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| # Results Files Documentation |
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| This page provides an overview of the output files generated by the **WPEM** software for diffraction refinement, background fitting, amorphous component analysis, solid solution modeling, and simulation tasks. |
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| ## General Information |
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| All results are saved in the **working directory** (`work_dir`), which can be specified by the user during execution. If not specified, outputs default to the current directory. |
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| ### File Naming Conventions |
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| * **Prefix**: Indicates the task type (e.g., `XRD`, `Background`, `Amorphous`, etc.). |
| * **Suffix**: Usually includes a timestamp to prevent file overwriting. |
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| ## Output Files by Function |
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| ### 1. **Background Fitting** |
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| **Folder**: `ConvertedDocuments` |
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| * `bac.csv`: Fitted background intensities. |
| * `no_bac_intensity.csv`: Diffraction signals after background removal. |
| * `bac_points.csv`: Selected background points. |
| * `intensity_fft.csv`: Diffraction signals processed by Fast Fourier Transform. |
| * `de_backgroundfittingcurve.png`: Plot of the original data, fitted background, and background-subtracted signals. |
| * `backgroundfittingcurve.png`: Visualization showing the raw data, selected background points, and the fitted background curve. |
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| ### 2. **XRD Refinement** |
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| **Folder**: `WPEMFittingResults` |
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| * `CrystalSystem0_WPEMout_<time>.csv`: Refined crystal information, including: |
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| * `code`: Indicates Kα1 or Kα2 origin. |
| * `H`, `K`, `L`: Miller indices. |
| * `wi`, `Ai`, `L_gamma_i`, `G_sigma2_i`: Peak shape parameters (refer to the WPEM paper for details). |
| * `mu_i`: Peak positions. |
| * `intensity`: Peak intensities. |
| * `system0`, `system1`, etc.: Refers to different phases. |
| * `hkl0_<time>.csv`: Diffraction indices for each peak in phase 0. |
| * `WPEMfittingProfile_<time>.csv`: WPEM-generated fitting profile. |
| * `WPEMPeakParas_<time>.csv`: Peak location and shape parameters, with profile fitting quality metrics. |
| * `ResidualWPEM_fittingresult_<time>.png`: Plot comparing fitted results with experimental data. |
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| ### 3. **Amorphous Fitting** |
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| **Folder**: `DecomposedComponents` |
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| * `Amorphous.csv`: Extracted amorphous signals. |
| * `M_Amorphous_componentsX.csv`: Identified amorphous peak components (X = index). |
| * `upbackground.csv`: Updated background after amorphous subtraction. |
| * `Decomposed_peaks.png`: Visualization of decomposed crystalline and amorphous components. |
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| ### 4. **CIF Parsing** |
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| **Folder**: `output_xrd` |
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| * `NAMEHKL.csv`: Calculated diffraction indices, angles, and theoretical intensities. |
| * `NAME_Extinction_peak.csv`: List of extinction peaks caused by geometrical and systematic extinction. |
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| ### 5. **Solid Solution Modeling** |
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| **Folder**: `WPEMSitOpt` |
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| * `substitutional.png`: Fitting result of the optimized solid solution structure. |
| * `DecompositionPlot.png`: Overlay of decomposed peaks and experimental data. |
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| ### 6. **XRD Simulation** |
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| **Function**: `XRDSimulation` |
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| * `Simulated_XRDPattern.csv`: Simulated XRD pattern based on the provided CIF file. |
| * `SimulatedPeaks.csv`: Simulated peak positions and intensities. |
| * `SimulationPlot.png`: Visualization of the simulated XRD pattern. |
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| ### 7. **CIF Preprocessing** |
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| **Function**: `CIFpreprocess` |
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| * `Processed_CIF_LatticeConstants.csv`: Extracted lattice constants from CIF. |
| * `Processed_CIF_Structure.csv`: Atomic positions and unit cell parameters. |
| * `ProcessedCIFPlot.png`: Visualization of the crystal structure. |
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| ### 8. **Substitutional Search** |
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| **Function**: `SubstitutionalSearch` |
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| * `SubstitutionalSearchResults.csv`: Possible substitutional configurations and their likelihoods. |
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| ### 9. **XPS Analysis** |
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| **Folder**: `XPSFittingProfile` |
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| * `XPSfittingProfile_<time>.csv`: Fitted XPS spectrum data. |
| * `XPSPeakParas_<time>.csv`: Peak parameters including binding energies, areas, shapes, and fitting quality. |
| * `WPEM_fittingresult.png`: Decomposed results of individual photoelectron peaks. |
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| ### 10. **EXAFS Analysis** |
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| **Folder**: `XAFS` / `WXAFS` |
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| * `FFT_EXAFS_unknown.png`: Radial distribution function representing local atomic structure. |
| * `interactive_plot.html`: Interactive 2D wavelet transform visualization. |
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| ## Notes |
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| * All files are saved with descriptive names based on their function and timestamp. |
| * Figures are generated in `.png` format for easy interpretation. |
| * CSV files are widely compatible with data analysis tools such as Excel, Python, and MATLAB. |
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| For further reference and source code, please visit the [WPEM GitHub Repository](https://github.com/Bin-Cao/PyWPEM). |
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