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* Update webpage

* Update image tag

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Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
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bjorgve and github-actions[bot] authored Feb 18, 2024
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2 changes: 1 addition & 1 deletion binder/Dockerfile
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### DO NOT EDIT THIS FILE! This Is Automatically Generated And Will Be Overwritten ###
FROM ghcr.io/mrchemsoft/vampyr-coven:ec0227a8dcdc
FROM ghcr.io/bjorgve/vampyr-coven:63a2115f8e3a
4 changes: 2 additions & 2 deletions content/conf.py
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# a list of builtin themes.
#
html_theme = "sphinx_book_theme"
html_logo = "img/hylleraas-logo.png"
html_logo = "img/vampyr-logo.png"
html_title = "" # project
html_js_files = [
"https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js",
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"thebe": True,
"notebook_interface": "jupyterlab",
},
}
}
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12 changes: 10 additions & 2 deletions content/index.rst
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VAMPyR coven
=====================

This is a collection of notebooks for VAMPyR.
This is a collection of notebooks for VAMPyR, the Very Accurate Multiresolution Python Routines library. The repository holds Jupyter notebooks that demonstrate the use of VAMPyR for various scientific computations and simulations.

The setup notebook provides instructions for installing and configuring the VAMPyR library and its dependencies, ensuring the environment is prepared for all subsequent simulations.

.. toctree::
:hidden:
:maxdepth: 1

setup

The demos include:

- The beryllium atom notebook, where users can learn about quantum mechanical modeling of the beryllium atom, including setting up the atomic structure, calculating energy levels, and visualizing electron orbitals using VAMPyR.
- The harmonic oscillator evolution notebook guides users through the simulation of the time evolution of a quantum harmonic oscillator, demonstrating the use of VAMPyR to solve the Schrödinger equation and analyze system dynamics.
- The PCMSolvent notebook focuses on the application of the Polarizable Continuum Model (PCM) for simulating solvent effects. It shows how VAMPyR can be used to model the influence of a solvent as a polarizable continuum on a solute molecule.

These notebooks can be run directly in the browser for convenience, but for those who prefer or require local execution, it is also possible to download the repository and run the notebooks on one's own machine.

.. toctree::
:hidden:
:maxdepth: 1
:caption: Exercises
:caption: Demos

notebooks/beryllium_atom
notebooks/harmonic_oscillator_evolution
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Setting up your system
======================

In order to follow this workshop, you will need access to the VAMPyR python
package and the MRChem program.
To use the VAMPyR Python package, you have two main options: working online or setting up your local environment.

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.
For online access, `Binder <https://mybinder.org>`_ allows you to run the Jupyter notebooks in the cloud without any local setup.

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.
For local use, setting up your Python environment correctly is crucial. The `Conda package and environment manager <https://docs.conda.io/en/latest/>`_ is recommended for installing binary packages, including VAMPyR, in an isolated and reproducible software environment.

Please refer to the respective GitHub repositories for different ways of installing:
For installation instructions, please refer to the VAMPyR GitHub repository:

- `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!
To install Miniconda, follow the official `Miniconda installation instructions <https://docs.conda.io/en/latest/miniconda.html>`_.

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