Simulations of Strain on Nanomaterials
Principle Investigator: Dr. Charles Cornwell
HPC System: Spirit, Garnet
The visualization of this project begins with analyzing the LAMMPS simulation results. The dump files contains a list of all of the atoms in the simulation. The first thing that is extracted from the data is the 3D position and the energy value of each atom. To represent each atom on a rendered image, a sphere was generated in VTK using the 3D position as the center point of the sphere.
To create the appearace of a mesh, the atoms needed to be connected by tubes. Atoms that are within a certain distance of each other are connected. This is accomplished by a version of the k-nearest neightbor algorithm. The atoms are sorted into buckets which prevent a polynomial runtime complexity. Next, the straight line distance for each atom in the bucket is calculated. The distances within the desired range are converted into a tube that connects those two spheres inside VTK.
Colors are applied to the spheres and tubes based on the energy values collected from the dump files and saved into a PLY format. The PLY files were rendered using 3D Studio Max.