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Writing docstrings following pydocstring

This commit is contained in:
Atsushi Togo 2021-10-25 14:18:37 +09:00
parent 39765d0ae4
commit 5bc2d0513e
7 changed files with 37 additions and 157 deletions
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25
phonopy/phonon/modulation.py
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@ -33,7 +33,7 @@
# ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE. # POSSIBILITY OF SUCH DAMAGE.
from typing import List, Union from typing import Union
import numpy as np import numpy as np
@ -69,17 +69,22 @@ class Modulation:
self._derivative_order = derivative_order self._derivative_order = derivative_order
self._factor = factor self._factor = factor
self._u = []
self._eigvecs = []
self._eigvals = []
self._supercell = None
dim = self._get_dimension_3x3() dim = self._get_dimension_3x3()
self._supercell = get_supercell(self._primitive, dim) self._supercell = get_supercell(self._primitive, dim)
complex_dtype = "c%d" % (np.dtype("double").itemsize * 2)
self._u = np.zeros(
(len(self._phonon_modes), len(self._supercell), 3),
dtype=complex_dtype,
order="C",
)
self._eigvals = np.zeros(len(self._phonon_modes), dtype="double")
self._eigvecs = np.zeros(
(len(self._phonon_modes), len(self._primitive) * 3), dtype=complex_dtype
)
def run(self): def run(self):
"""Calculate modulations.""" """Calculate modulations."""
for ph_mode in self._phonon_modes: for i, ph_mode in enumerate(self._phonon_modes):
q, band_index, amplitude, argument = ph_mode q, band_index, amplitude, argument = ph_mode
eigvals, eigvecs = get_eigenvectors( eigvals, eigvecs = get_eigenvectors(
q, q,
@ -90,9 +95,9 @@ class Modulation:
nac_q_direction=self._nac_q_direction, nac_q_direction=self._nac_q_direction,
) )
u = self._get_displacements(eigvecs[:, band_index], q, amplitude, argument) u = self._get_displacements(eigvecs[:, band_index], q, amplitude, argument)
self._u.append(u) self._u[i] = u
self._eigvecs.append(eigvecs[:, band_index]) self._eigvecs[i] = eigvecs[:, band_index]
self._eigvals.append(eigvals[band_index]) self._eigvals[i] = eigvals[band_index]
def get_modulated_supercells(self): def get_modulated_supercells(self):
"""Return modulations.""" """Return modulations."""

4
phonopy/spectrum/dynamic_structure_factor.py
View File

@ -233,9 +233,9 @@ class DynamicStructureFactor:
freq_min=self._fmin, freq_min=self._fmin,
freq_max=self._fmax, freq_max=self._fmax,
) )
td.set_temperatures([self._T]) td.temperatures = [self._T]
td.run() td.run()
return td.get_thermal_displacements() return td.temperatures, td.thermal_displacements
def _phonon_structure_factor(self, Q_cart, G, DW, freq, eigvec): def _phonon_structure_factor(self, Q_cart, G, DW, freq, eigvec):
symbols = self._primitive.get_chemical_symbols() symbols = self._primitive.get_chemical_symbols()

8
test/conftest.py
View File

@ -247,7 +247,9 @@ def helper_methods():
class HelperMethods: class HelperMethods:
@classmethod @classmethod
def compare_cells_with_order(cls, cell, cell_ref, symprec=1e-5): def compare_cells_with_order(
cls, cell: PhonopyAtoms, cell_ref: PhonopyAtoms, symprec=1e-5
):
"""Compare two cells with the same orders of positions.""" """Compare two cells with the same orders of positions."""
np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=symprec) np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=symprec)
cls.compare_positions_with_order( cls.compare_positions_with_order(
@ -270,7 +272,9 @@ def helper_methods():
assert (dist < symprec).all() assert (dist < symprec).all()
@classmethod @classmethod
def compare_cells(cls, cell, cell_ref, symprec=1e-5): def compare_cells(
cls, cell: PhonopyAtoms, cell_ref: PhonopyAtoms, symprec=1e-5
):
"""Compare two cells where position orders can be different.""" """Compare two cells where position orders can be different."""
np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=symprec) np.testing.assert_allclose(cell.cell, cell_ref.cell, atol=symprec)

2
test/harmonic/test_derivative_dynmat.py
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@ -91,7 +91,7 @@ def _assert(ph: Phonopy, ref_vals, show=False):
dynmat = ph.dynamical_matrix dynmat = ph.dynamical_matrix
ddynmat = DerivativeOfDynamicalMatrix(dynmat) ddynmat = DerivativeOfDynamicalMatrix(dynmat)
ddynmat.run([0, 0.1, 0.1]) ddynmat.run([0, 0.1, 0.1])
ddm = ddynmat.get_derivative_of_dynamical_matrix() ddm = ddynmat.d_dynamical_matrix
condition = np.abs(ddm) > 1e-8 condition = np.abs(ddm) > 1e-8
vals = np.extract(condition, ddm).real vals = np.extract(condition, ddm).real
if show: if show:

17
test/harmonic/test_force_constants.py
View File

@ -1,6 +1,8 @@
"""Tests for routines in force_constants.py."""
import numpy as np import numpy as np
import pytest import pytest
from phonopy import Phonopy
from phonopy.harmonic.force_constants import cutoff_force_constants from phonopy.harmonic.force_constants import cutoff_force_constants
from phonopy.structure.cells import get_primitive from phonopy.structure.cells import get_primitive
@ -41,26 +43,30 @@ fc_1_10_compact_fcsym_ref = [
] ]
def test_fc(ph_nacl): def test_fc(ph_nacl: Phonopy):
"""Test of force constants calculation with fcsym by NaCl."""
fc_1_10 = ph_nacl.force_constants[1, 10] fc_1_10 = ph_nacl.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()])) # print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_ref, atol=1e-5) np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_ref, atol=1e-5)
def test_fc_nofcsym(ph_nacl_nofcsym): def test_fc_nofcsym(ph_nacl_nofcsym: Phonopy):
"""Test of force constants calculation without fcsym by NaCl."""
fc_1_10 = ph_nacl_nofcsym.force_constants[1, 10] fc_1_10 = ph_nacl_nofcsym.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()])) # print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_nofcsym_ref, atol=1e-5) np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_nofcsym_ref, atol=1e-5)
def test_fc_compact_fcsym(ph_nacl_compact_fcsym): def test_fc_compact_fcsym(ph_nacl_compact_fcsym: Phonopy):
"""Test of force constants calculation in compact format with fcsym by NaCl."""
fc_1_10 = ph_nacl_compact_fcsym.force_constants[1, 10] fc_1_10 = ph_nacl_compact_fcsym.force_constants[1, 10]
# print("".join(["%f, " % v for v in fc_1_10.ravel()])) # print("".join(["%f, " % v for v in fc_1_10.ravel()]))
np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_compact_fcsym_ref, atol=1e-5) np.testing.assert_allclose(fc_1_10.ravel(), fc_1_10_compact_fcsym_ref, atol=1e-5)
@pytest.mark.parametrize("is_compact", [False, True]) @pytest.mark.parametrize("is_compact", [False, True])
def test_fc_cutoff_radius(ph_nacl, ph_nacl_compact_fcsym, is_compact): def test_fc_cutoff_radius(ph_nacl: Phonopy, ph_nacl_compact_fcsym: Phonopy, is_compact):
"""Test of cutoff radius of force constants calculation by NaCl."""
if is_compact: if is_compact:
ph = ph_nacl_compact_fcsym ph = ph_nacl_compact_fcsym
else: else:
@ -83,8 +89,9 @@ def test_fc_cutoff_radius(ph_nacl, ph_nacl_compact_fcsym, is_compact):
[(False, False), (False, True), (True, False), (True, True)], [(False, False), (False, True), (True, False), (True, True)],
) )
def test_fc_cutoff_radius_svecs( def test_fc_cutoff_radius_svecs(
ph_nacl, ph_nacl_compact_fcsym, is_compact, store_dense_svecs ph_nacl: Phonopy, ph_nacl_compact_fcsym: Phonopy, is_compact, store_dense_svecs
): ):
"""Test of cutoff radius with dense-svecs format by NaCl."""
if is_compact: if is_compact:
ph = ph_nacl_compact_fcsym ph = ph_nacl_compact_fcsym
else: else:

136
test/interface/FORCE_SETS_NaCl
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@ -1,136 +0,0 @@
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2
test/interface/test_vasp.py
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@ -28,7 +28,7 @@ def test_parse_vasprun_xml():
"""Test parsing vasprun.xml with expat.""" """Test parsing vasprun.xml with expat."""
filename_vasprun = os.path.join(data_dir, "vasprun.xml.tar.bz2") filename_vasprun = os.path.join(data_dir, "vasprun.xml.tar.bz2")
_tar = tarfile.open(filename_vasprun) _tar = tarfile.open(filename_vasprun)
filename = os.path.join(data_dir, "FORCE_SETS_NaCl") filename = os.path.join(data_dir, "../FORCE_SETS_NaCl")
dataset = parse_FORCE_SETS(filename=filename) dataset = parse_FORCE_SETS(filename=filename)
for i, member in enumerate(_tar.getmembers()): for i, member in enumerate(_tar.getmembers()):
vr = Vasprun(_tar.extractfile(member), use_expat=True) vr = Vasprun(_tar.extractfile(member), use_expat=True)