Merge pull request #4 from bjorgve/move-to-content

Update

content/bibliography.bib

@@ -0,0 +1,85 @@
+@MISC{mrchem-zenodo,
+  author       = {Bast, Radovan and
+                  Bjorgve, Magnar and
+                  Di Remigio, Roberto and
+                  Durdek, Antoine and
+                  Frediani, Luca and
+                  Gerez, Gabriel and
+                  Jensen, Stig Rune and
+                  Juselius, Jonas and
+                  Monstad, Rune and
+                  Wind, Peter},
+  title        = {MRChem: MultiResolution Chemistry},
+  month        = dec,
+  year         = 2020,
+  publisher    = {Zenodo},
+  version      = {v1.0.1},
+  doi          = {10.5281/zenodo.4306059},
+  url          = {https://doi.org/10.5281/zenodo.4306059}
+}
+
+@MISC{mrcpp-zenodo,
+  author       = {Bast, Radovan and
+                  Bjorgve, Magnar and
+                  Di Remigio, Roberto and
+                  Durdek, Antoine and
+                  Frediani, Luca and
+                  Fossgaard, Eirik and
+                  Gerez, Gabriel and
+                  Jensen, Stig Rune and
+                  Juselius, Jonas and
+                  Monstad, Rune and
+                  Wind, Peter},
+  author       = {Frediani, Luca},
+  title        = {MRCPP: MultiResolution Computation Program Package},
+  month        = oct,
+  year         = 2020,
+  publisher    = {Zenodo},
+  version      = {v1.3.6},
+  doi          = {10.5281/zenodo.4139210},
+  url          = {https://doi.org/10.5281/zenodo.4139210}
+}
+
+@MISC{vampyr-zenodo,
+  author       = {Battistella, Evelin and
+                  Bjorgve, Magnar and
+                  Di Remigio, Roberto and
+                  Frediani, Luca and
+                  Gerez, Gabriel and
+                  Jensen, Stig Rune},
+  title        = {{VAMPyR: Very Accurate Multiresolution Python 
+                   Routines}},
+  month        = oct,
+  year         = 2020,
+  publisher    = {Zenodo},
+  version      = {v0.1.0rc0},
+  doi          = {10.5281/zenodo.4117603},
+  url          = {https://doi.org/10.5281/zenodo.4117603}
+}
+
+@BOOK{Szabo1996-vl,
+  title     = "{Modern Quantum Chemistry: Introduction to Advanced Electronic
+               Structure Theory}",
+  author    = "Szabo, Attila and Ostlund, Neil S",
+  publisher = "Courier Corporation",
+  series    = "Dover Books on Chemistry",
+  month     =  jul,
+  year      =  1996,
+  url       = "https://play.google.com/store/books/details?id=k-DcCgAAQBAJ",
+  language  = "en",
+  isbn      = "9780486691862",
+  lccn      = "lc96010775"
+}
+
+@BOOK{Helgaker2000-yb,
+  title     = "{Molecular Electronic-Structure Theory}",
+  author    = "Helgaker, Trygve and J{\o}rgensen, Poul and Olsen, Jeppe",
+  publisher = "Wiley",
+  edition   = "1 edition",
+  month     =  oct,
+  year      =  2000,
+  url       = "https://play.google.com/store/books/details?id=2G8vAQAAIAAJ",
+  language  = "en",
+  isbn      = "9780471967552"
+}
+

content/conf.py

@@ -0,0 +1,129 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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 = "Vampyr coven"
+copyright = "2024, The contributors"
+author = "The contributors"
+github_user = "MRChemSoft"
+github_repo_name = "vampyr-coven"  # auto-detected from dirname if blank
+github_version = "main"
+conf_py_path = "/content/"  # with leading and trailing slash
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    # githubpages just adds a .nojekyll file
+    "sphinx.ext.githubpages",
+    "sphinx_lesson",
+    # 'sphinx.ext.intersphinx',
+    "sphinxcontrib.bibtex",
+    "sphinx.ext.todo",
+    # "sphinx_thebe",
+]
+# configure myst_nb
+source_suffix = {".rst": "restructuredtext", ".ipynb": "myst-nb", ".myst": "myst-nb"}
+# configure sphinxcontrib.bibtex
+bibtex_bibfiles = ["bibliography.bib"]
+# Settings for myst_nb:
+# https://myst-nb.readthedocs.io/en/latest/use/execute.html#triggering-notebook-execution
+jupyter_execute_notebooks = "off"  # no notebook execution
+# jupyter_execute_notebooks = "auto"   # *only* execute if at least one output is missing.
+# jupyter_execute_notebooks = "force"  # *always* execute notebooks
+# jupyter_execute_notebooks = "cache"  # *cache* execution outputs
+
+# Add any paths that contain templates here, relative to this directory.
+# templates_path = ['_templates']
+
+# 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 = [
+    "README*",
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+    "jupyter_execute",
+    "*venv*",
+    "notebooks/solutions/*.ipynb",
+    "notebooks/visualization_*.ipynb"
+]
+
+# -- 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_book_theme"
+html_logo = "img/hylleraas-logo.png"
+html_title = ""  # project
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js",
+    "https://3Dmol.org/build/3Dmol-min.js"
+]
+# sphinx-book-theme options
+html_theme_options = {
+    "repository_url": f"https://github.com/{github_user}/{github_repo_name}",
+    "use_repository_button": True,
+    "use_issues_button": True,
+    "use_edit_page_button": True,
+    "repository_branch": "master",
+    "path_to_docs": "content",
+    "use_download_button": True,
+    "home_page_in_toc": True,
+    "launch_buttons": {
+        "binderhub_url": "https://mybinder.org",
+        "notebook_interface": "jupyterlab",
+    },
+}
+html_sidebars = {
+    "**": [ "sidebar-logo.html", "sbt-sidebar-nav.html", "sbt-sidebar-footer.html"]
+}
+# 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", "inputs"]
+# html_css_files = ["overrides.css"]
+# HTML context:
+from os.path import basename, dirname, realpath
+
+html_context = {
+    "display_github": True,
+    "github_user": github_user,
+    # Auto-detect directory name.  This can break, but
+    # useful as a default.
+    "github_repo": github_repo_name or basename(dirname(realpath(__file__))),
+    "github_version": github_version,
+    "conf_py_path": conf_py_path,
+}
+# Intersphinx mapping.  For example, with this you can use
+# :py:mod:`multiprocessing` to link straight to the Python docs of that module.
+# List all available references:
+#   python -msphinx.ext.intersphinx https://docs.python.org/3/objects.inv
+# intersphinx_mapping = {
+#    #'python': ('https://docs.python.org/3', None),
+#    #'sphinx': ('https://www.sphinx-doc.org/', None),
+#    }
+
+# the epilog
+rst_epilog = f"""
+.. role:: red
+.. role:: blue
+.. _MRChemSoft: https://github.com/MRChemSoft
+"""

content/index.rst

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+VAMPyR coven
+=====================
+
+This is a collection of notebooks for VAMPyR.
+
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+
+   setup
+
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: Exercises
+
+   notebooks/beryllium_atom
+   notebooks/harmonic_oscillator_evolution
+   notebooks/PCMSolvent

content/setup.rst

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+.. _setup:
+
+Setting up your system
+======================
+
+In order to follow this workshop, you will need access to the VAMPyR python
+package and the MRChem program.
+
+You can work on the VAMPyR content entirely online using `Binder <https://mybinder.org>`_
+to run the Jupyter notebooks in the cloud, but some of the MRChem exercises are best
+performed on a HPC cluster.
+
+If you prefer to work locally, you will need to set up your Python environment correctly:
+we recommend using the `Conda package and enviroment manager
+<https://docs.conda.io/en/latest/>`_, as it provides a convenient way to install
+binary packages, including VAMPyR and MRChem, in an isolated, reproducible software
+environment.
+
+Please refer to the respective GitHub repositories for different ways of installing:
+
+- `VAMPyR <https://github.com/MRChemSoft/vampyr/blob/master/README.md>`_
+- `MRChem <https://github.com/MRChemSoft/mrchem/blob/master/README.md>`_
+
+
+Install Miniconda
+^^^^^^^^^^^^^^^^^
+
+Follow the official `Miniconda
+<https://docs.conda.io/en/latest/miniconda.html>`_  installation instructions
+for your platform:
+
+- For Linux see https://docs.conda.io/en/latest/miniconda.html#linux-installers
+- For macOS see https://docs.conda.io/en/latest/miniconda.html#macosx-installers
+- For Windows see https://docs.conda.io/en/latest/miniconda.html#windows-installers
+
+For all platforms, make sure to select the **Python 3.8**, **64 bit** installer.
+
+
+Cloning the vampyr coven repository
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+If you want to run the exercise notebooks locally on your laptop, then you can
+clone our tutorial repository. We provide a conda environment
+complete with all the things you need to run the notebooks.
+
+Clone the repostory with::
+
+  $ git clone https://github.com/MRChemSoft/vampyr-coven.git
+
+Then move into this repository::
+
+  $ cd vampyr-coven
+
+To create the environment, use the instructions in the next section.
+Finally, launch a `Jupyter lab` instance with::
+
+  $ jupyter lab
+
+This should open up a new tab in your default browser.
+The notebooks can be found in `content/notebooks`.
+
+Creating an environment and installing packages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Once you have ``conda`` installed and correctly configured you can use the
+:download:`environment.yml <../environment.yml>` file to install the
+dependencies.  First save it to your hard drive by clicking the link, and then
+in a terminal (Anaconda Prompt on Windows) navigate to where you saved the file
+and type::
+
+  $ conda env create -f environment.yml
+
+
+You then need to activate the new environment by::
+
+  $ conda activate vampyr-coven
+
+
+Now you should have VAMPyR, MRChem, Python, JupyterLab and a few other packages installed!

content/zbibliography.rst

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+Bibliography
+------------
+
+.. bibliography:: bibliography.bib

environment.yml

@@ -1,4 +1,4 @@
-name: mw-coven
+name: vampyr-coven
 channels:
   - conda-forge
 dependencies: