/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/ |
H A D | interface.py | 173 return Structure.from_sites(self.substrate_sites) 196 return Structure.from_sites(self.film_sites) 222 struct_copy = Structure.from_sites(self) 326 s = Structure.from_sites(sites) 492 top_plane = Structure.from_sites(top_plane_sites)
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H A D | structure.py | 723 def from_sites( member in IStructure 1118 return Structure.from_sites(new_sites, charge=new_charge) 1661 return self.__class__.from_sites(sites, charge=self._charge) 1743 return self.__class__.from_sites(new_sites, charge=self._charge) 2170 subset_structure = Structure.from_sites(disordered_sites) 2270 return cls.from_sites(sites, charge=charge) 2430 return cls.from_sites(s) 2659 def from_sites( member in IMolecule 2727 return tuple(self.__class__.from_sites(cluster) for cluster in clusters) 3108 return cls.from_sites(m) [all …]
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H A D | surface.py | 343 s = Structure.from_sites(sites) 521 s = Structure.from_sites(sites) 916 self.oriented_unit_cell = Structure.from_sites(single, to_unit_cell=True)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/command_line/ |
H A D | enumlib_caller.py | 212 finder = SpacegroupAnalyzer(Structure.from_sites(ss), self.symm_prec) 411 structs.append(Structure.from_sites(sorted(sites)))
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/dports/science/py-abipy/abipy-0.9.0/abipy/iotools/ |
H A D | cube.py | 80 structure = Structure.from_sites(sites=sites)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/defects/ |
H A D | utils.py | 628 structure = Structure.from_sites(sites=constrained_sites) 788 new_s = Structure.from_sites(self.structure) 825 new_s = Structure.from_sites(self.structure) 835 s = Structure.from_sites(self.framework) 860 vis.set_structure(Structure.from_sites(self.structure))
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/structure_prediction/ |
H A D | volume_predictor.py | 205 reduced_structure = Structure.from_sites(sub_sites)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/core/tests/ |
H A D | test_structure.py | 1173 s = Structure.from_sites(self.structure, to_unit_cell=True) 1177 s = Structure.from_sites(self.structure) 1185 s = Structure.from_sites(self.structure) 1197 s = Structure.from_sites(s, charge=1) 1266 cluster = Molecule.from_sites(structure.extract_cluster([site])) 1653 cluster = Molecule.from_sites(mol.extract_cluster([mol[0]]))
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/transformations/ |
H A D | standard_transformations.py | 579 structure = Structure.from_sites(structure) 608 s = Structure.from_sites(structure)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/ |
H A D | structure_matcher.py | 653 ss = Structure.from_sites(s) 1150 temp = Structure.from_sites(sites) 1166 return Structure.from_sites(sites)
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H A D | dimensionality.py | 159 …component_structure = Structure.from_sites([bonded_structure.structure[n] for n in sorted(graph.no…
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H A D | molecule_matcher.py | 962 p_prime = Molecule.from_sites([p[i] for i in inds]) 1056 p_prime = Molecule.from_sites([p[i] for i in inds])
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H A D | path_finder.py | 140 sum_struct = Structure.from_sites(sum_struct, validate_proximity=False)
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H A D | adsorption.py | 215 surf_str = Structure.from_sites(self.surface_sites)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/tests/ |
H A D | test_adsorption.py | 41 self.asf_struct = AdsorbateSiteFinder(Structure.from_sites(self.slab_dict["111"].sites))
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H A D | test_molecule_matcher.py | 87 mol = Molecule.from_sites(struct) 130 mol = Molecule.from_sites(struct)
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H A D | test_structure_matcher.py | 477 s1 = Structure.from_sites([s1[i] for i in shuffle]) 569 s1 = Structure.from_sites([s1[i] for i in shuffle])
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/magnetism/ |
H A D | analyzer.py | 371 structure = Structure.from_sites(sites) 612 s = Structure.from_sites([self.structure[idx] for idx in sorted_indices])
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/symmetry/ |
H A D | analyzer.py | 425 prim = Structure.from_sites(new_sites) 451 return Structure.from_sites(new_sites) 453 return Structure.from_sites(new_sites)
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/dports/science/py-abipy/abipy-0.9.0/abipy/core/ |
H A D | structure.py | 717 structure = self.__class__.from_sites(self) 1158 return self.__class__.from_sites(sorted(self.sites, key=lambda site: site.specie.Z)) 1873 new_structure = self.__class__.from_sites(new_sites) 1939 new_structure = self.__class__.from_sites(new_sites)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/gb/ |
H A D | grain.py | 171 s = Structure.from_sites(sites) 219 return Structure.from_sites(top_sites) 230 return Structure.from_sites(bottom_sites) 305 s = Structure.from_sites(sites) 788 s_near_gb = Structure.from_sites(sites_near_gb) 791 gb_with_vac = Structure.from_sites(all_sites)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/lammps/ |
H A D | utils.py | 101 self.molecule = Molecule.from_sites(self.molecule.sites)
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H A D | data.py | 921 sites = Molecule.from_sites(sites)
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/dports/science/py-abipy/abipy-0.9.0/abipy/abio/ |
H A D | factories.py | 168 structure = Structure.from_sites(structure) 171 structure = Structure.from_sites(structure)
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/vis/ |
H A D | structure_vtk.py | 230 s = Structure.from_sites(structure, to_unit_cell=to_unit_cell)
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