def setup_nmr(molecule, prefs, path='', ids=[], max=50):
nmr_files = []
for conformer in molecule.conformers:
if (conformer.nmr_status == 'None' or conformer.nmr_status
== 'pre-submission') and conformer.opt_status == 'successful':
if prefs['NMR']['software'] == 'orca':
conformer.nmr_in = orcasub.make_nmrin(prefs, conformer.molid,
conformer.xyz,
conformer.types,
path + 'NMR/')
elif prefs['NMR']['software'] == 'g09':
conformer.nmr_in = g09sub.make_nmrcom(prefs, conformer.molid,
conformer.xyz,
conformer.types,
path + 'NMR/')
elif prefs['NMR']['software'] == 'g16':
conformer.nmr_in = g16sub.make_nmrcom(prefs, conformer.molid,
conformer.xyz,
conformer.types,
path + 'NMR/')
conformer.nmr_log = conformer.nmr_in.split('.')[0] + '.log'
conformer.nmr_status = 'pre-submission'
nmr_files.append('NMR/' + conformer.nmr_in.split('/')[-1])
if len(nmr_files) == 0:
print('No files to submit. . .')
sys.exit(0)
IN_ARRAY = 'NMR/NMR_IN_ARRAY.txt'
with open(path + IN_ARRAY, 'w') as f:
for file in nmr_files:
print(file, file=f)
system = prefs['comp']['system']
memory = prefs['NMR']['memory']
processors = prefs['NMR']['processors']
walltime = prefs['NMR']['walltime']
software = prefs['NMR']['software']
files = len(nmr_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) + '_NMR'
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 + 'NMR_' + molecule.molid + '_' + str(ck) + '.qsub'
elif prefs['comp']['system'] == 'slurm':
filename = path + 'NMR_' + molecule.molid + '_' + str(
ck) + '.slurm'
elif prefs['comp']['system'] == 'local':
filename = path + 'NMR_' + 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. . . .')
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 conformational_search(molecule, prefs, pickle_file, path=''):
# Read relevant preferences
iterations = prefs['conf_search']['iterations']
maxconfs = prefs['conf_search']['maxconfs']
RMSthresh = prefs['conf_search']['RMSthresh']
Ethresh = prefs['conf_search']['Ethresh']
system = prefs['comp']['system']
python_env = prefs['comp']['python_env']
aE_dir = prefs['comp']['aE_directory']
if system != 'local':
memory = prefs['conf_search']['memory']
processors = prefs['conf_search']['processors']
walltime = prefs['conf_search']['walltime']
else:
memory = 2
processors = 2
walltime = '100:00:00'
# Try reading pybel mol object from xyz named according to molname
try:
file = path + molecule.molid + '.xyz'
mol = next(pyb.readfile('xyz', file))
# If not, make a molecule xyz file and then read the pybel mol object
except:
file = path + molecule.molid + '_INIT.xyz'
xyz.nmrmol_to_xyz(molecule, file, num=-404)
mol = next(pyb.readfile('xyz', file))
smiles = mol.write("smi").split()[0]
scriptname = 'conf_search/do_confsearch.py'
confsearch.make_confsearch_script(scriptname,
pickle_file,
smiles,
iterations=iterations,
RMSthresh=RMSthresh,
maxconfs=maxconfs,
Ethresh=Ethresh,
path=path)
jobname = 'aE_' + molecule.molid + '_confsearch'
strings = HPCsub.make_HPC_header(jobname=jobname,
system=system,
nodes=1,
ppn=processors,
walltime=walltime,
mem=memory)
strings.append('conda activate {env:<10s}'.format(env=python_env))
strings.append('python {0:<10s}'.format(scriptname))
if prefs['comp']['system'] == 'PBS':
filename = path + 'confsearch_' + molecule.molid + '_' + '.qsub'
elif prefs['comp']['system'] == 'slurm':
filename = path + 'confsearch_' + molecule.molid + '_' + '.slurm'
elif prefs['comp']['system'] == 'local':
filename = path + 'confsearch_' + molecule.molid + '_' + '.sh'
with open(filename, 'w') as f:
for string in strings:
print(string, file=f)
print('Conformational search script + submission file produced')