diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS new file mode 100644 index 0000000..f478260 --- /dev/null +++ b/.github/CODEOWNERS @@ -0,0 +1,7 @@ +# These owners are the default owners for everything in +# the repo. Unless a later match takes precedence, +* @kousuke-nakano + +# @kousuke-nakano owns any files in the build/ directory at +# the root of the repository and any of its subdirectories. +# /doc/ @kousuke-nakano diff --git a/.github/workflows/website-deploy.yml b/.github/workflows/website-deploy.yml new file mode 100644 index 0000000..f5df97f --- /dev/null +++ b/.github/workflows/website-deploy.yml @@ -0,0 +1,33 @@ +# This workflow will deploy the sphinx document. + +name: sphinx-deploy-gh-pages + +on: + release: + types: [published] + +jobs: + sphinx-build: + runs-on: ubuntu-latest + steps: + - name: Install and Setup Python + uses: actions/setup-python@v3 + with: + python-version: 3.8 + + - name: Install python dependencies + run: pip install sphinx sphinx-rtd-theme + + - name: Checkout the project repository + uses: actions/checkout@v2 + + - name: Build the sphinx document. + working-directory: doc + run: | + make html + + - name: Deploy the sphinx document. + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: doc/build/html diff --git a/.github/workflows/website-sphinx-build-test.yml b/.github/workflows/website-sphinx-build-test.yml new file mode 100644 index 0000000..a80eafc --- /dev/null +++ b/.github/workflows/website-sphinx-build-test.yml @@ -0,0 +1,30 @@ +# This workflow will deploy the sphinx document. + +name: sphinx-deploy-gh-pages + +on: + push: + branches: [ "main", "devel" ] + pull_request: + branches: [ "main", "devel" ] + +jobs: + sphinx-build: + runs-on: ubuntu-latest + steps: + - name: Install and Setup Python + uses: actions/setup-python@v3 + with: + python-version: 3.8 + + - name: Install python dependencies + run: pip install sphinx sphinx-rtd-theme + + - name: Checkout the project repository + uses: actions/checkout@v2 + + - name: Build the sphinx document. + working-directory: doc + run: | + make html + diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..f0763f4 --- /dev/null +++ b/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +SPHINXPROJ = turborvb-website +SOURCEDIR = source +BUILDDIR = build + +# Put it first so that "make" without argument is like "make help". +help: + @$(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) \ No newline at end of file diff --git a/README.md b/README.md index 94eba3d..35bdccf 100644 --- a/README.md +++ b/README.md @@ -1 +1,34 @@ -# turborvb_website +TurboRVB website: +-------------------------------------- + +Source codes of our TurboRVB website. **Please do not include any confidential information because the source files are also public.** + +The html (build) files in the master branch are uploaded to the SISSA server (i.e., public). + +How to edit the website:: + +This document is composed by Sphinx, which is a documentation generator. i.e, it takes plain-text source files, and then generates HTML files. You can think of it as a program that takes plain-text files written in the ``reStructuredText`` format and outputs HTML:: + + reStructuredText -> via Sphinx -> HTML + +Therefore, you should be minimally familiar with ``reStructuredText``. + +Sphinx is coded based on python (but you do not need to familiarize yourself with python itself!). So, first you should install the sphinx modules using via pip:: + + pip install Sphinx + pip install sphinx_rtd_theme + +The document can be built just by typing:: + + make html + +in the root directory (i.e., TurboRVB_website/). The generated documents are put in:: + + html version : root -> build -> html -> index.html, etc... + +The source files (i.e., xxx.rst) are: + + rst files: root -> source -> index.rst, root -> source -> _sources -> ***.rst + +Note: The public and development branches are no longer used (will be deleted). + diff --git a/source/_sources/02Developers.rst b/source/_sources/02Developers.rst new file mode 100644 index 0000000..6fdb899 --- /dev/null +++ b/source/_sources/02Developers.rst @@ -0,0 +1,149 @@ +.. TurboRVB_manual documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Developers and Contributors +=========================================== + +Main developer +------------------------------------------- + +Dr. Sandro Sorella +######################### + +.. figure:: /_static/01photos/ss.jpg + :height: 150px + ++ `Personal website `__ ++ **International School for Advanced Studies (SISSA), Italy** + +Project PIs +------------------------------------------- + +Dr. Michele Casula +################################### + +.. figure:: /_static/01photos/mc.jpg + :height: 150px + ++ `Personal website `__ ++ **Sorbonne Universit´e, CNRS, France** + +Dr. Kosuke Nakano +################################### + +.. figure:: /_static/01photos/kn.jpg + :height: 150px + ++ `Personal website `__ ++ **International School for Advanced Studies (SISSA), Italy** ++ **Japan Advanced Institute of Science and Technology (JAIST), Japan** + +Contributors (alphabetic order) +------------------------------------------- + +Dr. Claudio Attaccalite +################################### + +.. figure:: /_static/01photos/cc.jpg + :height: 150px + ++ `Personal website `__ ++ **Aix-Marseille Universit´e, CNRS, France** + +Dr. Matteo Barborini +################################### + +.. figure:: /_static/01photos/an.jpg + :height: 100px + ++ **CNR-NANO, Italy** + +Dr. Andrea Tirelli +################################### + +.. figure:: /_static/01photos/at.jpg + :height: 150px + ++ `Personal website `__ ++ **International School for Advanced Studies (SISSA), Italy** + +Mr. Giacomo Tenti +################################### + +.. figure:: /_static/01photos/gt.jpg + :height: 150px + ++ **International School for Advanced Studies (SISSA), Italy** + +Dr. Luca Capriotti +################################### + +.. figure:: /_static/01photos/an.jpg + :height: 100px + ++ **New York University, United States of America** ++ **University College London, United Kingdom** + +Dr. Emanuele Coccia +################################### + +.. figure:: /_static/01photos/ec.jpg + :height: 150px + ++ **University of Trieste, Italy** + +Dr. Mario Dagrada +################################### + +.. figure:: /_static/01photos/md.jpg + :height: 150px + ++ `Personal website `__ ++ **Forescout Technologies, The Netherlands** + +Dr. Claudio Genovese +################################### + +.. figure:: /_static/01photos/an.jpg + :height: 100px + ++ **International School for Advanced Studies (SISSA), Italy** + +Dr. Oto Kohulák +################################### + +.. figure:: /_static/01photos/ok.jpg + :height: 150px + ++ **International School for Advanced Studies (SISSA), Italy** + +Dr. Ye Luo +################################### + +.. figure:: /_static/01photos/an.jpg + :height: 100px + ++ **Argonne National Laboratory, United States of America** + +Dr. Guglielmo Mazzola +################################### + +.. figure:: /_static/01photos/an.jpg + :height: 100px + ++ **University of Zurich, Switzerland** + +Dr. Andrea Zen +################################### + +.. figure:: /_static/01photos/az.jpg + :height: 150px + ++ **University College London, United Kingdom** + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/03Source_code.rst b/source/_sources/03Source_code.rst new file mode 100644 index 0000000..1ac2cab --- /dev/null +++ b/source/_sources/03Source_code.rst @@ -0,0 +1,39 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Source codes +=========================================== + +When you publish a paper using our code(s), please cite corresponding paper(s). + +- | `TurboRVB: a many-body toolkit for ab initio electronic simulations by quantum Monte Carlo `_ + | K. Nakano*, C. Attaccalite, M. Barborini, L. Capriotti, M. Casula*, E. Coccia, M. Dagrada, Y. Luo, G. Mazzola, A. Zen, and S. Sorella*, + | *J. Chem. Phys.* 152, 204121 (2020) + +- | Turbo-Genius: A Python suite implementing workflows of the ab-initio quantum Monte Carlo calculations + | K. Nakano*, et al. + | *In preparation* (2023). + + +TurboRVB +---------------------------------- +**TurboRVB** is an open-source project. The source code is available from the `GitHub repository `__. + +TurboGenius +---------------------------------- +**TurboGenius** is an open-source project. The source code is available from the `GitHub repository `__. + +TurboWorkflows +---------------------------------- +**TurboWorkflows** is an open-source project. The source code is available from the `GitHub repository `__. + +Tutorials +---------------------------------- +Tutorials are available from the `GitHub Pages `__. + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/04Publications.rst b/source/_sources/04Publications.rst new file mode 100644 index 0000000..5f64818 --- /dev/null +++ b/source/_sources/04Publications.rst @@ -0,0 +1,629 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Publications +=========================================== + +.. figure:: /_static/07logo/logo_sub.png + :width: 500px + +.. Preprint +.. #################### + +2023 +#################### + +.. 2023RAG +.. article + +- | Toward Chemical Accuracy Using the Jastrow Correlated Antisymmetrized Geminal Power Ansatz, + | A. Raghav, R. Maezono, K. Hongo, S. Sorella, K. Nakano + | `J. Chem. Theory Comput. 19, 2222-2229 (2023) `_ + +.. 2023MON +.. article + +- | Quantum phase diagram of high-pressure hydrogen, + | L. Monacelli, M. Casula, K. Nakano, S. Sorella, and F. Mauri + | `Nat. Phys. 19, 845–850 (2023) `_ + +2022 +#################### + +.. 2022AND +.. article + +- | High-pressure hydrogen by machine learning and quantum Monte Carlo, + | A. Tirelli, G. Tenti, K. Nakano, and S. Sorella, + | `Phys. Rev. B 106, L041105 (2022). `_ + +.. 2022NAK +.. article + +- | Space-warp coordinate transformation for efficient ionic force calculations in quantum Monte Carlo, + | K. Nakano, A. Raghav, and S. Sorella, + | `J. Chem. Phys. 156, 034101 (2022). `_ + +2021 +#################### + +.. 2021NAK +.. article + +- | Atomic forces by quantum Monte Carlo: Application to phonon dispersion calculations, + | K. Nakano, T. Morresi, M. Casula, R. Maezono, and S. Sorella, + | `Phys. Rev. B 103, L121110 (2021). `_ + | Selected as an **Editors' Suggestion** + + +2020 +#################### + +.. 2020MOT + +- | Ground-state properties of the hydrogen chain: insulator-to-metal transition, dimerization, and magnetic phases, + | M. Motta, C. Genovese, F. Ma, Z. Cui, R. Sawaya, G.K. Chan, N. Chepiga, P. Helms, C. Jiménez-Hoyos, A.J. Millis, U. Ray, E. Ronca, H. Shi, S. Sorella, E.M. Stoudenmire, S.R. White, and S. Zhang (Simons Collaboration on the Many-Electron Problem), + | `Phys. Rev. X 10, 031058 (2020). `_ + + +.. 2020GEN2 + +- | The nature of the chemical bond in the dicarbon molecule, + | C. Genovese and S. Sorella, + | `J. Chem. Phys. 153, 164301 (2020). `_ + +.. 2020GEN1 +.. article + +- | General correlated geminal ansatz for electronic structure calculations: exploiting Pfaffians in place of determinants, + | C. Genovese, T. Shirakawa, K. Nakano, and S. Sorella, + | `J. Chem. Theory Comput. 16, 6114-6131 (2020). `_ + +.. 2020NAK2 +.. article + +- | TurboRVB: a many-body toolkit for *ab-initio* electronic simulations by quantum Monte Carlo, + | K. Nakano, C. Attaccalite, M. Barborini, L. Capriotti, M. Casula, E. Coccia, M. Dagrada, C. Genovese, Y. Luo, G. Mazzola, A. Zen, and S. Sorella, + | `J. Chem. Phys. 152, 204121 (2020). `_ + +.. 2020NAK1 +.. article + +- | Speeding up ab initio diffusion Monte Carlo simulations by a smart lattice regularization, + | K. Nakano, R. Maezono, and S. Sorella, + | `Phys. Rev. B 101, 155106 (2020). `_ + + +2019 +#################### + +.. 2019ZEN +.. article + +- | A new scheme for fixed node diffusion quantum Monte Carlo with pseudopotentials: Improving reproducibility and reducing the trial-wave-function bias, + | A. Zen, J. Brandenburg, A. Michaelides, and D. Alfe, + | `J. Chem. Phys. 151, 134105 (2019). `_ + +.. 2019GEN +.. article + +- | Assessing the accuracy of the Jastrow antisymmetrized geminal power in the :math:`\rm{H}_{4}` model system, + | C. Genovese, A. Meninno, and S. Sorella, + | `J. Chem. Phys. 150, 084102 (2019). `_ + +.. 2019FER +.. article + +- | van der Waals forces stabilize low-energy polymorphism in :math:`{\mathrm{B}}_{2}{\mathrm{O}}_{3}`: Implications for the crystallization anomaly, + | G. Ferlat, M. Hellgren, F. Coudert, H. Hay, F. Mauri, and M. Casula, + | `Phys. Rev. Materials 3, 063603 (2019). `_ + +.. 2019NAK +.. article + +- | All-Electron Quantum Monte Carlo with Jastrow Single Determinant Ansatz: Application to the Sodium Dimer, + | K. Nakano, R. Maezono, and S. Sorella, + | `J. Chem. Theory Comput. 15, 4044--4055 (2019). `_ + + +2018 +#################### + +.. 2018SOR +.. article + +- | Correlation-Driven Dimerization and Topological Gap Opening in Isotropically Strained Graphene, + | S. Sorella, K. Seki, O. Brovko, T. Shirakawa, S. Miyakoshi, S. Yunoki, and E. Tosatti, + | `Phys. Rev. Lett. 121, 066402 (2018). `_ + +.. 2018DUP +.. article + +- | Fate of the open-shell singlet ground state in the experimentally accessible acenes: A quantum Monte Carlo study, + | N. Dupuy, and M. Casula, + | `J. Chem. Phys. 148, 134112 (2018). `_ + +.. 2018BAR +.. article + +- | Angle-resolved photoemission spectroscopy from first-principles quantum Monte Carlo, + | M. Barborini, S. Sorella, M. Rontani, and S. Corni, + | `J. Chem. Phys. 149, 154102 (2018). `_ + +.. 2018MAZ +.. article + +- | Phase diagram of hydrogen and a hydrogen-helium mixture at planetary conditions by Quantum Monte Carlo simulations, + | G. Mazzola, R. Helled, and S. Sorella, + | `Phys. Rev. Lett. 120, 025701 (2018). `_ + + +2017 +#################### + +.. 2017COC +.. article + +- | Theoretical :math:`S_{1}` :math:`\leftarrow` :math:`S_{0}` Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green's Function Theory, + | E. Coccia, D. Varsano, and L. Guidoni, + | `J. Chem. Theory Comput. 13, 4357--4367 (2017). `_ + +.. 2017MOU +.. article + +- | Fully quantum description of the zundel ion: combining variational quantum Monte Carlo with path integral langevin dynamics, + | F. Mouhat, S. Sorella, R. Vuilleumier, A. Saitta, and M. Casula, + | `J. Chem. Theory Comput. 13, 2400--2417 (2017). `_ + +.. 2017VAR +.. article + +- | Carbon nanotubes as excitonic insulators, + | D. Varsano, S. Sorella, D. Sangalli, M. Barborini, S. Corni, E. Molinari, and M. Rontani, + | `Nat. Commun. 8, 1461 (2017). `_ + +.. 2017MOT +.. article + +- | Towards the Solution of the Many-Electron Problem in Real Materials: Equation of State of the Hydrogen Chain with State-of-the-Art Many-Body Methods, + | M. Motta, D. Ceperley, G. Chan, J. Gomez, E. Gull, S. Guo, C. Jim\'enez-Hoyos, T. Lan, J. Li, F. Ma, A. Millis, N. Prokof'ev, U. Ray, G. Scuseria, S. Sorella, E. Stoudenmire, Q. Sun, I. Tupitsyn, S. White, D. Zgid, and S. Zhang, + | `Phys. Rev. X 7, 031059 (2017). `_ + +.. 2017MAZ +.. article + +- | Accelerating ab initio molecular dynamics and probing the weak dispersive forces in dense liquid hydrogen, + | G. Mazzola, and S. Sorella, + | `Phys. Rev. Lett. 118, 015703 (2017). `_ + +.. 2017BEC +.. book + +- | Quantum Monte Carlo approaches for correlated systems + | F. Becca, and S. Sorella, + | `Cambridge University Press (2017). `_ + + +2016 +#################### + +.. 2016CHU +.. article + +- | Role of electron correlation along the water splitting reaction + | S. Chu, E. Coccia, M. Barborini, and L. Guidoni, + | `J. Chem. Theory Comput. 12, 5803--5810 (2016). `_ + +.. 2016BAR2 +.. article + +- | Geometries of low spin states of multi-centre transition metal complexes through extended broken symmetry variational Monte Carlo, + | M. Barborini, and L. Guidoni, + | `J. Chem. Phys. 145, 124107 (2016). `_ + +.. 2016ZEN2 +.. article + +- | Boosting the accuracy and speed of quantum Monte Carlo: Size consistency and time step, + | A. Zen, S. Sorella, M. Gillan, A. Michaelides, and D. Alfe, + | `Phys. Rev. B 93, 241118 (2016). `_ + +.. 2016ZEN +.. article + +- | Toward accurate adsorption energetics on clay surfaces, + | A. Zen, L. Roch, S. Cox, X. Hu, S. Sorella, D. Alfe, and A. Michaelides, + | `J. Phys. Chem. C 120, 26402--26413 (2016). `_ + +.. 2016BUS +.. article + +- | Competing collinear magnetic structures in superconducting FeSe by first-principles quantum Monte Carlo calculations, + | B. Busemeyer, M. Dagrada, S. Sorella, M. Casula, and L. Wagner, + | `Phys. Rev. B 94, 035108 (2016). `_ + + +.. 2016BAR +.. article + +- | Correlation effects in scanning tunneling microscopy images of molecules revealed by quantum monte carlo, + | M. Barborini, S. Sorella, M. Rontani, and S. Corni, + | `J. Chem. Theory Comput. 12, 5339--5349 (2016). `_ + +.. 2016DAG +.. article + +- | Exact special twist method for quantum Monte Carlo simulations, + | M. Dagrada, S. Karakuzu, V. Vildosola, M. Casula, and S. Sorella, + | `Phys. Rev. B 94, 245108 (2016). `_ + + +2015 +#################### +.. 2015BAR3 +.. article + +- | Ground state geometries of polyacetylene chains from many-particle quantum mechanics, + | M. Barborini, and L. Guidoni, + | `J. Chem. Theory Comput. 11, 4109--4118 (2015). `_ + +.. 2015BAR2 +.. article + +- | :math:`\pi`-conjugation in trans-1,3-butadiene: static and dynamical electronic correlations described through Quantum Monte Carlo, + | M. Barborini, and L. Guidoni, + | `J. Chem. Theory Comput. 11, 508--517 (2015). `_ + +.. 2015BAR +.. article + +- | Investigating disjoint non-Kekule diradicals with quantum Monte Carlo: The tetramethyleneethane molecule through the jastrow antisymmetrized geminal power wave function, + | M. Barborini, and E. Coccia, + | `J. Chem. Theory Comput. 11, 5696--5704 (2015). `_ + +.. 2015ZEN2 +.. article + +- | Quantum Monte Carlo treatment of the charge transfer and diradical electronic character in a retinal chromophore minimal model, + | A. Zen, E. Coccia, S. Gozem, M. Olivucci, and L. Guidoni, + | `J. Chem. Theory Comput. 11, 992--1005 (2015). `_ + +.. 2015LUO +.. article + +- | Ab initio molecular dynamics with quantum Monte Carlo, + | Y. Luo, and S. Sorella, + | `Front. Mater. 2, 29 (2015). `_ + +.. 2015DUP +.. article + +- | Vertical and adiabatic excitations in anthracene from quantum Monte Carlo: Constrained energy minimization for structural and electronic excited-state properties in the JAGP ansatz, + | N. Dupuy, S. Bouaouli, F. Mauri, S. Sorella, and M. Casula, + | `J. Chem. Phys. 142, 214109 (2015). `_ + +.. 2015DEV +.. article + +- | Electronic origin of the volume collapse in cerium, + | N. Devaux, M. Casula, F. Decremps, and S. Sorella, + | `Phys. Rev. B 91, 081101 (2015). `_ + +.. 2015SOR +.. article + +- | Geminal embedding scheme for optimal atomic basis set construction in correlated calculations, + | S. Sorella, N. Devaux, M. Dagrada, G. Mazzola, and M. Casula, + | `J. Chem. Phys. 143, 244112 (2015). `_ + + +.. 2015MAZ +.. article + +- | Distinct metallization and atomization transitions in dense liquid hydrogen, + | G. Mazzola, and S. Sorella, + | `Phys. Rev. Lett. 114, 105701 (2015). `_ + + +.. 2015ZEN +.. article + +- | Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo, + | A. Zen, Y. Luo, G. Mazzola, L. Guidoni, and S. Sorella, + | `J. Chem. Phys. 142, 144111 (2015). `_ + + +2014 +#################### +.. 2014COC +.. article + +- | Ab initio geometry and bright excitation of carotenoids: quantum Monte Carlo and many body green's function theory calculations on peridinin, + | E. Coccia, D. Varsano, and L. Guidoni, + | `J. Chem. Theory Comput. 10, 501--506 (2014). `_ + +.. 2014DAG +.. article + +- | Quantum Monte Carlo study of the protonated water dimer, + | M. Dagrada, M. Casula, A. Saitta, S. Sorella, and F. Mauri, + | `J. Chem. Theory Comput. 10, 1980--1993 (2014). `_ + +.. 2014MAZ +.. article + +- | Unexpectedly high pressure for molecular dissociation in liquid hydrogen by electronic simulation, + | G. Mazzola, S. Yunoki, and S. Sorella, + | `Nat. Commun. 5, 3487 (2014). `_ + +.. 2014LUO +.. article + +- | Ab initio molecular dynamics with noisy forces: Validating the quantum Monte Carlo approach with benchmark calculations of molecular vibrational properties, + | Y. Luo, A. Zen, and S. Sorella, + | `J. Chem. Phys. 141, 194112 (2014). `_ + +.. 2014ZEN2 +.. article + +- | Properties of reactive oxygen species by quantum Monte Carlo, + | A. Zen, B. Trout, and L. Guidoni, + | `J. Chem. Phys. 141, 014305 (2014). `_ + +.. 2014ZEN +.. article + +- | Static and dynamical correlation in diradical molecules by quantum Monte Carlo using the Jastrow antisymmetrized geminal power ansatz, + | A. Zen, E. Coccia, Y. Luo, S. Sorella, and L. Guidoni, + | `J. Chem. Theory Comput. 10, 1048--1061 (2014). `_ + +2013 +#################### +.. 2013COC +.. article + +- | Protein field effect on the dark state of 11-cis retinal in rhodopsin by quantum Monte Carlo/molecular mechanics, + | E. Coccia, D. Varsano, and L. Guidoni, + | `J. Chem. Theory Comput. 9, 8--12 (2013). `_ + +.. 2013CAS +.. article + +- | Improper *s*-wave symmetry of the electronic pairing in iron-based superconductors by first-principles calculations, + | M. Casula, and S. Sorella, + | `Phys. Rev. B 88, 155125 (2013). `_ + +.. 2013ZEN +.. article + +- | Molecular properties by Quantum Monte Carlo: an investigation on the role of the wave function ansatz and the basis set in the water molecule, + | A. Zen, Y. Luo, S. Sorella, and L. Guidoni, + | `J. Chem. Theory Comput. 9, 4332--4350 (2013). `_ + + +2012 +#################### +.. 2012ZEN +.. article + +- | Optimized Structure and Vibrational Properties by Error Affected Potential Energy Surfaces, + | A. Zen, D. Zhelyazov, and L. Guidoni, + | `J. Chem. Theory Comput. 8, 4204--4215 (2012). `_ + + +.. 2012COC2 +.. article + +- | Quantum Monte Carlo study of the retinal minimal model :math:`\rm{C}_{5}\rm{H}_{6}\rm{NH}_{2}^{+}`, + | E. Coccia, and L. Guidoni, + | `J. Comput. Chem. 33, 2332--2339 (2012). `_ + +.. 2012BAR2 +.. article + +- | Reaction pathways by quantum Monte Carlo: Insight on the torsion barrier of 1,3-butadiene, and the conrotatory ring opening of cyclobutene, + | M. Barborini, and L. Guidoni, + | `J. Chem. Phys. 137, 224309 (2012). `_ + +.. 2012COC +.. article + +- | Molecular electrical properties from quantum Monte Carlo calculations: Application to ethyne, + | E. Coccia, O. Chernomor, M. Barborini, S. Sorella, and L. Guidoni, + | `J. Chem. Theory Comput. 8, 1952--1962 (2012). `_ + +.. 2012BAR +.. article + +- | Structural optimization by Quantum Monte Carlo: investigating the low-lying excited states of ethylene, + | M. Barborini, S. Sorella, and L. Guidoni, + | `J. Chem. Theory Comput. 8, 1260--1269 (2012). `_ + + +.. 2012MAZ +.. article + +- | Finite-temperature electronic simulations without the Born-Oppenheimer constraint, + | G. Mazzola, A. Zen, and S. Sorella, + | `J. Chem. Phys. 137, 134112 (2012). `_ + + +2011 +#################### +.. 2011STE +.. article + +- | Strong electronic correlation in the hydrogen chain: A variational Monte Carlo study, + | L. Stella, C. Attaccalite, S. Sorella, and A. Rubio, + | `Phys. Rev. B 84, 245117 (2011). `_ + +.. 2011SOR +.. article + +- | Ab initio calculations for the :math:`\beta`-tin diamond transition in silicon: Comparing theories with experiments, + | S. Sorella, M. Casula, L. Spanu, and A. Dal Corso, + | `Phys. Rev. B 83, 075119 (2011). `_ + +.. 2011MAR +.. article + +- | Fate of the Resonating Valence Bond in Graphene, + | M. Marchi, S. Azadi, and S. Sorella, + | `Phys. Rev. Lett. 107, 086807 (2011). `_ + + +2010 +#################### +.. 2010CAS +.. article + +- | Size-consistent variational approaches to nonlocal pseudopotentials: Standard and lattice regularized diffusion Monte Carlo methods revisited, + | M. Casula, S. Moroni, S. Sorella, and C. Filippi, + | `J. Chem. Phys. 132, 154113 (2010). `_ + +.. 2010AZA +.. article + +- | Systematically convergent method for accurate total energy calculations with localized atomic orbitals, + | S. Azadi, C. Cavazzoni, and S. Sorella, + | `Phys. Rev. B 82, 125112 (2010). `_ + +.. 2010SOR +.. article + +- | Algorithmic differentiation and the calculation of forces by quantum Monte Carlo, + | S. Sorella, and L. Capriotti, + | `J. Chem. Phys. 133, 234111 (2010). `_ + + +2009 +#################### +.. 2009NIS +.. article + +- | Resonating-valence-bond ground state of lithium nanoclusters, + | D. Nissenbaum, L. Spanu, C. Attaccalite, B. Barbiellini, and A. Bansil, + | `Phys. Rev. B 79, 035416 (2009). `_ + +.. 2009SPA +.. article + +- | Nature and Strength of Interlayer Binding in Graphite, + | L. Spanu, S. Sorella, and G. Galli, + | `Phys. Rev. Lett. 103, 196401 (2009). `_ + +.. 2009CAS +.. article + +- | A consistent description of the iron dimer spectrum with a correlated single-determinant wave function, + | M. Casula, M. Marchi, S. Azadi, and S. Sorella, + | `Chem. Phys. Lett. 477, 255--258 (2009). `_ + +.. 2009MAR +.. article + +- | Resonating valence bond wave function with molecular orbitals: Application to first-row molecules, + | M. Marchi, S. Azadi, M. Casula, and S. Sorella, + | `J. Chem. Phys. 131, 154116 (2009). `_ + + +2008 +#################### +.. 2008STE +.. article + +- | Dissecting the hydrogen bond: a quantum Monte Carlo approach + | F. Sterpone, L. Spanu, L. Ferraro, S. Sorella, and L. Guidoni, + | `J. Chem. Theory Comput. 4, 1428--1434 (2008). `_ + +.. 2008BEA +.. article + +- | Molecular hydrogen adsorbed on benzene: Insights from a quantum Monte Carlo study, + | T. Beaudet, M. Casula, J. Kim, S. Sorella, and R. Martin, + | `J. Chem. Phys. 129, 164711 (2008). `_ + +.. 2008ATT +.. article + +- | Stable liquid hydrogen at high pressure by a novel ab initio molecular-dynamics calculation, + | C. Attaccalite, and S. Sorella, + | `Phys. Rev. Lett. 100, 114501 (2008). `_ + + +2007 +#################### +.. 2007UMR +.. article + +- | Alleviation of the Fermion-Sign Problem by Optimization of Many-Body Wave Functions, + | C. Umrigar, J. Toulouse, C. Filippi, S. Sorella, and R. Hennig, + | `Phys. Rev. Lett. 98, 110201 (2007). `_ + +.. 2007SOR +.. article + +- | Weak binding between two aromatic rings: Feeling the van der Waals attraction by quantum Monte Carlo methods, + | S. Sorella, M. Casula, and D. Rocca, + | `J. Chem. Phys. 127, 014105 (2007). `_ + +2006 +#################### +.. 2006CAS +.. article + +- | Beyond the locality approximation in the standard diffusion Monte Carlo method + | M. Casula, + | `Phys. Rev. B 74, 161102 (2006). `_ + + +2005 +#################### +.. 2005CAS2 +.. article + +- | Resonating valence bond wave function: from lattice models to realistic systems + | M. Casula, S. Yunoki, C. Attaccalite, and S. Sorella, + | `Comput. Phys. Commun. 169, 386--393 (2005). `_ + +.. 2005CAS +.. article + +- | Diffusion Monte Carlo method with lattice regularization + | M. Casula, C. Filippi, and S. Sorella, + | `Phys. Rev. Lett. 95, 1--5 (2005). `_ + +.. 2005SOR +.. article + +- | Wave function optimization in the variational Monte Carlo method, + | S. Sorella, + | `Phys. Rev. B 71, 241103 (2005). `_ + + +2004 +#################### +.. 2004CAS +.. article + +- | Correlated geminal wave function for molecules: An efficient resonating valence bond approach, + | M. Casula, C. Attaccalite, and S. Sorella, + | `J. Chem. Phys. 121, 7110--7126 (2004). `_ + +2003 +#################### +.. 2003CAS +.. article + +- | Geminal wave functions with Jastrow correlation: A first application to atoms, + | M. Casula, and S. Sorella, + | `J. Chem. Phys. 119, 6500--6511 (2003). `_ + + + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/05PhD_Thesis.rst b/source/_sources/05PhD_Thesis.rst new file mode 100644 index 0000000..fe9b5fa --- /dev/null +++ b/source/_sources/05PhD_Thesis.rst @@ -0,0 +1,42 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +PhD thesis +=========================================== + +- | **Dr. Claudio Genovese**, 2020: + | Geminal Power in QMC, `pdf <../_static/02phd_thesis/claudio.pdf>`__ + +- | **Dr. Félix Mouhat**, 2018: + | Fully quantum dynamics of protonated water clusters, `pdf <../../_static/02phd_thesis/mouhat.pdf>`__ + +- | **Dr. Nicolas Dupuy**, 2016: + | Corrélations électroniques des acènes vers la limite de longue taille : Étude par Monte Carlo quantique (Electronic correlations in the acenes to ards the long-size limit: a Monte Carlo study), `pdf <../_static/02phd_thesis/dupuy.pdf>`__ + +- | **Dr. Henri Hay**, 2016: + | Étude de la structure et des propriétés des polymorphes de :math:`\rm{SiO}_{2}` et :math:`\rm{B}_{2}\rm{O}_{3}` par méthodes ab initio (Structural properties of :math:`\rm{SiO}_{2}` and :math:`\rm{B}_{2}\rm{O}_{3}` polymorphs by ab initio methods), `pdf <../../_static/02phd_thesis/hay.pdf>`__ + +- | **Dr. Mario Dagrada**, 2016: + | Improved quantum Monte Carlo simulations: from open to extended systems, `pdf <../_static/02phd_thesis/dagrada.pdf>`__ + +- | **Dr. Nicolas Dévaux**, 2015: + | Étude par Monte Carlo quantique de la transition α-γ du Cérium (Quantum Monte Carlo study of the α-γ transition in Cerium), `pdf <../_static/02phd_thesis/devaux.pdf>`__ + +- | **Dr. Guglielmo Mazzola**, 2014: + | Metallization and dissociation in high pressure liquid hydrogen by an efficient molecular dynamics with quantum Monte Carlo, `pdf <../_static/02phd_thesis/mazzola.pdf>`__ + +- | **Dr. Ye Luo**, 2014: + | Ab initio molecular dynamics of water by quantum Monte Carlo, `pdf <../_static/02phd_thesis/yeluo.pdf>`__ + +- | **Dr. Claudio Attaccalite**, 2005: + | RVB phase of hydrogen at high pressure: towards the first ab-initio Molecular Dynamics by Quantum Monte Carlo, `pdf <../_static/02phd_thesis/attacc.pdf>`__ + +- | **Dr. Michele Casula**, 2005: + | New QMC approaches for the simulation of electronic systems: a first application to aromatic molecules and transition metal compounds, `pdf <../_static/02phd_thesis/casula.pdf>`__ + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/06Presentations.rst b/source/_sources/06Presentations.rst new file mode 100644 index 0000000..efb4b2b --- /dev/null +++ b/source/_sources/06Presentations.rst @@ -0,0 +1,14 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Presentations +=========================================== + +To be available soon!! + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/07Basis_set_and_Pseudopotentials.rst b/source/_sources/07Basis_set_and_Pseudopotentials.rst new file mode 100644 index 0000000..19e9f7a --- /dev/null +++ b/source/_sources/07Basis_set_and_Pseudopotentials.rst @@ -0,0 +1,18 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Basis sets and Pseudopotentials +=========================================== + +- `Basis set exchange `_ +- `Energy-consistent pseudopotentials for QMC calculations `_ +- `Pseudopotentials developed for high accuracy correlated many-body methods `_ + +.. - `CASINO pseudopotential library `_ + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/08logos.rst b/source/_sources/08logos.rst new file mode 100644 index 0000000..b029b21 --- /dev/null +++ b/source/_sources/08logos.rst @@ -0,0 +1,30 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Logo collections +=========================================== + +TurboRVB +------------------------------------- + +.. figure:: /_static/07logo/logo.png + :width: 800px + +TurboGenius +------------------------------------- + +.. figure:: /_static/07logo/logo2.png + :width: 800px + +TurboWorkflows +------------------------------------- + +.. figure:: /_static/07logo/logo3.png + :width: 800px + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/09Useful_Links.rst b/source/_sources/09Useful_Links.rst new file mode 100644 index 0000000..ef90835 --- /dev/null +++ b/source/_sources/09Useful_Links.rst @@ -0,0 +1,42 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Useful Links +=========================================== + +Database +-------------------------------------- +- `Computational Chemistry Comparison and Benchmark DataBase `_ +- `The Benchmark Energy & Geometry Database `_ + +Data Analysis and Visualization +-------------------------------------- + +- `Gnuplot `_ +- `Xmgrace `_ +- `LabPlot `_ + +Molecules and Solids Visualization +-------------------------------------- +- `JMol `_ +- `XCrysDen `_ +- `Mercury `_ +- `VMD `_ +- `Atomic Simulation Environment `_ + +Free Scientific Books +-------------------------------------- +- `FreeScience.info `_ +- `The Net Advance of Physics `_ + +Crystal Structures +-------------------------------------- +- `Mineralogy Database `_ +- `Inorganic Crystal Structure Database `_ + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/_sources/10Workshops.rst b/source/_sources/10Workshops.rst new file mode 100644 index 0000000..a5cc4dc --- /dev/null +++ b/source/_sources/10Workshops.rst @@ -0,0 +1,78 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Workshops +=========================================== + +.. contents:: Table of Contents + :depth: 2 + +.. _workshop_summer_2023: + +Summer School on Quantum Monte Carlo methods 2024 +----------------------------------------------------------------------------------- +In preparation. + + +Summer School on Quantum Monte Carlo methods 2023 +----------------------------------------------------------------------------------- + +We held an in-person school on `quantum Monte Carlo with the TurboRVB code `__. The school was held from **July 3rd through 7th**, hosted by **SISSA, Trieste, Italy**, and organized in the frame of the TREX HPC European center of excellence. + +Lecturers +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- `Michele Casula `__ (IMPMC) +- `Kosuke Nakano `__ (NIMS) +- Saverio Moroni (SISSA) + +Date and place +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- 3-7 July 2023 +- `Scuola Internazionale Superiore di Studi Avanzati (SISSA) `__ +- Trieste, Italy + +.. _workshop_summer_2022: + +Summer School on Quantum Monte Carlo methods 2022 +----------------------------------------------------------------------------------- + +We held `QMC Hands-on Summer Workshop `__ on **20-23 June 2022** in Mojmírovce, Slovakia. + +Lecturers +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- Claudia Filippi (Universiteit Twente) +- Anthony Scemama (CNRS) +- Ivan Stich (Institute of Physics of the Slovak Academy of Sciences) +- Jan Brndiar (Institute of Physics of the Slovak Academy of Sciences) +- `Sandro Sorella `__ (SISSA) +- `Michele Casula `__ (IMPMC) +- `Kosuke Nakano `__ (SISSA, JAIST) +- `Andrea Tirelli `__ (SISSA) + +Date and place +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- 20-23 June 2022 +- Mojmírovce, Slovakia + + +.. _workshop_summer_2021: + +Summer School on Quantum Monte Carlo methods 2021 +----------------------------------------------------------------------------------- + +We held `TREX and SISSA Summer School on QMC with TurboRVB `__ on **12-16 July 2021** at International School for Advanced Studies (SISSA/Italy). + +Lecturers +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- `Sandro Sorella `__ (SISSA) +- `Michele Casula `__ (IMPMC) +- `Kosuke Nakano `__ (SISSA, JAIST) + +Date and place +^^^^^^^^^^^^^^^^^^^^^^^^^^^ +- 12-16 July 2021 +- Trieste, Italy (online) + + diff --git a/source/_sources/11Positions.rst b/source/_sources/11Positions.rst new file mode 100644 index 0000000..8bb7b14 --- /dev/null +++ b/source/_sources/11Positions.rst @@ -0,0 +1,32 @@ +.. TurboRVB_website documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Opening positions +=========================================== + +.. contents:: Table of Contents + :depth: 2 + +.. _positions: + +Postdoc position at SISSA +----------------------------------------------------------------------------------- +No opening position. + + +Postdoc position at CNRS +----------------------------------------------------------------------------------- +No opening position. + + +Postdoc position in TREX +----------------------------------------------------------------------------------- +No opening position. + + +Postdoc position at NIMS +----------------------------------------------------------------------------------- +No opening position. + diff --git a/source/_static/01photos/ak.jpg b/source/_static/01photos/ak.jpg new file mode 100644 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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('.')) +#import sphinx_bootstrap_theme +sys.path.insert(0, os.path.abspath('.')) +import sphinx_rtd_theme +import datetime + +# -- Project information ----------------------------------------------------- + +# The short X.Y version +today_date=datetime.datetime.today().strftime("%d/%m/%Y") +today_year=datetime.datetime.today().strftime("%Y") +version = 'Updated on {}'.format(today_date) +# The full version, including alpha/beta/rc tags +release = 'Updated on {}'.format(today_date) + +project = 'TurboRVB website' +copyright = f'{today_year}, Kosuke Nakano and collaborators.' +author = 'Kosuke Nakano' + +# -- 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.todo', 'sphinxcontrib_roles'] + +# For security reason, it is """SUPER""" important to set False !!!!!!!!!! +html_show_sourcelink = False +html_copy_source = False + +# Define roles as dict (define roles and its style on HTML) +roles = {'strike': "text-decoration: line-through;", + 'red': "color: red;", + 'blue': "color: blue;"} + +# To do +todo_include_todos = True + +# 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', '.README'] + +# 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 = 'en' + +# 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 = ['98presentations', '99logo_archived'] + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# sphinx.ext.jsmath +extensions += ['sphinx.ext.imgmath'] +imgmath_image_format='svg' +#extensions += ['sphinx.ext.jsmath'] + +# jsMath path +#jsmath_path = 'jsMath-3.6e/easy/load.js' + +# -- 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 = 'bootstrap' +#html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() +#html_theme_options = {'bootswatch_theme': "flatly"} + +html_theme = "sphinx_rtd_theme" +html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] +html_style = "css/my_theme.css" + +# 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 = 'TurboRVB_website' + + +# -- 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, 'turborvb_website.tex', 'turborvb_website_manual_documentation', + 'kosuke.nakano', '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, 'turborvb_website', 'TurboRVB_website 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, 'TurboRVB_website', 'TurboRVB_website Documentation', + author, 'TurboRVB_website', 'TurboRVB_website', + 'Miscellaneous'), +] diff --git a/source/index.rst b/source/index.rst new file mode 100644 index 0000000..c39acfd --- /dev/null +++ b/source/index.rst @@ -0,0 +1,60 @@ +.. TurboRVB_manual documentation master file, created by + sphinx-quickstart on Thu Jan 24 00:11:17 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to our TurboRVB website +=========================================== + +.. figure:: /_static/07logo/logo.png + :width: 800px + +News +######################## + +- | TurboRVB is now an `open-source project `_! +- | A. Raghav et al. have published a paper in `J. Chem. Theory Comput. 19, 2222-2229 (2023) `_. +- | E. Posenitskiy et al. have published a paper in `J. Chem. Phys. 158, 174801 (2023) `_. +- | L. Monacelli et al. have published a paper in `Nat. Phys. 19, 845–850 (2023) `_. +- | A. Tirelli et al. have published a paper in `Phys. Rev. B, 106, L041105 (2022) `_. +- | K. Nakano et al. have published a paper in `J. Chem. Phys. 156, 034101 (2022) `_. +- | K. Nakano et al. have published a paper in `Phys. Rev. B 103, L121110 (2021) `_. + | This paper has been selected as an **Editors' Suggestion**. + +Features +######################## + +`TurboRVB `__ is a computational package for **ab initio Quantum Monte Carlo (QMC) simulations** of both molecular and bulk electronic systems. +The code was initially launched by **Prof. Sandro Sorella** and **Prof. Michele Casula** and has been continuously developed by many contributors for over 20 years. The code implements two types of well established QMC algorithms: Variational Monte Carlo (VMC), and Diffusion Monte Carlo in its robust and efficient lattice regularized variant (LRDMC). + +The source codes of TurboRVB and other associated packages are available from :doc:`_sources/03Source_code`. + +TurboRVB is distinguishable from other QMC codes in the following features: + +- The code employs a resonating valence bond (RVB)-type wave function, such as the Jastrow Geminal/Jastrow Pfaffian. This wave function includes the correlation effect beyond the Jastrow-Slater wave function, which is commonly used in other QMC codes. + +- Implemented state-of-art optimization algorithms, such as the stochastic reconfiguration and the linear method, realize a stable optimization of the amplitude and nodal surface of many-body wave functions at the variational quantum Monte Carlo level. + +- The code implements the so-called lattice regularized diffusion Monte Carlo method, which provides a numerically stable diffusion quantum Monte Carlo calculation. + +- The implementation of an adjoint algorithmic differentiation allows us to differentiate many-body wave functions efficiently and to perform structural optimizations and calculate molecular dynamics. + +.. toctree:: + :maxdepth: 1 + :caption: Contents: + + _sources/02Developers.rst + _sources/03Source_code.rst + _sources/10Workshops.rst + _sources/11Positions.rst + _sources/04Publications.rst + _sources/05PhD_Thesis.rst + _sources/06Presentations.rst + _sources/07Basis_set_and_Pseudopotentials.rst + _sources/08logos.rst + _sources/09Useful_Links.rst + +.. + * :ref:`genindex` + * :ref:`modindex` + * :ref:`search` diff --git a/source/sphinxcontrib_roles.py b/source/sphinxcontrib_roles.py new file mode 100755 index 0000000..9a28568 --- /dev/null +++ b/source/sphinxcontrib_roles.py @@ -0,0 +1,43 @@ +# -*- coding: utf-8 -*- +import os +from docutils.parsers.rst import roles + + +def _define_role(name): + base_role = roles.generic_custom_role + role = roles.CustomRole(name, base_role, {'class': [name]}, []) + + roles.register_local_role(name, role) + + +def on_builder_inited(app): + for name in app.builder.config.roles: + _define_role(name) + + +def on_html_collect_pages(app): + if isinstance(app.builder.config.roles, dict) and app.builder.config.roles: + cssdir = os.path.join(app.builder.outdir, '_static') + cssfile = os.path.join(cssdir, 'roles.css') + if not os.path.exists(cssdir): + os.makedirs(cssdir) + + fd = open(cssfile, 'wt') + for name, style in app.builder.config.roles.items(): + fd.write("span.%s { %s }\n" % (name, style)) + fd.close() + + return () + + +def html_page_context(app, pagename, templatename, context, doctree): + if isinstance(app.builder.config.roles, dict) and app.builder.config.roles: + if 'css_files' in context: + context['css_files'].append('_static/roles.css') + + +def setup(app): + app.add_config_value('roles', [], 'html') + app.connect("builder-inited", on_builder_inited) + app.connect("html-collect-pages", on_html_collect_pages) + app.connect("html-page-context", html_page_context)