Added SRIM intermediate files, along with scripts to generate multipl…

…e instances of SRIM and average the data
shortlab · May 13, 2015 · 73e3a49 · 73e3a49
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diff --git a/problems/InjectedInterstitials/OutputFilesForAveraging/AverageOutputs.sh b/problems/InjectedInterstitials/OutputFilesForAveraging/AverageOutputs.sh
@@ -0,0 +1,110 @@
+#!/bin/bash
+
+## This script reads in SRIM output files, and averages their
+##output values. It is used when many, many SRIM simulations are desired,
+## and each only runs a few ions, but with a different random seed.
+
+function usage
+{
+    echo "usage: ./AverageOutputs <options>"
+    echo "    -p (string)     --prefix (string)      Output filename prefix"
+    echo "    -h       --help          Show this usage statement"
+}
+
+## Get the filename prefix from the user
+
+FilePrefix=""
+
+while [ "$1" != "" ]; do
+    case $1 in
+        -p | --prefix )         shift
+                                FilePrefix=$1
+                                ;;
+        -h | --help )           usage
+                                exit
+                                ;;
+        * )                     usage
+                                exit 1
+    esac
+    shift
+done
+
+## Go through each .TXT file that matches the user's specified prefix.
+## Trim it to the last 100 lines (the actual output). Then read in each
+## line, split it into space-separated terms, and keep a running
+## average. This effectively keeps a 100xN matrix in memory,
+## containing averaged output values aat each distance. Only read the first
+## column once, as all files contain identical depth information.
+
+Filename=
+
+## Define variables Data1 through Data100, to hold running totals of
+## whatever we are averaging
+
+    for i in {1..100}
+    do
+      declare Data$i=0
+    done
+
+FileNumber=0
+
+for Filename in "$FilePrefix"*.TXT; do
+
+    echo "Opening "$Filename" for averaging"
+
+## Use 'tail' to trim each file to the last 100 lines
+
+    tail -n 102 $Filename > temp.txt
+
+## Trim the last three lines if this is a VACANCY file
+
+    if [ "$FilePrefix" == "VACANCY" ]; then
+        head -n 100 temp.txt > data.txt
+    elif [ "$FilePrefix" == "RANGE" ]; then
+        tail -n 100 temp.txt > data.txt
+    fi
+
+## Open each file line-by-line
+
+    i=1
+
+    while read line; do
+        IFS='  ' read -a splitline <<< "$line"
+#        split(line, splitline, " ")
+#        echo ${splitline[2]}
+
+
+## Replce the 'E' in all numbers with a (*10**) for bc -le
+        D1=$(echo "${splitline[1]})" | sed -r 's/E/*10\^\(/g' | sed -r 's/\+//g')
+        D2=$(echo "${splitline[2]})" | sed -r 's/E/*10\^\(/g' | sed -r 's/\+//g')
+        var="Data$i"
+            if [ "$FilePrefix" == "VACANCY" ]; then
+#                echo "(("${!var}" * "$FileNumber" + "$D1" + "$D2") / ($FileNumber + 1))"
+#                echo "(("${!var}" * "$FileNumber" + "$D1" + "$D2") / ($FileNumber + 1))" | bc -l
+                declare "Data$i"="$(echo "(${!var} * $FileNumber + $D1 + $D2) / ($FileNumber + 1)" | bc -l)"
+            elif [ "$FilePrefix" == "RANGE" ]; then
+                declare "Data$i"="$(echo "(${!var} * $FileNumber + ($D1 / 10000000)) / ($FileNumber + 1)" | bc -l)"
+            fi
+       i=$((i+1))
+
+    done < data.txt
+
+## End the for loop
+
+    FileNumber=$((FileNumber+1))
+
+done
+
+## Finally, write out the distance vs. quantity information as a comma separated file.
+## Read the distance data (in Angstroms) from the original data.txt file.
+
+rm $FilePrefix-Averaged.csv
+i=1
+    while read line; do
+        IFS='  ' read -a splitline <<< "$line"
+        var="Data$i"
+        Distance=$(echo "${splitline[0]})" | sed -r 's/E/*10\^\(/g' | sed -r 's/\+//g')
+        Distance="$(echo "${Distance} / 10" | bc -l)"
+        echo "$Distance ${!var}" >> $FilePrefix-Averaged.csv
+        i=$((i+1))
+    done < data.txt
diff --git a/problems/InjectedInterstitials/OutputFilesForAveraging/RANGE-10163358.TXT b/problems/InjectedInterstitials/OutputFilesForAveraging/RANGE-10163358.TXT
@@ -0,0 +1,137 @@
+====== Fe (3500) into Fe                        =======
+        SRIM-2013.00
+==================================================
+      ION and final RECOIL ATOM Distributions     
+ See  SRIM Outputs\TDATA.txt for calculation details
+==================================================
+--------------------------------------------------------------------
+    Recoil/Damage Calculations made with Kinchin-Pease Estimates    
+--------------------------------------------------------------------
+----------------------------------------------------------------
+  There are NO RECOILS unless a full TRIM calculation is made.   
+----------------------------------------------------------------
+See file :  SRIM Outputs\TDATA.txt   for details of calculation
+ Ion    = Fe   Energy = 3500  keV
+============= TARGET MATERIAL ======================================
+Layer  1 : Fe
+Layer Width =     2.E+04 A   Layer # 1- Density = 8.481E22 atoms/cm3 = 7.865 g/cm3
+  Layer # 1- Fe = 100  Atomic Percent = 100  Mass Percent
+====================================================================
+ Total Ions calculated =10000.00
+ Ion Average Range =   107.3E+02 A   Straggling =   211.5E+01 A
+ Ion Lateral Range =   187.5E+01 A   Straggling =   234.1E+01 A
+ Ion Radial  Range =   295.3E+01 A   Straggling =   153.0E+01 A
+====================================================================
+ Transmitted Ions =;  Backscattered Ions =1
+ (These are not included in Skewne- and Kurtosis below.)
+
+ Range Skewne- = -000.9685  &= [-(X-Rp)^3]/[N*Straggle^3]
+ Range Kurtosis = 004.5458  &= [-(X-Rp)^4]/[N*Straggle^4]
+ Statistical definitions above are those used in VLSI implant modelling.
+====================================================================
+=================================================================
+  Table Distribution Units are >>>  (Atoms/cm3) / (Atoms/cm2)  <<<  
+=================================================================
+   DEPTH         Fe       Recoil     
+   (Ang.)       Ions     Distribution
+-----------  ----------  ------------
+200010.E-03  1.0000E+02  0.0000E+00
+400010.E-03  0.0000E+00  0.0000E+00
+600010.E-03  0.0000E+00  0.0000E+00
+800010.E-03  5.0000E+01  0.0000E+00
+100001.E-02  5.0000E+01  0.0000E+00
+120001.E-02  5.0000E+01  0.0000E+00
+140001.E-02  3.0000E+02  0.0000E+00
+160001.E-02  1.5000E+02  0.0000E+00
+180001.E-02  5.0000E+01  0.0000E+00
+200001.E-02  2.5000E+02  0.0000E+00
+220001.E-02  3.0000E+02  0.0000E+00
+240001.E-02  2.0000E+02  0.0000E+00
+260001.E-02  3.5000E+02  0.0000E+00
+280001.E-02  2.5000E+02  0.0000E+00
+300001.E-02  1.5000E+02  0.0000E+00
+320001.E-02  4.5000E+02  0.0000E+00
+340001.E-02  5.5000E+02  0.0000E+00
+360001.E-02  5.0000E+02  0.0000E+00
+380001.E-02  7.5000E+02  0.0000E+00
+400001.E-02  6.0000E+02  0.0000E+00
+420001.E-02  7.0000E+02  0.0000E+00
+440001.E-02  8.0000E+02  0.0000E+00
+460001.E-02  5.0000E+02  0.0000E+00
+480001.E-02  6.0000E+02  0.0000E+00
+500001.E-02  1.1500E+03  0.0000E+00
+520001.E-02  1.0500E+03  0.0000E+00
+540001.E-02  1.3000E+03  0.0000E+00
+560001.E-02  1.7500E+03  0.0000E+00
+580001.E-02  9.0000E+02  0.0000E+00
+600001.E-02  2.3000E+03  0.0000E+00
+620001.E-02  1.9500E+03  0.0000E+00
+640001.E-02  2.2000E+03  0.0000E+00
+660001.E-02  1.9500E+03  0.0000E+00
+680001.E-02  3.1000E+03  0.0000E+00
+700001.E-02  3.4000E+03  0.0000E+00
+720001.E-02  2.6500E+03  0.0000E+00
+740001.E-02  3.2500E+03  0.0000E+00
+760001.E-02  4.6500E+03  0.0000E+00
+780001.E-02  5.1000E+03  0.0000E+00
+800001.E-02  6.1500E+03  0.0000E+00
+820001.E-02  5.7500E+03  0.0000E+00
+840001.E-02  7.2000E+03  0.0000E+00
+860001.E-02  8.4000E+03  0.0000E+00
+880001.E-02  9.3000E+03  0.0000E+00
+900001.E-02  9.7000E+03  0.0000E+00
+920001.E-02  1.0800E+04  0.0000E+00
+940001.E-02  1.0550E+04  0.0000E+00
+960001.E-02  1.1900E+04  0.0000E+00
+980001.E-02  1.3950E+04  0.0000E+00
+100000.E-01  1.5250E+04  0.0000E+00
+102000.E-01  1.6150E+04  0.0000E+00
+104000.E-01  1.8000E+04  0.0000E+00
+106000.E-01  1.8450E+04  0.0000E+00
+108000.E-01  2.0250E+04  0.0000E+00
+110000.E-01  2.0600E+04  0.0000E+00
+112000.E-01  2.1100E+04  0.0000E+00
+114000.E-01  1.9400E+04  0.0000E+00
+116000.E-01  2.2900E+04  0.0000E+00
+118000.E-01  2.1650E+04  0.0000E+00
+120000.E-01  2.1300E+04  0.0000E+00
+122000.E-01  2.1100E+04  0.0000E+00
+124000.E-01  2.0350E+04  0.0000E+00
+126000.E-01  1.8950E+04  0.0000E+00
+128000.E-01  1.6500E+04  0.0000E+00
+130000.E-01  1.4450E+04  0.0000E+00
+132000.E-01  1.2700E+04  0.0000E+00
+134000.E-01  1.0200E+04  0.0000E+00
+136000.E-01  8.5500E+03  0.0000E+00
+138000.E-01  6.8500E+03  0.0000E+00
+140000.E-01  5.4000E+03  0.0000E+00
+142000.E-01  3.9000E+03  0.0000E+00
+144000.E-01  2.4500E+03  0.0000E+00
+146000.E-01  1.7000E+03  0.0000E+00
+148000.E-01  8.5000E+02  0.0000E+00
+150000.E-01  1.4000E+03  0.0000E+00
+152000.E-01  7.0000E+02  0.0000E+00
+154000.E-01  5.5000E+02  0.0000E+00
+156000.E-01  1.0000E+02  0.0000E+00
+158000.E-01  0.0000E+00  0.0000E+00
+160000.E-01  5.0000E+01  0.0000E+00
+162000.E-01  5.0000E+01  0.0000E+00
+164000.E-01  0.0000E+00  0.0000E+00
+166000.E-01  0.0000E+00  0.0000E+00
+168000.E-01  0.0000E+00  0.0000E+00
+170000.E-01  0.0000E+00  0.0000E+00
+172000.E-01  0.0000E+00  0.0000E+00
+174000.E-01  0.0000E+00  0.0000E+00
+176000.E-01  0.0000E+00  0.0000E+00
+178000.E-01  0.0000E+00  0.0000E+00
+180000.E-01  0.0000E+00  0.0000E+00
+182000.E-01  0.0000E+00  0.0000E+00
+184000.E-01  0.0000E+00  0.0000E+00
+186000.E-01  0.0000E+00  0.0000E+00
+188000.E-01  0.0000E+00  0.0000E+00
+190000.E-01  0.0000E+00  0.0000E+00
+192000.E-01  0.0000E+00  0.0000E+00
+194000.E-01  0.0000E+00  0.0000E+00
+196000.E-01  0.0000E+00  0.0000E+00
+198000.E-01  0.0000E+00  0.0000E+00
+200000.E-01  0.0000E+00  0.0000E+00
diff --git a/problems/InjectedInterstitials/OutputFilesForAveraging/RANGE-10248261.TXT b/problems/InjectedInterstitials/OutputFilesForAveraging/RANGE-10248261.TXT
@@ -0,0 +1,134 @@
+====== Fe (3500) into Fe                        =======
+        SRIM-2013.00
+==================================================
+      ION and final RECOIL ATOM Distributions     
+ See  SRIM Outputs\TDATA.txt for calculation details
+==================================================
+--------------------------------------------------------------------
+    Recoil/Damage Calculations made with Kinchin-Pease Estimates    
+--------------------------------------------------------------------
+----------------------------------------------------------------
+  There are NO RECOILS unless a full TRIM calculation is made.   
+----------------------------------------------------------------
+See file :  SRIM Outputs\TDATA.txt   for details of calculation
+ Ion    = Fe   Energy = 3500  keV
+============= TARGET MATERIAL ======================================
+Layer  1 : Fe
+Layer Width =     2.E+04 A   Layer # 1- Density = 8.481E22 atoms/cm3 = 7.865 g/cm3
+  Layer # 1- Fe = 100  Atomic Percent = 100  Mass Percent
+====================================================================
+ Total Ions calculated =10000.00
+ Ion Average Range =   107.6E+02 A   Straggling =   206.9E+01 A
+ Ion Lateral Range =   189.7E+01 A   Straggling =   237.5E+01 A
+ Ion Radial  Range =   296.9E+01 A   Straggling =   153.5E+01 A
+====================================================================
+ Range Skewne- = -000.8957  &= [-(X-Rp)^3]/[N*Straggle^3]
+ Range Kurtosis = 004.2190  &= [-(X-Rp)^4]/[N*Straggle^4]
+ Statistical definitions above are those used in VLSI implant modelling.
+====================================================================
+=================================================================
+  Table Distribution Units are >>>  (Atoms/cm3) / (Atoms/cm2)  <<<  
+=================================================================
+   DEPTH         Fe       Recoil     
+   (Ang.)       Ions     Distribution
+-----------  ----------  ------------
+200010.E-03  0.0000E+00  0.0000E+00
+400010.E-03  5.0000E+01  0.0000E+00
+600010.E-03  5.0000E+01  0.0000E+00
+800010.E-03  1.0000E+02  0.0000E+00
+100001.E-02  0.0000E+00  0.0000E+00
+120001.E-02  1.0000E+02  0.0000E+00
+140001.E-02  5.0000E+01  0.0000E+00
+160001.E-02  0.0000E+00  0.0000E+00
+180001.E-02  1.0000E+02  0.0000E+00
+200001.E-02  1.0000E+02  0.0000E+00
+220001.E-02  5.0000E+01  0.0000E+00
+240001.E-02  4.0000E+02  0.0000E+00
+260001.E-02  2.0000E+02  0.0000E+00
+280001.E-02  2.5000E+02  0.0000E+00
+300001.E-02  2.5000E+02  0.0000E+00
+320001.E-02  2.5000E+02  0.0000E+00
+340001.E-02  1.5000E+02  0.0000E+00
+360001.E-02  2.5000E+02  0.0000E+00
+380001.E-02  4.0000E+02  0.0000E+00
+400001.E-02  3.5000E+02  0.0000E+00
+420001.E-02  6.0000E+02  0.0000E+00
+440001.E-02  5.5000E+02  0.0000E+00
+460001.E-02  1.0500E+03  0.0000E+00
+480001.E-02  6.5000E+02  0.0000E+00
+500001.E-02  7.5000E+02  0.0000E+00
+520001.E-02  1.1500E+03  0.0000E+00
+540001.E-02  1.4000E+03  0.0000E+00
+560001.E-02  1.8000E+03  0.0000E+00
+580001.E-02  1.7500E+03  0.0000E+00
+600001.E-02  2.1000E+03  0.0000E+00
+620001.E-02  2.4500E+03  0.0000E+00
+640001.E-02  2.0500E+03  0.0000E+00
+660001.E-02  2.3000E+03  0.0000E+00
+680001.E-02  2.7500E+03  0.0000E+00
+700001.E-02  3.0500E+03  0.0000E+00
+720001.E-02  3.0500E+03  0.0000E+00
+740001.E-02  3.9500E+03  0.0000E+00
+760001.E-02  4.5000E+03  0.0000E+00
+780001.E-02  4.2500E+03  0.0000E+00
+800001.E-02  5.7000E+03  0.0000E+00
+820001.E-02  6.6500E+03  0.0000E+00
+840001.E-02  7.8500E+03  0.0000E+00
+860001.E-02  7.5000E+03  0.0000E+00
+880001.E-02  8.1000E+03  0.0000E+00
+900001.E-02  9.7500E+03  0.0000E+00
+920001.E-02  1.1850E+04  0.0000E+00
+940001.E-02  1.0200E+04  0.0000E+00
+960001.E-02  1.2050E+04  0.0000E+00
+980001.E-02  1.3700E+04  0.0000E+00
+100000.E-01  1.5000E+04  0.0000E+00
+102000.E-01  1.5800E+04  0.0000E+00
+104000.E-01  1.7150E+04  0.0000E+00
+106000.E-01  1.9650E+04  0.0000E+00
+108000.E-01  1.9250E+04  0.0000E+00
+110000.E-01  2.1050E+04  0.0000E+00
+112000.E-01  2.0550E+04  0.0000E+00
+114000.E-01  2.2800E+04  0.0000E+00
+116000.E-01  2.0950E+04  0.0000E+00
+118000.E-01  2.0150E+04  0.0000E+00
+120000.E-01  2.2250E+04  0.0000E+00
+122000.E-01  2.1800E+04  0.0000E+00
+124000.E-01  1.9500E+04  0.0000E+00
+126000.E-01  1.8900E+04  0.0000E+00
+128000.E-01  1.7400E+04  0.0000E+00
+130000.E-01  1.3950E+04  0.0000E+00
+132000.E-01  1.2700E+04  0.0000E+00
+134000.E-01  1.2050E+04  0.0000E+00
+136000.E-01  1.0400E+04  0.0000E+00
+138000.E-01  7.3500E+03  0.0000E+00
+140000.E-01  4.0500E+03  0.0000E+00
+142000.E-01  3.9000E+03  0.0000E+00
+144000.E-01  2.3500E+03  0.0000E+00
+146000.E-01  1.3500E+03  0.0000E+00
+148000.E-01  1.3000E+03  0.0000E+00
+150000.E-01  6.5000E+02  0.0000E+00
+152000.E-01  5.5000E+02  0.0000E+00
+154000.E-01  2.5000E+02  0.0000E+00
+156000.E-01  1.5000E+02  0.0000E+00
+158000.E-01  1.0000E+02  0.0000E+00
+160000.E-01  5.0000E+01  0.0000E+00
+162000.E-01  0.0000E+00  0.0000E+00
+164000.E-01  5.0000E+01  0.0000E+00
+166000.E-01  0.0000E+00  0.0000E+00
+168000.E-01  0.0000E+00  0.0000E+00
+170000.E-01  0.0000E+00  0.0000E+00
+172000.E-01  0.0000E+00  0.0000E+00
+174000.E-01  0.0000E+00  0.0000E+00
+176000.E-01  0.0000E+00  0.0000E+00
+178000.E-01  0.0000E+00  0.0000E+00
+180000.E-01  0.0000E+00  0.0000E+00
+182000.E-01  0.0000E+00  0.0000E+00
+184000.E-01  0.0000E+00  0.0000E+00
+186000.E-01  0.0000E+00  0.0000E+00
+188000.E-01  0.0000E+00  0.0000E+00
+190000.E-01  0.0000E+00  0.0000E+00
+192000.E-01  0.0000E+00  0.0000E+00
+194000.E-01  0.0000E+00  0.0000E+00
+196000.E-01  0.0000E+00  0.0000E+00
+198000.E-01  0.0000E+00  0.0000E+00
+200000.E-01  0.0000E+00  0.0000E+00