Introduction
Software
Experiment
Data processing
Post-processing and results evaluation
Advanced discussions
Below is an example of a GrainSpotter loop for NaCoF3 post-perovskite. You can run it by typing
gsLoop.sh > gsLoop.log
The output of the loop will be saved in gsLoop.log, with multiple outputs, one for each indexing.
The loop can run nLoops indexings (typically 3). Indexing are run in parallel. If you ask for 20 copies of indexings, they will run simultaneously. Make sure you do not overrun the capabilities of your computer otherwise it will become very slow!
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.
There is now a dedicated TIMEleSS tool to evaluate your indexing performance.
You wanted it?! Here is the source code for the loop above
#!/bin/bash # Starting GVE file startGVE=../HTC_04_02_3D_03_merge.gve # Starting GVE file crystalSymmetryCode=3 # Number of indexings nLoops=3 # Threshold for considering 2 grains are the same (in degrees) matchgrainThreshold=1 # Step in omega, in degrees omegastep=0.25 # 2 theta range min2theta=4.0 max2theta=17.0 # Wavelength wave=0.3738 # 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=/usr/bin/timelessExtractEulerAngles indexingStatistics=/usr/bin/timelessGSIndexingStatistics # 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 63 ! spacegroup [space group nr] etarange 0 360 ! etarange [min max] ! dsrange 0.0 2.0 ! dsrange [min max], reciprocal d-spacing range, multiple ranges can be specified tthrange $min2theta $max2theta ! tthrange [min max], multiple ranges can be specified domega $omegastep ! domega [stepsize] in omega, degrees omegarange -29.0 30.0 ! omegarange [min max] degrees, multiple ranges can be specified filespecs $2 $3 ! [gvecsfile grainsfile] cuts $4 $5 1.0 ! cuts [min_measuments min_completeness min_uniqueness] eulerstep 3 ! 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 !Nhkls_in_indexing 31 ! Nhkls_in_indexing [Nfamilies] : use first Nfamilies in indexing random $9 ! random sampling of orientation space trying 10000 sample points minfracg 0.99 ! stop search when minfracg (0..1) of the gvectors have been assigned to grains ! 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 () { local grainlist="" # Declaring this variable as local to be able to run multiple indexings in parallel 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 25 0.5 0.05 1.2 1.2 10000 $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..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 25 0.5 0.05 1.2 1.2 10000 $GrainSpotter index-$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" rm peaks_after_step-$j.gve done for i in {21..40} do j="$((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 25 0.5 0.07 2.0 2.0 10000 $GrainSpotter index-$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" rm peaks_after_step-$j.gve done for i in {41..60} do j="$((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 15 0.3 0.05 1.2 1.2 10000 $GrainSpotter index-$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" rm peaks_after_step-$j.gve done for i in {61..80} do j="$((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 15 0.3 0.07 2.0 2.0 10000 $GrainSpotter index-$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" rm peaks_after_step-$j.gve done rm peaks_after_step-80.gve $mergeGrains -c $crystalSymmetryCode -m $matchgrainThreshold -o merge $grainlist $extractEuler -o merge-grains-euler.txt merge-grains.log $indexingStatistics -i index-80.ini -l merge-grains.log -g ../$startGVE -w $wave } #----------------------------------------------------------------------------------------------- # # Indexing loop, runs tens of GrainSpotter iterations with decreasing tolerances # Runs in the current folder # #----------------------------------------------------------------------------------------------- for (( loop=1; loop<=$nLoops; loop++ )) 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 cd $folder indexing_loop > "../indexing-$loop.log" & cd .. echo "" echo "" echo "#" echo "# Done starting the indexing loop number $loop" echo "# Data saved in folder: Indexing-$loop" echo "# Log file is indexing-$loop.log" echo "#" echo "#----------------------------------------------------------------------------------------" echo "" echo "" done exit
