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ASR in 1D materials #174

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dae8044
Now it is doing the actual minimization in 1D
mesonepigreco Nov 9, 2023
be9df67
Fixing a bug in the minimization
mesonepigreco Jan 16, 2024
2bb5323
Merge branch 'master' into asr_1d
mesonepigreco Feb 7, 2024
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35 changes: 20 additions & 15 deletions Modules/Ensemble.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1722,7 +1722,8 @@ def update_weights_fourier(self, new_dynamical_matrix, newT, timer=None):

# Exclude translations
if not self.ignore_small_w:
trans_original = CC.Methods.get_translations(pols_original, super_struct0.get_masses_array())
trans_original = super_struct0.get_asr_modes(pols_original)
# trans_original = CC.Methods.get_translations(pols_original, super_struct0.get_masses_array())
else:
trans_original = np.abs(w_original) < CC.Phonons.__EPSILON_W__

Expand All @@ -1739,15 +1740,14 @@ def update_weights_fourier(self, new_dynamical_matrix, newT, timer=None):


if not self.ignore_small_w:
trans_mask = CC.Methods.get_translations(pols, super_structure.get_masses_array())
trans_mask = super_structure.get_asr_modes(pols)
# trans_mask = CC.Methods.get_translations(pols, super_structure.get_masses_array())
else:
trans_mask = np.abs(w_new) < CC.Phonons.__EPSILON_W__


# Check if the new dynamical matrix satisfies the sum rule
violating_sum_rule = (np.sum(trans_mask.astype(int)) != 3) or (np.sum(trans_original.astype(int)) != 3)
if self.ignore_small_w:
violating_sum_rule = np.sum(trans_mask.astype(int)) != np.sum(trans_original.astype(int))
violating_sum_rule = np.sum(trans_mask.astype(int)) != np.sum(trans_original.astype(int))


if violating_sum_rule:
Expand Down Expand Up @@ -1944,7 +1944,8 @@ def update_weights(self, new_dynamical_matrix, newT, update_q = False, timer=Non

# Exclude translations
if not self.ignore_small_w:
trans_original = CC.Methods.get_translations(pols_original, super_struct0.get_masses_array())
trans_original = super_struct0.get_asr_modes(pols_original)
# trans_original = CC.Methods.get_translations(pols_original, super_struct0.get_masses_array())
else:
trans_original = np.abs(w_original) < CC.Phonons.__EPSILON_W__

Expand All @@ -1961,15 +1962,15 @@ def update_weights(self, new_dynamical_matrix, newT, update_q = False, timer=Non


if not self.ignore_small_w:
trans_mask = CC.Methods.get_translations(pols, super_structure.get_masses_array())
trans_mask = super_structure.get_asr_modes(pols)
# trans_mask = CC.Methods.get_translations(pols, super_structure.get_masses_array())
else:
trans_mask = np.abs(w_new) < CC.Phonons.__EPSILON_W__


# Check if the new dynamical matrix satisfies the sum rule
violating_sum_rule = (np.sum(trans_mask.astype(int)) != 3) or (np.sum(trans_original.astype(int)) != 3)
if self.ignore_small_w:
violating_sum_rule = np.sum(trans_mask.astype(int)) != np.sum(trans_original.astype(int))
# violating_sum_rule = (np.sum(trans_mask.astype(int)) != 3) or (np.sum(trans_original.astype(int)) != 3)
violating_sum_rule = np.sum(trans_mask.astype(int)) != np.sum(trans_original.astype(int))


if violating_sum_rule:
Expand All @@ -1984,7 +1985,7 @@ def update_weights(self, new_dynamical_matrix, newT, update_q = False, timer=Non
DETAILS OF ERROR:
Number of translatinal modes in the original dyn = {}
Number of translational modes in the target dyn = {}
(They should be both 3)
(They should be both be the same - 3 in bulk)
""".format(np.sum(trans_original.astype(int)), np.sum(trans_mask.astype(int)))

print(ERR_MSG)
Expand Down Expand Up @@ -2706,7 +2707,8 @@ def get_preconditioned_gradient(self, subtract_sscha = True, return_error = Fals
w, pols = self.current_dyn.DiagonalizeSupercell()#supercell_dyn.DyagDinQ(0)

if not self.ignore_small_w:
trans = CC.Methods.get_translations(pols, super_struct.get_masses_array())
trans = super_struct.get_asr_modes(pols)
# trans = CC.Methods.get_translations(pols, super_struct.get_masses_array())
else:
trans = np.abs(w) < CC.Phonons.__EPSILON_W__

Expand Down Expand Up @@ -2946,7 +2948,8 @@ def get_stress_tensor(self, offset_stress = None, use_spglib = False):
wr, pols = self.current_dyn.DiagonalizeSupercell()

if not self.ignore_small_w:
trans = ~ CC.Methods.get_translations(pols, super_structure.get_masses_array())
trans = ~ super_structure.get_asr_modes(pols)
# trans = ~ CC.Methods.get_translations(pols, super_structure.get_masses_array())
else:
trans = np.abs(wr) > CC.Phonons.__EPSILON_W__

Expand Down Expand Up @@ -3374,7 +3377,8 @@ def get_odd_realspace(self):
w_sc, pols_sc = super_dyn.DyagDinQ(0)

# Remove translations
no_trans_mask = ~CC.Methods.get_translations(pols_sc, super_dyn.structure.get_masses_array())
no_trans_mask = ~super_dyn.structure.get_asr_modes(pols_sc)
# no_trans_mask = ~CC.Methods.get_translations(pols_sc, super_dyn.structure.get_masses_array())
w_sc = w_sc[no_trans_mask]
pols_sc = pols_sc[:, no_trans_mask]

Expand Down Expand Up @@ -3669,7 +3673,8 @@ def get_free_energy_hessian(self, include_v4 = False, get_full_hessian = True, v

# Get the translational modes
if not self.ignore_small_w:
trans = CC.Methods.get_translations(pols, super_structure.get_masses_array())
trans = super_structure.get_asr_modes(pols)
# trans = CC.Methods.get_translations(pols, super_structure.get_masses_array())
else:
trans = np.abs(w) < CC.Phonons.__EPSILON_W__

Expand Down
20 changes: 13 additions & 7 deletions Modules/SchaMinimizer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1502,10 +1502,11 @@ def finalize(self, verbose = 1, timer=None):
pols = self.ensemble.current_pols.copy()

#w, pols = super_dyn.DyagDinQ(0)
trans = CC.Methods.get_translations(pols, super_struct.get_masses_array())
trans = super_struct.get_asr_modes(pols)
# trans = CC.Methods.get_translations(pols, super_struct.get_masses_array())

for i in range(len(w)):
print ("Mode %5d: freq %16.8f cm-1 | is translation? " % (i+1, w[i] * __RyToCm__), trans[i])
print ("Mode %5d: freq %16.8f cm-1 | is asr? " % (i+1, w[i] * __RyToCm__), trans[i])

print ()

Expand Down Expand Up @@ -1533,7 +1534,8 @@ def check_imaginary_frequencies(self, timer=None):

# Get translations
if not self.ensemble.ignore_small_w:
trans_mask = ~CC.Methods.get_translations(pols, ss.get_masses_array())
trans_mask = ~ss.get_asr_modes(pols)
# trans_mask = ~CC.Methods.get_translations(pols, ss.get_masses_array())
else:
trans_mask = np.abs(w) > CC.Phonons.__EPSILON_W__

Expand All @@ -1554,7 +1556,8 @@ def check_imaginary_frequencies(self, timer=None):
#ss0 = self.ensemble.dyn_0.structure.generate_supercell(self.dyn.GetSupercell())

if not self.ensemble.ignore_small_w:
trans_mask = ~CC.Methods.get_translations(pold, ss.get_masses_array())
trans_mask = ~ss.get_asr_modes(pold)
# trans_mask = ~CC.Methods.get_translations(pold, ss.get_masses_array())
else:
trans_mask = np.abs(wold) > CC.Phonons.__EPSILON_W__

Expand Down Expand Up @@ -1938,7 +1941,8 @@ def ApplyLambdaTensor(current_dyn, matrix, T = 0):
w, pols = current_dyn.DyagDinQ(0)

# Get the translations
trans = ~CC.Methods.get_translations(pols, current_dyn.structure.get_masses_array())
trans = ~current_dyn.structure.get_asr_modes(pols)
# trans = ~CC.Methods.get_translations(pols, current_dyn.structure.get_masses_array())

# Restrict only to non translational modes
w = np.real(w[trans])
Expand Down Expand Up @@ -2002,7 +2006,8 @@ def ApplyFCPrecond(current_dyn, matrix, T = 0):
w, pols = current_dyn.DyagDinQ(0)

# Get the translations
trans = ~CC.Methods.get_translations(pols, current_dyn.structure.get_masses_array())
trans = ~current_dyn.structure.get_asr_modes(pols)
#trans = ~CC.Methods.get_translations(pols, current_dyn.structure.get_masses_array())

# Restrict only to non translational modes
w = np.real(w[trans])
Expand Down Expand Up @@ -2093,7 +2098,8 @@ def GetStructPrecond(current_dyn, ignore_small_w = False, w_pols = None):

# Select translations
if not ignore_small_w:
not_trans = ~CC.Methods.get_translations(pols, mass)
not_trans = ~current_dyn.structure.get_asr_modes(pols)
# not_trans = ~CC.Methods.get_translations(pols, mass)
else:
not_trans = np.abs(w) > CC.Phonons.__EPSILON_W__

Expand Down
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