Crystal Analysis Tool Guide

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Crystal Analysis Tool
Author Dr. Alexander Stukowski
Website https://gitlab.com/stuko/crystal-analysis-tool
Source GitLab
Category Atomic simulations of solids, primarily crystals
Help PDF manual


From the manual:

"Crystal Analysis Tool [is] a computer code that was developed to analyze the output of atomistic simulations of solids (primarily crystals). The code implements algorithms to:

  • identify lattice structures and defect structures formed by atoms,
  • find dislocation lines and determine their Burgers vectors (using the Dialocation Extraction Algorithm, DXA),
  • compute the atomic-level elastic and plastic deformation gradient fields to quantify plastic deformation and elastic lattice strains,
  • generate a geometric representation of the free surfaces of a solid and identify internal voids, measure surface area, porosity, etc."

Loading the module

Note that the order of loading is important; you must load gcc after mpi/openmpi otherwise you will see run time errors similar to /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found:

module load mpi/openmpi/2.1.0 gcc/5.4.0-alt crystal-analysis-tool/24a8da7