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Oleg Peil 2015-02-13 21:58:42 +01:00 committed by Michel Ferrero
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1
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*.pyc

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2 2 1 2
0.1333597E+02 0.2987800E-09 0.2987800E-09 0.2987800E-09 0.5000000E-15
1.000000000000000E-004
CAR
V
22 4 15
0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3703704E-01
1 -31.708596 -31.708596
2 -31.708596 -31.708596
3 -31.708596 -31.708596
4 -31.061475 -31.061475
5 -31.061475 -31.061475
6 -31.061475 -31.061475
7 -0.811953 -0.811953
8 2.607665 2.607665
9 2.607665 2.607665
10 6.002735 6.002735
11 6.002735 6.002735
12 6.002735 6.002735
13 8.013630 8.013630
14 8.013630 8.013630
15 9.361252 9.361252
0.3333333E+00 0.0000000E+00 0.0000000E+00 0.2222222E+00
1 -31.682851 -31.682851
2 -31.539793 -31.539793
3 -31.539793 -31.539793
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6 -31.215960 -31.215960
7 1.216017 1.216017
8 3.394994 3.394994
9 3.771669 3.771669
10 6.050595 6.050595
11 6.050595 6.050595
12 6.457025 6.457025
13 6.771661 6.771661
14 7.383619 7.383619
15 7.383620 7.383620
0.3333333E+00 0.3333333E+00 0.0000000E+00 0.4444444E+00
1 -31.935665 -31.935665
2 -31.782518 -31.782518
3 -31.447103 -31.447103
4 -31.284953 -31.284953
5 -31.234384 -31.234384
6 -31.067231 -31.067231
7 2.201004 2.201004
8 3.123182 3.123182
9 4.809697 4.809697
10 5.123957 5.123957
11 5.357025 5.357025
12 5.853431 5.853431
13 7.260017 7.260017
14 7.862532 7.862532
15 8.230907 8.230907
0.3333333E+00 0.3333333E+00 0.3333333E+00 0.2962963E+00
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29
python/converters/vasp/POSCAR Normal file
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LuNiO3, low-T, P2_1/n
1.0
5.1234998703 0.0000000000 0.0000000000
0.0000000000 5.5089001656 0.0000000000
-0.0166880521 0.0000000000 7.3551808822
Lu Ni O
4 4 12
Cartesian
5.00246185 0.42418531 1.86086070
0.10434997 5.08471473 5.49431996
2.67444393 3.17863552 1.81672974
2.43236789 2.33026481 5.53845136
2.56174994 0.00000000 0.00000000
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0.00000000 2.75445008 0.00000000
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3.11342985 0.20548193 5.47298991
3.55122302 1.72814193 0.39644425
1.55558880 3.78075840 6.95873661
4.12568276 4.48259185 3.28114617
0.98112906 1.02630815 4.07403471
0.93260966 1.11059427 6.94181952
4.17420208 4.39830581 0.41336136
1.60410812 3.86504444 4.09095181
3.50270370 1.64385573 3.26422908

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LuNiO3, low-T, P2_1/n
1.0
5.1234998703 0.0000000000 0.0000000000
0.0000000000 5.5089001656 0.0000000000
-0.0166880521 0.0000000000 7.3551808822
Lu Ni O
4 4 12
Kartesian
5.00246185 0.42418531 1.86086070
0.10434997 5.08471473 5.49431996
2.67444393 3.17863552 1.81672974
2.43236789 2.33026481 5.53845136
2.56174994 0.00000000 0.00000000
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2.55340591 0.00000000 3.67759044
0.00000000 2.75445008 0.00000000
0.56002379 2.54896816 1.79539968
4.54678788 2.95993201 5.55978141
1.99338212 5.30341824 1.88219076
3.11342985 0.20548193 5.47298991
3.55122302 1.72814193 0.39644425
1.55558880 3.78075840 6.95873661
4.12568276 4.48259185 3.28114617
0.98112906 1.02630815 4.07403471
0.93260966 1.11059427 6.94181952
4.17420208 4.39830581 0.41336136
1.60410812 3.86504444 4.09095181
3.50270370 1.64385573 3.26422908

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LuNiO3, low-T, P2_1/n
1.0
5.1234998703 0.0000000000 0.0000000000
0.0000000000 5.5089001656 0.0000000000
-0.0166880521 0.0000000000 7.3551808822
Lu Ni O
4 4 12
Direct
0.977199972 0.077000000 0.252999991
0.022800028 0.922999978 0.746999979
0.522800028 0.577000022 0.247000009
0.477199972 0.423000008 0.753000021
0.500000000 0.000000000 0.000000000
0.000000000 0.500000000 0.500000000
0.500000000 0.000000000 0.500000000
0.000000000 0.500000000 0.000000000
0.110100001 0.462700009 0.244100004
0.889899969 0.537299991 0.755900025
0.389899999 0.962700009 0.255899996
0.610100031 0.037299991 0.744099975
0.693300009 0.313699991 0.053900000
0.306699991 0.686300039 0.946099997
0.806699991 0.813699961 0.446099997
0.193300009 0.186300009 0.553900003
0.185100004 0.201600000 0.943799973
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0.314899981 0.701600015 0.556200027
0.685100019 0.298399985 0.443799973

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# Makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build-2.7
PAPER =
BUILDDIR = build
# Internal variables.
PAPEROPT_a4 = -D latex_paper_size=a4
PAPEROPT_letter = -D latex_paper_size=letter
ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
# the i18n builder cannot share the environment and doctrees with the others
I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext
help:
@echo "Please use \`make <target>' where <target> is one of"
@echo " html to make standalone HTML files"
@echo " dirhtml to make HTML files named index.html in directories"
@echo " singlehtml to make a single large HTML file"
@echo " pickle to make pickle files"
@echo " json to make JSON files"
@echo " htmlhelp to make HTML files and a HTML help project"
@echo " qthelp to make HTML files and a qthelp project"
@echo " devhelp to make HTML files and a Devhelp project"
@echo " epub to make an epub"
@echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
@echo " latexpdf to make LaTeX files and run them through pdflatex"
@echo " text to make text files"
@echo " man to make manual pages"
@echo " texinfo to make Texinfo files"
@echo " info to make Texinfo files and run them through makeinfo"
@echo " gettext to make PO message catalogs"
@echo " changes to make an overview of all changed/added/deprecated items"
@echo " linkcheck to check all external links for integrity"
@echo " doctest to run all doctests embedded in the documentation (if enabled)"
clean:
-rm -rf $(BUILDDIR)/*
html:
$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
dirhtml:
$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
@echo
@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
singlehtml:
$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
@echo
@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
pickle:
$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
@echo
@echo "Build finished; now you can process the pickle files."
json:
$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
@echo
@echo "Build finished; now you can process the JSON files."
htmlhelp:
$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
@echo
@echo "Build finished; now you can run HTML Help Workshop with the" \
".hhp project file in $(BUILDDIR)/htmlhelp."
qthelp:
$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
@echo
@echo "Build finished; now you can run "qcollectiongenerator" with the" \
".qhcp project file in $(BUILDDIR)/qthelp, like this:"
@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/plotools.qhcp"
@echo "To view the help file:"
@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/plotools.qhc"
devhelp:
$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
@echo
@echo "Build finished."
@echo "To view the help file:"
@echo "# mkdir -p $$HOME/.local/share/devhelp/plotools"
@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/plotools"
@echo "# devhelp"
epub:
$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
@echo
@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
latex:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo
@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
@echo "Run \`make' in that directory to run these through (pdf)latex" \
"(use \`make latexpdf' here to do that automatically)."
latexpdf:
$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
@echo "Running LaTeX files through pdflatex..."
$(MAKE) -C $(BUILDDIR)/latex all-pdf
@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
text:
$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
@echo
@echo "Build finished. The text files are in $(BUILDDIR)/text."
man:
$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
@echo
@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
texinfo:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo
@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
@echo "Run \`make' in that directory to run these through makeinfo" \
"(use \`make info' here to do that automatically)."
info:
$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
@echo "Running Texinfo files through makeinfo..."
make -C $(BUILDDIR)/texinfo info
@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
gettext:
$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
@echo
@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
changes:
$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
@echo
@echo "The overview file is in $(BUILDDIR)/changes."
linkcheck:
$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
@echo
@echo "Link check complete; look for any errors in the above output " \
"or in $(BUILDDIR)/linkcheck/output.txt."
doctest:
$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
@echo "Testing of doctests in the sources finished, look at the " \
"results in $(BUILDDIR)/doctest/output.txt."

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*
!/.gitignore

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[General]
EFERMI = -0.6
[Group 1]
SHELLS = 1 2
EMIN = -7.6
EMAX = 2.7
[Shell 1]
# Ni shell
IONS = 5 6 7 8
LSHELL = 2
RTRANSFORM =
0.0 0.0 0.0 0.0 1.0
0.0 0.0 1.0 0.0 0.0
[Shell 2]
# Oxygen shell
IONS = 9..20
LSHELL = 1

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Code Structure
##############
.. toctree::
vaspio
plotools
converter
The program consists of three main parts:
* :doc:`Import of data from VASP files </vaspio>`
* Processing of projectors according to an input config-file
* Conversion of the DFT data to TRIQS h5-file
Import of data from VASP files is implemented in `vaspio.py`. The data
is read from VASP files and then stored in objects in raw format
(i.e. practically no processing is done at this stage).
These objects are then combined into a dictionary which can be easily
passed to other routines.
The basic workflow is prescribed as follows:
* raw data is read from VASP files and passed to the main part
* in the main part the input config-file is read and the projectors are selected and process accordingly
* the processed data is stored into output text-files
* when the TRIQS-converter is requested the data is read from text-files and written into a h5-file in an appropriate format

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# -*- coding: utf-8 -*-
#
# plotools documentation build configuration file, created by
# sphinx-quickstart on Tue Feb 3 20:25:36 2015.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys, os
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.insert(0, os.path.abspath('../../'))
# -- General configuration -----------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
#needs_sphinx = '1.0'
# 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.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.pngmath', 'sphinx.ext.mathjax']
mathjax_path = 'http://cdn.mathjax.org/mathjax/latest/MathJax.js'
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix of source filenames.
source_suffix = '.rst'
# The encoding of source files.
#source_encoding = 'utf-8-sig'
# The master toctree document.
master_doc = 'index'
# General information about the project.
project = u'PLOVasp'
copyright = u'2015, Oleg E. Peil'
# 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 = '0.1'
# The full version, including alpha/beta/rc tags.
release = '0.1'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#language = None
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#today = ''
# Else, today_fmt is used as the format for a strftime call.
#today_fmt = '%B %d, %Y'
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = []
# The reST default role (used for this markup: `text`) to use for all documents.
#default_role = None
# If true, '()' will be appended to :func: etc. cross-reference text.
#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
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
# A list of ignored prefixes for module index sorting.
#modindex_common_prefix = []
# -- Options for HTML output ---------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
html_theme = 'default'
# 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 = {}
# Add any paths that contain custom themes here, relative to this directory.
#html_theme_path = []
# The name for this set of Sphinx documents. If None, it defaults to
# "<project> v<release> documentation".
#html_title = None
# A shorter title for the navigation bar. Default is the same as html_title.
#html_short_title = None
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#html_logo = None
# 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
# 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']
# 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'
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#html_use_smartypants = True
# Custom sidebar templates, maps document names to template names.
#html_sidebars = {}
# Additional templates that should be rendered to pages, maps page names to
# template names.
#html_additional_pages = {}
# If false, no module index is generated.
#html_domain_indices = True
# If false, no index is generated.
#html_use_index = True
# If true, the index is split into individual pages for each letter.
#html_split_index = False
# If true, links to the reST sources are added to the pages.
#html_show_sourcelink = True
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#html_show_sphinx = True
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#html_show_copyright = 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 = ''
# This is the file name suffix for HTML files (e.g. ".xhtml").
#html_file_suffix = None
# Output file base name for HTML help builder.
htmlhelp_basename = 'plotoolsdoc'
# -- Options for LaTeX output --------------------------------------------------
latex_elements = {
# The paper size ('letterpaper' or 'a4paper').
#'papersize': 'letterpaper',
# The font size ('10pt', '11pt' or '12pt').
#'pointsize': '10pt',
# Additional stuff for the LaTeX preamble.
#'preamble': '',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'plotools.tex', u'plotools Documentation',
u'Oleg E. Peil', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#latex_logo = None
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#latex_use_parts = False
# If true, show page references after internal links.
#latex_show_pagerefs = False
# If true, show URL addresses after external links.
#latex_show_urls = False
# Documents to append as an appendix to all manuals.
#latex_appendices = []
# If false, no module index is generated.
#latex_domain_indices = True
# -- Options for manual page output --------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
('index', 'plotools', u'plotools Documentation',
[u'Oleg E. Peil'], 1)
]
# If true, show URL addresses after external links.
#man_show_urls = False
# -- Options for Texinfo output ------------------------------------------------
# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
# dir menu entry, description, category)
texinfo_documents = [
('index', 'plotools', u'plotools Documentation',
u'Oleg E. Peil', 'plotools', 'One line description of project.',
'Miscellaneous'),
]
# Documents to append as an appendix to all manuals.
#texinfo_appendices = []
# If false, no module index is generated.
#texinfo_domain_indices = True
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#texinfo_show_urls = 'footnote'

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Input Config-file
=================
A config-file describes subsets of PLOs that are to be generated.
The PLOs are defined in terms of `shells` determined uniquely by an orbital
number `l` and a set of ions (nomrmally, of the same sort).
The shells are further combined into `groups` such that PLO in each group
are orthogonalized together. This allows to create several mutually orthogonal
subsets of PLOs. A group is characterized by a single projection energy window.
A config-file contains three types of sections:
- **[General]** : providing information applicable to all projected shells
(e.g. Fermi level)
- **[Shell <Ns>]** : each section like this describes a PLO shell, with the index
`Ns` used for referencing
- **[Group <Ng>]** : describes shell groups
..
It must contain at least one group defined by a section `[PLO Group 1]`.
There is also an optional section `[General]` containing options that concern
all PLO groups (e.g. `k`-mesh properties).
The format requirements are relatively flexible. A config-file must contain
at least one `[Shell]` section. If there is only one shell defined, it is possible
to specify the energy window by providing parameters `EMIN`, `EMAX` (see below)
right in this section, in which case a group
will be created automatically and the `[Group]` section can be omitted.
If, nevertheless, a group referencing the single shell is explicitly given
the energy window parameters provided in the `[Group]` have higher priority
and in case of conflict with `[Shell]` section a warning is issued.
An example of a config-file:
.. literalinclude:: adv_example.cfg
A config file must contain at least on group of PLOs. Each group is described
by a set of ions to which the projectors are applied, an atomic shell number
(:math:`l = 0,1,2,3` for `s,p,d,f`, respectively), and an energy window defining
the subset of bands from which the projectors are constructed.
In addition, one can define a real or complex transformation, which allows one
to produce projectors in a basis set different from the original one.
Below, the format of config-file is described.
All option names are case-insensitive.
Required parameters
-------------------
- **IONS**: ion indices as defined in POSCAR files
- **LSHELL**: atomic shell (values 0, 1, 2, 3 for `s,p,d,f` orbitals, respectively)
- **EMIN**, **EMAX**: the bottom and top of the energy window with respect to the Fermi level
Optional parameters
-------------------
- **RTRANSFORM**, **CTRANSFORM**: real or complex transformation matrix used to produce projectors
in a different basis; the number of columns is determined by the size of the atomic shell

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TRIQS Converter
###############
The converter provides an interface between a DFT code and TRIQS solvers.

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[General]
[PLO Group 1]
IONS = 5 6 7 8
EMIN = -0.6
EMAX = 2.7
LSHELL = 2
RTRANSFORM =
0.0 0.0 0.0 0.0 1.0
0.0 0.0 1.0 0.0 0.0

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.. plotools documentation master file, created by
sphinx-quickstart on Tue Feb 3 20:25:36 2015.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to PLOVasp's documentation!
====================================
PLOVasp documentation.
Contents:
.. toctree::
:maxdepth: 1
users_guide
code_struct
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

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.. highlight:: python
PLO tools
#########
Introduction
============
This set of tools is intended for processing of raw projectors read
from VASP. One of the main tasks is to generate an orthonormalized subset
of PLOs constructed according to the :doc:`config-file </config>`.
As an input this sub-library accepts a dictionary with parameters from
the config-file and a dictionary containing VASP-data objects.
Generally, the following workflow is adopted:
* The VASP data is checked for consistency.
* For each group of PLOs a corresponding subset of projectors and eigenvalues
is selected according to the config-file.
* The selected subsets of projectors are orthogonalized. In general, there are different ways
how it can be done (see :ref:`Orthogonalization<ortho>`).
Initial Processing
==================
Consistency check
-----------------
The purpose of a consistency check is to make sure that the VASP data passed
to PLOtools are complete and originating from the same calculation.
In particular, the following things are supposed to be checked:
* the basic dimensions, such as the number of bands, number of `k`-points, etc.,
are consistent for all data
* the `k`-point mesh are read both the IBZKPT and EIGENVAL and it is worth checking
that both sets are coinciding
* in case tetrahedron data is read from IBZKPT, the tetrahedron volume must be related
to the total volume of the unit cell as derived from POSCAR
* parameters in the config-file should pass trivial checks such as that the ion
list does not contain non-existing ions (boundary check for ion indices)
.. function:: check_vasp_data_consistency(conf_pars, vasp_data)
**Parameters**:
- *conf_pars* (dict) : dictionary of input parameters from conf-file
- *vasp_data* (dict) : dictionary containing all VASP data
**Returns**:
*None*
**Raises**:
A meaningful exception indicating an inconsistency in the input data
Selecting projector subsets
---------------------------
.. autoclass:: plotools.ProjectorSet
:members:
The class is using a helper function `select_bands()` for selecting a subset of bands.
.. function:: select_bands(eigvals, emin, emax)
**Parameters**:
- *eigvals* (numpy.array) : array of eigenvalues
- *emin*, *emax* (float) : energy window
**Returns**:
*ib_win*, *nb_min*, *nb_max* (numpy.array[int], int, int) :
lowest and highest indices of the selected bands
.. _ortho:
Orthogonalization
=================
At the second stage the selected projectors are orthogonalized (orthonormalized).
Orthogonalization can be performed in different ways if projection is made
on several ions or if several correlated shells per ion are considered.
In the case of several correlated ions per unit cell (and one correlated shell per ion)
at least two options can be considered:
#. Projectors are normalized for each ion separetely. In this case, corresponding
Wannier functions for different ions are generally not orthogonal.
#. Projectors are normalized for all ions in the unit cell simultaneously. This
ensures that the Wannier functions for different ions are mutually orthogonal.
If more than one shells is considered (say, `p` and `d` orbitals), the
normalization can be imposed either for a combined set of shells or for each shell
separately.
The way the normalization of a PLO group is done is controlled by two flags:
- **NORMALIZE** (True/False) : indicates whether the PLO group is normalized (True by default)
- **NORMION** (True/False) : indicates whether the PLO group is normalized on a per-ion basis
If there are several PLO groups defined, the convention is the following: All PLO groups
marked with `NORMALIZE = True` are orthogonalized with respect to each other.

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User's Guide
############
.. toctree::
config
Here the user interface of PLOVasp is described.

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.. sec_vaspio
VASP input-output
#################
The following VASP are used by PLOtools:
* PLOCAR: raw projectors generated by VASP-PLO interface
* EIGENVAL: Kohn-Sham eigenvalues as well as `k`-points with weights
* IBZKPT: `k`-point data (:math:`\Gamma`)

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Processing tools for PLOs generated by VASP.
The main purpose of this set of tools is to process raw data
generated by VASP and to convert data to the TRIQS format. The raw data
is read from files:
POSCAR (atomic positions)
EIGVAL (eignevalues)
PLOCAR (non-orthogonalized PLOs and Fermi-weights)
IBZKPT (k-points and tetrahedra)
An appropriate set of orthogonalized projectors is defined by
parameters defined in the config file (config-like syntax).
The config-file allows to define several groups of projectors.
Structure of PLOtools:
vaspio.py: reading of VASP-generated files
vaspio.py:
All VASP data are represented by objects which contain data read
from corresponding files. These objects will subsequently be used to
handle the data and convert it into a more functional internal representation.
Functions
read_lines(filename): generator yielding lines from a file <filename>
Classes:
Plocar: raw PLO data from PLOCAR file;
the data itself is read using an auxiliary C-routine 'read_plocar'
Poscar: structure data from POSCAR file
Kpoints: k-point data from IBZKPT file
note that k-point data is also contained in EIGENVAL file;
the two k-point sets will be checked for consistency.
Eigenval: Kohn-Sham eigenvalues as well as k-points with weights
Symmcar: symmetry operations stored by VASP into SYMMCAR file
ploortho.py (or projectors.py)
Set of routines for processing projectors. The functionality includes:
-- selecting a proper subset of non-orthogonalized projectors from the raw VASP input
-- transforming and orthogonalizing projectors
-- calculating DFT density matrix and local Hamiltonian
General design:
Input data: conf_pars (output of 'parse_input()'), VASP file descriptors (Eigenval, Plocar, etc.)
* A projector for a given k-point is described by class 'Projector'
PLOs project on a set or orbitals and a set of ions.
* Projector set is a container of 'Projector' objects.
Out of optimization purposes the projectors are stored in a multi-dimensional
array. A view in terms of Projector objects is, however, possible.

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makefile
*.so
*.o
*.pyc

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#include <Python.h>
#include <arrayobject.h>
#include <complex.h>
#include <string.h>
#define MAX_STR_LEN 512
static int verbose = 1;
typedef struct {
int nion;
int ns;
int nk;
int nb;
int nlmmax;
int nc_flag;
int isdouble;
} t_params;
static PyObject* io_read_plocar(PyObject *self, PyObject *args);
PyObject* create_par_dictionary(t_params* p);
PyArrayObject* create_plo_array(t_params* p);
PyArrayObject* create_ferw_array(t_params* p);
int read_arrays(FILE* fh, t_params* p, PyArrayObject* py_plo, PyArrayObject* py_ferw);
// Python module descriptor
static PyMethodDef c_plocar_io[] = {
{"read_plocar", io_read_plocar, METH_VARARGS,
"Reads from PLOCAR and returns PLOs"},
{NULL, NULL, 0, NULL}
};
PyMODINIT_FUNC
initc_plocar_io()
{
(void) Py_InitModule("c_plocar_io", c_plocar_io);
import_array();
}
/*
Main function.
Reads data from the specified file (default is 'PLOCAR')
and returns it as a Python tuple.
*/
static PyObject *
io_read_plocar(PyObject *self, PyObject *args)
{
PyArrayObject *py_plo = NULL;
PyArrayObject *py_ferw = NULL;
PyObject *par_dict = NULL;
PyObject *ret_tuple = NULL;
char *fname = "PLOCAR";
char errmsg[MAX_STR_LEN] = {"\0"};
FILE* fh;
int isdouble, prec;
t_params params;
if(!PyArg_ParseTuple(args, "|s", &fname))
return NULL;
if(verbose)
printf(" Reading PLO data from file: %s\n", fname);
//
// Read the header
//
fh = fopen(fname, "r");
if(fh == NULL) {
// Treat this error separately because no clean-up is necessary
strncpy(errmsg, "Error opening PLOCAR\n", MAX_STR_LEN);
strncat(errmsg, strerror(errno), MAX_STR_LEN);
PyErr_SetString(PyExc_IOError, errmsg);
return NULL;
}
if(!fread(&prec, 4, 1, fh)) goto ioerror;
if(!fread(&params.nion, 4, 1, fh)) goto ioerror;
if(!fread(&params.ns, 4, 1, fh)) goto ioerror;
if(!fread(&params.nk, 4, 1, fh)) goto ioerror;
if(!fread(&params.nb, 4, 1, fh)) goto ioerror;
if(!fread(&params.nlmmax, 4, 1, fh)) goto ioerror;
if(!fread(&params.nc_flag, 4, 1, fh)) goto ioerror;
switch(prec) {
case 8:
params.isdouble = 1;
if(verbose) printf(" Data in double precision\n");
break;
case 4:
params.isdouble = 0;
if(verbose) printf(" Data in single precision\n");
break;
default:
PyErr_SetString(PyExc_ValueError,
"Error reading PLOCAR: only 'prec = 4, 8' are supported");
goto error;
}
if(verbose) {
printf(" nion: %d\n", params.nion);
printf(" ns: %d\n", params.ns);
printf(" nk: %d\n", params.nk);
printf(" nb: %d\n", params.nb);
printf(" nlmmax: %d\n", params.nlmmax);
printf(" nc_flag: %d\n", params.nc_flag);
}
//
// Create parameter dictionary
//
par_dict = create_par_dictionary(&params);
//
// Create PLO and Fermi-weight arrays
//
py_plo = create_plo_array(&params);
py_ferw = create_ferw_array(&params);
//
// Read the data from file
//
if(read_arrays(fh, &params, py_plo, py_ferw)) goto ioerror;
//
// Create return tuple
//
ret_tuple = PyTuple_New(3);
if(PyTuple_SetItem(ret_tuple, 0, par_dict) < 0) {
PyErr_SetString(PyExc_ValueError,
"Error adding element to the return tuple (parameter dictionary)");
goto error;
}
if(PyTuple_SetItem(ret_tuple, 1, (PyObject *)py_plo) < 0) {
PyErr_SetString(PyExc_ValueError,
"Error adding element to the return tuple (PLO array)");
goto error;
}
if(PyTuple_SetItem(ret_tuple, 2, (PyObject *)py_ferw) < 0) {
PyErr_SetString(PyExc_ValueError,
"Error adding element to the return tuple (Fermi-weight array)");
goto error;
}
// Py_DECREF(par_dict);
fclose(fh);
return ret_tuple;
//
// Handle IO-errors
//
ioerror:
printf("Error number: %d\n", errno);
if(feof(fh)) {
PyErr_SetString(PyExc_IOError, "End-of-file reading PLOCAR");
}
else {
strncpy(errmsg, "Error reading PLOCAR\n", MAX_STR_LEN);
strncat(errmsg, strerror(errno), MAX_STR_LEN);
PyErr_SetString(PyExc_IOError, errmsg);
}
//
// Clean-up after an error
//
error:
fclose(fh);
Py_XDECREF(par_dict);
Py_XDECREF(py_plo);
Py_XDECREF(py_ferw);
Py_XDECREF(ret_tuple);
return NULL;
}
//
// Auxiliary functions
//
PyObject*
create_par_dictionary(t_params* p)
{
PyObject *par_dict = PyDict_New();
PyDict_SetItemString(par_dict, "nion", PyInt_FromLong((long)p->nion));
PyDict_SetItemString(par_dict, "ns", PyInt_FromLong((long)p->ns));
PyDict_SetItemString(par_dict, "nk", PyInt_FromLong((long)p->nk));
PyDict_SetItemString(par_dict, "nb", PyInt_FromLong((long)p->nb));
PyDict_SetItemString(par_dict, "nc_flag", PyInt_FromLong((long)p->nc_flag));
return par_dict;
}
PyArrayObject*
create_plo_array(t_params* p)
{
double complex *plo;
npy_intp *dims;
int ntot = p->nion * p->ns * p->nk * p->nb * p->nlmmax;
int ndim = 5;
plo = (double complex*)malloc(ntot * sizeof(double complex));
memset(plo, 0, ntot * sizeof(double complex));
dims = (npy_intp *)malloc(ndim * sizeof(npy_intp));
dims[0] = p->nion;
dims[1] = p->ns;
dims[2] = p->nk;
dims[3] = p->nb;
dims[4] = p->nlmmax;
return (PyArrayObject *)PyArray_SimpleNewFromData(ndim, dims, NPY_CDOUBLE, plo);
}
PyArrayObject*
create_ferw_array(t_params* p)
{
double *ferw;
npy_intp *dims;
int ntot = p->nion * p->ns * p->nk * p->nb;
int ndim = 4;
ferw = (double *)malloc(ntot * sizeof(double));
memset(ferw, 0, ntot * sizeof(double));
dims = (npy_intp *)malloc(ndim * sizeof(npy_intp));
dims[0] = p->nion;
dims[1] = p->ns;
dims[2] = p->nk;
dims[3] = p->nb;
return (PyArrayObject *)PyArray_SimpleNewFromData(ndim, dims, NPY_DOUBLE, ferw);
}
int read_arrays(FILE* fh, t_params* p, PyArrayObject* py_plo, PyArrayObject* py_ferw)
{
double complex *plo;
double *ferw;
int strd_plo[5], strd_ferw[4];
int ion, ik, ib, is, ilm;
int nlm;
long ind1, ind2;
float rtmp;
float complex rbuf[50];
double dtmp;
double complex dbuf[50];
// Initialize array pointers and strides
plo = (double complex *)py_plo->data;
strd_plo[0] = py_plo->strides[0] / sizeof(double complex);
strd_plo[1] = py_plo->strides[1] / sizeof(double complex);
strd_plo[2] = py_plo->strides[2] / sizeof(double complex);
strd_plo[3] = py_plo->strides[3] / sizeof(double complex);
strd_plo[4] = py_plo->strides[4] / sizeof(double complex);
ferw = (double *)py_ferw->data;
strd_ferw[0] = py_ferw->strides[0] / sizeof(double);
strd_ferw[1] = py_ferw->strides[1] / sizeof(double);
strd_ferw[2] = py_ferw->strides[2] / sizeof(double);
strd_ferw[3] = py_ferw->strides[3] / sizeof(double);
ind1 = 0;
ind2 = 0;
for(ion = 0; ion < p->nion; ion++) {
fread(&nlm, 4, 1, fh);
// printf(" nlm = %d\n", nlm);
for(is = 0; is < p->ns; is++)
for(ik = 0; ik < p->nk; ik++)
for(ib = 0; ib < p->nb; ib++) {
ind1 = strd_ferw[0] * ion + strd_ferw[1] * is + strd_ferw[2] * ik + strd_ferw[3] * ib;
ind2 = strd_plo[0] * ion + strd_plo[1] * is + strd_plo[2] * ik + strd_plo[3] * ib;
if(p->isdouble) {
if(fread(&dtmp, sizeof(double), 1, fh) < 1) goto error;
if(fread(dbuf, sizeof(double complex), nlm, fh) < nlm) goto error;
ferw[ind1] = dtmp;
// printf("%5d %5d %5d %5d %lf\n", ion, is, ik, ib, dtmp);
memcpy(plo + ind2, dbuf, nlm * sizeof(double complex));
}
else {
if(fread(&rtmp, sizeof(float), 1, fh) < 1) goto error;
if(fread(rbuf, sizeof(float complex), nlm, fh) < nlm) goto error;
ferw[ind1] = (double)rtmp;
// printf("%5d %5d %5d %5d %f\n", ion, is, ik, ib, rtmp);
// In this case destination and source arrays are not compatible,
// we have to copy element-wise
for(ilm = 0; ilm < nlm; ilm++) {
plo[ind2 + ilm] = (double complex)rbuf[ilm];
// printf("%5d %5d %f\n", ilm, ind2 + ilm, rbuf[ilm]);
}
} // if p->isdouble
}
}
return 0;
error:
return -1;
}

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CC=gcc
INC_FLAGS=-I/opt/local/Library/Frameworks/Python.framework/Versions/Current/include/python2.7 -I/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7/site-packages/numpy/core/include/numpy
LIB_FLAGS=-L/opt/local/Library/Frameworks/Python.framework/Versions/Current/lib/python2.7
c_plocar_io.so: c_plocar_io.c
$(CC) $< -fPIC -shared -o $@ $(INC_FLAGS) $(LIB_FLAGS) -lpython2.7
cp $@ ..

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import numpy as np
class Projector:
"""
Class describing a local-orbital projector.
"""
def __init__(self, matrix, ib1=1, ib2=None, nion=1):
self.p_matrix = matrix.astype(np.complex128)
self.norb, self.nb = matrix.shape
self.nion = nion
self.ib1 = ib1 - 1
if not ib2 is None:
self.ib2 = ib2 - 1
else:
self.ib2 = self.nb - 1
def project_up(self, mat):
return np.dot(self.p_matrix.conj().T, np.dot(mat, self.p_matrix))
def project_down(self, mat):
assert mat.shape == (self.nb, self.nb), " Matrix must match projector in size"
return np.dot(self.p_matrix, np.dot(mat, self.p_matrix.conj().T))
def orthogonalize(self):
"""
Orthogonalizes a projector.
Returns an overlap matrix and its eigenvalues for initial projectors.
"""
self.p_matrix, overlap, over_eig = orthogonalize_projector(self.p_matrix)
return (overlap, over_eig)
################################################################################
# orthogonalize_projector()
################################################################################
def orthogonalize_projector(p_matrix):
"""
Orthogonalizes a projector defined by a rectangular matrix `p_matrix`.
Parameters
----------
p_matrix (numpy.array[complex]) : matrix `Nm x Nb`, where `Nm` is
the number of orbitals, `Nb` number of bands
Returns
-------
Orthogonalized projector matrix, initial overlap matrix and its eigenvalues.
"""
overlap = np.dot(p_matrix, p_matrix.conj().T)
eig, eigv = np.linalg.eigh(overlap)
assert np.all(eig > 0.0), (" Negative eigenvalues of the overlap matrix:"
"projectors are ill-defined")
sqrt_eig = np.diag(1.0 / np.sqrt(eig))
shalf = np.dot(eigv, np.dot(sqrt_eig, eigv.conj().T))
p_ortho = np.dot(shalf, p_matrix)
return (p_ortho, overlap, eig)
################################################################################
# check_vasp_data_consistency()
################################################################################
def check_vasp_data_consistency(vasp_data):
"""
Check the consistency of the VASP data.
"""
pass
################################################################################
# select_bands()
################################################################################
def select_bands(eigvals, emin, emax):
"""
Select a subset of bands lying within a given energy window.
The band energies are assumed to be sorted in an ascending order.
Parameters
----------
eigvals (numpy.array) : all eigenvalues
emin, emax (float) : energy window
Returns
-------
ib_win, nb_min, nb_max :
"""
nk, nband, ns_band = eigvals.shape
ib_win = np.zeros((nk, ns_band, 2), dtype=np.int32)
nb_min = 10000000
nb_max = 0
for isp in xrange(ns_band):
for ik in xrange(nk):
for ib in xrange(nband):
en = eigvals[ik, ib, isp]
if en >= emin:
break
ib1 = ib
for ib in xrange(ib1, nb_max):
en = eigvals[ik, ib, isp]
if en <= emax:
break
ib2 = ib
ib_win[ik, isp, 0] = ib1
ib_win[ik, isp, 1] = ib2
nb_min = min(nb_min, ib1)
nb_max = max(nb_max, ib2)
return ib_win, nb_min, nb_max
################################################################################
#
# class ProjectorSet
#
################################################################################
class ProjectorSet:
"""
Container of projectors defined within a certain energy window.
The constructor selects a subset of projectors according to
the parameters from the config-file (passed in `pars`).
Parameters:
- pars (dict) : dictionary of parameters from the config-file for a given PLO group
- proj_raw (numpy.array) : array of raw projectors
- eigvals (numpy.array) : array of KS eigenvalues
"""
# def __init__(self, proj_set, nb_min, nb_max, ib_win):
# """
# Constructor.
#
# Parameters
# ----------
#
# proj_set (numpy.array) : projector array
# nb_min (int) : the lowest absolute band index
# nb_max (int) : the lowest absolute band index
# ib_win (numpy.array((nk, ns, 2), dtype=int)) : the lowest and highest band indices
# for a given `k`-point
# """
# self.proj_set = proj_set
# self.nb_min = nb_min
# self.nb_max = nb_max
# self.ib_win = ib_win
#################################################################################
# __init__()
#################################################################################
def __init__(self, pars, proj_raw, eigvals):
"""
Constructor
"""
ns = proj_raw.shape[1]
nk, nband, ns_band = eigvals.shape
self.lorb = pars['lshell']
self.lm_l = range(lorb**2, (lorb+1)**2)
nlm = len(self.lm_l)
self.emin = pars['emin']
self.emax = pars['emax']
# Determine the minimum and maximum band numbers
ib_win, nb_min, nb_max = select_bands(eigvals, self.emin, self.emax)
self.ib_win = ib_win
self.nb_min = nb_min
self.nb_max = nb_max
# Set the dimensions of the array
nb_win = self.nb_max - self.nb_min + 1
nion_sel = pars['ion_list'].shape[0]
self.proj_set = np.zeros((nion_sel, ns, nk, nb_win, nlm), dtype=np.complex128)
# Select projectors for a given energy window
for isp in xrange(ns):
for ik in xrange(nk):
# TODO: for non-collinear case something else should be done here
is_b = min(isp, ns_band)
ib1 = self.ib_win[ik, is_b, 0]
ib2 = self.ib_win[ik, is_b, 1] + 1
ib1_win = ib1 - self.nb_min
ib2_win = ib2 - self.nb_min
for ion, ion_sel in enumerate(pars['ion_list']):
self.proj_set[ion, isp, ik, ib1_win:ib2_win, :] = proj_raw[ion_sel, isp, ik, ib1:ib2, self.lm_l]
def generate_ortho_plos(conf_pars, vasp_data):
"""
Parameters
----------
conf_pars (dict) : dictionary of input parameters (from conf-file)
vasp_data (dict) : dictionary of object representing various VASP files
"""
check_vasp_data_consistency(vasp_data)
proj_raw = vaps_data['plocar'].plo
efermi = vasp_data['doscar'].efermi
# eigvals(nktot, nband, ispin) are defined with respect to the Fermi level
eigvals = vasp_data['eigenval'].eigs - efermi
proj_set_l = []
for pars in conf_pars:
proj_set = select_projectors(pars, proj_raw, eigvals)

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import ConfigParser
import numpy as np
import re
import sys
import vaspio
def issue_warning(message):
"""
Issues a warning.
"""
print
print " !!! WARNING !!!: " + message
print
################################################################################
################################################################################
#
# class ConfigParameters
#
################################################################################
################################################################################
class ConfigParameters:
r"""
Class responsible for parsing of the input config-file.
Parameters:
- *sh_required*, *sh_optional* : required and optional parameters of shells
- *gr_required*, *gr_optional* : required and optional parameters of groups
The dictionary contains a mapping of conf-file keywords to
a pair of objects:
1. internal name of a parameter
2. function used to convert an input string into data for a given parameter
"""
self.sh_required = {
'ions': ('ion_list', self.parse_ion_list),
'lshell': ('lshell', int)}
self.sh_optional = {
'rtransform': ('tmatrix', lambda s: self.parse_tmatrix(s, real=True)),
'ctransform': ('tmatrix', lambda s: self.parse_tmatrix(s, real=False))}
self.gr_required = {
'emin': ('emin', float),
'emax': ('emax', float)}
self.gr_optional = {
'normalize' : ('normalize', self.parse_logical),
'normion' : ('normion', self.parse_logical)}
################################################################################
#
# __init__()
#
################################################################################
def __init__(self, input_filename, verbosity=1):
self.verbosity = verbosity
self.cp = ConfigParser.ConfigParser()
self.cp.readfp(open(input_filename, 'r'))
self.conf_pars = {}
#
# Special parsers
#
################################################################################
#
# parse_string_ion_list()
#
################################################################################
def parse_string_ion_list(self, par_str):
"""
The ion list accepts two formats:
1). A list of ion indices according to POSCAR.
2). An element name, in which case all ions with
this name are included.
The second option requires an input from POSCAR file.
"""
try:
l_tmp = map(int, par_str.split())
# Subtract 1 so that VASP indices (starting with 1) are converted
# to Python indices (starting with 0)
ion_list = np.array(l_tmp) - 1
except ValueError:
err_msg = "Only an option with a list of ion indices is implemented"
raise NotImplementedError(err_msg)
return ion_list
################################################################################
#
# parse_string_logical()
#
################################################################################
def parse_string_logical(self, par_str):
"""
Logical parameters are given by string 'True' or 'False'
(case does not matter). In fact, only the first symbol matters so that
one can write 'T' or 'F'.
"""
assert par_str[0] in 'tf', "Logical parameters should be given by either 'True' or 'False'"
return par_str[0] == 't'
################################################################################
#
# parse_parameter_set()
#
################################################################################
def parse_parameter_set(self, section, param_set, exception=False):
"""
Parses required or optional parameter set from a section.
For required parameters `exception=True` must be set.
"""
parsed = {}
for par in param_set.keys():
try:
par_str = self.cp.get(section, par)
except ConfigParser.NoOptionError:
if exception:
message = "Required parameter '%s' not found in section [%s]"%(par, section)
raise ConfigParser.NoOptionError(message)
else:
continue
if self.verbosity > 0:
print " %s = %s"%(par, par_str)
key = param_set[par][0]
parse_fun = param_set[par][1]
parsed[key] = parse_fun(par_str)
return parsed
################################################################################
#
# parse_shells()
#
################################################################################
def parse_shells(self):
"""
Parses all [Shell] sections.
"""
# Find all [Shell] sections
# (note that ConfigParser transforms all names to lower case)
sections = self.cp.sections()
sh_patt = 'shell *([0-9]*)'
ismatch = lambda s: not re.match(sh_patt, s) is None
sec_shells = filter(ismatch, sections)
self.nshells = len(sec_shells)
assert self.nshells > 0, "No projected shells found in the input file"
if self.verbosity > 0:
print
if self.nshells > 1:
print " Found %i projected shells"%(self.nshells)
else:
print " Found 1 projected shell"
# Get shell indices
get_ind = lambda s: int(re.match(sh_patt, s).groups()[0])
try:
sh_inds = map(get_ind, sec_shells)
except ValueError:
raise ValueError("Failed to extract shell indices from a list: %s"%(sec_shells))
self.sh_sections = {ind: sec for ind, sec in sh_inds, sec_shells}
# Check that all indices are unique
assert len(sh_inds) == len(set(sh_inds)), "There must be no shell with the same index!"
# Ideally, indices should run from 1 to <nshells>
# If it's not the case, issue a warning
sh_inds.sort()
if sh_inds != range(1, len(sh_inds) + 1):
issue_warning("Shell indices are not uniform or not starting from 1. "
"This might be an indication of a incorrect setup."
# Parse shell parameters
self.shells = {}
for ind in sh_inds:
self.shells[ind] = {}
section = self.sh_sections[ind]
# Shell required parameters
if self.verbosity > 0:
print
print " Required shell parameters:"
parsed = self.parse_parameter_set(section, self.sh_required, exception=True)
self.shells[ind].update(parsed)
# Shell optional parameters
if self.verbosity > 0:
print
print " Optional shell parameters:"
parsed = self.parse_parameter_set(section, self.sh_optional, exception=False)
self.shells[ind].update(parsed)
# Group required parameters
# Must be given if no group is explicitly specified
# If in conflict with the [Group] section, the latter has a priority
if self.verbosity > 0:
print
print " Required group parameters:"
parsed = self.parse_parameter_set(section, self.gr_required, exception=False)
self.shells[ind].update(parsed)
# Group optional parameters
if self.verbosity > 0:
print
print " Optional group parameters:"
parsed = self.parse_parameter_set(section, self.gr_optional, exception=False)
self.shells[ind].update(parsed)
################################################################################
#
# parse_groups()
#
################################################################################
def parse_groups(self):
"""
Parses [Group] sections.
"""
# Find group sections
sections = self.cp.sections()
gr_patt = 'group *([0-9]*)'
ismatch = lambda s: not re.match(gr_patt, s) is None
sec_groups = filter(ismatch, sections)
self.ngroups = len(sec_groups)
# Special case: no groups is defined
if self.ngroups == 0:
# Check that 'nshells = 1'
assert self.nshells == 1, "At least one group must be defined if there are more than one shells."
# Otherwise create a single group taking group information from [Shell] section
self.groups = [{}]
# Check that the single '[Shell]' section contains enough information
# and move it to the `groups` dictionary
ind = self.sh_sections.keys()[0]
try:
for par in self.gr_required.keys():
key = self.gr_required[par][0]
value = self.shells[ind].pop(key)
self.groups[0][key] = value
except KeyError:
message = "One [Shell] section is specified but no explicit [Group] section is provided."
message += " In this case the [Shell] section must contain all required group information.\n"
message += " Required parameters are: %s"%(self.gr_required.keys())
raise KeyError(message)
# Do the same for optional group parameters, but do not raise an exception
for par in self.gr_required.keys():
try:
key = self.gr_required[par][0]
value = self.shells[ind].pop(key)
self.groups[0][key] = value
except KeyError:
continue
self.groups.update({'shells': [self.shells[ind]]})
################################################################################
#
# Main parser
# parse_logical()
#
################################################################################
def parse_input(self):
"""
Parses input conf-file.
"""
self.parse_shells()
self.parse_groups()
# Output list of dictionaries
output_pars = [{} for isec in xrange(nsections)]
for isec, section in enumerate(sections):
print "Section: %s"%(section)
for par in required.keys():
try:
par_str = cp.get(section, par)
except ConfigParser.NoOptionError:
raise SystemExit("*** Error: Required entry '%s' not found in the input file"%(par))
print " %s: %s"%(par, par_str)
key = required[par][0]
parse_fun = required[par][1]
output_pars[isec][key] = parse_fun(par_str)
print output_pars
print cp.get(section, 'rtransform').strip().split('\n')
return output_pars
if __name__ == '__main__':
narg = len(sys.argv)
if narg < 2:
raise SystemExit(" Usage: python pyconf.py <conf-file> [<path-to-vasp-calcultaion>]")
else:
filename = sys.argv[1]
if narg > 2:
vasp_dir = sys.argv[2]
if vasp_dir[-1] != '/':
vasp_dir += '/'
else:
vasp_dir = './'
# plocar = vaspio.Plocar()
# plocar.from_file(vasp_dir)
# poscar = vaspio.Poscar()
# poscar.from_file(vasp_dir)
# kpoints = vaspio.Kpoints()
# kpoints.from_file(vasp_dir)
eigenval = vaspio.Eigenval()
eigenval.from_file(vasp_dir)
doscar = vaspio.Doscar()
doscar.from_file(vasp_dir)
# pars = parse_input(filename)

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[General]
[PLO Group 1]
IONS = 5 6 7 8
#IONS = Ni
EMIN = -0.6
EMAX = 2.7
LSHELL = 2
RTRANSFORM =
0.0 0.0 0.0 0.0 1.0
0.0 0.0 1.0 0.0 0.0

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import numpy as np
import plocar_io.c_plocar_io as c_plocar_io
def read_lines(filename):
r"""
Generator of lines for a file
Parameters
----------
filename (str) : name of the file
"""
with open(filename, 'r') as f:
for line in f:
yield line
class Plocar:
r"""
Class containing raw PLO data from VASP.
Properties
----------
plo (numpy.array((nion, ns, nk, nb, nlmmax))) : raw projectors
"""
def from_file(self, vasp_dir='./', plocar_filename='PLOCAR'):
r"""
Reads non-normalized projectors from a binary file (`PLOCAR' by default)
generated by VASP PLO interface.
Parameters
----------
vasp_dir (str) : path to the VASP working directory [default = `./']
plocar_filename (str) : filename [default = `PLOCAR']
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
self.params, self.plo, self.ferw = c_plocar_io.read_plocar(vasp_dir + plocar_filename)
class Poscar:
"""
Class containing POSCAR data from VASP.
Properties
----------
nq (int) : total number of ions
ntypes ([int]) : number of ion types
nions (int) : a list of number of ions of each type
a_brav (numpy.array((3, 3), dtype=float)) : lattice vectors
q_types ([numpy.array((nions, 3), dtype=float)]) : a list of
arrays each containing fractional coordinates of ions of a given type
"""
def __init__(self):
self.q_cart = None
self.b_rec = None
def from_file(self, vasp_dir='./', poscar_filename='POSCAR'):
"""
Reads POSCAR and returns a dictionary.
Parameters
----------
vasp_dir (str) : path to the VASP working directory [default = `./']
plocar_filename (str) : filename [default = `PLOCAR']
"""
# Convenince local function
def readline_remove_comments():
return f.next().split('!')[0].strip()
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
f = read_lines(vasp_dir + poscar_filename)
# Comment line
comment = f.next().rstrip()
print " Found POSCAR, title line: %s"%(comment)
# Read scale
sline = readline_remove_comments()
ascale = float(sline[0])
# Read lattice vectors
self.a_brav = np.zeros((3, 3))
for ia in xrange(3):
sline = readline_remove_comments()
self.a_brav[ia, :] = map(float, sline.split())
# Negative scale means that it is a volume scale
if ascale < 0:
vscale = -ascale
vol = np.linalg.det(self.a_brav)
ascale = (vscale / vol)**(1.0/3)
self.a_brav *= ascale
# Depending on the version of VASP there could be
# an extra line with element names
sline = readline_remove_comments()
try:
# Old v4.6 format: no element names
self.nions = map(int, sline.split())
self.el_names = ['El%i'%(i) for i in xrange(len(nions))]
except ValueError:
# New v5.x format: read element names first
self.el_names = sline.split()
sline = readline_remove_comments()
self.nions = map(int, sline.split())
# Set the number of atom sorts (types) and the total
# number of atoms in the unit cell
self.ntypes = len(self.nions)
self.nq = sum(self.nions)
# Check for the line 'Selective dynamics' (and ignore it)
sline = readline_remove_comments()
if sline[0].lower() == 's':
sline = readline_remove_comments()
# Check whether coordinates are cartesian or fractional
cartesian = (sline[0].lower() in 'ck')
if cartesian:
brec = np.linalg.inv(self.a_brav.T)
# Read atomic positions
self.q_types = []
for it in xrange(self.ntypes):
q_at_it = np.zeros((self.nions[it], 3))
for iq in xrange(self.nions[it]):
sline = readline_remove_comments()
qcoord = map(float, sline.split()[:3])
if cartesian:
qcoord = np.dot(brec, qcoord)
q_at_it[iq, :] = qcoord
self.q_types.append(q_at_it)
print " Total number of ions:", self.nq
print " Number of types:", self.ntypes
print " Number of ions for each type:", self.nions
# print
# print " Coords:"
# for it in xrange(ntypes):
# print " Element:", el_names[it]
# print q_at[it]
################################################################
#
# Kpoints
#
################################################################
class Kpoints:
"""
Class describing k-points and optionally tetrahedra.
Properties
----------
nktot (int) : total number of k-points in the IBZ
kpts (numpy.array((nktot, 3), dtype=float)) : k-point vectors (fractional coordinates)
ntet (int) : total number of k-point tetrahedra
itet (numpy.array((ntet, 5), dtype=float) : array of tetrahedra
volt (float) : volume of a tetrahedron (the k-grid is assumed to
be uniform)
"""
#
# Reads IBZKPT file
#
def from_file(self, vasp_dir='./', ibz_filename='IBZKPT'):
"""
Reads from IBZKPT: k-points and optionally
tetrahedra topology (if present).
Parameters
----------
vasp_dir (str) : path to the VASP working directory [default = `./']
plocar_filename (str) : filename [default = `PLOCAR']
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
ibz_file = read_lines(vasp_dir + ibz_filename)
# Skip comment line
line = ibz_file.next()
# Number of k-points
line = ibz_file.next()
self.nktot = int(line.strip().split()[0])
print
print " {0:>26} {1:d}".format("Total number of k-points:", self.nktot)
self.kpts = np.zeros((self.nktot, 3))
# Skip comment line
line = ibz_file.next()
for ik in xrange(self.nktot):
line = ibz_file.next()
self.kpts[ik, :] = map(float, line.strip().split()[:3])
# Attempt to read tetrahedra
# Skip comment line ("Tetrahedra")
try:
line = ibz_file.next()
# Number of tetrahedra and volume = 1/(6*nkx*nky*nkz)
line = ibz_file.next()
sline = line.split()
self.ntet = int(sline[0])
self.volt = float(sline[1])
print " {0:>26} {1:d}".format("Total number of tetrahedra:", self.ntet)
# Traditionally, itet[it, 0] contains multiplicity
self.itet = np.zeros((self.ntet, 5), dtype=int)
for it in xrange(self.ntet):
line = ibz_file.next()
self.itet[it, :] = map(int, line.split()[:5])
except IOError, ValueError:
print " Error reading tetrahedra. No tetrahedron data is uesd"
self.ntet = 0
# data = { 'nktot': nktot,
# 'kpts': kpts,
# 'ntet': ntet,
# 'itet': itet,
# 'volt': volt }
#
# return data
################################################################
#
# Eigenval
#
################################################################
class Eigenval:
"""
Class containing Kohn-Sham-eigenvalues data from VASP (EIGENVAL file).
"""
def from_file(self, vasp_dir='./', eig_filename='EIGENVAL'):
"""
Reads eigenvalues from EIGENVAL. Note that the file also
contains k-points with weights. They are also stored and
then used to check the consistency of files read.
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
f = read_lines(vasp_dir + eig_filename)
# First line: only the first and the last number out of four
# are used; these are 'nions' and 'ispin'
sline = f.next()
self.nq = int(sline[0])
self.ispin = int(sline[3])
# Second line: cell volume and lengths of lattice vectors (skip)
sline = f.next()
# Third line: temperature (skip)
sline = f.next()
# Fourth and fifth line: useless
sline = f.next()
sline = f.next()
# Sixth line: NELECT, NKTOT, NBTOT
sline = f.next()
self.nelect = int(sline[0])
self.nktot = int(sline[1])
self.nband = int(sline[2])
# Set of eigenvalues and k-points
self.kpts = np.zeros((self.nktot, 3))
sefl.kwghts = np.zeros((self.nktot,))
self.eigs = np.zeros((self.nktot, self.nband, self.ispin))
for ik in xrange(self.nktot):
sline = f.next() # Empty line
sline = f.next() # k-point info
tmp = map(float, sline)
self.kpts[ik, :] = tmp[:3]
self.kwghts[ik] = tmp[3]
for ib in xrange(self.nband):
sline = f.next()
tmp = map(float, sline[1:self.ispin+1])
self.eigs[ik, ib, :] = tmp[:]
################################################################
#
# Doscar
#
################################################################
class Doscar:
"""
Class containing some data from DOSCAR
"""
def from_file(self, vasp_dir='./', eig_filename='DOSCAR'):
"""
Reads only E_Fermi from DOSCAR.
"""
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
f = read_lines(vasp_dir + eig_filename)
# Skip first 5 lines
for _ in xrange(5):
sline = f.next()
# Sixth line: EMAX, EMIN, NEDOS, EFERMI, 1.0
sline = f.next()
self.efermi = int(sline[3])
################################################################
#
# Reads SYMMCAR
#
################################################################
def read_symmcar(vasp_dir, symm_filename='SYMMCAR'):
"""
Reads SYMMCAR.
"""
# Shorthand for simple parsing
def extract_int_par(parname):
return int(re.findall(parname + '\s*=\s*(\d+)', line)[-1])
# Add a slash to the path name if necessary
if vasp_dir[-1] != '/':
vasp_dir += '/'
symmcar_exist = False
sym_file = read_lines(vasp_dir + symm_filename)
line = sym_file.next()
nrot = extract_int_par('NROT')
line = sym_file.next()
ntrans = extract_int_par('NPCELL')
# Lmax
line = sym_file.next()
lmax = extract_int_par('LMAX')
mmax = 2 * lmax + 1
# Nion
line = sym_file.next()
nion = extract_int_par('NION')
print " {0:>26} {1:d}".format("Number of rotations:", nrot)
print " {0:>26} {1:d}".format("Number of translations:", ntrans)
print " {0:>26} {1:d}".format("Number of ions:", nion)
print " {0:>26} {1:d}".format("L_max:", lmax)
rot_mats = np.zeros((nrot, lmax+1, mmax, mmax))
rot_map = np.zeros((nrot, ntrans, nion), dtype=np.int32)
for irot in xrange(nrot):
# Empty line
line = sym_file.next()
# IROT index (skip it)
line = sym_file.next()
# ISYMOP matrix (can be also skipped)
line = sym_file.next()
line = sym_file.next()
line = sym_file.next()
# Skip comment " Permutation map..."
line = sym_file.next()
# Permutations (in chunks of 20 indices per line)
for it in xrange(ntrans):
for ibl in xrange((nion - 1) / 20 + 1):
i1 = ibl * 20
i2 = (ibl + 1) * 20
line = sym_file.next()
rot_map[irot, it, i1:i2] = map(int, line.split())
for l in xrange(lmax + 1):
mmax = 2 * l + 1
# Comment: "L = ..."
line = sym_file.next()
for m in xrange(mmax):
line = sym_file.next()
rot_mats[irot, l, m, :mmax] = map(float, line.split()[:mmax])
data.update({ 'nrot': nrot, 'ntrans': ntrans,
'lmax': lmax, 'nion': nion,
'sym_rots': rot_mats, 'perm_map': rot_map })