scripts:v2xyz
Differences
This shows you the differences between two versions of the page.
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scripts:v2xyz [2010/02/17 10:27] prokop created |
scripts:v2xyz [2011/02/18 13:13] |
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| - | ==== usage ==== | ||
| - | * Copy v2xyz and xv2xyz to bin directory | ||
| - | * make sure that you have particular POTCAR in the direscotry with your CONTCAR or XDATCAR | ||
| - | * run v2xyz in the directory with CONTCAR and POTCAR to make CONTCAR.xyz | ||
| - | * run xv2xyz in the directory with CONTCAR and XDATCAR to make answer.xyz movie | ||
| - | |||
| - | ==== warning ==== | ||
| - | the scripts copy, overwrite and delete some files | ||
| - | * xv2xyz overide CONTCAR, it saves backup to CONTCAR.bak before | ||
| - | * v2xyz and xv2xyz create and delate files *.temp | ||
| - | |||
| - | |||
| - | ==== v2xyz: ==== | ||
| - | <code> | ||
| - | #!/bin/bash | ||
| - | input="CONTCAR" | ||
| - | output="CONTCAR.xyz" | ||
| - | jmena=`grep TITEL POTCAR | cut -b 15- | tr "\n" " "` # chenicke znacky prvku z POTCAR | ||
| - | pocty=`head -n 6 CONTCAR | tail -n 1` # pocty prvku v CONTCAR | ||
| - | echo $jmena | ||
| - | echo $pocty | ||
| - | |||
| - | i=0 | ||
| - | for s in $jmena; | ||
| - | do | ||
| - | str2ar[$i]=$s | ||
| - | let i=$i+1 | ||
| - | done | ||
| - | |||
| - | #prepare array of atom numbers per element | ||
| - | > elemcol.temp | ||
| - | i=0 | ||
| - | for s in $pocty; | ||
| - | do | ||
| - | ii=0 | ||
| - | while [ $ii -lt $s ] | ||
| - | do | ||
| - | echo ${str2ar[$i]} >> elemcol.temp # temporary file with element names | ||
| - | let ii=$ii+1 | ||
| - | done | ||
| - | let i=$i+1 | ||
| - | done | ||
| - | |||
| - | # Sum up pocet prvku | ||
| - | nprvku=`echo $pocty | tr " " "+" | bc` | ||
| - | echo $nprvku | ||
| - | |||
| - | # Extract geometry from vasp format | ||
| - | awk -v L=$nprvku 'BEGIN { | ||
| - | da=0.0 | ||
| - | db=0.0 | ||
| - | dc=0.0 | ||
| - | } | ||
| - | NR==1 {name = $0} | ||
| - | NR==2 {k=$1} | ||
| - | NR==3 {ax=$1; ay=$2; az=$3} | ||
| - | NR==4 {bx=$1; by=$2; bz=$3} | ||
| - | NR==5 {cx=$1; cy=$2; cz=$3} | ||
| - | (NR>8) && (NR<=8+L) { | ||
| - | a=$1; b=$2; c=$3; | ||
| - | | ||
| - | a=(a+da)%1 | ||
| - | b=(b+db)%1 | ||
| - | c=(c+dc)%1 | ||
| - | | ||
| - | #a=(a+da)%1-da | ||
| - | #b=(b+db)%1-db | ||
| - | #c=(c+dc)%1-dc | ||
| - | | ||
| - | |||
| - | x=k*(ax*a+bx*b+cx*c) | ||
| - | y=k*(ay*a+by*b+cy*c) | ||
| - | z=k*(az*a+bz*b+cz*c) | ||
| - | printf "%15.6f%15.6f%15.6f\n", x, y, z | ||
| - | }' $input > xyz.temp | ||
| - | |||
| - | # assemble the whole .xyz file | ||
| - | echo $nprvku > $output | ||
| - | head -n 1 $input >> $output | ||
| - | paste elemcol.temp xyz.temp >> $output | ||
| - | echo "" >> $output | ||
| - | |||
| - | # delete temporary files | ||
| - | rm *.temp | ||
| - | </code> | ||
| - | |||
| - | |||
| - | |||
| - | ==== v2xyz: ==== | ||
| - | * uses v2xyz | ||
| - | <code> | ||
| - | #! /bin/bash | ||
| - | |||
| - | cp CONTCAR CONTCAR.bak | ||
| - | |||
| - | lines=`cat XDATCAR | wc -l` | ||
| - | atoms=`awk -v L=$lines '(NR==6){atoms=0; for(i=1;i<=NF;i++){atoms+=$i};print atoms}' CONTCAR` | ||
| - | records=`awk -v L=$lines -v a=$atoms 'BEGIN{print (L-5)/(a+1)}' CONTCAR` | ||
| - | echo $lines $atoms $records | ||
| - | |||
| - | > answer-.xyz | ||
| - | for ir in `seq 1 $records`; do | ||
| - | echo "image: " $ir | ||
| - | cat CONTCAR.bak | head -8 > CONTCAR | ||
| - | awk -v ir=$ir -v a=$atoms '(NR>(ir-1)*(a+1)+5+1)&&(NR<=ir*(a+1)+5){print $0}' XDATCAR >> CONTCAR | ||
| - | |||
| - | v2xyz # call v2xyz, you should have script "v2xyz" in your /bin directory | ||
| - | |||
| - | awk -v ir=$ir '(NR>NL-2){if(NR==2){print "image #: ",ir}else{print $0}}' CONTCAR.xyz > temp | ||
| - | |||
| - | cat temp >> answer-.xyz | ||
| - | done | ||
| - | |||
| - | awk 'NR>(-1) {if (!($0=="")) print $0}' answer-.xyz > answer.xyz | ||
| - | echo "" >> answer.xyz | ||
| - | </code> | ||
scripts/v2xyz.txt ยท Last modified: 2011/02/18 13:13 (external edit)
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