diff-grok 1.2.0 → 1.3.0

package/src/examples/robertson.js

@@ -1,19 +0,0 @@
-/** Robertson chemical reaction, updated version (see https://archimede.uniba.it/~testset/problems/rober.php) */
-export const robertson = {
-    name: 'Robertson',
-    arg: { name: 't', start: 0, finish: 10e11, step: 2.5e6 },
-    initial: [1, 0, 0],
-    func: (t, y, output) => {
-        output[0] = -0.04 * y[0] + 1e4 * y[1] * y[2];
-        output[1] = 0.04 * y[0] - 1e4 * y[1] * y[2] - 3e7 * Math.pow(y[1], 2);
-        output[2] = 3e7 * Math.pow(y[1], 2);
-    },
-    tolerance: 1e-7,
-    solutionColNames: ['A', 'B', 'C'],
-};
-export const robertsonReferencePoint = new Float64Array([
-    0.2083340149701255E-7,
-    0.8333360770334713E-13,
-    0.9999999791665050,
-]);
-//# sourceMappingURL=robertson.js.map

package/src/examples/robertson.js.map

@@ -1 +0,0 @@
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package/src/examples/robertson.ts

@@ -1,19 +0,0 @@
-/** Robertson chemical reaction, updated version (see https://archimede.uniba.it/~testset/problems/rober.php) */
-export const robertson = {
-  name: 'Robertson',
-  arg: {name: 't', start: 0, finish: 10e11, step: 2.5e6},
-  initial: [1, 0, 0],
-  func: (t: number, y: Float64Array, output: Float64Array) => {
-    output[0] = -0.04 * y[0] + 1e4 * y[1] * y[2];
-    output[1] = 0.04 * y[0] - 1e4 * y[1] * y[2] - 3e7 * y[1]**2;
-    output[2] = 3e7 * y[1]**2;
-  },
-  tolerance: 1e-7,
-  solutionColNames: ['A', 'B', 'C'],
-};
-
-export const robertsonReferencePoint = new Float64Array([
-  0.2083340149701255E-7,
-  0.8333360770334713E-13,
-  0.9999999791665050,
-]);

package/src/examples/scripting.js

@@ -1,30 +0,0 @@
-import { getIVP, getJScode } from '../../index';
-/** Example. Solve the following initial value problem
-      dx / dt = x + y - cos(t)
-      dy / dt = x - y + sin(t)
-      x(0) = 1
-      y(0) = 0
-
-    on [0, 1] with the step 0.01.
- */
-/** Diff Grok model specifying the given problem */
-const model = `#name: Example
-#equations:
-  dx/dt = x + y - cos(t)
-  dy/dt = x - y + sin(t)
-
-#inits:
-  x = 1
-  y = 0
-
-#argument: t
-  start = 0
-  finish = 1
-  step = 0.01`;
-// Get parsed formulas
-const ivp = getIVP(model);
-console.log(ivp);
-// Get lines of JS-code specifying ODEs object
-const lines = getJScode(ivp);
-console.log(lines);
-//# sourceMappingURL=scripting.js.map

package/src/examples/scripting.js.map

@@ -1 +0,0 @@
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package/src/examples/scripting.ts

@@ -1,35 +0,0 @@
-import {getIVP, getJScode} from '../../index';
-
-/** Example. Solve the following initial value problem
-      dx / dt = x + y - cos(t)
-      dy / dt = x - y + sin(t)
-      x(0) = 1
-      y(0) = 0
-
-    on [0, 1] with the step 0.01.
- */
-
-/** Diff Grok model specifying the given problem */
-const model = `#name: Example
-#equations:
-  dx/dt = x + y - cos(t)
-  dy/dt = x - y + sin(t)
-
-#inits:
-  x = 1
-  y = 0
-
-#argument: t
-  start = 0
-  finish = 1
-  step = 0.01`;
-
-// Get parsed formulas
-const ivp = getIVP(model);
-
-console.log(ivp);
-
-// Get lines of JS-code specifying ODEs object
-const lines = getJScode(ivp);
-
-console.log(lines);

package/src/examples/vdpol.js

@@ -1,17 +0,0 @@
-/** Van der Pol oscillator (see https://archimede.uniba.it/~testset/problems/vdpol.php) */
-export const vdpol = {
-    name: 'van der Pol',
-    arg: { name: 't', start: 0, finish: 2000, step: 0.1 },
-    initial: [-1, 1],
-    func: (t, y, output) => {
-        output[0] = y[1];
-        output[1] = -y[0] + 1000 * (1 - y[0] * y[0]) * y[1];
-    },
-    tolerance: 1e-12,
-    solutionColNames: ['x1', 'x2'],
-};
-export const vdpolReferencePoint = new Float64Array([
-    1.706167732170469,
-    -0.8928097010248125E-3,
-]);
-//# sourceMappingURL=vdpol.js.map

package/src/examples/vdpol.js.map

@@ -1 +0,0 @@
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package/src/examples/vdpol.ts

@@ -1,17 +0,0 @@
-/** Van der Pol oscillator (see https://archimede.uniba.it/~testset/problems/vdpol.php) */
-export const vdpol = {
-  name: 'van der Pol',
-  arg: {name: 't', start: 0, finish: 2000, step: 0.1},
-  initial: [-1, 1],
-  func: (t: number, y: Float64Array, output: Float64Array) => {
-    output[0] = y[1];
-    output[1] = -y[0] + 1000 * (1 - y[0] * y[0]) * y[1];
-  },
-  tolerance: 1e-12,
-  solutionColNames: ['x1', 'x2'],
-};
-
-export const vdpolReferencePoint = new Float64Array([
-  1.706167732170469,
-  -0.8928097010248125E-3,
-]);

package/src/pipeline/basic-pipeline-creator.js.map

@@ -1 +0,0 @@
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package/src/pipeline/constants.js.map

@@ -1 +0,0 @@
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package/src/pipeline/constants.ts

@@ -1,21 +0,0 @@
-export const ARG_INP_COUNT = 3;
-export const ARG_COL_IDX = 0;
-export const CORRECTION_FACTOR = 0.5;
-export const DEFAULT_CORRECTION = 0.0000001;
-export const LOOP_PARAMS_CONT = 1;
-export const LOOP_MIN_COUNT = 1;
-
-/** Default argument names*/
-export enum ARG {
-  START = '_t0',
-  FINISH = '_t1',
-  STEP = '_h',
-};
-
-export const LOOP_COUNT_NAME = '_count';
-
-export const argName2IdxMap = new Map<string, number>([
-  [ARG.START, 0],
-  [ARG.FINISH, 1],
-  [ARG.STEP, 2],
-]);

package/src/pipeline/index.js.map

@@ -1 +0,0 @@
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package/src/pipeline/index.ts

@@ -1,7 +0,0 @@
-export {Pipeline, Wrapper, applyPipeline, getPipelineCreator} from './pipeline';
-export {getOutputCode, getOutputNames} from './output';
-export {PipelineCreator} from './pipeline-creator';
-export {BasicModelPipelineCreator} from './basic-pipeline-creator';
-export {CyclicModelPipelineCreator} from './loops-pipeline-creator';
-export {UpdatesModelPipelineCreator} from './updates-pipeline-creator';
-export {getInputVector} from './input';

package/src/pipeline/input.js.map

@@ -1 +0,0 @@
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package/src/pipeline/input.ts

@@ -1,55 +0,0 @@
-import {IVP} from '../scripting-tools';
-import {ARG_INP_COUNT, argName2IdxMap, LOOP_PARAMS_CONT, LOOP_COUNT_NAME} from './constants';
-
-/** Return inputs in a form of a vector */
-export function getInputVector(inputs: Record<string, number>, ivp: IVP): Float64Array {
-  const eqsCount = ivp.deqs.solutionNames.length;
-  const paramsCount = (ivp.params !== null) ? ivp.params.size : 0;
-  const loopParamsCount = (ivp.loop !== null) ? LOOP_PARAMS_CONT : 0;
-  const size = ARG_INP_COUNT + eqsCount + paramsCount + loopParamsCount;
-  const inputVector = new Float64Array(size);
-
-  // Argument
-  argName2IdxMap.forEach((index, key) => {
-    if (key in inputs)
-      inputVector[index] = inputs[key];
-    else
-      throw new Error(`Inconsistent inputs: "${key}" is missing`);
-  });
-
-  let idx = ARG_INP_COUNT;
-
-  // Init values
-  ivp.deqs.solutionNames.forEach((name) => {
-    if (name in inputs)
-      inputVector[idx] = inputs[name];
-    else
-      throw new Error(`Inconsistent inputs: "${name}" is missing`);
-
-    ++idx;
-  });
-
-  // Parameters
-  if (ivp.params !== null) {
-    ivp.params.forEach((_, name) => {
-      if (name in inputs)
-        inputVector[idx] = inputs[name];
-      else
-        throw new Error(`Inconsistent inputs: "${name}" is missing`);
-
-      ++idx;
-    });
-  }
-
-  // Loop params
-  if (ivp.loop !== null) {
-    if (LOOP_COUNT_NAME in inputs)
-      inputVector[idx] = inputs[LOOP_COUNT_NAME];
-    else
-      throw new Error(`Inconsistent inputs, loop repetitions count is not defined: "${LOOP_COUNT_NAME}" is missing`);
-
-    ++idx;
-  }
-
-  return inputVector;
-} // getInputVector

package/src/pipeline/loops-pipeline-creator.js.map

@@ -1 +0,0 @@
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package/src/pipeline/loops-pipeline-creator.ts

@@ -1,252 +0,0 @@
-/* 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';
-import {Pipeline, Wrapper} from './pipeline';
-import {PipelineCreator} from './pipeline-creator';
-
-import {argName2IdxMap, ARG, ARG_COL_IDX, CORRECTION_FACTOR, DEFAULT_CORRECTION, LOOP_MIN_COUNT} from './constants';
-
-/** Pipeline creator for cyclic model
- * @example
- * // This example shows how to apply pipelines and cyclic models.
- * // This approach can be used for in-webworkers analysis of models.
- * // Here, we consider pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model.
- * import * as DGL from 'diff-grok';
- *
- * // 1. Model specification
- * const model = `#name: PK-PD
- * #tags: model
- * #description: Pharmacokinetic-pharmacodynamic (PK-PD) simulation: two-compartment model
- * #equations:
- *   d(depot)/dt = -KA * depot
- *   d(centr)/dt = KA * depot - CL * C2 - Q * C2 + Q * C3
- *   d(peri)/dt  = Q * C2 - Q * C3
- *   d(eff)/dt  = Kin - Kout * (1 - C2/(EC50 + C2)) * eff
- *
- * #expressions:
- *   C2 = centr / V2
- *   C3 = peri / V3
- *
- * #loop:
- *   _count = 10 {caption: count; category: Dosing; min: 1; max: 20} [Number of doses]
- *   depot += dose
- *
- * #argument: t
- *   _t0 = 0 {units: h; caption: begin; category: Dosing; min: 0; max: 1} [Begin of dosing interval]
- *   _t1 = 12 {units: h; caption: end; category: Dosing; min: 5; max: 15} [End of dosing interval]
- *   _h = 1 {units: h; caption: step; category: Dosing; min: 0.01; max: 0.1} [Time step of simulation]
- *
- * #inits:
- *   depot = 0 {category: Initial values}
- *   centr = 0 {category: Initial values} [Central]
- *   peri = 0 {category: Initial values} [Peripheral]
- *   eff = 0.2 {category: Initial values} [Effective compartment rate]
- *
- * #parameters:
- *   dose = 1e4 {category: Dosing; min: 1e3; max: 2e4; step: 1e3} [Dosage]
- *   KA = 0.3 {caption: rate constant; category: Parameters; min: 0.1; max: 1}
- *   CL = 2 {caption: clearance; category: Parameters; min: 1; max: 5}
- *   V2 = 4 {caption: central volume; category: Parameters; min: 1; max: 10} [Central compartment volume]
- *   Q = 1 {caption: inter rate; category: Parameters; min: 0.1; max: 1} [Intercompartmental rate]
- *   V3 = 30 {caption: peri volume; category: Parameters; min: 20; max: 40} [Peripheral compartment volume]
- *   EC50 = 8 {caption: effect; category: Parameters; min: 1; max: 10}
- *   Kin = 0.2 {caption: Kin; category: Parameters; min: 0.1; max: 0.5} [The first-order production constant]
- *   Kout = 0.2 {caption: Kout; category: Parameters; min: 0.1; max: 0.5} [The first-order dissipation rate constant]
- *
- * #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 = {
- *     _count: 10,
- *     _t0: 0,
- *     _t1: 16,
- *     _h: 1,
- *     depot: 0,
- *     centr: 0,
- *     peri: 0,
- *     eff: 0.2,
- *     dose: 10000,
- *     KA: 0.63,
- *     CL: 3.2,
- *     V2: 6.58,
- *     Q: 0.622,
- *     V3: 35.6,
- *     EC50: 5.41,
- *     Kin: 0.272,
- *     Kout: 0.276,
- *   };
- *
- *   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 CyclicModelPipelineCreator extends PipelineCreator {
-  /**
-   * @param ivp - initial value problem to be solved
-   */
-  constructor(ivp: IVP) {
-    super(ivp);
-
-    if (ivp.loop === null)
-      throw new Error('Incorrect use of CyclicModelPipelineCreator: model has no loop');
-  }
-
-  /** Return computations pipeline corresponding to the given input vector
-   * @param inputs - input vector of the model
-   */
-  public getPipeline(inputs: Float64Array): Pipeline {
-    if (this.ivp.loop === null)
-      throw new Error('Incorrect use of CyclicModelPipelineCreator: model has no loop');
-
-    const argSize = argName2IdxMap.size;
-    const restricted = inputs.length - 1;
-    const repetitions = inputs[restricted];
-
-    if (repetitions < LOOP_MIN_COUNT)
-      throw new Error(`Incorrect repetitions count: ${repetitions}, expected: > 0`);
-
-    const preProcLines: string[] = [];
-
-    // Used math funcs
-    this.ivp.usedMathFuncs.forEach((idx) => {
-      if (idx !== POW_IDX)
-        preProcLines.push(`const ${MATH_FUNCS[idx]} = (x) => Math.${MATH_FUNCS[idx]}(x);`);
-      else
-        preProcLines.push(`const pow = (x, y) => Math.pow(x, y);`);
-    });
-
-    // Used math consts
-    this.ivp.usedMathConsts.forEach((idx) => {
-      preProcLines.push(`const ${MATH_CONSTS[idx]} = Math.${MATH_CONSTS[idx]};`);
-    });
-
-    // Model constants
-    if (this.ivp.consts !== null)
-      this.ivp.consts.forEach((input, name) => preProcLines.push(`const ${name} = ${input.value};`));
-
-    preProcLines.push(`const inputs = arguments[1].slice(0, ${restricted});`);
-
-    // Extract inputs
-    argName2IdxMap.forEach((idx, name) => preProcLines.push(`let ${name} = inputs[${idx}];`));
-
-    this.ivp.deqs.solutionNames.forEach((name, idx) => {
-      preProcLines.push(`let ${name} = inputs[${idx + argSize}];`);
-    });
-
-    if (this.ivp.params !== null) {
-      const shift = argSize + this.ivp.deqs.solutionNames.length;
-      let idx = 0;
-
-      this.ivp.params.forEach((_, name) => {
-        preProcLines.push(`let ${name} = inputs[${idx + shift}];`);
-        ++idx;
-      });
-    }
-
-    // Updates
-    this.ivp.loop.updates.forEach((expr) => preProcLines.push(`${expr};`));
-
-    // Input vector update
-    argName2IdxMap.forEach((idx, name) => preProcLines.push(`inputs[${idx}] = ${name};`));
-
-    this.ivp.deqs.solutionNames.forEach((name, idx) => {
-      preProcLines.push(`inputs[${idx + argSize}] = ${name};`);
-    });
-
-    if (this.ivp.params !== null) {
-      const shift = argSize + this.ivp.deqs.solutionNames.length;
-      let idx = 0;
-
-      this.ivp.params.forEach((_, name) => {
-        preProcLines.push(`inputs[${idx + shift}] = ${name};`);
-        ++idx;
-      });
-    }
-
-    preProcLines.push(`return inputs;`);
-
-    const postProcLines = [
-      'const solution = arguments[0];',
-      'const lastIdx = solution[0].length - 1;',
-      'const inputs = new Float64Array(arguments[1]);',
-      `const duration = inputs[${argName2IdxMap.get(ARG.FINISH)}] - inputs[${argName2IdxMap.get(ARG.START)}];`,
-      `inputs[${argName2IdxMap.get(ARG.START)}] = inputs[${argName2IdxMap.get(ARG.FINISH)}];`,
-      `inputs[${argName2IdxMap.get(ARG.FINISH)}] += duration;`,
-    ];
-
-    this.ivp.deqs.solutionNames.forEach((_, idx) => {
-      postProcLines.push(`inputs[${idx + argSize}] = solution[${idx + 1}][lastIdx];`);
-    });
-
-    postProcLines.push('return inputs;');
-
-    const preCode = preProcLines.join('\n');
-    const postCode = postProcLines.join('\n');
-
-    const wrappers = new Array<Wrapper>(repetitions);
-
-    for (let i = 0; i < repetitions; ++i) {
-      wrappers[i] = {
-        preproc: preCode,
-        out: null,
-        postproc: postCode,
-      };
-    }
-
-    wrappers[repetitions - 1].postproc = this.getArgumentCorrectionCode();
-
-    return {
-      wrappers: wrappers,
-      out: getOutputCode(this.ivp),
-    };
-  } // getPipeline
-
-  /** Return code for correction of an argument */
-  private getArgumentCorrectionCode(): string {
-    return `const arg = arguments[0][${ARG_COL_IDX}];
-    const length = arg.length;
-    const step = arg[1] - arg[0];
-    const correction = Math.min(step * ${CORRECTION_FACTOR}, ${DEFAULT_CORRECTION});
-    for (let i = 0; i < length - 1; ++i) {
-      if (arg[i + 1] - arg[i] < step)
-        arg[i] -= correction;
-    }
-    return arguments[0];`;
-  } // getArgumentCorrectionCode
-} // CyclicModelPipelineCreator

package/src/pipeline/output.js.map

@@ -1 +0,0 @@
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