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Introduce vertical bar symbol for fc-calculator str

This commit is contained in:
Atsushi Togo 2022-10-16 20:17:03 +09:00
parent f4c26db474
commit 0ba6cbfef9
6 changed files with 967 additions and 17 deletions
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73
phono3py/api_phono3py.py
View File

@ -50,6 +50,8 @@ from phonopy.harmonic.force_constants import (
from phonopy.interface.fc_calculator import get_fc2
from phonopy.structure.atoms import PhonopyAtoms
from phonopy.structure.cells import (
Primitive,
Supercell,
get_primitive,
get_primitive_matrix,
get_supercell,
@ -567,7 +569,7 @@ class Phono3py:
return self._interaction.dynamical_matrix
@property
def primitive(self):
def primitive(self) -> Primitive:
"""Return primitive cell.
Primitive
@ -586,7 +588,7 @@ class Phono3py:
return self.primitive
@property
def unitcell(self):
def unitcell(self) -> PhonopyAtoms:
"""Return Unit cell.
PhonopyAtoms
@ -605,7 +607,7 @@ class Phono3py:
return self.unitcell
@property
def supercell(self):
def supercell(self) -> Supercell:
"""Return supercell.
Supercell
@ -624,7 +626,7 @@ class Phono3py:
return self.supercell
@property
def phonon_supercell(self):
def phonon_supercell(self) -> Supercell:
"""Return supercell for fc2.
Supercell
@ -643,7 +645,7 @@ class Phono3py:
return self.phonon_supercell
@property
def phonon_primitive(self):
def phonon_primitive(self) -> Primitive:
"""Return primitive cell for fc2.
Primitive
@ -664,7 +666,7 @@ class Phono3py:
return self.phonon_primitive
@property
def symmetry(self):
def symmetry(self) -> Symmetry:
"""Return symmetry of supercell.
Symmetry
@ -683,7 +685,7 @@ class Phono3py:
return self.symmetry
@property
def primitive_symmetry(self):
def primitive_symmetry(self) -> Symmetry:
"""Return symmetry of primitive cell.
Symmetry
@ -702,7 +704,7 @@ class Phono3py:
return self.primitive_symmetry
@property
def phonon_supercell_symmetry(self):
def phonon_supercell_symmetry(self) -> Symmetry:
"""Return symmetry of supercell for fc2.
Symmetry
@ -1625,15 +1627,19 @@ class Phono3py:
"""
disp_dataset = self._dataset
if fc_calculator is not None:
fc3_calculator, fc3_calculator_options = self._extract_fc2_fc3_calculators(
fc_calculator, fc_calculator_options, 3
)
if fc3_calculator is not None:
disps, forces = get_displacements_and_forces_fc3(disp_dataset)
fc2, fc3 = get_fc3(
self._supercell,
self._primitive,
disps,
forces,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
fc_calculator=fc3_calculator,
fc_calculator_options=fc3_calculator_options,
is_compact_fc=is_compact_fc,
log_level=self._log_level,
)
@ -1711,15 +1717,19 @@ class Phono3py:
else:
p2s_map = None
if fc_calculator is not None:
fc2_calculator, fc2_calculator_options = self._extract_fc2_fc3_calculators(
fc_calculator, fc_calculator_options, 2
)
if fc2_calculator is not None:
disps, forces = get_displacements_and_forces(disp_dataset)
self._fc2 = get_fc2(
self._phonon_supercell,
self._phonon_primitive,
disps,
forces,
fc_calculator=fc_calculator,
fc_calculator_options=fc_calculator_options,
fc_calculator=fc2_calculator,
fc_calculator_options=fc2_calculator_options,
atom_list=p2s_map,
log_level=self._log_level,
)
@ -2558,3 +2568,38 @@ class Phono3py:
)
print(" But this frequency is forced to be zero.")
print("=" * 61)
def _extract_fc2_fc3_calculators(self, fc_calculator, fc_calculator_options, order):
"""Extract fc_calculator and fc_calculator_options for fc2 and fc3.
fc_calculator : str
FC calculator. "|" separates fc2 and fc3. First and last
parts separated correspond to fc2 and fc3 calculators, respectively.
fc_calculator_options : str
FC calculator options. "|" separates fc2 and fc3. First and last
parts separated correspond to fc2 and fc3 options, respectively.
order : int = 2 or 3
2 and 3 indicate fc2 and fc3, respectively.
"""
if fc_calculator is not None:
if "|" in fc_calculator:
_fc_calculator = fc_calculator.split("|")[order - 2]
if _fc_calculator == "":
_fc_calculator = None
else:
_fc_calculator = fc_calculator
else:
_fc_calculator = None
if fc_calculator_options is not None:
if "|" in fc_calculator_options:
_fc_calculator_options = fc_calculator_options.split("|")[order - 2]
if _fc_calculator_options == "":
_fc_calculator_options = None
else:
_fc_calculator_options = fc_calculator_options
else:
_fc_calculator_options = None
return _fc_calculator, _fc_calculator_options

2
phono3py/cui/phono3py_script.py
View File

@ -1165,7 +1165,7 @@ def main(**argparse_control):
)
if log_level > 1:
show_phono3py_cells(phono3py, settings)
show_phono3py_cells(phono3py)
elif log_level:
print(
"Use -v option to watch primitive cell, unit cell, "

4
phono3py/cui/show_log.py
View File

@ -89,7 +89,7 @@ def show_general_settings(
print(" %s" % v)
def show_phono3py_cells(phono3py: Phono3py, settings):
def show_phono3py_cells(phono3py: Phono3py):
"""Show crystal structures."""
primitive = phono3py.primitive
supercell = phono3py.supercell
@ -100,7 +100,7 @@ def show_phono3py_cells(phono3py: Phono3py, settings):
print_cell(primitive)
print("-" * 32 + " supercell " + "-" * 33)
print_cell(supercell, mapping=primitive.s2p_map)
if settings.phonon_supercell_matrix is not None:
if phono3py.phonon_supercell_matrix is not None:
print("-" * 19 + " primitive cell for harmonic phonon " + "-" * 20)
print_cell(phonon_primitive)
print("-" * 21 + " supercell for harmonic phonon " + "-" * 22)

85
test/conftest.py
View File

@ -207,6 +207,91 @@ def si_pbesol_iterha_111():
return phonopy.load(yaml_filename, log_level=1, produce_fc=False)
@pytest.fixture(scope="session")
def si_pbesol_111_222_fd(request):
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
* use alm if available on test side
"""
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
log_level=1,
)
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm_fd(request):
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
* use alm for fc2 if available on test side
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm|",
log_level=1,
)
@pytest.fixture(scope="session")
def si_pbesol_111_222_alm(request):
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
* use alm if available on test side
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="alm",
log_level=1,
)
@pytest.fixture(scope="session")
def si_pbesol_111_222_fd_alm(request):
"""Return Phono3py instance of Si 1x1x1.
* with symmetry
* full fc
* use alm for fc3 if available on test side
"""
pytest.importorskip("alm")
yaml_filename = os.path.join(current_dir, "phono3py_params_Si-111-222.yaml")
enable_v2 = request.config.getoption("--v1")
return phono3py.load(
yaml_filename,
store_dense_gp_map=enable_v2,
store_dense_svecs=enable_v2,
fc_calculator="|alm",
log_level=1,
)
@pytest.fixture(scope="session")
def nacl_pbe(request):
"""Return Phono3py instance of NaCl 2x2x2.

703
test/phono3py_params_Si-111-222.yaml Normal file
View File

@ -0,0 +1,703 @@
phono3py:
version: 2.4.1
frequency_unit_conversion_factor: 15.633302
symmetry_tolerance: 1.00000e-05
physical_unit:
atomic_mass: "AMU"
space_group:
type: "Fd-3m"
number: 227
Hall_symbol: "F 4d 2 3 -1d"
primitive_matrix:
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
supercell_matrix:
- [ 1, 0, 0 ]
- [ 0, 1, 0 ]
- [ 0, 0, 1 ]
primitive_cell:
lattice:
- [ 0.000000000000000, 2.716780015000000, 2.716780015000000 ] # a
- [ 2.716780015000000, 0.000000000000000, 2.716780015000000 ] # b
- [ 2.716780015000000, 2.716780015000000, 0.000000000000000 ] # c
points:
- symbol: Si # 1
coordinates: [ 0.875000000000000, 0.875000000000000, 0.875000000000000 ]
mass: 28.085500
- symbol: Si # 2
coordinates: [ 0.125000000000000, 0.125000000000000, 0.125000000000000 ]
mass: 28.085500
reciprocal_lattice: # without 2pi
- [ -0.184041400937646, 0.184041400937646, 0.184041400937646 ] # a*
- [ 0.184041400937646, -0.184041400937646, 0.184041400937646 ] # b*
- [ 0.184041400937646, 0.184041400937646, -0.184041400937646 ] # c*
unit_cell:
lattice:
- [ 5.433560030000000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 5.433560030000000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 5.433560030000000 ] # c
points:
- symbol: Si # 1
coordinates: [ 0.875000000000000, 0.875000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 2
coordinates: [ 0.875000000000000, 0.375000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 3
coordinates: [ 0.375000000000000, 0.875000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 4
coordinates: [ 0.375000000000000, 0.375000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 5
coordinates: [ 0.125000000000000, 0.125000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 5
- symbol: Si # 6
coordinates: [ 0.125000000000000, 0.625000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 5
- symbol: Si # 7
coordinates: [ 0.625000000000000, 0.125000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 5
- symbol: Si # 8
coordinates: [ 0.625000000000000, 0.625000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 5
supercell:
lattice:
- [ 5.433560030000000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 5.433560030000000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 5.433560030000000 ] # c
points:
- symbol: Si # 1
coordinates: [ 0.875000000000000, 0.875000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 2
coordinates: [ 0.875000000000000, 0.375000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 3
coordinates: [ 0.375000000000000, 0.875000000000000, 0.375000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 4
coordinates: [ 0.375000000000000, 0.375000000000000, 0.875000000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 5
coordinates: [ 0.125000000000000, 0.125000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 5
- symbol: Si # 6
coordinates: [ 0.125000000000000, 0.625000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 5
- symbol: Si # 7
coordinates: [ 0.625000000000000, 0.125000000000000, 0.625000000000000 ]
mass: 28.085500
reduced_to: 5
- symbol: Si # 8
coordinates: [ 0.625000000000000, 0.625000000000000, 0.125000000000000 ]
mass: 28.085500
reduced_to: 5
phonon_supercell_matrix:
- [ 2, 0, 0 ]
- [ 0, 2, 0 ]
- [ 0, 0, 2 ]
phonon_primitive_cell:
lattice:
- [ 0.000000000000000, 2.716780015000000, 2.716780015000000 ] # a
- [ 2.716780015000000, 0.000000000000000, 2.716780015000000 ] # b
- [ 2.716780015000000, 2.716780015000000, 0.000000000000000 ] # c
points:
- symbol: Si # 1
coordinates: [ 0.875000000000000, 0.875000000000000, 0.875000000000000 ]
mass: 28.085500
- symbol: Si # 2
coordinates: [ 0.125000000000000, 0.125000000000000, 0.125000000000000 ]
mass: 28.085500
reciprocal_lattice: # without 2pi
- [ -0.184041400937646, 0.184041400937646, 0.184041400937646 ] # a*
- [ 0.184041400937646, -0.184041400937646, 0.184041400937646 ] # b*
- [ 0.184041400937646, 0.184041400937646, -0.184041400937646 ] # c*
phonon_supercell:
lattice:
- [ 10.867120060000000, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 10.867120060000000, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 10.867120060000000 ] # c
points:
- symbol: Si # 1
coordinates: [ 0.437500000000000, 0.437500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 2
coordinates: [ 0.937500000000000, 0.437500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 3
coordinates: [ 0.437500000000000, 0.937500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 4
coordinates: [ 0.937500000000000, 0.937500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 5
coordinates: [ 0.437500000000000, 0.437500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 6
coordinates: [ 0.937500000000000, 0.437500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 7
coordinates: [ 0.437500000000000, 0.937500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 8
coordinates: [ 0.937500000000000, 0.937500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 9
coordinates: [ 0.437500000000000, 0.187500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 10
coordinates: [ 0.937500000000000, 0.187500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 11
coordinates: [ 0.437500000000000, 0.687500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 12
coordinates: [ 0.937500000000000, 0.687500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 13
coordinates: [ 0.437500000000000, 0.187500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 14
coordinates: [ 0.937500000000000, 0.187500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 15
coordinates: [ 0.437500000000000, 0.687500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 16
coordinates: [ 0.937500000000000, 0.687500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 17
coordinates: [ 0.187500000000000, 0.437500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 18
coordinates: [ 0.687500000000000, 0.437500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 19
coordinates: [ 0.187500000000000, 0.937500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 20
coordinates: [ 0.687500000000000, 0.937500000000000, 0.187500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 21
coordinates: [ 0.187500000000000, 0.437500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 22
coordinates: [ 0.687500000000000, 0.437500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 23
coordinates: [ 0.187500000000000, 0.937500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 24
coordinates: [ 0.687500000000000, 0.937500000000000, 0.687500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 25
coordinates: [ 0.187500000000000, 0.187500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 26
coordinates: [ 0.687500000000000, 0.187500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 27
coordinates: [ 0.187500000000000, 0.687500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 28
coordinates: [ 0.687500000000000, 0.687500000000000, 0.437500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 29
coordinates: [ 0.187500000000000, 0.187500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 30
coordinates: [ 0.687500000000000, 0.187500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 31
coordinates: [ 0.187500000000000, 0.687500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 32
coordinates: [ 0.687500000000000, 0.687500000000000, 0.937500000000000 ]
mass: 28.085500
reduced_to: 1
- symbol: Si # 33
coordinates: [ 0.062500000000000, 0.062500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 34
coordinates: [ 0.562500000000000, 0.062500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 35
coordinates: [ 0.062500000000000, 0.562500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 36
coordinates: [ 0.562500000000000, 0.562500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 37
coordinates: [ 0.062500000000000, 0.062500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 38
coordinates: [ 0.562500000000000, 0.062500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 39
coordinates: [ 0.062500000000000, 0.562500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 40
coordinates: [ 0.562500000000000, 0.562500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 41
coordinates: [ 0.062500000000000, 0.312500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 42
coordinates: [ 0.562500000000000, 0.312500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 43
coordinates: [ 0.062500000000000, 0.812500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 44
coordinates: [ 0.562500000000000, 0.812500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 45
coordinates: [ 0.062500000000000, 0.312500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 46
coordinates: [ 0.562500000000000, 0.312500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 47
coordinates: [ 0.062500000000000, 0.812500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 48
coordinates: [ 0.562500000000000, 0.812500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 49
coordinates: [ 0.312500000000000, 0.062500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 50
coordinates: [ 0.812500000000000, 0.062500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 51
coordinates: [ 0.312500000000000, 0.562500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 52
coordinates: [ 0.812500000000000, 0.562500000000000, 0.312500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 53
coordinates: [ 0.312500000000000, 0.062500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 54
coordinates: [ 0.812500000000000, 0.062500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 55
coordinates: [ 0.312500000000000, 0.562500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 56
coordinates: [ 0.812500000000000, 0.562500000000000, 0.812500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 57
coordinates: [ 0.312500000000000, 0.312500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 58
coordinates: [ 0.812500000000000, 0.312500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 59
coordinates: [ 0.312500000000000, 0.812500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 60
coordinates: [ 0.812500000000000, 0.812500000000000, 0.062500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 61
coordinates: [ 0.312500000000000, 0.312500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 62
coordinates: [ 0.812500000000000, 0.312500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 63
coordinates: [ 0.312500000000000, 0.812500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
- symbol: Si # 64
coordinates: [ 0.812500000000000, 0.812500000000000, 0.562500000000000 ]
mass: 28.085500
reduced_to: 33
phonon_displacements:
- atom: 1
displacement:
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displacement_pairs:
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displacement_id: 1
forces:
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pair_distance: 0.00000000
displacement:
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displacement_id: 2
forces:
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forces:
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pair_distance: 3.84210714
displacement:
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displacement_id: 4
forces:
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displacement:
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forces:
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forces:
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forces:
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displacement:
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displacement_id: 8
forces:
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117
test/phonon3/test_fc3.py
View File

@ -96,6 +96,123 @@ def test_fc3(si_pbesol_111: Phono3py):
np.testing.assert_allclose(ph.fc3[0, 1, 7], fc3_ref, atol=1e-8, rtol=0)
def test_phonon_smat_fd(si_pbesol_111_222_fd: Phono3py):
"""Test phonon smat with Si PBEsol 1x1x1-2x2x2."""
ph = si_pbesol_111_222_fd
fc3_ref = [
[
[1.07250822e-01, 1.86302073e-17, -4.26452855e-18],
[8.96414569e-03, -1.43046911e-01, -1.38498937e-01],
[-8.96414569e-03, -1.38498937e-01, -1.43046911e-01],
],
[
[-8.96414569e-03, -1.43046911e-01, -1.38498937e-01],
[-3.39457157e-02, -4.63315728e-17, -4.17779237e-17],
[-3.31746167e-01, -2.60025724e-02, -2.60025724e-02],
],
[
[8.96414569e-03, -1.38498937e-01, -1.43046911e-01],
[-3.31746167e-01, 2.60025724e-02, 2.60025724e-02],
[-3.39457157e-02, 3.69351540e-17, 5.94504191e-18],
],
]
np.testing.assert_allclose(ph.fc3[0, 1, 7], fc3_ref, atol=1e-8, rtol=0)
fc2_ref = [
[-0.20333398, -0.0244225, -0.0244225],
[-0.0244225, -0.02219682, -0.024112],
[-0.0244225, -0.024112, -0.02219682],
]
np.testing.assert_allclose(ph.fc2[0, 33], fc2_ref, atol=1e-6, rtol=0)
def test_phonon_smat_alm(si_pbesol_111_222_alm: Phono3py):
"""Test phonon smat and ALM with Si PBEsol 1x1x1-2x2x2."""
ph = si_pbesol_111_222_alm
fc3_ref = [
[
[0.10725082, 0.0, 0.0],
[-0.04225275, -0.09187669, -0.1386571],
[0.04225275, -0.1386571, -0.09187669],
],
[
[0.04225275, -0.09187669, -0.1386571],
[-0.17073504, 0.0, 0.0],
[-0.33192165, 0.02516976, 0.02516976],
],
[
[-0.04225275, -0.1386571, -0.09187669],
[-0.33192165, -0.02516976, -0.02516976],
[-0.17073504, 0.0, 0.0],
],
]
np.testing.assert_allclose(ph.fc3[0, 1, 7], fc3_ref, atol=1e-6, rtol=0)
fc2_ref = [
[-0.20333398, -0.0244225, -0.0244225],
[-0.0244225, -0.02219682, -0.024112],
[-0.0244225, -0.024112, -0.02219682],
]
np.testing.assert_allclose(ph.fc2[0, 33], fc2_ref, atol=1e-6, rtol=0)
def test_phonon_smat_alm_fd(si_pbesol_111_222_alm_fd: Phono3py):
"""Test phonon smat and ALM (fc2) FD (fc3) with Si PBEsol 1x1x1-2x2x2."""
ph = si_pbesol_111_222_alm_fd
fc3_ref = [
[
[1.07250822e-01, 1.86302073e-17, -4.26452855e-18],
[8.96414569e-03, -1.43046911e-01, -1.38498937e-01],
[-8.96414569e-03, -1.38498937e-01, -1.43046911e-01],
],
[
[-8.96414569e-03, -1.43046911e-01, -1.38498937e-01],
[-3.39457157e-02, -4.63315728e-17, -4.17779237e-17],
[-3.31746167e-01, -2.60025724e-02, -2.60025724e-02],
],
[
[8.96414569e-03, -1.38498937e-01, -1.43046911e-01],
[-3.31746167e-01, 2.60025724e-02, 2.60025724e-02],
[-3.39457157e-02, 3.69351540e-17, 5.94504191e-18],
],
]
np.testing.assert_allclose(ph.fc3[0, 1, 7], fc3_ref, atol=1e-6, rtol=0)
fc2_ref = [
[-0.20333398, -0.0244225, -0.0244225],
[-0.0244225, -0.02219682, -0.024112],
[-0.0244225, -0.024112, -0.02219682],
]
np.testing.assert_allclose(ph.fc2[0, 33], fc2_ref, atol=1e-6, rtol=0)
def test_phonon_smat_fd_alm(si_pbesol_111_222_fd_alm: Phono3py):
"""Test phonon smat and FD (fc2) ALM (fc3) with Si PBEsol 1x1x1-2x2x2."""
ph = si_pbesol_111_222_fd_alm
fc3_ref = [
[
[0.10725082, 0.0, 0.0],
[-0.04225275, -0.09187669, -0.1386571],
[0.04225275, -0.1386571, -0.09187669],
],
[
[0.04225275, -0.09187669, -0.1386571],
[-0.17073504, 0.0, 0.0],
[-0.33192165, 0.02516976, 0.02516976],
],
[
[-0.04225275, -0.1386571, -0.09187669],
[-0.33192165, -0.02516976, -0.02516976],
[-0.17073504, 0.0, 0.0],
],
]
np.testing.assert_allclose(ph.fc3[0, 1, 7], fc3_ref, atol=1e-6, rtol=0)
fc2_ref = [
[-0.20333398, -0.0244225, -0.0244225],
[-0.0244225, -0.02219682, -0.024112],
[-0.0244225, -0.024112, -0.02219682],
]
np.testing.assert_allclose(ph.fc2[0, 33], fc2_ref, atol=1e-6, rtol=0)
@pytest.mark.parametrize("pinv_solver", ["numpy", "lapacke"])
def test_fc3_lapacke_solver(si_pbesol_111: Phono3py, pinv_solver: str):
"""Test fc3 with Si PBEsol 1x1x1 using lapacke solver."""