fit_static Basic Example

Basic usage example fit_static utility. Yon can find example file from TRXASprefitpack-example fit_static subdirectory.

Peak position shifting

  1. Go to shift subdirectory. In shift subdirectory, you can find example_calc_peak.txt and example_1.txt files. First one is simplified version of thoretically calculated x-ray absorption spectrum peak and its intensity. Last one is the fake experimental x-ray absorption spectrum.

  2. Type fit_static -h. Then it prints help message. You can find detailed description of arguments in the utility section of this document.

  3. Type fit_staitc example 1 example_calc_peak.txt -1.25 -ls v --fwhm_G 0.5 --fwhm_L 2.0 -o example First positional argument is prefix of experimental spectrum file to fit and second positional argument is the number of scan to fit. In this example it reads example_1.txt file. If you set num_scan argument to 2, it will search example_2.txt file and read it if such file exists. Third positional argument is filename of theoretical line shape spectrum. In this example it reads example_calc_peak.txt to get peak position and intensity of theoretically calculated one. Last positional argument is peak_factor. When --scale_energy option argument is not set, it left shift peak positions to match experimental one. In this example, it sets -1.25 as initial peak_factor. The fist optional argument -ls or --line_shape is line shape of spectrum. In this example it uses v voigt profile. The second and third optional argument --fwhm_G and --fwhm_L are initial broadening parameter of gaussian and lorenzian part respectively. In this example, It set 0.5 as initial broadening parameter of gaussian part and 2.0 as initial broadening parameter of lorenzian part.

  4. After fitting process is finished, you can see both fitting result plot and report for fitting result in the console.

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  • Close all fitting result plot windows, after then you can find example_A.txt, example_base.txt, example_fit.txt and example_fit_report.txt.

example_A.txt contains peak intensity scaling factor of each spectrum.

example_base.txt contains fitted base line feature of experimental spectrum.

example_fit.txt contains fitted thoretically calculated spectrum.

example_fit_report.txt contains fitting result report.

Peak position scaling

  1. Go to scale subdirectory. In scale subdirectory, you can find example_calc_peak.txt and example_1.txt files. First one contains thoretically calculated IR peak information and last one is fake experimental IR spectrum.

  2. Type fit_staitc example 1 example_calc_peak.txt 0.95 -ls g --fwhm_G 15 --scale_energy -o example. Last positional argument is initial parameter of peak_factor. Since we set --scale_energy, it matchs peak position of thoretical spectrum to experimental one by uniformly scaling peak position instead of uniform shifting. In this example we use g gaussian peak shape, so we need not to set --fwhm_L initial lorenzian broadening parameter.

  3. After fitting process is finished, you can see both fitting result plot and report for fitting result in the console.

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  • Close all fitting result plot windows, then fitting results files will be generated.