Révision f43a1b4c
| b/global_script.sh | ||
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| 1 | 1 |
#!/bin/bash |
| 2 | 2 |
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user="$(pwd | awk -F"/" '{print $3}')"
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file_path="$(find /home/${user} -name "DockOnSurf_path")"
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file_path="$(find $HOME -name "DockOnSurf_path")" |
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echo $file_path
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### Mise en place de l'arborescence |
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|
| ... | ... | |
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${DockOnSurf_path}/modules/launch_cp2k_molecule_seule.sh $molecule
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### Attente jusqu'à ce que tous les calculs aient fini |
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mol="$(echo $molecule | cut -c1-10)" |
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while [ "$(qstat | grep $mol | wc -l)" != 0 ]; |
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do |
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sleep 30 |
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done |
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echo ' -- ALL CALCULATIONS FOR MOLECULE ALONE HAVE BEEN DONE --' |
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### Suppression des fichiers inutiles |
| ... | ... | |
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${DockOnSurf_path}/modules/launch_script+diss.sh $molecule
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### Attente jusqu'à ce que tous les calculs aient fini |
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mol2="$(echo $molecule | cut -c1-5)" |
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while [ "$(qstat | grep surf_${mol2} | wc -l)" != 0 ];
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do |
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sleep 30 |
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done |
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echo ' -- ALL CALCULATIONS FOR ADSORPTION STRUCTURES HAVE BEEN DONE --' |
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### Suppression des fichiers inutiles |
| ... | ... | |
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${DockOnSurf_path}/modules/script_grandes_molecules+diss.sh $molecule $num_center ${nb_at_surf} ${cutoff}
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echo ' -- CLUSTERING HAS BEEN DONE AND CLUSTER CENTERS CALCULATIONS HAVE BEEN LAUNCHED --' |
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### Attente jusqu'à ce que tous les calculs aient fini |
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while [ "$(qstat | grep surf_${mol2} | wc -l)" != 0 ];
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do |
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sleep 30 |
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done |
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echo ' -- ALL CLUSTER CENTERS CALCULATIONS HAVE BEEN DONE --' |
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| b/modules/launch_cp2k_molecule_seule.sh | ||
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| 16 | 16 |
sed "/PROJECT_NAME/c\PROJECT_NAME ${molecule}" ${CP2K_input_molecule} > ${Molecule_results_path}/${molecule}/${molecule}_1/${molecule}.inp
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sed "s/XXXX/${molecule}/g" ${CP2K_sub} > ${Molecule_results_path}/${molecule}/${molecule}_1/cp2k_gamma.j
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cp ${Molecule_results_path}/${molecule}_confs/xyz_files/${molecule}_1.xyz ${Molecule_results_path}/${molecule}/${molecule}_1/coord.xyz
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qsub cp2k_gamma.j |
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new_job_id=$(qsub cp2k_gamma.j | awk '{print $3}')
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echo "Submitted job $new_job_id" |
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jobs_owned+=($new_job_id) |
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for ((i=2; i<=n; i++)) ; do |
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mkdir ${Molecule_results_path}/${molecule}/${molecule}_$i
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| ... | ... | |
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ln ${Molecule_results_path}/${molecule}/${molecule}_1/cp2k_gamma.j .
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ln ${Molecule_results_path}/${molecule}/${molecule}_1/${molecule}.inp .
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cp ${Molecule_results_path}/${molecule}_confs/xyz_files/${molecule}_${i}.xyz coord.xyz
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qsub cp2k_gamma.j |
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new_job_id=$(qsub cp2k_gamma.j | awk '{print $3}')
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echo "Submitted job $new_job_id" |
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jobs_owned+=($new_job_id) |
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done |
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### Attente jusqu'à ce que tous les calculs aient fini |
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go_on=true |
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while [ $go_on == true ]; do |
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all_jobs=`qstat | tail -n+3 | awk '{print $1}'`
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for j1 in ${jobs_owned[@]} ; do
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for j2 in ${all_jobs[@]}; do
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if [ $j1 == $j2 ]; then |
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sleep 30 |
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continue 3 |
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fi |
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done |
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done |
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echo "loop finished" |
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go_on=false |
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done |
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| b/modules/launch_script+diss.sh | ||
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| 40 | 40 |
ln ${mol_dir}/${nom_de_la_molecule}_1/cp2k_gamma.j .
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ln ${mol_dir}/${nom_de_la_molecule}_1/surf_${nom_de_la_molecule}.inp .
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fi |
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qsub cp2k_gamma.j |
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new_job_id=$(qsub cp2k_gamma.j | awk '{print $3}')
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echo "Submitted job $new_job_id" |
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jobs_owned+=($new_job_id) |
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fi |
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done |
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### Attente jusqu'à ce que tous les calculs aient fini |
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go_on=true |
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while [ $go_on == true ]; do |
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all_jobs=`qstat | tail -n+3 | awk '{print $1}'`
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for j1 in ${jobs_owned[@]} ; do
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for j2 in ${all_jobs[@]}; do
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if [ $j1 == $j2 ]; then |
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sleep 30 |
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continue 3 |
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fi |
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done |
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done |
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echo "loop finished" |
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go_on=false |
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done |
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| b/modules/script_grandes_molecules+diss.sh | ||
|---|---|---|
| 354 | 354 |
sed -i 's/EPS_SCF/EPS_SCF\ 1E-07\ #/g' ${dir}/surf_${nom_de_la_molecule}.inp
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# launches the calculation |
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cd $dir/ |
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qsub ${mol_dir}/relaunched_calculations/cp2k_gamma.j
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new_job_id=$(qsub ${mol_dir}/relaunched_calculations/cp2k_gamma.j | awk '{print $3}')
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echo "Submitted job $new_job_id" |
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jobs_owned+=($new_job_id) |
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cd - |
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done |
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fi |
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### Attente jusqu'à ce que tous les calculs aient fini |
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go_on=true |
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while [ $go_on == true ]; do |
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all_jobs=`qstat | tail -n+3 | awk '{print $1}'`
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for j1 in ${jobs_owned[@]} ; do
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for j2 in ${all_jobs[@]}; do
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if [ $j1 == $j2 ]; then |
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sleep 30 |
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continue 3 |
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fi |
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done |
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done |
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echo "loop finished" |
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go_on=false |
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done |
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| 363 | 379 |
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Formats disponibles : Unified diff