diff-grok 1.2.0 → 1.3.1

package/docs/media/cyclic-model.ts

@@ -1,112 +0,0 @@
-/* eslint-disable max-len */
-/** 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 '../../index';
-
-/** 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
-
-#meta.solver: {method: 'rkdp'; maxTimeMs: 5000}`;
-
-/** 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!');
-}

package/docs/media/e5.js.map

@@ -1 +0,0 @@
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package/docs/media/e5.ts

@@ -1,36 +0,0 @@
- /** Kintetic constants for the E5 model */
- enum E5 {
-    K1 = 7.89e-10,
-    K2 = 1.13e9,
-    K3 = 1.1e7,
-    K4 = 1.13e3,
-  };
-
-/** The E5 model (chemical pyrolysis: https://archimede.uniba.it/~testset/report/e5.pdf) */
-export const e5 = {
-  name: 'E5',
-  arg: {name: 't', start: 0, finish: 1e13, step: 2.5e8},
-  initial: [0.00176, 0, 0, 0],
-  func: (t: number, y: Float64Array, output: Float64Array) => {
-    // extract function values
-    const y1 = y[0];
-    const y2 = y[1];
-    const y3 = y[2];
-    const y4 = y[3];
-
-    // compute output
-    output[0] = -E5.K1 * y1 - E5.K3 * y1 * y3;
-    output[1] = E5.K1 * y1 - E5.K2 * y2 * y3;
-    output[2] = E5.K1 * y1 - E5.K2 * y2 * y3 - E5.K3 * y1 * y3 + E5.K4 * y4;
-    output[3] = E5.K3 * y1 * y3 - E5.K4 * y4;
-  },
-  tolerance: 1e-6,
-  solutionColNames: ['y1', 'y2', 'y3', 'y4'],
-};
-
-export const e5ReferencePoint = new Float64Array([
-  0.1152903278711829E-290,
-  0.8867655517642120E-22,
-  0.8854814626268838E-22,
-  0,
-]);

package/docs/media/hires.js.map

@@ -1 +0,0 @@
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package/docs/media/hires.ts

@@ -1,40 +0,0 @@
-/** High Irradiance Responses of photomorphogenesis (see https://archimede.uniba.it/~testset/problems/hires.php) */
-export const hires = {
-  name: 'HIRES',
-  arg: {name: 't', start: 0, finish: 321.8122, step: 0.01},
-  initial: [1, 0, 0, 0, 0, 0, 0, 0.0057],
-  func: (t: number, y: Float64Array, output: Float64Array) => {
-    // extract function values
-    const y1 = y[0];
-    const y2 = y[1];
-    const y3 = y[2];
-    const y4 = y[3];
-    const y5 = y[4];
-    const y6 = y[5];
-    const y7 = y[6];
-    const y8 = y[7];
-
-    // compute output
-    output[0] = -1.71 * y1 + 0.43 * y2 + 8.32 * y3 + 0.0007;
-    output[1] = 1.71 * y1 - 8.75 * y2;
-    output[2] = -10.03 * y3 + 0.43 * y4 + 0.035 * y5;
-    output[3] = 8.32 * y2 + 1.71 * y3 - 1.12 * y4;
-    output[4] = -1.745 * y5 + 0.43 * y6 + 0.43 * y7;
-    output[5] = -280 * y6 * y8 + 0.69 * y4 + 1.71 * y5 - 0.43 * y6 + 0.69 * y7;
-    output[6] = 280 * y6 * y8 - 1.81 * y7;
-    output[7] = -280 * y6 * y8 + 1.81 * y7;
-  },
-  tolerance: 1e-10,
-  solutionColNames: ['y1', 'y2', 'y3', 'y4', 'y5', 'y6', 'y7', 'y8'],
-}; // hires
-
-export const hiresReferencePoint = new Float64Array([
-  0.7371312573325668E-3,
-  0.1442485726316185E-3,
-  0.5888729740967575E-4,
-  0.1175651343283149E-2,
-  0.2386356198831331E-2,
-  0.6238968252742796E-2,
-  0.2849998395185769E-2,
-  0.2850001604814231E-2,
-]);

package/docs/media/model-updates.js.map

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package/docs/media/model-updates.ts

@@ -1,122 +0,0 @@
-/* eslint-disable max-len */
-/** 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 '../../index';
-
-/** 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!');
-}

package/docs/media/orego.js.map

@@ -1 +0,0 @@
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package/docs/media/orego.ts

@@ -1,25 +0,0 @@
-/** The OREGO model (see https://archimede.uniba.it/~testset/report/orego.pdf) */
-export const orego = {
-  name: 'OREGO',
-  arg: {name: 't', start: 0, finish: 360, step: 0.01},
-  initial: [1, 2, 3],
-  func: (t: number, y: Float64Array, output: Float64Array) => {
-    // extract function values
-    const y1 = y[0];
-    const y2 = y[1];
-    const y3 = y[2];
-
-    // compute output
-    output[0] = 77.27 * (y2 - y1 * y2 + y1 - 0.000008375 * y1 * y1 );
-    output[1] = 1 / 77.27 * (-y2 - y1 * y2 + y3);
-    output[2] = 0.161 * (y1 - y3);
-  },
-  tolerance: 1e-8,
-  solutionColNames: ['y1', 'y2', 'y3'],
-};
-
-export const oregoReferencePoint = new Float64Array([
-  1.000814870318523,
-  1228.178521549917,
-  132.0554942846706,
-]);

package/docs/media/pipeline-use.js.map

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package/docs/media/pipeline-use.ts

@@ -1,98 +0,0 @@
-/* eslint-disable max-len */
-/** This example shows how to apply pipelines and models with customized outputs.
-    This approach can be used for in-webworkers analysis of models.
-
-    Here, we consider modeling queues: https://en.wikipedia.org/wiki/M/M/c_queue
-*/
-
-import * as DGL from '../../index';
-
-/** 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!');
-}
-

package/docs/media/pollution.js.map

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package/docs/media/pollution.ts

@@ -1,133 +0,0 @@
-  /** Kintetic constants for the Pollution model */
-  enum POL {
-    K1 = 0.35,
-    K2 = 26.6,
-    K3 = 1.23e4,
-    K4 = 8.6e-4,
-    K5 = 8.2e-4,
-    K6 = 1.5e4,
-    K7 = 1.3e-4,
-    K8 = 2.4e4,
-    K9 = 1.65e4,
-    K10 = 9e3,
-    K11 = 0.022,
-    K12 = 1.2e4,
-    K13 = 1.88,
-    K14 = 1.63e4,
-    K15 = 4.8e6,
-    K16 = 3.5e-4,
-    K17 = 0.0175,
-    K18 = 1e8,
-    K19 = 4.44e11,
-    K20 = 1240,
-    K21 = 2.1,
-    K22 = 5.78,
-    K23 = 0.0474,
-    K24 = 1780,
-    K25 = 3.12,
-  }; // POL
-
-/** The chemical reaction part of the air pollution model (https://archimede.uniba.it/~testset/report/pollu.pdf) */
-export const pollution = {
-  name: 'Pollution',
-  arg: {name: 't', start: 0, finish: 60, step: 0.002},
-  initial: [0, 0.2, 0, 0.04, 0, 0, 0.1, 0.3, 0.01, 0, 0, 0, 0, 0, 0, 0, 0.007, 0, 0, 0],
-  func: (t: number, y: Float64Array, output: Float64Array) => {
-    // extract function values
-    const y1 = y[0];
-    const y2 = y[1];
-    const y3 = y[2];
-    const y4 = y[3];
-    const y5 = y[4];
-    const y6 = y[5];
-    const y7 = y[6];
-    const y8 = y[7];
-    const y9 = y[8];
-    const y10 = y[9];
-    const y11 = y[10];
-    const y12 = y[11];
-    const y13 = y[12];
-    const y14 = y[13];
-    const y15 = y[14];
-    const y16 = y[15];
-    const y17 = y[16];
-    const y18 = y[17];
-    const y19 = y[18];
-    const y20 = y[19];
-
-    // evaluate expressions
-    const r1 = POL.K1 * y1;
-    const r2 = POL.K2 * y2 * y4;
-    const r3 = POL.K3 * y5 * y2;
-    const r4 = POL.K4 * y7;
-    const r5 = POL.K5 * y7;
-    const r6 = POL.K6 * y7 * y6;
-    const r7 = POL.K7 * y9;
-    const r8 = POL.K8 * y9 * y6;
-    const r9 = POL.K9 * y11 * y2;
-    const r10 = POL.K10 * y11 * y1;
-    const r11 = POL.K11 * y13;
-    const r12 = POL.K12 * y10 * y2;
-    const r13 = POL.K13 * y14;
-    const r14 = POL.K14 * y1 * y6;
-    const r15 = POL.K15 * y3;
-    const r16 = POL.K16 * y4;
-    const r17 = POL.K17 * y4;
-    const r18 = POL.K18 * y16;
-    const r19 = POL.K19 * y16;
-    const r20 = POL.K20 * y17 * y6;
-    const r21 = POL.K21 * y19;
-    const r22 = POL.K22 * y19;
-    const r23 = POL.K23 * y1 * y4;
-    const r24 = POL.K24 * y19 * y1;
-    const r25 = POL.K25 * y20;
-
-    // compute output
-    output[0] = -(r1 + r10 + r14 + r23 + r24) + (r2 + r3 + r9 + r11 + r12 + r22 + r25);
-    output[1] = -r2 - r3 - r9 - r12 + r1 + r21;
-    output[2] = -r15 + r1 + r17 + r19 + r22;
-    output[3] = -r2 - r16 - r17 - r23 + r15;
-    output[4] = -r3 +2 * r4 + r6 +r7 +r13 + r20;
-    output[5] = -r6 - r8 - r14 - r20 + r3 + 2 * r18;
-    output[6] = -r4 - r5 - r6 + r13;
-    output[7] = r4 + r5 + r6 + r7;
-    output[8] = -r7 - r8;
-    output[9] = -r12 +r7 + r9;
-    output[10] = -r9 - r10 + r8 + r11;
-    output[11] = r9;
-    output[12] = -r11 + r10;
-    output[13] = -r13 + r12;
-    output[14] = r14;
-    output[15] = -r18 - r19 + r16;
-    output[16] = -r20;
-    output[17] = r20;
-    output[18] = -r21 - r22 - r24 + r23 + r25;
-    output[19] = -r25 + r24;
-  },
-  tolerance: 1e-6,
-  solutionColNames: ['y1', 'y2', 'y3', 'y4', 'y5', 'y6', 'y7', 'y8', 'y9', 'y10', 'y11',
-    'y12', 'y13', 'y14', 'y15', 'y16', 'y17', 'y18', 'y19', 'y20'],
-}; // pollution
-
-export const pollutionReferencePoint = new Float64Array([
-  0.05646255480022769,
-  0.1342484130422339,
-  0.4139734331099427E-8,
-  0.5523140207484359E-2,
-  0.2018977262302196E-6,
-  0.1464541863493966E-6,
-  0.7784249118997964E-1,
-  0.3245075353396018,
-  0.7494013383880406E-2,
-  0.1622293157301561E-7,
-  0.1135863833257075E-7,
-  0.2230505975721359E-2,
-  0.2087162882798630E-3,
-  0.1396921016840158E-4,
-  0.8964884856898295E-2,
-  0.4352846369330103E-17,
-  0.6899219696263405E-2,
-  0.1007803037365946E-3,
-  0.1772146513969984E-5,
-  0.5682943292316392E-4,
-]);

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