Description.txt

This set of programs was developed to perform LAMMPS [1] molecular dynamics (MD) simulations of elastic deformation in nickel on OSU COE computer cluster. The goal was to compute elastic constants values for nickel and a nickel-chromium alloy, Ni20Cr at fixed pressures for a temperature range 0.0 - 873.15 K. 

The main program is NiElastic.py and the detailed description of this program set is included there. Besides python scripts, used are Linux shell commands, and a parallel LAMMPS submission script developed by my coworkers specifically for the COE cluster. The script includes important small modification that enables varying random seed used in LAMMPS every time a new simulation is submitted to the cluster. The script del_jobs.py is an automated program for deleting unwanted jobs from the cluster. The set currently uses a LAMMPS python tool to extract simulation data from LAMMPS log, log2txt.py. This script is in script repository of my group which path is added to my shell configuration file hence the program assumes it can be called directly and does not to be present in the directory where it is called.  

In short, this set modifies LAMMPS scripts changing number of atoms and simulation parameters, submits the jobs to the cluster, collects and processes the data when simulations terminate (with an option to rerun any failed ones), and computes the elastic constants as a function of temperature. 

These programs were used to generate 10-20 datasets for each temperature in the 0.0-873.15 K range with 50 K increment starting from 0.5. Simulations were performed with about 100 - 2,000 atoms. A slightly modified program set was used for Ni20Cr. After obtaining statistically sufficient amount of data, all the datasets were processed in a not included MATLAB program. Due to consistent naming convention this process was also automated. Sample results from python and MATLAB are included. Python results are from a single dataset, MATLAB results are the average and standard error of all the datasets for that particular material and number of atoms. 

Included programs run shearing and compression in LAMMPS in a single deformation stage that deforms the atoms in x and xy. There is a second deformation format entirely covered by NiElastic.py where three separate LAMMPS simulations are run, each with different deformation, in particular x, y, and yz. The choice of the format needs to be specified in NiElastic.py and affects the files that have to be present in the directory. For this problem, it was concluded that both formats yield similar results. 

Finally, NiElastic.py currently modifies the size of simulation box in LAMMPS. It is necessary to use a proper box size for given temperature in pressure as the assembly used in the simulations is NVT. It is not mentioned in the programs, but the volume (box size) for every p and T values used was obtained in a separate NPT simulation.        

[1] S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995) (http://lammps.sandia.gov/)