Chimie Théorique » scripts_chimie4psmn » DockOnSurf

#!/bin/bash

molecule=$1

n="$(find ${Molecule_results_path}/${molecule}_confs/xyz_files/${molecule}*.xyz | wc -l)"

if [ ! -d "${Molecule_results_path}/${molecule}" ]

then mkdir ${Molecule_results_path}/${molecule}

else 

	print 'problem there is already a directory for this molecule'

	exit

fi

mkdir ${Molecule_results_path}/${molecule}/${molecule}_1

cd ${Molecule_results_path}/${molecule}/${molecule}_1

sed "/PROJECT_NAME/c\PROJECT_NAME ${molecule}" ${CP2K_input_molecule} > ${Molecule_results_path}/${molecule}/${molecule}_1/${molecule}.inp

sed "s/XXXX/${molecule}/g" ${CP2K_sub} > ${Molecule_results_path}/${molecule}/${molecule}_1/cp2k_gamma.j

cp ${Molecule_results_path}/${molecule}_confs/xyz_files/${molecule}_1.xyz ${Molecule_results_path}/${molecule}/${molecule}_1/coord.xyz

qsub cp2k_gamma.j

for ((i=2; i<=n; i++)) ; do

	mkdir ${Molecule_results_path}/${molecule}/${molecule}_$i

	cd ${Molecule_results_path}/${molecule}/${molecule}_$i

	ln ${Molecule_results_path}/${molecule}/${molecule}_1/cp2k_gamma.j .

	ln ${Molecule_results_path}/${molecule}/${molecule}_1/${molecule}.inp .

	cp ${Molecule_results_path}/${molecule}_confs/xyz_files/${molecule}_${i}.xyz coord.xyz

	qsub cp2k_gamma.j

done