allomorph

Nanoparticle structure generation toolkit.

A package for generating monometallic to trimetallic nanoparticle structural datasets for machine learning applications.

Submodules

`load_ele_dict_from_file`(path)	Load an element dictionary from a JSON file.
`parse_ele_comb`(ele_comb[, ele_dict])	Parse a concatenated element combination string into individual symbols.
`validate_ele_dict`(ele_dict)	Validate a user-supplied element dictionary.
`gen_bnp`(obj, element1, element2, shape, ratio2, ...[, ...])	Generates a BNP alloy structure based on specified distribution type.
`write_bnp`(element1, element2, diameter, shape, ratio2, ...)	Generates and writes a specific BNP alloy structure.
`gen_hard_core_shell`(shell_atoms, core_atoms, del_cutoff)	Generate a hard core-shell structure by combining shell and core atoms.
`write_hard_core_shell`([replace, vis, ele_dict])	Orchestrates the generation of hard core-shell BNPs.
`gen_mnp`(shape, diameter, element, latConst[, ...])	Generates a monometallic nanoparticle structure based on specified shape.
`write_mnp`(element, diameter, lat_const, shape[, ...])	Write a monometallic nanoparticle to LAMMPS data and XYZ files.
`gen_tnp`(obj, element1, element2, element3, ele1Ratio, ...)	Generates a TNP alloy structure based on specified distribution types.
`write_tnp`(element1, element2, element3, diameter, ...)	Generates and writes TNP alloy structures.

allomorph.SHAPE_LIST = ['OT', 'SP', 'IC', 'CU', 'DH', 'TH', 'RD', 'TO', 'CO'][source]

allomorph.TNP_DISTRIB_LIST = ['L10R', 'CS', 'CL10S', 'CRALS', 'RRAL', 'CSRAL', 'CSL10', 'CRSR', 'LL10'][source]

allomorph.load_ele_dict_from_file(path)[source]

Load an element dictionary from a JSON file.

Parameters:: path – Path to a JSON file containing the element dictionary.
Returns:: Validated element dictionary.

allomorph.parse_ele_comb(ele_comb, ele_dict=None)[source]

Parse a concatenated element combination string into individual symbols.

Parameters:

ele_comb – String like ‘AuPtPd’ or ‘CuAgAu’.
ele_dict – Optional element dictionary to use for matching. If None, the built-in ELE_DICT is used.

Returns:

List of element symbols, e.g. [‘Au’, ‘Pt’, ‘Pd’].

Raises:

ValueError – If the string cannot be parsed.

allomorph.validate_ele_dict(ele_dict)[source]

Validate a user-supplied element dictionary.

Parameters:: ele_dict – Dictionary mapping element symbols to property dicts.
Returns:: The validated dictionary.
Raises:: ValueError – If required keys are missing or invalid.

allomorph.gen_bnp(obj, element1, element2, shape, ratio2, distrib, rseed, ele_dict=None)[source]: Generates a BNP alloy structure based on specified distribution type.

allomorph.write_bnp(element1, element2, diameter, shape, ratio2, distrib, replace=False, vis=False, ele_dict=None)[source]: Generates and writes a specific BNP alloy structure.

allomorph.gen_hard_core_shell(shell_atoms, core_atoms, del_cutoff)[source]: Generate a hard core-shell structure by combining shell and core atoms. Shell atoms overlapping with core atoms within del_cutoff are deleted.

allomorph.write_hard_core_shell(replace=False, vis=False, ele_dict=None)[source]: Orchestrates the generation of hard core-shell BNPs. Iterates through elements, sizes, and shapes.

allomorph.gen_mnp(shape, diameter, element, latConst, custom_shapes=None)[source]: Generates a monometallic nanoparticle structure based on specified shape.

allomorph.write_mnp(element, diameter, lat_const, shape, replace=False, vis=False, custom_shapes=None)[source]: Write a monometallic nanoparticle to LAMMPS data and XYZ files.

allomorph.gen_tnp(obj, element1, element2, element3, ele1Ratio, ele2Ratio, ele3Ratio, distrib1, distrib2, rseed=0, shape=None, ele_dict=None)[source]: Generates a TNP alloy structure based on specified distribution types.

allomorph.write_tnp(element1, element2, element3, diameter, shape, ele1Ratio, ele2Ratio, ele3Ratio, distrib1, distrib2, rep1=0, replace=False, vis=False, ele_dict=None)[source]: Generates and writes TNP alloy structures.