 3 6 4 2 1 5 4 1 2 3 6 5 4 1 2 6 3 5 4 1 3 2 6 5 4 1 3 6 2 5 4 1 6 2 3 5 4 1 6 3 2 5 4 2 1 3 6 5 4 2 1 6 3 5 4 2 3 1 6 5 4 2 3 6 1 5 4 2 6 1 3 5 4 2 6 3 1 5 4 3 1 2 6 5 4 3 1 6 2 5 4 3 2 1 6 5 4 3 2 6 1 5 4 3 6 1 2 5 4 3 6 2 1 5 4 6 1 2 3 5 4 6 1 3 2 5 4 6 2 1 3 5 4 6 2 3 1 5 4 6 3 1 2 5 4 6 3 2 1 5 6 1 2 3 4 5 6 1 2 4 3 5 6 1 3 2 4 5 6 1 3 4 2 5 6 1 4 2 3 5 6 1 4 3 2 5 6 2 1 3 4 5 6 2 1 4 3 5 6 2 3 1 4 5 6 2 3 4 1 5 6 2 4 1 3 5 6 2 4 3 1 5 6 3 1 2 4 5 6 3 1 4 2 5 6 3 2 1 4 5 6 3 2 4 1 5 6 3 4 1 2 5 6 3 4 2 1 5 6 4 1 2 3 5 6 4 1 3 2 5 6 4 2 1 3 5 6 4 2 3 1 5 6 4 3 1 2 5 6 4 3 2 1 6 1 2 3 4 5 6 1 2 3 5 4 6 1 2 4 3 5 6 1 2 4 5 3 6 1 2 5 3 4 6 1 2 5 4 3 6 1 3 2 4 5 6 1 3 2 5 4 6 1 3 4 2 5 6 1 3 4 5 2 6 1 3 5 2 4 6 1 3 5 4 2 6 1 4 2 3 5 6 1 4 2 5 3 6 1 4 3 2 5 6 1 4 3 5 2 6 1 4 5 2 3 6 1 4 5 3 2 6 1 5 2 3 4 6 1 5 2 4 3 6 1 5 3 2 4 6 1 5 3 4 2 6 1 5 4 2 3 6 1 5 4 3 2 6 2 1 3 4 5 6 2 1 3 5 4 6 2 1 4 3 5 6 2 1 4 5 3 6 2 1 5 3 4 6 2 1 5 4 3 6 2 3 1 4 5 6 2 3 1 5 4 6 2 3 4 1 5 6 2 3 4 5 1 6 2 3 5 1 4 6 2 3 5 4 1 6 2 4 1 3 5 6 2 4 1 5 3 6 2 4 3 1 5 6 2 4 3 5 1 6 2 4 5 1 3 6 2 4 5 3 1 6 2 5 1 3 4 6 2 5 1 4 3 6 2 5 3 1 4 6 2 5 3 4 1 6 2 5 4 1 3 6 2 5 4 3 1 6 3 1 2 4 5 6 3 1 2 5 4 6 3 1 4 2 5 6 3 1 4 5 2 6 3 1 5 2 4 6 3 1 5 4 2 6 3 2 1 4 5 6 3 2 1 5 4 6 3 2 4 1 5 6 3 2 4 5 1 6 3 2 5 1 4 6 3 2 5 4 1 6 3 4 1 2 5 6 3 4 1 5 2 6 3 4 2 1 5 6 3 4 2 5 1 6 3 4 5 1 2 6 3 4 5 2 1 6 3 5 1 2 4 6 3 5 1 4 2 6 3 5 2 1 4 6 3 5 2 4 1 6 3 5 4 1 2 6 3 5 4 2 1 6 4 1 2 3 5 6 4 1 2 5 3 6 4 1 3 2 5 6 4 1 3 5 2 6 4 1 5 2 3 6 4 1 5 3 2 6 4 2 1 3 5 6 4 2 1 5 3 6 4 2 3 1 5 6 4 2 3 5 1 6 4 2 5 1 3 6 4 2 5 3 1 6 4 3 1 2 5 6 4 3 1 5 2 6 4 3 2 1 5 6 4 3 2 5 1 6 4 3 5 1 2 6 4 3 5 2 1 6 4 5 1 2 3 6 4 5 1 3 2 6 4 5 2 1 3 6 4 5 2 3 1 6 4 5 3 1 2 6 4 5 3 2 1 6 5 1 2 3 4 6 5 1 2 4 3 6 5 1 3 2 4 6 5 1 3 4 2 6 5 1 4 2 3 6 5 1 4 3 2 6 5 2 1 3 4 6 5 2 1 4 3 6 5 2 3 1 4 6 5 2 3 4 1 6 5 2 4 1 3 6 5 2 4 3 1 6 5 3 1 2 4 6 5 3 1 4 2 6 5 3 2 1 4 6 5 3 2 4 1 6 5 3 4 1 2 6 5 3 4 2 1 6 5 4 1 2 3 6 5 4 1 3 2 6 5 4 2 1 3 6 5 4 2 3 1 6 5 4 3 1 2 6 5 4 3 2 1 + # end listOfSequences function det() { # the columns of the determinant file must be separated by tabs if ! test -f $1 then echo "usage: determinant file" echo "the columns of the determinant must be separated by tabulator" exit 1 fi determinant=$1 dimension=`wc -l $determinant | awk ' { print $1 } ' ` #echo "dimension of determinant is $dimension" if test $dimension -le 1 then echo "this determinant has dimension only $dimension" exit 1 fi function Factorial() { if test $1 = "0" then factorial=1 else i=$1 factorial=1 while test $i -gt 1 do factorial=`echo "$factorial $i" | awk ' { printf "%d", $1*$2 }' ` let i=i-1 done fi printf "%d \n" $factorial } # function Factorial bigDimension=`Factorial $dimension ` #echo "bigDimension is $bigDimension" #wc -l listOfSequences.txt test -f bubbleSort.awk && rm bubbleSort.awk cat > bubbleSort.awk <<+ BEGIN { sum = 0 } FILENAME != "listOfSequences.txt" { cca = split(\$0, meadow); for (k=1;k<=cca;k++) a[NR, k] = meadow[k] } FILENAME == "listOfSequences.txt" { cca = split(\$0,field) for(i=1;i<=cca;i++) { j = field[i] printf "%.20f * ", a[i,j] } transpositions = 0 for (ca=cca;ca>=1;ca--) { for(i=1; i field[i+1]) { auxiliary = field[i]; field[i] = field[i+1]; field[i+1] = auxiliary transpositions++ } } } if (FNR < $bigDimension) printf "%d + \\\\\n", (-1)^transpositions else printf "%d \n", (-1)^transpositions #sum += product*(-1)^transpositions } #END { printf "%.720g \n", sum } + awk -f bubbleSort.awk $1 listOfSequences.txt | bc -l rm bubbleSort.awk #rm listOfSequences.txt } # function det det0=` det matrix0.txt ` ; echo "det0 is $det0" det1=` det matrix1.txt ` ; echo "det1 is $det1" det2=` det matrix2.txt ` ; echo "det2 is $det2" det3=` det matrix3.txt ` ; echo "det3 is $det3" det4=` det matrix4.txt ` ; echo "det4 is $det4" det5=` det matrix5.txt ` ; echo "det5 is $det5" det6=` det matrix6.txt ` ; echo "det6 is $det6" isZero=`echo "$det0 == 0.0" | bc -l ` echo "isZero je $isZero" if test $isZero = "1" then echo "matrix0 is singular" else coeff1=` echo "$det1 / $det0 " | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "coeff1 je $coeff1" coeff2=` echo "$det2 / $det0 " | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "coeff2 je $coeff2" coeff3=` echo "$det3 / $det0 " | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "coeff3 je $coeff3" coeff4=` echo "$det4 / $det0 " | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "coeff4 je $coeff4" coeff5=` echo "$det5 / $det0 " | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "coeff5 je $coeff5" coeff6=` echo "$det6 / $det0 " | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "coeff6 je $coeff6" a2=$coeff1 b2=$coeff2 c=$coeff3 a1=$coeff4 b1=$coeff5 a0=$coeff6 # denominator = 4*a2*b2 - c**2 # nominatorX = c*b1 - 2*a1*b2 # nominatorY = c*a1 - 2*a2*b1 denominator=` echo "4 * $a2 * $b2 - ${c}^2" | bc -l | awk ' { printf "%.20f", $1 } '` echo "denominator je $denominator" isZero=`echo "$denominator == 0.0" | bc -l ` echo "isZero je $isZero" if test $isZero = "1" then echo "some singularity in minimum" else nominatorX=`echo "$c * $b1 - 2 * $a1 * $b2 " | bc -l | awk ' { printf "%.20f", $1 } '` nominatorY=`echo "$c * $a1 - 2 * $a2 * $b1 " | bc -l | awk ' { printf "%.20f", $1 } '` minX=` echo "$nominatorX $denominator" | awk ' { printf "%.20f", $1/$2 } ' ` minY=` echo "$nominatorY $denominator" | awk ' { printf "%.20f", $1/$2 } ' ` echo "minX je $minX" echo "minY je $minY" cAmin=`echo "$minX / 10.0" | bc -l | awk ' { printf "%.20f", $1 } ' ` bAmin=`echo "$minY / 10.0" | bc -l | awk ' { printf "%.20f", $1 } ' ` echo "cAmin je $cAmin" echo "bAmin je $bAmin" fi # for gnuplot a2=`echo "$coeff1 * 100.0 " | bc -l ` b2=`echo "$coeff2 * 100.0 " | bc -l ` c=`echo "$coeff3 * 100.0 " | bc -l ` a1=`echo "$coeff4 * 10.0 " | bc -l ` b1=`echo "$coeff5 * 10.0 " | bc -l ` a0=$coeff6 gnuA=` echo "100 * ( $cAmin / $cAOriginal ) - 100.0" | bc -l | awk ' { printf "%.10f", $1 } ' ` gnuB=` echo "100 * ( $bAmin / $bAOriginal ) - 100.0" | bc -l | awk ' { printf "%.10f", $1 } ' ` # once more compute parentDirectory=${mySCRATCH} echo "parent directory: " echo $parentDirectory cd ${parentDirectory} test -d ${parentDirectory}/ariel${case}Min && rm -rf ${parentDirectory}/ariel${case}Min mkdir ${parentDirectory}/ariel${case}Min cp -r $case ariel${case}Min/ cd ${parentDirectory}/ariel${case}Min/${case}/ echo "in $PWD" echo "erasing struct files except BACKUP.struct" for i in *\.struct do test $i = BACKUP.struct || rm $i done cp BACKUP.struct ${case}.struct cat > ariel${case}Min.txt <<+ 3 1 $gnuA + x optimize < ariel${case}Min.txt ; rm ariel${case}Min.txt mv ${case}_coa_*\.struct TEMPORARY.struct for i in *\.struct do if test $i == BACKUP.struct -o $i == TEMPORARY.struct then echo "not erasing $i" else rm $i fi done mv TEMPORARY.struct ${case}.struct cat > ariel${case}Min.txt <<+ 4 1 $gnuB + x optimize < ariel${case}Min.txt ; rm ariel${case}Min.txt mv ${case}_boa_*\.struct ${case}.struct test -f *.broyd* && rm *.broyd* test -f *.error* && rm *.error* Computing echo y | clean_lapw -s cd ${parentDirectory}/ariel${case}Min/${case} echo "in $PWD" newENE=`grep :ENE ${case}.scf | tail -1 | awk ' { print $9 } '` echo "energy in $1 : $newENE " Aa=` echo "$gnuA" | awk ' { printf "%.5f", $1 } ' ` Bb=` echo "$gnuB" | awk ' { printf "%.5f", $1 } ' ` echo "Aa in minimum is $Aa" echo "Bb in minimum is $Bb" # cp ${parentDirectory}/ariel${case}Min/${case}/${case}.scf ${parentDirectory}/${case}/A${Aa}B${Bb}.scf cp ${parentDirectory}/ariel${case}Min/${case}/${case}.scf ${parentDirectory}/${case}/C${Aa}D${Bb}.scf cp ${parentDirectory}/ariel${case}Min/${case}/${case}.scf ${parentDirectory}/ariel${case}Min/${case}/C${Aa}D${Bb}.scf oldENE=`sed '/^$/d' ENE | sort -k4 -n | head -1 | awk ' { printf "%.8f", $4 } ' ` isLower=` echo "$newENE < $oldENE " | bc -l ` if test $isLower = "1" then echo "energy in fitted minimum is lower than any other energy" rm -rf ${parentDirectory}/${case} mv ${parentDirectory}/ariel${case}Min/${case} ${parentDirectory}/ rmdir ${parentDirectory}/ariel${case}Min else echo "Warning: there is a lower energy than that in the fitted minimum" #rm -rf ${parentDirectory}/ariel${case}Min rm -rf ${parentDirectory}/${case} mv ${parentDirectory}/ariel${case}Min/${case} ${parentDirectory}/ rmdir ${parentDirectory}/ariel${case}Min fi fi # matrix0 is not singular cd ${parentDirectory}/${case} echo "once more in $PWD" echo " to make final file ENE and a graph" test -f ENE && rm ENE for i in C*D*\.scf do grep :LAT $i | tail -1 | awk ' { printf "%.6f \t %.6f \t %.6f \t", $5, $6, $7 } ' grep :ENE $i | tail -1 | awk ' { printf "%.6f \n", $9 } ' done > ENE cat ENE export GDFONTPATH=/usr/share/fonts/bitstream-vera # for Gnuplot true type fonts test -f ridiciProGnuplot && rm ridiciProGnuplot # ridici pro gnuplot means driver for gnuplot cat > ridiciProGnuplot <<+ pocetAtomu = 1 set terminal x11 font "rk16" auToAng = 0.529177249 set encoding iso set pointsize 2 hladina = `sed '/^\$/d' ENE | sort -k4 -n | head -1 | awk ' { printf "%.6f", -\$4 } ' ` print "hladina = ", hladina set title "`pwd | awk -F '/' ' { split(\$0,pole,"/") ; print pole[NF] } '`" set xlabel "c/a" set ylabel "b/a" set zlabel "E (eV/cell)" set ticslevel 0.02 set grid splot "ENE.cellShape" using (\$3/\$1):(\$2/\$1):((\$4 + hladina)*13.6058/pocetAtomu) w p pt 7 ti "" a2 = $a2 b2 = $b2 c = $c a1 = $a1 b1 = $b1 a0 = $a0 f(x,y) = a0 + a1*x + a2*x**2 + b1*y + b2*y**2 + c*x*y replot f(x,y) # replot "ENEpath" using (\$3/\$1):(\$2/\$1):((\$4 + hladina)*13.6058/pocetAtomu) w p pt 4 ti "ENEpath" replot "ENEactual" using (\$3/\$1):(\$2/\$1):((\$4 + hladina)*13.6058/pocetAtomu) w p pt 7 ti "" + # gnuplot -persist ridiciProGnuplot cp ridiciProGnuplot showPlot test -f ${case}_initial.struct && rm ${case}_initial.struct hostname echo y | clean_lapw 1> /dev/null 2> /dev/null rm ${mySCRATCH}/toDoList.txt cd ${parentDirectory}/${case} echo "in $PWD" if test -d hiddenBox -a -f hiddenBox/BACKUPvol.struct then echo "At last " echo "changing the orthorhombic cell shape for the initial reference volume" echo " The initial volume will be referred to later " mv ${case}.struct hiddenBox/ mv BACKUP.struct hiddenBox/ mv hiddenBox/BACKUPvol.struct $PWD/BACKUP.struct echo "erasing struct files except BACKUP.struct" for i in *\.struct do test $i = BACKUP.struct || rm $i done cp BACKUP.struct ${case}.struct test -f ariel${case}Min.txt && rm ariel${case}Min.txt cat > ariel${case}Min.txt <<+ 3 1 $gnuA + x optimize < ariel${case}Min.txt ; rm ariel${case}Min.txt mv ${case}_coa_*\.struct TEMPORARY.struct for i in *\.struct do if test $i == BACKUP.struct -o $i == TEMPORARY.struct then echo "not erasing $i" else rm $i fi done mv TEMPORARY.struct ${case}.struct cat > ariel${case}Min.txt <<+ 4 1 $gnuB + x optimize < ariel${case}Min.txt ; rm ariel${case}Min.txt mv ${case}_boa_*\.struct BACKUPvol.struct rm BACKUP.struct mv hiddenBox/${case}.struct $PWD/ mv ${case}.scf hiddenBox/ cd hiddenBox cp ${case}.scf A${step}.scf cd .. echo "After running cellShapeOrtho hiddenBox contains: " ls hiddenBox echo "erasing all scf files and replacing them by scf files from hiddenBox" rm *.scf cd hiddenBox mv * ../ cd .. echo "back from hiddenBox in $PWD" rmdir hiddenBox cp ENE ENE.cellShape cp showPlot showPlotCellShape else cp ENE ENE.cellShape fi # test -d hiddenBox -a -f hiddenBox/BACKUPvol.struct rm matrix*\.awk rm matrix*\.txt rm columnB\.txt rm ridiciProGnuplot test -f ENEactual && rm ENEactual ( grep :LAT ${case}.scf | tail -1 | awk ' { printf "%.5f \t %.5f \t %.5f \t", $5, $6, $7 } ' grep :ENE ${case}.scf | tail -1 | awk ' { print $9 } ' ) > ENEactual echo "script cellShapeOrtho in $PWD ends" hostname