scnc
/
phonopy
mirror of https://github.com/phonopy/phonopy.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Wrote docstrings in DynamcalMatrixGL class

This commit is contained in:
Atsushi Togo 2021-06-15 15:15:55 +09:00
parent 3dfdc6d58c
commit 20270f5bfc
1 changed files with 86 additions and 39 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

121
phonopy/harmonic/dynamical_matrix.py
View File

@ -474,6 +474,26 @@ class DynamicalMatrixNAC(DynamicalMatrix):
DeprecationWarning)
return self.nac_method
@property
def nac_params(self):
"""Return NAC basic parameters."""
return {'born': self.born,
'factor': self.factor,
'dielectric': self.dielectric}
@nac_params.setter
def nac_params(self, nac_params):
"""Set NAC parameters."""
self._set_nac_params(nac_params)
def set_nac_params(self, nac_params):
"""Set NAC parameters."""
warnings.warn(
"DynamicalMatrixNAC.set_nac_params() is deprecated."
"Use DynamicalMatrixNAC.nac_params attribute instead.",
DeprecationWarning)
self.nac_params = nac_params
@property
def symprec(self):
"""Return symmetry tolerance."""
@ -484,6 +504,16 @@ class DynamicalMatrixNAC(DynamicalMatrix):
"""Return log level."""
return self._log_level
def _set_nac_params(self, nac_params):
raise NotImplementedError()
def _set_basic_nac_params(self, nac_params):
"""Set basic NAC parameters."""
self._born = np.array(nac_params['born'], dtype='double', order='C')
self._unit_conversion = nac_params['factor']
self._dielectric = np.array(nac_params['dielectric'],
dtype='double', order='C')
def set_dynamical_matrix(self, q, q_direction=None):
"""Run dynamical matrix calculation at q-point."""
warnings.warn(
@ -492,12 +522,6 @@ class DynamicalMatrixNAC(DynamicalMatrix):
DeprecationWarning)
self.run(q, q_direction=q_direction)
def _set_basic_nac_params(self, nac_params):
self._born = np.array(nac_params['born'], dtype='double', order='C')
self._unit_conversion = nac_params['factor']
self._dielectric = np.array(nac_params['dielectric'],
dtype='double', order='C')
def _get_charge_sum(self, num_atom, q, born):
nac_q = np.zeros((num_atom, num_atom, 3, 3), dtype='double', order='C')
A = np.dot(q, born)
@ -510,6 +534,9 @@ class DynamicalMatrixNAC(DynamicalMatrix):
return (unit_conversion * 4.0 * np.pi / volume /
np.dot(q.T, np.dot(dielectric, q)))
def _compute_dynamical_matrix(self, q_red, q_direction):
raise NotImplementedError()
class DynamicalMatrixGL(DynamicalMatrixNAC):
"""Non analytical term correction (NAC) by Gonze and Lee."""
@ -567,10 +594,11 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
self._dd_q0 = None
if nac_params is not None:
self.set_nac_params(nac_params)
self.nac_params = nac_params
@property
def Gonze_nac_dataset(self):
"""Return Gonze-Lee NAC dataset."""
return (self._Gonze_force_constants,
self._dd_q0,
self._G_cutoff,
@ -578,9 +606,19 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
self._Lambda)
def get_Gonze_nac_dataset(self):
"""Return Gonze-Lee NAC dataset."""
warnings.warn(
"DynamicalMatrixGL.get_Gonze_nac_dataset() is deprecated."
"Use DynamicalMatrixGL.Gonze_nac_dataset attribute instead.",
DeprecationWarning)
return self.Gonze_nac_dataset
def set_nac_params(self, nac_params):
def _set_nac_params(self, nac_params):
"""Set and prepare NAC parameters.
This is called via DynamicalMatrixNAC.nac_params.
"""
self._set_basic_nac_params(nac_params)
if 'G_cutoff' in nac_params:
self._G_cutoff = nac_params['G_cutoff']
@ -598,18 +636,41 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
# self._H = self._get_H()
def make_Gonze_nac_dataset(self):
"""Prepare Gonze-Lee force constants.
Dipole-dipole interaction contribution is subtracted from
supercell force constants.
"""
try:
import phonopy._phonopy as phonoc
import phonopy._phonopy as phonoc # noqa F401
self._run_c_recip_dipole_dipole_q0()
except ImportError:
print("Python version of dipole-dipole calculation is not well "
"implemented.")
sys.exit(1)
self._run_Gonze_force_constants()
fc_shape = self._force_constants.shape
d2f = DynmatToForceConstants(self._pcell,
self._scell,
is_full_fc=(fc_shape[0] == fc_shape[1]))
dynmat = []
num_q = len(d2f.commensurate_points)
for i, q_red in enumerate(d2f.commensurate_points):
if self._log_level > 2:
print("%d/%d %s" % (i + 1, num_q, q_red))
self._run(q_red)
dm_dd = self._get_Gonze_dipole_dipole(q_red, None)
self._dynamical_matrix -= dm_dd
dynmat.append(self._dynamical_matrix)
d2f.dynamical_matrices = dynmat
d2f.run()
self._Gonze_force_constants = d2f.force_constants
self._Gonze_count = 0
def show_nac_message(self):
"""Show message on Gonze-Lee NAC parameters."""
print("Use NAC by Gonze et al. (no real space sum in current "
"implementation)")
print(" PRB 50, 13035(R) (1994), PRB 55, 10355 (1997)")
@ -618,10 +679,11 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
% (self._G_cutoff, len(self._G_list), self._Lambda))
def show_Gonze_nac_message(self):
warnings.warn("DynamicalMatrixGL.show_Gonze_nac_message is deprecated."
"""Show message on Gonze-Lee NAC parameters."""
warnings.warn(
"DynamicalMatrixGL.show_Gonze_nac_message() is deprecated."
"Use DynamicalMatrixGL.show_nac_message instead.",
DeprecationWarning)
self.show_nac_message()
def _compute_dynamical_matrix(self, q_red, q_direction):
@ -638,24 +700,6 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
dm_dd = self._get_Gonze_dipole_dipole(q_red, q_direction)
self._dynamical_matrix += dm_dd
def _run_Gonze_force_constants(self):
fc_shape = self._force_constants.shape
d2f = DynmatToForceConstants(self._pcell,
self._scell,
is_full_fc=(fc_shape[0] == fc_shape[1]))
dynmat = []
num_q = len(d2f.commensurate_points)
for i, q_red in enumerate(d2f.commensurate_points):
if self._log_level > 2:
print("%d/%d %s" % (i + 1, num_q, q_red))
self._run(q_red)
dm_dd = self._get_Gonze_dipole_dipole(q_red, None)
self._dynamical_matrix -= dm_dd
dynmat.append(self._dynamical_matrix)
d2f.dynamical_matrices = dynmat
d2f.run()
self._Gonze_force_constants = d2f.force_constants
def _get_Gonze_dipole_dipole(self, q_red, q_direction):
rec_lat = np.linalg.inv(self._pcell.cell) # column vectors
q_cart = np.array(np.dot(q_red, rec_lat.T), dtype='double')
@ -666,7 +710,7 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
dtype='double')
try:
import phonopy._phonopy as phonoc
import phonopy._phonopy as phonoc # noqa F401
C_recip = self._get_c_recip_dipole_dipole(q_cart, q_dir_cart)
except ImportError:
print("Python version of dipole-dipole calculation is not well "
@ -685,7 +729,7 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
return C_dd
def _get_c_recip_dipole_dipole(self, q_cart, q_dir_cart):
"""Reciprocal part of Eq.(71) on the right hand side
"""Reciprocal part of Eq.(71) on the right hand side.
This is subtracted from supercell force constants to create
short-range force constants. Only once at commensurate points.
@ -694,7 +738,6 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
to create full force constants. Called many times.
"""
import phonopy._phonopy as phonoc
pos = self._pcell.positions
@ -718,12 +761,11 @@ class DynamicalMatrixGL(DynamicalMatrixNAC):
return dd
def _run_c_recip_dipole_dipole_q0(self):
"""Reciprocal part of Eq.(71) second term on the right hand side
"""Reciprocal part of Eq.(71) second term on the right hand side.
Computed only once.
"""
import phonopy._phonopy as phonoc
pos = self._pcell.get_positions()
@ -887,9 +929,14 @@ class DynamicalMatrixWang(DynamicalMatrixNAC):
self._symprec = symprec
if nac_params is not None:
self.set_nac_params(nac_params)
self.nac_params = nac_params
def set_nac_params(self, nac_params):
def _set_nac_params(self, nac_params):
"""Set NAC parameters.
This is called via DynamicalMatrixNAC.nac_params.
"""
self._set_basic_nac_params(nac_params)
def show_nac_message(self):