Introduction
Software
Experiment
Data processing
Post-processing and results evaluation
Advanced discussions
This is an old revision of the document!
Below is an example of a GrainSpotter loop for olivine. You can run it by typing
gsLoop.sh > gsLoop.log
The output of the loop will be saved in gsLoop.log.
The loop can run nLoops indexings (typically 3). For each, the loop runs
At the end of the loop, all results for the corresponding loop number are saved in a folder called Indexing-$loop, where $loop is the loop number. Merged grains are in a file called merge-grains.log and their Euler angles in merge-grains-euler.txt.
A good start is to look for the number of assigned G-vectors. This command will do it
cat gsLoop.log | grep "Assigned gvectors"
It will print out something like
Assigned gvectors: 3915 Assigned gvectors: 3719 Assigned gvectors: 3719 Assigned gvectors: 3719 Assigned gvectors: 3719 Assigned gvectors: 3719 Assigned gvectors: 3719 Assigned gvectors: 3139 Assigned gvectors: 2997 Assigned gvectors: 2972 Assigned gvectors: 2950 Assigned gvectors: 2927 Assigned gvectors: 2873 Assigned gvectors: 2873 Assigned gvectors: 2873 Assigned gvectors: 2873 Assigned gvectors: 2873 Assigned gvectors: 1831 Assigned gvectors: 1831 Assigned gvectors: 1831 Assigned gvectors: 1817 Assigned gvectors: 2121 Assigned gvectors: 1454 Assigned gvectors: 1454 Assigned gvectors: 1454 Assigned gvectors: 1454 Assigned gvectors: 3915
3915 is the number of experimental G-vectors that could match our crystal structure. It decreases it time we generate a new GVE file based on a previous GrainSpotter indexing. When it increases back to 3915, it means that the loop fully started over. In the example above, we started from 3915 experimental G-Vectors, 1454 are left, we assigned approximately 60% of the experiment G-Vectors.
The ratio of assigned G-Vectors is not 100% trivial to calculate as the number of matching experimental G-vectors depends on your Δ2θ and nσ parameters in the GrainSpotter input file.
You wanted it?! Here is the source code for the loop above
<file bash gsLoop.sh> #!/bin/bash
# Starting GVE file startGVE=../LTC_05_01_s26_t50_ol-seb-edit.gve # Starting GVE file crystalSymmetryCode=3 # Number of indexings nLoops=3
# Update parameters above as well as in # - create_GS_init # - fine details in indexing_loop
# Location of executables GrainSpotter=/usr/local/bin/GrainSpotter.0.90 clearGVE=/usr/bin/timelessClearGVEGrains mergeGrains=/usr/bin/timelessGrainSpotterMerge extractEuler=timelessExtractEulerAngles
# Global parameter. Used to pass list of files between functions grainlist=“”
#———————————————————————————————– # # Call to create GrainSpotter input # 3 parameters # - first: name of GrainSpotter output file # - second: name gve file # - third: name of grain output file # - forth : min_measurments # - fifth : min_completeness # - sixth : sigma_tth # - seventh : sigma_eta # - eighth : sigma_omega # #———————————————————————————————– create_GS_init () { cat > $1 «- EOM spacegroup 62 ! spacegroup [space group nr] ! dsrange 0 0.34 ! dsrange [min max], d-spacing range, multiple ranges can be specified tthrange 2 10.2 ! tthrange [min max], multiple ranges can be specified ! tthrange 2 8.8 ! tthrange [min max], multiple ranges can be specified ! tthrange 9 10.2 ! tthrange [min max], multiple ranges can be specified tthrange 10.5 14.4 ! tthrange [min max], multiple ranges can be specified ! tthrange 14.6 17 ! tthrange [min max], multiple ranges can be specifie etarange 0 360 ! etarange [min max], multiple ranges can be specified domega 0.5 ! domega [stepsize] in omega, degrees omegarange -21 13 ! omegarange [min max] degrees, multiple ranges can be specified filespecs $2 $3 ! filespecs [gvecsfile grainsfile] cuts $4 $5 0.5 ! cuts [min_measuments min_completeness min_uniqueness] eulerstep 5 ! eulerstep [stepsize] : angle step size in Euler space uncertainties $6 $7 $8 ! uncertainties [sigma_tth sigma_eta sigma_omega] in degrees nsigmas 2 ! nsigmas [Nsig] : maximal deviation in sigmas ! minfracg 1 ! stop search when minfracg (0..1) of the gvectors have been assigned to grains ! Nhkls_in_indexing 15 ! Nhkls_in_indexing [Nfamilies] : use first Nfamilies in indexing random 100000 ! use randomly chosen orientation seeds #trials ! positionfit ! fit the position of the grain ! genhkl ! generate list of hkl's based on space group and cell parameters in gve file EOM }
#———————————————————————————————– # # Actual indexing loop # Runs tens of GrainSpotter iterations with decreasing tolerances # Runs in the current folder # #———————————————————————————————–
indexing_loop () {
echo “#” echo “#” echo “# Running first GS iteration. Starting from $startGVE, GS parameters in index-0.ini, grains saved in grains0.log” echo “#” echo “#” create_GS_init index-0.ini $startGVE grains-0.log 20 0.5 0.06 1 1 $GrainSpotter index-0.ini echo “#” echo “#” echo “# Done with iteration 0. New list of GVE will be peaks_after_step-0.gve” echo “#” echo “#” $clearGVE grains-0.log $startGVE peaks_after_step-0.gve grainlist=“grains-0.log”
for i in {1..5} do
j="$((i - 1))" echo "#" echo "#" echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" echo "#" echo "#" # Use from previous step and create grains$i.log create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.5 0.06 1 1 $GrainSpotter index-$i.ini echo "#" echo "#" echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" echo "#" echo "#" $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve grainlist="$grainlist grains-$i.log"
done
for i in {6..10} do
j="$((i - 1))" echo "#" echo "#" echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grain-$i.log" echo "#" echo "#" create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.5 0.06 2 2 $GrainSpotter index-$i.ini echo "#" echo "#" echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" echo "#" echo "#" # Remove peaks that have been indexed $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve grainlist="$grainlist grains-$i.log"
done
for i in {11..15} do
j="$((i - 1))" echo "#" echo "#" echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" echo "#" echo "#" create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.3 0.06 2 2 $GrainSpotter index-$i.ini echo "#" echo "#" echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" echo "#" echo "#" # Remove peaks that have been indexed $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve grainlist="$grainlist grains-$i.log"
done
for i in {16..20} do
j="$((i - 1))" echo "#" echo "#" echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" echo "#" echo "#" # Use from previous step and create grains$i.log create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.3 0.06 3 3 $GrainSpotter index-$i.ini # Remove peaks that have been indexed echo "#" echo "#" echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" echo "#" echo "#" $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve grainlist="$grainlist grains-$i.log"
done
for i in {21..25} do
j="$((i - 1))" echo "#" echo "#" echo "# Running GS iteration $i. Starting from peaks_after_step-$j.gve, GS parameters in index$i.ini, grains saved in grains-$i.log" echo "#" echo "#" # Use from previous step and create grains$i.log create_GS_init index-$i.ini peaks_after_step-$j.gve grains-$i.log 20 0.3 0.1 3 3 $GrainSpotter index-$i.ini # Remove peaks that have been indexed echo "#" echo "#" echo "# Done with iteration $i. New list of GVE will be peaks_after_step-$i.gve" echo "#" echo "#" $clearGVE grains-$i.log peaks_after_step-$j.gve peaks_after_step-$i.gve grainlist="$grainlist grains-$i.log"
done
}
#———————————————————————————————– # # Indexing loop, runs tens of GrainSpotter iterations with decreasing tolerances # Runs in the current folder # #———————————————————————————————–
for 1) do
echo "#----------------------------------------------------------------------------------------" echo "#" echo "# Full indexing loop number $loop" echo "# Data saved in folder: Indexing-$loop" echo "#" echo "#----------------------------------------------------------------------------------------" echo "" folder="Indexing-$loop" \rm -rf $folder mkdir $folder grainlist="" indexing_loop $mergeGrains -c $crystalSymmetryCode -o merge $grainlist $extractEuler -o merge-grains-euler.txt merge-grains.log mv grains-* $folder mv peaks_after_step* $folder mv merge-* $folder mv index-*.ini $folder echo "" echo "" echo "#----------------------------------------------------------------------------------------" echo "#" echo "# Done with indexing loop number $loop" echo "# Data saved in folder: Indexing-$loop" echo "#" echo "#----------------------------------------------------------------------------------------" echo "" echo ""
done
exit <file>
