atomate.qchem.fireworks package¶

Submodules¶

atomate.qchem.fireworks.core module¶

class atomate.qchem.fireworks.core.FrequencyFlatteningOptimizeFW(molecule=None, name='frequency flattening structure optimization', qchem_cmd='qchem', multimode='openmp', input_file='mol.qin', output_file='mol.qout', max_cores=32, qchem_input_params=None, max_iterations=10, max_molecule_perturb_scale=0.3, reversed_direction=False, db_file=None, parents=None, **kwargs)¶

Bases: fireworks.core.firework.Firework

__init__(molecule=None, name='frequency flattening structure optimization', qchem_cmd='qchem', multimode='openmp', input_file='mol.qin', output_file='mol.qout', max_cores=32, qchem_input_params=None, max_iterations=10, max_molecule_perturb_scale=0.3, reversed_direction=False, db_file=None, parents=None, **kwargs)¶

Iteratively optimize the given structure and flatten imaginary frequencies to ensure that the resulting structure is a true minima and not a saddle point.

Args:

molecule (Molecule): Input molecule. name (str): Name for the Firework. 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.

max_iterations (int): Number of perturbation -> optimization -> frequency: iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float): The maximum scaled perturbation that can be: applied to the molecule. Defaults to 0.3.
reversed_direction (bool): Whether to reverse the direction of the vibrational: frequency vectors. Defaults to False.

db_file (str): Path to file specifying db credentials to place output parsing. parents ([Firework]): Parents of this particular Firework. **kwargs: Other kwargs that are passed to Firework.__init__.

class atomate.qchem.fireworks.core.OptimizeFW(molecule=None, name='structure optimization', qchem_cmd='qchem', multimode='openmp', input_file='mol.qin', output_file='mol.qout', max_cores=32, qchem_input_params=None, db_file=None, parents=None, **kwargs)¶

Bases: fireworks.core.firework.Firework

__init__(molecule=None, name='structure optimization', qchem_cmd='qchem', multimode='openmp', input_file='mol.qin', output_file='mol.qout', max_cores=32, qchem_input_params=None, db_file=None, parents=None, **kwargs)¶

Optimize the given structure.