# Open SourceMolecular Dynamics

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exercises:2018_uzh_cmest:first_simulation_run

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 exercises:2018_uzh_cmest:first_simulation_run [2018/09/17 12:52]127.0.0.1 external edit exercises:2018_uzh_cmest:first_simulation_run [2018/09/19 15:12] (current)tmueller 2018/09/19 15:12 tmueller 2018/09/17 12:52 external edit 2018/09/19 15:12 tmueller 2018/09/17 12:52 external edit Line 87: Line 87: <​code>​ <​code>​ - $cp2k.sopt -i energy.inp -o energy.out +$ cp2k.popt -i energy.inp -o energy.out ​ - ​Alternatively you can run it using <​code>​$cp2k.sopt -i energy.inp | tee energy.out​ which will write the output simultaneously to a file ''​energy.out''​ and show it in the terminal.​ + ​Alternatively you can run it using <​code>​$ cp2k.popt -i energy.inp | tee energy.out​ which will write the output simultaneously to a file ''​energy.out''​ and show it in the terminal.​ === 3. Step === === 3. Step === Line 160: Line 160: <​code>​ <​code>​ - $cp2k.sopt -i energy_dist2A.inp -o energy_dist2A.out +$ cp2k.popt -i energy_dist2A.inp -o energy_dist2A.out ​ Line 278: Line 278: for d in $(seq 2 0.1 4); do for d in$(seq 2 0.1 4); do sed -e "s|4 0 0|${d} 0 0|" energy.inp > energy_${d}A.inp sed -e "s|4 0 0|${d} 0 0|" energy.inp > energy_${d}A.inp - cp2k.sopt -i energy_${d}A.inp -o energy_${d}A.out + cp2k.popt -i energy_${d}A.inp -o energy_${d}A.out awk '/​Total FORCE_EVAL/ { print $9; }' energy_${d}A.out awk '/​Total FORCE_EVAL/ { print $9; }' energy_${d}A.out done done Line 287: Line 287: * ''​sed -e "s|4 0 0|$d 0 0|" energy.inp''​ looks for ''​4 0 0''​ in the file ''​energy.inp''​ (the original file from above) and replaces ''​4 0 0''​ by ''​$d 0 0''​ (that is: ''​2.0'',​ ''​2.1'',​ ''​2.2'',​ ...) * ''​sed -e "s|4 0 0|$d 0 0|" energy.inp''​ looks for ''​4 0 0''​ in the file ''​energy.inp''​ (the original file from above) and replaces ''​4 0 0''​ by ''​$d 0 0''​ (that is: ''​2.0'',​ ''​2.1'',​ ''​2.2'',​ ...) * ... and using ''>​ energy_${d}A.out''​ we redirect the output of the ''​sed''​ command to new files ''​energy_2.0A.out'',​ ''​energy_2.1A.out'',​ etc. * ... and using ''>​ energy_${d}A.out''​ we redirect the output of the ''​sed''​ command to new files ''​energy_2.0A.out'',​ ''​energy_2.1A.out'',​ etc. - * Then we run ''​cp2k.sopt''​ as shown before on those new input files and write the output to new output files as well + * Then we run ''​cp2k.popt''​ as shown before on those new input files and write the output to new output files as well * Using ''​awk''​ we extract the energy from the output file * Using ''​awk''​ we extract the energy from the output file 