コード例 #1
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 def setUpClass(cls):
     cls.bcc = CrystalStructure("Fe",
                                bravais_basis="bcc",
                                lattice_constants=[2.7])
     cls.fcc = CrystalStructure("Fe",
                                bravais_basis="fcc",
                                lattice_constants=[3.6])
コード例 #2
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 def test_occupy_lattice(self):
     basis_Mg = CrystalStructure("Mg",
                                 bravais_basis="fcc",
                                 lattice_constant=4.2)
     basis_O = CrystalStructure("O",
                                bravais_basis="fcc",
                                lattice_constant=4.2)
     basis_O.scaled_positions += [0., 0., 0.5]
     basis = basis_Mg + basis_O
     basis.center_coordinates_in_unit_cell()
     orig_basis = basis.copy()
     self.assertEqual(basis.get_chemical_formula(), "Mg4O4")
     Mg_indices = basis.select_index("Mg")
     O_indices = basis.select_index("O")
     basis.occupy_lattice(Na=Mg_indices)
     self.assertEqual(basis.get_chemical_formula(), "Na4O4")
     basis.occupy_lattice(Cl=O_indices)
     self.assertEqual(basis.get_chemical_formula(), "Cl4Na4")
     self.assertTrue(np.array_equal(basis.select_index("Na"), Mg_indices))
     self.assertTrue(np.array_equal(basis.select_index("Cl"), O_indices))
     orig_basis.set_repeat([2, 2, 2])
     Mg_indices = orig_basis.select_index("Mg")
     O_indices = orig_basis.select_index("O")
     orig_basis.occupy_lattice(Cl=O_indices, Na=Mg_indices)
     self.assertEqual(orig_basis.get_chemical_formula(), "Cl32Na32")
     orig_basis.occupy_lattice(H=O_indices[0])
     self.assertEqual(orig_basis.get_chemical_formula(), "Cl31HNa32")
コード例 #3
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 def setUp(self):
     self.bcc = CrystalStructure("Fe",
                                 bravais_basis='bcc',
                                 lattice_constants=[2.7])
     self.fcc = CrystalStructure("Fe",
                                 bravais_basis='fcc',
                                 lattice_constants=[3.6])
コード例 #4
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 def test__getitem__(self):
     self.assertEqual(self.CO2[0].symbol, 'C')
     self.assertEqual(self.C3[2].position.tolist(), [0, 2, 0])
     self.assertTrue((self.C3[1:].positions == np.array([[0, 0, 2],
                                                         [0, 2, 0]])).all())
     short_basis = self.CO2[0]
     self.assertIsInstance(short_basis, Atom)
     short_basis = self.CO2[[0]]
     self.assertIsInstance(short_basis, Atoms)
     self.assertEqual(short_basis.indices[0], 0)
     self.assertEqual(len(short_basis.species), 1)
     short_basis = self.CO2[[2]]
     self.assertIsInstance(short_basis, Atoms)
     self.assertEqual(short_basis.indices[0], 0)
     self.assertEqual(len(short_basis.species), 1)
     basis_Mg = CrystalStructure("Mg",
                                 bravais_basis="fcc",
                                 lattice_constant=4.2)
     basis_O = CrystalStructure("O",
                                bravais_basis="fcc",
                                lattice_constant=4.2)
     basis_O.positions += [0., 0., 0.5]
     basis = basis_Mg + basis_O
     basis.center_coordinates_in_unit_cell()
     basis.set_repeat([3, 3, 3])
     mg_indices = basis.select_index("Mg")
     o_indices = basis.select_index("O")
     basis_new = basis[mg_indices] + basis[o_indices]
     self.assertEqual(len(basis_new._tag_list),
                      len(basis[mg_indices]) + len(basis[o_indices]))
     self.assertEqual(basis_new.get_spacegroup()["Number"], 225)
コード例 #5
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 def test_get_scaled_positions(self):
     basis_Mg = CrystalStructure("Mg",
                                 bravais_basis="fcc",
                                 lattice_constant=4.2)
     self.assertTrue(
         np.array_equal(basis_Mg.scaled_positions,
                        basis_Mg.get_scaled_positions()))
コード例 #6
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ファイル: test_murnaghan.py プロジェクト: t-brink/pyiron
 def setUpClass(cls):
     cls.file_location = os.path.dirname(os.path.abspath(__file__))
     cls.project = Project(os.path.join(cls.file_location, "test_murnaghan"))
     cls.basis = CrystalStructure(
         element="Fe", bravais_basis="fcc", lattice_constant=3.5
     )
     cls.project.remove_jobs_silently(recursive=True)
コード例 #7
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ファイル: test_neighbors.py プロジェクト: t-brink/pyiron
 def test_get_global_shells(self):
     structure = CrystalStructure(elements='Al', lattice_constants=4, bravais_basis='fcc').repeat(2)
     neigh = structure.get_neighbors()
     self.assertTrue(np.array_equal(neigh.shells, neigh.get_global_shells()))
     structure += Atoms(elements='C', positions=[[0, 0, 0.5*4]])
     neigh = structure.get_neighbors()
     self.assertFalse(np.array_equal(neigh.shells, neigh.get_global_shells()))
     structure = CrystalStructure(elements='Al', lattice_constants=4, bravais_basis='fcc').repeat(2)
     neigh = structure.get_neighbors()
     shells = neigh.get_global_shells()
     structure.positions += 0.01*(np.random.random((len(structure), 3))-0.5)
     neigh = structure.get_neighbors()
     self.assertTrue(np.array_equal(shells, neigh.get_global_shells(cluster_by_vecs=True, cluster_by_distances=True)))
     neigh.reset_clusters()
     self.assertTrue(np.array_equal(shells, neigh.get_global_shells(cluster_by_vecs=True)))
     self.assertFalse(np.array_equal(shells, neigh.get_global_shells()))
コード例 #8
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 def setUpClass(cls):
     cls.file_location = os.path.dirname(os.path.abspath(__file__))
     cls.project = Project(
         os.path.join(cls.file_location, "testing_murnaghan_non_modal"))
     cls.basis = CrystalStructure(element="Fe",
                                  bravais_basis="bcc",
                                  lattice_constant=2.8)
     cls.project.remove_jobs(recursive=True)
コード例 #9
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 def test_set_empty_states(self):
     atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
     self.job.structure = atoms
     self.job.set_empty_states(n_empty_states=10)
     self.assertEqual(self.job.input.incar["NBANDS"], 15)
     self.job.structure = atoms.repeat([3, 1, 1])
     self.job.set_empty_states(n_empty_states=10)
     self.assertEqual(self.job.input.incar["NBANDS"], 25)
コード例 #10
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ファイル: test_neighbors.py プロジェクト: t-brink/pyiron
 def test_cluster_analysis(self):
     basis = CrystalStructure("Al", bravais_basis="fcc", lattice_constants=4.2).repeat(10)
     neigh = basis.get_neighbors(num_neighbors=100)
     key, counts = neigh.cluster_analysis(id_list=[0,1], return_cluster_sizes=True)
     self.assertTrue(np.array_equal(key[1], [0,1]))
     self.assertEqual(counts[0], 2)
     key, counts = neigh.cluster_analysis(id_list=[0,int(len(basis)/2)], return_cluster_sizes=True)
     self.assertTrue(np.array_equal(key[1], [0]))
     self.assertEqual(counts[0], 1)
コード例 #11
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 def test_set_structure(self):
     self.assertEqual(self.job.structure, None)
     atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
     self.job.structure = atoms
     self.assertEqual(self.job.structure, atoms)
     self.job.structure = None
     self.assertEqual(self.job.structure, None)
     self.job.structure = atoms
     self.assertEqual(self.job.structure, atoms)
コード例 #12
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ファイル: test_neighbors.py プロジェクト: t-brink/pyiron
 def test_get_shell_matrix(self):
     structure = CrystalStructure(elements='Fe', lattice_constants=2.83, bravais_basis='bcc').repeat(2)
     structure[0] = 'Ni'
     neigh = structure.get_neighbors(num_neighbors=8)
     mat = neigh.get_shell_matrix()
     self.assertEqual(mat[0].sum(), 8*len(structure))
     mat = neigh.get_shell_matrix(chemical_pair=['Fe', 'Ni'])
     self.assertEqual(mat[0].sum(), 16)
     mat = neigh.get_shell_matrix(chemical_pair=['Ni', 'Ni'])
     self.assertEqual(mat[0].sum(), 0)
コード例 #13
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ファイル: test_atomistic.py プロジェクト: samk07/pyiron
 def setUpClass(cls):
     cls.execution_path = os.path.dirname(os.path.abspath(__file__))
     cls.project = Project(os.path.join(cls.execution_path, "test_job"))
     cls.job = AtomisticGenericJob(
         project=ProjectHDFio(project=cls.project, file_name="test_job"),
         job_name="test_job",
     )
     cls.job.structure = CrystalStructure(
         element="Al", bravais_basis="fcc", lattice_constants=4
     ).repeat(4)
コード例 #14
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 def test_parent_index(self):
     basis_Mg = CrystalStructure("Mg",
                                 bravais_basis="fcc",
                                 lattice_constant=4.2)
     basis_O = CrystalStructure("O",
                                bravais_basis="fcc",
                                lattice_constant=4.2)
     basis_O.positions += [0., 0., 0.5]
     basis = basis_Mg + basis_O
     basis.center_coordinates_in_unit_cell()
     basis.set_repeat([2, 2, 2])
     o_indices = basis.select_index("O")
     pse = PeriodicTable()
     pse.add_element("O", "O_up", spin="up")
     o_up = pse.element("O_up")
     basis[o_indices] = o_up
     self.assertTrue(np.array_equal(o_indices, basis.select_index(o_up)))
     self.assertEqual(len(basis.select_index("O")), 0)
     self.assertTrue(
         np.array_equal(o_indices, basis.select_parent_index("O")))
コード例 #15
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 def test_run(self):
     job = self.project.create_job(
         self.project.job_type.AtomisticExampleJob, "job_test")
     basis = CrystalStructure(element="Fe",
                              bravais_basis="bcc",
                              lattice_constant=2.83)
     basis.set_initial_magnetic_moments([2, 2])
     job.structure = basis
     phono = self.project.create_job("PhonopyJob", "phono")
     phono.ref_job = job
     structure = phono.list_structures()[0]
     magmoms = structure.get_initial_magnetic_moments()
     self.assertAlmostEqual(sum(magmoms - 2), 0)
コード例 #16
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 def test_repeat(self):
     basis_Mg = CrystalStructure("Mg",
                                 bravais_basis="fcc",
                                 lattice_constant=4.2)
     basis_O = CrystalStructure("O",
                                bravais_basis="fcc",
                                lattice_constant=4.2)
     basis_O.scaled_positions += [0., 0., 0.5]
     basis = basis_Mg + basis_O
     basis.center_coordinates_in_unit_cell()
     basis.add_tag(selective_dynamics=[True, True, True])
     basis.selective_dynamics[basis.select_index("O")] = [
         False, False, False
     ]
     len_before = len(basis)
     sel_dyn_before = np.array(basis.selective_dynamics.list())
     self.assertTrue(
         np.alltrue(
             np.logical_not(
                 np.alltrue(sel_dyn_before[basis.select_index("O")],
                            axis=1))))
     self.assertTrue(
         np.alltrue(
             np.alltrue(sel_dyn_before[basis.select_index("Mg")], axis=1)))
     basis.set_repeat([3, 3, 2])
     sel_dyn_after = np.array(basis.selective_dynamics.list())
     len_after = len(basis)
     self.assertEqual(basis.get_spacegroup()["Number"], 225)
     self.assertEqual(len_before * 18, len_after)
     self.assertEqual(len(sel_dyn_before) * 18, len(sel_dyn_after))
     self.assertTrue(
         np.alltrue(
             np.logical_not(
                 np.alltrue(sel_dyn_after[basis.select_index("O")],
                            axis=1))))
     self.assertTrue(
         np.alltrue(
             np.alltrue(sel_dyn_after[basis.select_index("Mg")], axis=1)))
コード例 #17
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ファイル: project.py プロジェクト: ares201005/pyiron
    def create_structure(element, bravais_basis, lattice_constant):
        """
        
        Args:
            element: 
            bravais_basis: 
            lattice_constant: 

        Returns:

        """
        return CrystalStructure(element=element,
                                bravais_basis=bravais_basis,
                                lattice_constants=[lattice_constant])
コード例 #18
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 def test_Chemical_Element_to_and_from_hdf_with_None_Parent(self):
     pr = Project(
         os.path.join(os.path.dirname(os.path.abspath(__file__)),
                      "test_periodic_table"))
     basis = CrystalStructure(element="Ni",
                              bravais_basis="fcc",
                              lattice_constant=3.7)
     ham = pr.create_job(pr.job_type.Lammps, "lammps_test_2")
     test_ham = pr.create_job(pr.job_type.Lammps, "lammps_test_2")
     ham.structure = basis
     ham.to_hdf()
     test_ham.from_hdf()
     self.assertEqual(test_ham["input/structure/species"][0],
                      ham["input/structure/species"][0])
     ham.remove()
コード例 #19
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 def test_Chemical_Element_to_and_from_hdf(self):
     ni_up = self.pse.add_element("Ni", "Ni_up", spin="up")
     pr = Project(
         os.path.join(os.path.dirname(os.path.abspath(__file__)),
                      'test_periodic_table'))
     basis = CrystalStructure(element=ni_up,
                              bravais_basis='fcc',
                              lattice_constant=3.7)
     ham = pr.create_job(pr.job_type.Lammps, 'lammps_test_1')
     test_ham = pr.create_job(pr.job_type.Lammps, 'lammps_test_1')
     ham.structure = basis
     ham.to_hdf()
     test_ham.from_hdf()
     self.assertEqual(test_ham['input/structure/species'][0],
                      ham['input/structure/species'][0])
     ham.remove()
コード例 #20
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    def test_write_magmoms(self):
        magmom = np.arange(8.)
        magmom_ncl = np.zeros([8, 3])
        magmom_ncl[:, 0] = magmom / 2
        magmom_ncl[:, 1] = magmom
        magmom_ncl[:, 2] = magmom ** 2

        magmom_str = "0.0   1.0   2.0   3.0   4.0   5.0   6.0   7.0"
        magmom_ncl_str =\
            "0.0 0.0 0.0   0.5 1.0 1.0   1.0 2.0 4.0   1.5 3.0 9.0   " \
            "2.0 4.0 16.0   2.5 5.0 25.0   3.0 6.0 36.0   3.5 7.0 49.0"

        self.job.structure = CrystalStructure("Fe", BravaisBasis="bcc", a=2.83)
        self.job.structure = self.job.structure.repeat(2)

        self.job.structure.set_initial_magnetic_moments(magmom)

        self.job.input.incar["ISPIN"] = 1
        self.job.write_magmoms()
        self.assertIsNone(self.job.input.incar["MAGMOM"])
        self.assertEqual(self.job.input.incar["ISPIN"], 1)

        del self.job.input.incar["ISPIN"]
        self.job.write_magmoms()
        self.assertEqual(self.job.input.incar["ISPIN"], 2)
        self.assertEqual(self.job.input.incar["MAGMOM"], magmom_str)

        del self.job.input.incar["MAGMOM"]
        self.job.structure.set_initial_magnetic_moments(magmom_ncl)
        self.job.set_spin_constraint(lamb=1.0, rwigs_dict={"Fe": 2.5}, direction=True, norm=True)
        self.job.write_magmoms()
        self.assertEqual(self.job.input.incar["LNONCOLLINEAR"], True)
        self.assertEqual(self.job.input.incar["MAGMOM"], magmom_ncl_str)
        self.assertEqual(self.job.input.incar["M_CONSTR"], magmom_ncl_str)

        del self.job.input.incar["MAGMOM"]
        del self.job.input.incar["M_CONSTR"]
        del self.job.input.incar["LNONCOLLINEAR"]
        del self.job.input.incar["RWIGS"]

        self.assertRaises(ValueError, self.job.write_magmoms)

        self.job.input.incar["RWIGS"] = "2.5"
        del self.job.input.incar["LAMBDA"]

        self.assertRaises(ValueError, self.job.write_magmoms)
コード例 #21
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 def test_run(self):
     job = self.project.create_job(
         'HessianJob', "job_test"
     )
     basis = CrystalStructure(
         element="Fe", bravais_basis="bcc", lattice_constant=2.85
     )
     basis.set_initial_magnetic_moments([2]*len(basis))
     job.set_reference_structure(basis)
     phono = job.create_job("PhonopyJob", "phono")
     structure = phono.list_structures()[0]
     magmoms = structure.get_initial_magnetic_moments()
     self.assertAlmostEqual(sum(magmoms-2), 0)
     rep = phono._phonopy_supercell_matrix().diagonal().astype(int)
     job._reference_structure.set_repeat(rep)
     job.structure.set_repeat(rep)
     job.set_force_constants(1)
コード例 #22
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def create_structure(element, bravais_basis, lattice_constant):
    """
    Create a crystal structure using pyiron's native crystal structure generator

    Args:
        element (str): Element name
        bravais_basis (str): Basis type
        lattice_constant (float/list): Lattice constants

    Returns:
        pyiron.atomistics.structure.atoms.Atoms: The required crystal structure

    """
    return CrystalStructure(
        element=element,
        bravais_basis=bravais_basis,
        lattice_constants=[lattice_constant],
    )
コード例 #23
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ファイル: test_neighbors.py プロジェクト: t-brink/pyiron
 def test_get_neighbors(self):
     struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc').repeat(10)
     cell = struct.cell.copy()
     cell += np.random.random((3,3))-0.5
     struct.positions += np.random.random((len(struct), 3))-0.5
     struct.set_cell(cell, scale_atoms=True)
     neigh = struct.get_neighbors()
     self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
     myself = np.ones_like(neigh.indices)
     myself = myself*np.arange(len(myself))[:,np.newaxis]
     dist = struct.get_distances(myself.flatten(), neigh.indices.flatten(), mic=True)
     self.assertAlmostEqual(np.absolute(dist-neigh.distances.flatten()).max(), 0)
     vecs = struct.get_distances(myself.flatten(), neigh.indices.flatten(), mic=True, vector=True)
     self.assertAlmostEqual(np.absolute(vecs-neigh.vecs.reshape(-1, 3)).max(), 0)
     dist = struct.get_scaled_positions()
     dist = dist[:,np.newaxis,:]-dist[np.newaxis,:,:]
     dist -= np.rint(dist)
     dist = np.einsum('nmi,ij->nmj', dist, struct.cell)
     dist = np.linalg.norm(dist, axis=-1).flatten()
     dist = dist[dist>0]
     self.assertAlmostEqual(neigh.distances.min(), dist.min())
     struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc').repeat(10)
     struct.pbc = False
     cell = struct.cell.copy()
     cell += np.random.random((3,3))-0.5
     struct.set_cell(cell, scale_atoms=True)
     neigh = struct.get_neighbors()
     self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
     myself = np.ones_like(neigh.indices)
     myself = myself*np.arange(len(myself))[:,np.newaxis]
     dist = np.linalg.norm(struct.positions[myself]-struct.positions[neigh.indices], axis=-1)
     self.assertAlmostEqual(np.absolute(dist-neigh.distances).max(), 0)
     struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc').repeat(10)
     neigh = struct.get_neighbors()
     self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
     self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
     self.assertAlmostEqual(neigh.vecs[0, neigh.shells[0]==1].sum(), 0)
     struct = CrystalStructure(elements='Fe', lattice_constants=2.85, bravais_basis='bcc')
     neigh = struct.get_neighbors()
     self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
     struct = CrystalStructure(elements='Al', lattice_constants=4.04, bravais_basis='bcc').repeat(10)
     neigh = struct.get_neighbors()
     self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
     self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
     self.assertAlmostEqual(neigh.vecs[0, neigh.shells[0]==1].sum(), 0)
     struct = CrystalStructure(elements='Al', lattice_constants=4.04, bravais_basis='bcc')
     neigh = struct.get_neighbors()
     self.assertAlmostEqual(np.absolute(neigh.distances-np.linalg.norm(neigh.vecs, axis=-1)).max(), 0)
     self.assertAlmostEqual(neigh.vecs[neigh.shells==1].sum(), 0)
     with self.assertRaises(ValueError):
         struct.get_neighbors(num_neighbors=0)
コード例 #24
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ファイル: test_sqs.py プロジェクト: t-brink/pyiron
 def test_run(self):
     try:  # Only test if the machine has access to sqsgenerator -- at time of writing Windows doesn't
         job = self.project.create_job(
             'SQSJob', "job_test"
         )
         structure = CrystalStructure("Al", bravais_basis="fcc", lattice_constant=4)
         job.structure = structure
         with self.assertRaises(ValueError):
             job.validate_ready_to_run()
         job.input.mole_fractions = dict()
         structure[0] = 'Sc'
         job.structure = structure
         job.validate_ready_to_run()
         job.input.mole_fractions = dict()
         mole_fractions = {'Al': 0.5, 'Sc': 0.5}
         job.input.mole_fractions = mole_fractions.copy()
         job.structure = structure
         job.validate_ready_to_run()
         self.assertAlmostEqual(job.input.mole_fractions['Al'], mole_fractions['Al'])
     except ImportError:
         pass
コード例 #25
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 def setUpClass(cls):
     cls.execution_path = os.path.dirname(os.path.abspath(__file__))
     cls.project = Project(os.path.join(cls.execution_path, "test_vasp"))
     cls.job = cls.project.create_job("Vasp", "trial")
     cls.job_spin = cls.project.create_job("Vasp", "spin")
     cls.job_spin.structure = CrystalStructure("Fe", BravaisBasis="bcc", a=2.83)
     cls.job_spin.structure = cls.job_spin.structure.repeat(2)
     cls.job_spin.structure[2] = "Se"
     cls.job_spin.structure[3] = "O"
     cls.job_metadyn = cls.project.create_job("VaspMetadyn", "trial_metadyn")
     cls.job_complete = Vasp(
         project=ProjectHDFio(project=cls.project, file_name="vasp_complete"),
         job_name="vasp_complete",
     )
     poscar_file = posixpath.join(
         cls.execution_path, "../static/vasp_test_files/full_job_sample/POSCAR"
     )
     cls.job_complete.structure = read_atoms(poscar_file, species_from_potcar=True)
     poscar_file = posixpath.join(
         cls.execution_path, "../static/vasp_test_files/poscar_samples/POSCAR_metadyn"
     )
     cls.job_metadyn.structure = read_atoms(poscar_file)
コード例 #26
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 def test_get_nelect(self):
     atoms = CrystalStructure("Pt", BravaisBasis="fcc", a=3.98)
     self.job.structure = atoms
     self.assertEqual(self.job.get_nelect(), 10)
コード例 #27
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ファイル: test_neighbors.py プロジェクト: t-brink/pyiron
 def test_get_bonds(self):
     basis = CrystalStructure("Al", bravais_basis="fcc", lattice_constants=4.2).repeat(5)
     neigh = basis.get_neighbors(num_neighbors=20)
     bonds = neigh.get_bonds()
     self.assertTrue(np.array_equal(np.sort(bonds[0]['Al'][0]),
                     np.sort(neigh.indices[0, neigh.shells[0]==1])))
コード例 #28
0
    def test__add__(self):
        cell = np.eye(3) * 10.0
        basis_0 = Atoms(["O"], scaled_positions=[[0.5, 0.5, 0.5]], cell=cell)
        basis_1 = Atoms(["H"],
                        scaled_positions=[[0.75, 0.75, 0.75]],
                        cell=cell)
        basis_2 = Atoms(["H"],
                        scaled_positions=[[0.25, 0.25, 0.25]],
                        cell=cell)
        basis_3 = Atoms(["H", "O", "N"],
                        scaled_positions=[[0.35, 0.35, 0.35], [0., 0., 0.],
                                          [0., 0., 0.1]],
                        cell=cell)

        pse = PeriodicTable()
        pse.add_element("O", "O_up", spin="up")
        o_up = pse.element("O_up")
        basis_4 = Atoms([o_up],
                        scaled_positions=[[0.27, 0.27, 0.27]],
                        cell=np.eye(3) * 20.0)
        b = basis_0 + basis_1
        self.assertEqual(b.get_chemical_formula(), "HO")
        b = basis_0 + basis_1 + basis_2
        self.assertEqual(b.get_chemical_formula(), "H2O")
        b += basis_2
        self.assertEqual(b.get_chemical_formula(), "H3O")
        b = basis_0 + basis_1 + basis_2 + basis_3
        self.assertEqual(b.get_chemical_formula(), "H3NO2")
        self.assertTrue(
            np.array_equal(b.scaled_positions[b.select_index("N")],
                           [[0., 0., 0.1]]))
        self.assertTrue(
            np.allclose(
                b.scaled_positions[b.select_index("H")],
                [[0.75, 0.75, 0.75], [0.25, 0.25, 0.25], [0.35, 0.35, 0.35]]))
        self.assertTrue(
            np.allclose(b.scaled_positions[b.select_index("O")],
                        [[0.5, 0.5, 0.5], [0., 0., 0.]]))
        b.set_repeat([2, 2, 2])
        self.assertEqual(b.get_chemical_formula(), "H24N8O16")
        b += basis_4
        self.assertEqual(b.get_chemical_formula(), "H24N8O16O_up")
        self.assertTrue(
            np.allclose(b.scaled_positions[b.select_index(o_up)],
                        [[0.27, 0.27, 0.27]]))
        COX = self.C2 + Atom("O", position=[0, 0, -2])
        COX += Atom("O", position=[0, 0, -4])
        COX += COX
        n_objects = len(set(COX.get_species_objects()))
        n_species = len(set(COX.get_chemical_elements()))
        self.assertEqual(n_objects, n_species)
        self.assertEqual(n_objects, 2)
        self.assertEqual(n_species, 2)
        basis_Mg = CrystalStructure("Mg",
                                    bravais_basis="fcc",
                                    lattice_constant=4.2)
        basis_O = CrystalStructure("O",
                                   bravais_basis="fcc",
                                   lattice_constant=4.2)
        # basis_O.set_relative()
        basis_O.scaled_positions += [0., 0., 0.5]
        basis = basis_Mg + basis_O
        self.assertEqual(len(basis._tag_list),
                         len(basis_Mg._tag_list) + len(basis_O._tag_list))
        basis.center_coordinates_in_unit_cell()
        self.assertEqual(basis.get_spacegroup()["Number"], 225)