def process_optimisation(molecule, prefs, path=''):
good = 0
bad = 0
for conformer in molecule.conformers:
if prefs['optimisation']['software'] == 'orca':
status = orcaread.get_opt_status(conformer.opt_log)
elif prefs['optimisation']['software'] == 'g09':
status = g09read.get_opt_status(conformer.opt_log)
elif prefs['optimisation']['software'] == 'g16':
status = g16read.get_opt_status(conformer.opt_log)
if status == 'successful':
good +=1
conformer.read_structure(conformer.opt_log.split('.')[0] + '.xyz', type='xyz')
conformer.read_opt(conformer.opt_log, type=prefs['optimisation']['software'])
#files_to_delete = glob.glob(conformer.opt_log.split('.')[0] + '*.tmp')
#for file in files_to_delete:
# os.remove(file)
else:
bad += 1
if conformer.opt_status != status:
conformer.nmr_status = 'None'
conformer.opt_status = status
string = 'Conformer {molid:^3s} status: {status:^10s} | Energy {energy:<10.4f}'.format(molid=str(conformer.molid),
status=conformer.opt_status,
energy=conformer.energy)
print(string)
print(good, ' successful optimisations, ', bad, ' failed, out of ', good+bad)
def test_orcaget_opt_status():
file = 'tests/test_store/TST_pass_orca_opt.log'
status = orcaread.get_opt_status(file)
assert status == 'successful'
# Dont actually have a failed one yet
'''
def setup_resubmission(molecule, prefs, path=''):
for conformer in molecule.conformers:
optstatus = orcaread.get_opt_status(conformer.opt_log)
if optstatus != 'successful':
conformer.opt_in = orcasub.make_optin(prefs, conformer,
path + 'optimisation/')
conformer.opt_log = conformer.optin.split('.')[0] + '.log'
conformer.opt_status = 'pre-submission'
opt_files.append(conformer.opt_in)
nmrstatus = orcaread.get_nmr_status(conformer.nmr_log)
if conformer.nmr_status != 'successful' and conformer.opt_status == 'successful':
conformer.nmr_in = orcasub.make_nmrin(prefs, conformer,
path + 'nmr/')
conformer.nmr_log = conformer.nmr_in.split('.') + '.log'
conformer.nmr_status = 'pre-submission'
nmr_files.append(conformer.nmr_in)
for tag, in_files in zip(['OPT', 'NMR'], [opt_files, nmr_files]):
system = prefs['comp']['system']
if tag == 'OPT':
memory = prefs['opt']['memory']
processors = prefs['opt']['processors']
walltime = prefs['opt']['walltime']
if tag == 'NMR':
memory = prefs['nmr']['memory']
processors = prefs['nmr']['processors']
walltime = prefs['nmr']['walltime']
files = len(in_files)
chunks = HPCsub.get_chunks(files)
for ck in range(chunks):
start = (ck * max) + 1
end = ((ck + 1) * max)
if end > files:
end = files
jobname = 'aE_' + molecule.molid + '_' + str(ck) + tag + '_RESUB'
header = HPCsub.make_HPC_header(jobname=jobname,
system=system,
nodes=1,
ppn=processors,
walltime=walltime,
mem=memory)
strings = HPCsub.make_orca_batch_submission(
prefs, in_files, start, end, ck)
if prefs['comp']['system'] == 'PBS':
filename = path + 'RESUB_' + tag + '_' + molecule.molid + '_' + str(
ck) + '.qsub'
elif prefs['comp']['system'] == 'slurm':
filename = path + 'RESUB_' + tag + '_' + molecule.molid + '_' + str(
ck) + '.slurm'
elif prefs['comp']['system'] == 'localbox':
filename = path + 'RESUB_' + tag + '_' + molecule.molid + '_' + str(
ck) + '.sh'
with open(filename, 'w') as f:
for string in header:
print(string, file=f)
for string in strings:
print(string, file=f)
print('Created ', len(chunks), ' ', tag, 'resubmission files. . .')