chiN.append(chi[itterlist[chi_loc]])
WDIR_fieldpath = os.path.join(WDIR,fieldpath)
if p==0 or args.chainbool==False:
fieldsin_path = os.path.join(args.seed_path,f'{Phase}_fields.in')
shutil.copy(fieldsin_path,WDIR_fieldpath)
else:
shutil.copy(fieldsin_path,WDIR_fieldpath)
#replace list for make input file
REPLACE_lIST = [fieldpath,chain_list,chiN,d,args.chain_label,args.contour_step,args.timestep,args.stressscale,\
args.forcescale,args.initial_box_size[q],[args.number_of_planewaves[q]],args.reference_length,\
args.cell_updater,args.force_tol,args.stress_tol,args.field_updater]
make_input(Phase,REPLACE_lIST,WDIR)
#make submit file incase you want to run the simulation individually
make_submit(args,Phase)
if args.submitpolyfts:
os.chdir(WDIR)
cmd="qsub submit.sh"
subprocess.call(cmd.split())
os.chdir(IDIR)
time.sleep(1)
#runpolyfts for serial
if args.runpolyfts:
if args.NThreads[q]==1:
os.chdir(WDIR)
print('Delete!')
continue
if reparam_itter_store_count[i] == len(param_full_order):
break
Box_initial = 10
if reparam_itter_store_count[i] == 0:
paramlist = [dS, DT, lambda_stress, lambda_force]
replace_list.append([field_path,chain_list,chiN,npw,\
Box_initial,d,jobname,paramlist[0],\
paramlist[1],paramlist[2],paramlist[3]])
else:
DT = DT * tune
paramlist = [dS, DT, lambda_stress, lambda_force]
replace_list.append([field_path,chain_list,chiN,npw,\
Box_initial,d,jobname,paramlist[0],\
paramlist[1],paramlist[2],paramlist[3]])
WDIR_NAME = 'L_' + str(Ssweep[i])
WDIR = os.path.join(IDIR, WDIR_NAME)
jobstatus = 0
os.makedirs(WDIR)
make_input(phase, replace_list[i], WDIR)
past_field_dir.append(WDIR)
print('pass')
i += 1
itter = +1
chain_list+=sidechain_list
#pass internal checks
check_equality(len(chain_list)==0,False,"Need more than 0 chains")
for l in range(0,len(chain_list),1):
check_equality(len(chain_list[l])>6,False,"Too many side chain inputs")
check_equality(len(chain_list)!=0,True,"Need more than 0 chains")
list_of_checks = [[len(chain_list[l][2]),len(chain_list[l][3]),'check chain species and composition'],\
[np.isclose(np.sum(chain_list[l][3]),1),True,'backbone composition does not sum to 1']]
for checkchecks in list_of_checks:
check_equality(checkchecks[0],checkchecks[1],checkchecks[2])
REPLACE_lIST = [fieldpath,chain_list,chiN,d,chain_label,dS,dt,stress_scale,\
force_scale,InitialL0Guess[k],SpaceGroup[k]]
make_input(PhaseList[k],REPLACE_lIST,WDIR)
if NThreads[k] == 1:
submitfile='SEEDS/submit.sh'
elif NThreads[k] == -1:
if PhaseList[k] != 'SIGMA':
submitfile='SEEDS/submitGPU.sh'
else:
submitfile='SEEDS/submitGPU-P100.sh'
else:
submitfile='SEEDS/submitPLL.sh'
with open('%s/submit.sh' % WDIR, 'w') as fout:
