Chimie Théorique » scripts_chimie4psmn » DockOnSurf

#!/bin/bash

nom_de_la_molecule=$1

mol_dir=${MolOnSurf_results_path}/${nom_de_la_molecule}

list_errors=()

if [ -e ${mol_dir}/errors ]

then

	nb_lines="$(cat ${mol_dir}/errors | wc -l)"

	for ((line=1; line<=$nb_lines; line++ )) ; do

		err_dir="$(awk -v var="$line" 'NR == var' ${mol_dir}/errors | awk '{print $2}')"

		list_errors+=(${err_dir})

	done

fi

lg_liste=${#list_errors[@]}

sed "s/XXXX/surf_${nom_de_la_molecule}/g" ${CP2K_sub} > ${mol_dir}/${nom_de_la_molecule}_1/cp2k_gamma.j

sed "s/molecule/${nom_de_la_molecule}/g" ${CP2K_input_MolOnSurf} > ${mol_dir}/${nom_de_la_molecule}_1/surf_${nom_de_la_molecule}.inp

for dir in ${mol_dir}/${nom_de_la_molecule}* ; do

	i_error=0

	if [ -e ${mol_dir}/errors ]

	then 

		for ((j=0; j<$lg_liste; j++)) ; do

			if [[ "$dir" == *"${list_errors[$j]}" ]]

			then 

				i_error=1 

				echo "error"

			fi

		done

	fi

	if [ "$i_error" -eq "0" ]

	then 

		cd $dir

		if [ "${dir}" != "${mol_dir}/${nom_de_la_molecule}_1"  ]

		then 

			ln ${mol_dir}/${nom_de_la_molecule}_1/cp2k_gamma.j .

			ln ${mol_dir}/${nom_de_la_molecule}_1/surf_${nom_de_la_molecule}.inp .

		fi

		qsub cp2k_gamma.j

	fi

done