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OpenLAMMPSToolbox

Introduction

OpenLAMMPSToolbox is a collection of CLI tools used for pre- and post processing Molecular Dynamics (MD) simulations meant to be used alongside Sandia National Lab's Large Scale Atomic/Molecular Massively Parallel Simulator.

Post-processing Capabilities

The post-processing functions implemented follow a sequential command line interface for ease of use. Run the 'olt_postprocessing' executable and follow the subsequent prompts.

~/projects/openlammpstoolbox$ ./olt_postprocessing

Implemented post-processing functions include:

  1. Highlighting defects (DEFECT)
  2. Highligting displaced atoms (DISPLACEMENT)
  3. Sorting atoms by id, coordinates, or per-atom compute data (SORT)
  4. Selecting atoms by change in per-atom compute data (SUBSET)
Additional features:
  • Automatic detection of dump file format. 'xyz' and custom LAMMPS Dump file type compatibility currently implemented
  • Writing files in custom LAMMPS dump file format
  • Compatibility to handle all stored per-atom compute data

Python Scripts

  1. Creating cubic, periodic, and crystalline structure files
  2. Generating defects within structure files
  3. Selecting subset of atoms for 'group' type input file commands
Note: Run the Python files with the '-h' command to learn about input parameters. 
python3 ./python/main(...).py -h

Examples

  • Creating FCC Nickel structure: 
    • ~/projects/openlammpstoolbox$ python3 ./python/mainCubicCreate.py FCC 67 67 67 3.52 3.52 3.52
    Structure of FCC Nickel rendered using OVITO
  • Creating 15 Frenkel defect pairs in FCC Nickel: 
    • python3 ./python/mainDefectCreate.py NiFCC_SingleCrystal.lmp  Frenkel 15 -coord_num 12
    15 Frenkel defects in FCC Nickel rendered using OVITO

Installation and Build

OpenLAMMPSToolbox was made for Linux systems. For Windows devices use of WSL2 is recommended.
Clone the repository onto your device:

git clone https://github.com/JovinRyan/OpenLAMMPSToolbox.git

Navigate to the repository:

cd ~/projects/openlammpstoolbox

Create the build/ directory to house CMake files and:

mkdir build/

Run the cmake command in the build directory to generate the make file:

cd build/
cmake ../CMakeLists.txt

Run the make command to compile the C++ source files and generate the OpenLAMMPSToolbox ./olt_ executable:

make