make all formcheck files
module load gaussian
for f in `ls *.chk | sed -e 's/.chk//'`; do formchk $f.chk $f.fchk; done
get density and esp
module load gaussian
for file in `ls *.fchk | sed -e 's/.fchk//'`; do echo $file'_dens.cube'; cubegen 0 density $file.fchk $file'_dens.cube' 0 h; echo $file'_esp.cube'; cubegen 0 potential $file.fchk $file'_esp.cube' 0 h; done
Submit all jobs
for f in `ls *.job`; do qsub $f; done
Make cube files
for f in `ls *.fchk | sed -e 's/.fchk//'`; do sh newscript $f; done
Convert all line endings to unix (remove ^M characters)
dos2unix *.gjf
Convert all line endings to dos
unix2dos *.log
convert all gjfs in current dir to TD
for f in `ls *.gjf | sed -e 's/.gjf//'`; do sed $f.gjf -i -e 's/opt/td/' -e 's/\.chk/_TD.chk/' && mv $f.gjf $f'_TD.gjf'; done
Convert 0 charge 1 multiplicity to 1 charge 2 multiplicity assuming "_$charge" naming scheme
for f in `ls *_0.gjf | sed -e's/_0.gjf//'`; do sed $f'_0.gjf' -e 's/0.chk/1.chk/' -e 's/^0 1/1 2/' > $f'_1.gjf' ; done
Convert 0 charge 1 multiplicity to 2 charge 1 multiplicity
for f in `ls *_0.gjf | sed -e's/_0.gjf//'`; do sed $f'_0.gjf' -e 's/0.chk/2.chk/' -e 's/^0 1/2 1/' > $f'_2.gjf' ; done
Copy all logs to logs/
rsync --progress -az $CG:/home/ccollins/done/*.log logs/
Copy all fchk to fchk/
rsync --progress -az $CG:/home/ccollins/done/*.fchk fchk/
Change allocation number
for f in `ls *.job`; do sed $f -i -e 's/CHE120042/CHE130042/'; done
Add nprocshared to gjf
for f in `ls *.gjf`; do sed $f -i -e 's/%mem/%nprocshared=8\n%mem/'; done
Add opt
for f in `ls *.gjf`; do sed $f -i -e 's/B3LYP/opt B3LYP/I'; done
Get all incomplete logs
grep -L "Normal termination of Gaussian" *
Change Gordon jobs to work on Trestles (add ppn=16)
for f in `ls *.job`; do sed $f -i -e 's/node=1^/node=1:ppn=16/'; done
Parse, Prep, Build
./build; python clean_data.py; python run.py