dara.cif2str module

dara.cif2str module#

Convert CIF to Str format for BGMN.

exception CIF2StrError[source]#

Bases: Exception

CIF2Str error.

check_wyckoff(spacegroup_setting, structure)[source]#

Check if a given spacegroup setting is valid for a structure.

Parameters:

  • spacegroup_setting (dict[str, Any]) – the spacegroup setting

  • structure (SymmetrizedStructure) – the symmetrized structure

Return type:

tuple[list[dict[str, Any]], int]

Returns:

the settings of the elements and the number of errors

cif2str(cif_path, phase_name_suffix='', working_dir=None, *, lattice_range=0.1, gewicht='0_0', rp=4, k1='0_0^0.01', k2='0_0^0.01', b1='0_0^0.01', lebail=False)[source]#

Convert CIF to Str format.

Parameters:

  • cif_path (Path) – the path to the CIF file

  • phase_name_suffix (str) – the suffix of the phase name

  • working_dir (Path | None) – the folder to hold the processed str file

  • lattice_range (float) – the range of the lattice parameters to be refined

  • gewicht (str) – the weight fraction of the phase to be refined. Options: 0_0, SPHAR0, and SPHAR2. If 0_0, then no preferred orientation. Read more in the BGMN manual.

  • rp (int) – the peak function to be used in the refinement. Read more in the BGMN manual.

  • k1 (str) – the first peak parameter to be refined. Read more in the BGMN manual.

  • k2 (str) – the second peak parameter to be refined. Read more in the BGMN manual.

  • b1 (str) – the third peak parameter to be refined. Read more in the BGMN manual.

  • lebail (bool) – whether to use the Le Bail method

Return type:

Path

An example of the output .str file:

PHASE=BariumzirconiumtinIVoxide105053 // ICSD_43137 Reference=ICSD_43137 // Formula=Ba1_O3_Sn0.5_Zr0.5 // SpacegroupNo=221 HermannMauguin=P4/m-32/m Setting=1 Lattice=Cubic // PARAM=A=0.416280_0.412117^0.420443 // RP=4 k1=0 k2=0 PARAM=B1=0_0^0.01 GEWICHT=SPHAR4 // GOAL:BariumzirconiumtinIVoxide105053=GEWICHT*ifthenelse(ifdef(d),exp(my*d*3/4),1) // E=BA+2 Wyckoff=b x=0.500000 y=0.500000 z=0.500000 TDS=0.010000 E=(ZR+4(0.5000),SN+4(0.5000)) Wyckoff=a x=0.000000 y=0.000000 z=0.000000 TDS=0.010000 E=O-2 Wyckoff=d x=0.500000 y=0.000000 z=0.000000 TDS=0.010000

get_lattice_parameters_from_lattice(lattice, crystal_system)[source]#

Get lattice parameters from lattice based on the type of lattice. :rtype: dict[str, float]

Note

The lattice parameters are in nm

get_std_position(spacegroup_setting, wyckoff_letter, positions)[source]#

Get the standard position of a site based on the hall number and wyckoff notation.

Return type:

tuple[list[float], bool]

make_lattice_parameters_str(spacegroup_setting, structure, lattice_range)[source]#

Make the lattice parameters string.

Return type:

str

make_peak_parameter_str(k1, k2, b1, gewicht, rp)[source]#

Make the peak parameter string.

Return type:

str

make_spacegroup_setting_str(spacegroup_setting)[source]#

Make the spacegroup setting string.

Return type:

str

process_specie_string(sp)[source]#

Reverse the charge notation of a species.

Return type:

str