/dports/science/py-phonopy/phonopy-2.11.0/phonopy/harmonic/ |
H A D | force_constants.py | 57 return force_constants 94 force_constants, 111 force_constants = force_constants.round(decimals=decimals) 113 return force_constants 141 fc_shape = force_constants.shape 385 force_constants, 405 force_constants[:] = fc_new 485 force_constants[i, j] = (force_constants[i, j] + 499 if force_constants.shape[0] == force_constants.shape[1]: 611 if force_constants.shape[0] != force_constants.shape[1]: [all …]
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H A D | dynamical_matrix.py | 132 force_constants, argument 157 self._set_force_constants(force_constants) 221 def force_constants(self): member in DynamicalMatrix 230 return self.force_constants 382 force_constants, argument 411 force_constants, 563 force_constants, argument 594 force_constants, 683 self._Gonze_force_constants = d2f.force_constants 909 force_constants, argument [all …]
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/dports/science/phonopy/phonopy-2.11.0/phonopy/harmonic/ |
H A D | force_constants.py | 57 return force_constants 94 force_constants, 111 force_constants = force_constants.round(decimals=decimals) 113 return force_constants 141 fc_shape = force_constants.shape 385 force_constants, 405 force_constants[:] = fc_new 485 force_constants[i, j] = (force_constants[i, j] + 499 if force_constants.shape[0] == force_constants.shape[1]: 611 if force_constants.shape[0] != force_constants.shape[1]: [all …]
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H A D | dynamical_matrix.py | 132 force_constants, argument 157 self._set_force_constants(force_constants) 221 def force_constants(self): member in DynamicalMatrix 230 return self.force_constants 382 force_constants, argument 411 force_constants, 563 force_constants, argument 594 force_constants, 683 self._Gonze_force_constants = d2f.force_constants 909 force_constants, argument [all …]
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/dports/science/py-phonopy/phonopy-2.11.0/test/harmonic/ |
H A D | test_force_constants.py | 3 from phonopy.harmonic.force_constants import cutoff_force_constants 21 fc_1_10 = ph_nacl.force_constants[1, 10] 27 fc_1_10 = ph_nacl_nofcsym.force_constants[1, 10] 33 fc_1_10 = ph_nacl_compact_fcsym.force_constants[1, 10] 47 fc_orig = ph.force_constants.copy() 49 changed = (np.abs(fc_orig - ph.force_constants) > 1e-8) 50 ph.force_constants = fc_orig 68 fc = ph.force_constants.copy() 75 changed = (np.abs(ph.force_constants - fc) > 1e-8)
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H A D | test_dynmat_to_fc.py | 67 ph333.force_constants = fc333 97 np.testing.assert_allclose(ph.force_constants, d2f.force_constants, 116 np.testing.assert_allclose(ph.force_constants, d2f.force_constants,
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/dports/science/phonopy/phonopy-2.11.0/test/harmonic/ |
H A D | test_force_constants.py | 3 from phonopy.harmonic.force_constants import cutoff_force_constants 21 fc_1_10 = ph_nacl.force_constants[1, 10] 27 fc_1_10 = ph_nacl_nofcsym.force_constants[1, 10] 33 fc_1_10 = ph_nacl_compact_fcsym.force_constants[1, 10] 47 fc_orig = ph.force_constants.copy() 49 changed = (np.abs(fc_orig - ph.force_constants) > 1e-8) 50 ph.force_constants = fc_orig 68 fc = ph.force_constants.copy() 75 changed = (np.abs(ph.force_constants - fc) > 1e-8)
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H A D | test_dynmat_to_fc.py | 67 ph333.force_constants = fc333 97 np.testing.assert_allclose(ph.force_constants, d2f.force_constants, 116 np.testing.assert_allclose(ph.force_constants, d2f.force_constants,
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/dports/science/py-hiphive/hiphive-0.7.1/hiphive/structure_generation/ |
H A D | phonon.py | 119 def __init__(self, masses, force_constants): argument 121 if len(force_constants.shape) == 4: # assume shape = (n_atoms, n_atoms, 3, 3) 122 force_constants = force_constants.transpose(0, 2, 1, 3) 123 force_constants = force_constants.reshape(3 * n_atoms, 3 * n_atoms) 128 D *= force_constants
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/dports/science/py-phonopy/phonopy-2.11.0/example/NaCl/ |
H A D | NaCl-read_write_fc.py | 16 force_constants = parse_FORCE_CONSTANTS() variable 17 phonon.force_constants = force_constants 19 write_FORCE_CONSTANTS(phonon.force_constants,
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/dports/science/phonopy/phonopy-2.11.0/example/NaCl/ |
H A D | NaCl-read_write_fc.py | 16 force_constants = parse_FORCE_CONSTANTS() variable 17 phonon.force_constants = force_constants 19 write_FORCE_CONSTANTS(phonon.force_constants,
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/dports/science/py-abipy/abipy-0.9.0/abipy/dfpt/ |
H A D | converters.py | 173 force_constants=None, force_sets=None, born=None, argument 242 if force_sets is None and force_constants is None: 247 if isinstance(force_constants, str): 248 force_constants = parse_FORCE_CONSTANTS(filename=force_constants) 249 elif force_constants is not None: 250 force_constants = np.array(force_constants) 285 force_constants = force_constants[:, sc_mapping] 287 if force_constants is not None: 288 phonon.set_force_constants(force_constants) 296 phonon.set_force_constants(phonon.force_constants * fc_factor) [all …]
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/dports/science/py-hiphive/hiphive-0.7.1/hiphive/calculators/ |
H A D | ase_calculator.py | 12 from hiphive.force_constants import SortedForceConstants 46 self.force_constants = dd(list) 61 self.force_constants[key].append(fc.transpose(argsort)) 69 self.force_constants, 125 self.force_constants[key], 135 fc_dict_str = '{{{}: {}, ...}}'.format(self.clusters[0], self.force_constants[0])
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/dports/science/py-phonopy/phonopy-2.11.0/phonopy/ |
H A D | file_IO.py | 52 from phonopy.harmonic.force_constants import similarity_transformation 283 def write_FORCE_CONSTANTS(force_constants, argument 302 lines = get_FORCE_CONSTANTS_lines(force_constants, p2s_map=p2s_map) 307 def get_FORCE_CONSTANTS_lines(force_constants, p2s_map=None): argument 311 indices = np.arange(force_constants.shape[0], dtype='intc') 314 fc_shape = force_constants.shape 319 for vec in force_constants[i][j]: 325 def write_force_constants_to_hdf5(force_constants, argument 359 w.create_dataset('force_constants', data=force_constants, 388 force_constants[i, j] = tensor [all …]
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/dports/science/phonopy/phonopy-2.11.0/phonopy/ |
H A D | file_IO.py | 52 from phonopy.harmonic.force_constants import similarity_transformation 283 def write_FORCE_CONSTANTS(force_constants, argument 302 lines = get_FORCE_CONSTANTS_lines(force_constants, p2s_map=p2s_map) 307 def get_FORCE_CONSTANTS_lines(force_constants, p2s_map=None): argument 311 indices = np.arange(force_constants.shape[0], dtype='intc') 314 fc_shape = force_constants.shape 319 for vec in force_constants[i][j]: 325 def write_force_constants_to_hdf5(force_constants, argument 359 w.create_dataset('force_constants', data=force_constants, 388 force_constants[i, j] = tensor [all …]
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/dports/science/py-phonopy/phonopy-2.11.0/phonopy/unfolding/ |
H A D | core.py | 37 from phonopy.harmonic.force_constants import compact_fc_to_full_fc 327 fc_shape = ph_in.force_constants.shape 329 ph.force_constants = ph_in.force_constants.copy() 331 ph.force_constants = compact_fc_to_full_fc( 332 ph_in, ph_in.force_constants)
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/dports/science/phonopy/phonopy-2.11.0/phonopy/unfolding/ |
H A D | core.py | 37 from phonopy.harmonic.force_constants import compact_fc_to_full_fc 327 fc_shape = ph_in.force_constants.shape 329 ph.force_constants = ph_in.force_constants.copy() 331 ph.force_constants = compact_fc_to_full_fc( 332 ph_in, ph_in.force_constants)
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/dports/science/py-ase/ase-3.22.0/ase/md/ |
H A D | velocitydistribution.py | 191 force_constants, argument 284 dynamical_matrix = force_constants * rminv[:, None] * rminv[None, :] 369 force_constants, argument 414 force_constants=force_constants,
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/dports/science/py-phono3py/phono3py-1.22.3/phono3py/sscha/ |
H A D | sscha.py | 80 force_constants, argument 98 _fc2 = np.array(np.transpose(force_constants, axes=[0, 2, 1, 3]), 126 def force_constants(self): member in SupercellPhonon 281 matrix = self._d2f.force_constants 287 matrix = self._d2f.force_constants 355 self._force_constants = supercell_phonon.force_constants 465 self._force_constants = supercell_phonon.force_constants
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/dports/science/py-phonopy/phonopy-2.11.0/phonopy/cui/ |
H A D | load_helper.py | 166 phonon.force_constants = fc 176 elif phonon.forces is None and phonon.force_constants is None: 189 phonon.force_constants = _fc 194 if phonon.force_constants is None:
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/dports/science/phonopy/phonopy-2.11.0/phonopy/cui/ |
H A D | load_helper.py | 166 phonon.force_constants = fc 176 elif phonon.forces is None and phonon.force_constants is None: 189 phonon.force_constants = _fc 194 if phonon.force_constants is None:
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/dports/science/py-phonopy/phonopy-2.11.0/test/phonon/ |
H A D | test_random_displacements.py | 195 ph.force_constants) 226 np.testing.assert_allclose(rd.force_constants, ph.force_constants,
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/dports/science/phonopy/phonopy-2.11.0/test/phonon/ |
H A D | test_random_displacements.py | 195 ph.force_constants) 226 np.testing.assert_allclose(rd.force_constants, ph.force_constants,
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/dports/science/py-phonopy/phonopy-2.11.0/phonopy/phonon/ |
H A D | random_displacements.py | 101 force_constants, argument 153 force_constants, supercell, primitive) 260 def force_constants(self): member in RandomDisplacements 270 self._force_constants = d2f.force_constants 287 self._uu_inv = np.array(d2f.force_constants, dtype='double', order='C') 291 matrix = d2f.force_constants
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/dports/science/phonopy/phonopy-2.11.0/phonopy/phonon/ |
H A D | random_displacements.py | 101 force_constants, argument 153 force_constants, supercell, primitive) 260 def force_constants(self): member in RandomDisplacements 270 self._force_constants = d2f.force_constants 287 self._uu_inv = np.array(d2f.force_constants, dtype='double', order='C') 291 matrix = d2f.force_constants
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