atomate.qchem.workflows.base package¶
Submodules¶
atomate.qchem.workflows.base.double_FF_opt module¶
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atomate.qchem.workflows.base.double_FF_opt.get_wf_double_FF_opt(molecule, pcm_dielectric, max_cores=32, qchem_input_params=None, name='douple_FF_opt', qchem_cmd='>>qchem_cmd<<', db_file='>>db_file<<', **kwargs)¶ Returns a workflow to the torsion potential for a molecule.
- Firework 1 : write QChem input for an FF optimization,
- run FF_opt QCJob, parse directory and insert into db, pass relaxed molecule to fw_spec and on to fw2,
- Firework 2 : write QChem input for an optimization in the
- presence of a PCM, using the molecule passed from fw1,
run FF_opt QCJob, parse directory and insert into db
- Args:
molecule (Molecule): input molecule to be optimized and run. pcm_dielectric (float): The PCM dielectric constant. max_cores (int): Maximum number of cores to parallelize over.
Defaults to 32.- qchem_input_params (dict): Specify kwargs for instantiating
- the input set parameters.
qchem_cmd (str): Command to run QChem. db_file (str): path to file containing the database credentials. kwargs (keyword arguments): additional kwargs to be passed to Workflow
- Returns:
- Workflow
atomate.qchem.workflows.base.torsion_potential module¶
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atomate.qchem.workflows.base.torsion_potential.get_wf_torsion_potential(molecule, atom_indexes, angles, rem, name='torsion_potential', qchem_cmd='qchem', multimode='openmp', input_file='mol.qin', output_file='mol.qout', max_cores=32, db_file=None, **kwargs)¶ Returns a workflow to the torsion potential for a molecule.
- Firework 1 : write QChem input for an optimization,
- run Qchem, parse output and insert into db, pass relaxed molecule to fw_spec and on to fw2,
- Firework 2 : rotate molecule torsion to a particular angle,
- write QChem input for an optimization, run Qchem, parse output and insert into db
last Firework : add analysis code at some point
- Args:
molecule (Molecule): Input molecule (needs to be a pymatgen molecule object) atom_indexes (list of ints): list of atom indexes in the torsion angle to be rotated (i.e. [6, 8, 9, 10]) angles (list of floats): list of all the torsion angles to run rem (list of two rem dictionaries): a list with two rem dictionaries, one for the first optimization and one for the second constrained optimization name (str): Name for the workflow. qchem_cmd (str): Command to run QChem. Defaults to qchem. multimode (str): Parallelization scheme, either openmp or mpi. input_file (str): Name of the QChem input file. Defaults to mol.qin. output_file (str): Name of the QChem output file. Defaults to mol.qout. max_cores (int): Maximum number of cores to parallelize over. Defaults to 32. qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
For example, if you want to change the DFT_rung, you should provide: {“DFT_rung”: …}. Defaults to None.db_file (str): Path to file specifying db credentials to place output parsing. **kwargs: Other kwargs that are passed to Firework.__init__.
Returns: Workflow