PolyPal: A parallel microscale virtual specimen generator
Description
We present an open source program, PolyPal, that can generate a polycrystalline virtual specimen in the micrometer scale for atomistic calculations and visualization. Unlike regular meshes or perfect lattices, atomic positions in polycrystalline materials need to be defined before calculations, and the capability of an atom-generation code is evaluated by the maximum size of the virtual specimen it can generate as well as by the efficiency of the necessary input-output process. Present atom-generation codes are implemented in a serial fashion, and the maximum size of the virtual specimen is limited by the on-board memory. Furthermore, it is difficult to handle a single position file with billions of atoms not only because it takes a long time to read in a row but also full domain decomposition takes hours. PolyPal addresses these challenges with a fully parallelized MPI input-output scheme that supports multiple export options on a Linux cluster. It has no limit in the system size with virtually perfect scalability. Additionally by controlling the size distribution and homogeneity of grains, the program can simulate different microstructures, as typically found in the bulk system or in thin-film samples, prepared with different fabrication processes. PolyPal will harness molecular dynamics codes in the coming age of the exascale computing.