From abe21ac98ca8612c5d5cdf66ba0ef33439084400 Mon Sep 17 00:00:00 2001 From: Simon Gravelle Date: Fri, 17 Nov 2023 23:59:10 +0100 Subject: [PATCH] small correction --- .../tutorials/level0/lennard-jones-fluid.rst | 18 +++++++++++------- 1 file changed, 11 insertions(+), 7 deletions(-) diff --git a/docs/sphinx/source/tutorials/level0/lennard-jones-fluid.rst b/docs/sphinx/source/tutorials/level0/lennard-jones-fluid.rst index 3cae44ff..221f638b 100644 --- a/docs/sphinx/source/tutorials/level0/lennard-jones-fluid.rst +++ b/docs/sphinx/source/tutorials/level0/lennard-jones-fluid.rst @@ -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 @@ -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 (#) @@ -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 @@ -873,6 +877,10 @@ 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 @@ -880,10 +888,6 @@ Restarting from a saved configuration 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