def _run_qchem_on_alcf(self, log_file_object=None):
parent_qcinp = QcInput.from_file(self.input_file)
njobs = len(parent_qcinp.jobs)
return_codes = []
alcf_cmds = []
qc_jobids = []
for i, j in enumerate(parent_qcinp.jobs):
qsub_cmd = copy.deepcopy(self.current_command)
sub_input_filename = "alcf_{}_{}".format(i+1, self.input_file)
sub_output_filename = "alcf_{}_{}".format(i+1, self.output_file)
sub_log_filename = "alcf_{}_{}".format(i+1, self.qclog_file)
qsub_cmd[-2] = sub_input_filename
sub_qcinp = QcInput([copy.deepcopy(j)])
if "scf_guess" in sub_qcinp.jobs[0].params["rem"] and \
sub_qcinp.jobs[0].params["rem"]["scf_guess"] == "read":
sub_qcinp.jobs[0].params["rem"].pop("scf_guess")
if i > 0:
if isinstance(j.mol, str) and j.mol == "read":
prev_qcout_filename = "alcf_{}_{}".format(i+1-1, self.output_file)
prev_qcout = QcOutput(prev_qcout_filename)
prev_final_mol = prev_qcout.data[0]["molecules"][-1]
j.mol = prev_final_mol
sub_qcinp.write_file(sub_input_filename)
logging.info("The command to run QChem is {}".format(' '.join(qsub_cmd)))
alcf_cmds.append(qsub_cmd)
p = subprocess.Popen(qsub_cmd,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out, err = p.communicate()
qc_jobid = int(out.strip())
qc_jobids.append(qc_jobid)
cqwait_cmd = shlex.split("cqwait {}".format(qc_jobid))
subprocess.call(cqwait_cmd)
output_file_name = "{}.output".format(qc_jobid)
cobaltlog_file_name = "{}.cobaltlog".format(qc_jobid)
with open(cobaltlog_file_name) as f:
cobaltlog_last_line = f.readlines()[-1]
exit_code_pattern = re.compile("an exit code of (?P<code>\d+);")
m = exit_code_pattern.search(cobaltlog_last_line)
if m:
rc = float(m.group("code"))
else:
rc = -99999
return_codes.append(rc)
for name_change_trial in range(10):
if not os.path.exists(output_file_name):
message = "{} is not found in {}, {}th wait " \
"for 5 mins\n".format(
output_file_name,
os.getcwd(), name_change_trial)
logging.info(message)
if log_file_object:
log_file_object.writelines([message])
time.sleep(60 * 5)
pass
else:
message = "Found qchem output file {} in {}, change file " \
"name\n".format(output_file_name,
os.getcwd(),
name_change_trial)
logging.info(message)
if log_file_object:
log_file_object.writelines([message])
break
log_file_object.flush()
os.fsync(log_file_object.fileno())
shutil.move(output_file_name, sub_output_filename)
shutil.move(cobaltlog_file_name, sub_log_filename)
overall_return_code = min(return_codes)
with open(self.output_file, "w") as out_file_object:
for i, job_cmd, rc, qc_jobid in zip(range(njobs), alcf_cmds, return_codes, qc_jobids):
sub_output_filename = "alcf_{}_{}".format(i+1, self.output_file)
sub_log_filename = "alcf_{}_{}".format(i+1, self.qclog_file)
with open(sub_output_filename) as sub_out_file_object:
header_lines = ["Running Job {} of {} {}\n".format(i + 1, njobs, self.input_file),
" ".join(job_cmd) + "\n"]
if i > 0:
header_lines = ['', ''] + header_lines
sub_out = sub_out_file_object.readlines()
out_file_object.writelines(header_lines)
out_file_object.writelines(sub_out)
if rc < 0 and rc != -99999:
out_file_object.writelines(["Application {} exit codes: {}\n".format(qc_jobid, rc), '\n', '\n'])
if log_file_object:
with open(sub_log_filename) as sub_log_file_object:
sub_log = sub_log_file_object.readlines()
log_file_object.writelines(sub_log)
return overall_return_code
def main():
import argparse
parser = argparse.ArgumentParser(
description="Run A QChem Job for a QChem Input File")
parser.add_argument("-i",
"--input",
dest="input",
type=str,
required=True,
help="the QChem output file with imaginary frequency")
parser.add_argument("-o",
"--output",
dest="output",
type=str,
required=True,
help="the QChem input file with perturbed geometry")
parser.add_argument("-s",
"--scale",
dest="scale",
type=float,
default=0.3,
help="the scale factor to perturb molecule")
parser.add_argument("-r",
"--reverse",
dest="reverse",
action="store_true",
help="use reversed direction to perturb molecule")
parser.add_argument("-v",
"--verbose",
dest="verbose",
action="store_true",
help="print parameters")
options = parser.parse_args()
qcout = QcOutput(options.input)
charge = None
spin_multiplicity = None
for d in qcout.data:
j = d["input"]
if j.charge is not None:
charge = j.charge
if j.spin_multiplicity is not None:
spin_multiplicity = j.spin_multiplicity
if qcout.data[-1]['frequencies'][0]["frequency"] < -0.00:
old_mol = qcout.data[-1]["molecules"][-1]
vib_mode = qcout.data[-1]['frequencies'][0]["vib_mode"]
if options.verbose:
if options.reverse:
direction_text = "User forward direction"
else:
direction_text = "User reversed direction"
print("{} with scale factor {}".format(direction_text,
options.scale))
new_mol = perturb_molecule(old_mol,
vib_mode,
reversed_direction=options.reverse,
perturb_scale=options.scale)
qctask_freq = qcout.data[-1]["input"]
qctask_freq.mol = "read"
qctask_freq.charge = charge
qctask_freq.spin_multiplicity = spin_multiplicity
qctask_opt = copy.deepcopy(qctask_freq)
qctask_opt.params["rem"]["jobtype"] = "opt"
qctask_opt.params["rem"].pop("scf_guess", None)
qctask_opt.mol = new_mol
qcinp = QcInput([qctask_opt, qctask_freq])
qcinp.write_file(options.output)
else:
raise ValueError(
"Must have an imaginary frequency to perturb the molecule")
def _run_qchem_on_alcf(self, log_file_object=None):
parent_qcinp = QcInput.from_file(self.input_file)
njobs = len(parent_qcinp.jobs)
return_codes = []
alcf_cmds = []
qc_jobids = []
for i, j in enumerate(parent_qcinp.jobs):
qsub_cmd = copy.deepcopy(self.current_command)
sub_input_filename = "alcf_{}_{}".format(i + 1, self.input_file)
sub_output_filename = "alcf_{}_{}".format(i + 1, self.output_file)
sub_log_filename = "alcf_{}_{}".format(i + 1, self.qclog_file)
qsub_cmd[-2] = sub_input_filename
sub_qcinp = QcInput([copy.deepcopy(j)])
if "scf_guess" in sub_qcinp.jobs[0].params["rem"] and \
sub_qcinp.jobs[0].params["rem"]["scf_guess"] == "read":
sub_qcinp.jobs[0].params["rem"].pop("scf_guess")
if i > 0:
if isinstance(j.mol, str) and j.mol == "read":
prev_qcout_filename = "alcf_{}_{}".format(
i + 1 - 1, self.output_file)
prev_qcout = QcOutput(prev_qcout_filename)
prev_final_mol = prev_qcout.data[0]["molecules"][-1]
j.mol = prev_final_mol
sub_qcinp.write_file(sub_input_filename)
logging.info("The command to run QChem is {}".format(
' '.join(qsub_cmd)))
alcf_cmds.append(qsub_cmd)
p = subprocess.Popen(qsub_cmd,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out, err = p.communicate()
qc_jobid = int(out.strip())
qc_jobids.append(qc_jobid)
cqwait_cmd = shlex.split("cqwait {}".format(qc_jobid))
subprocess.call(cqwait_cmd)
output_file_name = "{}.output".format(qc_jobid)
cobaltlog_file_name = "{}.cobaltlog".format(qc_jobid)
with open(cobaltlog_file_name) as f:
cobaltlog_last_line = f.readlines()[-1]
exit_code_pattern = re.compile(
"an exit code of (?P<code>\d+);")
m = exit_code_pattern.search(cobaltlog_last_line)
if m:
rc = float(m.group("code"))
else:
rc = -99999
return_codes.append(rc)
for name_change_trial in range(10):
if not os.path.exists(output_file_name):
message = "{} is not found in {}, {}th wait " \
"for 5 mins\n".format(
output_file_name,
os.getcwd(), name_change_trial)
logging.info(message)
if log_file_object:
log_file_object.writelines([message])
time.sleep(60 * 5)
pass
else:
message = "Found qchem output file {} in {}, change file " \
"name\n".format(output_file_name,
os.getcwd(),
name_change_trial)
logging.info(message)
if log_file_object:
log_file_object.writelines([message])
break
log_file_object.flush()
os.fsync(log_file_object.fileno())
shutil.move(output_file_name, sub_output_filename)
shutil.move(cobaltlog_file_name, sub_log_filename)
overall_return_code = min(return_codes)
with open(self.output_file, "w") as out_file_object:
for i, job_cmd, rc, qc_jobid in zip(range(njobs), alcf_cmds,
return_codes, qc_jobids):
sub_output_filename = "alcf_{}_{}".format(
i + 1, self.output_file)
sub_log_filename = "alcf_{}_{}".format(i + 1, self.qclog_file)
with open(sub_output_filename) as sub_out_file_object:
header_lines = [
"Running Job {} of {} {}\n".format(
i + 1, njobs, self.input_file),
" ".join(job_cmd) + "\n"
]
if i > 0:
header_lines = ['', ''] + header_lines
sub_out = sub_out_file_object.readlines()
out_file_object.writelines(header_lines)
out_file_object.writelines(sub_out)
if rc < 0 and rc != -99999:
out_file_object.writelines([
"Application {} exit codes: {}\n".format(
qc_jobid, rc), '\n', '\n'
])
if log_file_object:
with open(sub_log_filename) as sub_log_file_object:
sub_log = sub_log_file_object.readlines()
log_file_object.writelines(sub_log)
return overall_return_code
def main():
import argparse
parser = argparse.ArgumentParser(
description="Run A QChem Job for a QChem Input File")
parser.add_argument("-f",
"--filename",
dest="filename",
type=str,
required=True,
help="the QChem input filename")
parser.add_argument("-e",
"--eliminate",
dest="eli_img",
action="store_true",
help="whether to eliminate imaginary frequency")
parser.add_argument("-b",
"--mixed_basis",
dest="mixed_basis",
type=json.loads,
required=False,
help="The mixed basis as a dict")
parser.add_argument("-a",
"--mixed_aux_basis",
dest="mixed_aux_basis",
type=json.loads,
required=False,
help="The mixed auxiliary basis as a dict")
parser.add_argument("-s",
"--solvent",
dest="solvent",
type=str,
required=False,
help="the implicit solvent")
parser.add_argument("-n",
"--run_name",
dest="run_name",
type=str,
default=None,
help="the implicit solvent")
options = parser.parse_args()
call_qchem_task(options.filename,
options.solvent,
options.mixed_basis,
options.mixed_aux_basis,
run_name=options.run_name)
if options.eli_img:
base_filename = os.path.splitext(options.filename)[0]
output_filename = base_filename + ".qcout"
qcout = QcOutput(output_filename)
charge = None
spin_multiplicity = None
for d in qcout.data:
j = d["input"]
if j.charge is not None:
charge = j.charge
if j.spin_multiplicity is not None:
spin_multiplicity = j.spin_multiplicity
if qcout.data[-1]['frequencies'][0]["frequency"] < -0.00:
os.system("tar czvf img_freq_1.tar.gz *")
old_mol = qcout.data[-1]["molecules"][-1]
vib_mode = qcout.data[-1]['frequencies'][0]["vib_mode"]
new_mol = perturb_molecule(old_mol, vib_mode)
qctask_freq = qcout.data[-1]["input"]
qctask_freq.mol = "read"
qctask_freq.charge = charge
qctask_freq.spin_multiplicity = spin_multiplicity
qctask_opt = copy.deepcopy(qctask_freq)
qctask_opt.params["rem"]["jobtype"] = "opt"
qctask_opt.params["rem"].pop("scf_guess", None)
qctask_opt.mol = new_mol
qcinp = QcInput([qctask_opt, qctask_freq])
eli_file_1 = base_filename + "_eli_img_1.qcinp"
qcinp.write_file(eli_file_1)
call_qchem_task(eli_file_1,
options.solvent,
options.mixed_basis,
options.mixed_aux_basis,
run_name=options.run_name)
output_filename = base_filename + "_eli_img_1.qcout"
qcout = QcOutput(output_filename)
if qcout.data[-1]['frequencies'][0]["frequency"] < -0.00:
os.system("tar czvf img_freq_2.tar.gz *")
old_mol = qcout.data[-1]["molecules"][-1]
vib_mode = qcout.data[-1]['frequencies'][0]["vib_mode"]
new_mol = perturb_molecule(old_mol, vib_mode)
qctask_freq = qcout.data[-1]["input"]
qctask_freq.mol = "read"
qctask_freq.charge = charge
qctask_freq.spin_multiplicity = spin_multiplicity
qctask_opt = copy.deepcopy(qctask_freq)
qctask_opt.params["rem"]["jobtype"] = "opt"
qctask_opt.params["rem"].pop("scf_guess", None)
qctask_opt.mol = new_mol
qcinp = QcInput([qctask_opt, qctask_freq])
for j in qcinp.jobs:
j.set_dft_grid(128, 302)
j.set_integral_threshold(12)
if j.params["rem"]["jobtype"] == "opt":
j.scale_geom_opt_threshold(0.1, 0.1, 0.1)
j.set_geom_max_iterations(100)
eli_file_2 = base_filename + "_eli_img_2.qcinp"
qcinp.write_file(eli_file_2)
call_qchem_task(eli_file_2,
options.solvent,
options.mixed_basis,
options.mixed_aux_basis,
run_name=options.run_name)
output_filename = base_filename + "_eli_img_2.qcout"
qcout = QcOutput(output_filename)
if qcout.data[-1]['frequencies'][0]["frequency"] < -0.00:
os.system("tar czvf img_freq_3.tar.gz *")
old_mol = qcout.data[-1]["molecules"][-1]
vib_mode = qcout.data[-1]['frequencies'][0]["vib_mode"]
new_mol = perturb_molecule(old_mol, vib_mode)
qctask_freq = qcout.data[-1]["input"]
qctask_freq.mol = "read"
qctask_freq.charge = charge
qctask_freq.spin_multiplicity = spin_multiplicity
qctask_opt = copy.deepcopy(qctask_freq)
qctask_opt.params["rem"]["jobtype"] = "opt"
qctask_opt.params["rem"].pop("scf_guess", None)
qctask_opt.mol = new_mol
qcinp = QcInput([qctask_opt, qctask_freq])
for j in qcinp.jobs:
j.set_dft_grid(90, 590)
j.set_integral_threshold(12)
if j.params["rem"]["jobtype"] == "opt":
j.scale_geom_opt_threshold(0.1, 0.1, 0.1)
j.set_geom_max_iterations(100)
eli_file_3 = base_filename + "_eli_img_3.qcinp"
qcinp.write_file(eli_file_3)
call_qchem_task(eli_file_3,
options.solvent,
options.mixed_basis,
options.mixed_aux_basis,
run_name=options.run_name)