Python SpacegroupAnalyzer.get_point_group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_point_group [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_spacegroup_symbol()
     sa.get_spacegroup_number()
     sa.get_point_group()
     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_point_group [as 别名]
    def symmetrize_slab(self, slab, tol=1e-3):

        """
        This method checks whether or not the two surfaces of the slab are
        equivalent. If the point group of the slab has an inversion symmetry (ie.
        belong to one of the Laue groups), then it is assumed that the surfaces
        should be equivalent. Otherwise, sites at the bottom of the slab will be
        removed until the slab is symmetric. Note that this method should only be
        limited to elemental structures as the removal of sites can destroy the
        stoichiometry of the slab. For non-elemental structures, use is_polar().
        Arg:
            slab (Structure): A single slab structure
            tol (float): Tolerance for SpaceGroupanalyzer.
        Returns:
            Slab (structure): A symmetrized Slab object.
        """

        laue = ["-1", "2/m", "mmm", "4/m", "4/mmm",
                "-3", "-3m", "6/m", "6/mmm", "m-3", "m-3m"]

        sg = SpacegroupAnalyzer(slab, symprec=tol)
        pg = sg.get_point_group()

        if str(pg) in laue:
            return slab
        else:
            asym = True

            while asym or (len(slab) < len(self.parent)):

                # Keep removing sites from the bottom one by one until both
                # surfaces are symmetric or the number of sites removed has
                # exceeded 10 percent of the original slab

                c_dir = [site[2] for i, site in enumerate(slab.frac_coords)]

                slab.remove_sites([c_dir.index(min(c_dir))])

                # Check if the altered surface is symmetric

                sg = SpacegroupAnalyzer(slab, symprec=tol)
                pg = sg.get_point_group()

                if str(pg) in laue:
                    asym = False

        if len(slab) < len(self.parent):
            warnings.warn("Too many sites removed, please use a larger slab size.")

        return slab

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_point_group [as 别名]
def create_structure_db_info(structure, spacegroup=None):
    # Figure out the symmetry group
    if not spacegroup:
        spacegroup = SpacegroupAnalyzer(structure, normalised_symmetry_precision(structure), -1)

    d = dict()
    # Set the composition and formulas for the system
    comp = structure.composition
    el_amt = structure.composition.get_el_amt_dict()
    d.update({"unit_cell_formula": comp.to_dict,
              "reduced_cell_formula": comp.to_reduced_dict,
              "elements": list(el_amt.keys()),
              "nelements": len(el_amt),
              "pretty_formula": comp.reduced_formula,
              "anonymous_formula": comp.anonymized_formula,
              "nsites": comp.num_atoms,
              "chemsys": "-".join(sorted(el_amt.keys()))})

    d["spacegroup"] = {"symbol": unicode(spacegroup.get_spacegroup_symbol(),
                                         errors="ignore"),
                       "number": spacegroup.get_spacegroup_number(),
                       "point_group": unicode(spacegroup.get_point_group(),
                                              errors="ignore"),
                       "source": "spglib",
                       "crystal_system": spacegroup.get_crystal_system(),
                       "hall": spacegroup.get_hall()}

    return 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_point_group [as 别名]
    def test_tensor(self):
        """Initialize Tensor"""

        lattice = Lattice.hexagonal(4,6)
        #rprimd = np.array([[0,0.5,0.5],[0.5,0,0.5],[0.5,0.5,0]])
        #rprimd = rprimd*10
        #lattice = Lattice(rprimd)
        structure = Structure(lattice, ["Ga", "As"],
                                      [[0, 0, 0], [0.5, 0.5, 0.5]])

        #finder = SymmetryFinder(structure)
        finder = SpacegroupAnalyzer(structure)

        spacegroup = finder.get_spacegroup()
        pointgroup = finder.get_point_group()

        cartesian_tensor = [[2,3,1.2],[3,4,1.0],[1.2,1.0,6]]

        tensor = Tensor.from_cartesian_tensor(cartesian_tensor,lattice.reciprocal_lattice,space="g")
        red_tensor = tensor.reduced_tensor
        tensor2 = Tensor(red_tensor,lattice.reciprocal_lattice,space="g")
        assert(((np.abs(tensor2.cartesian_tensor)-np.abs(cartesian_tensor)) < 1E-8).all())

        self.assertTrue(tensor==tensor2)
        print(tensor)

        #print("non-symmetrized cartesian_tensor = ",tensor2.cartesian_tensor)
        tensor2.symmetrize(structure)

        #print("symmetrized_cartesian_tensor = ",tensor2.cartesian_tensor)

        self.serialize_with_pickle(tensor)

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_point_group [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, ANGLE_TOLERANCE)
            sf.get_spacegroup()
            sgnum = sf.get_spacegroup_number() if sf.get_spacegroup_number() \
                else -1
            sgsym = sf.get_spacegroup_symbol() if sf.get_spacegroup_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()

            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_point_group [as 别名]
    def run_task(self, fw_spec):
        btrap_dir = os.path.join(os.getcwd(), "boltztrap")
        bta = BoltztrapAnalyzer.from_files(btrap_dir)
        d = bta.as_dict()
        d["boltztrap_dir"] = btrap_dir

        # 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"]

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

        # add the spacegroup
        sg = SpacegroupAnalyzer(Structure.from_dict(d["structure"]), 0.1)
        d["spacegroup"] = {"symbol": sg.get_spacegroup_symbol(),
                           "number": sg.get_spacegroup_number(),
                           "point_group": sg.get_point_group(),
                           "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:
            with open(os.path.join(btrap_dir, "boltztrap.json"), "w") as f:
                f.write(json.dumps(d, default=DATETIME_HANDLER))
        else:
            mmdb = MMDb.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_point_group [as 别名]
    def test_symmetrization(self):

        # Restricted to elemental materials due to the risk of
        # broken stoichiometry. For compound materials, use is_polar()

        # Get all slabs for P6/mmm Ti and Fm-3m Ag up to index of 2

        all_Ti_slabs = generate_all_slabs(self.ti, 2, 10, 10, bonds=None,
                                          tol=1e-3, max_broken_bonds=0,
                                          lll_reduce=False, center_slab=False,
                                          primitive=True, max_normal_search=2,
                                          symmetrize=True)

        all_Ag_fcc_slabs = generate_all_slabs(self.agfcc, 2, 10, 10, bonds=None,
                                              tol=1e-3, max_broken_bonds=0,
                                              lll_reduce=False, center_slab=False,
                                              primitive=True, max_normal_search=2,
                                              symmetrize=True)

        all_slabs = [all_Ti_slabs, all_Ag_fcc_slabs]

        for i, slabs in enumerate(all_slabs):

            assymetric_count = 0
            symmetric_count = 0

            for i, slab in enumerate(slabs):
                sg = SpacegroupAnalyzer(slab)
                pg = sg.get_point_group()

                # Check if a slab is symmetric
                if str(pg) not in self.laue_groups:
                    assymetric_count += 1
                else:
                    symmetric_count += 1

            # Check if slabs are all symmetric
            self.assertEqual(assymetric_count, 0)
            self.assertEqual(symmetric_count, len(slabs))

# 需要导入模块: from pymatgen.symmetry.analyzer import SpacegroupAnalyzer [as 别名]
# 或者: from pymatgen.symmetry.analyzer.SpacegroupAnalyzer import get_point_group [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_spacegroup_symbol(),
         "number": sg.get_spacegroup_number(),
         "point_group": sg.get_point_group(),
         "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_point_group [as 别名]
class SpacegroupAnalyzerTest(PymatgenTest):

    def setUp(self):
        p = Poscar.from_file(os.path.join(test_dir, 'POSCAR'))
        self.structure = p.structure
        self.sg = SpacegroupAnalyzer(self.structure, 0.001)
        self.disordered_structure = self.get_structure('Li10GeP2S12')
        self.disordered_sg = SpacegroupAnalyzer(self.disordered_structure, 0.001)
        s = p.structure.copy()
        site = s[0]
        del s[0]
        s.append(site.species_and_occu, site.frac_coords)
        self.sg3 = SpacegroupAnalyzer(s, 0.001)
        graphite = self.get_structure('Graphite')
        graphite.add_site_property("magmom", [0.1] * len(graphite))
        self.sg4 = SpacegroupAnalyzer(graphite, 0.001)

    def test_get_space_symbol(self):
        self.assertEqual(self.sg.get_spacegroup_symbol(), "Pnma")
        self.assertEqual(self.disordered_sg.get_spacegroup_symbol(),
                         "P4_2/nmc")
        self.assertEqual(self.sg3.get_spacegroup_symbol(), "Pnma")
        self.assertEqual(self.sg4.get_spacegroup_symbol(), "R-3m")

    def test_get_space_number(self):
        self.assertEqual(self.sg.get_spacegroup_number(), 62)
        self.assertEqual(self.disordered_sg.get_spacegroup_number(), 137)
        self.assertEqual(self.sg4.get_spacegroup_number(), 166)

    def test_get_hall(self):
        self.assertEqual(self.sg.get_hall(), '-P 2ac 2n')
        self.assertEqual(self.disordered_sg.get_hall(), 'P 4n 2n -1n')

    def test_get_pointgroup(self):
        self.assertEqual(self.sg.get_point_group(), 'mmm')
        self.assertEqual(self.disordered_sg.get_point_group(), '4/mmm')

    def test_get_symmetry_dataset(self):
        ds = self.sg.get_symmetry_dataset()
        self.assertEqual(ds['international'], 'Pnma')

    def test_get_crystal_system(self):
        crystal_system = self.sg.get_crystal_system()
        self.assertEqual('orthorhombic', crystal_system)
        self.assertEqual('tetragonal', self.disordered_sg.get_crystal_system())

    def test_get_symmetry_operations(self):
        fracsymmops = self.sg.get_symmetry_operations()
        symmops = self.sg.get_symmetry_operations(True)
        self.assertEqual(len(symmops), 8)
        latt = self.structure.lattice
        for fop, op in zip(fracsymmops, symmops):
            for site in self.structure:
                newfrac = fop.operate(site.frac_coords)
                newcart = op.operate(site.coords)
                self.assertTrue(np.allclose(latt.get_fractional_coords(newcart),
                                            newfrac))
                found = False
                newsite = PeriodicSite(site.species_and_occu, newcart, latt,
                                       coords_are_cartesian=True)
                for testsite in self.structure:
                    if newsite.is_periodic_image(testsite, 1e-3):
                        found = True
                        break
                self.assertTrue(found)

    def test_get_refined_structure(self):
        for a in self.sg.get_refined_structure().lattice.angles:
            self.assertEqual(a, 90)
        refined = self.disordered_sg.get_refined_structure()
        for a in refined.lattice.angles:
            self.assertEqual(a, 90)
        self.assertEqual(refined.lattice.a, refined.lattice.b)
        s = self.get_structure('Li2O')
        sg = SpacegroupAnalyzer(s, 0.001)
        self.assertEqual(sg.get_refined_structure().num_sites, 4 * s.num_sites)

    def test_get_symmetrized_structure(self):
        symm_struct = self.sg.get_symmetrized_structure()
        for a in symm_struct.lattice.angles:
            self.assertEqual(a, 90)
        self.assertEqual(len(symm_struct.equivalent_sites), 5)

        symm_struct = self.disordered_sg.get_symmetrized_structure()
        self.assertEqual(len(symm_struct.equivalent_sites), 8)
        self.assertEqual([len(i) for i in symm_struct.equivalent_sites],
                         [16,4,8,4,2,8,8,8])
        s1 = symm_struct.equivalent_sites[1][1]
        s2 = symm_struct[symm_struct.equivalent_indices[1][1]]
        self.assertEqual(s1, s2)
        self.assertEqual(self.sg4.get_symmetrized_structure()[0].magmom, 0.1)

    def test_find_primitive(self):
        """
        F m -3 m Li2O testing of converting to primitive cell
        """
        parser = CifParser(os.path.join(test_dir, 'Li2O.cif'))
        structure = parser.get_structures(False)[0]
        s = SpacegroupAnalyzer(structure)
        primitive_structure = s.find_primitive()
#.........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_point_group [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_spacegroup_symbol(),
                               "number": sg.get_spacegroup_number(),
                               "point_group": sg.get_point_group(),
                               "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