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docs/sphinx/source/tutorials/level1/breaking-a-carbon-nanotube.rst

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@@ -33,9 +33,8 @@ Pulling on a carbon nanotube
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.. container:: abstract
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The difference between classical and reactive force fields
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is illustrated through this tutorial.
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With a classical force field, the bonds between atoms
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are unbreakable. With the reactive
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is illustrated in this tutorial. With a classical force field, the bonds
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between atoms are unbreakable. With the reactive
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force field (named AIREBO :cite:`stuart2000reactive`),
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the breaking of the chemical bonds is possible when
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the imposed deformation is strong enough.

docs/sphinx/source/tutorials/level1/lennard-jones-fluid.rst

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The very basics of LAMMPS through a simple example
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.. figure:: ../figures/level1/lennard-jones-fluid/lennard-jones-fluid-avatar-dark.webp
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:alt: binary lennard jones fluid simulated with LAMMPS
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:alt: The binary mixture simulated during Tutorial 1. The atoms of type 1 are represented as small green spheres and the atoms of type 2 as large blue spheres.
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:height: 250
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:align: right
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:class: only-dark
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.. figure:: ../figures/level1/lennard-jones-fluid/lennard-jones-fluid-avatar-light.webp
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:alt: binary lennard jones fluid simulated with LAMMPS
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:alt: The binary mixture simulated during Tutorial 1. The atoms of type 1 are represented as small green spheres and the atoms of type 2 as large blue spheres.
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:height: 250
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:align: right
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:class: only-light
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.. container:: abstract
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The system is a Lennard-Jones fluid made of neutral
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particles with two different diameters in a cubic box with periodic
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boundary conditions. In this tutorial, the temperature of the system is
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The system is a Lennard-Jones fluid composed of neutral particles with two
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different diameters, contained within a cubic box with periodic boundary conditions
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In this tutorial, the temperature of the system is
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maintained using a Langevin thermostat :cite:`schneider1978molecular`, and
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basic quantities are extracted from the system, including the potential and
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kinetic energies.
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.. container:: justify
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To run a simulation using LAMMPS, one needs to write a series of commands
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To run a simulation using LAMMPS, one needs to write a series of commands
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in an input script. For clarity, the input scripts written for this first
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tutorial will be divided into five categories which we are going to fill up
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one by one.
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Create a folder, call it *my-first-input/*, and then create a blank
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text file in it called *input.lammps*. Copy the following lines
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in *input.lammps*, where a line starting with a brace (#)
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is a comment that is ignored by LAMMPS:
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in *input.lammps*, where a line starting with a hash symbol (#)
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is a comment ignored by LAMMPS:
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.. code-block:: lammps
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.. container:: justify
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The first line, *units lj*, indicates that we want to
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use the system of unit called *LJ*, for Lennard-Jones, for
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use the unit system called *LJ* (Lennard-Jones), in
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which all quantities are unitless.
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.. admonition:: About Lennard-Jones (LJ) units
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.. container:: justify
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where :math:`r` is the inter-particles distance,
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:math:`\epsilon_{ij}` the depth of potential well that sets the interaction strength, and
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:math:`\sigma_{ij}` the distance parameter, or particle effective size.
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:math:`\epsilon_{ij}` is the depth of potential well that sets the interaction strength, and
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:math:`\sigma_{ij}` is the distance parameter or particle effective size.
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Here, the indexes *ij* refer to the particle types *i* and *j*.
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.. admonition:: About Lennard-Jones potential
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At this point, the *input.lammps* is a
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LAMMPS input script that does nothing.
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You can run it using LAMMPS to verify that the *input* contains
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no mistake by running the following command in the terminal
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no mistake by typing the following command in the terminal
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from the *my-first-input/* folder:
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.. code-block:: bw
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The *thermo_style custom* requires LAMMPS to print
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the system temperature (*temp*), potential energy (*pe*),
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kinetic energy (*ke*), total energy (*etotal*),
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and pressure (*press*). Finally, the *minimize* line
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asks LAMMPS to perform an energy minimization of the system.
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and pressure (*press*). Finally, the *minimize* command
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instructs LAMMPS to perform an energy minimization of the system.
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.. admonition:: About energy minimization
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:class: info
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of the repulsive part of the Lennard-Jones interaction
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potential. As the energy minimization progresses, the energy
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rapidly decreases and reaches a negative value, indicating that the atoms have been
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displaced at reasonable distances from each others.
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displaced at reasonable distances from each other.
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.. admonition:: On the temperature during energy minimization
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:class: info
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.. container:: justify
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The system is now ready. Let us continue filling up the
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input script and adding commands to perform a molecular dynamics
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simulation that will start from the final state of the previous energy
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minimization step.
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The system is now ready. Let us continue by completing the input script and adding commands to perform a molecular
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dynamics simulation, starting from the final state of the previous energy minimization step.
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.. admonition:: Background Information -- What is molecular dynamics?
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:class: info
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.. container:: justify
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The 2 *variables* are used to count
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The two *variables* are used to count
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the number of atoms of a specific group in the *region_cylinder_in* region.
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.. container:: justify

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