Merge branch 'release-1.10.10'

.travis.yml

@@ -3,7 +3,6 @@ sudo: false
 dist: trusty
 python:
  - '2.7'
- - '3.4'
  - '3.5'
 
 cache: apt
@@ -22,19 +21,50 @@ before_install:
  - conda config --add channels jochym
 
 install:
- - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy python-ase spglib scipy yaml pyyaml future
+ - conda install --yes python=$TRAVIS_PYTHON_VERSION pip numpy python-ase spglib scipy yaml pyyaml future anaconda-client anaconda-build
  - git describe --tags --dirty
- - git describe --tags --dirty | sed -e 's/\([.0-9]*\)-\(.*\)-g.*/\2/' -e 's/^v//g' > __nanoversion__.txt
+ - git describe --tags --dirty | sed -e 's/\([.0-9]*\)-\(.*\)-g.*/\2/' -e 's/^[vr]//g' > __nanoversion__.txt
  - python setup.py install
 
 script: "( cd test/phonopy ; for d in * ; do ( cd $d ; for f in test_*.py ; do python $f ; done ) ; done )"
 
 deploy:
- skip_cleanup: true
- provider: pypi
- user: jochym
- password:
- secure: 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
- on:
- branch: master
- python: 2.7
+ # testing pypi
+ - provider: pypi
+ server: https://testpypi.python.org/pypi
+ skip_cleanup: true
+ distributions: sdist
+ user: jochym
+ password:
+ secure: "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"
+ on:
+ branch: rc
+ tags: false
+ python: 2.7
+ # testing anaconda
+ - provider: script
+ skip_cleanup: true
+ script: anaconda -t $ANACONDA_TOKEN build trigger --test-only --branch rc jochym/phonopy
+ on:
+ branch: rc
+ tags: false
+ python: 2.7
+ # production pypi
+ - provider: pypi
+ skip_cleanup: true
+ distributions: sdist
+ user: jochym
+ password:
+ secure: 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
+ on:
+ branch: master
+ tags: false
+ python: 2.7 
+ # production anaconda
+ - provider: script
+ skip_cleanup: true
+ script: anaconda -t $ANACONDA_TOKEN build trigger --branch master jochym/phonopy
+ on:
+ branch: master
+ tags: false
+ python: 2.7

MANIFEST.in

@@ -2,3 +2,4 @@ graft c/harmonic_h
 graft c/spglib_h
 graft c/kspclib_h
 graft example
+include __nanoversion__.txt

README.md

@@ -1,6 +1,9 @@
 [![Binstar Badge](https://anaconda.org/jochym/phonopy/badges/version.svg)](https://binstar.org/jochym/phonopy)
 [![Binstar Badge](https://anaconda.org/jochym/phonopy/badges/installer/conda.svg)](https://anaconda.org/jochym/phonopy)
 [![Binstar Badge](https://anaconda.org/jochym/phonopy/badges/build.svg)](https://anaconda.org/jochym/phonopy/builds)
+[![Build Status](https://travis-ci.org/jochym/phonopy.svg?branch=master)](https://travis-ci.org/jochym/phonopy)
+[![PyPI](https://img.shields.io/pypi/v/phonopy.svg?maxAge=2592000)](https://pypi.python.org/pypi/phonopy)
+[![PyPI](https://img.shields.io/pypi/dm/phonopy.svg?maxAge=2592000)]()
 
 phonopy
 =======

__nanoversion__.txt

@@ -0,0 +1 @@
+0

anharmonic/file_IO.py

@@ -625,6 +625,7 @@ def write_kappa_to_hdf5(temperature,
  mesh,
  frequency=None,
  group_velocity=None,
+ gv_by_gv=None,
  heat_capacity=None,
  kappa=None,
  mode_kappa=None,
@@ -656,6 +657,8 @@ def write_kappa_to_hdf5(temperature,
  w.create_dataset('frequency', data=frequency)
  if group_velocity is not None:
  w.create_dataset('group_velocity', data=group_velocity)
+ if gv_by_gv is not None:
+ w.create_dataset('gv_by_gv', data=gv_by_gv)
  if heat_capacity is not None:
  w.create_dataset('heat_capacity', data=heat_capacity)
  if kappa is not None:

anharmonic/phonon3/__init__.py

@@ -1,7 +1,7 @@
 import numpy as np
 from phonopy.structure.symmetry import Symmetry
 from phonopy.structure.cells import get_supercell, get_primitive
-from phonopy.structure.atoms import Atoms
+from phonopy.structure.atoms import PhonopyAtoms as Atoms
 from phonopy.units import VaspToTHz
 from phonopy.harmonic.force_constants import (get_fc2, set_permutation_symmetry,
  set_translational_invariance)

anharmonic/phonon3/conductivity_RTA.py

@@ -82,6 +82,7 @@ def get_thermal_conductivity_RTA(
 def _write_gamma(br, interaction, i, filename=None, verbose=True):
  grid_points = br.get_grid_points()
  group_velocities = br.get_group_velocities()
+ gv_by_gv = br.get_gv_by_gv()
  mode_heat_capacities = br.get_mode_heat_capacities()
  ave_pp = br.get_averaged_pp_interaction()
  mesh = br.get_mesh_numbers()
@@ -108,6 +109,7 @@ def _write_gamma(br, interaction, i, filename=None, verbose=True):
  mesh,
  frequency=frequencies,
  group_velocity=group_velocities[i],
+ gv_by_gv=gv_by_gv[i],
  heat_capacity=mode_heat_capacities[:, i],
  gamma=gamma[j, :, i],
  gamma_isotope=gamma_isotope_at_sigma,
@@ -135,6 +137,7 @@ def _write_gamma(br, interaction, i, filename=None, verbose=True):
  mesh,
  frequency=frequencies,
  group_velocity=group_velocities[i, k],
+ gv_by_gv=gv_by_gv[i, k],
  heat_capacity=mode_heat_capacities[:, i, k],
  gamma=gamma[j, :, i, k],
  gamma_isotope=gamma_isotope_at_sigma,
@@ -176,6 +179,7 @@ def _write_kappa(br, interaction, filename=None, log_level=0):
  mesh_divisors = br.get_mesh_divisors()
  frequencies = br.get_frequencies()
  gv = br.get_group_velocities()
+ gv_by_gv = br.get_gv_by_gv()
  mode_cv = br.get_mode_heat_capacities()
  ave_pp = br.get_averaged_pp_interaction()
  qpoints = br.get_qpoints()
@@ -218,6 +222,7 @@ def _write_kappa(br, interaction, filename=None, log_level=0):
  mesh,
  frequency=frequencies,
  group_velocity=gv,
+ gv_by_gv=gv_by_gv,
  heat_capacity=mode_cv,
  kappa=kappa_at_sigma,
  mode_kappa=mode_kappa[i],
@@ -357,6 +362,7 @@ def __init__(self,
 
  self._frequencies = None
  self._gv = None
+ self._gv_sum2 = None
  self._gamma = None
  self._gamma_iso = None
  self._gamma_unit_conversion = gamma_unit_conversion
@@ -428,12 +434,17 @@ def set_kappa_at_sigmas(self):
  gv_sum2[:, l] * cv[k, l] / (g_sum[l] * 2) *
  self._conversion_factor)
 
+ self._gv_sum2[i] = gv_sum2.T
+
  self._mode_kappa /= self._num_sampling_grid_points
  self._kappa = self._mode_kappa.sum(axis=2).sum(axis=2)
 
  def get_mode_heat_capacities(self):
  return self._cv
 
+ def get_gv_by_gv(self):
+ return self._gv_sum2
+
  def get_number_of_ignored_phonon_modes(self):
  return self._num_ignored_phonon_modes
 
@@ -494,6 +505,7 @@ def _allocate_values(self):
  num_grid_points,
  num_band0), dtype='double')
  self._gv = np.zeros((num_grid_points, num_band0, 3), dtype='double')
+ self._gv_sum2 = np.zeros((num_grid_points, num_band0, 6), dtype='double')
  self._cv = np.zeros(
  (len(self._temperatures), num_grid_points, num_band0), dtype='double')
  if self._isotope is not None:

c/_phono3py.c

@@ -426,7 +426,7 @@ static PyObject * py_get_imag_self_energy_with_g(PyObject *self, PyObject *args)
  Darray* fc3_normal_squared = convert_to_darray(fc3_normal_squared_py);
  double* gamma = (double*)PyArray_DATA(gamma_py);
  const double* g = (double*)PyArray_DATA(g_py);
- const char* g_zero = (double*)PyArray_DATA(g_zero_py);
+ const char* g_zero = (char*)PyArray_DATA(g_zero_py);
  const double* frequencies = (double*)PyArray_DATA(frequencies_py);
  const int* grid_point_triplets = (int*)PyArray_DATA(grid_point_triplets_py);
  const int* triplet_weights = (int*)PyArray_DATA(triplet_weights_py);

c/_phonopy.c

@@ -223,7 +223,8 @@ static PyObject * py_get_dynamical_matrix(PyObject *self, PyObject *args)
  m,
  s2p_map,
  p2s_map,
- NULL);
+ NULL,
+ 1);
 
  Py_RETURN_NONE;
 }
@@ -287,7 +288,8 @@ static PyObject * py_get_nac_dynamical_matrix(PyObject *self, PyObject *args)
  m,
  s2p_map,
  p2s_map,
- charge_sum);
+ charge_sum,
+ 1);
 
  free(charge_sum);