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# Minimal makefile for Sphinx documentation
#
# You can set these variables from the command line.
SPHINXOPTS =
SPHINXBUILD = sphinx-build
SOURCEDIR = source
BUILDDIR = build
# Put it first so that "make" without argument is like "make help".
help:
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
.PHONY: help Makefile
# Catch-all target: route all unknown targets to Sphinx using the new
# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
%: Makefile
@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

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Parallel efficiency
===================
The determinant selection, MR-PT2 and diagonalization are parallelized with distributed parallelism.
Benchmarks for the [NH2-CH-NH2]+ molecule are presented with up to 200 nodes (9600 cores) on the
`Irene` supercomputer.
.. _Irene: http://www-hpc.cea.fr/en/complexe/tgcc-Irene.htm

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# -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup --------------------------------------------------------------
# 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.
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- Project information -----------------------------------------------------
project = 'Quantum Package'
copyright = '2018, A. Scemama, E. Giner'
author = 'A. Scemama, E. Giner'
# The short X.Y version
version = '1.0'
# The full version, including alpha/beta/rc tags
release = '1.0'
# -- 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.mathjax',
'sphinx.ext.githubpages',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# The suffix(es) of source filenames.
# You can specify multiple suffix as a list of string:
#
# source_suffix = ['.rst', '.md']
source_suffix = '.rst'
# The master toctree document.
master_doc = 'index'
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = None
# -- 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 = 'sphinx_rtd_theme'
# 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 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']
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# The default sidebars (for documents that don't match any pattern) are
# defined by theme itself. Builtin themes are using these templates by
# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
# 'searchbox.html']``.
#
# html_sidebars = {}
# -- Options for HTMLHelp output ---------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = 'QuantumPackagedoc'
# -- 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': '',
# Latex figure (float) alignment
#
# 'figure_align': 'htbp',
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
# author, documentclass [howto, manual, or own class]).
latex_documents = [
(master_doc, 'QuantumPackage.tex', 'Quantum Package Documentation',
'A. Scemama, E. Giner, T. Applencourt, Y. Garniron', 'manual'),
]
# -- Options for manual page output ------------------------------------------
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
(master_doc, 'quantumpackage', 'Quantum Package Documentation',
[author], 1)
]
# -- 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 = [
(master_doc, 'QuantumPackage', 'Quantum Package Documentation',
author, 'QuantumPackage', 'One line description of project.',
'Miscellaneous'),
]
# -- Options for Epub output -------------------------------------------------
# Bibliographic Dublin Core info.
epub_title = project
# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''
# A unique identification for the text.
#
# epub_uid = ''
# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']
# -- Extension configuration -------------------------------------------------

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.. Quantum Package documentation master file, created by
sphinx-quickstart on Thu Oct 18 11:53:23 2018.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
===============
Quantum Package
===============
.. image:: _static/qp.png
:align: center
:alt: Quantum Package
.. toctree::
:maxdepth: 2
:caption: Contents:
intro
interfaces
benchmarks
installation
programming
references
license
Indices and tables
==================
* :ref:`genindex`
* :ref:`search`

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Installation
============
Set up the environment::
./configure <config_file>
For example you can type::
./configure config/gfortran.cfg
This command will :
- Download and install all the requirements.
Installing `OCaml`_ and the `Core`_ library may take some time (up to 20min on an old machine).
- Create the file which contains all the dependencies for the binaries.
It's not a Makefile, but a `Ninja`_ file (so don't type ``make`` is hopeless, type ``ninja`` instead)
By default, the OCaml compiler and libraries will be installed in ``$HOME/.opam``.
If you want to install it somewhere else, you can change this by setting the ``$OPAMROOT``
environment variable to the location of your choice.
For more info about the OCaml installation, you can visit the `Opam website <https://opam.ocaml.org/doc/Install.html>`_.
Compiling Flags
---------------
``<config_file>`` is the path to the file which contains all the flags useful for the compilation : optimization flags, Lapack libary, etc. We have two default configuration files in ``$QP_ROOT/config`` : ``ifort.cfg`` and ``gfortran.cfg``. Copy these files to create a new config file adapted to your architecture.
Note that the `popcnt` instruction accelerates *a lot* the programs, so the
SSE4.2, AVX or AVX2 instruction sets should be enabled if possible.
If you encounter an error saying that your Fortran compiler can't produce
executables, it means that the program was built using an instruction set
not supported by the current processor. In that case, use the ``-xHost`` option
of the Intel Fortran compiler, or the ``-march=native`` option of gfortran.
Set environment variables
-------------------------
A configuration file named ``quantum_package.rc`` will be created.
To finish the installation and to start using the quantum package, source this file in your shell::
source quantum_package.rc
And you can also source it inside your ``.bashrc`` file, or create a system-wide module file.
If you use a C-shell, you will have to translate the ``quantum_package.rc`` file into
C-shell syntax and source it in your shell.
Add some modules
----------------
The quantum package has **no executable out of the box**. You need to install (and then compile) some modules. The ``qp_module.py`` will help you::
qp_module.py create -n <name> [<children_modules>...]
qp_module.py download -n <name> [<path_folder>...]
qp_module.py install <name>...
qp_module.py list (--installed | --available-local)
qp_module.py uninstall <name>
For exemple you can type ::
qp_module.py install Full_CI_ZMQ
This will install the `Full_CI_ZMQ` module. All the modules are installed in the ``$QP_ROOT/src/``, and all the available modules are in ``$QP_ROOT/plugins/``
Compiling the Fortran
---------------------
Just type ``ninja`` if you are in ``$QP_ROOT`` (or ``ninja -f $QP_ROOT/build.ninja`` elsewhere). The compilation will take approximately 5 min.
.. _Ninja: https://ninja-build.org/
.. _OCaml: http://ocaml.org/
.. _Core: https://opensource.janestreet.com/core/

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Interfaces
==========
`Molden`_
3D plots of Molecular Orbitals
FCIDUMP
Interface with the FCI-QMC program `NECI`_, or the semi-stochastic Heat-Bath CI
program `Dice`_.
`GAMESS`_ / Gaussian
Using the resultsFile Python library, the geometr and molecular orbitals can be read.
This is useful to make calculations with CAS-SCF orbitals
`QMCPack`_ / `CHAMP`_ / `QMC=Chem`_
Trial wave functions can be used for Quantum Monte Carlo, with or without pseudo-potentials.
.. _Molden: http://cheminf.cmbi.ru.nl/molden/
.. _GAMESS: https://www.msg.chem.iastate.edu/gamess/
.. _QMC=Chem: https://github.com/scemama/qmcchem
.. _CHAMP: https://www.utwente.nl/en/tnw/ccp/research/CHAMP.html
.. _NECI: https://github.com/ghb24/NECI_STABLE
.. _Dice: https://sanshar.github.io/Dice/
.. _QMCPack: https://qmcpack.org

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Introduction
============
What it is
""""""""""
The |qp| is an open-source programming environment for quantum chemistry,
especially for `wave function methods <https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods>`_.
The main goal is the development of selected configuration interaction (sCI)
methods and multi-reference perturbation theory (MR-PT) in the
determinant-driven paradigm. The determinant-driven framework allows the
programmer to include any arbitrary set of determinants in the variational
space, and thus gives a complete freedom in the methodological development. All
the programs are developed with the `IRPF90`_ code generator, which simplifies
the development of new programs.
What it is not
""""""""""""""
The |qp| is *not* a general purpose quantum chemistry program.
First of all, it is a library. The users of the |qp| should develop
their own programs.
The |qp| has been designed specifically for sCI, so all the
algorithms which are programmed are not adapted to run SCF or DFT calculations
on thousands of atoms.
The |qp| is *not* a massive production code. For conventional
methods such as Hartree-Fock CISD or MP2, the users are recommended to use the
existing standard production codes which are designed to make these methods run
fast. Again, the role of the |qp| is to make life simple for the
developer. Once a new method is developed and tested, the developer is encouraged
to consider re-expressing it with an integral-driven formulation, and to
implement the new method is open-source production codes, such as `NWChem`_
or `GAMESS`_.
Applications
""""""""""""
Multiple programs were developed with the |qp|, such as:
- Selected Full-CI + Epstein-Nesbet PT2 (CIPSI)
- Hybrid stochastic/deterministic MR-PT2
- CIS, CISD, MP2
- Selected CISD
- Jeziorsky-Monkhorst MR-PT2
- Selected CAS+SD
- Selected difference-dedicated CI (DD-CI)
- Multi-Reference Coupled Cluster (MR-CCSD)
- CIPSI with range-separated DFT
All these programs can generate ground and excited states, and spin pure wave functions
(eigenstates of S²).
.. Links ..
.. _IRPF90: http://irpf90.ups-tlse.fr
.. _NWChem: http://www.nwchem-sw.org/
.. _GAMESS: https://www.msg.chem.iastate.edu/gamess/
.. |qp| replace:: Quantum Package

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License
=======
.. include:: LICENSE
:literal:

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Programming the Quantum Package
===============================

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References
^^^^^^^^^^^
Articles for which the Quantum Package was used