LAMMPS-Molecular-Dynamics-Simulator/C2/Simulation-of-Lennard-Jones-Bulk-Liquid/English

Title of script: Simulation of Lennard-Jones Bulk Liquid

Author: Dr.Snehalatha Kaliappan, Prasad Baddi

Keywords: LAMMPS, Simulation, Lennard-Jones bulk liquid, input file, video tutorial

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Simulation of Lennard-Jones Bulk Liquid.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to, Understand the structure of the input script to simulate Lennard-Jones bulk liquid.
Slide Number 3 Learning Objectives	In this tutorial, we will learn to, Initialize, setup simulation box, create atoms, minimize energy and equilibration. Run the simulation.
Slide Number 4 System Requirement	To record this tutorial, I am using, Ubuntu Linux OS version 22.04 Latest stable version of LAMMPS (LAMMPS Stable Release 29 Aug 2024)
Slide Number 5 Prerequisite	To follow this tutorial learner must be familiar with, basic computer operations on Linux OS.
Slide number 6 Code file	The following input file is required to practice this tutorial: LJBulk.txt This file is provided in the Code files link of this tutorial page.
Slide Number 7 LJ Bulk Liquid simulations	Here are some specific reasons for choosing the Lennard-jones simulations. Simplicity and Computational Efficiency Benchmarking and Model Testing Risk-Free Exploration of Scenarios Compatibility with Broader Systems For detailed explanation please refer to the Additional Reading material provided along with this tutorial.
Open the input file LJBulk.txt in gedit texttext editor.	Running simulations in LAMMPS require an input file. Download the input file provided along with this tutorial and save it on your system. Here I have opened the input file in a text editor.
Cursor on each section and highlight.	The input script is divided into four sections:  Initialization System definition Simulation settings Running a simulation
Cursor on the input file.	Now let us look at what needs to be defined in each section:
Cursor on Initialization section. Line 3: units lj	Initialization The units command sets the style of the units for the quantities specified in the input script, data file, and output. Here we have specified as lj.
Line 4: dimension 3	The dimension command sets the dimension of the simulation. Here we have 3, since we require the simulation in 3D. You can set it as 2, if you require a 2D simulation.
Line 5: boundary p p p	The boundary command sets the boundary conditions of the simulation box. here, p refers periodic
Line 6: atom_style atomic	The atom_style command defines necessary per-atom attributes for simulation models and data handling.
Cursor on System definition section. Line 12: region box block 0 20 0 20 0 20 units box region liquid block 1 19 1 19 1 10 create_atoms1 random 1754 12345 liquid mass 1 1.0	System definition: Here we define a geometric region of space in x, y and z direction. We specified number 20 here. This number can be small or big, depending on the requirement of the simulation box.
Line 13: It is on line 14create_box 1 box	Defining simulation box Here 1 indicates the number of atom types present in the system. For example, if the system consists of 3 types of particles, then 1 should be replaced with 3 and so on.
Line 16: region liquid block 1 19 1 19 1 10	Defining a geometric region to place the liquid atoms. Here, liquid is a group ID, the numbers are positioned low and high in X, Y and Z directions. We have defined 1 as low and 19 as high. Based on this number we have to calculate the number of type 1 atoms as defined in the next line.
Line 17: create_atoms1 random 1926 12345 liquid	Creation of liquid atoms in the defined region “liquid”.  Example: create_atoms 1 random 1926 12345 liquid Here, 1926 is the number of type 1 atoms. Please see the Additional Reading material for details of calculating this number. 12345 is the random number to put the type 1 particles randomly in the defined region liquid.
Line 18:It is on line 19 mass 1 1.0	Defining the mass of the particle. Here, 1 and 1.0 represents type “1” particle and mass of the particle respectively
Line 24: pair_style lj/cut 2.5	Next in Simulation Settings: cutoff calculates the pairwise distances within the mentioned cutoff.
Line 30: group liq type 1	Here we enter the numbers that describe how atom pairs interact. Here, all type 1 particles are grouped with a group ID liq.
Line 34: minimize 1e-6 1e-6 10000 10000	Running a simulation: Minimization of the system to remove the overlap between the particles. These numbers indicate tolerance, force tolerance, max iteration, max evaluations.
Line 38: neighbor 0.3 bin Line 39: neigh_modify every 1 delay 0 check yes page 100000 one 5000	Building of pairwise neighbor lists. This command sets parameters that affect the building of pairwise neighbor lists.
Line 44: dump 1 liq atom 5 output.atom	Storing the position of all the coordinates to the file. Here 5 is the frequency of printing the output file and in the end gives the name for the output file. Here we are naming it output.atom.
Line 46: thermo_style custom step etotal	Logging the desired data during the simulation. Here, other parameters can also be printed, and will be discussed in the upcoming tutorials.
Line 48: timestep 0.005 Line 49: thermo 5	The timestep command sets the timestep size for the simulation. The thermo command computes and prints the desired thermodynamic information like: temperature, energy, pressure at the mentioned interval of time. Number 5 here indicates the frequency of printing output.
Line 53: fix 1 liq npt temp 0.8 0.8 100 iso 1 1 100	In LAMMPS, a fix is any operation that is applied to the system during timestepping or minimization The npt command performs the time integration using equations of motion to generate positions and velocities for atoms. In an npt ensemble: the number of particles, pressure of the system and temperature of the system are held constant.
Line 55: run 10	Here 10 indicates timesteps_number. The large number will make the simulation more clear to visualize . The time taken to complete the simulation will also increase. For the sake of simplicity we have indicated 10 timesteps
Cursor on the input file. Close the text editor.	Now let me demonstrate how to run this input file. Close the text editor.
Go to the folder where input file is located. Open the folder and show the input file.	I have saved the input file in a folder in my home directory. Navigate to the input file location.
Right click on the folder containing the input file. From the context menu choose Open in Terminal option.	As LAMMPS is already installed in your computer. Right click on the folder containing the input file. From the context menu choose Open in Terminal option.
Cursor on the terminal.	Alternatively you can open the terminal and navigate to the path leading to the input file.
At the prompt type “ lmp_serial -in Ljbulk.txt” Press enter	Type the following command at the prompt to run the input file. lmp_serial -in LJbulk.txt Windows users can open the command prompt, type the command and proceed as shown. Press enter
Cursor on the terminal. Open the folder containing the input file to show log.lammps and output.atom..	The output is seen on the terminal. Two output files are generated, log.lammps and output.atom. These files will be saved in the same folder where your input file is located.
Cursor on the folder.	The analysis and visualization of the output file will be covered in the upcoming tutorial.
	This brings us to the end of this tutorial.
Slide Number 8 Summary	Let's summarize.
Slide Number 9 Assignment Edit the line in the System Definition section as follows region liquid block 1 25 1 25 1 15	As an assignment, Edit the line in the System Definition section as follows Calculate the number of atoms and replace the number in the subsequent line. Save and run the input file.
Slide Number 10 Thank you	Thank you

Contributors and Content Editors

Madhurig, Snehalathak