Add grain boundary generator

pymatgen/core/tests/test_grain_boundary_generator.py

@@ -0,0 +1,225 @@
+from __future__ import division, unicode_literals
+
+__author__ = 'Xiang-Guo Li'
+__copyright__ = 'Copyright 2018, The Materials Virtual Lab'
+__email__ = 'xil110@eng.ucsd.edu'
+__date__ = '05/18/18'
+
+from pymatgen.util.testing import PymatgenTest
+import os
+import numpy as np
+from pymatgen import Structure
+from pymatgen.core.grain_boundary_generator import GBGenerator
+
+test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
+                        "test_files", "grain_boundary")
+
+
+class Test_grain_boundary_generator(PymatgenTest):
+    @classmethod
+    def setUpClass(cls):
+        cls.Cu_prim = Structure.from_file(os.path.join(test_dir, "Cu_mp-30_primitive.cif"))
+        cls.GB_Cu_prim = GBGenerator(cls.Cu_prim)
+        cls.Cu_conv = Structure.from_file(os.path.join(test_dir,
+                                                       "Cu_mp-30_conventional_standard.cif"))
+        cls.GB_Cu_conv = GBGenerator(cls.Cu_conv)
+        cls.Be = Structure.from_file(os.path.join(test_dir,
+                                                  "Be_mp-87_conventional_standard.cif"))
+        cls.GB_Be = GBGenerator(cls.Be)
+        cls.Pa = Structure.from_file(os.path.join(test_dir,
+                                                  "Pa_mp-62_conventional_standard.cif"))
+        cls.GB_Pa = GBGenerator(cls.Pa)
+        cls.Br = Structure.from_file(os.path.join(test_dir,
+                                                  "Br_mp-23154_conventional_standard.cif"))
+        cls.GB_Br = GBGenerator(cls.Br)
+        cls.Bi = Structure.from_file(os.path.join(test_dir,
+                                                  "Bi_mp-23152_primitive.cif"))
+        cls.GB_Bi = GBGenerator(cls.Bi)
+
+    def test_gb_from_parameters(self):
+        # from fcc primitive cell,axis[1,2,3],sigma 9.
+        gb_cu_123_prim1 = self.GB_Cu_prim.gb_from_parameters([1, 2, 3],
+                                                             123.74898859588858,
+                                                             expand_times=2)
+        lat_mat1 = gb_cu_123_prim1.lattice.matrix
+        c_vec1 = np.cross(lat_mat1[0], lat_mat1[1]) / np.linalg.norm(np.cross(lat_mat1[0], lat_mat1[1]))
+        c_len1 = np.dot(lat_mat1[2], c_vec1)
+        vol_ratio = gb_cu_123_prim1.volume / self.Cu_prim.volume
+        self.assertAlmostEqual(vol_ratio, 9 * 2 * 2, 8)
+        # test expand_times
+        gb_cu_123_prim2 = self.GB_Cu_prim.gb_from_parameters([1, 2, 3],
+                                                             123.74898859588858,
+                                                             expand_times=4)
+        lat_mat2 = gb_cu_123_prim2.lattice.matrix
+        c_vec2 = np.cross(lat_mat2[0], lat_mat2[1]) / np.linalg.norm(np.cross(lat_mat2[0], lat_mat2[1]))
+        c_len2 = np.dot(lat_mat2[2], c_vec2)
+        self.assertAlmostEqual(c_len2 / c_len1, 2)
+        # test vacuum layer
+        gb_cu_123_prim3 = self.GB_Cu_prim.gb_from_parameters([1, 2, 3],
+                                                             123.74898859588858,
+                                                             expand_times=4,
+                                                             vacuum_thickness=1.5)
+        lat_mat3 = gb_cu_123_prim3.lattice.matrix
+        c_vec3 = np.cross(lat_mat3[0], lat_mat3[1]) / np.linalg.norm(np.cross(lat_mat3[0], lat_mat3[1]))
+        c_len3 = np.dot(lat_mat3[2], c_vec3)
+        self.assertAlmostEqual(c_len3 - c_len2, 1.5 * 2)
+
+        # from fcc conventional cell,axis [1,2,3], siamg 9
+        gb_cu_123_conv1 = self.GB_Cu_conv.gb_from_parameters([1, 2, 3],
+                                                             123.74898859588858,
+                                                             expand_times=4,
+                                                             vacuum_thickness=1.5)
+        lat_mat1 = gb_cu_123_conv1.lattice.matrix
+        self.assertAlmostEqual(np.dot(lat_mat1[0], [1, 2, 3]), 0)
+        self.assertAlmostEqual(np.dot(lat_mat1[1], [1, 2, 3]), 0)
+        # test normal
+        gb_cu_123_conv2 = self.GB_Cu_conv.gb_from_parameters([1, 2, 3],
+                                                             123.74898859588858,
+                                                             expand_times=4,
+                                                             vacuum_thickness=1.5,
+                                                             normal=True)
+        lat_mat2 = gb_cu_123_conv2.lattice.matrix
+        c_vec2 = np.cross(lat_mat2[0], lat_mat2[1]) / np.linalg.norm(np.cross(lat_mat2[0], lat_mat2[1]))
+        ab_len2 = np.linalg.norm(np.cross(lat_mat2[2], c_vec2))
+        self.assertAlmostEqual(ab_len2, 0)
+        # test plane
+        gb_cu_123_conv3 = self.GB_Cu_conv.gb_from_parameters([1, 2, 3],
+                                                             123.74898859588858,
+                                                             expand_times=4,
+                                                             vacuum_thickness=1.5,
+                                                             plane=[1, 3, 1])
+        lat_mat3 = gb_cu_123_conv3.lattice.matrix
+        self.assertAlmostEqual(np.dot(lat_mat3[0], [1, 3, 1]), 0)
+        self.assertAlmostEqual(np.dot(lat_mat3[1], [1, 3, 1]), 0)
+
+        # from hex cell,axis [1,1,1], sigma 21
+        gb_Be_111_1 = self.GB_Be.gb_from_parameters([1, 1, 1],
+                                                    128.246619878345,
+                                                    ratio=[12, 5],
+                                                    expand_times=4,
+                                                    vacuum_thickness=1.5,
+                                                    plane=[1, 2, 1])
+        lat_priv = self.Be.lattice.matrix
+        lat_mat1 = np.matmul(gb_Be_111_1.lattice.matrix, np.linalg.inv(lat_priv))
+        self.assertAlmostEqual(np.dot(lat_mat1[0], [1, 2, 1]), 0)
+        self.assertAlmostEqual(np.dot(lat_mat1[1], [1, 2, 1]), 0)
+        # test volume associated with sigma value
+        gb_Be_111_2 = self.GB_Be.gb_from_parameters([1, 1, 1], 128.246619878345, ratio=[12, 5],
+                                                    expand_times=4)
+        vol_ratio = gb_Be_111_2.volume / self.Be.volume
+        self.assertAlmostEqual(vol_ratio, 21 * 2 * 4)
+        # test ratio = None, axis [0,0,1], sigma 7
+        gb_Be_111_3 = self.GB_Be.gb_from_parameters([0, 0, 1], 21.786789298261812,
+                                                    ratio=[12, 5],
+                                                    expand_times=4)
+        gb_Be_111_4 = self.GB_Be.gb_from_parameters([0, 0, 1], 21.786789298261812, ratio=None,
+                                                    expand_times=4)
+        self.assertTupleEqual(gb_Be_111_3.lattice.abc, gb_Be_111_4.lattice.abc)
+        self.assertTupleEqual(gb_Be_111_3.lattice.angles, gb_Be_111_4.lattice.angles)
+        gb_Be_111_5 = self.GB_Be.gb_from_parameters([3, 1, 0], 180.0, ratio=[12, 5],
+                                                    expand_times=4)
+        ouc_supercell_gb_Be_111_6 = self.GB_Be.gb_from_parameters([3, 1, 0], 180.0, ratio=None,
+                                                                  expand_times=4)
+        gb_Be_111_6 = ouc_supercell_gb_Be_111_6[2]
+        self.assertTupleEqual(gb_Be_111_5.lattice.abc, gb_Be_111_6.lattice.abc)
+        self.assertTupleEqual(gb_Be_111_5.lattice.angles, gb_Be_111_6.lattice.angles)
+
+        # gb from tetragonal cell, axis[1,1,1], sigma 15
+        gb_Pa_111_1 = self.GB_Pa.gb_from_parameters([1, 1, 1], 86.17744627072565, ratio=[4, 5],
+                                                    expand_times=4)
+        vol_ratio = gb_Pa_111_1.volume / self.Pa.volume
+        self.assertAlmostEqual(vol_ratio, 15 * 2 * 4)
+
+        # gb from orthorhombic cell, axis[1,1,1], sigma 93
+        gb_Br_111_1 = self.GB_Br.gb_from_parameters([1, 1, 1], 95.55344419565849,
+                                                    ratio=[10, 20, 21],
+                                                    expand_times=4)
+        vol_ratio = gb_Br_111_1.volume / self.Br.volume
+        self.assertAlmostEqual(vol_ratio, 93 * 2 * 4)
+
+        # gb from rhombohedra cell, axis[1,2,0], sigma 81
+        gb_Bi_120_1 = self.GB_Bi.gb_from_parameters([1, 2, 0], 63.612200038756995,
+                                                    ratio=[39, 10],
+                                                    expand_times=4)
+        vol_ratio = gb_Bi_120_1.volume / self.Bi.volume
+        self.assertAlmostEqual(vol_ratio, 81 * 2 * 4)
+
+    def test_gb_from_matrices(self):
+        mat1 = np.array([[30, -11, -41], [20, 3, -48], [-7, -1, 17]])
+        mat2 = np.array([[10, -31, 41], [20, -31, 20], [-7, 11, -7]])
+        gb_Br_111_1 = self.GB_Br.gb_from_matrices(mat1, mat2, expand_times=4,
+                                                  vacuum_thickness=3)
+        lat_conv = self.Br.lattice.matrix
+        lat_mat1 = np.rint(np.matmul(gb_Br_111_1.lattice.matrix, np.linalg.inv(lat_conv))).astype(int)
+        self.assertListEqual(list(lat_mat1[0]), list(mat1[0]))
+        self.assertListEqual(list(lat_mat1[1]), list(mat1[1]))
+
+    def test_enum_sigma_cubic(self):
+        true_100 = [5, 13, 17, 25, 29, 37, 41]
+        true_110 = [3, 9, 11, 17, 19, 27, 33, 41, 43]
+        true_111 = [3, 7, 13, 19, 21, 31, 37, 39, 43, 49]
+        sigma_100 = list(GBGenerator.enum_sigma_cubic(50, [1, 0, 0]).keys())
+        sigma_110 = list(GBGenerator.enum_sigma_cubic(50, [1, 1, 0]).keys())
+        sigma_111 = list(GBGenerator.enum_sigma_cubic(50, [1, 1, 1]).keys())
+        sigma_222 = list(GBGenerator.enum_sigma_cubic(50, [2, 2, 2]).keys())
+        sigma_888 = list(GBGenerator.enum_sigma_cubic(50, [8, 8, 8]).keys())
+
+        self.assertListEqual(sorted(true_100), sorted(sigma_100))
+        self.assertListEqual(sorted(true_110), sorted(sigma_110))
+        self.assertListEqual(sorted(true_111), sorted(sigma_111))
+        self.assertListEqual(sorted(true_111), sorted(sigma_222))
+        self.assertListEqual(sorted(true_111), sorted(sigma_888))
+
+    def test_enum_sigma_hex(self):
+        true_100 = [17, 18, 22, 27, 38, 41]
+        true_001 = [7, 13, 19, 31, 37, 43, 49]
+        true_210 = [10, 11, 14, 25, 35, 49]
+        sigma_100 = list(GBGenerator.enum_sigma_hex(50, [1, 0, 0], [8, 3]).keys())
+        sigma_001 = list(GBGenerator.enum_sigma_hex(50, [0, 0, 1], [8, 3]).keys())
+        sigma_210 = list(GBGenerator.enum_sigma_hex(50, [2, 1, 0], [8, 3]).keys())
+        sigma_420 = list(GBGenerator.enum_sigma_hex(50, [4, 2, 0], [8, 3]).keys())
+        sigma_840 = list(GBGenerator.enum_sigma_hex(50, [8, 4, 0], [8, 3]).keys())
+
+        self.assertListEqual(sorted(true_100), sorted(sigma_100))
+        self.assertListEqual(sorted(true_001), sorted(sigma_001))
+        self.assertListEqual(sorted(true_210), sorted(sigma_210))
+        self.assertListEqual(sorted(true_210), sorted(sigma_420))
+        self.assertListEqual(sorted(true_210), sorted(sigma_840))
+
+    def test_enum_sigma_tet(self):
+        true_100 = [5, 37, 41, 13, 3, 15, 39, 25, 17, 29]
+        true_331 = [9, 3, 21, 39, 7, 31, 43, 13, 19, 37, 49]
+        sigma_100 = list(GBGenerator.enum_sigma_tet(50, [1, 0, 0], [9, 1]).keys())
+        sigma_331 = list(GBGenerator.enum_sigma_tet(50, [3, 3, 1], [9, 1]).keys())
+
+        self.assertListEqual(sorted(true_100), sorted(sigma_100))
+        self.assertListEqual(sorted(true_331), sorted(sigma_331))
+
+    def test_enum_sigma_ort(self):
+        true_100 = [41, 37, 39, 5, 15, 17, 13, 3, 25, 29]
+        sigma_100 = list(GBGenerator.enum_sigma_ort(50, [1, 0, 0], [270, 30, 29]).keys())
+
+        self.assertListEqual(sorted(true_100), sorted(sigma_100))
+
+    def test_enum_sigma_rho(self):
+        true_100 = [7, 11, 43, 13, 41, 19, 47, 31]
+        sigma_100 = list(GBGenerator.enum_sigma_rho(50, [1, 0, 0], [15, 4]).keys())
+
+        self.assertListEqual(sorted(true_100), sorted(sigma_100))
+
+    def test_get_trans_mat(self):
+        mat1, mat2 = GBGenerator.get_trans_mat([1, 1, 1], 95.55344419565849, lat_type='o', ratio=[10, 20, 21],
+                                               surface=[21, 20, 10], normal=True)
+        self.assertAlmostEqual(np.dot(mat1[0], [21, 20, 10]), 0)
+        self.assertAlmostEqual(np.dot(mat1[1], [21, 20, 10]), 0)
+        self.assertAlmostEqual(np.linalg.det(mat1), np.linalg.det(mat2))
+        ab_len1 = np.linalg.norm(np.cross(mat1[2], [1, 1, 1]))
+        self.assertAlmostEqual(ab_len1, 0)
+
+    def test_get_rotation_angle_from_sigma(self):
+        true_angle = [12.680383491819821, 167.3196165081802]
+        angle = GBGenerator.get_rotation_angle_from_sigma(41, [1, 0, 0], lat_type='o', ratio=[270, 30, 29])
+        self.assertArrayAlmostEqual(true_angle, angle)
+        close_angle = [36.86989764584403, 143.13010235415598]
+        angle = GBGenerator.get_rotation_angle_from_sigma(6, [1, 0, 0], lat_type='o', ratio=[270, 30, 29])
+        self.assertArrayAlmostEqual(close_angle, angle)

test_files/grain_boundary/Be_mp-87_conventional_standard.cif

@@ -0,0 +1,28 @@
+# generated using pymatgen
+data_Be
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   2.27983889
+_cell_length_b   2.27983889
+_cell_length_c   3.52777283
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   120.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Be
+_chemical_formula_sum   Be2
+_cell_volume   15.8795999213
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Be  Be1  1  0.333333  0.666667  0.750000  1
+  Be  Be2  1  0.666667  0.333333  0.250000  1

test_files/grain_boundary/Bi_mp-23152_primitive.cif

@@ -0,0 +1,28 @@
+# generated using pymatgen
+data_Bi
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.79829946
+_cell_length_b   4.79829946
+_cell_length_c   4.79829946
+_cell_angle_alpha   57.26305593
+_cell_angle_beta   57.26305593
+_cell_angle_gamma   57.26305593
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Bi
+_chemical_formula_sum   Bi2
+_cell_volume   73.1939584902
+_cell_formula_units_Z   2
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Bi  Bi1  1  0.765615  0.765615  0.765615  1
+  Bi  Bi2  1  0.234385  0.234385  0.234385  1

test_files/grain_boundary/Br_mp-23154_conventional_standard.cif

@@ -0,0 +1,34 @@
+# generated using pymatgen
+data_Br
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   4.25864728
+_cell_length_b   8.45219038
+_cell_length_c   8.74379641
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Br
+_chemical_formula_sum   Br8
+_cell_volume   314.732056167
+_cell_formula_units_Z   8
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Br  Br1  1  0.857527  0.000000  0.617751  1
+  Br  Br2  1  0.142473  0.000000  0.382249  1
+  Br  Br3  1  0.642473  0.000000  0.117751  1
+  Br  Br4  1  0.357527  0.000000  0.882249  1
+  Br  Br5  1  0.357527  0.500000  0.617751  1
+  Br  Br6  1  0.642473  0.500000  0.382249  1
+  Br  Br7  1  0.142473  0.500000  0.117751  1
+  Br  Br8  1  0.857527  0.500000  0.882249  1

test_files/grain_boundary/Cu_mp-30_conventional_standard.cif

@@ -0,0 +1,30 @@
+# generated using pymatgen
+data_Cu
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   3.61640724
+_cell_length_b   3.61640724
+_cell_length_c   3.61640724
+_cell_angle_alpha   90.00000000
+_cell_angle_beta   90.00000000
+_cell_angle_gamma   90.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Cu
+_chemical_formula_sum   Cu4
+_cell_volume   47.2968251068
+_cell_formula_units_Z   4
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cu  Cu1  1  0.000000  0.000000  0.000000  1
+  Cu  Cu2  1  0.000000  0.500000  0.500000  1
+  Cu  Cu3  1  0.500000  0.000000  0.500000  1
+  Cu  Cu4  1  0.500000  0.500000  0.000000  1

test_files/grain_boundary/Cu_mp-30_primitive.cif

@@ -0,0 +1,27 @@
+# generated using pymatgen
+data_Cu
+_symmetry_space_group_name_H-M   'P 1'
+_cell_length_a   2.55718608
+_cell_length_b   2.55718608
+_cell_length_c   2.55718608
+_cell_angle_alpha   60.00000000
+_cell_angle_beta   60.00000000
+_cell_angle_gamma   60.00000000
+_symmetry_Int_Tables_number   1
+_chemical_formula_structural   Cu
+_chemical_formula_sum   Cu1
+_cell_volume   11.8242062767
+_cell_formula_units_Z   1
+loop_
+ _symmetry_equiv_pos_site_id
+ _symmetry_equiv_pos_as_xyz
+  1  'x, y, z'
+loop_
+ _atom_site_type_symbol
+ _atom_site_label
+ _atom_site_symmetry_multiplicity
+ _atom_site_fract_x
+ _atom_site_fract_y
+ _atom_site_fract_z
+ _atom_site_occupancy
+  Cu  Cu1  1  0.000000  0.000000  0.000000  1