| /dports/science/py-phonopy/phonopy-2.11.0/scripts/ |
| H A D | phonopy-vasp-born | 58 supercell_matrix=None,
110 if args.supercell_matrix:
111 vals = [int(x) for x in args.supercell_matrix.split()]
113 supercell_matrix = np.reshape(np.array(vals, dtype='intc'), (3, 3))
115 supercell_matrix = np.diag(np.array(vals, dtype='intc'))
120 supercell_matrix = np.eye(3, dtype='intc')
132 supercell_matrix=supercell_matrix,
139 supercell_matrix=supercell_matrix,
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| H A D | phonopy-gruneisen | 196 supercell_matrix = [int(x) for x in args.supercell_dimension.split()]
197 if len(supercell_matrix) == 9:
198 supercell_matrix = np.array(supercell_matrix).reshape(3, 3)
199 elif len(supercell_matrix) == 3:
200 supercell_matrix = np.diag(supercell_matrix)
204 if np.linalg.det(supercell_matrix) < 1:
245 supercell_matrix=supercell_matrix,
258 supercell_matrix=supercell_matrix,
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| /dports/science/phonopy/phonopy-2.11.0/scripts/ |
| H A D | phonopy-vasp-born | 58 supercell_matrix=None,
110 if args.supercell_matrix:
111 vals = [int(x) for x in args.supercell_matrix.split()]
113 supercell_matrix = np.reshape(np.array(vals, dtype='intc'), (3, 3))
115 supercell_matrix = np.diag(np.array(vals, dtype='intc'))
120 supercell_matrix = np.eye(3, dtype='intc')
132 supercell_matrix=supercell_matrix,
139 supercell_matrix=supercell_matrix,
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| H A D | phonopy-gruneisen | 196 supercell_matrix = [int(x) for x in args.supercell_dimension.split()]
197 if len(supercell_matrix) == 9:
198 supercell_matrix = np.array(supercell_matrix).reshape(3, 3)
199 elif len(supercell_matrix) == 3:
200 supercell_matrix = np.diag(supercell_matrix)
204 if np.linalg.det(supercell_matrix) < 1:
245 supercell_matrix=supercell_matrix,
258 supercell_matrix=supercell_matrix,
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| /dports/science/py-phonopy/phonopy-2.11.0/phonopy/cui/ |
| H A D | collect_cell_info.py | 42 def collect_cell_info(supercell_matrix=None, argument
53 supercell_matrix,
86 supercell_matrix,
120 def _fallback_to_phonopy_yaml(supercell_matrix, argument
155 if supercell_matrix is None:
207 supercell_matrix, argument
219 if phpy.supercell_matrix is None:
220 _supercell_matrix = supercell_matrix
222 _supercell_matrix = phpy.supercell_matrix
231 _supercell_matrix = supercell_matrix
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| H A D | load.py | 44 supercell_matrix=None, argument
207 supercell_matrix=supercell_matrix,
224 smat = phpy_yaml.supercell_matrix
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| H A D | load_helper.py | 47 supercell_matrix=None, argument
66 smat = supercell_matrix
79 smat = supercell_matrix
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| /dports/science/phonopy/phonopy-2.11.0/phonopy/cui/ |
| H A D | collect_cell_info.py | 42 def collect_cell_info(supercell_matrix=None, argument
53 supercell_matrix,
86 supercell_matrix,
120 def _fallback_to_phonopy_yaml(supercell_matrix, argument
155 if supercell_matrix is None:
207 supercell_matrix, argument
219 if phpy.supercell_matrix is None:
220 _supercell_matrix = supercell_matrix
222 _supercell_matrix = phpy.supercell_matrix
231 _supercell_matrix = supercell_matrix
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| H A D | load.py | 44 supercell_matrix=None, argument
207 supercell_matrix=supercell_matrix,
224 smat = phpy_yaml.supercell_matrix
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| H A D | load_helper.py | 47 supercell_matrix=None, argument
66 smat = supercell_matrix
79 smat = supercell_matrix
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| /dports/science/py-ase/ase-3.22.0/ase/build/ |
| H A D | supercells.py | 165 supercell_matrix = P
166 supercell = clean_matrix(supercell_matrix @ prim.cell)
169 lattice_points_frac = lattice_points_in_supercell(supercell_matrix)
180 n_target = int(np.round(np.linalg.det(supercell_matrix) * len(prim)))
193 def lattice_points_in_supercell(supercell_matrix): argument
213 d_points = np.dot(diagonals, supercell_matrix)
225 frac_points = np.dot(all_points, np.linalg.inv(supercell_matrix))
231 assert len(tvects) == round(abs(np.linalg.det(supercell_matrix)))
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| /dports/science/py-phonopy/phonopy-2.11.0/phonopy/harmonic/ |
| H A D | dynmat_to_fc.py | 47 def get_commensurate_points(supercell_matrix): # wrt primitive cell argument
64 smat = np.array(supercell_matrix, dtype=int)
75 def get_commensurate_points_in_integers(supercell_matrix): argument
97 smat = np.array(supercell_matrix, dtype=int)
133 def ph2fc(ph_orig, supercell_matrix): argument
145 smat = shape_supercell_matrix(supercell_matrix)
239 supercell_matrix = np.linalg.inv(self._pcell.primitive_matrix)
240 supercell_matrix = np.rint(supercell_matrix).astype('intc')
243 supercell_matrix)
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| /dports/science/phonopy/phonopy-2.11.0/phonopy/harmonic/ |
| H A D | dynmat_to_fc.py | 47 def get_commensurate_points(supercell_matrix): # wrt primitive cell argument
64 smat = np.array(supercell_matrix, dtype=int)
75 def get_commensurate_points_in_integers(supercell_matrix): argument
97 smat = np.array(supercell_matrix, dtype=int)
133 def ph2fc(ph_orig, supercell_matrix): argument
145 smat = shape_supercell_matrix(supercell_matrix)
239 supercell_matrix = np.linalg.inv(self._pcell.primitive_matrix)
240 supercell_matrix = np.rint(supercell_matrix).astype('intc')
243 supercell_matrix)
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/tests/ |
| H A D | test_phonopy.py | 102 supercell_matrix = [[2, 0, 0], [0, 1, 0], [0, 0, 2]]
103 … = get_displaced_structures(pmg_structure=pmg_s, atom_disp=0.01, supercell_matrix=supercell_matrix)
125 supercell_matrix=supercell_matrix,
139 self.supercell_matrix = np.eye(3) * 2
145 self.supercell_matrix,
158 self.supercell_matrix,
171 self.supercell_matrix,
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/io/ |
| H A D | phonopy.py | 259 def get_displaced_structures(pmg_structure, atom_disp=0.01, supercell_matrix=None, yaml_fname=None,… argument
283 if supercell_matrix is None:
284 supercell_matrix = np.eye(3) * np.array((1, 1, 1))
286 phonon = Phonopy(unitcell=ph_structure, supercell_matrix=supercell_matrix)
319 supercell_matrix: np.ndarray,
342 phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, **kwargs)
369 supercell_matrix: np.ndarray,
390 phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, **kwargs)
401 supercell_matrix: np.ndarray,
425 … phonon = Phonopy(structure_phonopy, supercell_matrix=supercell_matrix, symprec=symprec, **kwargs)
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| /dports/science/py-phono3py/phono3py-1.22.3/phono3py/cui/ |
| H A D | show_log.py | 49 supercell_matrix = phono3py.supercell_matrix
65 if (np.diag(np.diag(supercell_matrix)) - supercell_matrix).any():
67 for v in supercell_matrix:
70 print("Supercell (dim): %s" % np.diag(supercell_matrix))
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| H A D | load.py | 48 supercell_matrix=None, argument
239 supercell_matrix=supercell_matrix,
261 smat = ph3py_yaml.supercell_matrix
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| /dports/science/py-phonopy/phonopy-2.11.0/example/ase/ |
| H A D | 8Si-phonon.py | 30 def phonopy_pre_process(cell, supercell_matrix=None): argument
32 if supercell_matrix is None:
35 smat = supercell_matrix
87 phonon = phonopy_pre_process(cell, supercell_matrix=np.eye(3, dtype='intc'))
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| /dports/science/phonopy/phonopy-2.11.0/example/ase/ |
| H A D | 8Si-phonon.py | 30 def phonopy_pre_process(cell, supercell_matrix=None): argument
32 if supercell_matrix is None:
35 smat = supercell_matrix
87 phonon = phonopy_pre_process(cell, supercell_matrix=np.eye(3, dtype='intc'))
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| /dports/science/py-phonopy/phonopy-2.11.0/phonopy/structure/ |
| H A D | symmetry.py | 382 supercell_matrix=None, argument
429 supercell_matrix=supercell_matrix,
441 supercell_matrix=None, argument
512 supercell_matrix=supercell_matrix,
573 supercell_matrix=None, argument
579 supercell_matrix=supercell_matrix,
590 supercell_matrix=None, argument
596 if supercell_matrix is None:
599 smat = supercell_matrix
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| /dports/science/phonopy/phonopy-2.11.0/phonopy/structure/ |
| H A D | symmetry.py | 382 supercell_matrix=None, argument
429 supercell_matrix=supercell_matrix,
441 supercell_matrix=None, argument
512 supercell_matrix=supercell_matrix,
573 supercell_matrix=None, argument
579 supercell_matrix=supercell_matrix,
590 supercell_matrix=None, argument
596 if supercell_matrix is None:
599 smat = supercell_matrix
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| /dports/science/py-abipy/abipy-0.9.0/abipy/dfpt/ |
| H A D | converters.py | 30 def abinit_to_phonopy(anaddbnc, supercell_matrix, symmetrize_tensors=False, output_dir_path=None, argument
87 phonon = Phonopy(phon_at, supercell_matrix, primitive_matrix=np.eye(3), nac_params=nac_params,
172 def phonopy_to_abinit(unit_cell, supercell_matrix, out_ddb_path, ngqpt=None, qpt_list=None, argument
257 phonon = Phonopy(phon_at, supercell_matrix, primitive_matrix=primitive_matrix, nac_params=None,
485 def tdep_to_abinit(unit_cell, fc_path, supercell_matrix, supercell, out_ddb_path, ngqpt=None, argument
539 … phonopy_to_abinit(unit_cell=unit_cell, force_constants=fc, supercell_matrix=supercell_matrix, ngq…
669 supercell_matrix=None, argument
679 supercell_matrix=supercell_matrix,
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| /dports/science/py-phono3py/phono3py-1.22.3/phono3py/interface/ |
| H A D | calculator.py | 72 def get_additional_info_to_write_supercells(interface_mode, supercell_matrix): argument
76 additional_info['supercell_matrix'] = supercell_matrix
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| /dports/science/py-abipy/abipy-0.9.0/abipy/dfpt/tests/ |
| H A D | test_converters.py | 61 …ddb_conv = phonopy_to_abinit(unit_cell=structure, supercell_matrix=scm, qpt_list=qpoints.frac_coor…
100 …ddb_conv = phonopy_to_abinit(unit_cell=structure, supercell_matrix=scm, qpt_list=qpoints.frac_coor…
130 ddb = phonopy_to_abinit(unit_cell=unit_cell, supercell_matrix=scm, ngqpt=ngqpt,
145 …phonon_orig = Phonopy(unitcell=phonon_conv.unitcell, supercell_matrix=scm, primitive_matrix=np.eye…
181 ddb = tdep_to_abinit(unit_cell=unit_cell, fc_path=fc_path, supercell_matrix=np.eye(3)*5,
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| /dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/util/ |
| H A D | coord.py | 268 def lattice_points_in_supercell(supercell_matrix): argument
292 d_points = np.dot(diagonals, supercell_matrix)
304 frac_points = np.dot(all_points, np.linalg.inv(supercell_matrix))
307 assert len(tvects) == round(abs(np.linalg.det(supercell_matrix)))
|