def test_make_optin():
prefs = get_dummy_prefs()
mol = get_random_mol()
molname = 'dummy_mol'
infile = orcasub.make_optin(prefs, molname, mol.xyz, mol.types)
# Check file was created
assert os.path.isfile(infile)
os.remove(infile)
infile = g09sub.make_optcom(prefs, molname, mol.xyz, mol.types)
# Check file was created
#assert os.path.isfile(infile)
#os.remove(infile)
infile = g16sub.make_optcom(prefs, molname, mol.xyz, mol.types)
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. . .')
def setup_optimisation(molecule, prefs, path='', max=50):
opt_files = []
for conformer in molecule.conformers:
if conformer.redundant:
continue
if prefs['optimisation']['software'] == 'orca':
conformer.opt_in = orcasub.make_optin(prefs, conformer.molid, conformer.xyz, conformer.types,
path + 'optimisation/')
elif prefs['optimisation']['software'] == 'g09':
conformer.opt_in = g09sub.make_optcom(prefs, conformer.molid, conformer.xyz, conformer.types,
path + 'optimisation/')
elif prefs['optimisation']['software'] == 'g16':
conformer.opt_in = g16sub.make_optcom(prefs, conformer.molid, conformer.xyz, conformer.types,
path + 'optimisation/')
conformer.opt_log = conformer.opt_in.split('.')[0] + '.log'
conformer.opt_status = 'pre-submission'
opt_files.append('optimisation/' + conformer.opt_in.split('/')[-1])
if len(opt_files) == 0:
print('No files to submit. . .')
sys.exit(0)
IN_ARRAY = 'optimisation/OPT_IN_ARRAY.txt'
with open(path + IN_ARRAY, 'w') as f:
for file in opt_files:
print(file, file=f)
system = prefs['comp']['system']
memory = prefs['optimisation']['memory']
processors = prefs['optimisation']['processors']
walltime = prefs['optimisation']['walltime']
software = prefs['optimisation']['software']
files = len(opt_files)
chunks = HPCsub.get_chunks(files)
qsub_names = []
for ck in range(chunks):
start = (ck * max) + 1
end = ((ck + 1) * max)
if end > files:
end = files
#header = HPCsub.make_HPC_header(jobname=jobname, system=system, nodes=1, ppn=processors, walltime=walltime, mem=memory)
jobname = 'aE_' + molecule.molid + '_' + str(ck) + '_optimisation'
strings = HPCsub.make_HPC_batch_submission(prefs, molecule.molid, IN_ARRAY, start, end, software=software,
jobname=jobname, nodes=1, ppn=processors, walltime=walltime, mem=memory)
if prefs['comp']['system'] == 'PBS':
filename = path + 'OPT_' + molecule.molid + '_' + str(ck) + '.qsub'
elif prefs['comp']['system'] == 'slurm':
filename = path + 'OPT_' + molecule.molid + '_' + str(ck) + '.slurm'
elif prefs['comp']['system'] == 'local':
filename = path + 'OPT_' + molecule.molid + '_' + str(ck) + '.sh'
with open(filename, 'w') as f:
for string in strings:
print(string, file=f)
qsub_names.append(filename)
print('Created ', chunks, ' submission files. . .')
if prefs['comp']['system'] == 'PBS':
print('Submit the calculations using:')
for file in qsub_names:
print('qsub ', file)
elif prefs['comp']['system'] == 'PBS':
print('Submit the calculations using:')
for file in qsub_names:
print('bash ', file)
elif prefs['comp']['system'] == 'slurm':
print('Havent finished this yet, good luck pal. . . .')