Output Files

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_<timestamp>.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_<timestamp>.csv: Complete list of Miller indices for all reflections in phase 0

  • WPEMfittingProfile_<timestamp>.csv: Calculated diffraction profile from WPEM refinement

  • WPEMPeakParas_<timestamp>.csv: Summary of peak parameters and goodness-of-fit statistics

  • ResidualWPEM_fittingresult_<timestamp>.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_<timestamp>.csv: Fitted XPS spectrum with individual peak contributions

  • XPSPeakParas_<timestamp>.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:

Contents