Pick one of 14 operations, then supply an XRD intensity CSV, a CIF by URL or inline text, a wavelength preset such as CuKa1Ka2, and the two-theta range.

You provide an operation along with XRD data, a CIF structure, or both. The operation you choose is what most affects the result, since it determines which of those inputs are required and how the pattern is processed.

PyWPEM inputs and parameters

Common parameters

Parameter	Type	Default	Description
`operation`	string	required	One of the 14 operation names above
`wavelength_preset`	string	`"CuKa1Ka2"`	X-ray source preset — see table below
`custom_wavelengths`	number[]	--	Custom wavelength(s) in Å, used when `wavelength_preset` is `"custom"`
`two_theta_min`	number	`10`	Minimum 2-theta angle (degrees)
`two_theta_max`	number	`90`	Maximum 2-theta angle (degrees)
`two_theta_step`	number	`0.02`	Angular step size (degrees)

Not every operation reads all of these — wavelength_preset/custom_wavelengths and the two-theta range mainly matter for simulate_xrd, preprocess_cif, and fit_amorphous.

Wavelength presets (`wavelength_preset`)

Preset key	Source	Wavelength (Å)
`CuKa1Ka2`	Cu K-alpha doublet (default, most common lab setup)	1.5406 / 1.5444
`CuKa`	Cu K-alpha (weighted average)	1.5418
`MoKa`	Mo K-alpha (single-crystal diffraction)	0.7107
`CoKa`	Co K-alpha (reduces fluorescence from Fe-containing samples)	1.7902
`FeKa`	Fe K-alpha	1.9373
`CrKa`	Cr K-alpha (stress analysis, texture)	2.291
`AgKa`	Ag K-alpha (high-energy, deep penetration)	0.5594
`custom`	User-defined — supply `custom_wavelengths`	--

XRD data input

For operations requiring experimental data:

Parameter	Type	Description
`xrd_data_url`	string	S3 URL to an XRD intensity CSV (`two_theta`, `intensity` columns)

There is no inline/raw-text alternative for this field — upload the CSV and pass its URL.

CIF structure input

For operations requiring crystal structure data:

Parameter	Type	Description
`cif_url`	string	URL to a CIF file — from the COD (`crystallography.net/cod/XXXXXXX.cif`), CCDC, ICDD, or S3. Do not use a PubChem 3D-conformer URL — it serves an HTML page, not a CIF file.
`cif_content`	string	Inline CIF file content (alternative to `cif_url`)

CIF requirements

Must include _cell_length_a/b/c and _cell_angle_alpha/beta/gamma
Must include _atom_site_fract_x/y/z coordinates
Must include _symmetry_space_group_name_H-M or equivalent

Operation-specific parameters

fit_background

Parameter	Type	Default	Description
`background_segments`	integer	`5`	Number of segments for piecewise background fitting

simulate_xrd

Parameter	Type	Default	Description
`grain_size_nm`	number	--	Crystallite grain size for peak broadening (nm, 5-100)
`replace_atom`	string	--	Atom to replace for solid-solution simulation (e.g., `"Cu2+"`)
`substitute_atom`	string	--	Substituting atom (e.g., `"Ti4+"`)
`substitution_ratio`	number	`0.1`	Fraction of atoms to replace (0-1)

refine_xrd

Parameter	Type	Default	Description
`background_url`	string	--	S3 URL to a background CSV (from `fit_background`)
`no_background_url`	string	--	S3 URL to a background-subtracted CSV (from `fit_background`)
`variance`	number	--	Background variance (from the `fit_background` result)
`phases`	array	required	Phases to refine — one or more objects with `name` (required), `cif_url`, and `fixed` (keep lattice fixed)
`max_iterations`	integer	`40`	Maximum refinement iterations
`beta`	number	`0.8`	Initial Lorentzian fraction in the pseudo-Voigt peak profile (0-1)

fit_amorphous

Parameter	Type	Default	Description
`num_components`	integer	`1`	Number of Gaussian components for amorphous fitting

calculate_rdf

Parameter	Type	Default	Description
`density_atoms_per_cc`	number	--	Atomic density for RDF calculation (atoms per cubic cm)
`scattering_factor`	number	--	Scattering factor for RDF normalization
`r_max`	number	`10`	Maximum radial distance for RDF (Å)

fit_xps

Parameter	Type	Default	Description
`xps_data_url`	string	required	S3 URL to XPS intensity data (`binding_energy`, `intensity` columns)
`peaks`	array	required	Peaks to fit — objects with `atom`, `orbital`, and `binding_energy` (all required)

fit_exafs

Parameter	Type	Default	Description
`xafs_data_url`	string	required	S3 URL to XAFS data (`energy`, `mu` columns)
`power`	number	`2`	k-weighting power for the EXAFS transform
`k_cutoff`	number	`12`	k-space cutoff for the Fourier transform (Å⁻¹)
`transform_type`	string	`"fourier"`	`"fourier"` or `"wavelet"`

generate_crystal_graph

Parameter	Type	Default	Description
`graph_type`	string	`"connectivity"`	`"connectivity"` (bond-based, CGCNN/standard GNN), `"voronoi"` (dense/amorphous phases), or `"distance"` (MEGNet-style continuous edges)
`max_neighbors`	integer	`12`	Maximum neighbors per atom in the graph
`cutoff_distance`	number	`5.0`	Distance cutoff for neighbor search (Å)

search_substitutional_sites

Parameter	Type	Default	Description
`target_element`	string	required	Element to substitute (e.g., `"Fe"`)
`substitute_element`	string	required	Substituting element (e.g., `"Co"`)
`energy_threshold`	number	`1.0`	Maximum formation energy threshold (eV)

This operation requires cif_url specifically (not cif_content).

plot_components

Parameter	Type	Default	Description
`plot_type`	string	required	`"xrd"`, `"xps"`, `"exafs"`, `"rdf"`, or `"amorphous"`
`components`	integer[]	--	Component indices to include in the plot
`show_residual`	boolean	`true`	Show the residual curve
`title`	string	--	Custom plot title

convert_file_format

Parameter	Type	Default	Description
`input_url`	string	required	S3 URL to the input file
`input_format`	string	required	`"csv"`, `"xy"`, `"xye"`, `"cif"`, `"json"`, `"raw"`, or `"brml"`
`output_format`	string	required	Same set of values as `input_format`

compute_graph_matrix

Parameter	Type	Default	Description
`matrix_operation`	string	`"to_adjacency"`	`"to_matrix"`, `"to_adjacency"`, or `"laplacian"`
`normalize`	boolean	`false`	Normalize the matrix

split_ml_datasets

Parameter	Type	Default	Description
`data_url`	string	--	S3 URL to the dataset to split
`data_urls`	string[]	--	Multiple S3 URLs to merge and split (alternative to `data_url`)
`train_ratio`	number	`0.8`	Fraction of data for the training set
`val_ratio`	number	`0.1`	Fraction of data for the validation set
`test_ratio`	number	`0.1`	Fraction of data for the test set
`stratify_column`	string	--	Column name for stratified splitting
`random_seed`	integer	`42`	Random seed for reproducible splits

Input validation

operation is always required; every other field is operation-dependent
CIF files must parse without syntax errors
refine_xrd requires at least one entry in phases
fit_xps requires at least one entry in peaks, each with atom, orbital, and binding_energy

PyWPEM inputs and parameters