mrkllntschpp/lammps-tutorials

LAMMPS tutorials for Beginners

LAMMPS tutorials for Beginners

Run LAMMPS in your browser

These tutorials were recreated from my original tutorials at Mississippi State University (MSU) Center for Advanced Vehicular Systems (CAVS) website with updates to codes within Jupyter Notebooks. I hope this helps with everyone's learning curves for LAMMPS! Thanks.

• Click here to open Tutorial 1. Run LAMMPS! Learn how to calculate the minimum energy lattice structure
• Click here to open Tutorial 2. Run LAMMPS! Learn how to feed variables through the command line and mine log file for values to plot in MATLAB or Python
• Click here to open Tutorial 3. Run LAMMPS! Learn how to deform a simulation cell in tension and visualize the results
• Click here to open Tutorial 4. Run LAMMPS! Learn how to deform a simulation cell in compression and visualize the results
• Click here to open Tutorial 5. Run LAMMPS! Learn how to make a grain boundary
• Click here to open Tutorial 6. Run LAMMPS! Learn how to strain a grain boundary until fracture
• Click here to open Tutorial 7. Run LAMMPS! Learn how to compute a number of per-atom metrics for use outside LAMMPS
• Click here to open Tutorial 8. Run LAMMPS! Learn how to add a 100-united atom polymer chain to LAMMPS

I've even tried to update the scripts here to some of the newer LAMMPS versions. So far so good!

Beginner to Python, Anaconda, Jupyter Notebooks, too?

• Click here for a brief intro

lammps-tutorials's Issues

Energy minimization without lattice constant change

Hello,

Thank you for providing such comprehensive list of tutorials for LAMMPS. I am just starting out with LAMMPS and I am finding your tutorial very useful.

In tutorial 1, you show how to perform energy minimization and obtain the optimized lattice parameter for Al lattice.

I was wondering, if there is way to perform energy minimization in LAMMPS where only the atoms are free to relax while the lattice shape and volume doesn't change. If you are familiar with VASP input, this would be equivalent to setting ISIF = 2.

I tried looking it up online and so far I haven't found any direct method of doing it.

I want to know if such energy minimizations are possible in LAMMPS and if so could you please give me some hints on how to do it.

Thank you!

delete_atoms command with ID issues

Hello,
Thanks for all these great tutorials! I got stuck with the delete_atoms command. I am looking at the LAMMPS documentation and comparing codes and I can't see where I am going wrong, yet I continue to get the error "ERROR: Could not find delete_atoms group ID (../delete_atoms.cpp:306)
Last command: delete_atoms overlap 0.35 region lower upper"
I get this error right after it starts the displacing atoms section. I copied my code directly from your code posted on this tutorial, so I am confused with what is happening.

is:issue is:open files not reading

after opening the correct folder in the terminal and running the code, lmp_serial -in in.lmp, the file is not opening. is there a specific way the files should be organized so that lammps is able to read it or is there another issue here.

Question about minimumenergy in tutorial-5

Dear sir,

Thanks for your input file to calculate the energy of grain boundary.
I have an question in tutorial-5.
Why the minimumenergy is euqal to -3.36? This item should be the atomic energy in bulk. How did you get this value?

Kind regards,
Meng Zhang

How to achieve polycrystalline stretching?

Thank you for the tutorial. Have tried so far, but how to achieve polycrystalline stretching? It has always been a problem.

The polycrystalline structure uses random grains created by Atomsk software. The above is the structure file. I have tried calculations, but the performance at the grain boundary is not very good. So ask you for help.

Write to Fe_unitcell.xsf

Bcc Fe oriented X=[100] Y=[010] Z=[001].

CRYSTAL
PRIMVEC
2.85530000 0.00000000 0.00000000
0.00000000 2.85530000 0.00000000
0.00000000 0.00000000 2.85530000
CONVVEC
2.85530000 0.00000000 0.00000000
0.00000000 2.85530000 0.00000000
0.00000000 0.00000000 2.85530000
PRIMCOORD
2 1
26 0.00000000 0.00000000 0.00000000
26 1.42765000 1.42765000 1.42765000

Fe_voronoiRandom.txt
box 100 100 25
random 10

Fe_polycrystal.lmp is generated by the following command

atomsk --polycrystal Fe_unitcell.xsf Fe_voronoiRandom.txt Fe_polycrystal.cfg lmp -wrap

Happy New Year!
Sincerely

confusion with strain rate units

Before I begin, thanks a lot for making these tutorials available. I've a doubt here. In tutorial 3, after the initial equilibration, the simulation box is deformed

in the x-direction at a strain rate of 10^10 1/s

That is implemented in the LAMMPS script in the following lines

units 		metal
...
timestep 0.001  #in picosecond 
... 
variable srate equal 1.0e10
variable srate1 equal "v_srate / 1.0e12"
fix 2 all deform 1 x erate ${srate1} units box remap x

How do you calculate the factor of 1.0e12 ? Isn't the timestep dt involved here in some way?

How to realize the 110 direction stretching?

Thank you very much for this tutorial. According to this tutorial, I have realized the tensile mechanical properties of BCC(body centered cubic) Fe block (x - < 100 >, Y - < 010 >, Z - < 001 >).

But I couldn't achieve it when I tried the tensile mechanical properties of another crystal oriented Fe block (x - < 110 >, Y - < 110 >, Z - < 001 >). I have tried to modify the system temperature, cutoff
and other parameters, but I still can't. I have to ask you for help. I hope you can help me.

Thank you!

In tutorial 6 the link to is no longer valid

Describe the bug
As https://icme.hpc.msstate.edu/mediawiki/index.php.1.html was archived in favour of https://www.cavs.msstate.edu/icme/ the link to certain files no longer work.

To Reproduce
https://icme.hpc.msstate.edu/mediawiki/index.php/Fe_110_sig3.txt

Expected behavior
It could be replaced with a link to the Github repository:
https://raw.githubusercontent.com/mrkllntschpp/lammps-tutorials/master/Fe_110_sig3.txt

Additional context
Maybe other links are effected as well.

Coarse grain polymer MD Simulation?

How to write input script for single polymer chain of polycarbonate in for MD simulation in lammps?