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Phono3py github repostory was moved to phonopy/phono3py from atztogo/phono3py. These updates were made following this migration.

This commit is contained in:
Atsushi Togo 2020-05-02 16:50:52 +09:00
parent 11bc6b0ca0
commit b880b6e748
12 changed files with 29 additions and 28 deletions
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6
.travis.yml
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@ -59,7 +59,7 @@ deploy:
password:
secure: "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"
on:
repo: atztogo/phono3py
repo: phonopy/phono3py
branch: rc
tags: false
python: 2.7
@ -69,7 +69,7 @@ deploy:
skip_cleanup: true
script: conda/anaconda_deploy.sh rc $ANACONDA_TOKEN2 $TRAVIS_BRANCH
on:
repo: atztogo/phono3py
repo: phonopy/phono3py
branch: rc
tags: false
# python: 2.7
@ -92,7 +92,7 @@ deploy:
skip_cleanup: true
script: conda/anaconda_deploy.sh main $ANACONDA_TOKEN2 $TRAVIS_BRANCH
on:
repo: atztogo/phono3py
repo: phonopy/phono3py
branch: master
tags: false
# python: 2.7

2
README.md
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@ -1,5 +1,5 @@
# phono3py
A simulation package of phonon-phonon interaction related properties. Phono3py user documetation is found at http://atztogo.github.io/phono3py/.
A simulation package of phonon-phonon interaction related properties. Phono3py user documetation is found at http://phonopy.github.io/phono3py/.
## Mailing list for questions

4
conda/meta.yaml
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@ -3,7 +3,7 @@ package:
version: version_from_shell
source:
git_url: https://github.com/atztogo/phono3py.git
git_url: https://github.com/phonopy/phono3py.git
git_branch: {{ environ.get('GIT_BRANCH','master') }}
build:
@ -70,7 +70,7 @@ test:
# - nose
about:
home: https://atztogo.github.io/phono3py/
home: https://phonopy.github.io/phono3py/
license: BSD
summary: 'A simulation package of phonon-phonon interaction related properties'

11
doc/command-options.rst
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@ -84,7 +84,7 @@ Supercell and primitive cell
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Supercell size is specified. See the
detail at http://atztogo.github.io/phonopy/setting-tags.html#dim .
detail at http://phonopy.github.io/phonopy/setting-tags.html#dim .
.. _dim_fc2_option:
@ -135,7 +135,7 @@ usual phono3py run without ``--dim-fc2`` option.
Transformation matrix from a non-primitive cell to the primitive
cell. See phonopy ``PRIMITIVE_AXES`` tag (``--pa`` option) at
http://atztogo.github.io/phonopy/setting-tags.html#primitive-axis
http://phonopy.github.io/phonopy/setting-tags.html#primitive-axis
Displacement creation
---------------------
@ -390,7 +390,8 @@ Phonon triples are chosen on the grid points on the sampling mesh
specified by this option. This mesh is made along reciprocal
axes and is always Gamma-centered.
Except for that this mesh is always Gamma-centered, the setting is in
the same way as written here, https://atztogo.github.io/phonopy/setting-tags.html#mesh-mp-or-mesh-numbers.
the same way as written here,
https://phonopy.github.io/phonopy/setting-tags.html#mesh-mp-or-mesh-numbers.
..
``--md``
@ -604,7 +605,7 @@ contribution to the thermal conducitivity is considered negligible.
Temperatures at equal interval are specified by ``--tmax``,
``--tmin``, ``--tstep``. See phonopy's document for the same tags at
http://atztogo.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep
http://phonopy.github.io/phonopy/setting-tags.html#tprop-tmin-tmax-tstep
.
::
@ -638,7 +639,7 @@ first line of ``BORN`` file.
This is used with ``--nac`` to specify the direction to polarize in
reciprocal space. See the detail at
http://atztogo.github.io/phonopy/setting-tags.html#q-direction .
http://phonopy.github.io/phonopy/setting-tags.html#q-direction .
.. _normal_umklapp_option:

4
doc/crystal.rst
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@ -17,9 +17,9 @@ specified::
When the file name of the unit cell is different from the default one
(see :ref:`default_unit_cell_file_name_for_calculator`), ``-c`` option
is used to specify the file name. CRYSTAL unit cell file parser used in
phono3py is the same as that in phonopy. It reads a limited number of
phono3py is the same as that in phonopy. It reads a limited number of
keywords that are documented in the phonopy web site
(http://atztogo.github.io/phonopy/crystal.html#crystal-interface).
(http://phonopy.github.io/phonopy/crystal.html#crystal-interface).
.. _crystal_workflow:

4
doc/examples.rst
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@ -8,9 +8,9 @@ Examples
:local:
Example files are found at
https://github.com/atztogo/phono3py/tree/master/example. The same are
https://github.com/phonopy/phono3py/tree/master/example. The same are
found in the example directory of the phono3py package downloaded at
https://github.com/atztogo/phono3py/archive/master.zip.
https://github.com/phonopy/phono3py/archive/master.zip.
Examples of silicon with VASP and Pwscf as calculators are given in

4
doc/index.rst
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@ -20,7 +20,7 @@ Some papers that may introduce phono3py well:
- Introduction to phono3py application:
https://doi.org/10.1103/PhysRevB.97.224306 (open access).
The source code is found at https://github.com/atztogo/phono3py
The source code is found at https://github.com/phonopy/phono3py
(BSD-3-Clause). The code is written in Python extended with C and
written as:
@ -35,7 +35,7 @@ written as:
:ref:`TURBOMOLE <turbomole_interface>`, and Abinit
are built in (see :ref:`calculator_interfaces`).
- API is prepared to operate from Python script (`example
<https://github.com/atztogo/phono3py/blob/master/example/Si-PBEsol/Si.py>`_)
<https://github.com/phonopy/phono3py/blob/master/example/Si-PBEsol/Si.py>`_)
Some tools to analyze the calculated results are prepared (see
:ref:`auxiliary_tools`).

12
doc/install.rst
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@ -14,7 +14,7 @@ performance is achieved by using the phono3py conda package (see
Installation of phonopy before the installation of phono3py is
required. See how to install phonopy at
https://atztogo.github.io/phonopy/install.html. Phono3py relies on
https://phonopy.github.io/phonopy/install.html. Phono3py relies on
phonopy, so please use the latest release of phonopy when installing
phono3py.
@ -186,7 +186,7 @@ needed.
The other option is using git to clone the phonopy repository from github::
% git clone https://github.com/atztogo/phono3py.git
% git clone https://github.com/phonopy/phono3py.git
% cd phono3py
2. Set up C-libraries for python C-API and python codes. This can be
@ -199,7 +199,7 @@ needed.
3. Set :envvar:`$PATH` and :envvar:`$PYTHONPATH`
``PATH`` and ``PYTHONPATH`` are set in the same way as phonopy, see
https://atztogo.github.io/phonopy/install.html#building-using-setup-py.
https://phonopy.github.io/phonopy/install.html#building-using-setup-py.
.. _install_an_example:
@ -281,8 +281,8 @@ This installation instruction supposes linux x86-64 environment.
% mkdir dev
% cd dev
% git clone https://github.com/atztogo/phonopy.git
% git clone https://github.com/atztogo/phono3py.git
% git clone https://github.com/phonopy/phonopy.git
% git clone https://github.com/phonopy/phono3py.git
% cd phonopy
% git checkout develop
% python setup.py build
@ -324,4 +324,4 @@ Trouble shooting
1. Phonopy version should be the latest to use the latest phono3py.
2. There are other pitfalls, see
https://atztogo.github.io/phonopy/install.html#trouble-shooting.
https://phonopy.github.io/phonopy/install.html#trouble-shooting.

2
doc/qe.rst
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@ -20,7 +20,7 @@ When the file name of the unit cell is different from the default one
is used to specify the file name. QE (pw) unit cell file parser used in
phono3py is the same as that in phonopy. It can read
only limited number of keywords that are shown in the phonopy web site
(http://atztogo.github.io/phonopy/qe.html#qe-interface).
(http://phonopy.github.io/phonopy/qe.html#qe-interface).
.. _qe_workflow:

2
doc/turbomole.rst
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@ -16,7 +16,7 @@ When the file name of the unit cell is different from the default one
is used to specify the file name. TURBOMOLE unit cell file parser used in
phono3py is the same as that in phonopy. It reads a limited number of
keywords that are documented in the phonopy web site
(http://atztogo.github.io/phonopy/turbomole.html#turbomole-interface).
(http://phonopy.github.io/phonopy/turbomole.html#turbomole-interface).
.. _turbomole_workflow:

2
phono3py/cui/load.py
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@ -107,7 +107,7 @@ def load(phono3py_yaml=None, # phono3py.yaml-like must be the first argument.
shape=(3, 3), dtype=float.
When 'F', 'I', 'A', 'C', or 'R' is given instead of a 3x3 matrix,
the primitive matrix defined at
https://atztogo.github.io/spglib/definition.html
https://spglib.github.io/spglib/definition.html
is used.
phonon_supercell_matrix : array_like, optional
Supercell matrix used for fc2. In phono3py, supercell matrix for fc3

4
setup.py
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@ -302,7 +302,7 @@ if __name__ == '__main__':
description='This is the phono3py module.',
author='Atsushi Togo',
author_email='atz.togo@gmail.com',
url='http://atztogo.github.io/phono3py/',
url='http://phonopy.github.io/phono3py/',
packages=packages_phono3py,
install_requires=['numpy', 'scipy', 'PyYAML', 'matplotlib',
'h5py', 'phonopy>=2.4.3'],
@ -317,7 +317,7 @@ if __name__ == '__main__':
description='This is the phono3py module.',
author='Atsushi Togo',
author_email='atz.togo@gmail.com',
url='http://atztogo.github.io/phono3py/',
url='http://phonopy.github.io/phono3py/',
packages=packages_phono3py,
requires=['numpy', 'scipy', 'PyYAML', 'matplotlib', 'h5py',
'phonopy'],