A practical guide on how to use FDMNES software to do XANES
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You can download FDMNES from here: http://neel.cnrs.fr/spip.php?article3137&lang=en
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FDMNES is precompiled so there is no need to compile it.
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For post processing, you need Athena software which can be downloaded from here: http://bruceravel.github.io/demeter/#windows
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There are several problems regarding the Mac version installation of Athena, and it is recommended to install the Windows version of it.
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First of all, you need to set the path to your input file(s) in fdmfile.txt file.
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The actual input file format is .txt.
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Output files: filename_conv.txt contains the energies and intensities of the spectrum and filename_bav.txt is the log file which contains more detailed information about the calculations.
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Sample input/output files can be found here: https://github.com/bzkarimi/XANES/tree/master/Sample-files
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./mpirun_fdmnes -np 16: To run the parallel version of FDMNES.
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HOST_NUM_FOR_MUMPS=4 ./mpirun_fdmnes -np 20: 20 MPI processes, which fdmnes divides into 5 groups of 4 processes in each. One group calculates one energy value by parallel MUMPS solver with 4 parallel processes.
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./mpirun_fdmnes -h: For getting help.
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Sample submission script: https://github.com/bzkarimi/Scripts/blob/master/HPC/fdmnes-hoffman.sh
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You have to normalize the intensities before you plot the spectrum (filename_conv.txt). This can be done automatically using Athena software. You just need to open filename_conv.txt with Athena and click on normalize. Then you can save the new data into a new file.
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Note: When you open your raw file (filename_conv.txt) with Athena, it asks which column in your data corresponds to E (first column) and which column corresponds to intensity (second column).
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Linear Combination Fitting (LCF): In order to do LCF, you have to open all files that you want to use (Standards and the one that you want to do the fitting). Once you have all your files open in Athena simply choose the spectrum that you want to do LCF on, then choose Linear Combination Fitting from the menu. The software automatically sets the other files as standards. The initial coefficients for each standard is equal to each other. Once you do LCF you can obtain the new coefficients and extract the fitted spectrum data.
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Note: Make sure that you do LCF on the normalized spectrum not the raw ones.