diff-grok 1.0.9 → 1.1.0

package/src/pipeline/updates-pipeline-creator.ts

@@ -1,3 +1,5 @@
+/* eslint-disable max-len */
+
 import {IVP} from '../scripting-tools';
 import {MATH_CONSTS, MATH_FUNCS, POW_IDX} from '../scripting-tools/scripting-tools';
 import {getOutputCode} from './output';
@@ -6,8 +8,133 @@ import {PipelineCreator} from './pipeline-creator';
 
 import {argName2IdxMap, ARG, ARG_COL_IDX, CORRECTION_FACTOR, DEFAULT_CORRECTION} from './constants';
 
-/** Pipeline creator for model with updates */
+/** Pipeline creator for model with updates
+ * @example
+ * // This example shows how to apply pipelines and models with updates.
+ * // This approach can be used for in-webworkers analysis of models.
+ * // Here, we consider gluconic acid (GA) production by Aspergillus niger modeling.
+ *
+ * import * as DGL from 'diff-grok';
+ *
+ * // 1. Model specification
+ * const model = `#name: GA-production
+ * #tags: model
+ * #description: Gluconic acid (GA) production by Aspergillus niger modeling
+ *
+ * #equations:
+ *    dX/dt = rX
+ *    dS/dt = -gamma * rX - lambda * X
+ *    dO/dt = Kla * (Cod - O) - delta * rX - phi * X
+ *    dP/dt = alpha * rX + beta * X
+ *
+ * #expressions:
+ *    mu = muM * S / (Ks + S) * O / (Ko + O)
+ *    rX = mu * X
+ *
+ * #argument: t, 1-st stage
+ *    _t0 = 0 {units: h; caption: initial; category: Misc} [Start of the process]
+ *    _t1 = 60 {units: h; caption: 1-st stage; category: Durations; min: 20; max: 80} [Duration of the 1-st stage]
+ *    step = 0.1 {units: h; caption: step; category: Misc; min: 0.01; max: 1} [Time step of simulation]
+ *
+ * #update: 2-nd stage
+ *    duration = overall - _t1
+ *    S += 70
+ *
+ * #inits:
+ *    X = 5 {units: kg/m³; caption: biomass; category: Initial concentrations; min: 1; max: 10} [Aspergillus niger biomass]
+ *    S = 150 {units: kg/m³; caption: glucose; category: Initial concentrations; min: 50; max: 200} [Glucose]
+ *    O = 7 {units: kg/m³; caption: oxygen; category: Initial concentrations; min: 1; max: 10} [Dissolved oxygen]
+ *    P = 0 {units: kg/m³; caption: acid; category: Initial concentrations; min: 0; max: 0.1} [Gluconic acid]
+ *
+ * #output:
+ *    t {caption: time}
+ *    X {caption: biomass}
+ *    S {caption: glucose}
+ *    O {caption: oxygen}
+ *    P {caption: acid}
+ *
+ * #parameters:
+ *    overall = 100 {units: h; category: Durations; min: 100; max: 140} [Overall duration]
+ *    muM = 0.668 {units: 1/h; category: Parameters} [Monod type model parameter]
+ *    alpha = 2.92 {category: Parameters} [Monod type model parameter]
+ *    beta = 0.131 {units: 1/h; category: Parameters} [Monod type model parameter]
+ *    gamma = 2.12 {category: Parameters} [Monod type model parameter]
+ *    lambda = 0.232 {units: 1/h; category: Parameters} [Monod type model parameter]
+ *    delta = 0.278 {category: Parameters} [Monod type model parameter]
+ *    phi = 4.87e-3 {units: 1/h; category: Parameters} [Monod type model parameter]
+ *    Ks = 1.309e2 {units: g/L; category: Parameters} [Monod type model parameter]
+ *    Ko = 3.63e-4 {units: g/L; category: Parameters} [Monod type model parameter]
+ *    Kla = 1.7e-2 {units: 1/s; category: Parameters} [Volumetric mass transfer coefficient]
+ *    Cod = 15 {units: kg/m³; category: Parameters} [Liquid phase dissolved oxygen saturation concentration]
+ *
+ *  #tolerance: 1e-9`;
+ *
+ * // 2. Generate IVP-objects: for the main thread & for computations in webworkers
+ * const ivp = DGL.getIVP(model);
+ * const ivpWW = DGL.getIvp2WebWorker(ivp);
+ *
+ * // 3. Perform computations
+ * try {
+ *   // 3.1) Extract names of outputs
+ *   const outputNames = DGL.getOutputNames(ivp);
+ *   const outSize = outputNames.length;
+ *
+ *   // 3.2) Set model inputs
+ *   const inputs = {
+ *     _t0: 0,
+ *     _t1: 60,
+ *     _h: 1,
+ *     X: 5,
+ *     S: 150,
+ *     O: 7,
+ *     P: 0,
+ *     overall: 100,
+ *     muM: 0.668,
+ *     alpha: 2.92,
+ *     beta: 0.131,
+ *     gamma: 2.12,
+ *     lambda: 0.232,
+ *     delta: 0.278,
+ *     phi: 4.87e-3,
+ *     Ks: 1.309e2,
+ *     Ko: 3.63e-4,
+ *     Kla: 1.7e-2,
+ *     Cod: 15,
+ *   };
+ *
+ *   const inputVector = DGL.getInputVector(inputs, ivp);
+ *
+ *   // 3.3) Create a pipeline
+ *   const creator = DGL.getPipelineCreator(ivp);
+ *   const pipeline = creator.getPipeline(inputVector);
+ *
+ *   // 3.4) Apply pipeline to perform computations
+ *   const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+ *
+ *   // 3.5) Print results
+ *
+ *   // 3.5.1) Table header
+ *   let line = '     ';
+ *   outputNames.forEach((name) => line += name + '         ');
+ *   console.log(line);
+ *
+ *   // 3.5.2) Table with solution  const length = solution[0].length;
+ *   for (let i = 0; i < length; ++i) {
+ *       line = '';
+ *
+ *       for (let j = 0; j < outSize; ++j)
+ *         line += solution[j][i].toFixed(8) + '     ';
+ *
+ *     console.log(line);
+ *   }
+ * } catch (err) {
+ *   console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+ * }
+ */
 export class UpdatesModelPipelineCreator extends PipelineCreator {
+  /**
+   * @param ivp - initial value problem to be solved
+   */
   constructor(ivp: IVP) {
     super(ivp);
 
@@ -15,7 +142,9 @@ export class UpdatesModelPipelineCreator extends PipelineCreator {
       throw new Error('Incorrect use of UpdatesModelPipelineCreator: model has no updates');
   }
 
-  /** Return computations pipeline */
+  /** Return computations pipeline corresponding to the given input vector
+   * @param inputs - input vector of the model
+  */
   public getPipeline(inputs: Float64Array): Pipeline {
     if (this.ivp.updates === null)
       throw new Error('Incorrect use of UpdatesModelPipelineCreator: model has no updates');

package/src/scripting-tools/constants.js

@@ -1,9 +1,15 @@
 // Control constants
+/** @internal */
 export const CONTROL_TAG = '#';
+/** @internal */
 export const CONTROL_TAG_LEN = CONTROL_TAG.length;
+/** @internal */
 export const DF_NAME = 'df';
+/** @internal */
 export const MAX_LINE_CHART = 4;
-/** Control expressions for the problem specifying */
+/** Control expressions for the problem specifying
+ * @internal
+*/
 export var CONTROL_EXPR;
 (function (CONTROL_EXPR) {
     CONTROL_EXPR["NAME"] = "#name";
@@ -26,7 +32,9 @@ export var CONTROL_EXPR;
     CONTROL_EXPR["INPUTS"] = "#meta.inputs";
 })(CONTROL_EXPR || (CONTROL_EXPR = {}));
 ;
-/** Loop consts */
+/** Loop consts
+ * @internal
+ * */
 export var LOOP;
 (function (LOOP) {
     LOOP[LOOP["MIN_LINES_COUNT"] = 1] = "MIN_LINES_COUNT";
@@ -35,7 +43,9 @@ export var LOOP;
     LOOP[LOOP["MIN_COUNT"] = 1] = "MIN_COUNT";
 })(LOOP || (LOOP = {}));
 ;
-/** UPDATE consts */
+/** UPDATE consts
+ * @internal
+ */
 export var UPDATE;
 (function (UPDATE) {
     UPDATE[UPDATE["MIN_LINES_COUNT"] = 1] = "MIN_LINES_COUNT";
@@ -43,11 +53,15 @@ export var UPDATE;
     UPDATE["DURATION"] = "_duration";
 })(UPDATE || (UPDATE = {}));
 ;
-/** Ranges of the solver options */
+/** Ranges of the solver options
+ * @internal
+ */
 export const SOLVER_OPTIONS_RANGES = new Map([
     ['maxTime', { min: 1, max: 10000 }],
     ['scale', { min: 0.5, max: 1 }],
 ]);
+/** @internal */
 export const TINY = 0.0001;
+/** @internal */
 export const STEP_RATIO = 0.5;
 //# sourceMappingURL=constants.js.map

package/src/scripting-tools/constants.js.map

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package/src/scripting-tools/constants.ts

@@ -1,10 +1,19 @@
 // Control constants
+/** @internal */
 export const CONTROL_TAG = '#';
+
+/** @internal */
 export const CONTROL_TAG_LEN = CONTROL_TAG.length;
+
+/** @internal */
 export const DF_NAME = 'df';
+
+/** @internal */
 export const MAX_LINE_CHART = 4;
 
-/** Control expressions for the problem specifying */
+/** Control expressions for the problem specifying
+ * @internal
+*/
 export enum CONTROL_EXPR {
     NAME = '#name',
     TAGS = '#tags',
@@ -26,7 +35,9 @@ export enum CONTROL_EXPR {
     INPUTS = '#meta.inputs',
 };
 
-/** Loop consts */
+/** Loop consts
+ * @internal
+ * */
 export enum LOOP {
   MIN_LINES_COUNT = 1,
   COUNT_IDX = 0,
@@ -34,18 +45,25 @@ export enum LOOP {
   MIN_COUNT = 1,
 };
 
-/** UPDATE consts */
+/** UPDATE consts
+ * @internal
+ */
 export enum UPDATE {
   MIN_LINES_COUNT = 1,
   DURATION_IDX = 0,
   DURATION = '_duration',
 };
 
-/** Ranges of the solver options */
+/** Ranges of the solver options
+ * @internal
+ */
 export const SOLVER_OPTIONS_RANGES = new Map([
   ['maxTime', {min: 1, max: 10000}],
   ['scale', {min: 0.5, max: 1}],
 ]);
 
+/** @internal */
 export const TINY = 0.0001;
+
+/** @internal */
 export const STEP_RATIO = 0.5;

package/src/scripting-tools/index.js.map

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package/src/scripting-tools/index.ts

@@ -1,7 +1,8 @@
 export {DF_NAME, CONTROL_EXPR, MAX_LINE_CHART} from './constants';
 
-export {getIVP, getScriptLines, getScriptParams, getJScode, IVP, Input, SCRIPTING,
+export {DifEqs, getIVP, getScriptLines, getScriptParams, getJScode, IVP, Input, SCRIPTING,
   BRACE_OPEN, BRACE_CLOSE, BRACKET_OPEN, BRACKET_CLOSE, ANNOT_SEPAR, CONTROL_SEP,
-  STAGE_COL_NAME, ARG_INPUT_KEYS, DEFAULT_SOLVER_SETTINGS, getFunc4worker} from './scripting-tools';
+  STAGE_COL_NAME, ARG_INPUT_KEYS, DEFAULT_SOLVER_SETTINGS, getFunc4worker, Loop, Update,
+  Output, Arg} from './scripting-tools';
 
 export {ModelError} from './model-error';

package/src/scripting-tools/model-error.js

@@ -1,4 +1,6 @@
-/** Diff Studio model error */
+/** Diff Studio model error
+ * @internal
+ */
 export class ModelError extends Error {
     constructor(message, helpUrl, toHighlight) {
         super(message);

package/src/scripting-tools/model-error.js.map

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package/src/scripting-tools/model-error.ts

@@ -1,4 +1,6 @@
-/** Diff Studio model error */
+/** Diff Studio model error
+ * @internal
+ */
 export class ModelError extends Error {
   private helpUrl: string;
   private toHighlight: string | undefined = undefined;

package/src/scripting-tools/scripting-tools.js

@@ -10,32 +10,48 @@
 import { CONTROL_TAG, CONTROL_TAG_LEN, CONTROL_EXPR, LOOP, UPDATE, MAX_LINE_CHART, SOLVER_OPTIONS_RANGES, TINY, STEP_RATIO } from './constants';
 import { ModelError } from './model-error';
 // Scripting specific constants
+/** @internal */
 export const CONTROL_SEP = ':';
 const COMMA = ',';
 const EQUAL_SIGN = '=';
 const DIV_SIGN = '/';
 const SERVICE = '_';
+/** @internal */
 export const BRACE_OPEN = '{';
+/** @internal */
 export const BRACE_CLOSE = '}';
+/** @internal */
 export const BRACKET_OPEN = '[';
+/** @internal */
 export const BRACKET_CLOSE = ']';
+/** @internal */
 export const ANNOT_SEPAR = ';';
 const DEFAULT_TOL = '0.00005';
+/** @internal */
 export const DEFAULT_SOLVER_SETTINGS = '{}';
 const COMMENT_SEQ = '//';
+/** @internal */
 export const STAGE_COL_NAME = `_Stage`;
 const INCEPTION = 'Inception';
-/** Elementary math tools */
+/** Elementary math tools
+ * @internal
+ */
 export const MATH_FUNCS = ['pow', 'sin', 'cos', 'tan', 'asin', 'acos', 'atan', 'sqrt', 'exp', 'log', 'sinh', 'cosh', 'tanh'];
+/** @internal */
 export const POW_IDX = MATH_FUNCS.indexOf('pow');
+/** @internal */
 export const MATH_CONSTS = ['PI', 'E'];
 /** Default meta */
 const defaultMetas = `//meta.runOnOpen: true
 //meta.runOnInput: true
 //meta.features: {"sens-analysis": true, "fitting": true}`;
-/** Input keys of Arg */
+/** Input keys of Arg
+ * @internal
+ */
 export const ARG_INPUT_KEYS = ['initial', 'final', 'step'];
-/** Scripting specific constants */
+/** Scripting specific constants
+ * @internal
+ */
 export var SCRIPTING;
 (function (SCRIPTING) {
     SCRIPTING["ARG_NAME"] = "name";
@@ -379,7 +395,100 @@ function getOutput(lines, begin, end) {
     } // for i
     return res;
 } // getOutput
-/** Get initial value problem specification given in the text */
+/** Return initial value problem specification given in the text
+ * @param text - declarative specification of initial value problem
+ * @example
+ *  // Here, we consider modeling queues: https://en.wikipedia.org/wiki/M/M/c_queue
+ * import * as DGL from 'diff-grok';
+ *
+ * // 1. Model specification: the M|M|2|2 model
+ * const model = `#name: M|M|2|2
+ * #description: Modelling the system with two servers & two waiting places (EXPLAINED)
+ *
+ * #equations:
+ *   dp0/dt = -la * p0 + mu * p1
+ *   dp1/dt = la * p0 - (la + mu) * p1 + 2 * mu * p2
+ *   dp2/dt = la * p1 - (la + 2 * mu) * p2 + 2 * mu * p3
+ *   dp3/dt = la * p2 - (la + 2 * mu) * p3 + 2 * mu * p4
+ *
+ * #expressions:
+ *   la = 1 / arrival
+ *   mu = 1 / service
+ *   p4 = 1 - p0 - p1 - p2 - p3
+ *   busy = 1 - p0 - p1
+ *   queue = p3 + 2 * p4
+ *
+ * #argument: t
+ *   _t0 = 0     {min: 0;      max: 10;   caption: start;   category: Time; units: min}  [Initial time of simulation]
+ *   _t1 = 60    {min: 20;     max: 100;  caption: finish;  category: Time; units: min}  [Final time of simulation]
+ *   _h  = 1     {min: 0.01;   max: 0.1;  caption: step;    category: Time; units: min}  [Time step of simulation]
+ *
+ * #inits:
+ *   p0 = 1   {min: 0; max: 1; category: Initial state; caption: empty}   [Probability that initially there are NO customers]
+ *   p1 = 0   {min: 0; max: 1; category: Initial state; caption: single}  [Probability that initially there is ONE customer]
+ *   p2 = 0   {min: 0; max: 1; category: Initial state; caption: two}     [Probability that initially there are TWO customers]
+ *   p3 = 0   {min: 0; max: 1; category: Initial state; caption: three}   [Probability that initially there are THREE customers]
+ *
+ * #output:
+ *   t     {caption: Time, min}
+ *   p0    {caption: P(Empty)}
+ *   busy  {caption: P(Full load)}
+ *   queue {caption: E(Queue)}
+ *
+ * #parameters:
+ *   arrival = 10   {min: 1; max: 100; category: Means; caption: arrival;  units: min} [Mean arrival time]
+ *   service = 100  {min: 1; max: 100; category: Means; caption: service; units: min} [Mean service time]`;
+ *
+ * // 2. Generate IVP-objects: for the main thread & for computations in webworkers
+ * const ivp = DGL.getIVP(model);
+ * const ivpWW = DGL.getIvp2WebWorker(ivp);
+ *
+ *  // 3. Perform computations
+ * try {
+ *   // 3.1) Extract names of outputs
+ *   const outputNames = DGL.getOutputNames(ivp);
+ *   const outSize = outputNames.length;
+ *
+ *   // 3.2) Set model inputs
+ *   const inputs = {
+ *     _t0: 0, // Initial time of simulation
+ *     _t1: 60, // Final time of simulation
+ *     _h: 1, // Time step of simulation
+ *     p0: 1, // Probability that initially there are NO customers
+ *     p1: 0, // Probability that initially there is ONE customer
+ *     p2: 0, // Probability that initially there are TWO customers
+ *     p3: 0, // Probability that initially there are THREE customers
+ *     arrival: 10, // Mean arrival time
+ *     service: 100, // Mean service time
+ *   };
+ *   const inputVector = DGL.getInputVector(inputs, ivp);
+ *
+ *  // 3.3) Create a pipeline
+ *   const creator = DGL.getPipelineCreator(ivp);
+ *   const pipeline = creator.getPipeline(inputVector);
+ *
+ *   // 3.4) Apply pipeline to perform computations
+ *   const solution = DGL.applyPipeline(pipeline, ivpWW, inputVector);
+ *   // 3.5) Print results
+ *
+ *   // 3.5.1) Table header
+ *   let line = '';
+ *   outputNames.forEach((name) => line += name + '      ');
+ *   console.log(line);
+ *
+ *   // 3.5.2) Table with solution
+ *   const length = solution[0].length;
+ *   for (let i = 0; i < length; ++i) {
+ *     line = '';
+ *
+ *     for (let j = 0; j < outSize; ++j)
+ *       line += solution[j][i].toFixed(8) + '     ';
+ *     console.log(line);
+ *   }
+ * } catch (err) {
+ *   console.log('Simulation failed: ', err instanceof Error ? err.message : 'Unknown problem!');
+ * }
+ */
 export function getIVP(text) {
     // The current Initial Value Problem (IVP) specification
     let name;
@@ -549,7 +658,9 @@ function getAnnot(ivp, toAddViewers = true, toAddEditor = false) {
         res.push(defaultMetas);
     return res;
 } // getAnnot
-/** Returns math functions arguments string */
+/** Returns math functions arguments string
+ * @internal
+ */
 function getMathArg(funcIdx) {
     return (funcIdx > POW_IDX) ? '(x)' : '(x, y)';
 }
@@ -835,14 +946,18 @@ function getScriptMainBody(ivp) {
         return getScriptMainBodyUpdateCase(ivp);
     return getScriptMainBodyBasic(ivp);
 }
-/** Return JS-script lines */
+/** Return JS-script lines
+ * @internal
+ */
 export function getScriptLines(ivp, toAddViewers = true, toAddEditor = false) {
     const res = getAnnot(ivp, toAddViewers, toAddEditor).concat(getScriptMainBody(ivp));
     if (ivp.outputs)
         return res.concat(getCustomOutputLines(ivp));
     return res;
 }
-/** Return parameters of JS-script */
+/** Return parameters of JS-script
+ * @internal
+ */
 export function getScriptParams(ivp) {
     const res = {};
     if (ivp.loop)
@@ -975,7 +1090,22 @@ function checkCorrectness(ivp) {
     // 5. Check solver settings
     checkSolverSettings(ivp.solverSettings);
 } // checkCorrectness
-/** */
+/** Return JavaScript code that solves the given initial value problem
+ * @param ivp - initial value problem to be solved
+ * @example
+ * import {getIVP, getJScode} from 'diff-grok';
+ *
+ * const model = `
+ *   #name: Example
+ *   #equations:
+ *      dx/dt = x + y - cos(t)
+ *      dy/dt = x - y + sin(t)
+ *   ...
+ * `;
+ *
+ * const ivp = getIVP(model);
+ * const lines = getJScode(ivp);
+ */
 export function getJScode(ivp) {
     const res = [];
     // 1. Math functions
@@ -1027,6 +1157,6 @@ export function getJScode(ivp) {
     res.push('};');
     return res;
 } // getJScode
-/** */
+/** @internal */
 export function getFunc4worker(ivp) { }
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