Python surface.SlabGenerator类代码示例

 def apply_transformation(self, structure):
     sg = SlabGenerator(structure, self.miller_index, self.min_slab_size,
                        self.min_vacuum_size, self.lll_reduce, 
                        self.center_slab, self.primitive,
                        self.max_normal_search)
     slab = sg.get_slab(self.shift, self.tol)
     return slab

    def test_normal_search(self):
        fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
                                        [[0, 0, 0]])
        for miller in [(1, 0, 0), (1, 1, 0), (1, 1, 1), (2, 1, 1)]:
            gen = SlabGenerator(fcc, miller, 10, 10)
            gen_normal = SlabGenerator(fcc, miller, 10, 10,
                                       max_normal_search=max(miller))
            slab = gen_normal.get_slab()
            self.assertAlmostEqual(slab.lattice.alpha, 90)
            self.assertAlmostEqual(slab.lattice.beta, 90)
            self.assertGreaterEqual(len(gen_normal.oriented_unit_cell),
                                    len(gen.oriented_unit_cell))

        graphite = self.get_structure("Graphite")
        for miller in [(1, 0, 0), (1, 1, 0), (0, 0, 1), (2, 1, 1)]:
            gen = SlabGenerator(graphite, miller, 10, 10)
            gen_normal = SlabGenerator(graphite, miller, 10, 10,
                                       max_normal_search=max(miller))
            self.assertGreaterEqual(len(gen_normal.oriented_unit_cell),
                                    len(gen.oriented_unit_cell))

        sc = Structure(Lattice.hexagonal(3.32, 5.15), ["Sc", "Sc"],
                       [[1/3, 2/3, 0.25], [2/3, 1/3, 0.75]])
        gen = SlabGenerator(sc, (1, 1, 1), 10, 10, max_normal_search=1)
        self.assertAlmostEqual(gen.oriented_unit_cell.lattice.angles[1], 90)

    def generate_slabs(self, film_millers, substrate_millers):
        """
        Generates the film/substrate slab combinations for a set of given
        miller indicies

        Args:
            film_millers(array): all miller indices to generate slabs for
                film
            substrate_millers(array): all miller indicies to generate slabs
                for substrate
        """

        for f in film_millers:
            film_slab = SlabGenerator(self.film, f, 20, 15,
                                      primitive=False).get_slab()
            film_vectors = reduce_vectors(film_slab.lattice_vectors()[0],
                                               film_slab.lattice_vectors()[1])
            film_area = vec_area(*film_vectors)

            for s in substrate_millers:
                substrate_slab = SlabGenerator(self.substrate, s, 20, 15,
                                               primitive=False).get_slab()
                substrate_vectors = reduce_vectors(
                    substrate_slab.lattice_vectors()[0],
                    substrate_slab.lattice_vectors()[1])
                substrate_area = vec_area(*substrate_vectors)

                yield [film_area, substrate_area, film_vectors,
                       substrate_vectors, f, s]

    def test_surface_sites_and_symmetry(self):
        # test if surfaces are equivalent by using
        # Laue symmetry and surface site equivalence

        for bool in [True, False]:
            # We will also set the slab to be centered and
            # off centered in order to test the center of mass
            slabgen = SlabGenerator(self.agfcc, (3, 1, 0), 10, 10,
                                    center_slab=bool)
            slab = slabgen.get_slabs()[0]
            surf_sites_dict = slab.get_surface_sites()
            self.assertEqual(len(surf_sites_dict["top"]),
                             len(surf_sites_dict["bottom"]))
            total_surf_sites = sum([len(surf_sites_dict[key])
                                    for key in surf_sites_dict.keys()])
            self.assertTrue(slab.is_symmetric())
            self.assertEqual(total_surf_sites / 2, 4)
            self.assertTrue(slab.have_equivalent_surfaces())

            # Test if the ratio of surface sites per area is
            # constant, ie are the surface energies the same
            r1 = total_surf_sites / (2 * slab.surface_area)
            slabgen = SlabGenerator(self.agfcc, (3, 1, 0), 10, 10,
                                    primitive=False)
            slab = slabgen.get_slabs()[0]
            surf_sites_dict = slab.get_surface_sites()
            total_surf_sites = sum([len(surf_sites_dict[key])
                                    for key in surf_sites_dict.keys()])
            r2 = total_surf_sites / (2 * slab.surface_area)
            self.assertArrayEqual(r1, r2)

 def test_dipole_and_is_polar(self):
     self.assertArrayAlmostEqual(self.zno55.dipole, [0, 0, 0])
     self.assertFalse(self.zno55.is_polar())
     cscl = self.get_structure("CsCl")
     cscl.add_oxidation_state_by_element({"Cs": 1, "Cl": -1})
     slab = SlabGenerator(cscl, [1, 0, 0], 5, 5,
                          lll_reduce=False, center_slab=False).get_slab()
     self.assertArrayAlmostEqual(slab.dipole, [-4.209, 0, 0])
     self.assertTrue(slab.is_polar())

 def test_get_orthogonal_c_slab(self):
     TeI = Structure.from_file(get_path("icsd_TeI.cif"),
                               primitive=False)
     trclnc_TeI = SlabGenerator(TeI, (0, 0, 1), 10, 10)
     TeI_slabs = trclnc_TeI.get_slabs()
     slab = TeI_slabs[0]
     norm_slab = slab.get_orthogonal_c_slab()
     self.assertAlmostEqual(norm_slab.lattice.angles[0], 90)
     self.assertAlmostEqual(norm_slab.lattice.angles[1], 90)

 def __init__(self, strt, hkl=[1,1,1], min_thick=10, min_vac=10,
              supercell=[1,1,1], name=None, adsorb_on_species=None,
              adatom_on_lig=None, ligand=None, displacement=1.0,
              surface_coverage=None, scell_nmax=10,
              coverage_tol=0.25, solvent=None, 
              start_from_slab=False, validate_proximity=False,
              to_unit_cell=False, coords_are_cartesian=False,
              primitive=True, from_ase=False,
              x_shift=0, y_shift=0, rot=[0,0,0],
              center_slab=True):
     self.from_ase = from_ase
     vac_extension = 0
     if ligand is not None:
         vac_extension = ligand.max_dist
     if isinstance(strt, Structure) and not isinstance(strt, Slab):
         self.min_vac = min_vac + vac_extension
         if self.from_ase:
             strt = get_ase_slab(strt,
                                 hkl=hkl,
                                 min_thick=min_thick,
                                 min_vac=min_vac + vac_extension, 
                                 center_slab=center_slab)
         else:
             strt = SlabGenerator(strt, hkl, min_thick,
                                  min_vac + vac_extension,
                                  center_slab=center_slab,
                                  primitive = primitive).get_slab()
         strt.make_supercell(supercell)
     else:
         self.min_vac = min_vac
     Slab.__init__(self, strt.lattice, strt.species_and_occu,
                   strt.frac_coords,
                   miller_index=strt.miller_index,
                   oriented_unit_cell=strt.oriented_unit_cell,
                   shift=strt.shift, scale_factor=strt.scale_factor,
                   validate_proximity=validate_proximity,
                   to_unit_cell=to_unit_cell,
                   coords_are_cartesian=coords_are_cartesian,
                   site_properties=strt.site_properties,
                   energy=strt.energy )
     self.strt= strt
     self.name = name
     self.hkl = hkl
     self.min_thick = min_thick
     self.supercell = supercell
     self.ligand = ligand
     self.slab = strt
     self.displacement = displacement
     self.solvent = solvent
     self.surface_coverage = surface_coverage
     self.adsorb_on_species = adsorb_on_species
     self.adatom_on_lig = adatom_on_lig
     self.scell_nmax = scell_nmax
     self.coverage_tol = coverage_tol
     self.x_shift = x_shift
     self.y_shift = y_shift
     self.rot = rot

def get_dimensionality(structure, max_hkl=2, el_radius_updates=None,
                       min_slab_size=5, min_vacuum_size=5,
                       standardize=True, bonds=None):
    """
    This method returns whether a structure is 3D, 2D (layered), or 1D (linear 
    chains or molecules) according to the algorithm published in Gorai, P., 
    Toberer, E. & Stevanovic, V. Computational Identification of Promising 
    Thermoelectric Materials Among Known Quasi-2D Binary Compounds. J. Mater. 
    Chem. A 2, 4136 (2016).
    
    Note that a 1D structure detection might indicate problems in the bonding
    algorithm, particularly for ionic crystals (e.g., NaCl)
    
    Users can change the behavior of bonds detection by passing either
    el_radius_updates to update atomic radii for auto-detection of max bond 
    distances, or bonds to explicitly specify max bond distances for atom pairs.
    Note that if you pass both, el_radius_updates are ignored.
    
    Args:
        structure: (Structure) structure to analyze dimensionality for 
        max_hkl: (int) max index of planes to look for layers
        el_radius_updates: (dict) symbol->float to update atomic radii
        min_slab_size: (float) internal surface construction parameter
        min_vacuum_size: (float) internal surface construction parameter
        standardize (bool): whether to standardize the structure before 
            analysis. Set to False only if you already have the structure in a 
            convention where layers / chains will be along low <hkl> indexes.
        bonds ({(specie1, specie2): max_bond_dist}: bonds are
                specified as a dict of tuples: float of specie1, specie2
                and the max bonding distance. For example, PO4 groups may be
                defined as {("P", "O"): 3}.

    Returns: (int) the dimensionality of the structure - 1 (molecules/chains), 
        2 (layered), or 3 (3D)

    """
    if standardize:
        structure = SpacegroupAnalyzer(structure). \
            get_conventional_standard_structure()

    if not bonds:
        bonds = get_max_bond_lengths(structure, el_radius_updates)

    num_surfaces = 0
    for h in range(max_hkl):
        for k in range(max_hkl):
            for l in range(max_hkl):
                if max([h, k, l]) > 0 and num_surfaces < 2:
                    sg = SlabGenerator(structure, (h, k, l),
                                       min_slab_size=min_slab_size,
                                       min_vacuum_size=min_vacuum_size)
                    slabs = sg.get_slabs(bonds)
                    for _ in slabs:
                        num_surfaces += 1

    return 3 - min(num_surfaces, 2)

 def test_normal_search(self):
     fcc = Structure.from_spacegroup("Fm-3m", Lattice.cubic(3), ["Fe"],
                                     [[0, 0, 0]])
     for miller in [(1, 0, 0), (1, 1, 0), (1, 1, 1), (2, 1, 1)]:
         gen = SlabGenerator(fcc, miller, 10, 10)
         gen_normal = SlabGenerator(fcc, miller, 10, 10,
                                    max_normal_search=max(miller))
         slab = gen_normal.get_slab()
         self.assertAlmostEqual(slab.lattice.alpha, 90)
         self.assertAlmostEqual(slab.lattice.beta, 90)
         self.assertGreaterEqual(len(gen_normal.oriented_unit_cell),
                                 len(gen.oriented_unit_cell))

 def test_triclinic_TeI(self):
     # Test case for a triclinic structure of TeI. Only these three
     # Miller indices are used because it is easier to identify which
     # atoms should be in a surface together. The closeness of the sites
     # in other Miller indices can cause some ambiguity when choosing a
     # higher tolerance.
     numb_slabs = {(0, 0, 1): 5, (0, 1, 0): 3, (1, 0, 0): 7}
     TeI = Structure.from_file(get_path("icsd_TeI.cif"),
                               primitive=False)
     for k, v in numb_slabs.items():
         trclnc_TeI = SlabGenerator(TeI, k, 10, 10)
         TeI_slabs = trclnc_TeI.get_slabs()
         self.assertEqual(v, len(TeI_slabs))

    def setUp(self):

        if "PMG_VASP_PSP_DIR" not in os.environ:
            os.environ["PMG_VASP_PSP_DIR"] = test_dir
        s = PymatgenTest.get_structure("Li2O")
        gen = SlabGenerator(s, (1, 0, 0), 10, 10)
        self.slab = gen.get_slab()
        self.bulk = self.slab.oriented_unit_cell

        vis_bulk = MVLSlabSet(self.bulk, bulk=True)
        vis = MVLSlabSet(self.slab)

        self.d_bulk = vis_bulk.all_input
        self.d_slab = vis.all_input

    def setUp(self):

        if "VASP_PSP_DIR" not in os.environ:
            os.environ["VASP_PSP_DIR"] = test_dir
        s = PymatgenTest.get_structure("Li2O")
        gen = SlabGenerator(s, (1, 0, 0), 10, 10)
        vis_bulk = MVLSlabSet(bulk=True)
        vis = MVLSlabSet()
        vis_bulk_gpu = MVLSlabSet(bulk=True, gpu=True)

        self.slab = gen.get_slab()
        self.bulk = self.slab.oriented_unit_cell
        self.d_bulk = vis_bulk.get_all_vasp_input(self.bulk)
        self.d_slab = vis.get_all_vasp_input(self.slab)
        self.d_bulk_gpu = vis_bulk_gpu.get_all_vasp_input(self.bulk)

    def setUp(self):
        s = self.get_structure("Li2O")
        gen = SlabGenerator(s, (1, 0, 0), 10, 10)
        self.slab = gen.get_slab()
        self.bulk = self.slab.oriented_unit_cell

        vis_bulk = MVLSlabSet(self.bulk, bulk=True)
        vis = MVLSlabSet(self.slab)
        vis_dipole = MVLSlabSet(self.slab, auto_dipole=True)

        self.d_bulk = vis_bulk.get_vasp_input()
        self.d_slab = vis.get_vasp_input()
        self.d_dipole = vis_dipole.get_vasp_input()
        self.vis = vis
        warnings.simplefilter("ignore")

    def setUp(self):
        if "PMG_VASP_PSP_DIR" not in os.environ:
            os.environ["PMG_VASP_PSP_DIR"] = test_dir
        s = PymatgenTest.get_structure("Li2O")
        gen = SlabGenerator(s, (1, 0, 0), 10, 10)
        self.slab = gen.get_slab()
        self.bulk = self.slab.oriented_unit_cell

        vis_bulk = MVLSlabSet(self.bulk, bulk=True)
        vis = MVLSlabSet(self.slab)
        vis_dipole = MVLSlabSet(self.slab, auto_dipole=True)

        self.d_bulk = vis_bulk.all_input
        self.d_slab = vis.all_input
        self.d_dipole = vis_dipole.all_input
        self.vis = vis
        warnings.simplefilter("ignore")

    def test_get_orthogonal_c_slab_site_props(self):
        TeI = Structure.from_file(get_path("icsd_TeI.cif"),
                                  primitive=False)
        trclnc_TeI = SlabGenerator(TeI, (0, 0, 1), 10, 10)
        TeI_slabs = trclnc_TeI.get_slabs()
        slab = TeI_slabs[0]
        # Add site property to slab
        sd_list = [[True, True, True] for site in slab.sites]
        new_sp = slab.site_properties
        new_sp['selective_dynamics'] = sd_list
        slab_with_site_props = slab.copy(site_properties=new_sp)

        # Get orthogonal slab
        norm_slab = slab_with_site_props.get_orthogonal_c_slab()

        # Check if site properties is consistent (or kept)
        self.assertEqual(slab_with_site_props.site_properties, norm_slab.site_properties)