pymatgen.io.cif module
Wrapper classes for Cif input and output from Structures.
- class CifBlock(data, loops, header)[source]
Bases:
objectObject 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 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)
- class CifFile(data, orig_string=None, comment=None)[source]
Bases:
objectReads and parses CifBlocks from a .cif file or string
- Parameters:
data (dict) – Of CifBlock objects.
orig_string (str) – The original cif string.
comment (str) – Comment string.
- class CifParser(filename, occupancy_tolerance=1.0, site_tolerance=0.0001, frac_tolerance=0.0001)[source]
Bases:
objectParses 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.
frac_tolerance (float) – This tolerance is used to determine is a coordinate should be rounded to an ideal value. E.g., 0.6667 is rounded to 2/3. This is desired if symmetry operations are going to be applied. However, for very large CIF files, this may need to be set to 0.
- static from_string(cif_string, **kwargs)[source]
Creates a CifParser from a string.
- Parameters:
cif_string (str) – String representation of a CIF.
**kwargs – Passthrough of all kwargs supported by CifParser.
- 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
- static get_lattice_no_exception(data, length_strings=('a', 'b', 'c'), angle_strings=('alpha', 'beta', 'gamma'), lattice_type=None)[source]
Take a dictionary of CIF data and returns a pymatgen Lattice object
- Parameters:
data – a dictionary of the CIF file
length_strings – The strings that are used to identify the length parameters in the CIF file.
angle_strings – The strings that are used to identify the angles in the CIF file.
lattice_type – The type of lattice. This is a string, and can be any of the following:
- Returns:
Lattice object
- 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
- class CifWriter(struct, symprec=None, write_magmoms=False, significant_figures=8, angle_tolerance=5.0, refine_struct=True)[source]
Bases:
objectA 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.