Added references

docs/INSTALL.md

@@ -0,0 +1,6 @@
+Requirements for the documentation
+==================================
+
+      pip install sphinx
+      pip install sphinx_rtd_theme
+      pip install sphinxcontrib-bibtex

docs/source/applications.rst

@@ -0,0 +1,20 @@
+Research made with the Quantum Package
+======================================
+
+- A Mountaineering Strategy to Excited States: Highly Accurate Reference Energies and Benchmarks :cite:`Loos_2018`
+- Deterministic Construction of Nodal Surfaces within Quantum Monte Carlo: The Case of {FeS} :cite:`Scemama_2018`
+- Excitation energies from diffusion Monte Carlo using selected configuration interaction nodes :cite:`Scemama_2018.2`
+- Perturbatively Selected Configuration-Interaction Wave Functions for Efficient Geometry Optimization in Quantum Monte Carlo :cite:`Dash_2018`
+- Selected configuration interaction dressed by perturbation :cite:`Garniron_2018`
+- A Jeziorski-Monkhorst fully uncontracted multi-reference perturbative treatment. I. Principles, second-order versions, and tests on ground state potential energy curves :cite:`Giner_2017`
+- Alternative definition of excitation amplitudes in multi-reference state-specific coupled cluster :cite:`Garniron_2017`
+- Hybrid stochastic-deterministic calculation of the second-order perturbative contribution of multireference perturbation theory :cite:`Garniron_2017.2`
+- Orthogonal Valence Bond Hamiltonians incorporating dynamical correlation effects :cite:`Giner_2017.2`
+- A simple approach to the state-specific {MR}-{CC} using the intermediate Hamiltonian formalism :cite:`Giner_2016`
+- Communication: Toward an improved control of the fixed-node error in quantum Monte Carlo: The case of the water molecule :cite:`Caffarel_2016`
+- Using CIPSI Nodes in Diffusion Monte Carlo :cite:`Caffarel_2016.2`
+- Fixed-node diffusion Monte Carlo potential energy curve of the fluorine molecule F2 using selected configuration interaction trial wavefunctions :cite:`Giner_2015`
+- Accurate nonrelativistic ground-state energies of 3d transition metal atoms :cite:`Scemama_2014`
+- Spin Density Distribution in Open-Shell Transition Metal Systems: A Comparative Post-Hartree-Fock, Density Functional Theory, and Quantum Monte Carlo Study of the CuCl2 Molecule :cite:`Caffarel_2014`
+- Using perturbatively selected configuration interaction in quantum Monte Carlo calculations :cite:`Giner_2013`
+- An efficient implementation of Slater-Condon rules :cite:`Scemama2013Nov`

docs/source/benchmarks.rst

@@ -7,3 +7,6 @@ Benchmarks for the [NH2-CH-NH2]+ molecule are presented with up to 200 nodes (96
 
 .. _Irene: http://www-hpc.cea.fr/en/complexe/tgcc-Irene.htm
 
+
+.. include:: work.rst
+

docs/source/conf.py

@@ -41,6 +41,8 @@ release = '1.0'
 extensions = [
     'sphinx.ext.mathjax',
     'sphinx.ext.githubpages',
+    'sphinxcontrib.bibtex'
+
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -98,12 +100,18 @@ html_static_path = ['_static']
 # 'searchbox.html']``.
 #
 # html_sidebars = {}
+html_sidebars = {
+  '**': [
+    'globaltoc.html',
+    'searchbox.html',
+  ]
+}
 
 
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'QuantumPackagedoc'
+htmlhelp_basename = 'QuantumPackage'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -131,7 +139,7 @@ latex_elements = {
 #  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'),
+     'A. Scemama, E. Giner', 'manual'),
 ]
 
 
@@ -176,3 +184,4 @@ epub_exclude_files = ['search.html']
 
 
 # -- Extension configuration -------------------------------------------------
+

docs/source/index.rst

@@ -16,6 +16,7 @@ Quantum Package
    :caption: Contents:
 
    intro
+   applications
    interfaces
    benchmarks
    installation

docs/source/references.rst

@@ -1,6 +1,9 @@
 References
 ^^^^^^^^^^^
 
-Articles for which the Quantum Package was used
+.. rubric:: References
+
+.. bibliography:: refs.bib
+   :style: unsrt
 
 

docs/source/refs.bib

@@ -0,0 +1,216 @@
+@article{Scemama2013Nov,
+        author = {Scemama, Anthony and Giner, Emmanuel},
+        title = {{An efficient implementation of Slater-Condon rules}},
+        journal = {arXiv},
+        year = {2013},
+        month = {Nov},
+        eprint = {1311.6244},
+        url = {https://arxiv.org/abs/1311.6244}
+}
+
+@article{Loos_2018,
+	doi = {10.1021/acs.jctc.8b00406},
+	url = {https://doi.org/10.1021%2Facs.jctc.8b00406},
+	year = 2018,
+	month = {jul},
+	publisher = {American Chemical Society ({ACS})},
+	volume = {14},
+	number = {8},
+	pages = {4360--4379},
+	author = {Pierre-Fran{\c{c}}ois Loos and Anthony Scemama and Aymeric Blondel and Yann Garniron and Michel Caffarel and Denis Jacquemin},
+	title = {A Mountaineering Strategy to Excited States: Highly Accurate Reference Energies and Benchmarks},
+	journal = {Journal of Chemical Theory and Computation}
+}
+@article{Scemama_2018,
+	doi = {10.1021/acs.jctc.7b01250},
+	url = {https://doi.org/10.1021%2Facs.jctc.7b01250},
+	year = 2018,
+	month = {jan},
+	publisher = {American Chemical Society ({ACS})},
+	volume = {14},
+	number = {3},
+	pages = {1395--1402},
+	author = {Anthony Scemama and Yann Garniron and Michel Caffarel and Pierre-Fran{\c{c}}ois Loos},
+	title = {Deterministic Construction of Nodal Surfaces within Quantum Monte Carlo: The Case of {FeS}},
+	journal = {Journal of Chemical Theory and Computation}
+}
+@article{Scemama_2018.2,
+	doi = {10.1063/1.5041327},
+	url = {https://doi.org/10.1063%2F1.5041327},
+	year = 2018,
+	month = {jul},
+	publisher = {{AIP} Publishing},
+	volume = {149},
+	number = {3},
+	pages = {034108},
+	author = {Anthony Scemama and Anouar Benali and Denis Jacquemin and Michel Caffarel and Pierre-Fran{\c{c}}ois Loos},
+	title = {Excitation energies from diffusion Monte Carlo using selected configuration interaction nodes},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Dash_2018,
+	doi = {10.1021/acs.jctc.8b00393},
+	url = {https://doi.org/10.1021%2Facs.jctc.8b00393},
+	year = 2018,
+	month = {jun},
+	publisher = {American Chemical Society ({ACS})},
+	volume = {14},
+	number = {8},
+	pages = {4176--4182},
+	author = {Monika Dash and Saverio Moroni and Anthony Scemama and Claudia Filippi},
+	title = {Perturbatively Selected Configuration-Interaction Wave Functions for Efficient Geometry Optimization in Quantum Monte Carlo},
+	journal = {Journal of Chemical Theory and Computation}
+}
+@article{Garniron_2018,
+	doi = {10.1063/1.5044503},
+	url = {https://doi.org/10.1063%2F1.5044503},
+	year = 2018,
+	month = {aug},
+	publisher = {{AIP} Publishing},
+	volume = {149},
+	number = {6},
+	pages = {064103},
+	author = {Yann Garniron and Anthony Scemama and Emmanuel Giner and Michel Caffarel and Pierre-Fran{\c{c}}ois Loos},
+	title = {Selected configuration interaction dressed by perturbation},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Giner_2017,
+	doi = {10.1063/1.4984616},
+	url = {https://doi.org/10.1063%2F1.4984616},
+	year = 2017,
+	month = {jun},
+	publisher = {{AIP} Publishing},
+	volume = {146},
+	number = {22},
+	pages = {224108},
+	author = {Emmanuel Giner and Celestino Angeli and Yann Garniron and Anthony Scemama and Jean-Paul Malrieu},
+	title = {A Jeziorski-Monkhorst fully uncontracted multi-reference perturbative treatment. I. Principles, second-order versions, and tests on ground state potential energy curves},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Garniron_2017,
+	doi = {10.1063/1.4980034},
+	url = {https://doi.org/10.1063%2F1.4980034},
+	year = 2017,
+	month = {apr},
+	publisher = {{AIP} Publishing},
+	volume = {146},
+	number = {15},
+	pages = {154107},
+	author = {Yann Garniron and Emmanuel Giner and Jean-Paul Malrieu and Anthony Scemama},
+	title = {Alternative definition of excitation amplitudes in multi-reference state-specific coupled cluster},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Garniron_2017.2,
+	doi = {10.1063/1.4992127},
+	url = {https://doi.org/10.1063%2F1.4992127},
+	year = 2017,
+	month = {jul},
+	publisher = {{AIP} Publishing},
+	volume = {147},
+	number = {3},
+	pages = {034101},
+	author = {Yann Garniron and Anthony Scemama and Pierre-Fran{\c{c}}ois Loos and Michel Caffarel},
+	title = {Hybrid stochastic-deterministic calculation of the second-order perturbative contribution of multireference perturbation theory},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Giner_2017.2,
+	doi = {10.1016/j.comptc.2017.03.001},
+	url = {https://doi.org/10.1016%2Fj.comptc.2017.03.001},
+	year = 2017,
+	month = {sep},
+	publisher = {Elsevier {BV}},
+	volume = {1116},
+	pages = {134--140},
+	author = {E. Giner and C. Angeli and A. Scemama and J.-P. Malrieu},
+	title = {Orthogonal Valence Bond Hamiltonians incorporating dynamical correlation effects},
+	journal = {Computational and Theoretical Chemistry}
+}
+@article{Giner_2016,
+	doi = {10.1063/1.4940781},
+	url = {https://doi.org/10.1063%2F1.4940781},
+	year = 2016,
+	month = {feb},
+	publisher = {{AIP} Publishing},
+	volume = {144},
+	number = {6},
+	pages = {064101},
+	author = {E. Giner and G. David and A. Scemama and J. P. Malrieu},
+	title = {A simple approach to the state-specific {MR}-{CC} using the intermediate Hamiltonian formalism},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Caffarel_2016,
+	doi = {10.1063/1.4947093},
+	url = {https://doi.org/10.1063%2F1.4947093},
+	year = 2016,
+	month = {apr},
+	publisher = {{AIP} Publishing},
+	volume = {144},
+	number = {15},
+	pages = {151103},
+	author = {Michel Caffarel and Thomas Applencourt and Emmanuel Giner and Anthony Scemama},
+	title = {Communication: Toward an improved control of the fixed-node error in quantum Monte Carlo: The case of the water molecule},
+	journal = {The Journal of Chemical Physics}
+}
+@incollection{Caffarel_2016.2,
+	doi = {10.1021/bk-2016-1234.ch002},
+	url = {https://doi.org/10.1021%2Fbk-2016-1234.ch002},
+	year = 2016,
+	month = {jan},
+	publisher = {American Chemical Society},
+	pages = {15--46},
+	author = {Michel Caffarel and Thomas Applencourt and Emmanuel Giner and Anthony Scemama},
+	title = {Using CIPSI Nodes in Diffusion Monte Carlo},
+	booktitle = {{ACS} Symposium Series}
+}
+@article{Giner_2015,
+	doi = {10.1063/1.4905528},
+	url = {https://doi.org/10.1063%2F1.4905528},
+	year = 2015,
+	month = {jan},
+	publisher = {{AIP} Publishing},
+	volume = {142},
+	number = {4},
+	pages = {044115},
+	author = {Emmanuel Giner and Anthony Scemama and Michel Caffarel},
+	title = {Fixed-node diffusion Monte Carlo potential energy curve of the fluorine molecule F2 using selected configuration interaction trial wavefunctions},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Scemama_2014,
+	doi = {10.1063/1.4903985},
+	url = {https://doi.org/10.1063%2F1.4903985},
+	year = 2014,
+	month = {dec},
+	publisher = {{AIP} Publishing},
+	volume = {141},
+	number = {24},
+	pages = {244110},
+	author = {A. Scemama and T. Applencourt and E. Giner and M. Caffarel},
+	title = {Accurate nonrelativistic ground-state energies of 3d transition metal atoms},
+	journal = {The Journal of Chemical Physics}
+}
+@article{Caffarel_2014,
+	doi = {10.1021/ct5004252},
+	url = {https://doi.org/10.1021%2Fct5004252},
+	year = 2014,
+	month = {nov},
+	publisher = {American Chemical Society ({ACS})},
+	volume = {10},
+	number = {12},
+	pages = {5286--5296},
+	author = {Michel Caffarel and Emmanuel Giner and Anthony Scemama and Alejandro Ram{\'{\i}}rez-Sol{\'{\i}}s},
+	title = {Spin Density Distribution in Open-Shell Transition Metal Systems: A Comparative Post-Hartree-Fock, Density Functional Theory, and Quantum Monte Carlo Study of the CuCl2 Molecule},
+	journal = {Journal of Chemical Theory and Computation}
+}
+@article{Giner_2013,
+	doi = {10.1139/cjc-2013-0017},
+	url = {https://doi.org/10.1139%2Fcjc-2013-0017},
+	year = 2013,
+	month = {sep},
+	publisher = {Canadian Science Publishing},
+	volume = {91},
+	number = {9},
+	pages = {879--885},
+	author = {Emmanuel Giner and Anthony Scemama and Michel Caffarel},
+	title = {Using perturbatively selected configuration interaction in quantum Monte Carlo calculations},
+	journal = {Canadian Journal of Chemistry}
+}
+

docs/source/work.rst

@@ -0,0 +1,3 @@
+
+.. image:: http://craniointernational.com/wp-content/uploads/2018/01/work-in-progress.jpg
+