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| # Parameters and Functions Documentation |
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| ## Module: WPEM |
| WPEM is the main call interface for diffraction refinement and analysis software, including various functions and subroutines for XRD analysis, background fitting, amorphous fitting, and more. |
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| ### Author |
| - **Bin CAO** |
| Email: [bincao4-c@my.cityu.edu.hk](mailto:bincao4-c@my.cityu.edu.hk) |
| GitHub: [https://github.com/Bin-Cao/PyWPEM](https://github.com/Bin-Cao/PyWPEM) |
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| ## Functions Overview |
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| ### 1. `WPEMsolver` |
| **From:** `EMBraggOpt.EMBraggSolver` |
| Solver for XRD profile refinement and analysis. |
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| ### 2. `TwiceFilter`, `convert_file`, `read_xrdml` |
| **From:** `Background.BacDeduct` |
| - **`TwiceFilter`**: Applies filtering techniques for background adjustments. |
| - **`convert_file`**: Converts XRD data files to the required format. |
| - **`read_xrdml`**: Reads `.xrdml` files for diffraction data. |
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| ### 3. `Amorphous_fitting` |
| **From:** `Amorphous.fitting.AmorphousFitting` |
| Fitting routine for amorphous phase diffraction data. |
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| ### 4. `RadialDistribution` |
| **From:** `Amorphous.QuantitativeCalculation.AmorphousRDF` |
| Calculates the radial distribution function (RDF) for amorphous materials. |
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| ### 5. `Decomposedpeaks` |
| **From:** `DecomposePlot.plot` |
| Decomposes diffraction peaks for detailed analysis. |
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| ### 6. `XRD_profile` |
| **From:** `XRDSimulation.Simulation` |
| Simulates XRD profiles for given crystal structures. |
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| ### 7. `profile` |
| **From:** `Extinction.XRDpre` |
| Generates XRD profiles with customizable parameters. |
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| ### 8. `BgolearnOpt` |
| **From:** `StructureOpt.SiteOpt` |
| Performs optimization for substitutional search and refinement. |
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| ### 9. `XPSsolver` |
| **From:** `WPEMXPS.XPSEM` |
| Solver for X-ray Photoelectron Spectroscopy (XPS) data refinement. |
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| ### 10. `EXAFS` |
| **From:** `WPEMXAS.EXAFS` |
| Performs Extended X-ray Absorption Fine Structure (EXAFS) analysis. |
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| ### 11. `CrystalGraph` |
| **From:** `GraphStructure.graph` |
| Generates crystal graphs for structural analysis. |
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| ## Executable Information |
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| ### Execution Information |
| - **Software Name**: WPEM (Diffraction Refinement Software) |
| - **Author**: Bin Cao, Advanced Materials Thrust, Hong Kong University of Science and Technology (Guangzhou) ｜ Department of physics, City University of Hong Kong |
| - **URL**: [https://github.com/Bin-Cao/WPEM](https://github.com/Bin-Cao/WPEM) |
| - **Execution Time**: Dynamically generated at runtime. |
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| ## Key Functions |
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| ### `XRDfit` |
| #### Parameters: |
| - **`wavelength`**: List of diffraction wavelengths. |
| - **`Var`**: Statistical variance of the background. |
| - **`Lattice_constants`**: Initial lattice constants for refinement. |
| - **`no_bac_intensity_file`**, **`original_file`**, **`bacground_file`**: Input data files. |
| - **`two_theta_range`**: Range of diffraction angles to analyze. |
| - **`density_list`**: Densities of crystals (optional). |
| - **`MODEL`**: Mode of analysis (`'REFINEMENT'` or `'ANALYSIS'`). |
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| #### Returns: |
| - Refined lattice constants, R-factor values, and runtime details. |
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| ### `BackgroundFit` |
| #### Parameters: |
| - **`intensity_csv`**: Input XRD data file. |
| - **`LFctg`, `lowAngleRange`, `bac_num`, `bac_split`**: Background filter parameters. |
| - **`window_length`, `polyorder`, `mode`**: Polynomial fitting settings. |
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| #### Returns: |
| - Background distribution statistics. |
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| --- |
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| ### `FileTypeCovert` |
| #### Parameters: |
| - **`file_name`**: Source file name. |
| - **`file_type`**: Format of the input file (`'dat'` or `'xrdml'`). |
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| #### Returns: |
| - Converted data. |
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| --- |
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| ### `Amorphous_fit` |
| #### Parameters: |
| - **`mix_component`**: Number of amorphous peaks. |
| - **`amor_file`**: Amorphous data file. |
| - **`ang_range`**: Angle range for refinement. |
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| #### Returns: |
| - Amorphous fit results. |
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| --- |
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| ### `CryGraph` |
| #### Parameters: |
| - **`folder_path`**: Path to save CIF files. |
| - **`BK_boundary_condition`**: Whether to apply Bon Kaman boundary conditions. |
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| #### Returns: |
| - Crystal structure graphs. |
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| --- |
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| ### Additional Functions |
| - **`AmorphousRDFun`**: Computes radial distribution function for amorphous phases. |
| - **`Plot_Components`**: Visualizes decomposed XRD components. |
| - **`XRDSimulation`**: Simulates XRD patterns for given CIF files. |
| - **`CIFpreprocess`**: Processes CIF files for XRD analysis. |
| - **`SubstitutionalSearch`**: Conducts substitutional optimization searches. |
| - **`XPSfit`**: Fits XPS data for electron binding energy analysis. |
| - **`EXAFSfit`**: Performs EXAFS analysis for structural and bonding studies. |
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