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@Ktera1988
Ktera1988 authored Jan 31, 2021
1 parent ff02863 commit cad11c0
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6 changes: 2 additions & 4 deletions fl_chemts/job_sub.sh
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#!/bin/sh
#$ -S /bin/bash
#$ -cwd
#$ -pe impi 30 #minimum 2
#$ -pe impi 1200 #minimum 2
##$ -par 20 -pe impi 1200
##$ -mods l_hard h_vmem 9G
##$ -mods l_hard mem_req 9G
Expand All @@ -16,11 +16,9 @@ ulimit -s unlimited

source /home/terayama/.bashrc

#export PATH="/home/yang/anaconda2/bin:$PATH"
#export PATH="/home/terayama/anaconda3/bin:$PATH"

source activate py2
export KERAS_BACKEND=tensorflow
## -pe impi argument 2161 is automatically transferred to the number of executable processes. Note, however, that -bootstrap sge is required.
mpiexec -bootstrap sge -n 30 python mpi_thread_chemts_tree_vl_0218.py
mpiexec -bootstrap sge -n 1200 python mpi_thread_chemts_tree_vl.py
source deactivate
123 changes: 52 additions & 71 deletions fl_chemts/mpi_thread_chemts_tree_vl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -413,11 +413,9 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
state=['&']
"""selection step"""
node_pool=[]

lock.acquire()


print 'time', time.time() -start_time, 'node.expanded', node.expanded, 'node.nodeadded', node.nodeadded, 'len(node.childNodes)', len(node.childNodes), len(node.expanded)
#print 'node.expanded', node.expanded, 'node.nodeadded', node.nodeadded, 'len(node.childNodes)', len(node.childNodes), len(node.expanded)
while len(node.expanded)>0 and node.nodeadded==[] and len(node.childNodes)==len(node.expanded):
#node.num_thread_visited+=1
#node.virtual_loss+=0
Expand Down Expand Up @@ -490,7 +488,7 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
#print('\\n was tried to added... skip')
lock.release()
continue
print "m is:",m
#print "m is:",m

lock.release()

Expand All @@ -512,7 +510,7 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
lock.acquire()
maxnum+=1
ind_mol+=1
print('ind_mol', ind_mol)
#print('ind_mol', ind_mol)
#lock.release()
#"""simulation step"""
#lock.acquire()
Expand Down Expand Up @@ -550,7 +548,7 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
lock.acquire()
free_core_id.append(data[2])
use_core_id.remove(data[2])
print('data[0]', data[0],'index', ind_mol, 'data[2]', data[2], 'dest_core', dest_core)
print('data[2]', data[2], 'dest_core', dest_core)
lock.release()
except:
print('comm.recv failed.')
Expand All @@ -572,17 +570,6 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
continue
#lock.release()
print('free_core_id', free_core_id)
#with open('/home/yang/DP-ChemTS/csvresult.csv','wb') as file:
# for line in text:
# file.write(line)
# file.write('\n')
#lock.acquire()
#result_test.append[data]
#free_core_id.append(data[2])
#with open('/home/yang/csvfile.csv','wb') as file:
# for line in result_test:
# file.write(str(line))
# file.write('\n')
#lock.release()
re = 0
tag = status.Get_tag()
Expand All @@ -609,10 +596,10 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
elif objective == 'WL':
re = (np.tanh(0.003*(data[0]-400)) + 1)/2
elif objective == 'WLFL':
fl_target = 1200
fl_target = 600
w_fl = 0.8
w_fl_intensity = 0.2
wl_target = 700
wl_target = 300
w_wl = 0.8
w_wl_intensity = 0.2

Expand Down Expand Up @@ -666,6 +653,44 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
s1_wavelength_list_list.append(data[15])
s1_strength_list_list.append(data[16])

with open('csvcom_.csv','wb') as file:
for line1 in wave_compounds:
file.write(str(line1))
file.write('\n')
with open('csvwave_.csv','wb') as file:
for line2 in wave:
file.write(str(line2))
file.write('\n')

with open(output_file,'wb') as file:
file.write('#Search strategy, '+ts_strategy+', search_parameter, '+str(search_parameter)+', alpha, '+str(alpha)+', objective,'+str(objective)+', parallel simulations, '+str(num_simulations)+', gaussian parallel, '+str(gau_parallel)+', simulation_time (h), '+str(simulation_time/3600)+', num_rollout, '+str(num_rollout)+'charge_check, '+str(charge_check)+'SA_score_check, '+str(SA_score_check)+'\n')
file.write('#Compound, index, wavelength, uv_intensity, s1_wavelength, s1_strength, reward, deen, gap, mol_weight, logP, SA_score, TS depth, wavelength_list, intensity_list, s1_wl_list, s1_strength_list \n')
for i in range(len(wave_compounds)):
file.write(str(wave_compounds[i])+', ')
file.write(str(index_list[i])+', ')
file.write(str(wave[i])+', ')
file.write(str(uv_intensity_list[i])+', ')
file.write(str(s1_wavelength_list[i])+', ')
file.write(str(s1_strength_list[i])+', ')
file.write(str(reward_list[i])+', ')
file.write(str(deen_list[i])+', ')
file.write(str(gap_list[i])+', ')
file.write(str(mol_weight_list[i])+', ')
file.write(str(logP_list[i])+', ')
file.write(str(SA_score_list[i])+', ')
file.write(str(depth_list[i])+', ')
for wl_i in wl_list_list[i]:
file.write(str(wl_i)+', ')
for int_i in intensity_list_list[i]:
file.write(str(int_i)+', ')
for wl_i in s1_wavelength_list_list[i]:
file.write(str(wl_i)+', ')
for int_i in s1_strength_list_list[i]:
file.write(str(int_i)+', ')
file.write('\n')



lock.release()
if data[0]==-1000:
#re=-1
Expand All @@ -691,48 +716,6 @@ def ChemTS_run(rootnode,result_queue,lock,chem_model,ts_strategy,search_paramete
lock.release()


#output
print('End-of-loop')
"""
with open('csvcom_.csv','w') as file:
for line1 in wave_compounds:
file.write(str(line1))
file.write('\n')
with open('csvwave_.csv','w') as file:
for line2 in wave:
file.write(str(line2))
file.write('\n')
with open(output_file,'w') as file:
file.write('#Search strategy, '+ts_strategy+', search_parameter, '+str(search_parameter)+', alpha, '+str(alpha)+', objective,'+str(objective)+', parallel simulations, '+str(num_simulations)+', gaussian parallel, '+str(gau_parallel)+', simulation_time (h), '+str(simulation_time/3600)+', num_rollout, '+str(num_rollout)+'charge_check, '+str(charge_check)+'SA_score_check, '+str(SA_score_check)+'\n')
file.write('#Compound, index, wavelength, uv_intensity, s1_wavelength, s1_strength, reward, deen, gap, mol_weight, logP, SA_score, TS depth, wavelength_list, intensity_list, s1_wl_list, s1_strength_list \n')
for i in range(len(wave_compounds)):
file.write(str(wave_compounds[i])+', ')
file.write(str(index_list[i])+', ')
file.write(str(wave[i])+', ')
file.write(str(uv_intensity_list[i])+', ')
file.write(str(s1_wavelength_list[i])+', ')
file.write(str(s1_strength_list[i])+', ')
file.write(str(reward_list[i])+', ')
file.write(str(deen_list[i])+', ')
file.write(str(gap_list[i])+', ')
file.write(str(mol_weight_list[i])+', ')
file.write(str(logP_list[i])+', ')
file.write(str(SA_score_list[i])+', ')
file.write(str(depth_list[i])+', ')
for wl_i in wl_list_list[i]:
file.write(str(wl_i)+', ')
for int_i in intensity_list_list[i]:
file.write(str(int_i)+', ')
for wl_i in s1_wavelength_list_list[i]:
file.write(str(wl_i)+', ')
for int_i in s1_strength_list_list[i]:
file.write(str(int_i)+', ')
file.write('\n')
"""


result_queue.put([all_compounds,wave_compounds,depth,wave,maxnum,uv_intensity_list,deen_list,gap_list,reward_list,index_list,mol_weight_list,logP_list,SA_score_list,depth_list])

def charge_check(mol):
Expand Down Expand Up @@ -806,7 +789,7 @@ def gaussion_workers(chem_model,val,gau_parallel,charge_check):
m=None
#if m!=None and len(task[i])<=81:

#print('Gaussian worker, check fin. ', str(new_compound[0]),ind)

if m!=None:
try:
stable=tansfersdf(str(new_compound[0]),ind)
Expand All @@ -815,14 +798,14 @@ def gaussion_workers(chem_model,val,gau_parallel,charge_check):
if stable==1.0:
cd_path = os.getcwd()
try:
SDFinput = 'CheckMolopt'+str(ind)+'.sdf'
SDFinput = 'CheckMolopt'+str(ind)+'.sdf'
#wavelength=GauTDDFT_ForDFT('B3LYP', '3-21G*', 1, 'CheckMolopt'+str(ind)+'.sdf')
#calc_sdf = GaussianDFTRun('B3LYP', '3-21G*', gau_parallel, 'OPT fluor energy deen uv homolumo', SDFinput, 0)
calc_sdf = GaussianDFTRun('STO-3G', '3-21G*', gau_parallel, 'OPT fluor energy deen uv homolumo', SDFinput, 0)
#STO3G
calc_sdf = GaussianDFTRun('B3LYP', '3-21G*', gau_parallel, 'OPT fluor energy deen uv homolumo', SDFinput, 0)
outdic = calc_sdf.run_gaussian()
wavelength = outdic['uv'][0]
s1_wavelength = outdic['S1 Wavelength and Oscillator strengths'][0]

print('ind', ind, 'wavelength', wavelength)
if os.path.isfile('CheckMol'+str(ind)+'.sdf'):
shutil.move('CheckMol'+str(ind)+'.sdf', 'dft_result')
if os.path.isfile('CheckMolopt'+str(ind)+'.sdf'):
Expand Down Expand Up @@ -915,16 +898,15 @@ def gaussion_workers(chem_model,val,gau_parallel,charge_check):

ts_strategy = 'puct' #'uct', 'puct'
search_parameter = 0.25 #If ts_strategy=='uct', 0 < search_parameter < 1. If ts_strategy=='puct', default value is 5 (AlphaGo).
num_simulations = 29 # core - 1, max: 2560 (skylake)
num_simulations = 1199 # core - 1, max: 2560 (skylake)
gau_parallel = 1
num_rollout = 3 #3
num_rollout = 3
simulation_time = 3600*120 # 3600*24 # max: 168h
alpha = 1 # alph*mean + (1 - alpha)*max + bais
objective = 'WLFL' # 'WL_IT', 'HL', 'WL'
charge_check = True # True or False
SA_score_check = True # True or False
output_file = 'csvresult_FP_'+ts_strategy+'_C'+str(search_parameter)+'_alpha'+str(alpha)+'_obj'+objective+'_para'+str(num_simulations)+'_time'+str(simulation_time/3600)+'h_rollout'+str(num_rollout)+'_CC'+str(charge_check)+'_SA'+str(SA_score_check)+'_210130_test.csv'

output_file = 'csvresult_FP_'+ts_strategy+'_C'+str(search_parameter)+'_alpha'+str(alpha)+'_obj'+objective+'_para'+str(num_simulations)+'_time'+str(simulation_time/3600)+'h_rollout'+str(num_rollout)+'_CC'+str(charge_check)+'_SA'+str(SA_score_check)+'.csv'

thread_pool=[]
lock=Lock()
Expand Down Expand Up @@ -991,4 +973,3 @@ def gaussion_workers(chem_model,val,gau_parallel,charge_check):
#else:
# while True:
# time.sleep(30)

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