Dislocation Mobility

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< Back to Homework 2 (2013) Overview
< Back to Homework 2 (2015) Overview

Contents

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. [1].

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.

References

  1. S. Groh, E.B. Marin, M.F. Horstemeyer, H.M. Zbib. Multiscale modeling of the plasticity in an aluminum single crystal, International Journal of Plasticity Volume 25, Issues 8, August 1, 2009, Pages 1456-1473 Science Direct
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