xtalforge-wasm 0.0.2 → 1.0.0-rc.1

package/package.json

@@ -5,7 +5,7 @@
     "Jose Ivan Gonzalez <jigonzalez930209@gmail.com>"
   ],
   "description": "WebAssembly bindings for xtalforge.",
-  "version": "0.0.2",
+  "version": "1.0.0-rc.1",
   "license": "MIT OR Apache-2.0",
   "repository": {
     "type": "git",

package/xtalforge_wasm.d.ts

@@ -1,6 +1,42 @@
 /* tslint:disable */
 /* eslint-disable */
 
+/**
+ * A stateful session an assistant drives in the browser.
+ */
+export class AgentSession {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Name of the active document.
+     */
+    active_name(): string | undefined;
+    /**
+     * Names of the open documents as JSON.
+     */
+    documents_json(): string;
+    /**
+     * Creates an empty session.
+     */
+    constructor();
+    /**
+     * Runs one verb with a JSON object and returns the answer as JSON.
+     *
+     * # Errors
+     *
+     * Returns a JavaScript object with `code` and `message` properties.
+     */
+    run(verb: string, arguments_json: string): string;
+    /**
+     * One document as structure JSON.
+     *
+     * # Errors
+     *
+     * Returns a JavaScript object with `code` and `message` properties.
+     */
+    structure_json(name?: string | null): string;
+}
+
 /**
  * An undoable structure document in the browser.
  */
@@ -73,6 +109,25 @@ export class WasmDocument {
     readonly history: Array<any>;
 }
 
+/**
+ * Runtime capability report as JSON.
+ */
+export function agent_capabilities(): string;
+
+/**
+ * Runs a JSON script against a fresh session and returns the answers.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript object with `code` and `message` properties.
+ */
+export function agent_run(script_json: string): string;
+
+/**
+ * The verb catalogue as JSON.
+ */
+export function agent_verbs(): string;
+
 /**
  * Angle `i-j-k` in degrees, using minimum images.
  *
@@ -131,6 +186,16 @@ export function build_c20_info(): any;
  */
 export function build_c60_info(): any;
 
+/**
+ * Builds a disordered carbon from a recipe.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for an unsupported net, a bad repeat or a
+ * surface that cannot be meshed.
+ */
+export function build_carbon_recipe_info(net: string, repeat_x: number, repeat_y: number, repeat_z: number, density: number, radius_ratio: number, coverage: number, seed: number, hydrogen: number, fluorine: number, oxygen: number): any;
+
 /**
  * Builds a graphene sheet and returns its summary.
  *
@@ -275,7 +340,7 @@ export function ff_optimize_info(text: string, minimizer: string, max_steps: num
  *
  * Returns a JavaScript `Error` for invalid text or a failed step.
  */
-export function ff_prepare_info(text: string, minimize: boolean, charges: boolean, ewald: boolean, vibrations: boolean): any;
+export function ff_prepare_info(text: string, minimize: boolean, charges: boolean, ewald: boolean, vibrations: boolean, merge_duplicates?: boolean | null, order_disorder?: boolean | null, remove_solvent?: boolean | null, check_charge_balance?: boolean | null, hydrogens?: boolean | null, check_close_contacts?: boolean | null): any;
 
 /**
  * Returns harmonic thermochemistry.
@@ -503,13 +568,37 @@ export function powder_automatic_info(text: string, pattern_text: string): any;
 export function powder_cells_info(number: number): any;
 
 /**
- * Refines positions with a whole-pattern least-squares step.
+ * Finds peaks and indexes the metric families of a measured XY pattern.
+ *
+ * Returns `{ peaks: [{ two_theta, intensity, fwhm }], candidates: [{ system,
+ * a, b, c, alpha, beta, gamma, m20, f_n, coverage, completeness }] }`.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or a failed search.
+ */
+export function powder_index_info(pattern_text: string, wavelength: number, max_index: number, tolerance: number): any;
+
+/**
+ * Fits a Pawley model: free intensities, cell, zero shift and width model.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or a failed fit.
+ */
+export function powder_pawley_info(text: string, pattern_text: string, profile: string): any;
+
+/**
+ * Refines a phase with the McCusker stages.
+ *
+ * The March-Dollase axis is the `c` axis. Returns `rwp`, `converged`,
+ * `iterations`, `stages`, `parameters` and `parameter_esds`.
  *
  * # Errors
  *
  * Returns a JavaScript `Error` for invalid text or a failed fit.
  */
-export function powder_refine_info(text: string, pattern_text: string, refine_positions: boolean): any;
+export function powder_refine_info(text: string, pattern_text: string, refine_positions: boolean, refine_adps: boolean, refine_occupancies: boolean, refine_zero: boolean, refine_cell: boolean, refine_width: boolean, refine_texture: boolean, doublet: boolean): any;
 
 /**
  * Builds the standardized primitive cell.

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 {
-    WasmDocument, angle, asymmetrize_info, bonds, brillouin_zone, build_c20_info, build_c60_info, build_graphene_info, build_mof_info, build_nanotube_info, cell_volume, change_setting_info, convert_structure, detect_symmetry, diagnose_info, distance, element_info, ff_charges_info, ff_energy, ff_ir_info, ff_optimize_info, ff_prepare_info, ff_thermo_info, ff_types_info, ff_vibrations_info, groups, hydrogens_info, kpath_info, lattice_info, lattice_minimum_image, layer_group_info, limits_bounds, limits_check, lower_to_subgroup_info, 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_refine_info, primitive_info, project_info, project_pack, pxrd_info, read_cif, read_structure, reduce_info, ribbon_info, rietx_inventory_info, rings, scene_summary, schwarzite_info, set_space_group_info, slab_info, slab_text, standardize_info, structure_info, subgroups_info, supercell_info, supercell_text, to_p1_info, tolerance_ladder_info, torsion, twist_info, version, workspace_archive, workspace_read_archive, wyckoff_info, zeo_parse_info, ztc_info
+    AgentSession, WasmDocument, agent_capabilities, agent_run, agent_verbs, angle, asymmetrize_info, bonds, brillouin_zone, build_c20_info, build_c60_info, build_carbon_recipe_info, build_graphene_info, build_mof_info, build_nanotube_info, cell_volume, change_setting_info, convert_structure, detect_symmetry, diagnose_info, distance, element_info, ff_charges_info, ff_energy, ff_ir_info, ff_optimize_info, ff_prepare_info, ff_thermo_info, ff_types_info, ff_vibrations_info, groups, hydrogens_info, kpath_info, lattice_info, lattice_minimum_image, layer_group_info, limits_bounds, limits_check, lower_to_subgroup_info, 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_pawley_info, powder_refine_info, primitive_info, project_info, project_pack, pxrd_info, read_cif, read_structure, reduce_info, ribbon_info, rietx_inventory_info, rings, scene_summary, schwarzite_info, set_space_group_info, slab_info, slab_text, standardize_info, structure_info, subgroups_info, supercell_info, supercell_text, to_p1_info, tolerance_ladder_info, torsion, twist_info, version, workspace_archive, workspace_read_archive, wyckoff_info, zeo_parse_info, ztc_info
 } from "./xtalforge_wasm_bg.js";

package/xtalforge_wasm_bg.js

@@ -1,3 +1,126 @@
+/**
+ * A stateful session an assistant drives in the browser.
+ */
+export class AgentSession {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        AgentSessionFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_agentsession_free(ptr, 0);
+    }
+    /**
+     * Name of the active document.
+     * @returns {string | undefined}
+     */
+    active_name() {
+        const ret = wasm.agentsession_active_name(this.__wbg_ptr);
+        let v1;
+        if (ret[0] !== 0) {
+            v1 = getStringFromWasm0(ret[0], ret[1]);
+            wasm.__wbindgen_free(ret[0], ret[1] * 1, 1);
+        }
+        return v1;
+    }
+    /**
+     * Names of the open documents as JSON.
+     * @returns {string}
+     */
+    documents_json() {
+        let deferred1_0;
+        let deferred1_1;
+        try {
+            const ret = wasm.agentsession_documents_json(this.__wbg_ptr);
+            deferred1_0 = ret[0];
+            deferred1_1 = ret[1];
+            return getStringFromWasm0(ret[0], ret[1]);
+        } finally {
+            wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+        }
+    }
+    /**
+     * Creates an empty session.
+     */
+    constructor() {
+        const ret = wasm.agentsession_new();
+        this.__wbg_ptr = ret;
+        AgentSessionFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Runs one verb with a JSON object and returns the answer as JSON.
+     *
+     * # Errors
+     *
+     * Returns a JavaScript object with `code` and `message` properties.
+     * @param {string} verb
+     * @param {string} arguments_json
+     * @returns {string}
+     */
+    run(verb, arguments_json) {
+        let deferred4_0;
+        let deferred4_1;
+        try {
+            let ptr0, len0, ptr1, len1;
+            try {
+                ptr0 = passStringToWasm0(verb, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+                len0 = WASM_VECTOR_LEN;
+                ptr1 = passStringToWasm0(arguments_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+                len1 = WASM_VECTOR_LEN;
+            } catch (e) {
+                if (ptr1) { wasm.__wbindgen_free(ptr1, len1 * 1, 1); }
+                if (ptr0) { wasm.__wbindgen_free(ptr0, len0 * 1, 1); }
+                throw e;
+            }
+            const ret = wasm.agentsession_run(this.__wbg_ptr, ptr0, len0, ptr1, len1);
+            var ptr3 = ret[0];
+            var len3 = ret[1];
+            if (ret[3]) {
+                ptr3 = 0; len3 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred4_0 = ptr3;
+            deferred4_1 = len3;
+            return getStringFromWasm0(ptr3, len3);
+        } finally {
+            wasm.__wbindgen_free(deferred4_0, deferred4_1, 1);
+        }
+    }
+    /**
+     * One document as structure JSON.
+     *
+     * # Errors
+     *
+     * Returns a JavaScript object with `code` and `message` properties.
+     * @param {string | null} [name]
+     * @returns {string}
+     */
+    structure_json(name) {
+        let deferred3_0;
+        let deferred3_1;
+        try {
+            var ptr0 = isLikeNone(name) ? 0 : passStringToWasm0(name, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+            var len0 = WASM_VECTOR_LEN;
+            const ret = wasm.agentsession_structure_json(this.__wbg_ptr, ptr0, len0);
+            var ptr2 = ret[0];
+            var len2 = ret[1];
+            if (ret[3]) {
+                ptr2 = 0; len2 = 0;
+                throw takeFromExternrefTable0(ret[2]);
+            }
+            deferred3_0 = ptr2;
+            deferred3_1 = len2;
+            return getStringFromWasm0(ptr2, len2);
+        } finally {
+            wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+        }
+    }
+}
+if (Symbol.dispose) AgentSession.prototype[Symbol.dispose] = AgentSession.prototype.free;
+
 /**
  * An undoable structure document in the browser.
  */
@@ -163,6 +286,70 @@ export class WasmDocument {
 }
 if (Symbol.dispose) WasmDocument.prototype[Symbol.dispose] = WasmDocument.prototype.free;
 
+/**
+ * Runtime capability report as JSON.
+ * @returns {string}
+ */
+export function agent_capabilities() {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        const ret = wasm.agent_capabilities();
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
+/**
+ * Runs a JSON script against a fresh session and returns the answers.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript object with `code` and `message` properties.
+ * @param {string} script_json
+ * @returns {string}
+ */
+export function agent_run(script_json) {
+    let deferred3_0;
+    let deferred3_1;
+    try {
+        const ptr0 = passStringToWasm0(script_json, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.agent_run(ptr0, len0);
+        var ptr2 = ret[0];
+        var len2 = ret[1];
+        if (ret[3]) {
+            ptr2 = 0; len2 = 0;
+            throw takeFromExternrefTable0(ret[2]);
+        }
+        deferred3_0 = ptr2;
+        deferred3_1 = len2;
+        return getStringFromWasm0(ptr2, len2);
+    } finally {
+        wasm.__wbindgen_free(deferred3_0, deferred3_1, 1);
+    }
+}
+
+/**
+ * The verb catalogue as JSON.
+ * @returns {string}
+ */
+export function agent_verbs() {
+    let deferred1_0;
+    let deferred1_1;
+    try {
+        const ret = wasm.agent_verbs();
+        deferred1_0 = ret[0];
+        deferred1_1 = ret[1];
+        return getStringFromWasm0(ret[0], ret[1]);
+    } finally {
+        wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
+    }
+}
+
 /**
  * Angle `i-j-k` in degrees, using minimum images.
  *
@@ -283,6 +470,46 @@ export function build_c60_info() {
     return takeFromExternrefTable0(ret[0]);
 }
 
+/**
+ * Builds a disordered carbon from a recipe.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for an unsupported net, a bad repeat or a
+ * surface that cannot be meshed.
+ * @param {string} net
+ * @param {number} repeat_x
+ * @param {number} repeat_y
+ * @param {number} repeat_z
+ * @param {number} density
+ * @param {number} radius_ratio
+ * @param {number} coverage
+ * @param {number} seed
+ * @param {number} hydrogen
+ * @param {number} fluorine
+ * @param {number} oxygen
+ * @returns {any}
+ */
+export function build_carbon_recipe_info(net, repeat_x, repeat_y, repeat_z, density, radius_ratio, coverage, seed, hydrogen, fluorine, oxygen) {
+    const val2 = +repeat_x;
+    const val3 = +repeat_y;
+    const val4 = +repeat_z;
+    const val5 = +density;
+    const val6 = +radius_ratio;
+    const val7 = +coverage;
+    const val8 = +seed;
+    const val9 = +hydrogen;
+    const val10 = +fluorine;
+    const val11 = +oxygen;
+    const ptr0 = passStringToWasm0(net, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.build_carbon_recipe_info(ptr0, len0, val2, val3, val4, val5, val6, val7, val8, val9, val10, val11);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * Builds a graphene sheet and returns its summary.
  *
@@ -664,16 +891,22 @@ export function ff_optimize_info(text, minimizer, max_steps, force_tolerance, ce
  * @param {boolean} charges
  * @param {boolean} ewald
  * @param {boolean} vibrations
+ * @param {boolean | null} [merge_duplicates]
+ * @param {boolean | null} [order_disorder]
+ * @param {boolean | null} [remove_solvent]
+ * @param {boolean | null} [check_charge_balance]
+ * @param {boolean | null} [hydrogens]
+ * @param {boolean | null} [check_close_contacts]
  * @returns {any}
  */
-export function ff_prepare_info(text, minimize, charges, ewald, vibrations) {
+export function ff_prepare_info(text, minimize, charges, ewald, vibrations, merge_duplicates, order_disorder, remove_solvent, check_charge_balance, hydrogens, check_close_contacts) {
     const val2 = +minimize;
     const val3 = +charges;
     const val4 = +ewald;
     const val5 = +vibrations;
     const ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
     const len0 = WASM_VECTOR_LEN;
-    const ret = wasm.ff_prepare_info(ptr0, len0, val2, val3, val4, val5);
+    const ret = wasm.ff_prepare_info(ptr0, len0, val2, val3, val4, val5, isLikeNone(merge_duplicates) ? 0xFFFFFF : merge_duplicates ? 1 : 0, isLikeNone(order_disorder) ? 0xFFFFFF : order_disorder ? 1 : 0, isLikeNone(remove_solvent) ? 0xFFFFFF : remove_solvent ? 1 : 0, isLikeNone(check_charge_balance) ? 0xFFFFFF : check_charge_balance ? 1 : 0, isLikeNone(hydrogens) ? 0xFFFFFF : hydrogens ? 1 : 0, isLikeNone(check_close_contacts) ? 0xFFFFFF : check_close_contacts ? 1 : 0);
     if (ret[2]) {
         throw takeFromExternrefTable0(ret[1]);
     }
@@ -1238,7 +1471,71 @@ export function powder_cells_info(number) {
 }
 
 /**
- * Refines positions with a whole-pattern least-squares step.
+ * Finds peaks and indexes the metric families of a measured XY pattern.
+ *
+ * Returns `{ peaks: [{ two_theta, intensity, fwhm }], candidates: [{ system,
+ * a, b, c, alpha, beta, gamma, m20, f_n, coverage, completeness }] }`.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or a failed search.
+ * @param {string} pattern_text
+ * @param {number} wavelength
+ * @param {number} max_index
+ * @param {number} tolerance
+ * @returns {any}
+ */
+export function powder_index_info(pattern_text, wavelength, max_index, tolerance) {
+    const val2 = +wavelength;
+    const val3 = +max_index;
+    const val4 = +tolerance;
+    const ptr0 = passStringToWasm0(pattern_text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    const len0 = WASM_VECTOR_LEN;
+    const ret = wasm.powder_index_info(ptr0, len0, val2, val3, val4);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
+/**
+ * Fits a Pawley model: free intensities, cell, zero shift and width model.
+ *
+ * # Errors
+ *
+ * Returns a JavaScript `Error` for invalid text or a failed fit.
+ * @param {string} text
+ * @param {string} pattern_text
+ * @param {string} profile
+ * @returns {any}
+ */
+export function powder_pawley_info(text, pattern_text, profile) {
+    let ptr0, len0, ptr1, len1, ptr2, len2;
+    try {
+        ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        len0 = WASM_VECTOR_LEN;
+        ptr1 = passStringToWasm0(pattern_text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        len1 = WASM_VECTOR_LEN;
+        ptr2 = passStringToWasm0(profile, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        len2 = WASM_VECTOR_LEN;
+    } catch (e) {
+        if (ptr2) { wasm.__wbindgen_free(ptr2, len2 * 1, 1); }
+        if (ptr1) { wasm.__wbindgen_free(ptr1, len1 * 1, 1); }
+        if (ptr0) { wasm.__wbindgen_free(ptr0, len0 * 1, 1); }
+        throw e;
+    }
+    const ret = wasm.powder_pawley_info(ptr0, len0, ptr1, len1, ptr2, len2);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
+/**
+ * Refines a phase with the McCusker stages.
+ *
+ * The March-Dollase axis is the `c` axis. Returns `rwp`, `converged`,
+ * `iterations`, `stages`, `parameters` and `parameter_esds`.
  *
  * # Errors
  *
@@ -1246,10 +1543,24 @@ export function powder_cells_info(number) {
  * @param {string} text
  * @param {string} pattern_text
  * @param {boolean} refine_positions
+ * @param {boolean} refine_adps
+ * @param {boolean} refine_occupancies
+ * @param {boolean} refine_zero
+ * @param {boolean} refine_cell
+ * @param {boolean} refine_width
+ * @param {boolean} refine_texture
+ * @param {boolean} doublet
  * @returns {any}
  */
-export function powder_refine_info(text, pattern_text, refine_positions) {
+export function powder_refine_info(text, pattern_text, refine_positions, refine_adps, refine_occupancies, refine_zero, refine_cell, refine_width, refine_texture, doublet) {
     const val3 = +refine_positions;
+    const val4 = +refine_adps;
+    const val5 = +refine_occupancies;
+    const val6 = +refine_zero;
+    const val7 = +refine_cell;
+    const val8 = +refine_width;
+    const val9 = +refine_texture;
+    const val10 = +doublet;
     let ptr0, len0, ptr1, len1;
     try {
         ptr0 = passStringToWasm0(text, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
@@ -1261,7 +1572,7 @@ export function powder_refine_info(text, pattern_text, refine_positions) {
         if (ptr0) { wasm.__wbindgen_free(ptr0, len0 * 1, 1); }
         throw e;
     }
-    const ret = wasm.powder_refine_info(ptr0, len0, ptr1, len1, val3);
+    const ret = wasm.powder_refine_info(ptr0, len0, ptr1, len1, val3, val4, val5, val6, val7, val8, val9, val10);
     if (ret[2]) {
         throw takeFromExternrefTable0(ret[1]);
     }
@@ -2044,6 +2355,9 @@ export function __wbindgen_init_externref_table() {
     table.set(1026, true);
     table.set(1027, false);
 }
+const AgentSessionFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_agentsession_free(ptr, 1));
 const WasmDocumentFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_wasmdocument_free(ptr, 1));
@@ -2163,6 +2477,10 @@ function handleError(f, args) {
     }
 }
 
+function isLikeNone(x) {
+    return x === undefined || x === null;
+}
+
 function passArray32ToWasm0(arg, malloc) {
     const ptr = malloc(arg.length * 4, 4) >>> 0;
     getUint32ArrayMemory0().set(arg, ptr / 4);