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Tune Manual

6.0 - TUNE - Isotropic simulations & optimizations

The TUNE program optimizes the values of simulation parameters to produce a calculated spectrum with minimum residual error as compared to the experimental spectrum. The text input_file contains experimental, simulation, and parameter output filenames, optimization settings and starting simulation parameters. TUNE can either be used to produce a single simulation or an optimized simulation. TUNE also has the AUTO SIMULATE function. This is used to pick out potential simulations from a very large set of possibilities for a single isotropic EPR spectrum, particularly those which display a a complex pattern of many lines.


Usage: tune filename
Example: tune testdata.tun


The filename "testdata.tun" refers to an ASCII parameter file which contains all the information TUNE needs to execute. The format of this file is displayed later in this document. Information text will be printed to the screen until notification that the program has finished. You can then examine the output files for results. Creating the Input Files Create the parameter and spectrum input files. You can create the parameter file using either a text editor or by using functions functions provided by both the SimEPR and WinSIM programs. You will need both a parameter (.tun) file and an experimental spectrum file (.lmb, .exp, or .spc). For instance:


test01.tun ASCII parameter file
test01.lmb binary experimental spectrum data file


Now run the program as a command line program.


6.0.1 Format of the TUNE input file

The tune input-file is ASCII text and contains the following information: experimental file name, simulation file name, simulation parameters, optimization parameters. All letters may be either upper-case or lower-case. The order of the parameters is generally insignificant. All optimization flags are of the form 1= Optimize, 0= Remain Constant. An example:


Parameters Description
Tune input file. unneeded title
---------------------------------------------------- unneeded divider
F0: 0 spectrum file types
F1: test01.lmb experimental data file name
F2: test01.sim simulation data file name
F3: test01.epr text parameter output file
---------------------------------------------------- Unneeded divider
LMB fit parameters  
HF: 1 Regular hcc analysis: 1= on, 0= off
PA: 0 Parametric hcc analysis: 1= on, 0= off
ST: 0 Step type: 0, 1, 2
NL: 7 Number of levels of iteration
---------------------------------------------------- Unneeded divider
Simplex fit parameters  
RS: 4 Number of Restarts
IT: 600 Max iterations per restart
TL: 0.01000 Fractional Tolerance
---------------------------------------------------- Unneeded divider
Continuous wave fit range  
DS: 1 Data start, low data point of CW fit range
DE: 4096 Data end, high data point of CW fit range
---------------------------------------------------- Unneeded divider
Parameter constraints  
CHF: 0, 10 hcc: flag, % deviation allowed
CLW: 0, 10 linewidth: flag, % deviation allowed
CGS: 0, 10 g-shift: flag, % deviation allowed
CRI: 0, 10 intensity: flag, % deviation allowed
---------------------------------------------------- Unneeded divider
Spectral parameters  
SM: 1 0=simple, 1=Nitroxide calculations
FT: 0 0=Continuous Wave, 1=Fourier
FF: 256 FT combined frequency, unneeded if FT=0
HA: 1 Harmonic: 0, 1, 2
MA: 1.333 Modulation amplitude in Gauss
TC: 0.5 ratio: time constant (ms) / scan time (s).
---------------------------------------------------- Unneeded divider
SP: 1 Species start identifier
LW: 0.100, 0 LW value, optimization flag
LS: 6.000, 1 Line shape value, opt. flag
RI: 118.000, 1 Relative intensity, opt. flag
GS: -0.012, 1 G-shift value, opt. flag
NX: 16.0, 1 Nitroxide coupling
N1: 0.45, 1 Nitroxide low field line width
N2: 0.55, 1 Nitroxide mid field line width
N3: 0.65, 1 Nitroxide high field line width
aa: 0.718, 0.5, 1, 1 hcc value, spin, number, optimization flag
aa: 4.089, 0.5, 1, 1 "
aa: 5.270, 0.5, 3, 1 "
---------------------------------------------------- unneeded divider
SP: 2 species start identifier
LW: 0.100, 0
LS: 0.000, 1
RI: 50.000, 1
GS: -0.037, 1
NX: 13.5, 1
N1: 0.67, 1
N2: 0.72, 1
aa: 0.54, 0.5, 3, 1
aa: 4.75, 0.5, 3, 1
aa: 0.556, 0.5, 1, 1
same as above...


6.0.2 TUNE output

TUNE produces three output files, in our example:


test01.epr ASCII text printout of simulation parameters
test01.out ASCII parameter file which can again be used with TUNE
test01.sim Simulation spectrum data file, same format as experimental data file


The text parameter output-file is a printout of the beginning and ending simulation parameters, SSR measurement, final Spearman's rank Correlation Coefficient, input and output filenames, and on the job time. This file can be read on screen or output to a printer, perhaps using the Reporter program. The simulation data output file can be loaded into the main EPR or WinSIM programs for viewing, comparing, and plotting.


6.1 - REPORTER - View and print text data files

This is a small Microsoft Windows program to view and edit text files with the .EPR suffix, normally the output of TUNE. In the MS-Windows properties box that accompanies each program icon, you should set the directory as the one most likely to contain these files. 


Conversion to HTML by DRD. Jan, 1996