Crystal Analysis Tool (draft)

If you are a windows user – please ensure you create your jobscript ON THE CSF directly using gedit. This will prevent your job going into error (Eqw). Text files created on windows have hidden characters that linux cannot read. For further information please see the guide to using the system from windows, in particular the section about text & batch submission script files.

Overview

Crystal Analysis Tool is a package for analysing the output of atomistic simulation of crystalline solids. It can be used to identify lattice structures and defects and to determine additional properties.

Restrictions on use

While the tool is freely available to download, the README contains the following copyright statement:

Copyright 2012-2013, Alexander Stukowski
All rights reserved. Contact the author for permission to use, copy, modify or redistribute this software.

THIS SOFTWARE IS PROVIDED "AS IS", IN THE HOPE THAT IT WILL BE USEFUL, BUT WITHOUT ANY WARRANTY;
WITHOUT EVEN THE IMPLIED WARRANTY OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PRUPOSE. IN NO EVENT SHALL
THE AUTHOR BE LIABLE FOR ANY DAMAGES WHATSOEVER ARISING OUT OF THE USE OF OR INABILITY TO USE THIS SOFTWARE.

This product includes software developed by Silicon Graphics, Inc.,  
licensed under the SGI Free Software License B (http://oss.sgi.com/projects/FreeB/) 

Setup procedure

To use Crystal Analysis Tool, load the modulefile into your environment as follows:

module load apps/gcc/crystal-analysis-tool/0.9.20

Running the application

The executable is named CrystalAnalysis. Please do not run this on the login node; follow the instruction below to submit a batch job instead.

Parallel batch job submission

Example job

$ ls
jobscript  npAu.dump.gz

#!/bin/bash --login
#$ -cwd
#$ -pe smp.pe 8
#$ -N npAu

module load apps/gcc/crystal-analysis-tool/0.9.20

# Name of the simulation snapshot file:
inputFile="npAu.dump.gz"

# List of structure patterns to search for:
patterns="fcc,fcc_isf,fcc_triple_sf,fcc_quad_sf,fcc_coherent_twin"

# Neighbor list cutoff radius:
cutoff=3.6

# Base name of output files:
outputFile=$(basename $inputFile .dump.gz)

# Run analysis program:
mpirun -np $NSLOTS CrystalAnalysis \
   -catalog $CATOOL_DB \
   -patterns $patterns \
   -cutoff $cutoff \
   -cell ${outputFile}.cell.vtk \
   -atoms id,type,x,y,z,pattern,cluster ${outputFile}.atoms.dump.gz \
   -scounts ${outputFile}.counts.txt \
   -defectsurface ${outputFile}.defectsurface.vtk \
   -defectsurfacecap ${outputFile}.defectsurfacecap.vtk \
   -dislocations ${outputFile}.dislocations.vtk \
   -output ${outputFile}.ca \
   $inputFile > ${outputFile}.log

The environment variable CATOOL_DB is defined in the modulefile for your convenience.

$ ls -ltr
total 47236
-rw-r--r-- 1 me mygroup  7099468 Dec  7 13:04 npAu.dump.gz
-rwxr-xr-x 1 me mygroup      969 Jan  2 10:03 jobscript
-rw-r--r-- 1 me mygroup        0 Jan  2 10:03 npAu.o68110
-rw-r--r-- 1 me mygroup      198 Jan  2 10:03 npAu.e68110
-rw-r--r-- 1 me mygroup      361 Jan  2 10:03 npAu.cell.vtk
-rw-r--r-- 1 me mygroup      173 Jan  2 10:04 npAu.counts.txt
-rw-r--r-- 1 me mygroup  9502680 Jan  2 10:04 npAu.atoms.dump.gz
-rw-r--r-- 1 me mygroup 16644529 Jan  2 10:04 npAu.ca
-rw-r--r-- 1 me mygroup 13713294 Jan  2 10:04 npAu.defectsurface.vtk
-rw-r--r-- 1 me mygroup     3380 Jan  2 10:04 npAu.log
-rw-r--r-- 1 me mygroup   713889 Jan  2 10:04 npAu.dislocations.vtk
-rw-r--r-- 1 me mygroup   666228 Jan  2 10:04 npAu.defectsurfacecap.vtk