Meetings

2014 Summer School Tutorial

Material Surfaces, Grain Boundaries and Interfaces: Role of Interatomic Potentials in Enabling Atomic-Scale Simulations

Wednesday, May 21

 


 

On this page:

General Information
Overview of how to run calculations using LAMMPS.

Linux Installation
Executables and links to downloads for the Linux OS.

Windows Installation
Executables and links to downloads for the Windows operating system.

General Information

Introduction: This tutorial compares the behavior of the Cu Σ5(310) tilt grain boundary in molecular dynamics simulations where the forces are determined using three different potentials: Lennard-Jones (LJ), the embedded atom method (EAM), and COMB.

Usage: To start the LAMMPS program from the command line, the basic command is set up as follows
 

./lmp_intx0 < in....
where lmp_intx0 is the name of the executable file, and in... stands for the name of an input file. A specific example for a Windows installation, could be:
 
lmp_serial < in.lj
where in.lj is the input filename chosen for a Lennard-Jones. More information about Windows installations for serial and parallel calculations can be found below.

Though a LAMMPS executable is provided, it is recommended that the user download and compile the LAMMPS executable himself/herself from the LAMMPS website. Windows installers can also be downloaded.

Structure information: The structure provided was made based on the principles discussed in Refs 1 and 2. If you want to simulate a different material other than the example provided (Cu-with lattice constant 3.615 Å), it is possible to modify the lattice constant and the box sizes.

For example,

#region whole block xmin xmax ymin ymax  zmin zmax (latt_a) units box

should be modified as:

New xmax=(xmax*New_latt_a/3.615)

Similarly, it is possible for ymin, ymax, and the zmax to be reset to the new lattice constant of the material of interest. Additionally, the cohesive energy of the material (line 72 of the script, variable minimumenergy which is set equal to -3.540000) should be modified.

Post-processing: The .cfg files can be visualized/animated using the atomeye software. The atomeye manual provides instructions on how to generate a movie of the simulation results. The grain-boundary energy is printed in the log.lammps file. The effect of temperature can be investigated by changing the variable tmp. Note the change in the potential energy profile throughout the grain-boundary structure. This potential energy profile can be determined at various temperatures by using (Caps-lock on+1) in the \ keyboard. Generally, the final structures of each run are compared. (See Fig. 3 of Ref. 3 for example).

References:

  1. LAMMPS_Help3 website
     
  2. Tschopp et al., "Asymmetric tilt grain boundary structure and energy in copper and aluminum", Phil. Mag. 87, 3871 (2007).
     
  3. E. Vincent-Aublant , J-M. Delaye, L. Van Brutzel, "Self-diffusion near symmetrical tilt grain boundaries in UO2 matrix: A molecular dynamics simulation study", J. Nucl. Mat. 392, 114 (2009).
     

 

 

Linux Installation for LAMMPS

We have provdide here the following two archives that you can download and unpack that include the input files for this tutorial and also the LAMMPS executable file suitable for a Linux system.

Download tutorial files in TAR format.

Download tutorial files in ZIP format.

However it is suggested to go to the LAMMPS website and download the executable or source files directly from their download page.

To download only the input files needed for the tutorial (no executable), please use this link.

 


 

Windows Installation for LAMMPS

Pre-compiled Windows installers for the LAMMPS software are generated and availabe at the Installer repository for LAMMPS. Here we have collected the latest downloads from that page. Generally two downloads are needed: the LAMMPS installer itself, and the MPICH software for parallel calculations.

For a 32-bit system:

Latest LAMMPS installer version for 32-bit Windows

32-bit MPICH2 software (not needed for serial calculations)

For a 64-bit system:

Latest LAMMPS installer version for 64-bit Windows

64-bit MPICH2 software (not needed for serial calculations)

 

Input files

After installing LAMMPS, you can download the input files needed for the tutorial.

The installer should put the LAMMPS executable in your system path. So after unzipping the input files, you can then open a command prompt and change to the input files directory to run LAMMPS.

Example commands:

A serial calculation on a windows installation can be invoked at the command prompt by using, for example:

lmp_serial < in.comb

assuming of course that there is an input file called in.comb in your current directory.

Starting a parallel calculation requires the starting of the MPICH software as described here.

Manual

Further information can be found in the LAMMPS software manual which is installed along with the software in the DOC subdirectory, or you can download a copy here.