diff --git a/.dependencies/lammpstutorials-inputs b/.dependencies/lammpstutorials-inputs index f1592294..5cf1ff47 160000 --- a/.dependencies/lammpstutorials-inputs +++ b/.dependencies/lammpstutorials-inputs @@ -1 +1 @@ -Subproject commit f1592294274e5d9c368349f0e7381d1cc7d37cf7 +Subproject commit 5cf1ff474d31a377d1cb96e4dbc838b908e48f19 diff --git a/docs/sphinx/source/index.rst b/docs/sphinx/source/index.rst index 5879eb0f..8aea34a9 100644 --- a/docs/sphinx/source/index.rst +++ b/docs/sphinx/source/index.rst @@ -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 diff --git a/docs/sphinx/source/non-tutorials/scope.rst b/docs/sphinx/source/non-tutorials/scope.rst index 9be13601..fcff0e0c 100644 --- a/docs/sphinx/source/non-tutorials/scope.rst +++ b/docs/sphinx/source/non-tutorials/scope.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}. \ No newline at end of file +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}. \ No newline at end of file diff --git a/docs/sphinx/source/tutorial8/avatars/avatar-dm.webp b/docs/sphinx/source/tutorial8/avatars/avatar-dm.webp new file mode 100644 index 00000000..09b01315 Binary files /dev/null and b/docs/sphinx/source/tutorial8/avatars/avatar-dm.webp differ diff --git a/docs/sphinx/source/tutorial8/avatars/avatar.webp b/docs/sphinx/source/tutorial8/avatars/avatar.webp new file mode 100644 index 00000000..ac2e28a5 Binary files /dev/null and b/docs/sphinx/source/tutorial8/avatars/avatar.webp differ diff --git a/docs/sphinx/source/tutorial8/figures/REACT-composite-dm.png b/docs/sphinx/source/tutorial8/figures/REACT-composite-dm.png new file mode 100644 index 00000000..8b3f240e Binary files /dev/null and b/docs/sphinx/source/tutorial8/figures/REACT-composite-dm.png differ diff --git a/docs/sphinx/source/tutorial8/figures/REACT-composite.png b/docs/sphinx/source/tutorial8/figures/REACT-composite.png new file mode 100644 index 00000000..6fef91bd Binary files /dev/null and b/docs/sphinx/source/tutorial8/figures/REACT-composite.png differ diff --git a/docs/sphinx/source/tutorial8/introduction.rst b/docs/sphinx/source/tutorial8/introduction.rst index 4dccec16..cd7b9d82 100644 --- a/docs/sphinx/source/tutorial8/introduction.rst +++ b/docs/sphinx/source/tutorial8/introduction.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. \ No newline at end of file +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. \ No newline at end of file diff --git a/docs/sphinx/source/tutorial8/tutorial.rst b/docs/sphinx/source/tutorial8/tutorial.rst index d14c4f3b..569bd746 100644 --- a/docs/sphinx/source/tutorial8/tutorial.rst +++ b/docs/sphinx/source/tutorial8/tutorial.rst @@ -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