xtalforge-wasm 1.1.0 → 1.2.0

package/package.json

@@ -5,7 +5,7 @@
     "Jose Ivan Gonzalez <jigonzalez930209@gmail.com>"
   ],
   "description": "WebAssembly bindings for xtalforge.",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",

package/xtalforge_wasm.d.ts

@@ -109,6 +109,15 @@ export class WasmDocument {
     readonly history: Array<any>;
 }
 
+/**
+ * Adsorption sites as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or tolerance.
+ */
+export function adsorption_sites(text: string, format_hint: string, tolerance: number): string;
+
 /**
  * Runtime capability report as JSON.
  */
@@ -156,6 +165,15 @@ export function asymmetrize_info(text: string, symprec: number): any;
  */
 export function asymmetrize_text(text: string, symprec: number): string;
 
+/**
+ * Bond-valence sums as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or cutoff.
+ */
+export function bond_valence_sums(text: string, format_hint: string, cutoff: number): string;
+
 /**
  * Perceives the bonds of a structure.
  *
@@ -374,6 +392,33 @@ export function change_setting_text(text: string, hall_number: number): string;
  */
 export function convert_structure(text: string, format_hint: string, format: string): string;
 
+/**
+ * Convex hull as JSON from a JSON list of phases.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for an invalid phase list.
+ */
+export function convex_hull(entries_json: string): string;
+
+/**
+ * Coordination shell and shape measures as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or an out-of-range index.
+ */
+export function coordination(text: string, format_hint: string, index: number, strategy: string, cutoff: number, solid_angle: number): string;
+
+/**
+ * Applies a strain, gradient, volume or density and returns structure JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or deformation options.
+ */
+export function deform(text: string, format_hint: string, options_json: string): string;
+
 /**
  * Detects the space group and returns the dataset as a JS object.
  *
@@ -407,6 +452,24 @@ export function diagnose_info(text: string, symbol: string): any;
  */
 export function distance(text: string, i: number, j: number): number;
 
+/**
+ * Site edits; returns structure JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or edit options.
+ */
+export function edit_structure(text: string, format_hint: string, options_json: string): string;
+
+/**
+ * Elastic tensor from UFF stress finite differences as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or strain.
+ */
+export function elastic_tensor(text: string, format_hint: string, strain: number): string;
+
 /**
  * Reference data for an element by symbol or atomic number.
  *
@@ -417,6 +480,15 @@ export function distance(text: string, i: number, j: number): number;
  */
 export function element_info(input: string): any;
 
+/**
+ * Equation-of-state fit as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for an unknown model or too few points.
+ */
+export function eos_fit(options_json: string): string;
+
 /**
  * Returns QEq, EQeq or EEQ2019 charges (`qeq`, `eqeq`, `eeq`).
  *
@@ -498,6 +570,24 @@ export function ff_types_info(text: string): Array<any>;
  */
 export function ff_vibrations_info(text: string, step: number): any;
 
+/**
+ * Similarity of two fingerprints.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text.
+ */
+export function fingerprint_similarity(first: string, second: string, format_hint: string, r_max: number, bin_width: number): number;
+
+/**
+ * Equality classes of a list of structure texts.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text.
+ */
+export function group_structures(structures: string[], format_hint: string, options_json: string): string;
+
 /**
  * Finds the functional groups of a structure.
  *
@@ -528,6 +618,34 @@ export function hydrogens_info(text: string, distance: number): any;
  */
 export function hydrogens_text(text: string, distance: number): string;
 
+/**
+ * Linear interpolation between matched structures; returns a JSON array of
+ * structure documents.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` when the structures do not match.
+ */
+export function interpolate(first: string, second: string, images: number, format_hint: string, options_json: string): string;
+
+/**
+ * Interstitial candidates as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or options.
+ */
+export function interstitials(text: string, format_hint: string, species: string, options_json: string): string;
+
+/**
+ * Kabsch alignment; points are a flat `xyzxyz...` array.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for mismatched or non-finite point sets.
+ */
+export function kabsch_alignment(points: Float64Array | number[], reference: Float64Array | number[]): string;
+
 /**
  * Returns the Bravais type and band path of a structure.
  *
@@ -547,6 +665,15 @@ export function kpath_info(text: string): any;
  */
 export function lattice_info(a: number, b: number, c: number, alpha: number, beta: number, gamma: number): any;
 
+/**
+ * Commensurate 2D lattice matches as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or options.
+ */
+export function lattice_matches(film: string, substrate: string, format_hint: string, options_json: string): string;
+
 /**
  * Minimum-image fractional vector and distance.
  *
@@ -612,6 +739,15 @@ export function lower_to_subgroup_text(text: string, subgroup_number: number, to
  */
 export function magnetic_group_info(text: string, symprec: number): any;
 
+/**
+ * Matches two structures and returns the match record as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or tolerances.
+ */
+export function match_structures(first: string, second: string, format_hint: string, options_json: string): string;
+
 /**
  * Builds an ASCII STL string.
  *
@@ -660,6 +796,33 @@ export function neighbors(text: string, cutoff: number): Array<any>;
  */
 export function net_invariants_info(text: string, tolerance: number): Array<any>;
 
+/**
+ * Supercell closest to a cube; returns structure JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for an invalid cell count.
+ */
+export function optimal_supercell(text: string, cells: number, format_hint: string): string;
+
+/**
+ * Orderings of partial occupancies as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for a structure without partial occupancy.
+ */
+export function orderings(text: string, format_hint: string, options_json: string): string;
+
+/**
+ * Oxidation states as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or cutoff.
+ */
+export function oxidation_states(text: string, format_hint: string, cutoff: number): string;
+
 /**
  * Returns the JSON schema of a built-in parameter preset.
  *
@@ -669,6 +832,24 @@ export function net_invariants_info(text: string, tolerance: number): Array<any>
  */
 export function param_schema(name: string): any;
 
+/**
+ * Periodic RMSD for an explicit atom mapping.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or an incomplete mapping.
+ */
+export function periodic_rmsd(first: string, second: string, mapping: Uint32Array | number[], format_hint: string): number;
+
+/**
+ * Places a molecule on an adsorption site and returns structure JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or an out-of-range site.
+ */
+export function place_molecule(slab: string, molecule: string, format_hint: string, options_json: string): string;
+
 /**
  * Detects the molecular point group of a finite structure.
  *
@@ -815,6 +996,24 @@ export function project_pack(text: string): Uint8Array;
  */
 export function pxrd_info(text: string, radiation: string, max_two_theta: number, step: number): any;
 
+/**
+ * Total and partial RDF as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or range.
+ */
+export function radial_distribution(text: string, format_hint: string, r_max: number, bin_width: number, smoothing: number): string;
+
+/**
+ * Random displacements with a fixed seed; returns structure JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or options.
+ */
+export function rattle(text: string, format_hint: string, options_json: string): string;
+
 /**
  * Reads a CIF and returns its summary object.
  *
@@ -958,6 +1157,15 @@ export function set_space_group_text(text: string, symbol: string, mode: string)
  */
 export function slab_info(text: string, h: number, k: number, l: number, layers: number, vacuum: number): any;
 
+/**
+ * Every termination of a surface as JSON with structure documents.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or a degenerate plane.
+ */
+export function slab_terminations(text: string, format_hint: string, options_json: string): string;
+
 /**
  * Cuts a slab and returns it as CIF text.
  *
@@ -968,6 +1176,24 @@ export function slab_info(text: string, h: number, k: number, l: number, layers:
  */
 export function slab_text(text: string, h: number, k: number, l: number, layers: number, vacuum: number): string;
 
+/**
+ * SQS generation as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for a structure without binary disorder.
+ */
+export function special_quasirandom(text: string, format_hint: string, options_json: string): string;
+
+/**
+ * Stacks a film on a substrate; returns structure JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for empty slabs or invalid options.
+ */
+export function stack_slabs(film: string, substrate: string, format_hint: string, options_json: string): string;
+
 /**
  * Standardizes a structure to the conventional cell.
  *
@@ -986,6 +1212,15 @@ export function standardize_info(text: string, symprec: number): any;
  */
 export function standardize_text(text: string, symprec: number): string;
 
+/**
+ * Structure fingerprint as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or range.
+ */
+export function structure_fingerprint(text: string, format_hint: string, r_max: number, bin_width: number): string;
+
 /**
  * Summary of a structure JSON document.
  *
@@ -1005,6 +1240,15 @@ export function structure_info(text: string): any;
  */
 export function subgroups_info(hall_number: number, epsilon: number): Array<any>;
 
+/**
+ * Symmetry-unique substitutions as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or species.
+ */
+export function substitutions(text: string, format_hint: string, species: string, min_image: number): string;
+
 /**
  * Builds a supercell and returns its summary object.
  *
@@ -1074,11 +1318,38 @@ export function torsion(text: string, i: number, j: number, k: number, l: number
  */
 export function twist_info(n: number, m: number, theta: number, layers: number): any;
 
+/**
+ * Symmetry-unique Miller indices as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or a bad index bound.
+ */
+export function unique_miller_indices(text: string, format_hint: string, options_json: string): string;
+
+/**
+ * Symmetry-unique vacancies as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or distance.
+ */
+export function vacancies(text: string, format_hint: string, min_image: number): string;
+
 /**
  * Version of the workspace.
  */
 export function version(): string;
 
+/**
+ * Periodic Voronoi cells as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or cutoff.
+ */
+export function voronoi(text: string, format_hint: string, cutoff: number): string;
+
 /**
  * Archives run records (a JSON array) into an in-memory ZIP.
  *
@@ -1097,6 +1368,15 @@ export function workspace_archive(records_json: string): Uint8Array;
  */
 export function workspace_read_archive(bytes: Uint8Array | number[]): Array<any>;
 
+/**
+ * Wulff construction as JSON.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or surface energies.
+ */
+export function wulff(text: string, format_hint: string, options_json: string): string;
+
 /**
  * Returns Wyckoff assignments.
  *

package/xtalforge_wasm.js

@@ -5,5 +5,5 @@ import { __wbg_set_wasm } from "./xtalforge_wasm_bg.js";
 __wbg_set_wasm(wasm);
 wasm.__wbindgen_start();
 export {
-    AgentSession, WasmDocument, agent_capabilities, agent_run, agent_verbs, angle, asymmetrize_info, asymmetrize_text, bonds, brillouin_zone, build_c20_info, build_c20_text, build_c60_info, build_c60_text, build_carbon_recipe_info, build_carbon_text, build_graphene_info, build_graphene_text, build_mof_info, build_mof_text, build_nanotube_info, build_nanotube_text, build_polymer_text, build_ribbon_text, build_schwarzite_text, build_twist_text, build_ztc_text, cell_volume, change_setting_info, change_setting_text, convert_structure, detect_symmetry, diagnose_info, distance, element_info, ff_charges_info, ff_energy, ff_ir_info, ff_optimize_info, ff_optimize_text, ff_prepare_info, ff_thermo_info, ff_types_info, ff_vibrations_info, groups, hydrogens_info, hydrogens_text, kpath_info, lattice_info, lattice_minimum_image, layer_group_info, limits_bounds, limits_check, lower_to_subgroup_info, lower_to_subgroup_text, magnetic_group_info, mesh_stl, mof_blocks_info, mof_topologies_info, neighbors, net_invariants_info, param_schema, pointgroup_info, polymer_info, porosity_info, powder_automatic_info, powder_cells_info, powder_index_info, powder_lebail_info, powder_pawley_info, powder_pawley_width_info, powder_refine_info, primitive_info, primitive_text, project_info, project_pack, pxrd_info, read_cif, read_structure, reduce_info, reduce_text, ribbon_info, rietx_inventory_info, rings, scene_data, scene_summary, schwarzite_info, set_space_group_info, set_space_group_text, slab_info, slab_text, standardize_info, standardize_text, structure_info, subgroups_info, supercell_info, supercell_text, to_p1_info, to_p1_text, tolerance_ladder_info, torsion, twist_info, version, workspace_archive, workspace_read_archive, wyckoff_info, zeo_parse_info, ztc_info
+    AgentSession, WasmDocument, adsorption_sites, agent_capabilities, agent_run, agent_verbs, angle, asymmetrize_info, asymmetrize_text, bond_valence_sums, bonds, brillouin_zone, build_c20_info, build_c20_text, build_c60_info, build_c60_text, build_carbon_recipe_info, build_carbon_text, build_graphene_info, build_graphene_text, build_mof_info, build_mof_text, build_nanotube_info, build_nanotube_text, build_polymer_text, build_ribbon_text, build_schwarzite_text, build_twist_text, build_ztc_text, cell_volume, change_setting_info, change_setting_text, convert_structure, convex_hull, coordination, deform, detect_symmetry, diagnose_info, distance, edit_structure, elastic_tensor, element_info, eos_fit, ff_charges_info, ff_energy, ff_ir_info, ff_optimize_info, ff_optimize_text, ff_prepare_info, ff_thermo_info, ff_types_info, ff_vibrations_info, fingerprint_similarity, group_structures, groups, hydrogens_info, hydrogens_text, interpolate, interstitials, kabsch_alignment, kpath_info, lattice_info, lattice_matches, lattice_minimum_image, layer_group_info, limits_bounds, limits_check, lower_to_subgroup_info, lower_to_subgroup_text, magnetic_group_info, match_structures, mesh_stl, mof_blocks_info, mof_topologies_info, neighbors, net_invariants_info, optimal_supercell, orderings, oxidation_states, param_schema, periodic_rmsd, place_molecule, pointgroup_info, polymer_info, porosity_info, powder_automatic_info, powder_cells_info, powder_index_info, powder_lebail_info, powder_pawley_info, powder_pawley_width_info, powder_refine_info, primitive_info, primitive_text, project_info, project_pack, pxrd_info, radial_distribution, rattle, read_cif, read_structure, reduce_info, reduce_text, ribbon_info, rietx_inventory_info, rings, scene_data, scene_summary, schwarzite_info, set_space_group_info, set_space_group_text, slab_info, slab_terminations, slab_text, special_quasirandom, stack_slabs, standardize_info, standardize_text, structure_fingerprint, structure_info, subgroups_info, substitutions, supercell_info, supercell_text, to_p1_info, to_p1_text, tolerance_ladder_info, torsion, twist_info, unique_miller_indices, vacancies, version, voronoi, workspace_archive, workspace_read_archive, wulff, wyckoff_info, zeo_parse_info, ztc_info
 } from "./xtalforge_wasm_bg.js";