# Output Files This document provides a comprehensive overview of output files generated by PyXplore during various analysis workflows, including diffraction refinement, background fitting, amorphous component analysis, solid solution modeling, and simulation tasks. --- ## General Information ### Output Directory All results are saved in the working directory (`work_dir`), which can be specified by the user during execution. If not specified, outputs are saved to the current working directory. ### File Naming Conventions Output files follow a systematic naming convention: - **Prefix**: Indicates the analysis type (e.g., `XRD`, `Background`, `Amorphous`) - **Suffix**: Includes a timestamp to prevent file overwriting and enable version tracking - **Extension**: Reflects the file format (`.csv` for data, `.png` for visualizations) --- ## Output Files by Analysis Type ### 1. Background Fitting **Output Directory**: `ConvertedDocuments` This module generates files related to background subtraction and data preprocessing: - **`bac.csv`**: Fitted background intensity values as a function of 2θ - **`no_bac_intensity.csv`**: Background-subtracted diffraction intensities - **`bac_points.csv`**: Automatically selected background points used for fitting - **`intensity_fft.csv`**: Fast Fourier Transform processed diffraction signals for noise reduction - **`de_backgroundfittingcurve.png`**: Visualization showing original data, fitted background, and background-subtracted signals - **`backgroundfittingcurve.png`**: Diagnostic plot displaying raw data, selected background points, and fitted background curve --- ### 2. XRD Profile Refinement **Output Directory**: `WPEMFittingResults` The WPEM refinement module produces the following output files: - **`CrystalSystem0_WPEMout_.csv`**: Comprehensive refinement results containing: - `code`: Radiation source identifier (Kα1 or Kα2) - `H`, `K`, `L`: Miller indices for each reflection - `wi`: Lorentzian weight parameter in pseudo-Voigt function - `Ai`: Integrated peak intensity - `L_gamma_i`: Lorentzian width parameter (FWHM) - `G_sigma2_i`: Gaussian variance parameter - `mu_i`: Peak center position (2θ) - `intensity`: Calculated peak intensity - `system0`, `system1`, etc.: Phase identifiers for multi-phase systems - **`hkl0_.csv`**: Complete list of Miller indices for all reflections in phase 0 - **`WPEMfittingProfile_.csv`**: Calculated diffraction profile from WPEM refinement - **`WPEMPeakParas_.csv`**: Summary of peak parameters and goodness-of-fit statistics - **`ResidualWPEM_fittingresult_.png`**: Comparison plot showing experimental data, fitted profile, and residual difference --- ### 3. Amorphous Phase Analysis **Output Directory**: `DecomposedComponents` Files generated during amorphous component fitting: - **`Amorphous.csv`**: Extracted amorphous scattering contribution - **`M_Amorphous_componentsX.csv`**: Individual amorphous peak components (X denotes component index) - **`upbackground.csv`**: Revised background after amorphous phase subtraction - **`Decomposed_peaks.png`**: Visualization showing separation of crystalline and amorphous contributions --- ### 4. CIF File Processing **Output Directory**: `output_xrd` Outputs from crystallographic information file (CIF) parsing: - **`NAMEHKL.csv`**: Calculated diffraction data including Miller indices, 2θ angles, d-spacings, and theoretical intensities - **`NAME_Extinction_peak.csv`**: List of systematically extinct reflections due to space group symmetry --- ### 5. Solid Solution Structure Optimization **Output Directory**: `WPEMSitOpt` Results from solid solution refinement: - **`substitutional.png`**: Optimized fitting results for solid solution structure - **`DecompositionPlot.png`**: Overlay of decomposed peak contributions and experimental data --- ### 6. XRD Pattern Simulation **Function**: `XRDSimulation` Theoretical diffraction pattern generation from crystal structures: - **`Simulated_XRDPattern.csv`**: Complete simulated XRD pattern based on input CIF file - **`SimulatedPeaks.csv`**: Peak positions, intensities, and Miller indices for all reflections - **`SimulationPlot.png`**: Graphical representation of the simulated diffraction pattern --- ### 7. CIF File Preprocessing **Function**: `CIFpreprocess` Crystallographic information extraction and processing: - **`Processed_CIF_LatticeConstants.csv`**: Extracted lattice parameters (a, b, c, α, β, γ) - **`Processed_CIF_Structure.csv`**: Atomic coordinates, occupancies, and unit cell parameters - **`ProcessedCIFPlot.png`**: Crystal structure visualization --- ### 8. Substitutional Site Analysis **Function**: `SubstitutionalSearch` Results from substitutional site optimization: - **`SubstitutionalSearchResults.csv`**: Evaluated substitutional configurations with probability scores and structural parameters --- ### 9. XPS Data Analysis **Output Directory**: `XPSFittingProfile` X-ray photoelectron spectroscopy fitting results: - **`XPSfittingProfile_.csv`**: Fitted XPS spectrum with individual peak contributions - **`XPSPeakParas_.csv`**: Detailed peak parameters including: - Binding energies - Peak areas and intensities - Full width at half maximum (FWHM) - Peak shape parameters (Gaussian/Lorentzian ratio) - Goodness-of-fit statistics - **`WPEM_fittingresult.png`**: Deconvoluted spectrum showing individual photoelectron peaks and overall fit --- ### 10. EXAFS Data Analysis **Output Directory**: `XAFS` or `WXAFS` Extended X-ray absorption fine structure analysis outputs: - **`FFT_EXAFS_unknown.png`**: Fourier-transformed EXAFS spectrum showing radial distribution function and local coordination environment - **`interactive_plot.html`**: Interactive 2D wavelet transform visualization for time-frequency analysis of EXAFS oscillations --- ## File Format Notes ### Data Files All numerical data are saved in CSV (comma-separated values) format, ensuring compatibility with: - Spreadsheet software (Microsoft Excel, LibreOffice Calc) - Programming environments (Python, MATLAB, R) - Data visualization tools (Origin, Igor Pro) ### Visualization Files Graphical outputs are generated in PNG format with publication-quality resolution (300 DPI minimum). Interactive visualizations are provided in HTML format for dynamic exploration. ### Timestamp Format Timestamps in filenames follow the format `YYYYMMDD_HHMMSS` to ensure chronological ordering and prevent file conflicts. --- ## Additional Resources For detailed information on file structures, data formats, and analysis workflows, please refer to: - [PyWPEM GitHub Repository](https://github.com/Bin-Cao/PyWPEM) - [Author's Website](https://bin-cao.github.io/) - WPEM methodology publications (see references.bib)