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Updated document, installation, and packaging related files.

This commit is contained in:
Atsushi Togo 2020-07-22 15:40:36 +09:00
parent 8ce43ddb71
commit 8b3f265b67
23 changed files with 503 additions and 138 deletions
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2
.travis.yml
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@ -55,7 +55,7 @@ before_install:
source $(conda info --root)/etc/profile.d/conda.sh;
fi;
- conda install --yes -c conda-forge python=$TRAVIS_PYTHON_VERSION;
- conda install --yes -c conda-forge gcc_linux-64 gxx_linux-64 matplotlib pyyaml scipy numpy spglib h5py setuptools_scm conda-build pip pytest;
- conda install --yes -c conda-forge gcc_linux-64 gxx_linux-64 matplotlib-base pyyaml scipy numpy spglib h5py setuptools_scm conda-build pip pytest;
- if [[ "$TRAVIS_PYTHON_VERSION" != "2.7" ]]; then
pip install cp2k-input-tools;
fi;

4
build-wheels.sh
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@ -4,7 +4,7 @@ set -e -x
yum install -y hdf5 freetype freetype-devel pkgconfig libpng-devel
for PYBIN in /opt/python/*/bin; do
if [[ ! $PYBIN == *"34"* ]]; then
if [[ ! $PYBIN == *"34"* ]] && [[ ! $PYBIN == *"39"* ]]; then
"${PYBIN}/pip" install -r /io/dev-requirements.txt
"${PYBIN}/pip" wheel /io/ -w wheelhouse/
fi
@ -17,7 +17,7 @@ done
# Install packages and test
for PYBIN in /opt/python/*/bin/; do
if [[ ! $PYBIN == *"34"* ]]; then
if [[ ! $PYBIN == *"34"* ]] && [[ ! $PYBIN == *"39"* ]]; then
"${PYBIN}/pip" install phonopy --no-index -f /io/wheelhouse
(cd "$HOME"; "${PYBIN}/nosetests" phonopy)
fi

8
conda/meta.yaml
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@ -28,19 +28,19 @@ requirements:
build:
- python
- numpy
- matplotlib
- pyyaml
- h5py
- setuptools
- pip
- spglib
run:
- python
- pip
- numpy
- matplotlib
- matplotlib-base
- pyyaml
- h5py
- spglib
- scipy
test:
# Python imports

1
dev-requirements.txt
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@ -1,2 +1 @@
nose
numpy

10
doc/changelog.rst
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@ -3,6 +3,16 @@
Change Log
==========
July-22-2020: Version 2.7.0
---------------------------
* Spglib was removed from phonopy source code tree. Now phonopy
depends on spglib. So spglib has to be installed separately. But
for normal cases, it is handled by the package manager.
* A new way of using phonopy from command line is proposed at
:ref:`phonopy_load_command`.
* Slightly changed the behaviour of ``--include-all`` option to that
force constants are not stored when force sets are stored.
May-3-2020: Version 2.6.1
-------------------------
* Release for pypi and conda packaging

4
doc/conf.py
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@ -45,9 +45,9 @@ copyright = u'2009, Atsushi Togo'
# built documents.
#
# The short X.Y version.
version = '2.6'
version = '2.7'
# The full version, including alpha/beta/rc tags.
release = '2.6.1'
release = '2.7.0'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.

1
doc/index.rst
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@ -92,6 +92,7 @@ Documentation
auxiliary-tools
external-tools
phonopy-module
phonopy-load
formulation
citation
reference

134
doc/install.rst
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@ -3,6 +3,8 @@
Installation
=============
**From phonopy v2.7.0, spglib has to be installed separately.**
.. contents::
:depth: 3
:local:
@ -18,7 +20,7 @@ system is set-up (see `details about conda setting up
of phonopy is super easy for any of Linux, MacOSX, and Windows.
To install::
% conda install -c conda-forge phonopy h5py
% conda install -c conda-forge phonopy
This phonopy's conda package is prepared and maintained by
Paweł T. Jochym at conda-forge channel (please be aware that this is
@ -41,7 +43,7 @@ environment).
% conda create -n phonopy -c conda-forge python=3
% conda activate phonopy
% conda install -c conda-forge phonopy h5py
% conda install -c conda-forge phonopy
To exit from this conda's environment::
@ -72,28 +74,6 @@ To use this phonopy, entering this environment is necessary like below.
| __/ | | | | (_) | |
\___|_| |_| \___/|_|
Using pip
---------
Installation of phonopy via pip is not very recommended. :ref:`install_conda`
as rewritten above is recommended.
Phonopy pip wheel is not prepared for most of the systems. So before
installing phonopy using pip, Python C-API compilation environment has
to be prepared. Then phonopy is installed using pip by::
% pip install phonopy
If you see the error message like below in the installation process::
_phonopy.c:35:20: fatal error: Python.h: No such file or directory
development tools for building python module are additionally
necessary and are installed using OS's package management system,
e.g.,::
sudo apt-get install python-dev
.. _install_from_source:
From source code
@ -104,9 +84,10 @@ System requirement
The procedure to setup phonopy is explained in this section. It is
supposed that phonopy is installed on the recent linux distribution
like Ubuntu or Fedora with Python version 2.6 or later. Python version
3.4 or later is expected to work. Mac OS X users may use conda packages.
Windows users should use conda packages as well.
like Ubuntu or Fedora with Python version 2.7 or later. Python version
3.4 or later is expected to work. Mac OS X users may use conda
(conda-forge channel) packages. Windows users should use conda
(conda-forge channel) packages as well.
Prepare the following Python libraries:
@ -120,27 +101,25 @@ And optionally the following:
* cp2k-input-tools, for the CP2K force calculator backend
Installing required packages by conda
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
By Ubuntu package manager
^^^^^^^^^^^^^^^^^^^^^^^^^^
The python libraries can be installed using conda. Conda packages are
distributed in binary. Minimum setup of conda envrironment is done by
miniconda, which is downloaded at https://conda.io/miniconda.html. It
is strongly recommended to create conda's virtual environment by
``conda create -n <venvname>`` as written above. The installation of
necessary libraries is done as follows::
The most recommended system is Ubuntu linux version 14.04 (64-bit) or
later. The python libraries are installed by::
% conda install -c conda-forge numpy scipy h5py pyyaml matplotlib-base spglib
% sudo apt-get install python-dev python-numpy python-matplotlib python-yaml python-h5py
If you need a compiler, for usual 64-bit linux system::
``python-scipy`` is also required to use ``phonopy-qha`` or
``DEBYE_MODEL`` tag.
% conda install -c conda-forge gcc_linux-64
By conda
^^^^^^^^^
For macOS::
The python libraries may be also installed using pip or
conda. Conda packages are distributed in binary and recommended often
more than pip. The installation of necessary libraries is done as
follows::
% conda install numpy scipy h5py pyyaml matplotlib
% conda install -c conda-forge clang_osx-64
.. _install_setup_py:
@ -152,76 +131,23 @@ special compiler or special options, phonopy is built using
setup.py. In this case, manual modification of ``setup.py`` may be
needed.
1. Download the source code at
1. Get the source code from github
https://pypi.python.org/pypi/phonopy
::
and extract it::
% git clone https://github.com/phonopy/phonopy.git
% cd phonopy
% git checkout master
% tar xvfz phonopy-1.11.12.31.tar.gz
% cd phonopy-1.11.12.31
The other option is using git to clone the phonopy repository from github::
% git clone https://github.com/phonopy/phonopy.git
% cd phonopy
2. Set up C-libraries for python C-API and python codes. This can be
done as follows:
Run ``setup.py`` script::
% python setup.py install --user
Watching carefully where the phonopy commands and library are
installed. Those locations can be ``~/.local/bin`` and
``~/.local/lib`` directories, respectively.
3. Assuming the installation location is those shown in the step 2,
set ``$PATH`` and ``$PYTHONPATH``::
export PYTHONPATH=~/.local/lib:$PYTHONPATH
export PATH=~/.local/bin:$PATH
or if ``PYTHONPATH`` is not yet set in your system::
export PYTHONPATH=~/.local/lib
export PATH=~/.local/bin:$PATH
in your ``.bashrc`` (or maybe ``.bash_profile``), ``.zshenv``, or
other script for the other shells.
2. Run ``setup.py`` script
::
% python setup.py build
% pip install -e .
.. _install_trouble_shooting:
Multithreading support
-----------------------
Two kinds of multithreadings can be used in phonopy.
1. Multithreaded BLAS linked numpy
Phonopy uses numpy to run singular value decomposition in the
calculation of force constants and diagonalizaion of dynamical
matrices. For these, numpy internally calls the LAPACK
routines. Therefore if a user installs a numpy that is linked with
multithreaded BLAS, these parts are multithreaded. For example, MKL
linked numpy is easily installed using conda.
2. OpenMP support in phonopy and spglib
OpenMP are applied in the symmetry finding of spglib and the
distribution of symmetry reduced force constants elements to full
force constants elements in phonopy. When a chosen supercell is
very large and there are many cores on a computer, these parts may
work well to reduce the computational time. In the default phonopy
setting, this is not activated. To enable this, it is necessary to
build phonopy using modified ``setup.py`` in which ``with_openmp =
False`` must be changed to ``with_openmp = True``. For this,
currently only gcc is supported.
Trouble shooting
-----------------

59
doc/phonopy-load.rst Normal file
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@ -0,0 +1,59 @@
.. _phonopy_load_command:
phonopy-load command
====================
At phonopy v2.7.0, ``phonopy-load`` command is installed. This behaves
similarly to ``phonopy.load`` (:ref:`phonopy_load`) in the phonopy
python module. The main aim of introducing this command is to provide
uniform usage over many different force calculators. Once
``phonopy_disp.yaml`` is created, the later operations will be the
same using this command.
The following default behaviours are changed from that of those
of ``phonopy`` command:
1. ``phonopy_xxx.yaml`` type file is always necessary by a way of (2)
or (3).
2. The first argument of the command is used to give a ``phonopy_xxx.yaml``
type file.
3. The file names of ``phonopy_params.yaml``, ``phonopy_disp.yaml``,
``phonopy.yaml`` are the default file
names and these files are searched in the current directory. The
preference order is as given here.
4. ``-c`` option (read crystal structure) does not exist.
5. Use of dommand options is recommended, but phonopy configuration
file can be read using ``--config`` option.
6. If parameters for non-analytical term correction (NAC) are
found, NAC is automatically enabled. This can be disabled by
``--nonac`` option.
7. When force constants are calculated from displacements and forces
dataset, force constants are automatically symmetrized. To disable
this, ``--no-sym-fc`` option is used.
Examples
--------
In the NaCl-qe example,
::
% phonopy --qe -d --dim 2 2 2 --pa auto -c NaCl.in
% phonopy -f NaCl-00{1,2}.out
With these commands, ``phonopy_disp.yaml`` and ``FORCE_SETS`` are
created. After this step, it is unnecessary to specify ``--qe`` option
to run with ``phonopy-load``. The following command works to draw band
structure.
::
% phonopy-load --band auto -p
Data in ``FORCE_SETS`` and ``BORN`` stored in
``phonopy_xxx.yaml`` file can be used as follows::
% phonopy-load --include-all
% mkdir test && cd test
% mv ../phonopy.yaml phonopy_data.yaml
% phonopy-load phonopy_data.yaml --band auto -p

2
doc/phonopy-module.rst
View File

@ -191,6 +191,8 @@ written in the yaml file, the argument ``settings`` is set as follows::
phonon.save(settings={'force_constants': True})
.. _phonopy_load:
Shortcut to load input files (``phonopy.load``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

1
doc/setting-tags.rst
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@ -1576,3 +1576,4 @@ This is set by default when the ``phonopy`` script is run in ``displacements`` m
All available data covered by the other ``include`` flags can be written to the yaml
summary file using the ``--include-all`` flag or by setting ``INCLUDE_ALL = .TRUE.``.
Force constants are not stored when force sets are stored.

2
example/NaCl/NaCl-band-gv.py
View File

@ -11,7 +11,7 @@ def append_band(bands, q_start, q_end):
bands.append(band)
phonon = phonopy.load(unitcell_filename="POSCAR",
phonon = phonopy.load(unitcell_filename="POSCAR-unitcell",
born_filename="BORN",
force_sets_filename="FORCE_SETS",
supercell_matrix=[[2, 0, 0],

2
example/NaCl/NaCl-band.py
View File

@ -7,7 +7,7 @@ phonon = phonopy.load(supercell_matrix=[[2, 0, 0],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
unitcell_filename="POSCAR",
unitcell_filename="POSCAR-unitcell",
force_sets_filename="FORCE_SETS",
born_filename="BORN")
points = get_band_qpoints(

2
example/NaCl/NaCl-dynmat.py
View File

@ -10,7 +10,7 @@ phonon = phonopy.load(supercell_matrix=[[2, 0, 0],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
unitcell_filename="POSCAR",
unitcell_filename="POSCAR-unitcell",
force_sets_filename="FORCE_SETS",
born_filename="BORN")

2
example/NaCl/NaCl-gv.py
View File

@ -2,7 +2,7 @@ import numpy as np
import phonopy
import matplotlib.pyplot as plt
phonon = phonopy.load(unitcell_filename="POSCAR",
phonon = phonopy.load(unitcell_filename="POSCAR-unitcell",
born_filename="BORN",
force_sets_filename="FORCE_SETS",
supercell_matrix=[[2, 0, 0],

4
example/NaCl/NaCl-read_write_fc.py
View File

@ -7,7 +7,7 @@ phonon = phonopy.load(supercell_matrix=[[2, 0, 0],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
unitcell_filename="POSCAR",
unitcell_filename="POSCAR-unitcell",
force_sets_filename="FORCE_SETS",
born_filename="BORN")
write_FORCE_CONSTANTS(phonon.get_force_constants(),
@ -16,5 +16,5 @@ write_FORCE_CONSTANTS(phonon.get_force_constants(),
force_constants = parse_FORCE_CONSTANTS()
phonon.force_constants = force_constants
phonon.symmetrize_force_constants()
write_FORCE_CONSTANTS(phonon.get_force_constants(),
write_FORCE_CONSTANTS(phonon.force_constants,
filename="FORCE_CONSTANTS_NEW")

2
example/NaCl/NaCl-yaml.py
View File

@ -7,7 +7,7 @@ phonon = phonopy.load(supercell_matrix=[[2, 0, 0],
primitive_matrix=[[0, 0.5, 0.5],
[0.5, 0, 0.5],
[0.5, 0.5, 0]],
unitcell_filename="POSCAR",
unitcell_filename="POSCAR-unitcell",
force_sets_filename="FORCE_SETS",
born_filename="BORN")
phpy_yaml = PhonopyYaml(calculator='vasp',

2
example/NaCl/NaCl.py
View File

@ -13,7 +13,7 @@ def append_band(bands, q_start, q_end):
# NaCl crystal structure is read from POSCAR.
unitcell = read_vasp("POSCAR")
unitcell = read_vasp("POSCAR-unitcell")
# This can be given via a PhonopyAtoms class as follows:
# unitcell = PhonopyAtoms(symbols=(['Na'] * 4 + ['Cl'] * 4),
# cell=(np.eye(3) * 5.6903014761756712),

356
example/NaCl/phonopy_disp.yaml Normal file
View File

@ -0,0 +1,356 @@
phonopy:
version: 2.7.0
frequency_unit_conversion_factor: 15.633302
symmetry_tolerance: 1.00000e-05
configuration:
cell_filename: "POSCAR-unitcell"
create_displacements: ".true."
primitive_axes: "auto"
dim: "2 2 2"
physical_unit:
atomic_mass: "AMU"
length: "angstrom"
force_constants: "eV/angstrom^2"
space_group:
type: "Fm-3m"
number: 225
Hall_symbol: "-F 4 2 3"
primitive_matrix:
- [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
- [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
supercell_matrix:
- [ 2, 0, 0 ]
- [ 0, 2, 0 ]
- [ 0, 0, 2 ]
primitive_cell:
lattice:
- [ 0.000000000000000, 2.845150738087836, 2.845150738087836 ] # a
- [ 2.845150738087836, 0.000000000000000, 2.845150738087836 ] # b
- [ 2.845150738087836, 2.845150738087836, 0.000000000000000 ] # c
points:
- symbol: Na # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 22.989769
- symbol: Cl # 2
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 35.453000
reciprocal_lattice: # without 2pi
- [ -0.175737613233118, 0.175737613233118, 0.175737613233118 ] # a*
- [ 0.175737613233118, -0.175737613233118, 0.175737613233118 ] # b*
- [ 0.175737613233118, 0.175737613233118, -0.175737613233118 ] # c*
unit_cell:
lattice:
- [ 5.690301476175671, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 5.690301476175671, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 5.690301476175671 ] # c
points:
- symbol: Na # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 2
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 3
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Cl # 5
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 5
- symbol: Cl # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 5
- symbol: Cl # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 5
- symbol: Cl # 8
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 5
supercell:
lattice:
- [ 11.380602952351342, 0.000000000000000, 0.000000000000000 ] # a
- [ 0.000000000000000, 11.380602952351342, 0.000000000000000 ] # b
- [ 0.000000000000000, 0.000000000000000, 11.380602952351342 ] # c
points:
- symbol: Na # 1
coordinates: [ 0.000000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 2
coordinates: [ 0.500000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 3
coordinates: [ 0.000000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 4
coordinates: [ 0.500000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 5
coordinates: [ 0.000000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 6
coordinates: [ 0.500000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 7
coordinates: [ 0.000000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 8
coordinates: [ 0.500000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 9
coordinates: [ 0.000000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 10
coordinates: [ 0.500000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 11
coordinates: [ 0.000000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 12
coordinates: [ 0.500000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 13
coordinates: [ 0.000000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 14
coordinates: [ 0.500000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 15
coordinates: [ 0.000000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 16
coordinates: [ 0.500000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 17
coordinates: [ 0.250000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 18
coordinates: [ 0.750000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 19
coordinates: [ 0.250000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 20
coordinates: [ 0.750000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 21
coordinates: [ 0.250000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 22
coordinates: [ 0.750000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 23
coordinates: [ 0.250000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 24
coordinates: [ 0.750000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 25
coordinates: [ 0.250000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 26
coordinates: [ 0.750000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 27
coordinates: [ 0.250000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 28
coordinates: [ 0.750000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 29
coordinates: [ 0.250000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 30
coordinates: [ 0.750000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 31
coordinates: [ 0.250000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Na # 32
coordinates: [ 0.750000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 22.989769
reduced_to: 1
- symbol: Cl # 33
coordinates: [ 0.250000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 34
coordinates: [ 0.750000000000000, 0.250000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 35
coordinates: [ 0.250000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 36
coordinates: [ 0.750000000000000, 0.750000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 37
coordinates: [ 0.250000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 38
coordinates: [ 0.750000000000000, 0.250000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 39
coordinates: [ 0.250000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 40
coordinates: [ 0.750000000000000, 0.750000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 41
coordinates: [ 0.250000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 42
coordinates: [ 0.750000000000000, 0.000000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 43
coordinates: [ 0.250000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 44
coordinates: [ 0.750000000000000, 0.500000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 45
coordinates: [ 0.250000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 46
coordinates: [ 0.750000000000000, 0.000000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 47
coordinates: [ 0.250000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 48
coordinates: [ 0.750000000000000, 0.500000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 49
coordinates: [ 0.000000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 50
coordinates: [ 0.500000000000000, 0.250000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 51
coordinates: [ 0.000000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 52
coordinates: [ 0.500000000000000, 0.750000000000000, 0.000000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 53
coordinates: [ 0.000000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 54
coordinates: [ 0.500000000000000, 0.250000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 55
coordinates: [ 0.000000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 56
coordinates: [ 0.500000000000000, 0.750000000000000, 0.500000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 57
coordinates: [ 0.000000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 58
coordinates: [ 0.500000000000000, 0.000000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 59
coordinates: [ 0.000000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 60
coordinates: [ 0.500000000000000, 0.500000000000000, 0.250000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 61
coordinates: [ 0.000000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 62
coordinates: [ 0.500000000000000, 0.000000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 63
coordinates: [ 0.000000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
- symbol: Cl # 64
coordinates: [ 0.500000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 35.453000
reduced_to: 33
displacements:
- atom: 1
displacement:
[ 0.0100000000000000, 0.0000000000000000, 0.0000000000000000 ]
- atom: 33
displacement:
[ 0.0100000000000000, 0.0000000000000000, 0.0000000000000000 ]

11
phonopy/api_phonopy.py
View File

@ -1243,7 +1243,6 @@ class Phonopy(object):
axs = ImageGrid(fig, 111, # similar to subplot(111)
nrows_ncols=(1, n),
axes_pad=0.11,
add_all=True,
label_mode="L")
self._band_structure.plot(axs)
return plt
@ -1622,21 +1621,16 @@ class Phonopy(object):
axs = ImageGrid(fig, 111, # similar to subplot(111)
nrows_ncols=(1, n),
axes_pad=0.11,
add_all=True,
label_mode="L")
self._band_structure.plot(axs[:-1])
if pdos_indices is None:
freqs = self._total_dos.frequency_points
dos = self._total_dos.dos
self._total_dos.plot(axs[-1],
xlabel="",
ylabel="",
draw_grid=False,
flip_xy=True)
else:
freqs = self._pdos.frequency_points
dos = self._pdos.projected_dos
self._pdos.plot(axs[-1],
indices=pdos_indices,
xlabel="",
@ -2507,10 +2501,7 @@ class Phonopy(object):
else:
animation.write_v_sim(amplitude=amplitude_,
factor=self._factor)
if (anime_type == 'arc' or
anime_type == 'xyz' or
anime_type == 'jmol' or
anime_type == 'poscar'):
if anime_type in ('arc', 'xyz', 'jmol', 'poscar'):
if band_index is None or amplitude is None or num_div is None:
msg = ("Parameters are not correctly set for animation.")
raise RuntimeError(msg)

4
phonopy/cui/phonopy_argparse.py
View File

@ -117,6 +117,10 @@ def get_parser(fc_symmetry=False,
parser.add_argument(
"-c", "--cell", dest="cell_filename", metavar="FILE", default=None,
help="Read unit cell")
if load_phonopy_yaml:
parser.add_argument(
"--config", dest="conf_filename", metavar="FILE", default=None,
help="Phonopy configuration file")
parser.add_argument(
"--cutoff-freq", "--cutoff-frequency", dest="cutoff_frequency",
type=float, default=None,

27
phonopy/cui/phonopy_script.py
View File

@ -1336,28 +1336,43 @@ def read_phonopy_settings(args, argparse_control, log_level):
"""Read phonopy settings"""
load_phonopy_yaml = argparse_control.get('load_phonopy_yaml', False)
conf_filename = None
if len(args.filename) > 0:
file_exists(args.filename[0], log_level)
if load_phonopy_yaml:
if load_phonopy_yaml:
if args.conf_filename:
conf_filename = args.conf_filename
phonopy_conf_parser = PhonopyConfParser(
filename=args.conf_filename, args=args,
default_settings=argparse_control)
else:
phonopy_conf_parser = PhonopyConfParser(
args=args, default_settings=argparse_control)
if len(args.filename) > 0:
file_exists(args.filename[0], log_level)
cell_filename = args.filename[0]
else:
cell_filename = phonopy_conf_parser.settings.cell_filename
else:
if len(args.filename) > 0:
if is_file_phonopy_yaml(args.filename[0]):
phonopy_conf_parser = PhonopyConfParser(args=args)
cell_filename = args.filename[0]
else:
conf_filename = args.filename[0]
phonopy_conf_parser = PhonopyConfParser(
filename=args.filename[0], args=args)
cell_filename = phonopy_conf_parser.settings.cell_filename
else:
phonopy_conf_parser = PhonopyConfParser(args=args)
cell_filename = phonopy_conf_parser.settings.cell_filename
else:
phonopy_conf_parser = PhonopyConfParser(args=args)
cell_filename = phonopy_conf_parser.settings.cell_filename
confs = phonopy_conf_parser.confs.copy()
settings = phonopy_conf_parser.settings
if log_level > 0 and conf_filename is not None:
print("Phonopy configuration was read from \"%s\"." %
conf_filename)
return settings, confs, cell_filename

1
requirements.txt
View File

@ -2,3 +2,4 @@ numpy==1.16.5
PyYAML==5.1.2
matplotlib==2.2.4
h5py==2.10.0
spglib==1.15.1