Source code for httk.external.pyspglib_ext

#    The high-throughput toolkit (httk)
#    Copyright (C) 2012-2015 Rickard Armiento
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU Affero General Public License as
#    published by the Free Software Foundation, either version 3 of the
#    License, or (at your option) any later version.
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    GNU Affero General Public License for more details.
#    You should have received a copy of the GNU Affero General Public License
#    along with this program.  If not, see <>.

  pyspglib external module

import os, sys

from httk.core import citation
citation.add_ext_citation('spglib / pyspglib', "(Author list to be added)")

from httk import config
from httk.external.command import Command
from httk.external.subimport import submodule_import_external
import httk

    pyspglib_path = config.get('paths', 'pyspglib')
except Exception:
    pyspglib_path = None

    spglib_path = config.get('paths', 'spglib')
except Exception:
    spglib_path = None

pyspg_major_verion = None
pyspg_minor_verion = None

[docs]def ensure_pyspg_is_imported(): if pyspglib_path == "False" and spglib_path == "False": raise Exception("httk.external.ase_glue: module ase_glue imported, but ase is disabled in configuration file.") if pyspg_major_version is None: raise Exception("httk.external.pyspglib_ext imported, but could not access pyspg.")
try: if pyspglib_path is not None and spglib_path is not None: # Import spglib from pyspglib, with some magic to enable use of pyspglib.Atoms for the pyspglib ASE atoms emulation class pyspglib = submodule_import_external(os.path.join(pyspglib_path, 'lib', 'python'), 'pyspglib') from pyspglib import spglib atoms = submodule_import_external(os.path.join(spglib_path, 'python', 'ase', 'test'), 'atoms') spglib.Atoms = atoms.Atoms del atoms # Lets not pollute the namespace pyspg_major_version = spglib.__version__.split('.')[0] pyspg_minor_version = spglib.__version__.split('.')[1] else: try: external = config.get('general', 'allow_system_libs') except Exception: external = 'yes' if external == 'yes': # Note: this type of import will miss the spglib 'fake' atom object which is a problem. Probably should # not use this type of import from pyspglib import spglib sys.stderr.write('WARNING: spglib imported in httk.external without any path given in httk.cfg, this means no spglib.Atoms object exists.\n') pyspg_major_version = spglib.__version__.split('.')[0] pyspg_minor_version = spglib.__version__.split('.')[1] else: pass except Exception: pass
[docs]def structure_to_spglib_atoms(struct): ensure_pyspg_is_imported() symbols = [] for i in range(len(struct.coordgroups)): name = httk.htdata.periodictable.atomic_symbol(struct.assignments[i]) symbols += [name]*struct.counts[i] print("SYMBOLS", symbols, struct.N) cell = struct.cell.to_floats() scaled_positions = struct.coords atoms = spglib.Atoms(symbols=symbols, cell=cell, scaled_positions=scaled_positions, pbc=True) return atoms
[docs]def analysis(struct, symprec=1e-5): ensure_pyspg_is_imported() atoms = structure_to_spglib_atoms(struct) val = spglib.get_spacegroup(atoms) print("Spacegroup is:", val) val = spglib.refine_cell(atoms, symprec=symprec) print("Primitive", val)
[docs]def primitive(struct, symprec=1e-5): ensure_pyspg_is_imported() atoms = structure_to_spglib_atoms(struct) prim = spglib.refine_cell(atoms, symprec=symprec) sg = spglib.get_spacegroup(atoms) struct = httk.iface.spglib_if.spglib_out_to_struct(prim) struct.comment = "Spacegroup: "+sg return struct