Merge pull request #102 from lammpstutorials/add-tutorial-8

Add tutorial 8

Author: simongravelle

.dependencies/lammpstutorials-inputs

@@ -21,6 +21,7 @@ lammpstutorials by Simon Gravelle : LAMMPS courses for beginners
     tutorial5/reactive-silicon-dioxide.rst
     tutorial6/water-adsorption-in-silica.rst
     tutorial7/free-energy-calculation.rst
+    tutorial8/reactive-molecular-dynamics.rst
 
 .. toctree::
     :maxdepth: 2

docs/sphinx/source/index.rst

@@ -3,7 +3,7 @@
 Scope
 *****
 
-This set of tutorials consists of seven tutorials arranged in order of
+This set of tutorials consists of eight tutorials arranged in order of
 increasing difficulty.  The novelties associated with each tutorial are
 briefly described below.
 
@@ -59,8 +59,7 @@ an energy barrier, this tutorial describes a protocol
 for addressing energy landscapes that are difficult to sample using
 classical MD or MC methods.
 
-..
-    In :ref:`bond-react-label`, a CNT embedded in
-    nylon-6,6 polymer melt is simulated.  The
-    REACTER protocol is used to model the polymerization of nylon, and the formation
-    of water molecules is tracked over time~\cite{gissinger2020reacter}.
+In :ref:`bond-react-label`, a CNT embedded in
+nylon-6,6 polymer melt is simulated.  The
+REACTER protocol is used to model the polymerization of nylon, and the formation
+of water molecules is tracked over time~\cite{gissinger2020reacter}.

docs/sphinx/source/non-tutorials/scope.rst

@@ -1,19 +1,19 @@
-.. figure:: avatars/avatar_light.webp
+.. figure:: avatars/avatar.webp
     :height: 250
-    :alt: Lennard Jones atoms simulated with LAMMPS
+    :alt: Carbon nanotube (CNT) embedded in a polymer melt composed of polystyrene with LAMMPS
     :class: only-light
     :align: right
 
-.. figure:: avatars/avatar_dark.webp
+.. figure:: avatars/avatar-dm.webp
     :height: 250
-    :alt: Lennard Jones atoms simulated with LAMMPS
+    :alt: Carbon nanotube (CNT) embedded in a polymer melt composed of polystyrene with LAMMPS
     :class: only-dark
     :align: right
 
-The goal of this tutorial is to create a model of a carbon nanotube (CNT) embedded
-in a polymer melt made of polystyrene (PS) (Fig.~\ref{fig:REACT}).  The
-REACTER protocol is used to simulate the polymerization of styrene monomers, and the
-polymerization reaction is followed in time :cite:`gissinger2017polymer, gissinger2020reacter, gissinger2024molecular`.
-In contrast with AIREBO :ref:`carbon-nanotube-label`
-and ReaxFF :ref:`reactive-silicon-dioxide-label`, the REACTER
-protocol relies on the use of a *classical* force field.
+The goal of this tutorial is to create a model of a carbon nanotube (CNT)
+embedded in a polymer melt composed of polystyrene (PS). The REACTER
+protocol is used to simulate the polymerization of styrene monomers, and the
+polymerization reaction is tracked over time :cite:`gissinger2017polymer,
+gissinger2020reacter, gissinger2024molecular`. In contrast to AIREBO
+:ref:`carbon-nanotube-label` and ReaxFF :ref:`reactive-silicon-dioxide-label`,
+the REACTER protocol relies on the use of a *classical* force field.

docs/sphinx/source/tutorial8/avatars/avatar-dm.webp

@@ -1,9 +1,9 @@
 Creating the system
 ===================
 
-To begin this tutorial, select ``Start Tutorial 8`` from the
-``Tutorials`` menu of LAMMPS--GUI and follow the instructions.
-The editor should display the following content corresponding to **mixing.lmp**:
+To begin this tutorial, select ``Start Tutorial 8`` from the ``Tutorials`` menu
+of LAMMPS--GUI and follow the instructions. The editor should display the
+following content corresponding to **mixing.lmp**:
 
 .. code-block:: lammps
 
@@ -29,9 +29,13 @@ of the cross coefficients:
 
 .. math::
 
-    \sigma_{ij} & = & 2^{-1/6} (\sigma^6_i+\sigma_j^6)^{1/6}, ~ \text{and}
+    \sigma_{ij} = 2^{-1/6} (\sigma^6_i+\sigma_j^6)^{1/6},
 
-    \epsilon_{ij} & = & \dfrac{2 \sqrt{\epsilon_i \epsilon_j} \sigma^3_i \sigma^3_j}{\sigma^6_i+\sigma_j^6}.
+and
+
+.. math::
+
+    \epsilon_{ij} = \dfrac{2 \sqrt{\epsilon_i \epsilon_j} \sigma^3_i \sigma^3_j}{\sigma^6_i+\sigma_j^6}.
 
 Let us read the |CNT_data_8| file, which contains a periodic single-walled
 CNT.  Add the following line to **mixing.lmp**:
@@ -170,7 +174,7 @@ The third reaction uses the prefix ``P-P``,
 - |P_P_post_mol_8|,
 - |P_P_rxnmap_8|.
 
-Here, the file names for each reaction use the abbreviation `M' for monomer and `P'
+Here, the file names for each reaction use the abbreviation ``M`` for monomer and ``P``
 for polymer.
 
 .. |M_M_pre_mol_8| raw:: html
@@ -275,9 +279,19 @@ based on the atom map **M-M.rxnmap**.  Implementation details about each reactio
 such as the reaction distance cutoffs and the frequency with which to search for
 reaction sties, are also specified in this command.
 
-ADD REACT-final FIGURE: Final configuration.
-The atoms from the formed polymer named ``c1``, ``c2``, and
-``c3`` are colored in pink.
+.. figure:: figures/REACT-composite-dm.png
+    :class: only-dark
+    :alt: Evolution of reacting species
+
+.. figure:: figures/REACT-composite.png
+    :class: only-light
+    :alt: Evolution of reacting species
+
+..  container:: figurelegend
+
+    Figure: Initial (left) and final (right) configuration.
+    The atoms from the formed polymer named ``c1``, ``c2``, and
+    ``c3`` are colored in pink.
 
 .. admonition:: Note
     :class: non-title-info