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/dports/science/py-phonopy/phonopy-2.11.0/phonopy/harmonic/
H A Dforce_constants.py57 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 …]
H A Ddynamical_matrix.py132 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 …]
/dports/science/phonopy/phonopy-2.11.0/phonopy/harmonic/
H A Dforce_constants.py57 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 …]
H A Ddynamical_matrix.py132 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 …]
/dports/science/py-phonopy/phonopy-2.11.0/test/harmonic/
H A Dtest_force_constants.py3 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)
H A Dtest_dynmat_to_fc.py67 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,
/dports/science/phonopy/phonopy-2.11.0/test/harmonic/
H A Dtest_force_constants.py3 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)
H A Dtest_dynmat_to_fc.py67 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,
/dports/science/py-hiphive/hiphive-0.7.1/hiphive/structure_generation/
H A Dphonon.py119 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
/dports/science/py-phonopy/phonopy-2.11.0/example/NaCl/
H A DNaCl-read_write_fc.py16 force_constants = parse_FORCE_CONSTANTS() variable
17 phonon.force_constants = force_constants
19 write_FORCE_CONSTANTS(phonon.force_constants,
/dports/science/phonopy/phonopy-2.11.0/example/NaCl/
H A DNaCl-read_write_fc.py16 force_constants = parse_FORCE_CONSTANTS() variable
17 phonon.force_constants = force_constants
19 write_FORCE_CONSTANTS(phonon.force_constants,
/dports/science/py-abipy/abipy-0.9.0/abipy/dfpt/
H A Dconverters.py173 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 …]
/dports/science/py-hiphive/hiphive-0.7.1/hiphive/calculators/
H A Dase_calculator.py12 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])
/dports/science/py-phonopy/phonopy-2.11.0/phonopy/
H A Dfile_IO.py52 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 …]
/dports/science/phonopy/phonopy-2.11.0/phonopy/
H A Dfile_IO.py52 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 …]
/dports/science/py-phonopy/phonopy-2.11.0/phonopy/unfolding/
H A Dcore.py37 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)
/dports/science/phonopy/phonopy-2.11.0/phonopy/unfolding/
H A Dcore.py37 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)
/dports/science/py-ase/ase-3.22.0/ase/md/
H A Dvelocitydistribution.py191 force_constants, argument
284 dynamical_matrix = force_constants * rminv[:, None] * rminv[None, :]
369 force_constants, argument
414 force_constants=force_constants,
/dports/science/py-phono3py/phono3py-1.22.3/phono3py/sscha/
H A Dsscha.py80 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
/dports/science/py-phonopy/phonopy-2.11.0/phonopy/cui/
H A Dload_helper.py166 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:
/dports/science/phonopy/phonopy-2.11.0/phonopy/cui/
H A Dload_helper.py166 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:
/dports/science/py-phonopy/phonopy-2.11.0/test/phonon/
H A Dtest_random_displacements.py195 ph.force_constants)
226 np.testing.assert_allclose(rd.force_constants, ph.force_constants,
/dports/science/phonopy/phonopy-2.11.0/test/phonon/
H A Dtest_random_displacements.py195 ph.force_constants)
226 np.testing.assert_allclose(rd.force_constants, ph.force_constants,
/dports/science/py-phonopy/phonopy-2.11.0/phonopy/phonon/
H A Drandom_displacements.py101 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
/dports/science/phonopy/phonopy-2.11.0/phonopy/phonon/
H A Drandom_displacements.py101 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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