Computational Multiscale Modeling (151-0520-00L) May 16, 2018

Spring 2018 Prof. Dennis M. Kochmann, ETH Zürich

Project #4

assigned: Wednesday, May 16th, 2018

due: Wednesday, June 6th, 2018, 17:00
please hand in to one of the TAs in LEE N203

For the final project, we will use the most widely used open-source MD code, the so-called Large-Scale
Atomic/Molecular Massively Parallel Simulator or LAMMPS developed by Sandia National Labs.

(a) Installing LAMMPS on your machine or using the class server

Instructions for download and installation can be found on the LAMMPS website. If you are working on
MAC OS, we recommend that you use Homebrew to download, build and configure LAMMPS. Detailed
information can also be found in the LAMMPS manual.
Alternatively, you can log into our class server, where LAMMPS has already been installed.

(b) Running LAMMPS examples

We suggest that you run one of the example problems from the LAMMPS folder as a test (typically found
in /usr/local/share/lammps/examples). Have a look at the examples/README for short descriptions
of the 30 examples. Try to run your first example, for example indent.
For example, when using the class server, from the LAMMPS folder you may type the following commands

cp -r /opt/lammps-16Mar18/examples/indent/ .
cd indent
cp /opt/lammps-16Mar18/src/lmp_mpi .
./lmp_mpi < in.indent

If you are working locally on your own machine, you need to replace lmp_mpi with the LAMMPS
executable.

(c) Description of input files

While you are running your first example, have a look at the input file, for example in.indent. This file
contains a list of instructions executed by LAMMPS. Feel free to have a look at the LAMMPS online
manual for a complete description of all the available commands.
Start to play with the commands in your input file example. For example, uncomment the dump image
and dump_modify commands in order to create images of the results of your simulation. In the indenta-
tion problem, try to change the indentation depth, the size or shape of indenter, the size of the system,
etc.

Problem 1: Compute the lattice spacing of fcc Cu (40 points).

As a benchmark case, let us – as on Project 3 – identify the equilibrium spacing a0 as the minimizer of the
interaction energy E(a) in a Cu fcc lattice at 0K, using the potential of Foiles et al. (1986). For that purpose,
we will adapt this online tutorial. The tutorial equilibrates an atomic crystal using an EAM potential. You need
to change the potential’s definition in the input file in order to compute the lattice spacing for Cu. Compute

1
Computational Multiscale Modeling (151-0520-00L) May 16, 2018
Spring 2018 Prof. Dennis M. Kochmann, ETH Zürich

the energy of fcc Cu for various values of the lattice spacing a, and compute the bulk modulus analologously
to Project 3. Compare your results to those of Project 3.
Hint: You can adapt the Matlab script given in Part 2 of the online tutorial (a python script can be provided
if you wish to use python). Note that Matlab is not installed on the class server (so either use it on your
machine or use python on the server).

Problem 2: Molecular Dynamics (40 points).

Next, let us simulate a finite-temperature canonical (N V T ) ensemble of Cu, using the same potential as
above. Repurposing the same initialization part for the input script as in Problem 1, now using the fix nvt
command1 , write a new input script in order to perform simulations at finite temperature using explicit time
integration:

• Run the simulation at a fixed temperature (e.g., 300K).

• Plot the evolution of the system’s potential and kinetic energy and temperature over time.
Hint: Use the thermo and thermo_style commands and output data from the log file.

• Compute the radial distribution function using the compute rdf command2 . Output this last result
using the fix ave/time command and plot the distribution.

Perform the same setup at a different temperature and compare your results.

Problem 3: Simulating a mechanical indentation test (20 points).

Finally, let us simulate an indentation test into a 2D block at finite temperature as a realistic boundary value
problem, using periodic boundary conditions on the lateral sides and the microcanonical (N V E) ensemble to
simulate adiabatic conditions. Start from the indent example provided with the LAMMPS distribution and
adapt it in order to output and plot the force exerted on the indenter as a function of its position. By dumping
graphics files, you can also import results into Paraview.

total: 100 points

1
http://lammps.sandia.gov/doc/fix nh.html
2
http://lammps.sandia.gov/doc/compute rdf.html