© 2020 Yanwei Wang
Getting Started with LAMMPS
Yanwei Wang
Department of Chemical and Materials Engineering
School of Engineering and Digital Sciences
Nazarbayev University
© 2020 Yanwei Wang
What is LAMMPS?
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❑ LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator and is a popular molecular dynamics program from Sandia
National Laboratories.
❑ Authors of LAMMPS: https://lammps.sandia.gov/authors.html
❑ How to cite LAMMPS: https://lammps.sandia.gov/cite.html
❑ Homepage of LAMMPS: https://lammps.sandia.gov/index.html
❑ The LAMMPS Manual: https://lammps.sandia.gov/doc/Manual.html
❑ LAMMPS Tutorials: https://lammps.sandia.gov/tutorials.html
❑ LAMMPS Workshops: https://lammps.sandia.gov/workshops.html
Lots of presentations to
spend your spare time
Bookmark this page!
© 2020 Yanwei Wang
❑ Download an executable for Windows
https://lammps.sandia.gov/doc/Install_windows.html
❑There are installer packages for 32-bit and 64-bit versions of Windows available. So,
which version should we install? It depends on the system type of your computer.
Install LAMMPS on Windows 10
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© 2020 Yanwei Wang
Install LAMMPS on Windows 10
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http://packages.lammps.org/windows.html
I am using a 64-bit windows laptop, so I should
download the 64-bit version
It is always a good idea to download the Latest stable versions
© 2020 Yanwei Wang
Install LAMMPS on Windows 10
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Latest stable versions 64-bit Windows download area
Latest version
Let’s download the latest stable version:
LAMMPS-64bit-stable.exe
© 2020 Yanwei Wang
Install LAMMPS on Windows 10
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Double-click on
the LAMMPS-
64bit-stable.exe
file that you have
downloaded.Click on More info
Run Anyway
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© 2020 Yanwei Wang
Install LAMMPS on Windows 10
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Let’s go to the folder where LAMMPS is installed and see what we’ve got
LAMMPS 64-bit 3Mar2020 Setup: Completed!
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© 2020 Yanwei Wang
Install LAMMPS on Windows 10
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Homework: Try to understand what you have got in each folder
© 2020 Yanwei Wang
My first LAMMPS Simulation
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❑ Create a New Folder in your “Documents”. Name it “Lammps”.
❑ Create in “Lammps” a subfolder “melt”
❑ Copy files “in.chain” and “data.chain” from “C:\Program Files\LAMMPS
64-bit 3Mar2020\Benchmarks” to “melt”, the new folder that you have
just created. If you did everything as I told you to, the directory of Folder
“melt” should be “C:\Users\dell\Documents\LAMMPS\melt”
Those are the typical input files for a LAMMPS simulation.
© 2020 Yanwei Wang
My first LAMMPS Simulation
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❑ Both “in.chain” and “data.chain” are simple text files, you may open
them with Notepad.
❑ To increase your work efficiency, I recommend that you install a more
power text editor, such as Notepad++ or Sublime Text. To learn more,
Google “Top 5 Best Text Editor For Windows In 2019”
© 2020 Yanwei Wang
My first LAMMPS Simulation
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in.chaindata.chain
© 2020 Yanwei Wang
My first LAMMPS Simulation
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❑ The LAMMPS executable files can be found in the folder
C:\Program Files\LAMMPS 64-bit 3Mar2020\bin
❑ It is troublesome if we run those executable files every time from that
“bin” folder. A better idea is to add the path “C:\Program Files\LAMMPS
64-bit 3Mar2020” to our system as system environment variables.
❑ If you are using windows 10, search “edit the system environment
variables” in the start.
© 2020 Yanwei Wang
My first LAMMPS Simulation
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© 2020 Yanwei Wang
My first LAMMPS Simulation
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Double-click on “Path”
Click on “New”, and add the path
“C:\Program Files\LAMMPS 64-bit 3Mar2020\bin”
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© 2020 Yanwei Wang
My first LAMMPS Simulation
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❑ If you are using windows 10, search “PowerShell” in the start.
“dell” is my username, which in
your case will be your username.
https://devblogs.microsoft.com/scripting/table-of-basic-powershell-commands/Table of Basic PowerShell Commands
You should learn some basic shell
commands. If you are familiar with basic
UNIX commands, they are very similar.
© 2020 Yanwei Wang
My first LAMMPS Simulation
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Change your work directory to the
“melt” folder. You may simply type
“cd Doc” and type the magic “Tab”
key.
Type “ls’ to see what is in that
folder
Type “pwd” to see your current
work directory
© 2020 Yanwei Wang
My first LAMMPS Simulation
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Now you ready for (maybe) your
first LAMMPS simulation.
Type “lmp” and try the magic “Tab”
key
When all is done, type the “Enter”
key to run your Lammps simulation.
“-in” can be replaced by “-i”
© 2020 Yanwei Wang
My first LAMMPS Simulation
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This is also a text file. Open it with
Notepad or my favorite Notepad++,
and see what is in there.
Congratulations! You have conducted your
first LAMMPS simulation successfully.
Read this page https://lammps.sandia.gov/bench.html#chain
to learn more about this benchmark test.
Send me know your
results. Let’s see whose
computer has the best
performance ☺
© 2020 Yanwei Wang
❑ Copy from “C:\Program Files\LAMMPS 64-bit 3Mar2020\Examples”
folder “colloid”, “dreiding”, and “peptide” to your “LAMMPS” folder
More Examples
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© 2020 Yanwei Wang
If the current work directory of your PowerShell is “C:\Users\dell\Documents\LAMMPS\melt”. Then, you
may type “cd ..” to go the upper-level folder. Let’s practice those Unix-like commands again.
More Examples
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http://linuxcommand.org/tlcl.php
© 2020 Yanwei Wang21
More Examples
Type the “Enter” key to run
your Lammps simulation.
Now let’s try to modify the “in.colloid” file and run the simulation again.
Go to your /LAMMPS/colloid folder, and open “in.colloid” with Notepad++.
© 2020 Yanwei Wang22
More Examples
Remove the hashtag # and save
the file.
CTRL+S also works.
© 2020 Yanwei Wang23
More Examples You may use the arrow ↑ on your keyboard to
repeat the previous commands.
Run the simulation again and see what you
have got in your folder
C:\Users\dell\Documents\LAMMPS\colloid
© 2020 Yanwei Wang24
More Examples
© 2020 Yanwei Wang25
More Examples
Let’s try another example.
© 2020 Yanwei Wang26
More Examples
And another one
© 2020 Yanwei Wang
Homework
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❑ Repeat the simulations described in this tutorial
❑ Try to go through all the input and output files of your LAMMPS
simulations
© 2020 Yanwei Wang
Further readings
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❑ This is a set of nice tutorials created by the Center for Advanced
Vehicular Systems (CAVS) group at Mississippi State University:
LAMMPS tutorials
https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_tutorials
© 2020 Yanwei Wang
If Windows PowerShell isn’t power enough
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Try Cygwin or Ubuntu on Windows 10
❑ Install Ubuntu on Windows 10 Cygwin https://cygwin.com/
www.nu.edu.kz © 2020 Yanwei Wang