PRMContainer¶

FOX.io.read_prm¶

A class for reading and generating .prm parameter files.

Index¶

`PRMContainer`([filename, atoms, bonds, …])	A container for managing prm files.
`PRMContainer.read`(filename[, encoding])	Construct a new instance from this object’s class by reading the content of filename.
`PRMContainer.write`([filename, encoding])	Write the content of this instance to filename.
`PRMContainer.overlay_mapping`(prm_name, param_df)	Update a set of parameters, prm_name, with those provided in param_df.
`PRMContainer.overlay_cp2k_settings`(cp2k_settings)	Extract forcefield information from PLAMS-style CP2K settings.

API¶

class FOX.io.read_prm.PRMContainer(filename=None, atoms=None, bonds=None, angles=None, dihedrals=None, improper=None, impropers=None, nonbonded=None, nonbonded_header=None, nbfix=None, hbond=None)[source]¶

A container for managing prm files.

pd_printoptions¶

A dictionary with Pandas print options. See Options and settings.

Type:	`dict` [`str`, `object`], private

CP2K_TO_PRM¶

A mapping providing tools for converting CP2K settings to .prm-compatible values. See CP2K_TO_PRM.

Type:	`Mapping` [`str`, `PRMMapping`]

classmethod PRMContainer.read(filename, encoding=None, **kwargs)[source]¶

Construct a new instance from this object’s class by reading the content of filename.

Parameters:

filename (str, bytes, os.PathLike or a file object) – The path+filename or a file object of the to-be read .psf file. In practice, any iterable can substitute the role of file object as long iteration returns either strings or bytes (see encoding).
encoding (str, optional) – Encoding used to decode the input (e.g. "utf-8"). Only relevant when a file object is supplied to filename and the datastream is not in text mode.
**kwargs (Any) – Optional keyword arguments that will be passed to both PRMContainer._read_iterate() and PRMContainer._read_postprocess().

See also

PRMContainer._write_iterate(): Write the content of this instance to an opened datastream.
PRMContainer._get_writer(): Take a write() method and ensure its first argument is properly encoded.

Return type:	`None`

PRMContainer.overlay_mapping(prm_name, param_df, units=None)[source]¶

Update a set of parameters, prm_name, with those provided in param_df.

Examples

>>> from FOX import PRMContainer

>>> prm = PRMContainer(...)

>>> param_dict = {}
>>> param_dict['epsilon'] = {'Cd Cd': ..., 'Cd Se': ..., 'Se Se': ...}  # epsilon
>>> param_dict['sigma'] = {'Cd Cd': ..., 'Cd Se': ..., 'Se Se': ...}  # sigma

>>> units = ('kcal/mol', 'angstrom')  # input units for epsilon and sigma

>>> prm.overlay_mapping('nonbonded', param_dict, units=units)

Parameters:

prm_name (str) – The name of the parameter of interest. See the keys of PRMContainer.CP2K_TO_PRM for accepted values.
param_df (pandas.DataFrame or nested Mapping) – A DataFrame or nested mapping with the to-be added parameters. The keys should be a subset of PRMContainer.CP2K_TO_PRM[prm_name]["columns"]. If the index/nested sub-keys consist of strings then they’ll be split and turned into a pandas.MultiIndex. Note that the resulting values are not sorted.
units (Iterable [str], optional) – An iterable with the input units of each column in param_df. If None, default to the defaults specified in PRMContainer.CP2K_TO_PRM[prm_name]["unit"].

Return type:

None

PRMContainer.overlay_cp2k_settings(cp2k_settings)[source]¶

Extract forcefield information from PLAMS-style CP2K settings.

Performs an inplace update of this instance.

Examples

Example input value for cp2k_settings. In the provided example the cp2k_settings are directly extracted from a CP2K .inp file.

>>> import cp2kparser  # https://github.com/nlesc-nano/CP2K-Parser

>>> filename = str(...)

>>> cp2k_settings: dict = cp2kparser.read_input(filename)
>>> print(cp2k_settings)
{'force_eval': {'mm': {'forcefield': {'nonbonded': {'lennard-jones': [...]}}}}}

Parameters:	cp2k_settings (`Mapping`) – A Mapping with PLAMS-style CP2K settings.