dockonsurf / modules / script_grandes_molecules+diss.sh @ f43a1b4c
Historique | Voir | Annoter | Télécharger (12,6 ko)
| 1 |
#!/bin/bash |
|---|---|
| 2 |
|
| 3 |
########################## |
| 4 |
#### Arguments input #### |
| 5 |
########################## |
| 6 |
|
| 7 |
nom_de_la_molecule=$1 |
| 8 |
atom_nb=$2 |
| 9 |
nb_surf=$3 |
| 10 |
cutoff=$4 |
| 11 |
|
| 12 |
|
| 13 |
############################################################# |
| 14 |
#### Creation of the working diretory and initialisation #### |
| 15 |
############################################################# |
| 16 |
|
| 17 |
|
| 18 |
mol_dir=${MolOnSurf_results_path}/${nom_de_la_molecule}
|
| 19 |
|
| 20 |
list_errors=() |
| 21 |
|
| 22 |
mkdir ${mol_dir}/analyse
|
| 23 |
|
| 24 |
|
| 25 |
############################################################### |
| 26 |
#### Extraction of structures needed from file *-pos-1.xyz #### |
| 27 |
############################################################### |
| 28 |
|
| 29 |
|
| 30 |
num=0 |
| 31 |
|
| 32 |
for dir in ${mol_dir}/* ; do
|
| 33 |
if [ ! -e $dir/*-pos-1.xyz ] |
| 34 |
then list_errors+=($dir) |
| 35 |
else |
| 36 |
name="$(echo $dir | awk -F/ '{print $NF}')"
|
| 37 |
mkdir ${mol_dir}/analyse/${name}_$num
|
| 38 |
|
| 39 |
|
| 40 |
####################################### |
| 41 |
#### Get last geometry of mol+surf #### |
| 42 |
####################################### |
| 43 |
|
| 44 |
|
| 45 |
n_line="$(grep -n "i =" ${dir}/*-pos-1.xyz | awk 'END{print}' | awk 'NF=1{print}' | awk 'sub(".$", "")')"
|
| 46 |
n_line_1="$(expr $n_line - 1)" |
| 47 |
awk -v ligne="$n_line_1" 'NR>=ligne{print}' ${dir}/*-pos-1.xyz > ${mol_dir}/analyse/${name}_$num/last_geo.xyz
|
| 48 |
|
| 49 |
|
| 50 |
####################################################### |
| 51 |
#### Recenter the mol+surf on one atom without pbc #### |
| 52 |
####################################################### |
| 53 |
|
| 54 |
|
| 55 |
${DockOnSurf_path}/modules/recenter_only.py ${mol_dir}/analyse/${name}_$num ${atom_nb}
|
| 56 |
recentered_temp_file=${mol_dir}/analyse/${name}_$num/recentered_only.xyz
|
| 57 |
|
| 58 |
|
| 59 |
##################################################### |
| 60 |
#### Get the molecule alone centered on one atom #### |
| 61 |
##################################################### |
| 62 |
|
| 63 |
nb_surf2="$(expr ${nb_surf} + 2 )"
|
| 64 |
nbligne="$(awk 'END{print NR}' ${recentered_temp_file})"
|
| 65 |
for ((a=3; a<=nbligne; a++)) ; do |
| 66 |
z="$(awk '{print NR,$0}' ${recentered_temp_file}| awk 'NR == nligne {print}' nligne="$a" | awk '{print $1}')"
|
| 67 |
if (( $(echo "$z > ${nb_surf2}" | bc -l) ))
|
| 68 |
then awk 'NR == nligne {print}' nligne="$a" ${recentered_temp_file} >> ${mol_dir}/analyse/${name}_$num/temp_file.xyz
|
| 69 |
fi |
| 70 |
done |
| 71 |
|
| 72 |
temp_file=${mol_dir}/analyse/${name}_$num/temp_file.xyz
|
| 73 |
awk 'END{print NR}' ${temp_file} > ${mol_dir}/analyse/${name}_$num/molecule_seule.xyz
|
| 74 |
mol_seule_file=${mol_dir}/analyse/${name}_$num/molecule_seule.xyz
|
| 75 |
echo ' ' >> ${mol_seule_file}
|
| 76 |
cat ${temp_file} >> ${mol_seule_file}
|
| 77 |
rm ${temp_file}
|
| 78 |
|
| 79 |
|
| 80 |
############################################################## |
| 81 |
### Apply pbc conditions to surface only in mol+surf file #### |
| 82 |
############################################################## |
| 83 |
|
| 84 |
|
| 85 |
${DockOnSurf_path}/modules/recenter_periodicity.py ${mol_dir}/analyse/${name}_$num ${atom_nb}
|
| 86 |
recentered_periodicity_file=${mol_dir}/analyse/${name}_$num/recentered_periodicity.xyz
|
| 87 |
|
| 88 |
for ((a=3; a<=nbligne; a++)) ; do |
| 89 |
z="$(awk '{print NR,$0}' ${recentered_temp_file}| awk 'NR == nligne {print}' nligne="$a" | awk '{print $1}')"
|
| 90 |
if (( $(echo "$z <= ${nb_surf2}" | bc -l) ))
|
| 91 |
then awk 'NR == nligne {print}' nligne="$a" ${recentered_periodicity_file} >> ${mol_dir}/analyse/${name}_$num/temp_file.xyz
|
| 92 |
fi |
| 93 |
done |
| 94 |
|
| 95 |
awk 'NR <= 2{print}' ${recentered_periodicity_file} > ${mol_dir}/analyse/${name}_$num/recentered_pbc.xyz
|
| 96 |
cat ${mol_dir}/analyse/${name}_$num/temp_file.xyz >> ${mol_dir}/analyse/${name}_$num/recentered_pbc.xyz
|
| 97 |
awk 'NR > 2{print}' ${mol_seule_file} >> ${mol_dir}/analyse/${name}_$num/recentered_pbc.xyz
|
| 98 |
|
| 99 |
rm ${mol_dir}/analyse/${name}_$num/temp_file.xyz
|
| 100 |
rm ${recentered_periodicity_file}
|
| 101 |
rm ${recentered_temp_file}
|
| 102 |
|
| 103 |
|
| 104 |
num=$((num+1)) |
| 105 |
|
| 106 |
fi |
| 107 |
done |
| 108 |
|
| 109 |
echo "All structures files have been created" |
| 110 |
|
| 111 |
|
| 112 |
################################################################################# |
| 113 |
#### RMSD calculation of molecules without surface to create the RMSD matrix #### |
| 114 |
################################################################################# |
| 115 |
|
| 116 |
|
| 117 |
matrix_file=${mol_dir}/analyse/matrice_RMSD_mol_seule.txt
|
| 118 |
|
| 119 |
touch ${matrix_file}
|
| 120 |
|
| 121 |
for ((i=0; i<$num; i++)) ; do |
| 122 |
echo >> ${matrix_file}
|
| 123 |
done |
| 124 |
|
| 125 |
for ((i=1; i<=$num; i++)) ; do |
| 126 |
for ((j=$i; j<=$num; j++)) ; do |
| 127 |
if (( $(echo "$i == $j" | bc -l) )) |
| 128 |
then |
| 129 |
add_to_line="$(awk -v ii="$i" 'NR==ii {print}' ${matrix_file})"
|
| 130 |
add_to_line+=' 0' |
| 131 |
sed -i "${i}c $add_to_line" ${matrix_file}
|
| 132 |
else |
| 133 |
num_i="$(expr $i - 1)" |
| 134 |
num_j="$(expr $j - 1)" |
| 135 |
RMSD_mol_seule_i_j="$(${DockOnSurf_path}/modules/calculate_rmsd --reorder ${mol_dir}/analyse/${nom_de_la_molecule}*_${num_i}/molecule_seule.xyz ${mol_dir}/analyse/${nom_de_la_molecule}*_${num_j}/molecule_seule.xyz)"
|
| 136 |
add_to_i_line="$(awk -v ii="$i" 'NR==ii {print}' ${matrix_file})"
|
| 137 |
add_to_i_line+=' -' |
| 138 |
add_to_i_line+=$RMSD_mol_seule_i_j |
| 139 |
sed -i "${i}c $add_to_i_line" ${matrix_file}
|
| 140 |
add_to_j_line="$(awk -v jj="$j" 'NR==jj {print}' ${matrix_file})"
|
| 141 |
add_to_j_line+=' -' |
| 142 |
add_to_j_line+=$RMSD_mol_seule_i_j |
| 143 |
sed -i "${j}c $add_to_j_line" ${matrix_file}
|
| 144 |
fi |
| 145 |
done |
| 146 |
done |
| 147 |
|
| 148 |
echo "RMSD matrix for molecules without surface has been calculated" |
| 149 |
|
| 150 |
|
| 151 |
############################################################### |
| 152 |
#### Clustering of the molecule structures without surface #### |
| 153 |
############################################################### |
| 154 |
|
| 155 |
|
| 156 |
cluster_molecule_file=${mol_dir}/analyse/cluster_molecule.txt
|
| 157 |
|
| 158 |
${DockOnSurf_path}/modules/clustering.py ${matrix_file} > ${cluster_molecule_file}
|
| 159 |
|
| 160 |
echo "Clustering of molecules has been done" |
| 161 |
|
| 162 |
|
| 163 |
################################################################################### |
| 164 |
#### Separation of the clusters found for the molecule alone and re-clustering #### |
| 165 |
################################################################################### |
| 166 |
|
| 167 |
|
| 168 |
nb_clusters="$(awk 'END{print NR}' ${cluster_molecule_file})"
|
| 169 |
|
| 170 |
sed -i 's/\[/ /g' ${cluster_molecule_file}
|
| 171 |
sed -i 's/\]/ /g' ${cluster_molecule_file}
|
| 172 |
|
| 173 |
mkdir ${mol_dir}/analyse/cluster_centers_energy
|
| 174 |
|
| 175 |
s=1 |
| 176 |
|
| 177 |
line_cluster_group="$(awk '{print NR,$0}' ${cluster_molecule_file} | grep "Cluster\ groups:" | awk '{print $1}')"
|
| 178 |
line_first_cluster="$(expr ${line_cluster_group} + 1 )"
|
| 179 |
|
| 180 |
for ((k=${line_first_cluster}; k<=${nb_clusters}; k++)) ; do
|
| 181 |
|
| 182 |
|
| 183 |
################################ |
| 184 |
#### Separation of clusters #### |
| 185 |
################################ |
| 186 |
|
| 187 |
|
| 188 |
awk -v ligne="$k" 'NR==ligne{print}' ${cluster_molecule_file} > ${mol_dir}/analyse/array
|
| 189 |
sed -i 's/^ *//' ${mol_dir}/analyse/array
|
| 190 |
sed -i 's/ / /g' ${mol_dir}/analyse/array
|
| 191 |
sed -i 's/ / /g' ${mol_dir}/analyse/array
|
| 192 |
sed -i 's/ / /g' ${mol_dir}/analyse/array
|
| 193 |
sed -i 's/ / /g' ${mol_dir}/analyse/array
|
| 194 |
readarray -d " " cluster < ${mol_dir}/analyse/array
|
| 195 |
|
| 196 |
mkdir ${mol_dir}/analyse/cluster_molecule_$s
|
| 197 |
cluster_dir=${mol_dir}/analyse/cluster_molecule_$s
|
| 198 |
|
| 199 |
for numero in ${cluster[*]} ; do
|
| 200 |
mv ${mol_dir}/analyse/${nom_de_la_molecule}*_${numero} ${cluster_dir}/.
|
| 201 |
done |
| 202 |
a=0 |
| 203 |
for dir2 in ${cluster_dir}/${nom_de_la_molecule}* ; do
|
| 204 |
mv $dir2 ${dir2}_$a
|
| 205 |
a=$((a+1)) |
| 206 |
done |
| 207 |
|
| 208 |
rm ${mol_dir}/analyse/array
|
| 209 |
|
| 210 |
|
| 211 |
###################################################################### |
| 212 |
#### Calculation of RMSD for mol+surf and creation of RMSD matrix #### |
| 213 |
###################################################################### |
| 214 |
|
| 215 |
|
| 216 |
cluster_matrix_file=${cluster_dir}/matrice_RMSD_cluster.txt
|
| 217 |
touch ${cluster_matrix_file}
|
| 218 |
|
| 219 |
len=${#cluster[@]}
|
| 220 |
len_cluster="$(expr $len - 1)" |
| 221 |
|
| 222 |
for ((i=1; i<=${len_cluster}; i++)) ; do
|
| 223 |
echo >> ${cluster_matrix_file}
|
| 224 |
done |
| 225 |
|
| 226 |
for ((i=1; i<=${len_cluster}; i++)) ; do
|
| 227 |
for ((j=$i; j<=${len_cluster}; j++)) ; do
|
| 228 |
if (( $(echo "$i == $j" | bc -l) )) |
| 229 |
then |
| 230 |
add_to_line="$(awk -v ii="$i" 'NR==ii {print}' ${cluster_matrix_file})"
|
| 231 |
add_to_line+=' 0' |
| 232 |
sed -i "${i}c $add_to_line" ${cluster_matrix_file}
|
| 233 |
else |
| 234 |
num_i="$(expr $i - 1)" |
| 235 |
num_j="$(expr $j - 1)" |
| 236 |
RMSD_mol_surf_i_j="$(${DockOnSurf_path}/modules/calculate_rmsd --reorder ${cluster_dir}/${nom_de_la_molecule}*_${num_i}/recentered_pbc.xyz ${cluster_dir}/${nom_de_la_molecule}*_${num_j}/recentered_pbc.xyz)"
|
| 237 |
add_to_i_line="$(awk -v ii="$i" 'NR==ii {print}' ${cluster_matrix_file})"
|
| 238 |
add_to_i_line+=' -' |
| 239 |
add_to_i_line+=$RMSD_mol_surf_i_j |
| 240 |
sed -i "${i}c $add_to_i_line" ${cluster_matrix_file}
|
| 241 |
add_to_j_line="$(awk -v jj="$j" 'NR==jj {print}' ${cluster_matrix_file})"
|
| 242 |
add_to_j_line+=' -' |
| 243 |
add_to_j_line+=$RMSD_mol_surf_i_j |
| 244 |
sed -i "${j}c $add_to_j_line" ${cluster_matrix_file}
|
| 245 |
fi |
| 246 |
done |
| 247 |
done |
| 248 |
|
| 249 |
|
| 250 |
####################### |
| 251 |
#### Re-clustering #### |
| 252 |
####################### |
| 253 |
|
| 254 |
|
| 255 |
cluster_molsurf_file=${cluster_dir}/cluster_molsurf.txt
|
| 256 |
${DockOnSurf_path}/modules/clustering.py ${cluster_matrix_file} > ${cluster_molsurf_file}
|
| 257 |
|
| 258 |
|
| 259 |
################################################# |
| 260 |
#### Get the cluster centers (min of energy) #### |
| 261 |
################################################# |
| 262 |
|
| 263 |
|
| 264 |
nb_cluster_molsurf="$(awk 'END{print NR}' ${cluster_molsurf_file})"
|
| 265 |
line_cluster_group2="$(awk '{print NR,$0}' ${cluster_molsurf_file} | grep "Cluster\ groups:" | awk '{print $1}')"
|
| 266 |
line_first_cluster2="$(expr ${line_cluster_group2} + 1 )"
|
| 267 |
|
| 268 |
for ((a=${line_first_cluster2}; a<=${nb_cluster_molsurf}; a++)); do
|
| 269 |
awk -v ligne="$a" 'NR==ligne{print}' ${cluster_molsurf_file} > ${cluster_dir}/array
|
| 270 |
sed -i 's/\[/ /g' ${cluster_dir}/array
|
| 271 |
sed -i 's/\]/ /g' ${cluster_dir}/array
|
| 272 |
sed -i 's/^ *//' ${cluster_dir}/array
|
| 273 |
sed -i 's/ / /g' ${cluster_dir}/array
|
| 274 |
readarray -d " " cluster_struct < ${cluster_dir}/array
|
| 275 |
|
| 276 |
E_min=0 |
| 277 |
numero_mol_E_min=t |
| 278 |
|
| 279 |
for struct_nb in ${cluster_struct[*]} ; do
|
| 280 |
energie="$(awk 'NR==2{E=$NF} END{print E}' ${cluster_dir}/*_${struct_nb}/last_geo.xyz)"
|
| 281 |
if (( $(echo $energie '<' $E_min | bc -l) )) |
| 282 |
then |
| 283 |
E_min=$energie |
| 284 |
numero_mol_E_min=$struct_nb |
| 285 |
fi |
| 286 |
done |
| 287 |
|
| 288 |
cp -r ${cluster_dir}/${nom_de_la_molecule}*_${numero_mol_E_min} ${mol_dir}/analyse/cluster_centers_energy/.
|
| 289 |
done |
| 290 |
|
| 291 |
s=$((s+1)) |
| 292 |
done |
| 293 |
|
| 294 |
for dir in ${mol_dir}/analyse/cluster_centers_energy/${nom_de_la_molecule}* ; do
|
| 295 |
nb_champs="$(echo $dir | awk -F "_" '{print NF}')"
|
| 296 |
nb_limit="$(expr $nb_champs - 2)" |
| 297 |
name="$(echo $dir | cut -d '_' -f-$nb_limit)" |
| 298 |
mv $dir $name |
| 299 |
done |
| 300 |
|
| 301 |
echo "Clustering of structures mol+surf has been done" |
| 302 |
|
| 303 |
|
| 304 |
################################################### |
| 305 |
#### Determination of calculations to relaunch #### |
| 306 |
################################################### |
| 307 |
|
| 308 |
Energy_min=0 |
| 309 |
|
| 310 |
for structure in ${mol_dir}/analyse/cluster_centers_energy/*; do
|
| 311 |
Energy="$(awk 'NR==2{E=$NF} END{print E}' $structure/last_geo.xyz)"
|
| 312 |
if (( $(echo $Energy '<' $Energy_min | bc -l) )) |
| 313 |
then Energy_min=$Energy |
| 314 |
fi |
| 315 |
done |
| 316 |
|
| 317 |
Limit_energy="$(echo $Energy_min + ${cutoff}/27.2 | bc -l)" #limit of energy to relaunch the calculation 0.25eV more than min
|
| 318 |
|
| 319 |
mkdir ${mol_dir}/relaunched_calculations
|
| 320 |
|
| 321 |
for structure in ${mol_dir}/analyse/cluster_centers_energy/*; do
|
| 322 |
Energy="$(awk 'NR==2{E=$NF} END{print E}' $structure/last_geo.xyz)"
|
| 323 |
if (( $(echo $Energy '<' $Limit_energy | bc -l) )) |
| 324 |
then cp -r $structure ${mol_dir}/relaunched_calculations/.
|
| 325 |
fi |
| 326 |
done |
| 327 |
|
| 328 |
|
| 329 |
#################################### |
| 330 |
#### Launching the calculations #### |
| 331 |
#################################### |
| 332 |
|
| 333 |
n="$(find ${mol_dir}/relaunched_calculations/${nom_de_la_molecule}* -type d | wc -l)"
|
| 334 |
|
| 335 |
echo $n "clusters centers with energy lower than Emin+$cutoff eV have been found" |
| 336 |
echo "Relaunch the calculations ?" |
| 337 |
read answer |
| 338 |
|
| 339 |
if [[ $answer = "yes" ]] |
| 340 |
then |
| 341 |
cp ${mol_dir}/${nom_de_la_molecule}_1/cp2k_gamma.j ${mol_dir}/relaunched_calculations/.
|
| 342 |
|
| 343 |
for dir in ${mol_dir}/relaunched_calculations/${nom_de_la_molecule}*; do
|
| 344 |
# takes the restart file of the previous calculation as input file for re-optimization |
| 345 |
conf=$(echo $dir | rev | cut -d/ -f1 | rev ) |
| 346 |
cp ${mol_dir}/$conf/surf_${nom_de_la_molecule}-1.restart ${dir}/surf_${nom_de_la_molecule}.inp
|
| 347 |
topo_line=$(grep -n \&TOPOLOGY ${dir}/surf_${nom_de_la_molecule}.inp | cut -d: -f1)
|
| 348 |
sed -i "$topo_line,$(($topo_line+5))d" ${dir}/surf_${nom_de_la_molecule}.inp
|
| 349 |
# changes the optimization criterions for more precise re-optimization |
| 350 |
sed -i 's/MAX_FORCE/#MAX_FORCE/g' ${dir}/surf_${nom_de_la_molecule}.inp
|
| 351 |
sed -i 's/MAX_DR/#MAX_DR/g' ${dir}/surf_${nom_de_la_molecule}.inp
|
| 352 |
sed -i 's/RMS_DR/#RMS_DR/g' ${dir}/surf_${nom_de_la_molecule}.inp
|
| 353 |
sed -i 's/RMS_FORCE/#RMS_FORCE/g' ${dir}/surf_${nom_de_la_molecule}.inp
|
| 354 |
sed -i 's/EPS_SCF/EPS_SCF\ 1E-07\ #/g' ${dir}/surf_${nom_de_la_molecule}.inp
|
| 355 |
# launches the calculation |
| 356 |
cd $dir/ |
| 357 |
new_job_id=$(qsub ${mol_dir}/relaunched_calculations/cp2k_gamma.j | awk '{print $3}')
|
| 358 |
echo "Submitted job $new_job_id" |
| 359 |
jobs_owned+=($new_job_id) |
| 360 |
cd - |
| 361 |
done |
| 362 |
fi |
| 363 |
|
| 364 |
### Attente jusqu'à ce que tous les calculs aient fini |
| 365 |
go_on=true |
| 366 |
while [ $go_on == true ]; do |
| 367 |
all_jobs=`qstat | tail -n+3 | awk '{print $1}'`
|
| 368 |
for j1 in ${jobs_owned[@]} ; do
|
| 369 |
for j2 in ${all_jobs[@]}; do
|
| 370 |
if [ $j1 == $j2 ]; then |
| 371 |
sleep 30 |
| 372 |
continue 3 |
| 373 |
fi |
| 374 |
done |
| 375 |
done |
| 376 |
echo "loop finished" |
| 377 |
go_on=false |
| 378 |
done |
| 379 |
|