Python SpacegroupAnalyzer.get_space_group_number方法代码示例

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def add_snl(self, snl, force_new=False, snlgroup_guess=None):
        try:
            self.lock_db()
            snl_id = self._get_next_snl_id()

            spstruc = snl.structure.copy()
            spstruc.remove_oxidation_states()
            sf = SpacegroupAnalyzer(spstruc, SPACEGROUP_TOLERANCE)
            sf.get_space_group_operations()
            sgnum = sf.get_space_group_number() if sf.get_space_group_number() \
                else -1
            sgsym = sf.get_space_group_symbol() if sf.get_space_group_symbol() \
                else 'unknown'
            sghall = sf.get_hall() if sf.get_hall() else 'unknown'
            sgxtal = sf.get_crystal_system() if sf.get_crystal_system() \
                else 'unknown'
            sglatt = sf.get_lattice_type() if sf.get_lattice_type() else 'unknown'
            sgpoint = sf.get_point_group_symbol()

            mpsnl = MPStructureNL.from_snl(snl, snl_id, sgnum, sgsym, sghall,
                                           sgxtal, sglatt, sgpoint)
            snlgroup, add_new, spec_group = self.add_mpsnl(mpsnl, force_new, snlgroup_guess)
            self.release_lock()
            return mpsnl, snlgroup.snlgroup_id, spec_group
        except:
            self.release_lock()
            traceback.print_exc()
            raise ValueError("Error while adding SNL!")

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
 def test_tricky_structure(self):
     # for some reason this structure kills spglib1.9
     # 1.7 can't find symmetry either, but at least doesn't kill python
     s = Structure.from_file(os.path.join(test_dir, 'POSCAR.tricky_symmetry'))
     sa = SpacegroupAnalyzer(s, 0.1)
     sa.get_space_group_symbol()
     sa.get_space_group_number()
     sa.get_point_group_symbol()
     sa.get_crystal_system()
     sa.get_hall()

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
def create_saturated_interstitial_structure( interstitial_def, dist_tol=0.1):
    """
    this takes a Interstitial defect object and generates the
    sublattice for it based on the structure's space group.
    Useful for understanding multiplicity of an interstitial
    defect in thermodynamic analysis.

    NOTE: if large relaxation happens to interstitial or
        defect involves a complex then there may be additional
        degrees of freedom that need to be considered for
        the multiplicity.

    Args:
        dist_tol: changing distance tolerance of saturated structure,
                allowing for possibly overlapping sites
                but ensuring space group is maintained

    Returns:
        Structure object decorated with interstitial site equivalents
    """
    sga = SpacegroupAnalyzer( interstitial_def.bulk_structure.copy())
    sg_ops = sga.get_symmetry_operations( cartesian=True)

    # copy bulk structure to make saturated interstitial structure out of
    # artificially lower distance_tolerance to allow for distinct interstitials
    # with lower symmetry to be replicated - This is OK because one would never
    # actually use this structure for a practical calcualtion...
    saturated_defect_struct = interstitial_def.bulk_structure.copy()
    saturated_defect_struct.DISTANCE_TOLERANCE = dist_tol

    for sgo in sg_ops:
        new_interstit_coords = sgo.operate( interstitial_def.site.coords[:])
        poss_new_site = PeriodicSite(
                interstitial_def.site.specie,
                new_interstit_coords,
                saturated_defect_struct.lattice,
                to_unit_cell=True,
                coords_are_cartesian=True)
        try:
            #will raise value error if site already exists in structure
            saturated_defect_struct.append(
                        poss_new_site.specie, poss_new_site.coords,
                        coords_are_cartesian=True, validate_proximity=True)
        except ValueError:
            pass

    # do final space group analysis to make sure symmetry not lowered by saturating defect structure
    saturated_sga = SpacegroupAnalyzer( saturated_defect_struct)
    if saturated_sga.get_space_group_number() != sga.get_space_group_number():
        raise ValueError("Warning! Interstitial sublattice generation "
                         "has changed space group symmetry. Recommend "
                         "reducing dist_tol and trying again...")

    return saturated_defect_struct

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
 def set_space_group_from_structure(self, structure):
     spga = SpacegroupAnalyzer(structure=structure)
     self.crystal_system = spga.get_crystal_system()
     self.hall = spga.get_hall()
     self.number = spga.get_space_group_number()
     self.source = "spglib"
     self.symbol = spga.get_space_group_symbol()

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def set_material_data_from_structure(self, structure, space_group=True, symprec=1e-3, angle_tolerance=5):
        """
        Sets the fields of the Document using a Structure and Spglib to determine the space group properties

        Args:
            structure: A |Structure|
            space_group: if True sets the spacegroup fields using spglib_.
            symprec (float): Tolerance for symmetry finding.
            angle_tolerance (float): Angle tolerance for symmetry finding.
        """

        comp = structure.composition
        el_amt = structure.composition.get_el_amt_dict()
        self.unit_cell_formula = comp.as_dict()
        self.reduced_cell_formula = comp.to_reduced_dict
        self.elements = list(el_amt.keys())
        self.nelements = len(el_amt)
        self.pretty_formula = comp.reduced_formula
        self.anonymous_formula = comp.anonymized_formula
        self.nsites = comp.num_atoms
        self.chemsys = "-".join(sorted(el_amt.keys()))
        if space_group:
            sym = SpacegroupAnalyzer(structure, symprec=symprec, angle_tolerance=angle_tolerance)
            self.spacegroup = SpaceGroupDocument(crystal_system=sym.get_crystal_system(), hall=sym.get_hall(),
                                                 number=sym.get_space_group_number(), point_group=sym.get_point_group_symbol(),
                                                 symbol=sym.get_space_group_symbol(), source="spglib")

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def test_apply_transformation(self):
        trans = MagOrderingTransformation({"Fe": 5})
        p = Poscar.from_file(os.path.join(test_dir, 'POSCAR.LiFePO4'),
                             check_for_POTCAR=False)
        s = p.structure
        alls = trans.apply_transformation(s, 10)
        self.assertEqual(len(alls), 3)
        f = SpacegroupAnalyzer(alls[0]["structure"], 0.1)
        self.assertEqual(f.get_space_group_number(), 31)

        model = IsingModel(5, 5)
        trans = MagOrderingTransformation({"Fe": 5},
                                          energy_model=model)
        alls2 = trans.apply_transformation(s, 10)
        # Ising model with +J penalizes similar neighbor magmom.
        self.assertNotEqual(alls[0]["structure"], alls2[0]["structure"])
        self.assertEqual(alls[0]["structure"], alls2[2]["structure"])

        s = self.get_structure('Li2O')
        # Li2O doesn't have magnetism of course, but this is to test the
        # enumeration.
        trans = MagOrderingTransformation({"Li+": 1}, max_cell_size=3)
        alls = trans.apply_transformation(s, 100)
        # TODO: check this is correct, unclear what len(alls) should be
        self.assertEqual(len(alls), 12)

        trans = MagOrderingTransformation({"Ni": 5})
        alls = trans.apply_transformation(self.NiO.get_primitive_structure(),
                                          return_ranked_list=10)
        self.assertEqual(self.NiO_AFM_111.lattice, alls[0]["structure"].lattice)
        self.assertEqual(self.NiO_AFM_001.lattice, alls[1]["structure"].lattice)

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def run_task(self, fw_spec):
        additional_fields = self.get("additional_fields", {})

        # pass the additional_fields first to avoid overriding BoltztrapAnalyzer items
        d = additional_fields.copy()

        btrap_dir = os.path.join(os.getcwd(), "boltztrap")
        d["boltztrap_dir"] = btrap_dir

        bta = BoltztrapAnalyzer.from_files(btrap_dir)
        d.update(bta.as_dict())
        d["scissor"] = bta.intrans["scissor"]

        # trim the output
        for x in ['cond', 'seebeck', 'kappa', 'hall', 'mu_steps', 'mu_doping', 'carrier_conc']:
            del d[x]

        if not self.get("hall_doping"):
            del d["hall_doping"]

        bandstructure_dir = os.getcwd()
        d["bandstructure_dir"] = bandstructure_dir

        # add the structure
        v, o = get_vasprun_outcar(bandstructure_dir, parse_eigen=False, parse_dos=False)
        structure = v.final_structure
        d["structure"] = structure.as_dict()
        d["formula_pretty"] = structure.composition.reduced_formula
        d.update(get_meta_from_structure(structure))

        # add the spacegroup
        sg = SpacegroupAnalyzer(Structure.from_dict(d["structure"]), 0.1)
        d["spacegroup"] = {"symbol": sg.get_space_group_symbol(),
                           "number": sg.get_space_group_number(),
                           "point_group": sg.get_point_group_symbol(),
                           "source": "spglib",
                           "crystal_system": sg.get_crystal_system(),
                           "hall": sg.get_hall()}

        d["created_at"] = datetime.utcnow()

        db_file = env_chk(self.get('db_file'), fw_spec)

        if not db_file:
            del d["dos"]
            with open(os.path.join(btrap_dir, "boltztrap.json"), "w") as f:
                f.write(json.dumps(d, default=DATETIME_HANDLER))
        else:
            mmdb = VaspCalcDb.from_db_file(db_file, admin=True)

            # dos gets inserted into GridFS
            dos = json.dumps(d["dos"], cls=MontyEncoder)
            fsid, compression = mmdb.insert_gridfs(dos, collection="dos_boltztrap_fs",
                                                   compress=True)
            d["dos_boltztrap_fs_id"] = fsid
            del d["dos"]

            mmdb.db.boltztrap.insert(d)

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
 def print_spg(src='POSCAR'):
     """
     space group を return
     """
     srcpos = Poscar.from_file(src)
     finder = SpacegroupAnalyzer(srcpos.structure,
                                 symprec=5e-2, angle_tolerance=8)
     spg = finder.get_space_group_symbol()
     spg_num = finder.get_space_group_number()
     return spg, spg_num

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
def print_spg(src='POSCAR'):
    """
    空間群を出力
    """
    srcpos = Poscar.from_file(src)
    # srcpos.structure | fnc.echo
    finder = SpacegroupAnalyzer(srcpos.structure,
                                symprec=5e-2, angle_tolerance=8)
    # dir(finder) | fnc.echo
    # srcpos | fnc.echo
    # help(finder.get_space_group_symbol)
    # finder._space_group_data | fnc.echo
    spg = finder.get_space_group_symbol()
    spg_num = finder.get_space_group_number()
    print(spg)
    print(spg_num)

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def test_apply_transformation(self):
        trans = MagOrderingTransformation({"Fe": 5})
        p = Poscar.from_file(os.path.join(test_dir, "POSCAR.LiFePO4"), check_for_POTCAR=False)
        s = p.structure
        alls = trans.apply_transformation(s, 10)
        self.assertEqual(len(alls), 3)
        f = SpacegroupAnalyzer(alls[0]["structure"], 0.1)
        self.assertEqual(f.get_space_group_number(), 31)

        model = IsingModel(5, 5)
        trans = MagOrderingTransformation({"Fe": 5}, energy_model=model)
        alls2 = trans.apply_transformation(s, 10)
        # Ising model with +J penalizes similar neighbor magmom.
        self.assertNotEqual(alls[0]["structure"], alls2[0]["structure"])
        self.assertEqual(alls[0]["structure"], alls2[2]["structure"])

        s = self.get_structure("Li2O")
        # Li2O doesn't have magnetism of course, but this is to test the
        # enumeration.
        trans = MagOrderingTransformation({"Li+": 1}, max_cell_size=3)
        alls = trans.apply_transformation(s, 100)
        self.assertEqual(len(alls), 10)

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
 def set_output_data(self, d_calc, d):
     """
     set the 'output' key
     """
     d["output"] = {
         "structure": d_calc["output"]["structure"],
         "density": d_calc.pop("density"),
         "energy": d_calc["output"]["energy"],
         "energy_per_atom": d_calc["output"]["energy_per_atom"]}
     d["output"].update(self.get_basic_processed_data(d))
     sg = SpacegroupAnalyzer(Structure.from_dict(d_calc["output"]["structure"]), 0.1)
     if not sg.get_symmetry_dataset():
         sg = SpacegroupAnalyzer(Structure.from_dict(d_calc["output"]["structure"]), 1e-3, 1)
     d["output"]["spacegroup"] = {
         "source": "spglib",
         "symbol": sg.get_space_group_symbol(),
         "number": sg.get_space_group_number(),
         "point_group": sg.get_point_group_symbol(),
         "crystal_system": sg.get_crystal_system(),
         "hall": sg.get_hall()}
     if d["input"]["parameters"].get("LEPSILON"):
         for k in ['epsilon_static', 'epsilon_static_wolfe', 'epsilon_ionic']:
             d["output"][k] = d_calc["output"][k]

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def generate_doc(self, dir_name, vasprun_files):
        """
        Process aflow style runs, where each run is actually a combination of
        two vasp runs.
        """
        try:
            fullpath = os.path.abspath(dir_name)
            #Defensively copy the additional fields first.  This is a MUST.
            #Otherwise, parallel updates will see the same object and inserts
            #will be overridden!!
            d = {k: v for k, v in self.additional_fields.items()}
            d["dir_name"] = fullpath
            d["schema_version"] = VaspToDbTaskDrone.__version__
            d["calculations"] = [
                self.process_vasprun(dir_name, taskname, filename)
                for taskname, filename in vasprun_files.items()]
            d1 = d["calculations"][0]
            d2 = d["calculations"][-1]

            #Now map some useful info to the root level.
            for root_key in ["completed_at", "nsites", "unit_cell_formula",
                             "reduced_cell_formula", "pretty_formula",
                             "elements", "nelements", "cif", "density",
                             "is_hubbard", "hubbards", "run_type"]:
                d[root_key] = d2[root_key]
            d["chemsys"] = "-".join(sorted(d2["elements"]))

            #store any overrides to the exchange correlation functional
            xc = d2["input"]["incar"].get("GGA")
            if xc:
                xc = xc.upper()
            d["input"] = {"crystal": d1["input"]["crystal"],
                          "is_lasph": d2["input"]["incar"].get("LASPH", False),
                          "potcar_spec": d1["input"].get("potcar_spec"),
                          "xc_override": xc}
            vals = sorted(d2["reduced_cell_formula"].values())
            d["anonymous_formula"] = {string.ascii_uppercase[i]: float(vals[i])
                                      for i in range(len(vals))}
            d["output"] = {
                "crystal": d2["output"]["crystal"],
                "final_energy": d2["output"]["final_energy"],
                "final_energy_per_atom": d2["output"]["final_energy_per_atom"]}
            d["name"] = "aflow"
            p = d2["input"]["potcar_type"][0].split("_")
            pot_type = p[0]
            functional = "lda" if len(pot_type) == 1 else "_".join(p[1:])
            d["pseudo_potential"] = {"functional": functional.lower(),
                                     "pot_type": pot_type.lower(),
                                     "labels": d2["input"]["potcar"]}
            if len(d["calculations"]) == len(self.runs) or \
                    list(vasprun_files.keys())[0] != "relax1":
                d["state"] = "successful" if d2["has_vasp_completed"] \
                    else "unsuccessful"
            else:
                d["state"] = "stopped"
            d["analysis"] = get_basic_analysis_and_error_checks(d)

            sg = SpacegroupAnalyzer(Structure.from_dict(d["output"]["crystal"]),
                                    0.1)
            d["spacegroup"] = {"symbol": sg.get_space_group_symbol(),
                               "number": sg.get_space_group_number(),
                               "point_group": sg.get_point_group_symbol(),
                               "source": "spglib",
                               "crystal_system": sg.get_crystal_system(),
                               "hall": sg.get_hall()}
            d["last_updated"] = datetime.datetime.today()
            return d
        except Exception as ex:
            import traceback
            print(traceback.format_exc())
            logger.error("Error in " + os.path.abspath(dir_name) +
                         ".\n" + traceback.format_exc())

            return None

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def _gen_input_file(self):
        """
        Generate the necessary struct_enum.in file for enumlib. See enumlib
        documentation for details.
        """
        coord_format = "{:.6f} {:.6f} {:.6f}"
        # Using symmetry finder, get the symmetrically distinct sites.
        fitter = SpacegroupAnalyzer(self.structure, self.symm_prec)
        symmetrized_structure = fitter.get_symmetrized_structure()
        logger.debug("Spacegroup {} ({}) with {} distinct sites".format(
            fitter.get_space_group_symbol(),
            fitter.get_space_group_number(),
            len(symmetrized_structure.equivalent_sites))
        )

        """
        Enumlib doesn"t work when the number of species get too large. To
        simplify matters, we generate the input file only with disordered sites
        and exclude the ordered sites from the enumeration. The fact that
        different disordered sites with the exact same species may belong to
        different equivalent sites is dealt with by having determined the
        spacegroup earlier and labelling the species differently.
        """

        # index_species and index_amounts store mappings between the indices
        # used in the enum input file, and the actual species and amounts.
        index_species = []
        index_amounts = []

        # Stores the ordered sites, which are not enumerated.
        ordered_sites = []
        disordered_sites = []
        coord_str = []
        for sites in symmetrized_structure.equivalent_sites:
            if sites[0].is_ordered:
                ordered_sites.append(sites)
            else:
                sp_label = []
                species = {k: v for k, v in sites[0].species.items()}
                if sum(species.values()) < 1 - EnumlibAdaptor.amount_tol:
                    # Let us first make add a dummy element for every single
                    # site whose total occupancies don't sum to 1.
                    species[DummySpecie("X")] = 1 - sum(species.values())
                for sp in species.keys():
                    if sp not in index_species:
                        index_species.append(sp)
                        sp_label.append(len(index_species) - 1)
                        index_amounts.append(species[sp] * len(sites))
                    else:
                        ind = index_species.index(sp)
                        sp_label.append(ind)
                        index_amounts[ind] += species[sp] * len(sites)
                sp_label = "/".join(["{}".format(i) for i in sorted(sp_label)])
                for site in sites:
                    coord_str.append("{} {}".format(
                        coord_format.format(*site.coords),
                        sp_label))
                disordered_sites.append(sites)

        def get_sg_info(ss):
            finder = SpacegroupAnalyzer(Structure.from_sites(ss),
                                        self.symm_prec)
            return finder.get_space_group_number()

        target_sgnum = get_sg_info(symmetrized_structure.sites)
        curr_sites = list(itertools.chain.from_iterable(disordered_sites))
        sgnum = get_sg_info(curr_sites)
        ordered_sites = sorted(ordered_sites, key=lambda sites: len(sites))
        logger.debug("Disordered sites has sg # %d" % (sgnum))
        self.ordered_sites = []

        # progressively add ordered sites to our disordered sites
        # until we match the symmetry of our input structure
        if self.check_ordered_symmetry:
            while sgnum != target_sgnum and len(ordered_sites) > 0:
                sites = ordered_sites.pop(0)
                temp_sites = list(curr_sites) + sites
                new_sgnum = get_sg_info(temp_sites)
                if sgnum != new_sgnum:
                    logger.debug("Adding %s in enum. New sg # %d"
                                 % (sites[0].specie, new_sgnum))
                    index_species.append(sites[0].specie)
                    index_amounts.append(len(sites))
                    sp_label = len(index_species) - 1
                    for site in sites:
                        coord_str.append("{} {}".format(
                            coord_format.format(*site.coords),
                            sp_label))
                    disordered_sites.append(sites)
                    curr_sites = temp_sites
                    sgnum = new_sgnum
                else:
                    self.ordered_sites.extend(sites)

        for sites in ordered_sites:
            self.ordered_sites.extend(sites)

        self.index_species = index_species

        lattice = self.structure.lattice
#.........这里部分代码省略.........

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
    def _gen_input_file(self):
        """
        Generate the necessary struct_enum.in file for enumlib. See enumlib
        documentation for details.
        """
        coord_format = "{:.6f} {:.6f} {:.6f}"
        # Using symmetry finder, get the symmetrically distinct sites.
        fitter = SpacegroupAnalyzer(self.structure, self.symm_prec)
        symmetrized_structure = fitter.get_symmetrized_structure()
        logger.debug("Spacegroup {} ({}) with {} distinct sites".format(
            fitter.get_space_group_symbol(),
            fitter.get_space_group_number(),
            len(symmetrized_structure.equivalent_sites))
        )

        """
        Enumlib doesn"t work when the number of species get too large. To
        simplify matters, we generate the input file only with disordered sites
        and exclude the ordered sites from the enumeration. The fact that
        different disordered sites with the exact same species may belong to
        different equivalent sites is dealt with by having determined the
        spacegroup earlier and labelling the species differently.
        """

        # index_species and index_amounts store mappings between the indices
        # used in the enum input file, and the actual species and amounts.
        index_species = []
        index_amounts = []

        # Stores the ordered sites, which are not enumerated.
        ordered_sites = []
        disordered_sites = []
        coord_str = []
        for sites in symmetrized_structure.equivalent_sites:
            if sites[0].is_ordered:
                ordered_sites.append(sites)
            else:
                sp_label = []
                species = {k: v for k, v in sites[0].species_and_occu.items()}
                if sum(species.values()) < 1 - EnumlibAdaptor.amount_tol:
                    # Let us first make add a dummy element for every single
                    # site whose total occupancies don't sum to 1.
                    species[DummySpecie("X")] = 1 - sum(species.values())
                for sp in species.keys():
                    if sp not in index_species:
                        index_species.append(sp)
                        sp_label.append(len(index_species) - 1)
                        index_amounts.append(species[sp] * len(sites))
                    else:
                        ind = index_species.index(sp)
                        sp_label.append(ind)
                        index_amounts[ind] += species[sp] * len(sites)
                sp_label = "/".join(["{}".format(i) for i in sorted(sp_label)])
                for site in sites:
                    coord_str.append("{} {}".format(
                        coord_format.format(*site.coords),
                        sp_label))
                disordered_sites.append(sites)

        def get_sg_info(ss):
            finder = SpacegroupAnalyzer(Structure.from_sites(ss),
                                        self.symm_prec)
            return finder.get_space_group_number()

        curr_sites = list(itertools.chain.from_iterable(disordered_sites))
        min_sgnum = get_sg_info(curr_sites)
        logger.debug("Disordered sites has sgnum %d" % (
            min_sgnum))
        # It could be that some of the ordered sites has a lower symmetry than
        # the disordered sites.  So we consider the lowest symmetry sites as
        # disordered in our enumeration.
        self.ordered_sites = []
        to_add = []

        if self.check_ordered_symmetry:
            for sites in ordered_sites:
                temp_sites = list(curr_sites) + sites
                sgnum = get_sg_info(temp_sites)
                if sgnum < min_sgnum:
                    logger.debug("Adding {} to sites to be ordered. "
                                 "New sgnum {}"
                                 .format(sites, sgnum))
                    to_add = sites
                    min_sgnum = sgnum

        for sites in ordered_sites:
            if sites == to_add:
                index_species.append(sites[0].specie)
                index_amounts.append(len(sites))
                sp_label = len(index_species) - 1
                logger.debug("Lowest symmetry {} sites are included in enum."
                             .format(sites[0].specie))
                for site in sites:
                    coord_str.append("{} {}".format(
                        coord_format.format(*site.coords),
                        sp_label))
                disordered_sites.append(sites)
            else:
                self.ordered_sites.extend(sites)

#.........这里部分代码省略.........

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_space_group_number [as 别名]
 def get_sg(s):
     finder = SpacegroupAnalyzer(s, symprec=self.symprec)
     return finder.get_space_group_number()