Dislocation Mobility
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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
- ↑ 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