Chimie Théorique » scripts_chimie4psmn » DockOnSurf

#!/bin/bash

user="$(pwd | awk -F"/" '{print $3}')"

file_path="$(find /home/${user} -name "DockOnSurf_path")"

### Mise en place de l'arborescence

source ${file_path}

### Récupération des vecteurs de cellule

a1="$(grep "A\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^A/ {print}' | awk '{print $2}')"

if [[ $a1 =~ "E+00" ]]; then a1="$(echo $a1 | cut -d "E" -f1)"; fi ; export a1

a2="$(grep "A\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^A/ {print}' | awk '{print $3}')"

if [[ $a2 =~ "E+00" ]]; then a2="$(echo $a2 | cut -d "E" -f1)"; fi ; export a2

a3="$(grep "A\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^A/ {print}' | awk '{print $4}')"

if [[ $a3 =~ "E+00" ]]; then a3="$(echo $a3 | cut -d "E" -f1)"; fi ; export a3

b1="$(grep "B\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^B/ {print}' | awk '{print $2}')"

if [[ $b1 =~ "E+00" ]]; then b1="$(echo $b1 | cut -d "E" -f1)"; fi ; export b1

b2="$(grep "B\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^B/ {print}' | awk '{print $3}')"

if [[ $b2 =~ "E+00" ]]; then b2="$(echo $b2 | cut -d "E" -f1)"; fi ; export b2

b3="$(grep "B\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^B/ {print}' | awk '{print $4}')"

if [[ $b3 =~ "E+00" ]]; then b3="$(echo $b3 | cut -d "E" -f1)"; fi ; export b3

c1="$(grep "C\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^C/ {print}' | awk '{print $2}')"

if [[ $c1 =~ "E+00" ]]; then c1="$(echo $c1 | cut -d "E" -f1)"; fi ; export c1

c2="$(grep "C\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^C/ {print}' | awk '{print $3}')"

if [[ $c2 =~ "E+00" ]]; then c2="$(echo $c2 | cut -d "E" -f1)"; fi ; export c2

c3="$(grep "C\ " ${CP2K_input_MolOnSurf} | awk '$1 ~/^C/ {print}' | awk '{print $4}')"

if [[ $c3 =~ "E+00" ]]; then c3="$(echo $c3 | cut -d "E" -f1)"; fi ; export c3

### Paramètres initiaux

echo 'Name of the molecule (without .mol) '

read molecule

echo '' 

module load rdkit

### Generation des conformeres

${DockOnSurf_path}/modules/generation_conformeres.py $molecule 5000

echo ' -- CONFORMERS HAVE BEEN GENERATED --'

### Conversion des fichiers .mol en .xyz

${DockOnSurf_path}/modules/mol_to_xyz.sh $molecule

### Lancement des calculs pour les molecules seules

${DockOnSurf_path}/modules/launch_cp2k_molecule_seule.sh $molecule

### Attente jusqu'à ce que tous les calculs aient fini

mol="$(echo $molecule | cut -c1-10)"

while [ "$(qstat | grep $mol | wc -l)" != 0 ];

do 

	sleep 300

done

echo ' -- ALL CALCULATIONS FOR MOLECULE ALONE HAVE BEEN DONE --'

### Suppression des fichiers inutiles

rm -r ${Molecule_results_path}/${molecule}/*/*RESTART*

rm -r ${Molecule_results_path}/${molecule}/*/*restart*

rm -r ${Molecule_results_path}/${molecule}/*/*BFGS*

rm -r ${Molecule_results_path}/${molecule}/*/*.p*

echo ' '

echo ' -- RESULTS --'

min_energy_molecule=0

for struct in ${Molecule_results_path}/${molecule}/${molecule}*; do

	energy_molecule="$(awk '/ENERGY/{E=$NF} END{print E}' ${struct}/*${molecule}.out)"

	if [[ "${energy_molecule}" > "${min_energy_molecule}" ]]

	then 

		min_energy_molecule=${energy_molecule}

		numero_mol_stable="$(echo $struct | awk -F'/' '{print $NF}')"

	fi

done

echo "   Most stable structure for molecule alone: ${numero_mol_stable} with energy ${min_energy_molecule} Ha"

echo ' ' 

echo ' -- ARGUMENTS FOR ADSORPTION -- '

echo ' '

echo 'Name of the file to use for the surface (without .xyz) '

read surface

echo 'Number of the central atom of the molecule'

read center

read -a list_atom_1_mol -p 'List of atoms of the molecule to adsorb '

read -a list_atom_2_mol -p 'List of neighboring atoms of the molecule (linked to the atoms to adsorb) '

nombre_atom_mol=${#list_atom_1_mol[@]}

if [ ${#list_atom_2_mol[@]} != ${nombre_atom_mol} ]

then

	echo "  Problem: number of atoms different in the two lists"

	exit

fi

read -a list_atom_surf -p 'List of the atoms of the surface that can be adsorption sites '

echo 'Value of cutoff energy for reoptimisation (eV)'

read cutoff

echo '' 

### Adsorption de la molecule sur la surface

${DockOnSurf_path}/modules/script_add_adsorbate+diss.sh $molecule $surface "${list_atom_1_mol[*]}" "${list_atom_2_mol[*]}" "${list_atom_surf[*]}"

echo ' -- ADSORPTION SUTRUCTURES HAVE BEEN CALCULATED --'

# Changes labels of elements to its original definition, thus allowing different kinds of same element (Fe1 Fe2) with different properties (e.g. spin state in compounds with magnetic coupling) 

${DockOnSurf_path}/modules/fe_change.sh $molecule $surface ${MolOnSurf_results_path}/${molecule}

### Lancement des calculs pour les molecules adsorbees

${DockOnSurf_path}/modules/launch_script+diss.sh $molecule

### Attente jusqu'à ce que tous les calculs aient fini

mol2="$(echo $molecule | cut -c1-5)"

while [ "$(qstat | grep surf_${mol2} | wc -l)" != 0 ];

do 

	sleep 300

done

echo ' -- ALL CALCULATIONS FOR ADSORPTION STRUCTURES HAVE BEEN DONE --'

### Suppression des fichiers inutiles

rm -r ${MolOnSurf_results_path}/${molecule}/*/*RESTART*

rm -r ${MolOnSurf_results_path}/${molecule}/*/*BFGS*

rm -r ${MolOnSurf_results_path}/${molecule}/*/*.p*

### Clustering et lancement des structures centres des clusters

nb_at_surf="$(awk 'NR==1{print}' ${Surface_path}/${surface}.xyz)"

num_center="$(expr ${nb_at_surf} + $center )"

${DockOnSurf_path}/modules/script_grandes_molecules+diss.sh $molecule $num_center ${nb_at_surf} ${cutoff}

echo ' -- CLUSTERING HAS BEEN DONE AND CLUSTER CENTERS CALCULATIONS HAVE BEEN LAUNCHED --'

### Attente jusqu'à ce que tous les calculs aient fini

while [ "$(qstat | grep surf_${mol2} | wc -l)" != 0 ];

do

        sleep 300

done

echo ' -- ALL CLUSTER CENTERS CALCULATIONS HAVE BEEN DONE --'

echo " "

echo ' -- RESULTS --'

echo ' '

echo "Most stable structure for molecule alone: ${numero_mol_stable} with energy ${min_energy_molecule} Ha"

min_energy_global=0

for global_struct in ${MolOnSurf_results_path}/${molecule}/relaunched_calculations/* ; do

	if [[ "$global_struct" != *.inp ]]

	then

		if [[ "$global_struct" != *.j ]]

		then 

			energy_global="$(awk '/ENERGY/{E=$NF} END{print E}' ${global_struct}/*${molecule}.out)"

			if [[ "${energy_global}" > "${min_energy_global}" ]]

			then

				min_energy_global=${energy_global}

				numero_global_stable="$(echo ${global_struct} | awk -F'/' '{print $NF}')"

			fi

		fi

	fi

done

echo "Most stable structure for adsorption: ${numero_global_stable} with energy ${min_energy_global} Ha"