pymatgen.io.cif module

Wrapper classes for Cif input and output from Structures.

class CifBlock(data, loops, header)[source]

Bases: object

Object for storing cif data. All data is stored in a single dictionary. Data inside loops are stored in lists in the data dictionary, and information on which keys are grouped together are stored in the loops attribute.

Parameters
  • data – dict or OrderedDict of data to go into the cif. Values should be convertible to string, or lists of these if the key is in a loop

  • loops – list of lists of keys, grouped by which loop they should appear in

  • header – name of the block (appears after the data_ on the first line)

classmethod from_string(string)[source]

Reads CifBlock from string.

Parameters

string – String representation.

Returns

CifBlock

maxlen = 70[source]
class CifFile(data, orig_string=None, comment=None)[source]

Bases: object

Reads and parses CifBlocks from a .cif file or string

Parameters
  • data (OrderedDict) – Of CifBlock objects.å

  • orig_string (str) – The original cif string.

  • comment (str) – Comment string.

classmethod from_file(filename)[source]

Reads CifFile from a filename.

Parameters

filename – Filename

Returns

CifFile

classmethod from_string(string)[source]

Reads CifFile from a string.

Parameters

string – String representation.

Returns

CifFile

class CifParser(filename, occupancy_tolerance=1.0, site_tolerance=0.0001)[source]

Bases: object

Parses a CIF file. Attempts to fix CIFs that are out-of-spec, but will issue warnings if corrections applied. These are also stored in the CifParser’s errors attribute.

Parameters
  • filename (str) – CIF filename, bzipped or gzipped CIF files are fine too.

  • occupancy_tolerance (float) – If total occupancy of a site is between 1 and occupancy_tolerance, the occupancies will be scaled down to 1.

  • site_tolerance (float) – This tolerance is used to determine if two sites are sitting in the same position, in which case they will be combined to a single disordered site. Defaults to 1e-4.

as_dict()[source]
Returns

MSONable dict

static from_string(cif_string, occupancy_tolerance=1.0)[source]

Creates a CifParser from a string.

Parameters
  • cif_string (str) – String representation of a CIF.

  • occupancy_tolerance (float) – If total occupancy of a site is between 1 and occupancy_tolerance, the occupancies will be scaled down to 1.

Returns

CifParser

get_bibtex_string()[source]

Get BibTeX reference from CIF file. :param data: :return: BibTeX string

get_lattice(data, length_strings='a', 'b', 'c', angle_strings='alpha', 'beta', 'gamma', lattice_type=None)[source]

Generate the lattice from the provided lattice parameters. In the absence of all six lattice parameters, the crystal system and necessary parameters are parsed

get_magsymops(data)[source]

Equivalent to get_symops except for magnetic symmetry groups. Separate function since additional operation for time reversal symmetry (which changes magnetic moments on sites) needs to be returned.

get_structures(primitive=True, symmetrized=False)[source]

Return list of structures in CIF file. primitive boolean sets whether a conventional cell structure or primitive cell structure is returned.

Parameters
  • primitive (bool) – Set to False to return conventional unit cells. Defaults to True. With magnetic CIF files, will return primitive magnetic cell which may be larger than nuclear primitive cell.

  • symmetrized (bool) – If True, return a SymmetrizedStructure which will include the equivalent indices and symmetry operations used to create the Structure as provided by the CIF (if explicit symmetry operations are included in the CIF) or generated from information in the CIF (if only space group labels are provided). Note that currently Wyckoff labels and space group labels or numbers are not included in the generated SymmetrizedStructure, these will be notated as “Not Parsed” or -1 respectively.

Returns

List of Structures.

get_symops(data)[source]

In order to generate symmetry equivalent positions, the symmetry operations are parsed. If the symops are not present, the space group symbol is parsed, and symops are generated.

property has_errors[source]

Whether there are errors/warnings detected in CIF parsing.

Type

return

static parse_magmoms(data, lattice=None)[source]

Parse atomic magnetic moments from data dictionary

static parse_oxi_states(data)[source]

Parse oxidation states from data dictionary

class CifWriter(struct, symprec=None, write_magmoms=False, significant_figures=8, angle_tolerance=5.0, refine_struct=True)[source]

Bases: object

A wrapper around CifFile to write CIF files from pymatgen structures.

Parameters
  • struct (Structure) – structure to write

  • symprec (float) – If not none, finds the symmetry of the structure and writes the cif with symmetry information. Passes symprec to the SpacegroupAnalyzer. See also refine_struct.

  • write_magmoms (bool) – If True, will write magCIF file. Incompatible with symprec

  • significant_figures (int) – Specifies precision for formatting of floats. Defaults to 8.

  • angle_tolerance (float) – Angle tolerance for symmetry finding. Passes angle_tolerance to the SpacegroupAnalyzer. Used only if symprec is not None.

  • refine_struct – Used only if symprec is not None. If True, get_refined_structure is invoked to convert input structure from primitive to conventional.

property ciffile[source]

CifFile associated with the CifWriter.

Type

Returns

write_file(filename)[source]

Write the cif file.

str2float(text)[source]

Remove uncertainty brackets from strings and return the float.