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imrpove SiO tutorial
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simongravelle committed Oct 5, 2023
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -27,3 +27,4 @@ find more information on my [personal webpage](https://simongravelle.github.io/)

All the inputs, scripts, and data files are released under the
GNU general public license v3.0.

19 changes: 10 additions & 9 deletions docs/sphinx/source/tutorials/level3/water-adsorption-in-silica.rst
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Expand Up @@ -5,30 +5,29 @@ Water adsorption in silica

.. container:: hatnote

Using the grand canonical Monte Carlo method
Dealing with varying molecule number

.. figure:: ../figures/level3/water-adsorption-in-silica/main-light.png
:height: 250
:alt: Water molecule adsorbed in silica matrix
:alt: Water molecules adsorbed in silica SiO2 porous inorganic material
:class: only-light
:align: right

.. figure:: ../figures/level3/water-adsorption-in-silica/main-dark.png
:height: 250
:alt: Water molecule adsorbed in silica matrix
:alt: Water molecules adsorbed in silica SiO2 porous inorganic material
:class: only-dark
:align: right

.. container:: justify

The objective of this tutorial is to combine molecular
dynamics and grand canonical Monte Carlo simulations to
simulate the adsorption of water molecules in a cracked
silica.
compute the adsorption of water molecules in a cracked silica material.

This tutorial illustrates the use of the grand canonical
ensemble in molecular simulation, an ensemble in which the number of
molecule/atom is not constant.
ensemble in molecular simulation, an open ensemble in which the number of
molecules or atoms is not constant.

.. include:: ../../contact/recommand-lj.rst

Expand All @@ -39,9 +38,11 @@ Generation of the silica block

.. container:: justify

Let us generate a block of amorphous silica (SiO2). To do
Let us first generate a block of amorphous silica (SiO2). To do
so, we are going to replicate a building block containing 3
Si and 6 O atoms. The data file for the SiO atoms can be
Si and 6 O atoms.

The data file for the SiO atoms can be
downloaded by clicking |download_SiO.data|.
Save it in a folder called SilicaBlock. This data file
contains the coordinates of the atoms, their masses, and
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