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