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Merge branch 'refactoring' into develop

This commit is contained in:
Atsushi Togo 2021-10-25 17:43:02 +09:00
parent 767daebe5d c95d19c77f
commit ac7abb7e4b
369 changed files with 42095 additions and 35894 deletions
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13
.github/workflows/phonopy-pytest-conda.yml vendored
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@ -6,29 +6,28 @@ jobs:
build-linux:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
matrix:
python-version: [3.7, 3.8, 3.9]
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: 3.8
python-version: ${{ matrix.python-version }}
- name: Add conda to system path
run: |
# $CONDA is an environment variable pointing to the root of the miniconda directory
echo $CONDA/bin >> $GITHUB_PATH
- name: Install dependencies
run: |
conda install --yes -c conda-forge python=3.8
conda install --yes -c conda-forge gcc_linux-64 gxx_linux-64 matplotlib-base pyyaml scipy numpy spglib h5py setuptools_scm conda-build pip pytest codecov pytest-cov pytest
conda install --yes -c conda-forge python=${{ matrix.python-version }}
conda install --yes -c conda-forge gcc_linux-64 gxx_linux-64 matplotlib-base pyyaml scipy numpy spglib h5py pip pytest codecov pytest-cov pytest
- name: Install cp2k-input-tools
run: |
pip install cp2k-input-tools
- name: Setup phonopy
run: |
./get_nanoversion.sh
cat __nanoversion__.txt
python setup.py build
pip install -e .
- name: Test with pytest

13
.github/workflows/publish-to-test-pypi.yml vendored
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@ -1,19 +1,24 @@
name: publish PyPI and TestPyPI
on: push
on:
push:
branches:
- master
- rc
jobs:
build-linux:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
matrix:
python-version: [3.9, ]
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: 3.8
python-version: ${{ matrix.python-version }}
- name: Make sdist
run: |
./get_nanoversion.sh

53
.pre-commit-config.yaml Normal file
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@ -0,0 +1,53 @@
# See https://pre-commit.com for more informatio
# See https://pre-commit.com/hooks.html for more hooks
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.0.1
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-yaml
exclude: ^conda/
- id: check-added-large-files
- repo: https://github.com/pycqa/flake8
rev: 4.0.1
hooks:
- id: flake8
exclude: |
(?x)^(
test/phonon/test_irreps.py|
test/qha/test_electron.py|
phonopy/interface/cp2k.py
)$
args:
- "--max-line-length=88"
- "--ignore=E203,W503"
- id: flake8
files: |
(?x)^(
test/phonon/test_irreps.py|
test/qha/test_electron.py|
phonopy/interface/cp2k.py
)$
args:
- "--max-line-length=88"
- "--ignore=E203,W503,E501"
- repo: https://github.com/psf/black
rev: 21.9b0
hooks:
- id: black
args:
- --line-length=88
- repo: https://github.com/pycqa/pydocstyle
rev: 6.0.0
hooks:
- id: pydocstyle
- repo: https://github.com/pycqa/isort
rev: 5.8.0
hooks:
- id: isort
name: isort (python)

7
README.md
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@ -33,6 +33,13 @@ repository.
"python.linting.pycodestyleEnabled": false,
"python.linting.pydocstyleEnabled": true,
"python.formatting.provider": "black",
"python.formatting.blackArgs": ["--line-length=88"],
"python.sortImports.args": ["--profile", "black"],
"[python]": {
"editor.codeActionsOnSave": {
"source.organizeImports": true
},
}
```
## Documentation

26
conda/.binstar.yml
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@ -1,49 +1,49 @@
## The package attribure specifies a binstar package namespace to build the package to.
## The package attribure specifies a binstar package namespace to build the package to.
## This can be specified here or on the command line
package: phonopy
## You can also specify the account to upload to,
## you must be an admin of that account, this
## you must be an admin of that account, this
## defaults to your user account
# user: USERNAME
# user: USERNAME
#===============================================================================
# Build Matrix Options
# Thes options may be a single item, a list or empty
# The resulting number of builds is [platform * engine * env]
# The resulting number of builds is [platform * engine * env]
#===============================================================================
## The platforms to build on.
## platform defaults to linux-64
# platform:
## platform defaults to linux-64
# platform:
# - linux-64
# - linux-32
## The engine are the inital conda packages you want to run with
## The engine are the inital conda packages you want to run with
engine:
- python=2
- python=3
## The env param is an environment variable list
## The env param is an environment variable list
env:
- GIT_BRANCH=master
#===============================================================================
# Scrip options
# Thes options may be broken out into the before_script, script and after_script
# or not, that is up to you
# or not, that is up to you
#===============================================================================
## Run before the script
before_script:
- conda install anaconda-client --yes
## Put your main computations here!
## Put your main computations here!
script:
- conda update -n root conda conda-build --yes
- GIT_BRANCH=`git branch |grep '^*'|sed -e 's/^*\s\?//' -e 's/(HEAD [a-z ]* \(.*\))$/\1/'`
- conda build .
## This will run after the script regardless of the result of script
## BINSTAR_BUILD_RESULT=[succcess|failure]
## BINSTAR_BUILD_RESULT=[succcess|failure]
after_script:
- echo "The build was a $BINSTAR_BUILD_RESULT" | tee artifact1.txt
## This will be run only after a successfull build
@ -71,8 +71,8 @@ after_failure:
## Build Targets: Upload these files to your binstar package
## build targets may be a list of files (globs allows) to upload
## The special build targets 'conda' and 'pypi' may be used to
## upload conda builds
## The special build targets 'conda' and 'pypi' may be used to
## upload conda builds
## e.g. conda is an alias for /opt/anaconda/conda-bld/<os-arch>/*.tar.bz2
build_targets:
- conda

4
doc/Fleur.rst
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@ -50,7 +50,7 @@ A procedure of a Fleur-phonopy calculation may look as follows:
The resulting inp.xml is then run by the fleur command itself.
After successfull convergence, set the tag 'l_f' in the inp.xml to "T"
and add 'f_level="n"' behind it with n from {0,1,2,3}. This optional
tag ensures the write-out of the 'FORCES' file and setting it to
tag ensures the write-out of the 'FORCES' file and setting it to
{1,2,3} calculates additional refined force contibutions.
3) Create ``FORCE_SETS`` by::
@ -72,5 +72,5 @@ A procedure of a Fleur-phonopy calculation may look as follows:
if you prepared a band.conf file or::
% phonopy --fleur -c fleur_inpgen --dim="2 2 2" [other-OPTIONS] [setting-file]
if you want to set the path directly or specify a different file.

4
doc/_static/procedure.dot vendored
View File

@ -23,8 +23,8 @@ digraph phonopy {
Supercell -> "Force calc." [label = "(1)"];
Supercell -> "Force-constant calc." [label = "(2)"];
"Force calc." -> "Force constants" [label = "(1)"];
"Force-constant calc." -> "Force constants" [label = "(2)"];
"Force-constant calc." -> "Force constants" [label = "(2)"];
"Unit cell" -> "Phonopy post-process";
"Supercell size" -> "Phonopy post-process";
"Primitive cell size\n(optional)" -> "Phonopy post-process";

9
doc/citation.rst
View File

@ -13,7 +13,7 @@ If you have used phonopy, please cite the following article:
http://dx.doi.org/10.1016/j.scriptamat.2015.07.021 (Open access)
::
@article {phonopy,
Journal = {Scr. Mater.},
Year = {2015},
@ -43,7 +43,7 @@ Some papers where phonopy was used
Atsushi Togo and Isao Tanaka,
Phys. Rev. B, **87**, 184104-1-6 (2013)
* "Transition pathway of CO2 crystals under high pressures",
Atsushi Togo, Fumiyasu Oba, and Isao Tanaka,
@ -63,7 +63,7 @@ Some papers where phonopy was used
Atsushi Togo, Fumiyasu Oba, and Isao Tanaka, Phys. Rev. B, **78**, 134106 (2008)
``TDISP``, ``TDISPMAT`` tags: Root mean square thermal atomic displacement
``TDISP``, ``TDISPMAT`` tags: Root mean square thermal atomic displacement
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* "Neutron diffraction measurements and first-principles study of
@ -80,7 +80,7 @@ Some papers where phonopy was used
Volker L. Deringer, Ralf P. Stoffel, Atsushi Togo, Bernhard Eck,
Martin Mevencd and Richard Dronskowski, Cryst. Eng. Comm., (2014)
A short history of phonopy
---------------------------
@ -93,4 +93,3 @@ important part of the implementation is the symmetry handling. In
fropho, at first the symmetry finder in Abinit code was employed, but
later the symmetry finder was replaced by spglib
(http://spglib.sourceforge.net/).

125
doc/conf.py
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@ -1,3 +1,4 @@
"""Sphinx configuration of phonopy documentation."""
# -*- coding: utf-8 -*-
#
# phonopy documentation build configuration file, created by
@ -22,69 +23,69 @@ import sphinx_bootstrap_theme
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
extensions = ['sphinx.ext.mathjax']
extensions = ["sphinx.ext.mathjax"]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
templates_path = ["_templates"]
# The suffix of source filenames.
source_suffix = '.rst'
source_suffix = ".rst"
# The encoding of source files.
source_encoding = 'utf-8'
source_encoding = "utf-8"
# The master toctree document.
master_doc = 'index'
master_doc = "index"
# General information about the project.
project = u'phonopy'
copyright = u'2009, Atsushi Togo'
project = u"phonopy"
copyright = u"2009, Atsushi Togo"
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '2.11'
version = "2.11"
# The full version, including alpha/beta/rc tags.
release = '2.11.0'
release = "2.11.0"
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# today_fmt = '%B %d, %Y'
# List of documents that shouldn't be included in the build.
#unused_docs = []
# unused_docs = []
# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = ['_build']
exclude_trees = ["_build"]
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#add_function_parentheses = True
# add_function_parentheses = True
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#add_module_names = True
# add_module_names = True
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
pygments_style = "sphinx"
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# modindex_common_prefix = []
# -- Options for HTML output ---------------------------------------------------
@ -93,20 +94,18 @@ pygments_style = 'sphinx'
# Sphinx are currently 'default' and 'sphinxdoc'.
# html_theme = 'default'
# html_theme = 'nature'
html_theme = 'bootstrap'
html_theme = "bootstrap"
# html_theme = 'sphinxbootstrap4theme'
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
#html_theme_options = {}
# html_theme_options = {}
html_theme_options = {
# Navigation bar title. (Default: ``project`` value)
'navbar_title': "Phonopy",
"navbar_title": "Phonopy",
# Tab name for entire site. (Default: "Site")
'navbar_site_name': "Site",
"navbar_site_name": "Site",
# A list of tuples containing pages or urls to link to.
# Valid tuples should be in the following forms:
# (name, page) # a link to a page
@ -122,17 +121,13 @@ html_theme_options = {
# ("Tags", "setting-tags"),
# ("Options", "command-options"),
# ],
# Render the next and previous page links in navbar. (Default: true)
'navbar_sidebarrel': True,
"navbar_sidebarrel": True,
# Render the current pages TOC in the navbar. (Default: true)
'navbar_pagenav': True,
"navbar_pagenav": True,
# Global TOC depth for "site" navbar tab. (Default: 1)
# Switching to -1 shows all levels.
'globaltoc_depth': 1,
"globaltoc_depth": 1,
# Include hidden TOCs in Site navbar?
#
# Note: If this is "false", you cannot have mixed ``:hidden:`` and
@ -140,32 +135,27 @@ html_theme_options = {
# will break.
#
# Values: "true" (default) or "false"
'globaltoc_includehidden': "true",
"globaltoc_includehidden": "true",
# HTML navbar class (Default: "navbar") to attach to <div> element.
# For black navbar, do "navbar navbar-inverse"
# 'navbar_class': "navbar navbar-inverse",
'navbar_class': "navbar",
"navbar_class": "navbar",
# Fix navigation bar to top of page?
# Values: "true" (default) or "false"
'navbar_fixed_top': "true",
"navbar_fixed_top": "true",
# Location of link to source.
# Options are "nav" (default), "footer" or anything else to exclude.
# 'source_link_position': "nav",
'source_link_position': "footer",
"source_link_position": "footer",
# Bootswatch (http://bootswatch.com/) theme.
#
# Options are nothing with "" (default) or the name of a valid theme
# such as "amelia" or "cosmo".
# 'bootswatch_theme': "united",
'bootswatch_theme': "cerulean",
"bootswatch_theme": "cerulean",
# Choose Bootstrap version.
# Values: "3" (default) or "2" (in quotes)
'bootstrap_version': "3",
"bootstrap_version": "3",
}
# Add any paths that contain custom themes here, relative to this directory.
@ -175,10 +165,10 @@ html_theme_path = sphinx_bootstrap_theme.get_html_theme_path()
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
html_title = 'Phonopy v.%s' % release
html_title = "Phonopy v.%s" % release
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sideba.
@ -187,80 +177,79 @@ html_title = 'Phonopy v.%s' % release
# The name of an image file (within the static path) to use as favicon of the
# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#html_favicon = None
# html_favicon = None
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
html_static_path = ["_static"]
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
#html_last_updated_fmt = '%b %d, %Y'
# html_last_updated_fmt = '%b %d, %Y'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# html_additional_pages = {}
# If false, no module index is generated.
#html_use_modindex = True
# html_use_modindex = True
# If false, no index is generated.
#html_use_index = True
# html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# html_show_sourcelink = True
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it. The value of this option must be the
# base URL from which the finished HTML is served.
#html_use_opensearch = ''
# html_use_opensearch = ''
# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = ''
# html_file_suffix = ''
# Output file base name for HTML help builder.
htmlhelp_basename = 'phonopydoc'
htmlhelp_basename = "phonopydoc"
# -- Options for LaTeX output --------------------------------------------------
# The paper size ('letter' or 'a4').
#latex_paper_size = 'letter'
# latex_paper_size = 'letter'
# The font size ('10pt', '11pt' or '12pt').
#latex_font_size = '10pt'
# latex_font_size = '10pt'
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('documentation', 'phonopy.tex', u'phonopy manual',
u'Atsushi Togo', 'manual'),
("documentation", "phonopy.tex", u"phonopy manual", u"Atsushi Togo", "manual"),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# latex_use_parts = False
# Additional stuff for the LaTeX preamble.
#latex_preamble = ''
# latex_preamble = ''
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# latex_appendices = []
# If false, no module index is generated.
#latex_use_modindex = True
# latex_use_modindex = True

3
doc/reference.rst
View File

@ -134,8 +134,7 @@ DFPT
Currently there are several many implementations such as `Abinit
<http://www.abinit.org/>`_, `Quantum espresso
<http://www.quantum-espresso.org/>`_, `Elk
<http://elk.sourceforge.net/>`_, `Fleur
<https://www.flapw.de/>`_, etc. VASP can calculate force constants
<http://elk.sourceforge.net/>`_, etc. VASP can calculate force constants
using DFPT however only at Gamma-point.
For the study of basics

13
doc/turbomole.rst
View File

@ -28,7 +28,7 @@ parameter is not needed.
In this example, the Si crystal structure is defined with the conventional
unit cell of eight atoms and 3x3x3 supercells are created. For every supercell, the
interface creates a subdirectory with ``control`` and ``coord`` files.
Files in ``supercell`` contain the perfect supercell. The files in
Files in ``supercell`` contain the perfect supercell. The files in
``supercell-xxx`` (``xxx`` are numbers) contain the supercells with displacements.
File ``phonopy_disp.yaml`` is also generated, containing information about the
supercell and the displacements.
@ -37,8 +37,8 @@ parameter is not needed.
2) Complete TURBOMOLE inputs need to be prepared manually in the subdirectories.
Note that supercells with displacements must not be relaxed, because the
atomic forces induced by a small atomic displacement are what we need for
Note that supercells with displacements must not be relaxed, because the
atomic forces induced by a small atomic displacement are what we need for
phonon calculation. To get accurate forces, $scfconv should be at least 10.
Phonopy includes this data group automatically in the control file.
You also need to choose a k-point mesh for the force calculations.
@ -55,15 +55,15 @@ parameter is not needed.
% phonopy --turbomole -f supercell-*
Here ``supercell-*`` directories contain the TURBOMOLE output files
from the force calculations (only the file ``gradient`` is required).
Here ``supercell-*`` directories contain the TURBOMOLE output files
from the force calculations (only the file ``gradient`` is required).
To run this command, ``phonopy_disp.yaml`` has to be located in the current
directory because the information on atomic displacements stored in
this file are used to generate ``FORCE_SETS``. See some more
detail at :ref:`turbomole_force_sets_option`.
4) Now, Phonopy post-prcessing commands can be run. ``FORCE_SETS`` is
automatically read in. Note that here PRIMITIVE_AXES is defined in
automatically read in. Note that here PRIMITIVE_AXES is defined in
band.conf to create the phonon dispersions for the primitive cell.
Create phonon dispersion plot with:
@ -121,4 +121,3 @@ parameter is not needed.
For further settings and command options, see the general Phonopy documentation
:ref:`setting_tags` and :ref:`command_options`, respectively, and
for examples, see :ref:`examples_link`.

78
example/Al-Fleur/IO/out
View File

@ -1,8 +1,8 @@
This output is generated by fleur 32
* *
This output is generated by fleur 32
* *
* \:/ *
* | *
* *
* *
This is FLEUR version: fleur 32
@ -18,7 +18,7 @@ Compiler info:
flags : -ffree-line-length-none -Wno-missing-include-dirs -fno-sign-zero -fdefault-real-8 -fdefault-double-8 -fopenmp -I/home/alex/fleur/build/external/libxc-git
link flags: -lscalapack-openmpi;/usr/lib/x86_64-linux-gnu/libxml2.so;/usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so
No system architecture specified in Makefile
Additional flags are: CPP_MPI CPP_HDF
Additional flags are: CPP_MPI CPP_HDF
group operations on equivalent atoms:
@ -2776,11 +2776,11 @@ gmaxxc = 23.993715
3 49 48
4 49 48
5 49 48
neq= 1 ncore= 10.000000000000000
neq= 1 ncore= 20.000000000000000
neq= 4 ncore= 60.000000000000000
neq= 1 ncore= 70.000000000000000
neq= 1 ncore= 80.000000000000000
neq= 1 ncore= 10.000000000000000
neq= 1 ncore= 20.000000000000000
neq= 4 ncore= 60.000000000000000
neq= 1 ncore= 70.000000000000000
neq= 1 ncore= 80.000000000000000
zelec= 24.00000000
@ -3873,9 +3873,9 @@ FERHIS: Fermi-Energy by histogram:
--> new fermi energy : 0.282992 htr
valence charge : 24.000000 e
actual charge blw ef-8kt : 23.375000 e
actual charge blw ef+8kt : 24.000000 e
valence charge : 24.000000 e
actual charge blw ef-8kt : 23.375000 e
actual charge blw ef+8kt : 24.000000 e
number of occ. states : 250
sum of the valence weights : 12.000000
entropy : 0.257920 *kb htr/K = 0.00000 htr/K
@ -4032,7 +4032,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 1 (spin 1)
atom type 1 (spin 1)
kinetic energy= 0.239028865966E+03 sum of the eigenvalues= -0.129193450604E+03
0.00159165 electrons lost from core.
@ -4043,7 +4043,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 2 (spin 1)
atom type 2 (spin 1)
kinetic energy= 0.239028880915E+03 sum of the eigenvalues= -0.129193461967E+03
0.00159164 electrons lost from core.
@ -4054,7 +4054,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 3 (spin 1)
atom type 3 (spin 1)
kinetic energy= 0.239028895692E+03 sum of the eigenvalues= -0.129193473852E+03
0.00159163 electrons lost from core.
@ -4065,7 +4065,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 4 (spin 1)
atom type 4 (spin 1)
kinetic energy= 0.239028900208E+03 sum of the eigenvalues= -0.129193475630E+03
0.00159163 electrons lost from core.
@ -4076,7 +4076,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 5 (spin 1)
atom type 5 (spin 1)
kinetic energy= 0.239028898073E+03 sum of the eigenvalues= -0.129193472522E+03
0.00159163 electrons lost from core.
@ -4187,7 +4187,7 @@ FERHIS: Fermi-Energy by histogram:
FORCES: SURFACE CORRECTION FOR ATOM TYPE 5
FX_SF= 0.000000 0.000000 FY_SF= 0.000000 0.000000 FZ_SF= 0.000000 0.000000
***** TOTAL FORCES ON ATOMS *****
***** TOTAL FORCES ON ATOMS *****
TOTAL FORCE FOR ATOM TYPE= 1 X= 0.000 Y= 0.014 Z= 0.014
FX_TOT= 0.000000 FY_TOT=-0.000554 FZ_TOT=-0.000554
@ -5322,9 +5322,9 @@ FERHIS: Fermi-Energy by histogram:
--> new fermi energy : 0.282992 htr
valence charge : 24.000000 e
actual charge blw ef-8kt : 23.375000 e
actual charge blw ef+8kt : 24.000000 e
valence charge : 24.000000 e
actual charge blw ef-8kt : 23.375000 e
actual charge blw ef+8kt : 24.000000 e
number of occ. states : 250
sum of the valence weights : 12.000000
entropy : 0.257920 *kb htr/K = 0.00000 htr/K
@ -5481,7 +5481,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 1 (spin 1)
atom type 1 (spin 1)
kinetic energy= 0.239028865964E+03 sum of the eigenvalues= -0.129193450591E+03
0.00159165 electrons lost from core.
@ -5492,7 +5492,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 2 (spin 1)
atom type 2 (spin 1)
kinetic energy= 0.239028880912E+03 sum of the eigenvalues= -0.129193461952E+03
0.00159164 electrons lost from core.
@ -5503,7 +5503,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 3 (spin 1)
atom type 3 (spin 1)
kinetic energy= 0.239028895688E+03 sum of the eigenvalues= -0.129193473834E+03
0.00159163 electrons lost from core.
@ -5514,7 +5514,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 4 (spin 1)
atom type 4 (spin 1)
kinetic energy= 0.239028900205E+03 sum of the eigenvalues= -0.129193475615E+03
0.00159163 electrons lost from core.
@ -5525,7 +5525,7 @@ FERHIS: Fermi-Energy by histogram:
2. 0. 0.5 -3.4880 2.0000
2. 1. 0.5 -2.1098 2.0000
2. 1. 1.5 -2.0936 4.0000
atom type 5 (spin 1)
atom type 5 (spin 1)
kinetic energy= 0.239028898071E+03 sum of the eigenvalues= -0.129193472508E+03
0.00159163 electrons lost from core.
@ -5636,7 +5636,7 @@ FERHIS: Fermi-Energy by histogram:
FORCES: SURFACE CORRECTION FOR ATOM TYPE 5
FX_SF= 0.000000 0.000000 FY_SF= 0.000000 0.000000 FZ_SF= 0.000000 0.000000
***** TOTAL FORCES ON ATOMS *****
***** TOTAL FORCES ON ATOMS *****
TOTAL FORCE FOR ATOM TYPE= 1 X= 0.000 Y= 0.014 Z= 0.014
FX_TOT= 0.000000 FY_TOT=-0.000554 FZ_TOT=-0.000554
@ -5655,24 +5655,24 @@ Total execution time: 685sec
-------------------------------------------------
most relevant subroutines:
Total Run 352.70sec= 0h 5min 52sec -> 51.4%
MT part ->non-spherical setup 254.88sec= 0h 4min 14sec -> 37.2%
eigen ->Diagonalization 140.49sec= 0h 2min 20sec -> 20.5%
generation of new ->cdngen: cdncore 128.24sec= 0h 2min 8sec -> 18.7%
generation of pote->Force level 3 (IS) 32.48sec= 0h 0min 32sec -> 4.7%
abcof ->force contributions 27.26sec= 0h 0min 27sec -> 4.0%
cdnval ->Force level 2 23.35sec= 0h 0min 23sec -> 3.4%
generation of pote->Vxc in interstitial 13.17sec= 0h 0min 13sec -> 1.9%
MT part ->spherical setup 10.30sec= 0h 0min 10sec -> 1.5%
cdnval ->pwden 8.71sec= 0h 0min 8sec -> 1.3%
Total Run 352.70sec= 0h 5min 52sec -> 51.4%
MT part ->non-spherical setup 254.88sec= 0h 4min 14sec -> 37.2%
eigen ->Diagonalization 140.49sec= 0h 2min 20sec -> 20.5%
generation of new ->cdngen: cdncore 128.24sec= 0h 2min 8sec -> 18.7%
generation of pote->Force level 3 (IS) 32.48sec= 0h 0min 32sec -> 4.7%
abcof ->force contributions 27.26sec= 0h 0min 27sec -> 4.0%
cdnval ->Force level 2 23.35sec= 0h 0min 23sec -> 3.4%
generation of pote->Vxc in interstitial 13.17sec= 0h 0min 13sec -> 1.9%
MT part ->spherical setup 10.30sec= 0h 0min 10sec -> 1.5%
cdnval ->pwden 8.71sec= 0h 0min 8sec -> 1.3%
Sum: 144.6%
-------------------------------------------------
Total execution time: 685sec, minimal timing printed:13sec
0 Total Run 685.55sec= 0h 11min 25sec -> 100.0%
0 Total Run 685.55sec= 0h 11min 25sec -> 100.0%
0 measured in submodules: 332.85sec= 0h 5min 32sec
1 Iteration 685.30sec= 0h 11min 25sec -> 100.0%
1 Iteration 685.30sec= 0h 11min 25sec -> 100.0%
1 measured in submodules: 685.28sec= 0h 11min 25sec
2 generation of potential 56.28sec= 0h 0min 56sec -> 8.2% (2calls: 27.058sec - 29.221sec)
2 measured in submodules: 56.22sec= 0h 0min 56sec

6
example/Al-Fleur/supercell-001.in
View File

@ -2,9 +2,9 @@ Aluminium test Fleur
0.0000000000000000 7.6559999999999997 7.6559999999999997
7.6559999999999997 0.0000000000000000 7.6559999999999997
7.6559999999999997 7.6559999999999997 0.0000000000000000
1.0
1.0 1.0 1.0
1.0
1.0 1.0 1.0
8
13.1 0.0018471964 -0.0000000000 -0.0000000000
13.1 0.5000000000 0.0000000000 0.0000000000

39
example/Al-QHA/Al-QHA.py
View File

@ -1,8 +1,8 @@
#!/usr/bin/env python
"""Example of QHA calculation by Al."""
import numpy as np
import yaml
from yaml import CLoader as Loader
import numpy as np
from phonopy import PhonopyQHA
volumes = []
@ -15,24 +15,25 @@ for line in open("e-v.dat"):
entropy = []
cv = []
fe = []
for index in range(-5,6):
for index in range(-5, 6):
filename = "thermal_properties.yaml-%d" % index
print("Reading %s" % filename)
thermal_properties = yaml.load(open(filename),
Loader=Loader)['thermal_properties']
temperatures = [v['temperature'] for v in thermal_properties]
cv.append([v['heat_capacity'] for v in thermal_properties])
entropy.append([v['entropy'] for v in thermal_properties])
fe.append([v['free_energy'] for v in thermal_properties])
qha = PhonopyQHA(volumes,
energies,
temperatures=temperatures,
free_energy=np.transpose(fe),
cv=np.transpose(cv),
entropy=np.transpose(entropy),
t_max=400,
verbose=True)
thermal_properties = yaml.load(open(filename), Loader=Loader)["thermal_properties"]
temperatures = [v["temperature"] for v in thermal_properties]
cv.append([v["heat_capacity"] for v in thermal_properties])
entropy.append([v["entropy"] for v in thermal_properties])
fe.append([v["free_energy"] for v in thermal_properties])
qha = PhonopyQHA(
volumes,
energies,
temperatures=temperatures,
free_energy=np.transpose(fe),
cv=np.transpose(cv),
entropy=np.transpose(entropy),
t_max=400,
verbose=True,
)
# qha.plot_helmholtz_volume().show()
# qha.plot_volume_temperature().show()

2
example/Al-QHA/POSCAR--1
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR--2
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR--3
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR--4
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR--5
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

4
example/Al-QHA/POSCAR-0
View File

@ -1,5 +1,5 @@
Al
1.00000000000000
1.00000000000000
4.0393282180880821 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.0393282180880821 0.0000000000000000
0.0000000000000000 0.0000000000000000 4.0393282180880821
@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR-1
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR-2
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR-3
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR-4
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

2
example/Al-QHA/POSCAR-5
View File

@ -9,7 +9,7 @@ Direct
0.0000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.5000000000000000
0.5000000000000000 0.5000000000000000 0.0000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

1
example/Al-QHA/thermal_properties.yaml--1
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -378.9467176
entropy: 289.4736650
heat_capacity: 99.5473036

1
example/Al-QHA/thermal_properties.yaml--2
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -366.7327306
entropy: 283.3949646
heat_capacity: 99.5190804

1
example/Al-QHA/thermal_properties.yaml--3
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -355.1311761
entropy: 277.6245626
heat_capacity: 99.4887894

1
example/Al-QHA/thermal_properties.yaml--4
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -343.8208732
entropy: 272.0025819
heat_capacity: 99.4557211

1
example/Al-QHA/thermal_properties.yaml--5
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -333.0629769
entropy: 266.6590471
heat_capacity: 99.4204298

1
example/Al-QHA/thermal_properties.yaml-0
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -391.4467304
entropy: 295.6979666
heat_capacity: 99.5729516

1
example/Al-QHA/thermal_properties.yaml-1
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -404.3758647
entropy: 302.1390626
heat_capacity: 99.5963768

1
example/Al-QHA/thermal_properties.yaml-2
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -417.8333877
entropy: 308.8463804
heat_capacity: 99.6177832

1
example/Al-QHA/thermal_properties.yaml-3
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -431.7193088
entropy: 315.7698942
heat_capacity: 99.6372002

1
example/Al-QHA/thermal_properties.yaml-4
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -446.4389062
entropy: 323.1118308
heat_capacity: 99.6550383

1
example/Al-QHA/thermal_properties.yaml-5
View File

@ -5015,4 +5015,3 @@ thermal_properties:
free_energy: -462.0680669
entropy: 330.9100940
heat_capacity: 99.6713363

2
example/Al-hiphive/reference_data/POSCAR_prim
View File

@ -1,4 +1,4 @@
Al
Al
1.0000000000000000
0.0000000000000000 2.0000000000000000 2.0000000000000000
2.0000000000000000 0.0000000000000000 2.0000000000000000

34
example/Al2O3/Al2O3.py
View File

@ -1,9 +1,11 @@
import phonopy
"""Example by corundum Al2O3."""
import numpy as np
phonon = phonopy.load(unitcell_filename="POSCAR-unitcell",
supercell_matrix=[2, 2, 1],
log_level=1)
import phonopy
phonon = phonopy.load(
unitcell_filename="POSCAR-unitcell", supercell_matrix=[2, 2, 1], log_level=1
)
print("Space group: %s" % phonon.symmetry.get_international_table())
# Example to obtain dynamical matrix
@ -12,7 +14,7 @@ print(dmat)
# Example of band structure calculation
bands = []
q_start = np.array([1./3, 1./3, 0])
q_start = np.array([1.0 / 3, 1.0 / 3, 0])
q_end = np.array([0, 0, 0])
band = []
for i in range(51):
@ -20,30 +22,26 @@ for i in range(51):
bands.append(band)
q_start = np.array([0, 0, 0])
q_end = np.array([1./3, 1./3, 1./2])
q_end = np.array([1.0 / 3, 1.0 / 3, 1.0 / 2])
band = []
for i in range(51):
band.append(q_start + (q_end - q_start) / 50 * i)
bands.append(band)
print("\nPhonon dispersion:")
phonon.run_band_structure(bands,
with_eigenvectors=True,
labels=["X", r"$\Gamma$", "L"])
phonon.run_band_structure(bands, with_eigenvectors=True, labels=["X", r"$\Gamma$", "L"])
band_plot = phonon.plot_band_structure()
band_plot.show()
bs = phonon.get_band_structure_dict()
distances = bs['distances']
frequencies = bs['frequencies']
qpoints = bs['qpoints']
distances = bs["distances"]
frequencies = bs["frequencies"]
qpoints = bs["qpoints"]
for (qs_at_segments,
dists_at_segments,
freqs_at_segments) in zip(qpoints, distances, frequencies):
for (qs_at_segments, dists_at_segments, freqs_at_segments) in zip(
qpoints, distances, frequencies
):
for q, d, f in zip(qs_at_segments,
dists_at_segments,
freqs_at_segments):
for q, d, f in zip(qs_at_segments, dists_at_segments, freqs_at_segments):
print("# %f %f %f" % tuple(q))
print(("%s " + "%f " * len(f)) % ((d,) + tuple(f)))

6
example/Al2O3/BORN
View File

@ -1,4 +1,4 @@
# epsilon and Z* of atoms 1 13
3.27649624 -0.00000000 0.00000000 -0.00000000 3.27649624 0.00000000 0.00000000 0.00000000 3.21878866
2.96008813 -0.02948662 -0.00000000 0.02948662 2.96008813 -0.00000000 -0.00000000 0.00000000 2.92614183
-2.07328119 0.00000000 0.00000000 -0.00000000 -1.87350298 0.25811770 -0.00000000 0.35087130 -1.95076122
3.27649624 -0.00000000 0.00000000 -0.00000000 3.27649624 0.00000000 0.00000000 0.00000000 3.21878866
2.96008813 -0.02948662 -0.00000000 0.02948662 2.96008813 -0.00000000 -0.00000000 0.00000000 2.92614183
-2.07328119 0.00000000 0.00000000 -0.00000000 -1.87350298 0.25811770 -0.00000000 0.35087130 -1.95076122

16
example/Al2O3/FORCE_SETS
View File

@ -1,7 +1,7 @@
120
5
120
5
1
1
0.0059163718384140 0.0000000000000000 0.0080620434301498
-0.1266189400 0.0002383700 -0.1526970400
0.0075193700 0.0003911800 -0.0083948700
@ -124,7 +124,7 @@
-0.0011203800 0.0030566100 -0.0039680500
0.0003020400 -0.0000725200 -0.0003101900
1
1
-0.0059163718384140 0.0000000000000000 -0.0080620434301498
0.1259458600 0.0002316400 0.1538443800
-0.0074937800 -0.0003883900 0.0081817800
@ -247,7 +247,7 @@
0.0011789900 -0.0029341800 0.0039442000
-0.0002298100 0.0001892100 0.0003071200
49
49
-0.0050000000000000 0.0086602540378444 0.0000000000000000
0.0029185700 -0.0047305700 0.0029613700
-0.0008989700 -0.0004377200 0.0000403600
@ -370,7 +370,7 @@
-0.0001427000 0.0003438900 -0.0002439500
0.0002183600 0.0001754700 -0.0002816400
49
49
0.0050000000000000 -0.0086602540378444 0.0000000000000000
-0.0029323300 0.0047500500 -0.0031733500
0.0009065000 0.0004427100 -0.0002494700
@ -493,7 +493,7 @@
0.0002057400 -0.0002308800 0.0002477800
-0.0001509500 -0.0000635300 0.0002845500
49
49
0.0000000000000000 0.0000000000000000 0.0100000000000000
-0.0046446700 0.0060312600 -0.0030432100
0.0012550400 0.0006213400 -0.0009905300
@ -614,4 +614,4 @@
-0.0003822400 0.0004174900 0.0026145700
-0.0002608100 0.0002142700 0.0017369600
-0.0001888100 0.0002120200 0.0021701500
-0.0002879100 0.0001205600 0.0017374400
-0.0002879100 0.0001205600 0.0017374400

8
example/Al2O3/POSCAR-unitcell
View File

@ -1,9 +1,9 @@
generated by phonopy
1.00000000000000
generated by phonopy
1.00000000000000
4.7742263452989944 0.0000000000000000 -0.0000000000000000
-2.3871131726494972 4.1346012984458653 0.0000000000000000
-0.0000000000000000 0.0000000000000000 13.0113593913272219
Al O
Al O
12 18
Direct
0.3333333333333357 0.6666666666666643 0.0187603745624614
@ -36,7 +36,7 @@ Direct
-0.0000000000000000 0.6941913462119872 0.7500000000000000
0.0275246795453229 0.3608580128786515 0.9166666666666643
0.3058086537880128 0.3058086537880128 0.7500000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

14
example/CaTiO3/FORCE_SETS
View File

@ -1,7 +1,7 @@
40
4
40
4
1
1
0.0100000000000000 0.0000000000000000 0.0000000000000000
-0.0248901400 0.0000000000 0.0000000000
0.0167876400 0.0000000000 0.0000000000
@ -44,7 +44,7 @@
0.0002293600 0.0017021100 0.0000000000
0.0002211100 -0.0016919800 0.0000000000
9
9
0.0100000000000000 0.0000000000000000 0.0000000000000000
0.0030065200 0.0111566700 0.0111566700
0.0029655100 -0.0113176800 -0.0113176800
@ -87,7 +87,7 @@
0.0012204100 0.0000000000 0.0000169200
-0.0011237500 0.0000000000 -0.0000017100
17
17
0.0000000000000000 0.0100000000000000 0.0000000000000000
0.0000000000 -0.0035018100 -0.0071057000
0.0000000000 0.0001983200 -0.0016954400
@ -130,7 +130,7 @@
0.0000046600 0.0019401000 0.0000117900
-0.0000046600 0.0019401000 0.0000117900
17
17
0.0100000000000000 0.0000000000000000 0.0000000000000000
0.0096564900 -0.0001177700 -0.0001177700
-0.0071742700 0.0000165500 0.0000165500
@ -171,4 +171,4 @@
0.0148424900 0.0000000000 0.0263700600
0.0149355400 0.0000000000 -0.0260464500
-0.0000623900 0.0000000000 0.0025879300
-0.0000345000 0.0000000000 -0.0025610800
-0.0000345000 0.0000000000 -0.0025610800

8
example/Cr-castep/FORCE_SETS
View File

@ -1,7 +1,7 @@
16
1
16
1
1
1
0.0100000000000000 0.0000000000000000 0.0000000000000000
-0.0530093750 0.0000000000 -0.0000000000
0.0043906250 0.0000000000 0.0000000000
@ -18,4 +18,4 @@
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0.0058206250 -0.0058900000 0.0058900000
0.0065006250 -0.0052900000 -0.0052900000
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0.0058206250 0.0058900000 0.0058900000

10
example/Cr-castep/README
View File

@ -1,17 +1,17 @@
This is step-by-step example how to calculate phonon dispertion with CASTEP.
Spin-polarization example.
1. Generate supercell based on structrural parameters given in unitcell.cell
1. Generate supercell based on structrural parameters given in unitcell.cell
file by running:
% phonopy -d --dim="2 2 2" --castep -c unitcell.cell
In this example file unitcell.cell contains initial spin values in positions_frac BLOCK.
In this example file unitcell.cell contains initial spin values in positions_frac BLOCK.
As well as the value of the U parameter in LDA+U approximation.
2. Use make_displ_dirs.sh bash script to make directories with input files needed to
calculate FORCES for supercells.
2. Use make_displ_dirs.sh bash script to make directories with input files needed to
calculate FORCES for supercells.
% make_displ_dirs.sh supercell.param tail.cell
Please note file supercell.param is the standart CASTEP file with paremeters (convergence
Please note file supercell.param is the standart CASTEP file with paremeters (convergence
criteria, Ecut, functional name etc.). The file with name tail.cell contains k-mesh
description, U parameter value, symmetry operation E, and name of pseudopotential.

1
example/Cr-castep/tail.cell
View File

@ -24,4 +24,3 @@ SYMMETRY_TOL : 0.000001
kpoint_mp_grid : 8 8 8
kpoint_mp_offset : 0.00000000000000 0.00000000000000 0.00000000000000

7
example/Cr-castep/unitcell.cell
View File

@ -2,9 +2,9 @@
%BLOCK lattice_cart
ANG
3.20276584921909 0.00000000000000 0.00000000000000
0.00000000000000 3.20276584686211 0.00000000000000
0.00000000000000 0.00000000000000 3.20276584686211
3.20276584921909 0.00000000000000 0.00000000000000
0.00000000000000 3.20276584686211 0.00000000000000
0.00000000000000 0.00000000000000 3.20276584686211
%ENDBLOCK lattice_cart
%BLOCK cell_constraints
@ -120,4 +120,3 @@ SYMMETRY_TOL : 0.001000
kpoint_mp_grid : 8 8 8
kpoint_mp_offset : 0.500000000000000 0.500000000000000 0.500000000000000

8
example/Cr/FORCE_SETS
View File

@ -1,7 +1,7 @@
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0.0070706300 -0.0058273200 -0.0058273200
0.0065860300 0.0056186700 0.0056186700
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example/Cr/POSCAR-unitcell
View File

@ -7,4 +7,4 @@
2
Direct
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example/Cu-QHA/POSCAR-00
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@ -9,4 +9,4 @@ Direct
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example/Cu-QHA/POSCAR-01
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@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-02
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-03
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-04
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-05
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@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-06
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-07
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-08
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-09
View File

@ -9,4 +9,4 @@ Direct
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2
example/Cu-QHA/POSCAR-10
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@ -9,4 +9,4 @@ Direct
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4
example/Cu-QHA/thermal_properties.yaml-00
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 43.0804791128
natom: 4
volume: 43.0804791128
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-01
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 43.9779889420
natom: 4
volume: 43.9779889420
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-02
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 44.8754989139
natom: 4
volume: 44.8754989139
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-03
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 45.7730090104
natom: 4
volume: 45.7730090104
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-04
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 46.6705189090
natom: 4
volume: 46.6705189090
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-05
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 47.5680287744
natom: 4
volume: 47.5680287744
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-06
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 48.4655386547
natom: 4
volume: 48.4655386547
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-07
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 49.3630487614
natom: 4
volume: 49.3630487614
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-08
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 50.2605586587
natom: 4
volume: 50.2605586587
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-09
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 51.1580685636
natom: 4
volume: 51.1580685636
num_modes: 96000
num_integrated_modes: 96000

4
example/Cu-QHA/thermal_properties.yaml-10
View File

@ -6,8 +6,8 @@ unit:
entropy: J/K/mol
heat_capacity: J/K/mol
natom: 4
volume: 52.0555787437
natom: 4
volume: 52.0555787437
num_modes: 96000
num_integrated_modes: 96000

1
example/Graphene-siesta/Gr.fdf
View File

@ -39,4 +39,3 @@ AtomicCoordinatesFormat NotScaledCartesianAng
0.00000000000000 0.00000000000000 0.00000000000000 1 12.011000
1.27500000000000 0.73612159321677 0.00000000000000 1 12.011000
%endblock AtomicCoordinatesAndAtomicSpecies

100
example/LiF-nosym/FORCE_SETS
View File

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-0.0063925500 0.0000000000 -0.0000098400
0.0028668700 0.0000000000 0.0000033900
@ -2949,7 +2949,7 @@
0.0005311000 0.0000000000 0.0000000000
-0.0005495100 0.0000000000 0.0000000000
57
57
0.0000000000000000 0.0100000000000000 0.0000000000000000
0.0000000000 0.0063924800 -0.0000095500
0.0000000000 0.0007541300 -0.0000005200
@ -3016,7 +3016,7 @@
0.0000000000 0.0018436700 0.0000000000
0.0000000000 0.0005499100 0.0000000000
57
57
0.0000000000000000 -0.0100000000000000 0.0000000000000000
0.0000000000 -0.0063909200 -0.0000086800
0.0000000000 -0.0007519600 0.0000029000
@ -3083,7 +3083,7 @@
0.0000000000 -0.0018401500 0.0000000000
0.0000000000 -0.0005481400 0.0000000000
57
57
0.0000000000000000 0.0000000000000000 0.0100000000000000
0.0000000000 0.0000000000 0.0006009300
0.0000000000 0.0000000000 0.0000688000
@ -3150,7 +3150,7 @@
0.0000000000 0.0000000000 0.0018429500
0.0000000000 0.0000000000 0.0005496800
57
57
0.0000000000000000 0.0000000000000000 -0.0100000000000000
0.0000000000 0.0000000000 -0.0013465400
0.0000000000 0.0000000000 -0.0000781900

6
example/LiF-nosym/POSCAR
View File

@ -1,5 +1,5 @@
Li F
1.00000000000000
Li F
1.00000000000000
4.0611030011359448 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.0611030011359448 0.0000000000000000
0.0000000000000000 0.0000000000000000 4.0611030011359448
@ -13,7 +13,7 @@ Direct
0.5000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 0.5000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

10
example/MgB2/FORCE_SETS
View File

@ -1,7 +1,7 @@
54
2
54
2
1
1
0.0079439039403258 0.0000000000000000 0.0060740752536396
-0.0567291400 0.0000000000 -0.0437145000
0.0074057100 0.0000000000 -0.0008197500
@ -58,7 +58,7 @@
0.0008065100 0.0003768100 0.0008807300
-0.0005610100 0.0044479800 0.0031491600
19
19
0.0079439039403258 0.0000000000000000 0.0060740752536396
-0.0005500500 0.0026459600 0.0031424500
0.0001593800 -0.0000032100 0.0000341100
@ -113,4 +113,4 @@
0.0007799900 -0.0009255800 0.0002910800
0.0011407900 0.0003750100 -0.0002949900
0.0011504300 -0.0003563500 -0.0002993600
-0.0008333200 0.0000082200 0.0002940900
-0.0008333200 0.0000082200 0.0002940900

9
example/MgB2/MgB2.py
View File

@ -1,12 +1,13 @@
import phonopy
"""Example of calculation of irreps of MgB2."""
import numpy as np
phonon = phonopy.load(unitcell_filename="POSCAR-unitcell",
supercell_matrix=[3, 3, 2])
import phonopy
phonon = phonopy.load(unitcell_filename="POSCAR-unitcell", supercell_matrix=[3, 3, 2])
print("Space group: %s" % phonon.symmetry.get_international_table())
# Character table
phonon.set_irreps([1./3, 1./3, 0], 1e-4)
phonon.set_irreps([1.0 / 3, 1.0 / 3, 0], 1e-4)
ct = phonon.get_irreps()
band_indices = ct.get_band_indices()
characters = np.rint(ct.get_characters()).real

10
example/MgO/FORCE_SETS
View File

@ -1,7 +1,7 @@
64
2
64
2
1
1
0.0100000000000000 0.0000000000000000 0.0000000000000000
-0.1088198900 0.0000000000 0.0000000000
0.0156863000 0.0000000000 0.0000000000
@ -68,7 +68,7 @@
0.0012923900 0.0000000000 -0.0000070500
-0.0014169000 0.0000000000 -0.0000003800
33
33
0.0100000000000000 0.0000000000000000 0.0000000000000000
-0.0003358000 -0.0025844000 -0.0025844000
-0.0003213600 0.0025938900 0.0025938900
@ -133,4 +133,4 @@
-0.0001182900 0.0011847700 0.0000000000
-0.0001301700 -0.0011916700 0.0000000000
-0.0001182900 -0.0011847700 0.0000000000
-0.0001301700 0.0011916700 0.0000000000
-0.0001301700 0.0011916700 0.0000000000

6
example/MgO/POSCAR-unitcell
View File

@ -1,5 +1,5 @@
Mg O
1.00000000000000
Mg O
1.00000000000000
4.2555564654942897 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.2555564654942888 0.0000000000000000
0.0000000000000000 0.0000000000000000 4.2555564654942897
@ -13,7 +13,7 @@ Direct
0.5000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 0.5000000000000000
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00

4
example/NaCl-CRYSTAL/README
View File

@ -4,7 +4,7 @@ CRYSTAL output file is crystal.o. This is the default file name
for the CRYSTAL interface, so, the -c crystal.o parameter is not needed
CRYSTAL output file crystal.o includes the Born effective
charges and the dielectric tensor
charges and the dielectric tensor
(from FREQCALC-INTENS-INTCPHF, see the input in the beginning of crystal.o)
1) Create displaced supercells:
@ -24,7 +24,7 @@ charges and the dielectric tensor
5) Calculate phonon dispersion data into band.yaml and save band.pdf
Take the non-analytical correction into account using --nac (see BORN file):
phonopy --crystal --dim="4 4 4" -p -s --nac band.conf
Plot the phonon dispersion in cm^{-1} units:
(factor = CrystalToTHz * THzToCm = 15.633302 * 33.356410)
phonopy --crystal --dim="4 4 4" -p -s --nac --factor=521.47083 band.conf

70
example/NaCl-CRYSTAL/crystal.o
View File

@ -100,7 +100,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
PROCESS 10 OF 12 WORKING
PROCESS 11 OF 12 WORKING
*******************************************************************************
* *
* CRYSTAL17 *
@ -145,14 +145,14 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
* *
*******************************************************************************
EEEEEEEEEE STARTING DATE 10 06 2018 TIME 13:56:02.5
NaCl at the PBE0/SVP level of theory
NaCl at the PBE0/SVP level of theory
CRYSTAL CALCULATION
(INPUT ACCORDING TO THE INTERNATIONAL TABLES FOR X-RAY CRYSTALLOGRAPHY)
CRYSTAL FAMILY : CUBIC
CRYSTAL CLASS (GROTH - 1921) : CUBIC HEXAKISOCTAHEDRAL
CRYSTAL FAMILY : CUBIC
CRYSTAL CLASS (GROTH - 1921) : CUBIC HEXAKISOCTAHEDRAL
SPACE GROUP (CENTROSYMMETRIC) : F M 3 M
SPACE GROUP (CENTROSYMMETRIC) : F M 3 M
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - CONVENTIONAL CELL
A B C ALPHA BETA GAMMA
@ -187,7 +187,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
NUMBER OF SYMMETRY OPERATORS : 48
*******************************************************************************
* GEOMETRY EDITING - INPUT COORDINATES ARE GIVEN IN ANGSTROM
* GEOMETRY EDITING - INPUT COORDINATES ARE GIVEN IN ANGSTROM
*******************************************************************************
GEOMETRY NOW FULLY CONSISTENT WITH THE GROUP
@ -208,11 +208,11 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
PRIMITIVE CELL - CENTRING CODE 5/0 VOLUME= 43.197975 - DENSITY 2.228 g/cm^3
A B C ALPHA BETA GAMMA
A B C ALPHA BETA GAMMA
3.93845719 3.93845719 3.93845719 60.000000 60.000000 60.000000
*******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 2 - ATOMS IN THE UNIT CELL: 2
ATOM X/A Y/B Z/C
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 11 NA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
2 T 17 CL -5.000000000000E-01 5.000000000000E-01 5.000000000000E-01
@ -222,11 +222,11 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
*******************************************************************************
CRYSTALLOGRAPHIC CELL (VOLUME= 172.79190008)
A B C ALPHA BETA GAMMA
A B C ALPHA BETA GAMMA
5.56981957 5.56981957 5.56981957 90.000000 90.000000 90.000000
COORDINATES IN THE CRYSTALLOGRAPHIC CELL
ATOM X/A Y/B Z/C
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 11 NA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
2 T 17 CL -5.000000000000E-01 5.000000000000E-01 5.000000000000E-01
@ -305,50 +305,50 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
ATOM X(AU) Y(AU) Z(AU) N. TYPE EXPONENT S COEF P COEF D/F/G COEF
*******************************************************************************
1 NA 0.000 0.000 0.000
1 S
1 S
4.098E+03-5.854E-03 0.000E+00 0.000E+00
6.165E+02-4.365E-02 0.000E+00 0.000E+00
1.400E+02-1.943E-01 0.000E+00 0.000E+00
3.907E+01-4.869E-01 0.000E+00 0.000E+00
1.193E+01-4.188E-01 0.000E+00 0.000E+00
2 S
2 S
2.066E+01 8.595E-02 0.000E+00 0.000E+00
1.984E+00-5.636E-01 0.000E+00 0.000E+00
6.484E-01-5.195E-01 0.000E+00 0.000E+00
3 S
3 S
3.200E-01 1.000E+00 0.000E+00 0.000E+00
4- 7 SP
4- 7 SP
1.600E-01 1.000E+00 1.000E+00 0.000E+00
8- 10 P
8- 10 P
7.540E+01 0.000E+00 1.544E-02 0.000E+00
1.727E+01 0.000E+00 9.974E-02 0.000E+00
5.184E+00 0.000E+00 3.121E-01 0.000E+00
1.660E+00 0.000E+00 4.930E-01 0.000E+00
5.123E-01 0.000E+00 3.242E-01 0.000E+00
2 CL 5.263 5.263 5.263
11 S
11 S
1.045E+04 1.971E-03 0.000E+00 0.000E+00
1.572E+03 1.475E-02 0.000E+00 0.000E+00
3.571E+02 6.668E-02 0.000E+00 0.000E+00
1.003E+02 1.723E-01 0.000E+00 0.000E+00
3.081E+01 1.588E-01 0.000E+00 0.000E+00
12 S
12 S
5.192E+01-1.001E-01 0.000E+00 0.000E+00
5.705E+00 6.084E-01 0.000E+00 0.000E+00
2.351E+00 5.435E-01 0.000E+00 0.000E+00
13 S
13 S
4.973E-01 1.000E+00 0.000E+00 0.000E+00
14- 17 SP
14- 17 SP
2.100E-01 1.000E+00 1.000E+00 0.000E+00
18- 20 P
18- 20 P
3.077E+02 0.000E+00-8.780E-03 0.000E+00
7.210E+01 0.000E+00-6.356E-02 0.000E+00
2.253E+01 0.000E+00-2.402E-01 0.000E+00
7.899E+00 0.000E+00-4.780E-01 0.000E+00
2.877E+00 0.000E+00-3.852E-01 0.000E+00
21- 23 P
21- 23 P
7.736E-01 0.000E+00 1.000E+00 0.000E+00
24- 28 D
24- 28 D
6.500E-01 0.000E+00 0.000E+00 1.000E+00
INFORMATION **** SET_MPP **** PCRYSTAL CALCULATION
INFORMATION **** READM2 **** NEW DEFAULT: FOCK/KS MATRIX MIXING SET TO 30 %
@ -402,7 +402,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
25-C( 4 3 1) 26-C( 5 3 1) 27-C( 6 3 1) 28-C( 5 4 1)
29-C( 6 4 2)
DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
X Y Z X Y Z
0.0000000 5.2627168 5.2627168 -0.5969526 0.5969526 0.5969526
5.2627168 0.0000000 5.2627168 0.5969526 -0.5969526 0.5969526
@ -505,7 +505,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
EEEEEEEEEE INT_CALC TERMINATION DATE 10 06 2018 TIME 13:56:02.7
*******************************************************************************
NaCl at the PBE0/SVP level of theory
NaCl at the PBE0/SVP level of theory
CRYSTAL - SCF - TYPE OF CALCULATION : RESTRICTED CLOSED SHELL
*******************************************************************************
@ -1094,7 +1094,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
TENSOR IN PRINCIPAL AXES SYSTEM
AA 1.812611E+00 BB 1.812611E+00 CC 1.812612E+00
REFRACTIVE INDICES
REFRACTIVE INDICES
AA 1.346332E+00 BB 1.346332E+00 CC 1.346333E+00
OPTICALLY ISOTROPIC CRYSTAL
@ -1171,13 +1171,13 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
THERE ARE NO SYMMETRY ALLOWED DIRECTIONS
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT SYMM TELAPSE 36.91 TCPU 36.81
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT INT_SCREEN TELAPSE 36.91 TCPU 36.82
COMPUTING IR TENSOR ALONG DIRECTION X
COMPUTING IR TENSOR ALONG DIRECTION Y
COMPUTING IR TENSOR ALONG DIRECTION Z
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT IR TENSOR TELAPSE 106.00 TCPU 105.84
*******************************************************************************
* *
@ -1226,7 +1226,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
ATOMS ISOTOPIC MASS (AMU) FOR FREQUENCY CALCULATION
ATOMS ISOTOPIC MASS (AMU) FOR FREQUENCY CALCULATION
1 NA 22.9898 2 CL 34.9689
@ -1234,10 +1234,10 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
GENERATING FREQUENCIES. IN PRINCIPLE 3N+1 SCF + GRADIENT
CALCULATIONS ARE REQUIRED;
FOR EACH OF THEM THE REMAINING POINT SYMMETRY IS INDICATED.
POINT SYMMETRY PERMITS TO GENERATE GRADIENTS FOR DISPLACEMENT B
POINT SYMMETRY PERMITS TO GENERATE GRADIENTS FOR DISPLACEMENT B
STARTING FROM THE GRADIENT GENERATED BY DISPLACEMENT A.
N LABEL SYMBOL DISPLACEMENT SYM.
N LABEL SYMBOL DISPLACEMENT SYM.
1 EQUILIBRIUM GEOMETRY 48
@ -1303,7 +1303,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT INT_CALC TELAPSE 106.14 TCPU 105.98
*******************************************************************************
NaCl at the PBE0/SVP level of theory
NaCl at the PBE0/SVP level of theory
CRYSTAL - SCF - TYPE OF CALCULATION : RESTRICTED CLOSED SHELL
*******************************************************************************
@ -1540,7 +1540,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
(2) ONLY RELEVANT CLASSES ARE CONSIDERED IN THE CHARACTER TABLE
(3) SYMBOLS MAY NOT FULLY COINCIDE WITH THOSE FROM TEXT BOOKS.]
(P, D, RP, RD, STAND FOR PAIRING, DOUBLING, REAL PAIRING AND REAL DOUBLING
(P, D, RP, RD, STAND FOR PAIRING, DOUBLING, REAL PAIRING AND REAL DOUBLING
OF THE IRREPS (SEE MANUAL))
CLASS | GROUP OPERATORS (SEE SYMMOPS KEYWORD)
@ -1560,7 +1560,7 @@ Creating temporary directory /chemtemp/CRY_9310 on node compute-0-0.local
MULTIP | 1 3 8 6 6 1 3 8 6 6
-------------------------------------------------------------------------------
Fu | 3.00 -1.00 0.00 -1.00 1.00 -3.00 1.00 0.00 1.00 -1.00
Fu -(3, 2);
@ -1724,4 +1724,4 @@ CPHF RESTART data fort.31 saved as /home/antti/work/crypho/dev-examples/NaCl-CRY
Born charges BORN.DAT saved as /home/antti/work/crypho/dev-examples/NaCl-CRYSTAL-new/fq/crystal.born
IR tensor for IRREA TENS_IR.DAT saved as /home/antti/work/crypho/dev-examples/NaCl-CRYSTAL-new/fq/crystal.tensir
Temporary directory /chemtemp/CRY_9310 removed from node compute-0-0.local
Date: 2018-06-10 13:58:04
Date: 2018-06-10 13:58:04

62
example/NaCl-CRYSTAL/supercell-001.o
View File

@ -89,7 +89,7 @@ sent 65104283 bytes received 75 bytes 43402905.33 bytes/sec
total size is 65096084 speedup is 1.00
48 PROCESSORS WORKING
*******************************************************************************
* *
* CRYSTAL17 *
@ -134,10 +134,10 @@ total size is 65096084 speedup is 1.00
* *
*******************************************************************************
EEEEEEEEEE STARTING DATE 10 06 2018 TIME 14:30:18.6
Created by Phonopy CRYSTAL interface
Created by Phonopy CRYSTAL interface
GEOMETRY INPUT FROM EXTERNAL FILE (FORTRAN UNIT 34)
3D - CRYSTAL
3D - CRYSTAL
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - PRIMITIVE CELL
@ -282,11 +282,11 @@ total size is 65096084 speedup is 1.00
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
PRIMITIVE CELL - CENTRING CODE 1/0 VOLUME= 2764.670401 - DENSITY 2.228 g/cm^3
A B C ALPHA BETA GAMMA
A B C ALPHA BETA GAMMA
15.75382875 15.75382875 15.75382875 60.000000 60.000000 60.000000
*******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 128 - ATOMS IN THE UNIT CELL: 128
ATOM X/A Y/B Z/C
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 11 NA 6.347663261918E-04 1.293161595056E-20 -1.293161595056E-20
2 T 11 NA 2.500000000000E-01 2.019909446387E-18 -2.019909446387E-18
@ -419,7 +419,7 @@ total size is 65096084 speedup is 1.00
T = ATOM BELONGING TO THE ASYMMETRIC UNIT
*******************************************************************************
* GEOMETRY EDITING - INPUT COORDINATES ARE GIVEN IN ANGSTROM
* GEOMETRY EDITING - INPUT COORDINATES ARE GIVEN IN ANGSTROM
*******************************************************************************
GCALCO - MAX INDICES DIRECT LATTICE VECTOR 14 14 14
@ -430,11 +430,11 @@ total size is 65096084 speedup is 1.00
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
PRIMITIVE CELL - CENTRING CODE 1/0 VOLUME= 2764.670401 - DENSITY 2.228 g/cm^3
A B C ALPHA BETA GAMMA
A B C ALPHA BETA GAMMA
15.75382875 15.75382875 15.75382875 60.000000 60.000000 60.000000
*******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 128 - ATOMS IN THE UNIT CELL: 128
ATOM X/A Y/B Z/C
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 11 NA 6.347663261918E-04 -9.258804133146E-21 9.258804133146E-21
2 T 11 NA 2.500000000000E-01 -4.776101526044E-18 4.776101526044E-18
@ -718,21 +718,21 @@ total size is 65096084 speedup is 1.00
ATOM X(AU) Y(AU) Z(AU) N. TYPE EXPONENT S COEF P COEF D/F/G COEF
*******************************************************************************
1 NA 0.000 0.013 0.013
1 S
1 S
4.098E+03-5.854E-03 0.000E+00 0.000E+00
6.165E+02-4.365E-02 0.000E+00 0.000E+00
1.400E+02-1.943E-01 0.000E+00 0.000E+00
3.907E+01-4.869E-01 0.000E+00 0.000E+00
1.193E+01-4.188E-01 0.000E+00 0.000E+00
2 S
2 S
2.066E+01 8.595E-02 0.000E+00 0.000E+00
1.984E+00-5.636E-01 0.000E+00 0.000E+00
6.484E-01-5.195E-01 0.000E+00 0.000E+00
3 S
3 S
3.200E-01 1.000E+00 0.000E+00 0.000E+00
4- 7 SP
4- 7 SP
1.600E-01 1.000E+00 1.000E+00 0.000E+00
8- 10 P
8- 10 P
7.540E+01 0.000E+00 1.544E-02 0.000E+00
1.727E+01 0.000E+00 9.974E-02 0.000E+00
5.184E+00 0.000E+00 3.121E-01 0.000E+00
@ -802,29 +802,29 @@ total size is 65096084 speedup is 1.00
63 NA 31.576 26.314 26.314
64 NA 31.576 31.576 31.576
65 CL 5.263 21.051 21.051
641 S
641 S
1.045E+04 1.971E-03 0.000E+00 0.000E+00
1.572E+03 1.475E-02 0.000E+00 0.000E+00
3.571E+02 6.668E-02 0.000E+00 0.000E+00
1.003E+02 1.723E-01 0.000E+00 0.000E+00
3.081E+01 1.588E-01 0.000E+00 0.000E+00
642 S
642 S
5.192E+01-1.001E-01 0.000E+00 0.000E+00
5.705E+00 6.084E-01 0.000E+00 0.000E+00
2.351E+00 5.435E-01 0.000E+00 0.000E+00
643 S
643 S
4.973E-01 1.000E+00 0.000E+00 0.000E+00
644- 647 SP
644- 647 SP
2.100E-01 1.000E+00 1.000E+00 0.000E+00
648- 650 P
648- 650 P
3.077E+02 0.000E+00-8.780E-03 0.000E+00
7.210E+01 0.000E+00-6.356E-02 0.000E+00
2.253E+01 0.000E+00-2.402E-01 0.000E+00
7.899E+00 0.000E+00-4.780E-01 0.000E+00
2.877E+00 0.000E+00-3.852E-01 0.000E+00
651- 653 P
651- 653 P
7.736E-01 0.000E+00 1.000E+00 0.000E+00
654- 658 D
654- 658 D
6.500E-01 0.000E+00 0.000E+00 1.000E+00
66 CL 5.263 5.263 5.263
67 CL 5.263 10.525 10.525
@ -943,7 +943,7 @@ total size is 65096084 speedup is 1.00
*** K POINTS COORDINATES (OBLIQUE COORDINATES IN UNITS OF IS = 1)
1-R( 0 0 0)
DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
X Y Z X Y Z
0.0000000 21.0508672 21.0508672 -0.1492382 0.1492382 0.1492382
21.0508672 0.0000000 21.0508672 0.1492382 -0.1492382 0.1492382
@ -4093,7 +4093,7 @@ total size is 65096084 speedup is 1.00
EEEEEEEEEE INT_CALC TERMINATION DATE 10 06 2018 TIME 14:30:34.7
*******************************************************************************
Created by Phonopy CRYSTAL interface
Created by Phonopy CRYSTAL interface
CRYSTAL - SCF - TYPE OF CALCULATION : RESTRICTED CLOSED SHELL
*******************************************************************************
@ -4246,7 +4246,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 122.14 TCPU 121.20
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 122.14 TCPU 121.20
DIIS TEST: 0.58890E+00 AT SCF CYCLE 2 - DIIS ACTIVE - HISTORY: 2 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 1.661 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 1.661 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 122.33 TCPU 121.39
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 122.74 TCPU 121.80
INSULATING STATE
@ -4291,7 +4291,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 158.43 TCPU 157.45
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 158.43 TCPU 157.45
DIIS TEST: 0.56993E-03 AT SCF CYCLE 3 - DIIS ACTIVE - HISTORY: 3 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 2.492 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 2.492 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 158.62 TCPU 157.63
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 159.02 TCPU 158.04
INSULATING STATE
@ -4336,7 +4336,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 194.92 TCPU 193.88
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 194.92 TCPU 193.88
DIIS TEST: 0.96203E-05 AT SCF CYCLE 4 - DIIS ACTIVE - HISTORY: 4 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 3.322 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 3.322 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 195.13 TCPU 194.09
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 195.49 TCPU 194.46
INSULATING STATE
@ -4381,7 +4381,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 231.34 TCPU 230.26
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 231.34 TCPU 230.26
DIIS TEST: 0.15312E-06 AT SCF CYCLE 5 - DIIS ACTIVE - HISTORY: 5 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.153 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.153 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 231.53 TCPU 230.45
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 231.93 TCPU 230.85
INSULATING STATE
@ -4426,7 +4426,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 267.64 TCPU 266.51
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 267.64 TCPU 266.51
DIIS TEST: 0.69412E-09 AT SCF CYCLE 6 - DIIS ACTIVE - HISTORY: 6 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.983 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.983 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 267.85 TCPU 266.72
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 268.22 TCPU 267.09
INSULATING STATE
@ -4471,7 +4471,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 303.94 TCPU 302.76
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 303.94 TCPU 302.76
DIIS TEST: 0.19533E-09 AT SCF CYCLE 7 - DIIS ACTIVE - HISTORY: 7 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 5.814 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 5.814 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 304.15 TCPU 302.96
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 304.54 TCPU 303.35
INSULATING STATE
@ -4516,7 +4516,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 340.48 TCPU 339.25
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 340.48 TCPU 339.25
DIIS TEST: 0.28479E-12 AT SCF CYCLE 8 - DIIS ACTIVE - HISTORY: 8 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 6.645 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 6.645 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 340.68 TCPU 339.45
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 341.07 TCPU 339.84
INSULATING STATE
@ -4561,7 +4561,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 376.75 TCPU 375.47
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 376.75 TCPU 375.47
DIIS TEST: 0.43260E-13 AT SCF CYCLE 9 - DIIS ACTIVE - HISTORY: 9 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 7.475 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 7.475 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 376.96 TCPU 375.67
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 377.33 TCPU 376.05
INSULATING STATE
@ -4874,4 +4874,4 @@ MPPcrystal finished normally
SCF wavefunction fort.9 saved as /homeappl/home/anttikar/work/test/nacl/MPP/supercell-001.w
Temporary directory /tmp/anttikar/CRY_10144 removed from node c840
Temporary directory /tmp/anttikar/CRY_10144 removed from node c839
Date: 2018-06-10 14:40:13
Date: 2018-06-10 14:40:13

62
example/NaCl-CRYSTAL/supercell-002.o
View File

@ -89,7 +89,7 @@ sent 65104279 bytes received 75 bytes 43402902.67 bytes/sec
total size is 65096084 speedup is 1.00
48 PROCESSORS WORKING
*******************************************************************************
* *
* CRYSTAL17 *
@ -134,10 +134,10 @@ total size is 65096084 speedup is 1.00
* *
*******************************************************************************
EEEEEEEEEE STARTING DATE 10 06 2018 TIME 14:30:19.0
Created by Phonopy CRYSTAL interface
Created by Phonopy CRYSTAL interface
GEOMETRY INPUT FROM EXTERNAL FILE (FORTRAN UNIT 34)
3D - CRYSTAL
3D - CRYSTAL
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - PRIMITIVE CELL
@ -282,11 +282,11 @@ total size is 65096084 speedup is 1.00
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
PRIMITIVE CELL - CENTRING CODE 1/0 VOLUME= 2764.670401 - DENSITY 2.228 g/cm^3
A B C ALPHA BETA GAMMA
A B C ALPHA BETA GAMMA
15.75382875 15.75382875 15.75382875 60.000000 60.000000 60.000000
*******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 128 - ATOMS IN THE UNIT CELL: 128
ATOM X/A Y/B Z/C
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 11 NA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
2 T 11 NA 2.500000000000E-01 2.019909446387E-18 -2.019909446387E-18
@ -419,7 +419,7 @@ total size is 65096084 speedup is 1.00
T = ATOM BELONGING TO THE ASYMMETRIC UNIT
*******************************************************************************
* GEOMETRY EDITING - INPUT COORDINATES ARE GIVEN IN ANGSTROM
* GEOMETRY EDITING - INPUT COORDINATES ARE GIVEN IN ANGSTROM
*******************************************************************************
GCALCO - MAX INDICES DIRECT LATTICE VECTOR 14 14 14
@ -430,11 +430,11 @@ total size is 65096084 speedup is 1.00
*******************************************************************************
LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM
PRIMITIVE CELL - CENTRING CODE 1/0 VOLUME= 2764.670401 - DENSITY 2.228 g/cm^3
A B C ALPHA BETA GAMMA
A B C ALPHA BETA GAMMA
15.75382875 15.75382875 15.75382875 60.000000 60.000000 60.000000
*******************************************************************************
ATOMS IN THE ASYMMETRIC UNIT 128 - ATOMS IN THE UNIT CELL: 128
ATOM X/A Y/B Z/C
ATOM X/A Y/B Z/C
*******************************************************************************
1 T 11 NA 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00
2 T 11 NA 2.500000000000E-01 -4.776101526044E-18 4.776101526044E-18
@ -718,21 +718,21 @@ total size is 65096084 speedup is 1.00
ATOM X(AU) Y(AU) Z(AU) N. TYPE EXPONENT S COEF P COEF D/F/G COEF
*******************************************************************************
1 NA 0.000 0.000 0.000
1 S
1 S
4.098E+03-5.854E-03 0.000E+00 0.000E+00
6.165E+02-4.365E-02 0.000E+00 0.000E+00
1.400E+02-1.943E-01 0.000E+00 0.000E+00
3.907E+01-4.869E-01 0.000E+00 0.000E+00
1.193E+01-4.188E-01 0.000E+00 0.000E+00
2 S
2 S
2.066E+01 8.595E-02 0.000E+00 0.000E+00
1.984E+00-5.636E-01 0.000E+00 0.000E+00
6.484E-01-5.195E-01 0.000E+00 0.000E+00
3 S
3 S
3.200E-01 1.000E+00 0.000E+00 0.000E+00
4- 7 SP
4- 7 SP
1.600E-01 1.000E+00 1.000E+00 0.000E+00
8- 10 P
8- 10 P
7.540E+01 0.000E+00 1.544E-02 0.000E+00
1.727E+01 0.000E+00 9.974E-02 0.000E+00
5.184E+00 0.000E+00 3.121E-01 0.000E+00
@ -802,29 +802,29 @@ total size is 65096084 speedup is 1.00
63 NA 31.576 26.314 26.314
64 NA 31.576 31.576 31.576
65 CL 5.263 21.064 21.064
641 S
641 S
1.045E+04 1.971E-03 0.000E+00 0.000E+00
1.572E+03 1.475E-02 0.000E+00 0.000E+00
3.571E+02 6.668E-02 0.000E+00 0.000E+00
1.003E+02 1.723E-01 0.000E+00 0.000E+00
3.081E+01 1.588E-01 0.000E+00 0.000E+00
642 S
642 S
5.192E+01-1.001E-01 0.000E+00 0.000E+00
5.705E+00 6.084E-01 0.000E+00 0.000E+00
2.351E+00 5.435E-01 0.000E+00 0.000E+00
643 S
643 S
4.973E-01 1.000E+00 0.000E+00 0.000E+00
644- 647 SP
644- 647 SP
2.100E-01 1.000E+00 1.000E+00 0.000E+00
648- 650 P
648- 650 P
3.077E+02 0.000E+00-8.780E-03 0.000E+00
7.210E+01 0.000E+00-6.356E-02 0.000E+00
2.253E+01 0.000E+00-2.402E-01 0.000E+00
7.899E+00 0.000E+00-4.780E-01 0.000E+00
2.877E+00 0.000E+00-3.852E-01 0.000E+00
651- 653 P
651- 653 P
7.736E-01 0.000E+00 1.000E+00 0.000E+00
654- 658 D
654- 658 D
6.500E-01 0.000E+00 0.000E+00 1.000E+00
66 CL 5.263 5.263 5.263
67 CL 5.263 10.525 10.525
@ -943,7 +943,7 @@ total size is 65096084 speedup is 1.00
*** K POINTS COORDINATES (OBLIQUE COORDINATES IN UNITS OF IS = 1)
1-R( 0 0 0)
DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
DIRECT LATTICE VECTORS COMPON. (A.U.) RECIP. LATTICE VECTORS COMPON. (A.U.)
X Y Z X Y Z
0.0000000 21.0508672 21.0508672 -0.1492382 0.1492382 0.1492382
21.0508672 0.0000000 21.0508672 0.1492382 -0.1492382 0.1492382
@ -4093,7 +4093,7 @@ total size is 65096084 speedup is 1.00
EEEEEEEEEE INT_CALC TERMINATION DATE 10 06 2018 TIME 14:30:35.2
*******************************************************************************
Created by Phonopy CRYSTAL interface
Created by Phonopy CRYSTAL interface
CRYSTAL - SCF - TYPE OF CALCULATION : RESTRICTED CLOSED SHELL
*******************************************************************************
@ -4246,7 +4246,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 122.48 TCPU 121.58
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 122.48 TCPU 121.58
DIIS TEST: 0.58890E+00 AT SCF CYCLE 2 - DIIS ACTIVE - HISTORY: 2 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 1.661 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 1.661 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 122.67 TCPU 121.77
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 123.08 TCPU 122.17
INSULATING STATE
@ -4291,7 +4291,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 159.00 TCPU 158.05
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 159.00 TCPU 158.05
DIIS TEST: 0.56993E-03 AT SCF CYCLE 3 - DIIS ACTIVE - HISTORY: 3 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 2.492 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 2.492 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 159.19 TCPU 158.23
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 159.58 TCPU 158.63
INSULATING STATE
@ -4336,7 +4336,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 195.52 TCPU 194.51
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 195.52 TCPU 194.51
DIIS TEST: 0.96213E-05 AT SCF CYCLE 4 - DIIS ACTIVE - HISTORY: 4 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 3.322 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 3.322 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 195.73 TCPU 194.72
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 196.12 TCPU 195.11
INSULATING STATE
@ -4381,7 +4381,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 232.10 TCPU 231.02
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 232.10 TCPU 231.03
DIIS TEST: 0.15344E-06 AT SCF CYCLE 5 - DIIS ACTIVE - HISTORY: 5 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.153 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.153 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 232.29 TCPU 231.22
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 232.67 TCPU 231.59
INSULATING STATE
@ -4426,7 +4426,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 268.47 TCPU 267.32
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 268.47 TCPU 267.32
DIIS TEST: 0.86690E-09 AT SCF CYCLE 6 - DIIS ACTIVE - HISTORY: 6 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.983 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 4.983 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 268.66 TCPU 267.52
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 269.04 TCPU 267.90
INSULATING STATE
@ -4471,7 +4471,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 305.05 TCPU 303.82
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 305.05 TCPU 303.82
DIIS TEST: 0.25946E-09 AT SCF CYCLE 7 - DIIS ACTIVE - HISTORY: 7 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 5.814 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 5.814 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 305.22 TCPU 303.99
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 305.64 TCPU 304.42
INSULATING STATE
@ -4516,7 +4516,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 341.61 TCPU 340.31
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 341.61 TCPU 340.31
DIIS TEST: 0.29469E-12 AT SCF CYCLE 8 - DIIS ACTIVE - HISTORY: 8 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 6.645 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 6.645 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 341.79 TCPU 340.49
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 342.19 TCPU 340.89
INSULATING STATE
@ -4561,7 +4561,7 @@ total size is 65096084 speedup is 1.00
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 378.12 TCPU 376.75
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIIS TELAPSE 378.12 TCPU 376.75
DIIS TEST: 0.43931E-13 AT SCF CYCLE 9 - DIIS ACTIVE - HISTORY: 9 CYCLES
MAXIMUM MEMORY OCCUPIED BY DIIS: 7.475 Mb PER CORE
MAXIMUM MEMORY OCCUPIED BY DIIS: 7.475 Mb PER CORE
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_TRAF TELAPSE 378.30 TCPU 376.93
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT MPP_DIAG TELAPSE 378.69 TCPU 377.31
INSULATING STATE
@ -4874,4 +4874,4 @@ MPPcrystal finished normally
SCF wavefunction fort.9 saved as /homeappl/home/anttikar/work/test/nacl/MPP/supercell-002.w
Temporary directory /tmp/anttikar/CRY_10274 removed from node c719
Temporary directory /tmp/anttikar/CRY_10274 removed from node c718
Date: 2018-06-10 14:40:18
Date: 2018-06-10 14:40:18

2
example/NaCl-QE/NaCl-001.in
View File

@ -89,4 +89,4 @@ ATOMIC_POSITIONS crystal
Cl 0.0000000000000000 0.0000000000000000 0.7500000000000001
Cl 0.5000000000000000 0.0000000000000000 0.7500000000000001
Cl 0.0000000000000000 0.5000000000000000 0.7500000000000001
Cl 0.5000000000000000 0.5000000000000000 0.7500000000000001
Cl 0.5000000000000000 0.5000000000000000 0.7500000000000001

40
example/NaCl-QE/NaCl-001.out
View File

@ -1,10 +1,10 @@
Program PWSCF v.5.4.0 starts on 14Sep2016 at 16:22:52
Program PWSCF v.5.4.0 starts on 14Sep2016 at 16:22:52
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
@ -23,14 +23,14 @@
one sub-group per band group will be used
scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs)
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 644 644 165 49140 49140 6426
Max 645 645 167 49142 49142 6427
Sum 10309 10309 2661 786247 786247 102831
bravais-lattice index = 0
@ -51,14 +51,14 @@
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )
PseudoPot. # 1 for Na read from file:
@ -67,12 +67,12 @@
Pseudo is Projector augmented-wave, Zval = 9.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1121 points, 4 beta functions with:
Using radial grid of 1121 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for Cl read from file:
@ -81,12 +81,12 @@
Pseudo is Projector augmented-wave + core cor, Zval = 7.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1157 points, 4 beta functions with:
Using radial grid of 1157 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
Q(r) pseudized with 0 coefficients
atomic species valence mass pseudopotential
@ -189,7 +189,7 @@
starting charge 495.97294, renormalised to 512.00000
Starting wfc are 384 randomized atomic wfcs
Checking if some PAW data can be deallocated...
Checking if some PAW data can be deallocated...
total cpu time spent up to now is 4.7 secs
@ -425,7 +425,7 @@
0.00000000 0.00000427 0.00000000 0.00 0.63 0.00
0.00000000 0.00000000 0.00000427 0.00 0.00 0.63
init_run : 4.14s CPU 4.30s WALL ( 1 calls)
electrons : 98.15s CPU 99.00s WALL ( 1 calls)
forces : 1.60s CPU 1.65s WALL ( 1 calls)
@ -464,14 +464,14 @@
calbec : 9.12s CPU 9.13s WALL ( 53 calls)
fft : 0.73s CPU 0.77s WALL ( 167 calls)
fftw : 30.10s CPU 30.19s WALL ( 17922 calls)
Parallel routines
fft_scatter : 10.96s CPU 10.94s WALL ( 18089 calls)
PWSCF : 1m55.79s CPU 1m56.91s WALL
This run was terminated on: 16:24:49 14Sep2016
This run was terminated on: 16:24:49 14Sep2016
=------------------------------------------------------------------------------=
JOB DONE.

2
example/NaCl-QE/NaCl-002.in
View File

@ -89,4 +89,4 @@ ATOMIC_POSITIONS crystal
Cl 0.0000000000000000 0.0000000000000000 0.7500000000000001
Cl 0.5000000000000000 0.0000000000000000 0.7500000000000001
Cl 0.0000000000000000 0.5000000000000000 0.7500000000000001
Cl 0.5000000000000000 0.5000000000000000 0.7500000000000001
Cl 0.5000000000000000 0.5000000000000000 0.7500000000000001

40
example/NaCl-QE/NaCl-002.out
View File

@ -1,10 +1,10 @@
Program PWSCF v.5.4.0 starts on 14Sep2016 at 16:22:52
Program PWSCF v.5.4.0 starts on 14Sep2016 at 16:22:52
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
@ -23,14 +23,14 @@
one sub-group per band group will be used
scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs)
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 644 644 165 49140 49140 6426
Max 645 645 167 49142 49142 6427
Sum 10309 10309 2661 786247 786247 102831
bravais-lattice index = 0
@ -51,14 +51,14 @@
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )
PseudoPot. # 1 for Na read from file:
@ -67,12 +67,12 @@
Pseudo is Projector augmented-wave, Zval = 9.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1121 points, 4 beta functions with:
Using radial grid of 1121 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for Cl read from file:
@ -81,12 +81,12 @@
Pseudo is Projector augmented-wave + core cor, Zval = 7.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1157 points, 4 beta functions with:
Using radial grid of 1157 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
Q(r) pseudized with 0 coefficients
atomic species valence mass pseudopotential
@ -189,7 +189,7 @@
starting charge 495.97294, renormalised to 512.00000
Starting wfc are 384 randomized atomic wfcs
Checking if some PAW data can be deallocated...
Checking if some PAW data can be deallocated...
total cpu time spent up to now is 4.6 secs
@ -425,7 +425,7 @@
0.00000000 0.00000440 0.00000000 0.00 0.65 0.00
0.00000000 0.00000000 0.00000440 0.00 0.00 0.65
init_run : 4.08s CPU 4.24s WALL ( 1 calls)
electrons : 98.16s CPU 98.98s WALL ( 1 calls)
forces : 1.55s CPU 1.59s WALL ( 1 calls)
@ -464,14 +464,14 @@
calbec : 8.78s CPU 8.78s WALL ( 55 calls)
fft : 0.72s CPU 0.79s WALL ( 167 calls)
fftw : 30.29s CPU 30.37s WALL ( 17986 calls)
Parallel routines
fft_scatter : 8.82s CPU 8.78s WALL ( 18153 calls)
PWSCF : 1m55.67s CPU 1m56.72s WALL
This run was terminated on: 16:24:49 14Sep2016
This run was terminated on: 16:24:49 14Sep2016
=------------------------------------------------------------------------------=
JOB DONE.

150
example/NaCl-QE/NaCl.ph.out
View File

@ -1,10 +1,10 @@
Program PHONON v.5.4.0 starts on 14Sep2016 at 14:55: 8
Program PHONON v.5.4.0 starts on 14Sep2016 at 14:55: 8
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
@ -37,20 +37,20 @@
file Na.pbe-spn-kjpaw_psl.0.2.UPF: wavefunction(s) 2P 3P renormalized
file Cl.pbe-n-kjpaw_psl.0.1.UPF: wavefunction(s) 3S 3P renormalized
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 214 214 59 8198 8198 1195
Max 217 217 60 8200 8200 1198
Sum 2585 2585 717 98385 98385 14363
Check: negative/imaginary core charge= -0.000005 0.000000
Calculation of q = 0.0000000 0.0000000 0.0000000
bravais-lattice index = 0
lattice parameter (alat) = 10.7531 a.u.
@ -69,17 +69,17 @@
celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000
crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.0000 0.0000 0.0000 )
a(2) = ( 0.0000 1.0000 0.0000 )
a(3) = ( 0.0000 0.0000 1.0000 )
a(1) = ( 1.0000 0.0000 0.0000 )
a(2) = ( 0.0000 1.0000 0.0000 )
a(3) = ( 0.0000 0.0000 1.0000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.0000 0.0000 0.0000 )
b(2) = ( 0.0000 1.0000 0.0000 )
b(3) = ( 0.0000 0.0000 1.0000 )
b(1) = ( 1.0000 0.0000 0.0000 )
b(2) = ( 0.0000 1.0000 0.0000 )
b(3) = ( 0.0000 0.0000 1.0000 )
Atoms inside the unit cell:
Atoms inside the unit cell:
Cartesian axes
@ -93,9 +93,9 @@
7 Cl 35.4530 tau( 7) = ( 0.00000 0.50000 0.00000 )
8 Cl 35.4530 tau( 8) = ( 0.00000 0.00000 0.50000 )
Computing dynamical matrix for
Computing dynamical matrix for
q = ( 0.0000000 0.0000000 0.0000000 )
49 Sym.Ops. (with q -> -q+G )
@ -129,12 +129,12 @@
Pseudo is Projector augmented-wave, Zval = 9.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1121 points, 4 beta functions with:
Using radial grid of 1121 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for Cl read from file:
@ -143,12 +143,12 @@
Pseudo is Projector augmented-wave + core cor, Zval = 7.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Shape of augmentation charge: PSQ
Using radial grid of 1157 points, 4 beta functions with:
Using radial grid of 1157 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
Q(r) pseudized with 0 coefficients
Mode symmetry, O_h (m-3m) point group:
@ -203,7 +203,7 @@
End of electric fields calculation
Dielectric constant in cartesian axis
Dielectric constant in cartesian axis
( 2.472958201 0.000000000 0.000000000 )
( 0.000000000 2.472958201 0.000000000 )
@ -211,35 +211,35 @@
Effective charges (d Force / dE) in cartesian axis
atom 1 Na
atom 1 Na
Ex ( 1.09924 0.00000 0.00000 )
Ey ( 0.00000 1.09924 0.00000 )
Ez ( 0.00000 0.00000 1.09924 )
atom 2 Na
atom 2 Na
Ex ( 1.09924 0.00000 0.00000 )
Ey ( 0.00000 1.09922 0.00000 )
Ez ( 0.00000 0.00000 1.09922 )
atom 3 Na
atom 3 Na
Ex ( 1.09922 0.00000 0.00000 )
Ey ( 0.00000 1.09924 0.00000 )
Ez ( 0.00000 0.00000 1.09922 )
atom 4 Na
atom 4 Na
Ex ( 1.09922 0.00000 0.00000 )
Ey ( 0.00000 1.09922 0.00000 )
Ez ( 0.00000 0.00000 1.09924 )
atom 5 Cl
atom 5 Cl
Ex ( -1.11106 0.00000 0.00000 )
Ey ( 0.00000 -1.11106 0.00000 )
Ez ( 0.00000 0.00000 -1.11106 )
atom 6 Cl
atom 6 Cl
Ex ( -1.11114 0.00000 0.00000 )
Ey ( 0.00000 -1.11198 0.00000 )
Ez ( 0.00000 0.00000 -1.11198 )
atom 7 Cl
atom 7 Cl
Ex ( -1.11198 0.00000 0.00000 )
Ey ( 0.00000 -1.11114 0.00000 )
Ez ( 0.00000 0.00000 -1.11198 )
atom 8 Cl
atom 8 Cl
Ex ( -1.11198 0.00000 0.00000 )
Ey ( 0.00000 -1.11198 0.00000 )
Ez ( 0.00000 0.00000 -1.11114 )
@ -272,7 +272,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 2 modes # 4 5 6
@ -302,7 +302,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 3 modes # 7 8 9
@ -329,7 +329,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 4 modes # 10 11 12
@ -359,7 +359,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 5 modes # 13 14 15
@ -389,7 +389,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 6 modes # 16 17 18
@ -419,7 +419,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 7 modes # 19 20 21
@ -443,7 +443,7 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Representation # 8 modes # 22 23 24
@ -471,13 +471,13 @@
End of self-consistent calculation
Convergence has been achieved
Convergence has been achieved
Number of q in the star = 1
List of q in the star:
1 0.000000000 0.000000000 0.000000000
Dielectric constant in cartesian axis
Dielectric constant in cartesian axis
( 2.472958201 0.000000000 0.000000000 )
( 0.000000000 2.472958201 0.000000000 )
@ -485,42 +485,42 @@
Effective charges (d Force / dE) in cartesian axis
atom 1 Na
atom 1 Na
Ex ( 1.09924 0.00000 0.00000 )
Ey ( 0.00000 1.09924 0.00000 )
Ez ( 0.00000 0.00000 1.09924 )
atom 2 Na
atom 2 Na
Ex ( 1.09924 0.00000 0.00000 )
Ey ( 0.00000 1.09922 0.00000 )
Ez ( 0.00000 0.00000 1.09922 )
atom 3 Na
atom 3 Na
Ex ( 1.09922 0.00000 0.00000 )
Ey ( 0.00000 1.09924 0.00000 )
Ez ( 0.00000 0.00000 1.09922 )
atom 4 Na
atom 4 Na
Ex ( 1.09922 0.00000 0.00000 )
Ey ( 0.00000 1.09922 0.00000 )
Ez ( 0.00000 0.00000 1.09924 )
atom 5 Cl
atom 5 Cl
Ex ( -1.11106 0.00000 0.00000 )
Ey ( 0.00000 -1.11106 0.00000 )
Ez ( 0.00000 0.00000 -1.11106 )
atom 6 Cl
atom 6 Cl
Ex ( -1.11114 0.00000 0.00000 )
Ey ( 0.00000 -1.11198 0.00000 )
Ez ( 0.00000 0.00000 -1.11198 )
atom 7 Cl
atom 7 Cl
Ex ( -1.11198 0.00000 0.00000 )
Ey ( 0.00000 -1.11114 0.00000 )
Ez ( 0.00000 0.00000 -1.11198 )
atom 8 Cl
atom 8 Cl
Ex ( -1.11198 0.00000 0.00000 )
Ey ( 0.00000 -1.11198 0.00000 )
Ez ( 0.00000 0.00000 -1.11114 )
Diagonalizing the dynamical matrix
q = ( 0.000000000 0.000000000 0.000000000 )
q = ( 0.000000000 0.000000000 0.000000000 )
**************************************************************************
freq ( 1) = 1.098704 [THz] = 36.648806 [cm-1]
@ -551,21 +551,21 @@
Mode symmetry, O_h (m-3m) point group:
freq ( 1 - 3) = 36.6 [cm-1] --> T_1u G_15 G_4- I
freq ( 4 - 6) = 90.3 [cm-1] --> T_2u G_25 G_5-
freq ( 7 - 9) = 90.6 [cm-1] --> T_1u G_15 G_4- I
freq ( 10 - 12) = 145.3 [cm-1] --> T_1u G_15 G_4- I
freq ( 13 - 15) = 152.2 [cm-1] --> T_1u G_15 G_4- I
freq ( 16 - 18) = 156.3 [cm-1] --> T_2u G_25 G_5-
freq ( 19 - 21) = 165.3 [cm-1] --> T_1u G_15 G_4- I
freq ( 22 - 24) = 170.0 [cm-1] --> T_1u G_15 G_4- I
freq ( 1 - 3) = 36.6 [cm-1] --> T_1u G_15 G_4- I
freq ( 4 - 6) = 90.3 [cm-1] --> T_2u G_25 G_5-
freq ( 7 - 9) = 90.6 [cm-1] --> T_1u G_15 G_4- I
freq ( 10 - 12) = 145.3 [cm-1] --> T_1u G_15 G_4- I
freq ( 13 - 15) = 152.2 [cm-1] --> T_1u G_15 G_4- I
freq ( 16 - 18) = 156.3 [cm-1] --> T_2u G_25 G_5-
freq ( 19 - 21) = 165.3 [cm-1] --> T_1u G_15 G_4- I
freq ( 22 - 24) = 170.0 [cm-1] --> T_1u G_15 G_4- I
PHONON : 37m26.06s CPU 41m53.10s WALL
INITIALIZATION:
INITIALIZATION:
phq_setup : 0.04s CPU 0.04s WALL ( 1 calls)
phq_init : 11.31s CPU 11.80s WALL ( 1 calls)
phq_init : 11.31s CPU 11.80s WALL ( 1 calls)
set_drhoc : 0.41s CPU 0.41s WALL ( 3 calls)
init_vloc : 0.01s CPU 0.01s WALL ( 1 calls)
@ -574,32 +574,32 @@
dvanqq : 0.79s CPU 0.79s WALL ( 1 calls)
drho : 9.66s CPU 10.14s WALL ( 1 calls)
cmpt_qdipol : 0.00s CPU 0.00s WALL ( 1 calls)
DIELECTRIC CONSTANT AND EFFECTIVE CHARGES:
solve_e : 231.28s CPU 260.53s WALL ( 1 calls)
dielec : 0.01s CPU 0.03s WALL ( 1 calls)
zstar_eu : 45.23s CPU 48.31s WALL ( 1 calls)
DYNAMICAL MATRIX:
dynmat0 : 0.50s CPU 0.52s WALL ( 1 calls)
phqscf : 1957.25s CPU 2191.24s WALL ( 1 calls)
dynmatrix : 0.01s CPU 0.01s WALL ( 1 calls)
phqscf : 1957.25s CPU 2191.24s WALL ( 1 calls)
solve_linter : 1954.55s CPU 2188.36s WALL ( 8 calls)
drhodv : 2.69s CPU 2.76s WALL ( 8 calls)
dynmat0 : 0.50s CPU 0.52s WALL ( 1 calls)
dynmat_us : 0.19s CPU 0.19s WALL ( 1 calls)
d2ionq : 0.03s CPU 0.03s WALL ( 1 calls)
dynmatcc : 0.28s CPU 0.29s WALL ( 1 calls)
dynmat_us : 0.19s CPU 0.19s WALL ( 1 calls)
addusdynmat : 0.00s CPU 0.00s WALL ( 1 calls)
phqscf : 1957.25s CPU 2191.24s WALL ( 1 calls)
solve_linter : 1954.55s CPU 2188.36s WALL ( 8 calls)
solve_linter : 1954.55s CPU 2188.36s WALL ( 8 calls)
dvqpsi_us : 21.65s CPU 23.86s WALL ( 960 calls)
ortho : 8.57s CPU 9.23s WALL ( 3480 calls)
@ -613,27 +613,27 @@
newdq : 4.06s CPU 4.12s WALL ( 57 calls)
adddvscf : 4.46s CPU 4.63s WALL ( 2880 calls)
drhodvus : 0.03s CPU 0.04s WALL ( 8 calls)
dvqpsi_us : 21.65s CPU 23.86s WALL ( 960 calls)
dvqpsi_us_on : 5.03s CPU 5.22s WALL ( 960 calls)
cgsolve : 1933.54s CPU 2143.85s WALL ( 3480 calls)
ch_psi : 1855.46s CPU 2067.24s WALL ( 107294 calls)
ch_psi : 1855.46s CPU 2067.24s WALL ( 107294 calls)
h_psiq : 1589.26s CPU 1774.95s WALL ( 107294 calls)
last : 237.95s CPU 255.04s WALL ( 107294 calls)
h_psiq : 1589.26s CPU 1774.95s WALL ( 107294 calls)
firstfft : 703.09s CPU 762.54s WALL ( 2709650 calls)
secondfft : 638.03s CPU 724.92s WALL ( 2709650 calls)
add_vuspsi : 63.87s CPU 63.75s WALL ( 107294 calls)
incdrhoscf : 65.39s CPU 75.73s WALL ( 3480 calls)
addusdbec : 3.32s CPU 3.34s WALL ( 3960 calls)
drhodvus : 0.03s CPU 0.04s WALL ( 8 calls)
General routines
calbec : 156.15s CPU 168.19s WALL ( 235788 calls)
fft : 3.34s CPU 3.86s WALL ( 3904 calls)
@ -641,12 +641,12 @@
fftw : 1426.30s CPU 1568.29s WALL ( 5903780 calls)
davcio : 3.55s CPU 34.64s WALL ( 16934 calls)
write_rec : 0.13s CPU 1.76s WALL ( 65 calls)
PHONON : 37m26.06s CPU 41m53.10s WALL
This run was terminated on: 15:37: 1 14Sep2016
This run was terminated on: 15:37: 1 14Sep2016
=------------------------------------------------------------------------------=
JOB DONE.

2
example/NaCl-QE/disp.yaml
View File

@ -206,4 +206,4 @@ points:
mass: 35.453000
- symbol: Cl # 64
coordinates: [ 0.500000000000000, 0.500000000000000, 0.750000000000000 ]
mass: 35.453000
mass: 35.453000

25452
example/NaCl-VASPdfpt/OUTCAR
View File

File diff suppressed because it is too large Load Diff

2
example/NaCl-VASPdfpt/POSCAR
View File

@ -1,4 +1,4 @@
Na Cl
Na Cl
1.0
11.3806029523513423 0.0000000000000000 0.0000000000000000
0.0000000000000000 11.3806029523513423 0.0000000000000000

4
example/NaCl-VASPdfpt/POSCAR-unitcell
View File

@ -1,5 +1,5 @@
Na Cl
1.00000000000000
Na Cl
1.00000000000000
5.6903014761756712 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.6903014761756712 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.6903014761756712

16
example/NaCl-abinit/supercell-001.out
View File

@ -1,8 +1,8 @@
.Version 7.8.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu4.8 computer)
.Version 7.8.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu4.8 computer)
.Copyright (C) 1998-2014 ABINIT group .
.Copyright (C) 1998-2014 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
@ -16,7 +16,7 @@
.Starting date : Thu 30 Oct 2014.
- ( at 09h13 )
- input file -> NaCl.in
- output file -> NaCl.out
- root for input files -> NaCli
@ -47,10 +47,10 @@ _ WF disk file : 18.903 Mbytes ; DEN or POT disk file : 44.497 Mbytes.
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- outvars: echo of selected default values
- accesswff0 = 0 , fftalg0 =112 , wfoptalg0 = 10
-
- outvars: echo of global parameters not present in the input file
- outvars: echo of global parameters not present in the input file
- max_nthreads = 0
-
-outvars: echo values of preprocessed input variables --------
@ -1012,7 +1012,7 @@ _setup2: Arith. and geom. avg. npw (full set) are 4301.000 4301.000
== END DATASET(S) ==============================================================
================================================================================
-outvars: echo values of variables after computation --------
accesswff 1
acell 1.0000000000E+00 1.0000000000E+00 1.0000000000E+00 Bohr
@ -1407,7 +1407,7 @@ P mkmem 1
M. Torrent, M.J. Verstraete, G. Zerah, J.W. Zwanziger
Computer Phys. Comm. 180, 2582-2615 (2009).
Comment : the third generic paper describing the ABINIT project.
Note that a version of this paper, that is not formatted for Computer Phys. Comm.
Note that a version of this paper, that is not formatted for Computer Phys. Comm.
is available at http://www.abinit.org/about/ABINIT_CPC_v10.pdf .
The licence allows the authors to put it on the Web.

16
example/NaCl-abinit/supercell-002.out
View File

@ -1,8 +1,8 @@
.Version 7.8.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu4.8 computer)
.Version 7.8.2 of ABINIT
.(MPI version, prepared for a x86_64_linux_gnu4.8 computer)
.Copyright (C) 1998-2014 ABINIT group .
.Copyright (C) 1998-2014 ABINIT group .
ABINIT comes with ABSOLUTELY NO WARRANTY.
It is free software, and you are welcome to redistribute it
under certain conditions (GNU General Public License,
@ -16,7 +16,7 @@
.Starting date : Thu 30 Oct 2014.
- ( at 09h47 )
- input file -> NaCl.in
- output file -> NaCl.out
- root for input files -> NaCli
@ -47,10 +47,10 @@ _ WF disk file : 18.903 Mbytes ; DEN or POT disk file : 44.497 Mbytes.
------------- Echo of variables that govern the present computation ------------
--------------------------------------------------------------------------------
-
- outvars: echo of selected default values
- outvars: echo of selected default values
- accesswff0 = 0 , fftalg0 =112 , wfoptalg0 = 10
-
- outvars: echo of global parameters not present in the input file
- outvars: echo of global parameters not present in the input file
- max_nthreads = 0
-
-outvars: echo values of preprocessed input variables --------
@ -1016,7 +1016,7 @@ _setup2: Arith. and geom. avg. npw (full set) are 4301.000 4301.000
== END DATASET(S) ==============================================================
================================================================================
-outvars: echo values of variables after computation --------
accesswff 1
acell 1.0000000000E+00 1.0000000000E+00 1.0000000000E+00 Bohr
@ -1415,7 +1415,7 @@ P mkmem 1
M. Torrent, M.J. Verstraete, G. Zerah, J.W. Zwanziger
Computer Phys. Comm. 180, 2582-2615 (2009).
Comment : the third generic paper describing the ABINIT project.
Note that a version of this paper, that is not formatted for Computer Phys. Comm.
Note that a version of this paper, that is not formatted for Computer Phys. Comm.
is available at http://www.abinit.org/about/ABINIT_CPC_v10.pdf .
The licence allows the authors to put it on the Web.

10
example/NaCl-castep/FORCE_SETS
View File

@ -1,7 +1,7 @@
64
2
64
2
1
1
0.0100000000000000 -0.0000000000000000 0.0000000000000000
-0.0209792188 0.0000001562 -0.0000001563
0.0030307813 0.0000001562 -0.0000001563
@ -68,7 +68,7 @@
0.0002007812 0.0000001562 -0.0000001563
-0.0002092188 0.0000001562 0.0000098438
33
33
0.0100000000000000 -0.0000000000000000 0.0000000000000000
-0.0000604687 -0.0004000000 -0.0004006250
-0.0000704687 0.0004100000 0.0004093750
@ -133,4 +133,4 @@
-0.0000004687 0.0002100000 0.0000093750
-0.0000204687 -0.0002000000 -0.0000006250
-0.0000204687 -0.0002200000 -0.0000006250
-0.0000104687 0.0002100000 -0.0000006250
-0.0000104687 0.0002100000 -0.0000006250

12
example/NaCl-castep/README
View File

@ -1,16 +1,16 @@
This is step-by-step example how to calculate phonon dispertion with CASTEP.
1. Generate supercell based on structrural parameters given in unitcell.cell
1. Generate supercell based on structrural parameters given in unitcell.cell
file by running:
% phonopy -d --dim="2 2 2" --castep -c unitcell.cell
In this example file unitcell.cell contains initial spin values in positions_frac BLOCK.
In this example file unitcell.cell contains initial spin values in positions_frac BLOCK.
As well as the value of the U parameter in LDA+U approximation.
2. Use make_displ_dirs.sh bash script to make directories with input files needed to
calculate FORCES for supercells.
2. Use make_displ_dirs.sh bash script to make directories with input files needed to
calculate FORCES for supercells.
% make_displ_dirs.sh supercell.param tail.cell
Please note file supercell.param is the standart CASTEP file with paremeters (convergence
Please note file supercell.param is the standart CASTEP file with paremeters (convergence
criteria, Ecut, functional name etc.). The file with name tail.cell contains k-mesh
description, U parameter value, symmetry operation E, and name of pseudopotential.
@ -20,4 +20,4 @@ description, U parameter value, symmetry operation E, and name of pseudopotenti
% phonopy --castep -f displ-001/supercell.castep displ-002/supercell.castep
5. Finally plot phonon bandstructure by running the following command:
% phonopy --castep -c unitcell.cell -p band.conf
% phonopy --castep -c unitcell.cell -p band.conf

2
example/NaCl-castep/band.conf
View File

@ -1,4 +1,4 @@
DIM = 2 2 2
PRIMITIVE_AXIS = 0.0 0.5 0.5 0.5 0.0 0.5 0.5 0.5 0.0
BAND = 0.0 0.0 0.0 0.5 0.0 0.0 0.5 0.5 0.0 0.0 0.0 0.0 0.5 0.5 0.5
NAC = .TRUE.
NAC = .TRUE.

1
example/NaCl-castep/tail.cell
View File

@ -23,4 +23,3 @@ SYMMETRY_TOL : 0.000001
Na ../Na.upf
Cl ../Cl.upf
%ENDBLOCK SPECIES_POT

3
example/NaCl-castep/unitcell.cell
View File

@ -4,7 +4,7 @@
ANG
5.55590303034721 -0.230202827763682E-54 0.230202827763682E-54
-0.230202827763682E-54 5.55590303034721 0.230202827763682E-54
0.230202827763682E-54 0.230202827763682E-54 5.55590303034721
0.230202827763682E-54 0.230202827763682E-54 5.55590303034721
%ENDBLOCK lattice_cart
%BLOCK cell_constraints
@ -1000,4 +1000,3 @@ SYMMETRY_TOL : 0.001000
kpoint_mp_grid : 6 6 6
kpoint_mp_offset : 0.500000000000000 0.500000000000000 0.500000000000000

2
example/NaCl-gruneisen/NaCl-0.995/BORN
View File

@ -1,4 +1,4 @@
# epsilon and Z* of atoms 1 5
2.48825992 0.00000000 0.00000000 0.00000000 2.48825992 0.00000000 0.00000000 0.00000000 2.48825992
1.10127737 0.00000000 0.00000000 0.00000000 1.10127737 0.00000000 0.00000000 0.00000000 1.10127737
-1.10127737 0.00000000 0.00000000 0.00000000 -1.10127737 0.00000000 0.00000000 0.00000000 -1.10127737
-1.10127737 0.00000000 0.00000000 0.00000000 -1.10127737 0.00000000 0.00000000 0.00000000 -1.10127737

8
example/NaCl-gruneisen/NaCl-0.995/FORCE_SETS
View File

@ -1,7 +1,7 @@
64
2
64
2
1
1
0.0100000000000000 0.0000000000000000 0.0000000000000000
-0.0192589500 -0.0000000000 -0.0000000000
0.0029834700 -0.0000000000 -0.0000000000
@ -68,7 +68,7 @@
0.0002079000 -0.0000000000 -0.0000014200
-0.0002214600 -0.0000000000 -0.0000001100
33
33
0.0100000000000000 0.0000000000000000 0.0000000000000000
-0.0000700900 -0.0004286100 -0.0004286100
-0.0000676900 0.0004295500 0.0004295500

2
example/NaCl-gruneisen/NaCl-0.995/POSCAR-unitcell
View File

@ -13,4 +13,4 @@ Direct
0.5000000000000000 0.5000000000000000 0.5000000000000000
0.5000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 0.5000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 0.5000000000000000
0.0000000000000000 0.0000000000000000 0.5000000000000000

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