def run_job(settings, mol, job_name='gamess_job', work_dir=None):
"""
Call the Cp2K binary using plams interface.
:param settings: Job Settings.
:type settings: :class:`~qmflows.Settings`
:param mol: molecular Geometry
:type mol: plams Molecule
:param input_file_name: Optional name for the input.
:type input_file_name: String
:param out_file_name: Optional name for the output.
:type out_file_name: String
:return: Package.Result
"""
gamess_settings = Settings()
gamess_settings.input = settings.specific.gamess
job = plams.interfaces.gamess.GamessJob(molecule=mol,
name=job_name,
settings=gamess_settings)
r = job.run()
# Relative job path
relative_plams_path = '/'.join(r.job.path.split('/')[-2:])
result = Gamess_Result(gamess_settings,
mol,
r.job.name,
plams_dir=relative_plams_path,
work_dir=work_dir,
status=job.status)
return result
def run_job(settings, mol, job_name="dirac_job"):
dirac_settings = Settings()
dirac_settings.input = settings.specific.dirac
dirac_settings.ignore_molecule
job = plams.interfaces.thirdparty.dirac.DiracJob(
name=job_name, settings=dirac_settings, molecule=mol)
result = job.run()
# Relative job path
relative_plams_path = '/'.join(result.job.path.split('/')[-2:])
return DIRAC_Result(dirac_settings, mol, result.job.name,
plams_dir=relative_plams_path, status=job.status)
def run_job(settings, mol, job_name='cp2k_job', work_dir=None, **kwargs):
"""
Call the Cp2K binary using plams interface.
:param settings: Job Settings.
:type settings: :class:`~qmflows.Settings`
:param mol: molecular Geometry
:type mol: plams Molecule
:param hdf5_file: Path to the HDF5 file that contains the
numerical results.
:type hdf5_file: String
:param input_file_name: Optional name for the input.
:type input_file_name: String
:param out_file_name: Optional name for the output.
:type out_file_name: String
:param store_in_hdf5: wether to store the output arrays in HDF5 format.
:type store_in_hdf5: Bool
"""
# Yet another work directory
# Input modifications
cp2k_settings = Settings()
cp2k_settings.input = settings.specific.cp2k
# Add molecular coordinates
m = format_coord_xyz(mol) + '{:>8}'.format('&END')
cp2k_settings.input.force_eval.subsys['&COORD'] = m
# Create a Plams job
job = plams.interfaces.thirdparty.cp2k.Cp2kJob(name=job_name,
settings=cp2k_settings,
molecule=mol)
r = job.run()
work_dir = work_dir if work_dir is not None else job.path
warnings = parse_output_warnings(job_name, r.job.path,
parse_cp2k_warnings, cp2k_warnings)
result = CP2K_Result(cp2k_settings,
mol,
job_name,
r.job.path,
work_dir,
status=job.status,
warnings=warnings)
return result
def run_job(settings, mol, job_name='DFTBjob', nproc=None):
"""
Execute an DFTB job with the *ADF* quantum package.
:param settings: user input settings.
:type settings: |Settings|
:param mol: Molecule to run the simulation
:type mol: Plams Molecule
:parameter input_file_name: The user can provide a name for the
job input.
:type input_file_name: String
:parameter out_file_name: The user can provide a name for the
job output.
:type out_file_name: String
:returns: :class:`~qmflows.packages.SCM.DFTB_Result`
"""
dftb_settings = Settings()
if nproc:
dftb_settings.runscript.nproc = nproc
dftb_settings.input = settings.specific.dftb
job = plams.DFTBJob(name=job_name,
molecule=mol,
settings=dftb_settings)
# Check RKF status
try:
result = job.run()
name = result.job.name
path = result.job.path
except struct.error:
job.status = 'failed'
name = job_name
path = None
msg = "job:{} has failed.\nRKF is corrupted"
print(msg.format(job_name))
if job.status in ['failed', 'crashed']:
builtins.config.jm.remove_job(job)
return DFTB_Result(dftb_settings,
mol,
name,
plams_dir=path,
status=job.status)
def run_job(settings, mol, job_name="ORCAjob", work_dir=None, **kwargs):
orca_settings = Settings()
orca_settings.input = settings.specific.orca
# Running Orca with Plams
job = plams.interfaces.orca.ORCAJob(molecule=mol,
settings=orca_settings,
name=job_name)
result = job.run()
# Relative job path
relative_plams_path = '/'.join(result.job.path.split('/')[-2:])
return ORCA_Result(orca_settings,
mol,
result.job.name,
plams_dir=relative_plams_path,
status=job.status)
def run_job(settings, mol, job_name='ADFjob', nproc=None):
"""
Execute ADF job.
:param settings: user input settings.
:type settings: |Settings|
:param mol: Molecule to run the simulation
:type mol: Plams Molecule
:parameter input_file_name: The user can provide a name for the
job input.
:type input_file_name: String
:parameter out_file_name: The user can provide a name for the
job output.
:type out_file_name: String
:returns: :class:`~qmflows.packages.SCM.ADF_Result`
"""
adf_settings = Settings()
if nproc:
adf_settings.runscript.nproc = nproc
adf_settings.input = settings.specific.adf
job = plams.ADFJob(name=job_name, molecule=mol, settings=adf_settings)
result = job.run()
# Path to the tape 21 file
path_t21 = result._kf.path
# Relative path to the CWD
relative_path_t21 = '/'.join(path_t21.split('/')[-3:])
# Relative job path
relative_plams_path = '/'.join(result.job.path.split('/')[-2:])
adf_result = ADF_Result(adf_settings,
mol,
result.job.name,
relative_path_t21,
plams_dir=relative_plams_path,
status=job.status)
return adf_result
