Notes on SRIM:
Unattended (batch) operation and processing data files
Large parts of this are verbatim extracts from SRIM Documentation (v. 2003.20)
Physics of Recoil Cascades
…The number of displacement collisions records how many target atoms were set in motion in the
cascade with energies above their displacement energy (which you specified in the input program to
TRIM)... A vacancy is the hole left behind when a recoil atom moves from its original site. Next, the
table shows replacement collisions, which reduce the number of vacancies. If a moving atom strikes a
stationary target atom and transfers more than its displacement energy to it, and the initial atom, after
the collision, does not have enough energy to move onwards, and it is the same element as the atom it
struck, then it just replaces that atom in the target and there is no vacancy created. Although this may
sound complicated, this mechanism may reduce the total vacancies by up to 30%. The summation
goes:
Displacements = Vacancies + Replacement Collisions
…The calculation of cascades, target displacements, replacement collisions, etc. makes certain
assumptions which are defined explicitly below:
Assume an incident atom has atomic number Z1, and energy E. It has a collision within the target with
an atom of atomic number Z2. After the collision, the incident ion has energy E1 and the struck atom
has energy E2. Previously specified for the target are energies E d, the displacement energy, Eb, the
binding energy of a lattice atom to its site, and Ef, the final energy of a moving atom, below which it is
considered to be stopped.
A displacement occurs if E2>Ed (the hit atom is given enough energy to leave the site). A vacancy
occurs if both E1>Ed and E2>Ed (both atoms have enough energy to leave the site). Both atoms then
become moving atoms of the cascade. The energy, E2, of atom Z2 is reduced by Eb before it has
another collision. If E2<Ed, then the struck atom does not have enough energy and it will vibrate back
to its original site releasing E2 as phonons.
If E1<Ed and E2>Ed and Z1 = Z2, then the incoming atom will remain at the site and the collision is
called a replacement collision with E1 released as phonons. The atom in the lattice site remains the
same atom by exchange. This type of collision is common in single element targets with large recoil
cascades. If E1<Ed and E2>Ed and Z1Z2, then Z1 becomes a stopped interstitial atom.
Finally, if E1<Ed and E2<Ed, then Z1 becomes an interstitial and E1+E2 is released as phonons. If
your target has several different elements in it, and each has a different displacement energy, then E d
will change for each atom of the cascade hitting different target atoms.…
Quick vs. Full Calculations
TRIM allows the user to omit certain aspects of collision kinetics in order to increase the speed of the
calculation. "Full Damage Cascades" includes all normal kinetics of the ion penetrating the target. The
"Quick" calculation ignores target atom cascades and limits the calculation to the ion trajectories. The
"Sputtering" calculation includes special plots related to target atom sputtering. Finally, TRIM may be
run in a constrained mode, as explained below for calculating neutron, electron, and photon cascades.
(1) - Quick: Kinchen-Pease - This option should be used if you don't care about details of target
damage or sputtering. The damage calculated with this option will be the quick statistical estimates
based on the Kinchin-Pease formalism (see section Physics of Recoil Cascades for details about target
damage).. The following data will be calculated correctly: Final distribution of ions in the target,
Ionization energy loss by the ion into the target, Energy transferred to recoil atoms, Backscattered Ions
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6 February 2016
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and Transmitted Ions. You will get identical range results for each ion as when you use the Full
Damage Cascade option below, since the random number generator for the ions is separate from that
used for the recoils.
(2) - Full Cascades - This option follows every recoil until its energy drops below the lowest
displacement energy of any target atom. Hence all collisional damage to the target is analyzed. The one
exception is for very rare massive cascades which exceed 2000 atoms. At this point TRIM runs out of
memory, and an error message is posted indicating that the limit of 2000 atoms in a single cascade has
been exceeded. The calculation continues after the message is posted.
[My interpretation of this is that full cascades are necessary for any calculations used to assess target
damage (which is what we are concerned with), and quick calculations should only be used to get ion
ranges.]
Output Files relevant to Energy Loss
Energy Loss to Ionization
The datafile IONIZ.TXT, and the plot summaries the energy loss to the target electrons within the
target window.
This plot and file contains the energy given up to the target electrons. The data relating to "Ions" is the
direct energy transferred from the ion to the target electrons. The data relating to the "Recoils" is
energy transferred from recoiling target atoms to the target electrons.
====== Argon (10keV)
=======
SRIM-2003.20
========================================
Ion and Recoil IONIZATION
See SRIM Outputs\TDATA.txt for details
========================================
See file : SRIM Outputs\TDATA.txt
for calculation data
Ion
= Ar
Energy = 10 keV
============= TARGET MATERIAL ======================================
Layer 1 : PET
Layer Width = 10000.E+00 A ;
Layer # 1- Density = 9.631E22 atoms/cm3 = 1.397 g/cm3
Layer # 1- H = 36.3 Atomic Percent = 4.19 Mass Percent
Layer # 1- C = 45.4 Atomic Percent = 62.5 Mass Percent
Layer # 1- O = 18.1 Atomic Percent = 33.3 Mass Percent
====================================================================
Total Ions calculated =010000.00
===============================================================
Table Ionization Units are >>>> eV / Angstrom / Ion <<<<
===============================================================
TARGET
DEPTH
(Ang)
----------389000.E-05
777000.E-05
116500.E-04
…
IONIZ.
by
IONS
----------1039.20E-02
1039.11E-02
1020.97E-02
IONIZ.
by
RECOILS
----------2277.50E-03
4055.10E-03
5216.12E-03
Energy Loss to Phonons
The datafile PHONON.TXT, and the plot summaries the energy loss of the ions and recoiling target
atoms into target phonons. The energy loss to target phonons consists of the direct creation of phonons
by the ion, and the additional energy loss by target recoil atoms to phonons.
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====== Argon (10keV)
=======
SRIM-2003.20
========================================
Ion and Recoil PHONONS
See SRIM Outputs\TDATA.txt for calc. details
========================================
See file : SRIM Outputs\TDATA.txt calculation data
Ion
= Ar
Energy = 10 keV
============= TARGET MATERIAL ======================================
Layer 1 : PET
Layer Width =
1.E+04 AAA ;
Layer # 1- Density = 9.631E22 atoms/cm3 = 1.397 g/cm3
Layer # 1- H = 36.3 Atomic Percent = 4.19 Mass Percent
Layer # 1- C = 45.4 Atomic Percent = 62.5 Mass Percent
Layer # 1- O = 18.1 Atomic Percent = 33.3 Mass Percent
====================================================================
Total Ions calculated =10000.00
========================================================
Table Units are >>>> Phonons / Angstrom / Ion <<<<
========================================================
DEPTH
PHONONS
PHONONS
(Ang.)
by ION
by RECOILS
----------- ----------- ----------389000.E-05 126130.E-05 286503.E-05
777000.E-05 122127.E-05 555112.E-05
116500.E-04 123007.E-05 794211.E-05
155300.E-04 124469.E-05 988060.E-05
194100.E-04 127521.E-05 116107.E-04
…
Energy Loss to Vacancy Production
This plot and the files VACANCY.TXT and NOVAC.TXT, tabulate the energy loss to target
vacancies. Each target atom element is shown separately. The number of vacancies depends on the
Displacement Energy assigned to each target atom.
The file NOVAC.TXT tabulates replacement collisions. These are a special type of collision in which
the moving atom collides with an identical target atom, transfers an amount of energy greater than that
atom's displacement energy, and does not have enough energy to move on out of the lattice site. Hence
the original moving atom replaces the target atom, the target atom moves on, and since the two atoms
are the same atomic species, there is no final damage. The two atoms exchange places, but since they
are the same species there is no detectable change.
[I’m not sure what the primary knock-on atom column is – I think maybe it is the number of target
atoms recoiling (added to the cascade) in atoms/angstrom/ion, this column is not used for energy loss
calculations ]
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====== Argon (10keV)
=======
SRIM-2003.20
==========================================
Ion and Target VACANCY production
See SRIM Outputs\TDATA.txt for calc. details
==========================================
See file : SRIM Outputs\TDATA.txt for calculation data
Ion
= Ar
Energy = 10 keV
============= TARGET MATERIAL ======================================
Layer 1 : PET
Layer Width =
1.E+04 A ;
Layer # 1- Density = 9.631E22 atoms/cm3 = 1.397 g/cm3
Layer # 1- H = 36.3 Atomic Percent = 4.19 Mass Percent
Layer # 1- C = 45.4 Atomic Percent = 62.5 Mass Percent
Layer # 1- O = 18.1 Atomic Percent = 33.3 Mass Percent
====================================================================
Total Ions calculated =10000.00
Total Target Vacancies
= 141 /Ion
Total Target Displacements = 143 /Ion
Total Target Replacement Collisions = 2 /Ion
!!!! NOTE : 2nd Column below is number of Primary Knock-Ons !!!!
( PKO are number of Target Atoms Recoiling from the Ion. )
==========================================================
Table Units are >>>> Vacancies / Angstrom / Ion <<<<
==========================================================
TARGET
DEPTH
Ar
H
C
O
(Ang.)
Knock-Ons
Vacancies
Vacancies
Vacancies
----------- ----------- ----------- ----------- ----------389000.E-05 7002.62E-05 1216.75E-04 9412.60E-05 4420.04E-05
777000.E-05 1280.40E-04 1120.89E-04 1130.42E-04 5103.00E-05
116500.E-04 1277.05E-04 1198.71E-04 1297.92E-04 5484.47E-05
155300.E-04 1284.52E-04 1334.26E-04 1407.18E-04 6121.11E-05
194100.E-04 1301.79E-04 1464.13E-04 1561.03E-04 6657.24E-05
232900.E-04 1300.24E-04 1553.04E-04 1653.79E-04 7110.88E-05
…
====== Argon (10keV)
=======
SRIM-2003.20
=========================================
Replacement Collisions
See SRIM Outputs\TDATA.txt for calc. details
=========================================
See file: SRIM Outputs\TDATA.txt for data about the calculation
Ion
= Ar
Energy = 10 keV
============= TARGET MATERIAL ======================================
Layer 1 : PET
Layer Width =
1.E+04 AAA ;
Layer # 1- Density = 9.631E22 atoms/cm3 = 1.397 g/cm3
Layer # 1- H = 36.3 Atomic Percent = 4.19 Mass Percent
Layer # 1- C = 45.4 Atomic Percent = 62.5 Mass Percent
Layer # 1- O = 18.1 Atomic Percent = 33.3 Mass Percent
====================================================================
Total Ions calculated =10000.00
Total Target Vacancies
= 141 /Ion
Total Target Displacements = 143 /Ion
Total Target Replacement Collisions = 2 /Ion
================================================================
Table Energy Units are >>>> Number / Angstrom / Ion <<<<
================================================================
DEPTH (A)
Number
---------------------3890000.E-06
0000.030747
7770000.E-06
0000.007990
1165000.E-05
0000.003608
1553000.E-05
0000.003814
…
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6 February 2016
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Calculating Electronic and Nuclear LET
According to the discussion above, linear energy transfer (LET) can be calculated
from the SRIM output files:
Electronic LET =
eV/ion/Angstrom
Nuclear LET =
eV/ion/Angstrom
Ionization LET (Ion) + Ionization LET (Recoils)
IONIZ.TXT column 2
IONIZ.TXT column 3
Binding Energy LET + Phonon Energy LET
eV/ion/Angstrom
eV/ion/Angstrom
Binding Energy LET = Number of Displacements * Binding Energy, Eb
eV/ion/Angstrom
displ./ion/Angstrom
eV/displacement
Phonons (Ion)
+
Phonons (Recoils)
Phonon Energy LET =
eV/ion/Angstrom
PHONON.TXT column 2
PHONON.TXT column 3
For Full Cascades:
Number of Displacements= Number of Vacancies + Number of Replacements
displ./ion/Angstrom
displ./ion/Angstrom
displ./ion/Angstrom
Sum of Target Atom Vacancies
Number of Vacancies =
displ./ion/Angstrom
VACANCY.TXT sum: columns 3,4,+…
Replacements
Number of Replacements =
displ./ion/Angstrom
NOVAC.TXT column 2
For Quick Calculations:
Sum of Target Atom Vacancies
Number of Displacements =
displ./ion/Angstrom
VACANCY.TXT sum: columns 2+3
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Running TRIM automatically (batch mode) from SRIM help file
TRIM Monte Carlo calculations can be run without any keyboard inputs. This allows TRIM to be run
with sequential calculations for a group of related results (sometimes called "running in a batch
mode"). Between each run, the input file to TRIM is slightly altered, in order to make similar runs
which may be compared. This input file, TRIM.IN, controls the TRIM calculation.
Instructions:
Look at the SRIM file: TRIMAUTO which contains one number.
If the number is 1 then TRIM runs without input, and at completion is saves all datafiles and
terminates.
If any other number is in TRIMAUTO, or the file is not present, then TRIM runs normally.
Running TRIM in batch mode:
(1) Run a full TRIM calculation.
(1) Edit the file TRIM.IN, changing any parameters to vary the TRIM calculation.
Be sure to edit line #3, Ion Number, to the finite number ions to be calculated (not the default
99999).
Be sure to edit line #7 to obtain the desired output datafiles.
Be sure to edit line #13 to Plot Type = 5 (no plots) if you wish a rapid calculation.
(2) Run TRIM.EXE by executing it directly.
(3) When TRIM is completed, save or rename all the *.TXT files which have been generated.
(4) Repeat as needed
You will obtain all output files requested in TRIM.IN, line #7, plus two special groups:
*.TXT = Files containing all the data shown in the available plots
*.SAV = Files allowing the restart of TRIM where this calculation stopped.
You will have to alter file "SRIM Saves/TDATA.SAV", Line #10, "Ion Number Total" to a bigger
number
in order to continue calculations with TRIM using old data. This special change is required to sum a
group of TRIM calculations. See the Help section: Combining Multiple TRIM Calculations.
Example:
The following is a simple procedure for running TRIM in batch mode:
(1) Edit TRIM.IN to set the calculation.
(2) Start the batch job TRIM.EXT.
(3) While the calculation is progressing, you may still execute any of the TRIM functions.
(4) When TRIM finishes, change the file TRIM.IN to a new setup.
(5) Go to step (2) to continue
Running a set of SRIM simulations automatically
It is possible to run SRIM from the (Windows/DOS) command line. The documentation for this mode
is provided in the SRIM file: TRIMAUTO.TXT and in the help topic 'Auto-TRIM' available through the
help menu under 'TRIM FAQ and Solutions'.
In batch/non-interactive mode, SRIM will start and execute using the input data in the file TRIM.IN
which is in the main program directory where TRIM.EXE is located. TRIM.IN specifies all data
needed to run the simulation including the target composition, density and thickness, incident ion
species, charge and energy, which output files to produce and which calculation mode to use
(Quick/Full Cascades). Output files produced such as IONIZ.TXT, PHONON.TXT, VACANCY.TXT
and NOVAC.TXT are saved in the main directory, and are overwritten with each new simulation.
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First, read the documentation in TRIMAUTO.TXT so that you understand how to run SRIM on a single
input file(TRIM.IN) in non-interactive mode. The next step is to automate this process to run SRIM
automatically on a set of input files.
Instructions:
I have written two DOS batch files (MultiLET.bat and LET.bat, listings below) which will run
SRIM in non-interactive mode on a set of pre-prepared *.IN files, allowing unattended simulation of
many ion/energy/target combinations. To use these batch files, you need to do the following:
Note: In this description, the main SRIM directory is the directory where the file TRIM.EXE is
located, the data directory is where the input and output files are located.
1.
2.
3.
4.
5.
6.
Copy MultiLET.bat and LET.bat to the main directory.
Make a new directory which will contain the input and output data for the set of simulations.
This is the data directory.
Copy TRIMAUTO (from the main directory) to the data directory. Edit the file so that the first
line contains a "1", and the second line is the path of the data directory
Make a set of input files (following the format of TRIM.IN), one for each set of conditions
you wish to simulate (see below), and save them in the data directory. Make sure these files do
not have spaces in their filenames, and that the file extension is .IN
At a command prompt, cd to the main directory
At the command prompt type: MULTILET.bat datadirectory substituting the
pathname of the data directory. This will run SRIM in non-interactive mode using every *.IN
file in the data directory, moving all output files produced back to the data directory with
names prefixed with the name of the input file.
For example, running MultiLET.bat .\myData would run SRIM on all input files with
names like *.IN in the data directory .\myData. If there were two input files
.\myData\sim1.IN and \myData\sim2.IN in the data directory, the output files
would be .\myData\sim1_ioniz.txt, .\myData\sim2_ioniz.txt,
.\myData\sim1_phonon.txt etc.
Creating input files:
To create a set of input files, the easiest method is to first run SRIM in normal mode, setting up the
target, ion and simulation parameters to match one of the desired set of input conditions. Start the
simulation, then quit SRIM, opting to save the data so that SRIM can be re-started (this ensures the
input data is saved to TRIM.IN). Copy TRIM.IN (in the main directory) to the data directory, and
open the copy with a text editor. Check the SRIM documentation for details of the format of this file,
and alter the appropriate values to change the incident ion species, ion energy and calculation mode. If
you are not sure how to change a parameter, run SRIM again with the conditions you want and look at
how TRIM.IN in the main directory has changed. Save each *.IN file to the data directory with a
new name to reflect the simulation conditions, and repeat for each set of conditions. There are also
some example input files available in the SRIM documentation.
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6 February 2016
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Example input (TRIM.IN) file
Values that can are likely to vary between input files are highlighted:
Ion Z
use 1 for quick,
2 for full
calculations
Xmax (maximum
depth for output
values)
Ion M
Number of
ions simulated
Ion Energy
Bragg Correction
(change to match
target value below)
==> SRIM-2003.20 This file controls TRIM Calculations.
Ion: Z1 , M1, Energy (keV), Angle,Number,Bragg Corr,AutoSave Number.
18 39.962
2.5
0 20000 .9570329 10000
Cascades(1=No;2=Full;3=Sputt;4-5=Ions;6-7=Neutrons), Random Number Seed, Reminders
1
0
0
Diskfiles (0=no,1=yes): Ranges, Backscatt, Transmit, Sputtered, Recoils (0=none;1=Some;2=All
Details;>10=EXYZ Output)
0
0
0
0
0
Target material : Number of Elements & Layers
"Argon (2.5keV)
"
3
1
Target Energies (eV): Binding, Surface, Individual Displacement
3
2 10 28 28
PlotType (0-5); Plot Depths: Xmin, Xmax(Ang.) [=0 0 for Viewing Full Target]
5
0
230
Target Elements: Z Mass(amu)
Atom 1 = H =
1 1.008
Atom 2 = C =
6 12.011
Atom 3 = O =
8 15.999
Layer Layer Name /
Width Density H(1) C(6) O(8)
Numb. Description
(Ang) (g/cm3) Stoich Stoich Stoich
1 "PET"
10000 1.397 .363636 .454545 .181818
0 Target layer phases (0=Solid, 1=Gas)
0
Target
Target Compound Corrections (Bragg)
composition
.9570329
and binding
Target atom displacement energies (eV)
energies
10 28 28
Target atom lattice binding energies (eV)
3
3
3
Target atom surface binding energies (eV)
2 7.41
2
Stopping Power Version (1=2003, 0=2003)
0
Some Hints:
Depth Resolution: The number of depth values in the output files is fixed (at ?100), so to get good
depth resolution when simulating multiple incident ion species and/or energies, make sure you set
Xmax on line 13 (this corresponds the 'plot window' when running SRIM interactively) to a value just
beyond the maximum range of the incident. You can use the range calculation facility of SRIM to
determine appropriate Xmax values for each input file.
Oscillations at small depths: For low ion energies and/or heavy ions, you may see oscillations in the
output values at small depths (some Angstroms) - this will not go away by increasing the number of
ions simulated - it is due to effects of statistical sampling and the intermolecular spacing in the early
part of the ion trajectory - see TRIM FAQ in the help menu.
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Batch file listings:
MultiLET.bat
echo off
REM for each input file in the data directory *.IN
REM run LET.BAT to process the file in TRIM and move the output
REM pass data directory as first argument
echo working in data directory: %1
echo processing the following input files:
dir %1\*.IN
echo switching to batch mode in TRIM
move %1\trimauto >nul
FOR %%a in (%1\*.IN) do call:PROC_FILE %1 %%a
:PROC_FILE
@echo data directory: %1
@echo processing %~n2
call let.bat %1 %~n2
GOTO :EOF
LET.bat
echo off
REM run TRIM.EXE in main SRIM directory with
REM input file TRIM.IN from data directory input as %1
REM in auto mode according to TRIMAUTO
REM by replacing files and moving them to the correct location
REM first argument is data directory
REM second argument is stem of input and output file
REM data directory must contain a file stem.IN which is a TRIM.IN file
REM the results will be copied back to the data directory with the name
REM ioniz_stem.txt etc
REM note - all data files in the main SRIM directory will be overwritten
if not exist trim.exe echo 'Must run this from SRIM main directory'
REM echo data directory: %1
REM echo file stem %2
REM step 1: copy input file from data directory to main SRIM directory
if not exist %1\%2.in echo file %1\%2.in was not found
copy %1\%2.in TRIM.IN >nul
echo copied input file %2.in to main directory as TRIM.IN
REM step 2: run TRIM
trim.exe
echo finished running TRIM
REM step 3: copy output *.txt files back to data directory with new name
if not exist tdata.txt echo no summary results were saved...
move tdata.txt %1\tdata_%2.txt >nul
if exist %1\tdata_%2.txt echo results in: %1\tdata_%2.txt
if not exist ioniz.txt echo no ionization results were saved...
move ioniz.txt %1\ioniz_%2.txt >nul
if exist %1\ioniz_%2.txt echo results in: %1\ioniz_%2.txt
if not exist vacancy.txt echo no vacancy results were saved...
move vacancy.txt %1\vacancy_%2.txt >nul
if exist %1\vacancy_%2.txt echo results in: %1\vacancy_%2.txt
if not exist phonon.txt echo no phonon results were saved...
move phonon.txt %1\phonon_%2.txt >nul
if exist %1\phonon_%2.txt echo results in: %1\phonon_%2.txt
if not exist novac.txt echo no replacement results were saved...
move novac.txt %1\novac_%2.txt >nul
if exist %1\novac_%2.txt echo results in: %1\novac_%2.txt
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6 February 2016
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