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simongravelle committed Nov 17, 2023
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18 changes: 11 additions & 7 deletions docs/sphinx/source/tutorials/level0/lennard-jones-fluid.rst
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Expand Up @@ -23,8 +23,10 @@ Lennard Jones fluid

The objective of this tutorial is to use
LAMMPS to perform a simple molecular dynamics simulation
of a binary fluid in the NVT ensemble. The system is a simple Lennard-Jones fluid
made of neutral dots with a Langevin thermostating. The
of a binary fluid in the NVT ensemble. The system is
a simple Lennard-Jones fluid made of neutral
particles with different sizes. A Langevin thermostat is
applied to the particles. The
simulation box is cubic with periodic boundary conditions.

.. container:: abstract
Expand All @@ -48,6 +50,8 @@ The input script
this script will be divided into five categories which we are going to
fill up one by one.

.. container:: justify

Create a folder, call it *my-first-input*, and then create a blank
text file in it, called *input.lammps*. Copy the following lines
in *my-first-input/input.lammps*, where a line starting with a brace (#)
Expand Down Expand Up @@ -775,7 +779,7 @@ Restarting from a saved configuration
.. container:: justify

Add the following lines to *input.md.lammps*
(note the absence of mass and pair_coeff parameters):
(note the absence of mass and *pair_coeff* parameters):

.. code-block:: lammps
Expand Down Expand Up @@ -873,17 +877,17 @@ Restarting from a saved configuration
:alt: LAMMPS VMD tutorial molecular dynamics simulation
:class: only-dark

.. container:: figurelegend

Figure: Evolution of the atom populations during mixing.

.. container:: justify

After running *input.md.lammps* using LAMMPS, you can observe the number
of atoms in each region from the generated data files, as
well as the evolution of the coordination number due to
mixing:

.. container:: figurelegend

Figure: Evolution of the atom populations during mixing.

.. figure:: ../figures/level0/lennard-jones-fluid/mixing-light.png
:alt: Result tutorial molecular dynamics simulation: Energy plot over time
:class: only-light
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