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

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

CP2K_TO_PRM: :class:`Mapping<collections.abc.Mapping>` [:class:`str`, :class:`PRMMapping<FOX.io.cp2k_to_prm.PRMMapping>`]

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

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._read_iterate()
An abstract method for parsing the opened file in PRMContainer.read().
PRMContainer._read_postprocess()
Post processing the class instance created by PRMContainer.read().
Return type:PRMContainer
PRMContainer.write(filename=None, encoding=None, **kwargs)[source]

Write the content of this instance to 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. Contrary to _read_postprocess(), file objects can not be substituted for generic iterables.
  • 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 _write_iterate().

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:
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.

See also

PRMMapping()
PRMMapping A mapping providing tools for converting CP2K settings to .prm-compatible values.
Return type:None