diff --git a/docs/INSTALL.md b/docs/INSTALL.md new file mode 100644 index 00000000..a3a19f5f --- /dev/null +++ b/docs/INSTALL.md @@ -0,0 +1,6 @@ +Requirements for the documentation +================================== + + pip install sphinx + pip install sphinx_rtd_theme + pip install sphinxcontrib-bibtex diff --git a/docs/source/applications.rst b/docs/source/applications.rst new file mode 100644 index 00000000..6c908237 --- /dev/null +++ b/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` diff --git a/docs/source/benchmarks.rst b/docs/source/benchmarks.rst index 6a3ceaf0..9df2aeb1 100644 --- a/docs/source/benchmarks.rst +++ b/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 + diff --git a/docs/source/conf.py b/docs/source/conf.py index 29f09f48..f13e8f27 100644 --- a/docs/source/conf.py +++ b/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 ------------------------------------------------- + diff --git a/docs/source/index.rst b/docs/source/index.rst index be24ef7d..d9972917 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -16,6 +16,7 @@ Quantum Package :caption: Contents: intro + applications interfaces benchmarks installation diff --git a/docs/source/references.rst b/docs/source/references.rst index de2a6911..4ffc2be0 100644 --- a/docs/source/references.rst +++ b/docs/source/references.rst @@ -1,6 +1,9 @@ References ^^^^^^^^^^^ -Articles for which the Quantum Package was used +.. rubric:: References + +.. bibliography:: refs.bib + :style: unsrt diff --git a/docs/source/refs.bib b/docs/source/refs.bib new file mode 100644 index 00000000..0a6ff47d --- /dev/null +++ b/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} +} + diff --git a/docs/source/work.rst b/docs/source/work.rst new file mode 100644 index 00000000..3d7291f7 --- /dev/null +++ b/docs/source/work.rst @@ -0,0 +1,3 @@ + +.. image:: http://craniointernational.com/wp-content/uploads/2018/01/work-in-progress.jpg +