def set_final_dmat(self, entry_id, abinitout):
abo = AbinitOutput(abinitout)
if not abo.is_finished:
return None
dmatpawu = abo.get_dmatpawu()
if dmatpawu is None:
return None
odmatpawu = np.array(dmatpawu).reshape(-1, self.ndim, self.ndim)
oparams = dmatpawu2params(odmatpawu, self.ndim)
data = abo.get_energetics()
if data is None:
return None
nres2 = data['nres2'][-1]
etot = data['etot'][-1]
if not np.all(
np.sum(oparams['occupations'], axis=1) == np.array(
self.num_electrons_dftu)):
print(
'ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s'
% entry_id)
print('From the population : %s ' % self.num_electrons_dftu)
print('From %20s : %s ' % (abinitout, oparams['occupations']))
return self.pcdb.db.pychemia_entries.update({'_id': entry_id}, {
'$set': {
'properties.etot': etot,
'properties.nres2': nres2,
'properties.final_dmat': gs(oparams)
}
})
def move(self, entry_id, entry_jd, factor=0.2, in_place=False):
"""
Move one candidate with identifier 'entry_id' in the direction of another candidate 'entry_jd'
:param entry_id: Identifier of first entry (Origin)
:param entry_jd: Identifier of second entry (Target)
:param factor: Scale factor for change, 0 scale is the 'Origin' candidate, 1 is the 'Target' candidate
Intermediate values will change candidates accordingly
:param in_place: If True the candidate is changed keeping the identifier unchanged
:return:
"""
if self.is_evaluated(entry_id):
dmat1 = self.get_correlation_params(entry_id)
else:
dmat1 = self.get_correlation_params(entry_id, final=False)
if self.is_evaluated(entry_id):
dmat2 = self.get_correlation_params(entry_jd)
else:
dmat2 = self.get_correlation_params(entry_jd, final=False)
euler_angles1 = dmat1['euler_angles']
euler_angles2 = dmat2['euler_angles']
euler_angles_new = np.zeros(
(self.num_indep_matrices, int(self.ndim * (self.ndim - 1) / 2)))
for i in range(self.num_indep_matrices):
for j in range(int(self.ndim * (self.ndim - 1) / 2)):
angle1 = euler_angles1[i][j]
angle2 = euler_angles2[i][j]
if angle1 < angle2:
if angle2 - angle1 < angle1 - angle2 + 2 * np.pi:
direction = 1 # Forward
angle = angle2 - angle1
else:
direction = -1 # Backward
angle = angle1 - angle2 + 2 * np.pi
else:
if angle1 - angle2 < angle2 - angle1 + 2 * np.pi:
direction = -1 # Backward
angle = angle1 - angle2
else:
direction = 1
angle = angle2 - angle1 + 2 * np.pi
euler_angles_new[i, j] = angle1 + direction * factor * angle
if euler_angles_new[i, j] > np.pi:
euler_angles_new[i, j] -= -2 * np.pi
if euler_angles_new[i, j] < -np.pi:
euler_angles_new[i, j] += -2 * np.pi
newdata = dict(dmat1)
newdata['euler_angles'] = gs(euler_angles_new)
if in_place:
return self.update_dmat_inplace(entry_id, newdata)
else:
return self.new_entry(newdata, active=False)
def get_final_properties(self, path):
outputfile = get_final_abinit_out(path)
if outputfile is None:
raise ValueError("Not such dir: %s" % path)
# Reading the OUTPUT
abo = AbinitOutput(outputfile)
dmatpawu = abo.get_dmatpawu()
odmatpawu = np.array(dmatpawu).reshape(-1, self.ndim, self.ndim)
oparams = dmatpawu2params(odmatpawu, self.ndim)
if not abo.is_finished:
print('This output is not finished')
return None, None
data = abo.get_energetics()
nres2 = data['nres2'][-1]
etot = data['etot'][-1]
final_properties = None
if etot is not None and oparams is not None:
final_properties = {
'etot': etot,
'nres2': nres2,
'final_dmat': gs(oparams)
}
return final_properties, etot
def get_final_properties(self, path):
outputfile = get_final_abinit_out(path)
if outputfile is None:
raise ValueError("Not such dir: %s" % path)
# Reading the OUTPUT
abo = AbinitOutput(outputfile)
dmatpawu = abo.get_dmatpawu()
odmatpawu = np.array(dmatpawu).reshape(-1, self.ndim, self.ndim)
oparams = dmatpawu2params(odmatpawu, self.ndim)
if not abo.is_finished:
print('This output is not finished')
return None, None
data = abo.get_energetics()
nres2 = data['nres2'][-1]
etot = data['etot'][-1]
final_properties = None
if etot is not None and oparams is not None:
final_properties = {'etot': etot,
'nres2': nres2,
'final_dmat': gs(oparams)}
return final_properties, etot
def move(self, entry_id, entry_jd, factor=0.2, in_place=False):
"""
Move one candidate with identifier 'entry_id' in the direction of another candidate 'entry_jd'
:param entry_id: Identifier of first entry (Origin)
:param entry_jd: Identifier of second entry (Target)
:param factor: Scale factor for change, 0 scale is the 'Origin' candidate, 1 is the 'Target' candidate
Intermediate values will change candidates accordingly
:param in_place: If True the candidate is changed keeping the identifier unchanged
:return:
"""
if self.is_evaluated(entry_id):
dmat1 = self.get_correlation_params(entry_id)
else:
dmat1 = self.get_correlation_params(entry_id, final=False)
if self.is_evaluated(entry_id):
dmat2 = self.get_correlation_params(entry_jd)
else:
dmat2 = self.get_correlation_params(entry_jd, final=False)
euler_angles1 = dmat1['euler_angles']
euler_angles2 = dmat2['euler_angles']
euler_angles_new = np.zeros((self.num_indep_matrices, int(self.ndim*(self.ndim-1)/2)))
for i in range(self.num_indep_matrices):
for j in range(int(self.ndim*(self.ndim-1)/2)):
angle1 = euler_angles1[i][j]
angle2 = euler_angles2[i][j]
if angle1 < angle2:
if angle2 - angle1 < angle1 - angle2 + 2*np.pi:
direction = 1 # Forward
angle = angle2 - angle1
else:
direction = -1 # Backward
angle = angle1 - angle2 + 2*np.pi
else:
if angle1 - angle2 < angle2 - angle1 + 2*np.pi:
direction = -1 # Backward
angle = angle1 - angle2
else:
direction = 1
angle = angle2 - angle1 + 2*np.pi
euler_angles_new[i, j] = angle1 + direction*factor*angle
if euler_angles_new[i, j] > np.pi:
euler_angles_new[i, j] -= -2*np.pi
if euler_angles_new[i, j] < -np.pi:
euler_angles_new[i, j] += -2*np.pi
newdata = dict(dmat1)
newdata['euler_angles'] = gs(euler_angles_new)
if in_place:
return self.update_dmat_inplace(entry_id, newdata)
else:
return self.new_entry(newdata, active=False)
def set_final_dmat(self, entry_id, abinitout):
abo = AbinitOutput(abinitout)
if not abo.is_finished:
return None
dmatpawu = abo.get_dmatpawu()
if dmatpawu is None:
return None
odmatpawu = np.array(dmatpawu).reshape(-1, self.ndim, self.ndim)
oparams = dmatpawu2params(odmatpawu, self.ndim)
data = abo.get_energetics()
if data is None:
return None
nres2 = data['nres2'][-1]
etot = data['etot'][-1]
if not np.all(np.sum(oparams['occupations'], axis=1) == np.array(self.num_electrons_dftu)):
print('ERROR: Inconsistent number of DFT+U electrons for correlated orbitals: %s' % entry_id)
print('From the population : %s ' % self.num_electrons_dftu)
print('From %20s : %s ' % (abinitout, oparams['occupations']))
return self.pcdb.db.pychemia_entries.update({'_id': entry_id},
{'$set': {'properties.etot': etot,
'properties.nres2': nres2,
'properties.final_dmat': gs(oparams)}})