def run_job(self,
settings,
settings_2=None,
inputArgues=None,
others=None,
job_name='',
**kwargs):
"""
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:`~qmworks.packages.SCM.ADF_Result`
"""
fragmentset = Settings()
complexset = Settings()
fragmentset.input = settings.specific.fragment
complexset.input = settings_2.specific.complex
job = PyFragJob(fragmentset, complexset, inputArgues, others)
result = job.run()
return result
def run_job(settings, mol, job_name="DFTBjob"):
"""
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:`~qmworks.packages.SCM.DFTB_Result`
"""
dftb_settings = Settings()
dftb_settings.input = settings.specific.dftb
job = plams.DFTBJob(name=job_name,
molecule=mol,
settings=dftb_settings)
result = job.run()
if job.status in ["failed", "crashed"]:
builtins.config.jm.remove_job(job)
return DFTB_Result(dftb_settings,
mol,
result.job.name,
plams_dir=result.job.path)
def run_job(settings, mol, job_name="ADFjob"):
"""
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:`~qmworks.packages.SCM.ADF_Result`
"""
adf_settings = Settings()
adf_settings.input = settings.specific.adf
job = plams.ADFJob(name=job_name, molecule=mol, settings=adf_settings)
result = job.run()
path_t21 = result._kf.path
adf_result = ADF_Result(
adf_settings,
mol,
result.job.name,
path_t21,
plams_dir=result.job.path,
status=job.status,
)
return adf_result
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:`~qmworks.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.GamessJob(molecule=mol,
name=job_name,
settings=gamess_settings)
r = job.run()
result = Gamess_Result(
gamess_settings,
mol,
r.job.name,
plams_dir=r.job.path,
work_dir=work_dir,
status=job.status,
)
return result
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:`~qmworks.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
job = plams.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
result = CP2K_Result(cp2k_settings, mol, job_name, r.job.path,
work_dir, status=job.status)
return result
def run_job(self, settings, mol, job_name='DFTBjob'):
"""
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:`~qmworks.packages.SCM.DFTB_Result`
"""
dftb_settings = Settings()
dftb_settings.input = settings.specific.dftb
result = plams.DFTBJob(name=job_name,
molecule=mol,
settings=dftb_settings).run()
return DFTB_Result(dftb_settings,
mol,
result.job.name,
plams_dir=result.job.path)
def run_job(self, settings, mol, input_file_name=None, out_file_name=None):
dirac_settings = Settings()
dirac_settings.input = settings.specific.dirac
check_dirac_input(dirac_settings)
result = plams.DiracJob(settings=dirac_settings, molecule=mol).run()
return DIRAC_Result(dirac_settings, mol, result)
def run_job(self,
settings,
mol,
work_dir=None,
project_name=None,
hdf5_file="quantum.hdf5",
input_file_name=None,
out_file_name=None,
store_in_hdf5=True,
nHOMOS=None,
nLUMOS=None,
job_name='cp2k_job'):
"""
Call the Cp2K binary using plams interface.
:param settings: Job Settings.
:type settings: :class:`~qmworks.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
"""
cp2k_settings = Settings()
cp2k_settings.input = settings.specific.cp2k
job = plams.Cp2kJob(name=job_name,
settings=cp2k_settings,
molecule=mol)
runner = plams.JobRunner(parallel=True)
r = job.run(runner)
r.wait()
work_dir = work_dir if work_dir is not None else job.path
output_file = join(job.path, job._filename('out'))
if store_in_hdf5:
dump_to_hdf5(hdf5_file,
settings,
work_dir,
output_file,
nHOMOS,
nLUMOS,
project_name=project_name)
return CP2K_Result(cp2k_settings,
mol,
job_name,
r.job.path,
work_dir,
path_hdf5=hdf5_file,
project_name=project_name)
def run_job(self, settings, mol, job_name="ORCAjob"):
orca_settings = Settings()
orca_settings.input = settings.specific.orca
result = plams.ORCAJob(molecule=mol,
settings=orca_settings,
name=job_name).run()
return ORCA_Result(orca_settings, mol, result.job.name,
result.job.path)
def run_job(settings, mol, job_name="ORCAjob"):
orca_settings = Settings()
orca_settings.input = settings.specific.orca
job = plams.ORCAJob(molecule=mol, settings=orca_settings, name=job_name)
result = job.run()
return ORCA_Result(
orca_settings,
mol,
result.job.name,
plams_dir=result.job.path,
status=job.status,
)
def run_job(settings, mol, job_name="dirac_job"):
dirac_settings = Settings()
dirac_settings.input = settings.specific.dirac
dirac_settings.ignore_molecule
job = plams.DiracJob(name=job_name,
settings=dirac_settings,
molecule=mol)
result = job.run()
return DIRAC_Result(
dirac_settings,
mol,
result.job.name,
plams_dir=result.job.path,
status=job.status,
)
def run_job(self,
settings,
mol,
work_dir=None,
project_name=None,
hdf5_file="quantum.hdf5",
store_in_hdf5=True,
job_name='gamess_job'):
"""
Call the Cp2K binary using plams interface.
:param settings: Job Settings.
:type settings: :class:`~qmworks.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
"""
gamess_settings = Settings()
gamess_settings.input = settings.specific.gamess
job = plams.GamessJob(molecule=mol,
name=job_name,
settings=gamess_settings)
runner = plams.JobRunner(parallel=True)
r = job.run(runner)
r.wait()
return Gamess_Result(gamess_settings,
mol,
r.job.name,
plams_dir=r.job.path,
work_dir=work_dir,
path_hdf5=hdf5_file,
project_name=project_name)