pymatgen.io.res module

Provides parsing and read/write support for ShelX .res files as produced by the AIRSS code.

Converting from and back to pymatgen objects is expected to be reversible, i.e. you should get the same Structure or ComputedStructureEntry back. On the other hand, converting from and back to a string/file is not guaranteed to be reversible, i.e. a diff on the output would not be empty. The difference should be limited to whitespace, float precision, and the REM entries.

class AirssProvider(res: Res, parse_rems: Literal['gentle', 'strict'] = 'gentle')[source]

Bases: ResProvider

Provides access to the res file as does ResProvider. This class additionally provides access to fields in the TITL entry and various other fields found in the REM entries that AIRSS puts in the file. Values in the TITL entry that AIRSS could not get end up as 0. If the TITL entry is malformed, empty, or missing then attempting to construct this class from a res file will raise a ResError.

While AIRSS supports a number of geometry and energy solvers, CASTEP is the default. As such, fetching the information from the REM entries is only supported if AIRSS was used with CASTEP. The other properties that get put in the TITL should still be accessible even if CASTEP was not used.

The parse_rems attribute controls whether functions that fail to retrieve information from the REM entries should return None. If this is set to "strict", then a ParseError may be raised, but the return value will not be None. If it is set to anything else then None will be returned instead of raising an exception. This setting applies to all methods of this class that are typed to return an Optional type. Default is "gentle".

The from_str() and from_file() methods should be used instead of constructing this directly.

property appearances: int[source]

This is sometimes the number of times a structure was found in an AIRSS search. Using the cryan tool that comes with AIRSS may be a better approach than relying on this property.

as_dict(verbose: bool = True) dict[str, Any][source]

Get dict with title fields, structure and rems of this AirssProvider.

property energy: float[source]

Energy of the structure. With CASTEP, this is usually the enthalpy and is in eV.

property entry: ComputedStructureEntry[source]

Get this res file as a ComputedStructureEntry.

classmethod from_file(filename: str, parse_rems: Literal['gentle', 'strict'] = 'gentle') AirssProvider[source]

Construct a Provider from a file.

classmethod from_str(string: str, parse_rems: Literal['gentle', 'strict'] = 'gentle') AirssProvider[source]

Construct a Provider from a string.

get_airss_version() tuple[str, datetime.date] | None[source]

Retrieves the version of AIRSS that was used along with the build date (not compile date).

Returns:

(version string, date)

get_castep_version() str | None[source]

Retrieves the version of CASTEP that the res file was computed with from the REM entries.

Returns:

version string

get_cut_grid_gmax_fsbc() tuple[float, float, float, str] | None[source]

Retrieves the cut-off energy, grid scale, Gmax, and finite basis set correction setting from the REM entries.

Returns:

(cut-off, grid scale, Gmax, fsbc)

get_func_rel_disp() tuple[str, str, str] | None[source]

Retrieves the functional, relativity scheme, and dispersion correction from the REM entries.

Returns:

(functional, relativity, dispersion)

get_mpgrid_offset_nkpts_spacing() tuple[tuple[int, int, int], tuple[float, float, float], int, float] | None[source]

Retrieves the MP grid, the grid offsets, number of kpoints, and maximum kpoint spacing.

Returns:

(MP grid), (offsets), No. kpts, max spacing)

get_pspots() dict[str, str][source]

Retrieves the OTFG pseudopotential string that can be used to generate the pseudopotentials used in the calculation.

Returns:

dict[specie, potential]

get_run_start_info() tuple[datetime.date, str] | None[source]

Retrieves the run start date and the path it was started in from the REM entries.

Returns:

(date, path)

property integrated_absolute_spin_density: float[source]

Corresponds to the last Integrated |Spin Density| in the CASTEP file.

property integrated_spin_density: float[source]

Corresponds to the last Integrated Spin Density in the CASTEP file.

property pressure: float[source]

Pressure for the run. This is in GPa if CASTEP was used.

property seed: str[source]

The seed name, typically also the name of the res file.

property spacegroup_label: str[source]

The Hermann-Mauguin notation of the spacegroup with ascii characters. So no. 225 would be Fm-3m, and no. 194 would be P6_3/mmc.

property volume: float[source]

Volume of the structure. This is in cubic Angstroms if CASTEP was used.

exception ParseError[source]

Bases: RuntimeError

This exception indicates a problem was encountered during parsing due to unexpected formatting.

exception ResError[source]

Bases: ValueError

This exception indicates a problem was encountered while trying to retrieve a value or perform an action that a provider for the res file does not support.

class ResIO[source]

Bases: object

Class providing convenience methods for converting a Structure or ComputedStructureEntry to/from a string or file in the res format as used by AIRSS.

Note: Converting from and back to pymatgen objects is expected to be reversible, i.e. you should get the same Structure or ComputedStructureEntry back. On the other hand, converting from and back to a string/file is not guaranteed to be reversible, i.e. a diff on the output would not be empty. The difference should be limited to whitespace, float precision, and the REM entries.

If the TITL entry doesn’t exist or is malformed or empty, then you can only get a Structure. Attempting to get an Entry will raise a ResError.

classmethod entry_from_file(filename: str) ComputedStructureEntry[source]

Produce a pymatgen ComputedStructureEntry from a res file.

classmethod entry_from_str(string: str) ComputedStructureEntry[source]

Produce a pymatgen ComputedStructureEntry from contents of a res file.

classmethod entry_to_file(entry: ComputedStructureEntry, filename: str) None[source]

Write a pymatgen ComputedStructureEntry to a res file.

classmethod entry_to_str(entry: ComputedStructureEntry) str[source]

Produce the contents of a res file from a pymatgen ComputedStructureEntry.

classmethod structure_from_file(filename: str) Structure[source]

Produces a pymatgen Structure from a res file.

classmethod structure_from_str(string: str) Structure[source]

Produces a pymatgen Structure from contents of a res file.

classmethod structure_to_file(structure: Structure, filename: str) None[source]

Write a pymatgen Structure to a res file.

classmethod structure_to_str(structure: Structure) str[source]

Produce the contents of a res file from a pymatgen Structure.

class ResProvider(res: Res)[source]

Bases: MSONable

Provides access to elements of the res file in the form of familiar pymatgen objects.

The from_str() and from_file() methods should be used instead of constructing this directly.

classmethod from_file(filename: str) ResProvider[source]

Construct a Provider from a file.

classmethod from_str(string: str) ResProvider[source]

Construct a Provider from a string.

property lattice: Lattice[source]

Construct a Lattice from the res file.

property rems: list[str][source]

The full list of REM entries contained within the res file.

property sites: list[pymatgen.core.sites.PeriodicSite][source]

Construct a list of PeriodicSites from the res file.

property structure: Structure[source]

Construct a Structure from the res file.

class ResWriter(entry: Structure | ComputedStructureEntry)[source]

Bases: object

This class provides a means to write a Structure or ComputedStructureEntry to a res file.

This class can be constructed from either a pymatgen Structure or ComputedStructureEntry object.

property string: str[source]

The contents of the res file.

write(filename: str) None[source]

Write the res datat to a file.