mispr.hybrid.workflows package¶

Submodules¶

mispr.hybrid.workflows.core module¶

Define the DFT-MD hybrid workflow.

mispr.hybrid.workflows.core.run_hybrid_calcs(mol_operation_type, mol, mol_type, mol_data, box_data, ff_method=None, ff_params=None, mixture_type='number of molecules', db=None, name='hybrid_calculation', working_dir=None, opt_gaussian_inputs=None, freq_gaussian_inputs=None, esp_gaussian_inputs=None, solvent_gaussian_inputs=None, solvent_properties=None, cart_coords=True, oxidation_states=None, skips=None, box_data_type='cubic', data_file_name='data.mixture', analysis_list=None, analysis_settings=None, **kwargs)[source]¶

mispr.hybrid.workflows.nmr module¶

Define the DFT-MD workflow that extracts solvation structures and computes their nuclear magnetic resonances.

Return a workflow to run hybrid DFT/MD calculations, extract categorize atomic clusters around a particle of interest, and run the NMR calculations for the clusters that have the highest frequency of occurrence in solution.

Parameters:¶

mol_operation_type : list of str¶

Operation to perform for each molecule composing the liquid solution in order to process the input structure format. Length should correspond to the number of molecules/species composing the liquid solution. Supported commands:

get_from_mol: If the input is a pymatgen Molecule object.
get_from_file: If the input is any file format supported by Openabel and pymatgen.
get_from_gout_file: If the input is a Gaussian output file.
get_from_str: If the input is a string.
get_from_mol_db: If the input is an InChI representation of the molecule to be used to query the database.
get_from_gout: If the input is a pymatgen GaussianOutput object.
get_from_run_dict: If the input is a GaussianOutput dictionary.
get_from_run_id: If the input is a MongoDB document ID to be used to query the database.
get_from_run_query: If the input is a dictionary with criteria to search the database: e.g.
```
{'inchi': inchi,
 'type': type,
 'functional': func, ...}
```
get_from_pubchem: If the input is a common name for the molecule to be used in searching the PubChem database.
derive_molecule: Used for deriving a molecule by attaching a functional group at a site and the corresponding mol input should be a dictionary, e.g.
```
{'operation_type': <mol_operation_type for the base structure>,
 'mol': <base_mol>,
 'func_grp': func_group_name, ...}
```
link_molecules: Used for linking two structures by forming a bond at specific sites and the corresponding mol input should be a dictionary, e.g.
```
{'operation_type': ['get_from_file', 'get_from_mol_db'],
 'mol': ['mol1.xyz', 'mol_inchi'],
 'index': [3, 5],
 'bond_order': 1}
```

mol : list¶

Sources of structures making up the liquid solution, e.g. file path if mol_operation_type is specified as “get_from_file”, InChI string if mol_operation_type is specified as “get_from_mol_db”, etc.

Important

Order should match that in mol_operation_type.

mol_type : list of str¶

Type of each structure composing the liquid solution. Supported types: “Solvents”, “Solutes”. Used for calculating the number of molecules of each type if this information is not provided.

mol_data : list of int or list of dict¶

Format depends on mixture_type input. If mixture_type is “number of molecules”, mol_data should be a list of the number of molecules of each type. If mixture_type is “concentration”, mol_data should be a list of dict, where each dictionary should follow the format:

{'Initial Molarity': molarity_i,
 'Final Molarity': molarity_f,
 'Density': density,
 'Molar Weight': molar_weight
}

box_data : float, int, list (3,2), array (3,2), or LammpsBox¶

Definitions for box size. See box_data_type for info how to define this parameter.

ff_method : list of str, optional¶

Operation to perform for each molecule composing the liquid solution in order to process the force field parameters. Can be “get_from_esp”, “get_from_prmtop”, “get_from_dict”, “get_from_opls”. Defaults to “get_from_esp” for all molecules.

ff_params : list of str or dict, optional¶

Sources of the force field parameters for each molecule type; type depends on what is specified in the ff_method input; if “get_from_esp” is used, the corresponding ff_param should be an empty dictionary since the path to the ESP file is automatically detected from the ESP calculations that is performed at the beginning of the workflow; if “get_from_prmtop” is used, the corresponding ff_param should be the path to the prmtop file; if “get_from_dict” is used, the corresponding ff_param should be a dictionary, e.g.:

{
    "Labels": ["mg"],
    "Masses": OrderedDict({"mg": 24.305}),
    "Nonbond": [[0.8947000005260684, 1.412252647723565]],
    "Bonds": [],
    "Angles": [],
    "Dihedrals": [],
    "Impropers": [],
    "Improper Topologies": None,
    "Charges": np.asarray([2.0]),
}

If “get_from_opls” is used, the corresponding ff_param should be the path to the molecule PDB file.

mixture_type : str, optional¶

“concentration” or “number of molecules”; defaults to “number of molecules”.

db : str or dict, optional¶

Database credentials; could be provided as the path to the “db.json” file or in the form of a dictionary; if none is provided, attempts to get it from the configuration files.

name : str, optional¶

Name of the workflow. Defaults to “hybrid_calculation”.

working_dir : str, optional¶

Path of the working directory where any required input files can be found and output will be created.

opt_esp_gaussian_inputs : dict, optional¶

Dictionary of Gaussian input parameters for the optimization step of the ESP workflow; e.g.:

{
    "functional": "B3LYP",
    "basis_set": "6-31G(d)",
    "route_parameters": {"Opt": None},
    "link0_parameters": {
        "%chk": "checkpoint.chk",
        "%mem": "45GB",
        "%NProcShared": "24"}
}

The above default parameters will be used if not specified.

freq_esp_gaussian_inputs : dict, optional¶

Dictionary of Gaussian input parameters for the frequency step of the ESP workflow; default parameters will be used if not specified.

esp_gaussian_inputs : dict, optional¶

Sictionary of Gaussian input parameters for the ESP step of the ESP workflow; default parameters will be used if not specified.

opt_nmr_gaussian_inputs : dict, optioanl¶

Dictionary of Gaussian input parameters for the optimization step of the NMR workflow; default parameters will be used if not specified.

freq_nmr_gaussian_inputs : dict, optional¶

Dictionary of Gaussian input parameters for the frequency step of the NMR workflow; default parameters will be used if not specified.

nmr_gaussian_inputs : dict, optional¶

Dictionary of Gaussian input parameters for the NMR step of the NMR workflow; default parameters will be used if not specified.

esp_solvent_gaussian_inputs : str, optional¶

Gaussian input parameters corresponding to the implicit solvent model to be used in the ESP calculations, if any; e.g.:

"(Solvent=TetraHydroFuran)"

These parameters should only be specified here and not included in the main gaussian_inputs dictionary for each job (i.e. opt_gaussian_inputs, freq_esp_gaussian_inputs, etc.).

esp_solvent_properties : dict, optional¶

Additional input parameters to be used in the ESP calculations and relevant to the solvent model, if any; e.g., {“EPS”:12}.

nmr_solvent_gaussian_inputs : str, optional¶

Gaussian input parameters corresponding to the implicit solvent model to be used in the NMR calculations, if any; e.g.:

"(Solvent=TetraHydroFuran)"

These parameters should only be specified here and not included in the main gaussian_inputs dictionary for each job (i.e. opt_nmr_gaussian_inputs, freq_nmr_gaussian_inputs, etc.).

nmr_solvent_properties : dict, optional¶

Additional input parameters to be used in the NMR calculations and relevant to the solvent model, if any; e.g., {“EPS”:12}.

cart_coords : bool, optional¶

Uses cartesian coordinates in writing Gaussian input files if set to True, otherwise uses z-matrix. Defaults to True.

oxidation_states : dict, optional¶

Dictionary of oxidation states that can be used in setting the charge and spin multiplicity of the clusters extracted from MD simulations to be used in the NMR workflow.

skips : list of lists, optional¶

Type of DFT calculation to skip in the ESP workflow for each molecule; e.g. [“opt”, “freq”], [“opt”], [“freq”], or [].

box_data_type : str, optional¶

Can be one of the following: “cubic”, “rectangular”, or “LammpsBox”. If “cubic”, box_data must be a float or int; if “rectangular”, box_data must be an array-like with size (3,2); if “LammpsBox”, box_data must be a pymatgen.io.lammps.data.LammpsBox object. Defaults to “cubic”.

data_file_name : str, optional¶

Name of the LAMMPS data file to create and use; defaults to “data.mixture”.

analysis_list : list of str, optional¶

Type of MD analysis to perform after the MD simulations are finished; e.g.: [“diffusion”, “rdf”, “cn”, “clusters”] if user wants to perform diffusion, RDF, coordination number, and cluster analysis.

analysis_settings : list of dict, optional¶

Settings of the MD analysis steps; please refer to the mdproptools documentation for details of inputs used in the analysis functions; order of settings should correspond to the order used in analysis_list.

kwargs : keyword arguments¶

Additional kwargs to be passed to the workflow; e.g.: lammps recipe and recipe_settings; the defaults for these inputs are specified in the mispr/lammps/defaults.py.

Returns:¶

Workflow

mispr.hybrid.workflows package¶

Submodules¶

mispr.hybrid.workflows.core module¶

mispr.hybrid.workflows.nmr module¶

Module contents¶