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The tutorial 2nd

Introduces the process for refining multi-phase systems.

coding

1. Save your diffraction data to the root directory and rename the file to intensity.csv.

# import PyXplore package
from PyXplore import WPEM
import pandas as pd

2. Parse your diffraction data (2θ, intensity) and perform background processing.

intensity_csv = pd.read_csv(r'intensity.csv',header=None )
var = WPEM.BackgroundFit(intensity_csv,lowAngleRange=22,poly_n=8,bac_split=8,bac_num=600)

3. After running the code, a new folder named ConvertedDocuments will be created in the root directory. This folder contains the background information.

Copy the two important files — bac.csv and no_bac_intensity.csv — from ConvertedDocuments into the root directory, as they are required for the next steps.

4. After background subtraction, the next step is to parse the reference structure.

Save the reference .cif files in the root directory. For example, if your structures are Mn₂O₃ and RuO₂, place files named Mn2O3.cif and RuO2.cif in the root directory as the reference phases.

If you are unsure of the reference phases, you must first perform phase identification. For assistance, please visit our website: https://xqueryer.caobin.asia/

MnO_latt, AtomCoordinates,des = WPEM.CIFpreprocess(filepath='Mn2O3.cif',two_theta_range=(15,75))

RuO_latt, AtomCoordinates,des = WPEM.CIFpreprocess(filepath='RuO2.cif',two_theta_range=(15,75))

5. After running the code, a new folder named output_xrd will be generated.

Inside this folder, find the file named xxxHKL.csv. Copy it to the root directory and rename it sequentially as peak0.csv, peak1.csv, and so on. These files will be used in the refinement step.

# The wavelength is set according to the actual light source
wavelength = [1.540593, 1.544414]
# The file name of non-background data (2theta-intensity data)
no_bac_intensity_file = "no_bac_intensity.csv" 
# The file name of raw/original data (2theta-intensity data)
original_file = "intensity.csv"  
# The file name of background data (2theta-intensity data)
bacground_file = "bac.csv"  


# Input the initial lattice constants {a, b, c, α, β, γ}, whose values need to be assumed at initialization.
Lattice_constants = [MnO_latt,RuO_latt]

# Execute the model

WPEM.XRDfit(
    wavelength, var, Lattice_constants,no_bac_intensity_file, original_file, bacground_file, 
    subset_number=11,low_bound=20,up_bound=70,bta = 0.85,iter_max = 5, asy_C = 0,InitializationEpoch=0, 
    )

For demonstration purposes, the code uses `iter_max = 5` to reduce computational cost. However, for practical applications, it is recommended to set `iter_max` to at least 50 for more reliable results.