| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/lammps/ |
| H A D | utils.py | 79 start_monomer.translate_sites(range(len(start_monomer)), -monomer.cart_coords[s_head])
80 monomer.translate_sites(range(len(monomer)), -monomer.cart_coords[head])
81 end_monomer.translate_sites(range(len(end_monomer)), -monomer.cart_coords[e_head])
158 monomer.translate_sites(range(len(monomer)), translate_by)
364 mol.translate_sites(indices=range(len(mol)), vector=-mol.center_of_mass)
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/transformations/ |
| H A D | site_transformations.py | 221 s.translate_sites(idx, self.translation_vector[i], self.vector_in_frac_coords)
223 … s.translate_sites(self.indices_to_move, self.translation_vector, self.vector_in_frac_coords)
642 structure.translate_sites(**kwargs)
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/tests/ |
| H A D | test_structure_matcher.py | 247 self.struct_list[1].translate_sites([0], [0.4, 0.4, 0.2], frac_coords=True)
250 self.struct_list[1].translate_sites([0], [-0.4, -0.4, -0.2], frac_coords=True)
445 s2.translate_sites(range(len(s2)), match[3])
1070 …shift_s_struc.translate_sites(range(len(s_struc)), [0.2, 0.3, 0.4], frac_coords=True, to_unit_cell…
1092 …shift_ns_struc.translate_sites(range(len(ns_struc)), [0.0, 0.6, 0.3], frac_coords=True, to_unit_ce…
1151 …rotANDshift_ns_struc.translate_sites(range(len(ns_struc)), [0.0, 0.6, 0.3], frac_coords=True, to_u…
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/ |
| H A D | interface.py | 115 self.translate_sites(self.film_indices, [delta[0], delta[1], 0], to_unit_cell=True)
133 self.translate_sites(self.film_indices, [0, 0, delta], frac_coords=False, to_unit_cell=True)
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| H A D | surface.py | 987 slab.translate_sites(list(range(len(slab))), [0, 0, 0.5 - avg_c])
1275 slab.translate_sites(top_site_index, [0, 0, slab_ratio])
1276 slab.translate_sites(bottom_site_index, [0, 0, -slab_ratio])
1984 slab.translate_sites(all_indices, [0, 0, shift])
1990 slab.translate_sites(all_indices, [0, 0, shift])
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| H A D | structure.py | 3475 fgroup.translate_sites(list(range(len(fgroup))), origin - x.coords)
3607 def translate_sites( member in Structure
3715 self.translate_sites([i], get_rand_vec(), frac_coords=False)
4013 def translate_sites(self, indices: Sequence[int] = None, vector: ArrayLike = None): member in Molecule
4089 self.translate_sites([i], get_rand_vec())
4178 func_grp.translate_sites(list(range(len(func_grp))), origin - x.coords)
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/tests/ |
| H A D | test_structure.py | 903 self.structure.translate_sites([0, 1], [0.5, 0.5, 0.5], frac_coords=True)
906 self.structure.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=False)
909 self.structure.translate_sites([0], [0.5, 0.5, 0.5], frac_coords=True, to_unit_cell=False)
1538 self.mol.translate_sites([0, 1], [0.5, 0.5, 0.5])
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| H A D | test_surface.py | 314 slab.translate_sites([i for i, site in enumerate(slab)], [0, 0, -0.25])
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/ |
| H A D | structure_matcher.py | 1153 temp.translate_sites(list(range(len(temp))), t)
1158 temp.translate_sites(j, vec, to_unit_cell=False)
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| H A D | path_finder.py | 107 image.translate_sites(
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| H A D | adsorption.py | 402 molecule.translate_sites(vector=[-x, -y, -z])
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| H A D | surface_analysis.py | 1492 slab.translate_sites([i for i, site in enumerate(slab)], [0, 0, self.shift])
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/vasp/ |
| H A D | sets.py | 2448 s.translate_sites([i], t, to_unit_cell=False)
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| /dports/science/py-abipy/abipy-0.9.0/abipy/core/ |
| H A D | structure.py | 1622 self.translate_sites(indices=i, vector=eta * displ[i, :], frac_coords=True)
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