Dislocation Mobility

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Overview

• Run molecular dynamics simulations using the Modified Embedded Atom Method (MEAM) to dislocation velocity
• Using that velocity, calculate the dislocation drag coefficient.
• Execute calculations according to the work of Groh et. al. .

Instructions

LAMMPS Manual

• A comprehensive manual for LAMMPS can be found here.

LAMMPS Files/Executable for Aluminum (2013)

• Create a directory for running the MEAM calculations in LAMMPS.
• Navigate to

  /cavs/general/ICME_2013/Homework_2/LAMMPS

• COPY (do not move!) the following files into the directory you made for running LAMMPS.
  • lmp_4Jul10 - Basic LAMMPS executable configured for MEAM.
  • Al.meam - MEAM parameters for Aluminum.
  • meafile.al - Additional MEAM paramters for Aluminum.
  • atoms.fcc.edge.pad - Atomic configuration with dislocation included
  • in.VelocityDisloPADAl - LAMMPS input file

LAMMPS Files/Executable for Nickel (2015)

• Create a directory for running the MEAM calculations in LAMMPS.
• Place the library and parameter files for nickel that were created using the MPC routine
• Navigate to /scratch/ICME_2015/HW2/LAMMPS/
• COPY (do not move!) the following files into the directory you made for running LAMMPS.
  • Generate_PAD - Folder containing the atom positions file atoms.fcc.edge.pad to be used by LAMMPS
  • lmp_4Jul10 - Basic LAMMPS executable configured for MEAM.
  • Ni_DisCore_posVStme.py - Python script for generating a position vs. time curve
  • in.VelocityDisloPADNi_v4 - LAMMPS input file; the required names for the library and parameter files are found here

Execution

• If an atoms position file is not given navigate to the Generate_PAD folder

1. Run the disloc file

2. Inputs needed to generate atoms.fcc.edge.pad

FCC, element of your choice, 100 60 2 (this will generate ~71000 atoms), edge, PAD

disloc will exit with an error, but the necessary file will still be correctly created

• For Al HW only - Open the "Al.meam" file and input meam parameter values calculated from the MPC GUI.
• Embed the following command in a PBS script for the cluster Raptor:

   mpirun -np # PATH_TO_EXECUTABLE < NAME_OF_INPUT_FILE 

• Replace the '#' with the number of processors desired.
• Replace "PATH_TO_EXECUTABLE" with the path to the LAMMPS executable
• Replace "NAME_OF_INPUT_FILE" with the name of the LAMMPS input file (if you didnt change it, in.VelocityDisloPADElement)
• Submit the job to Raptor

Output and Post Processing

• The given LAMMPS input file is written to create several output files:
  • dump.all - All information every 10000 time steps
  • dump.minimize - Initial atomic configuration
  • dump.shear - X,Y,Z positions every 5000 time steps (small file)
  • dump.shear.unwrap - X,Y,Z positions and Ackland parameter every 500 time steps (big file)
  • dump.final - X positions and Ackland parameter for dislocation core every 500 time steps
• OVITO can be used for visualizing the output files from LAMMPS
  • Import the dump.shear.unwrap
  • Under "LAMMPS dump file" select File contains multiple timesteps
  • Drop down "Add modification" select Color coding
  • The dislocation core will be illustrated by the red/blue atoms in the center of the file
• Navigate to that working directory in a terminal and use the following command to process the output: python Element_DisCore_posVStme.py
• The python code outputs a dislocation core position vs time step curve in a .txt file.