d3tales_api.Workflows package
Submodules
d3tales_api.Workflows.D3TaLES_FW module
- class d3tales_api.Workflows.D3TaLES_FW.DihedRot(geometry='groundState', dihed_degree=0, parents=None, priority=None, name_tag='', **kwargs)[source]
Bases:
Firework- __init__(geometry='groundState', dihed_degree=0, parents=None, priority=None, name_tag='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.EmailEnd(parents=None, priority=None, name_tag='', identifier='', email='', username='', **kwargs)[source]
Bases:
Firework- __init__(parents=None, priority=None, name_tag='', identifier='', email='', username='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.EmailStart(parents=None, priority=None, name_tag='', identifier='', email='', username='', **kwargs)[source]
Bases:
Firework- __init__(parents=None, priority=None, name_tag='', identifier='', email='', username='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.Energy(species='groundState', geometry='groundState', parents=None, priority=None, name_tag='', solvent=None, **kwargs)[source]
Bases:
Firework- __init__(species='groundState', geometry='groundState', parents=None, priority=None, name_tag='', solvent=None, **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.InitializeMolecule(name='initial_molecule_data', parents=None, priority=None, name_tag='', **kwargs)[source]
Bases:
Firework- __init__(name='initial_molecule_data', parents=None, priority=None, name_tag='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.MolOpt(name='opt_mol', parents=None, priority=None, name_tag='', **kwargs)[source]
Bases:
Firework- __init__(name='opt_mol', parents=None, priority=None, name_tag='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.Optimization(species='groundState', geometry='opt_mol', solvent=None, parents=None, priority=None, name_tag='', **kwargs)[source]
Bases:
Firework- __init__(species='groundState', geometry='opt_mol', solvent=None, parents=None, priority=None, name_tag='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.TDDFT(species='groundState', solvent=None, parents=None, priority=None, name_tag='', solv_geom=False, **kwargs)[source]
Bases:
Firework- __init__(species='groundState', solvent=None, parents=None, priority=None, name_tag='', solv_geom=False, **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
- class d3tales_api.Workflows.D3TaLES_FW.WTuning(name='wtuning', parents=None, priority=None, name_tag='', **kwargs)[source]
Bases:
Firework- __init__(name='wtuning', parents=None, priority=None, name_tag='', **kwargs)[source]
- Args:
tasks (Firetask or [Firetask]): a list of Firetasks to run in sequence. spec (dict): specification of the job to run. Used by the Firetask. launches ([Launch]): a list of Launch objects of this Firework. archived_launches ([Launch]): a list of archived Launch objects of this Firework. state (str): the state of the FW (e.g. WAITING, RUNNING, COMPLETED, ARCHIVED) created_on (datetime): time of creation fw_id (int): an identification number for this Firework. parents (Firework or [Firework]): list of parent FWs this FW depends on. updated_on (datetime): last time the STATE was updated.
d3tales_api.Workflows.Gaussian module
- class d3tales_api.Workflows.Gaussian.RunGaussianDihedRot(*args, **kwargs)[source]
Bases:
GaussianBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
- class d3tales_api.Workflows.Gaussian.RunGaussianEnergy(*args, **kwargs)[source]
Bases:
GaussianBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
- class d3tales_api.Workflows.Gaussian.RunGaussianOpt(*args, **kwargs)[source]
Bases:
GaussianBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
- class d3tales_api.Workflows.Gaussian.RunGaussianTDDFT(*args, **kwargs)[source]
Bases:
GaussianBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
- class d3tales_api.Workflows.Gaussian.RunWtuning(*args, **kwargs)[source]
Bases:
FiretaskBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
d3tales_api.Workflows.Gromacs module
d3tales_api.Workflows.Initialize module
- class d3tales_api.Workflows.Initialize.EmailFinished(*args, **kwargs)[source]
Bases:
FiretaskBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
- class d3tales_api.Workflows.Initialize.EmailStarting(*args, **kwargs)[source]
Bases:
FiretaskBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
- class d3tales_api.Workflows.Initialize.MoleculeInit(*args, **kwargs)[source]
Bases:
FiretaskBase- run_task(fw_spec)[source]
This method gets called when the Firetask is run. It can take in a Firework spec, perform some task using that data, and then return an output in the form of a FWAction.
- Args:
- fw_spec (dict): A Firework spec. This comes from the master spec.
In addition, this spec contains a special “_fw_env” key that contains the env settings of the FWorker calling this method. This provides for abstracting out certain commands or settings. For example, “foo” may be named “foo1” in resource 1 and “foo2” in resource 2. The FWorker env can specify { “foo”: “foo1”}, which maps an abstract variable “foo” to the relevant “foo1” or “foo2”. You can then write a task that uses fw_spec[“_fw_env”][“foo”] that will work across all these multiple resources.
- Returns:
(FWAction)
d3tales_api.Workflows.ParamSet module
- class d3tales_api.Workflows.ParamSet.GaussianParameters(route_parameters=None, charge=None, multiplicity=None, basis_set=None, functional=None, input_parameters=None, link0_parameters=None)[source]
Bases:
MSONable
d3tales_api.Workflows.utils module
- d3tales_api.Workflows.utils.generate_gaussian_input(paramset=None, mol=None, dieze_tag='#P')[source]
- d3tales_api.Workflows.utils.get_central_dihed(rdk_mol)[source]
function for recording central dihedral atom numbers
- d3tales_api.Workflows.utils.get_db_geom(input_geometry_hash, error_raise=False)[source]
get input geometry from DB :param input_geometry_hash: str :return: pymatgen mol object
- d3tales_api.Workflows.utils.get_groundState(identifier, prop='charge')[source]
get input geometry frontend DB smiles :param identifier: str :param prop: str :return: int, ground state charge
- d3tales_api.Workflows.utils.get_tddft_excitations(logfile)[source]
Read a excitation energies after a TD-DFT calculation.
Returns:
- A list: A list of tuple for each transition such as
[(energie (eV), lambda (nm), oscillatory strength), … ]
- d3tales_api.Workflows.utils.orig_conditions(functional, basis_set, tuning_parameter=None, solvent=None)[source]
Dictionary of conditions (in accordance with D3TaLES backend schema)
- d3tales_api.Workflows.utils.orig_hash_id(_id, calculation_type, functional, basis_set, tuning_parameter=None, solvent=None)[source]
Hash ID
- d3tales_api.Workflows.utils.start_from_smiles(identifier)[source]
get input geometry frontend DB smiles :param identifier: str :return: pymatgen mol object
- d3tales_api.Workflows.utils.write_nto(tddft_log, excitation_num, tddft_chk=None)[source]
Run NTO analysis after a TDDFT calculation. https://gaussian.com/faq4/ :param tddft_log: str, path to TDDFT calculation log file :param excitation_num: int, number for excitation on which to run the NTO analysis :param tddft_chk: str, path to TDDFT calculation checkpoint file (assumed to be the same name as log if not specified)
d3tales_api.Workflows.wf_writer module
- d3tales_api.Workflows.wf_writer.d3tales_wf(paramset, identifier=None, smiles=None, wtune=True, solvent='acetonitrile', hf_mol_opt=False, email=None, username=None, wf_tag='', **kwargs)[source]
- d3tales_api.Workflows.wf_writer.hf_wf(paramset, identifier=None, smiles=None, hf_mol_opt=False, email=None, username=None, solvent=None, **kwargs)[source]
- d3tales_api.Workflows.wf_writer.huckaba_wf(paramset, identifier=None, smiles=None, solvent='DiMethylSulfoxide', wtune=True, hf_mol_opt=False, email=None, username=None, **kwargs)[source]
- d3tales_api.Workflows.wf_writer.just_anion(paramset, identifier=None, smiles=None, wtune=False, solvent='acetonitrile', hf_mol_opt=False, email=None, username=None, **kwargs)[source]
- d3tales_api.Workflows.wf_writer.just_initialize(paramset, identifier=None, smiles=None, solvent='acetonitrile', hf_mol_opt=False, email=None, username=None, **kwargs)[source]
- d3tales_api.Workflows.wf_writer.just_nmr(paramset, identifier=None, smiles=None, solvent='acetonitrile', hf_mol_opt=False, email=None, username=None, **kwargs)[source]
- d3tales_api.Workflows.wf_writer.just_tddft(paramset, identifier=None, smiles=None, wtune=False, solvent=None, hf_mol_opt=False, email=None, username=None, check_if_already_run=True, **kwargs)[source]
d3tales_api.Workflows.wtuning module
Code taken from the OCELOT API to transform molecule objects. https://github.com/caer200/ocelot_api Code copied from: https://github.com/caer200/ocelot_api/blob/master/ocelot/task/wtuning.py
originally written by Sean M. Ryno, Cheng Zhong, Haitao Sun, see /legacy/aw_tuning.py for a certain mol, get tuned w default keywords for gaussian ‘scf=(xqc,fermi,noincfock,ndamp=35,conver=6,vshift=500,novaracc)’ dev-ing
- class d3tales_api.Workflows.wtuning.WtuningJob(func='uLC-wHPBE', basis='def2tzvp', name='', nproc=16, mem=50, n_charge=0, n_spin=1, wdir='./', rps={'scf': {'conver': '6', 'fermi': '', 'ndamp': '35', 'noincfock': '', 'novaracc': '', 'vshift': '500', 'xqc': ''}}, scheme='Jh', wbmin=0.05, wbmax=0.5, abmin=0.05, abmax=0.5, gauss_cmd='g16')[source]
Bases:
object- __init__(func='uLC-wHPBE', basis='def2tzvp', name='', nproc=16, mem=50, n_charge=0, n_spin=1, wdir='./', rps={'scf': {'conver': '6', 'fermi': '', 'ndamp': '35', 'noincfock': '', 'novaracc': '', 'vshift': '500', 'xqc': ''}}, scheme='Jh', wbmin=0.05, wbmax=0.5, abmin=0.05, abmax=0.5, gauss_cmd='g16')[source]
- property alpha_iopstr
- property beta_iopstr
- property iop_route_params
- omega_FindC()[source]
Calculate scheme value from extracted data Set the optimization criterion (the value to minimize), available options are: J2—((HOMO-IP)^2+(A_HOMO+EA)^2) Jh—(HOMO-IP) Jl—(LUMO+EA) Jn2—((HOMO-IP)^2+(LUMO+EA)^2) O2—((A_HOMO-LUMO)^2+(C_LUMO-HOMO)^2) :return: Jn, Jl, Jh value (depending on scheme)
- static omega_extract(fn)[source]
Pull important data from Log Files after run :param fn: Filename of Log File to be read :return: Energies of Molecule, HOMO and LUMO in eV
- omega_format()[source]
Format IOp strings based off of omega value, then update route parameters dictionary and input filenames
- omega_gauss_do()[source]
Run Gaussian in subprocess and wait for termination. Extract data from output when done
- property omega_iopstr