diff-grok 1.0.10 → 1.1.0

package/.claude/settings.local.json

@@ -0,0 +1,11 @@
+{
+  "permissions": {
+    "allow": [
+      "Bash(npm run build:*)",
+      "Bash(npm run lint:*)",
+      "Bash(npx jest:*)",
+      "Bash(npm test:*)",
+      "Bash(npx eslint:*)"
+    ]
+  }
+}

package/CLAUDE.md

@@ -0,0 +1,98 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+**diff-grok** is a zero-dependency TypeScript library for solving initial value problems (IVPs) for ordinary differential equations (ODEs), focused on stiff equations. It implements Rosenbrock-Wanner type numerical methods and includes a declarative model scripting system.
+
+## Build & Development Commands
+
+```bash
+npm install          # Install dev dependencies
+npm run build        # Compile TypeScript (tsc)
+npm run lint         # ESLint check: eslint "./src/**/*.ts"
+npm run lint-fix     # Auto-fix lint issues
+npm test             # Run Jest test suite
+```
+
+Run a single test file:
+```bash
+npx jest src/tests/correctness.test.ts
+```
+
+## Architecture
+
+### Module Structure
+
+- **`index.ts`** — Single entry point; re-exports everything from the four modules below.
+
+- **`src/solver-tools/`** — Core numerical solvers
+  - **Implicit methods** (for stiff ODEs): `mrt` (Modified Rosenbrock Triple), `ros3prw`, `ros34prw`
+    - Require Jacobian computation and linear system solves
+    - Use LU decomposition for solving W*k = b at each stage
+  - **Automatic methods** (stiffness-detecting): `lsoda` (variable-order Nordsieck Adams/BDF with automatic switching)
+    - Automatically switch between non-stiff (Adams) and stiff (BDF) modes
+    - Use consecutive rejection counting (Adams→BDF) and periodic trial steps (BDF→Adams)
+  - **Explicit methods** (for non-stiff ODEs): `rk3` (Bogacki-Shampine 3(2)), `rk4` (Runge-Kutta-Fehlberg 4(5)), `ab5` (Adams-Bashforth-Moulton 5), `ab4` (Adams-Bashforth-Moulton 4), `rkdp` (Dormand-Prince 5(4))
+    - Only require function evaluations (no Jacobian)
+    - Include `hMax` constraint to prevent poor interpolation
+    - `ab5` and `ab4` are multistep predictor-corrector methods bootstrapped with RKF45
+  - Key types: `ODEs` (problem definition), `Func` (RHS function signature), `SolverMethod`
+  - `solver-defs.ts` — Type definitions, adaptive step constants, Jacobian/derivative computation
+  - `lin-alg-tools.ts` — Linear algebra routines (LU decomposition, matrix ops)
+  - `callbacks/` — Flow control during solving (iteration limits, time limits)
+
+- **`src/scripting-tools/`** — Declarative model parsing and JS code generation
+  - `scripting-tools.ts` — Main parser: converts model DSL text → `IVP` object → JavaScript code
+  - Model DSL uses `#name`, `#equations`, `#argument`, `#inits`, `#parameters`, `#constants`, `#expressions` blocks
+  - Entry functions: `getIVP()` (parse model string), `getJScode()` (generate JS from IVP)
+
+- **`src/pipeline/`** — Multi-stage simulation orchestration
+  - Three pipeline creators for different model types:
+    - `BasicModelPipelineCreator` — Single-stage models
+    - `CyclicModelPipelineCreator` — Loop/dosing models (PK-PD)
+    - `UpdatesModelPipelineCreator` — Multi-stage models with state transitions
+  - `applyPipeline()` runs the full computation pipeline
+
+- **`src/worker-tools/`** — WebWorker integration for browser parallel computation
+  - `getIvp2WebWorker()` serializes IVP for worker transfer; `solveIvp()` runs in worker
+
+### Data Flow
+
+1. Define problem as `ODEs` object (programmatic) or parse model string via `getIVP()`
+2. Call solver method (`mrt`/`ros3prw`/`ros34prw`/`rk3`/`rk4`/`ab5`/`ab4`/`rkdp`/`lsoda`) → returns `Float64Array[]` (argument values + solution columns)
+3. For complex models: create pipeline via `getPipelineCreator()` → `applyPipeline()`
+
+### Performance Patterns
+
+- Uses `Float64Array` throughout for memory efficiency
+- Pre-allocated buffers to minimize GC pressure
+- RHS function signature `(t, y, output) => void` writes to pre-allocated output array
+
+## Code Style
+
+- **ESLint config**: Google style base, 2-space indent, 120 char max line length
+- **Curly braces**: `"multi-or-nest"` — single-statement bodies don't need braces, multi-line do
+- **TypeScript strict mode** enabled
+- Commit messages: `feat:`, `fix:`, `docs:` prefixes (conventional style)
+
+## Testing
+
+Tests are in `src/tests/` using Jest with ts-jest:
+- `correctness.test.ts` — Validates solver accuracy against reference solutions (threshold: MAX_MAD = 0.1)
+  - Tests all methods (implicit + explicit + automatic) against 6 problems with known exact solutions (11 methods total)
+  - 3 non-stiff problems (1D, 2D, 3D) + 3 stiff problems (1D, 2D, 3D)
+- `performance.test.ts` — Benchmarks solver speed on stiff problems (timeout: 10,000ms)
+  - Tests implicit and automatic methods (MRT, ROS3PRw, ROS34PRw, LSODA)
+  - Test problems: Robertson, HIRES, VDPOL, OREGO, E5, Pollution
+- `pipeline.test.ts` — Pipeline integration tests (3 model types)
+- Method definitions in `test-defs.ts`: `methods` map (all 11 solvers), `implicitMethods` map (stiff-capable only)
+
+## Key Types
+
+```typescript
+type Func = (t: number, y: Float64Array, output: Float64Array) => void;
+type ODEs = { name, arg: {name, start, finish, step}, initial, func: Func, tolerance, solutionColNames };
+type SolverMethod = (odes: ODEs, callback?: Callback) => Float64Array[];
+```

package/README.MD

@@ -1,15 +1,31 @@
 # Diff Grok
 
-A lightweight TypeScript library for solving initial value problem ([IVP](https://en.wikipedia.org/wiki/Initial_value_problem)) for ordinary differential equations ([ODEs](https://en.wikipedia.org/wiki/Ordinary_differential_equation)) using numerical methods. This library focuses on solving [stiff equations](https://en.wikipedia.org/wiki/Stiff_equation).
+[![DOI](https://zenodo.org/badge/635090135.svg)](https://doi.org/10.5281/zenodo.17974378)
+[![Docs-stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://datagrok-ai.github.io/diff-grok/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://github.com/datagrok-ai/diff-grok/blob/main/LICENSE)
+[![Build Status](https://github.com/datagrok-ai/diff-grok/actions/workflows/libraries.yaml/badge.svg)](https://github.com/datagrok-ai/diff-grok/actions/workflows/libraries.yaml)
+[![Run tests](https://github.com/datagrok-ai/diff-grok/actions/workflows/test.yaml/badge.svg)](https://github.com/datagrok-ai/diff-grok/actions/workflows/test.yaml)
+
+A lightweight TypeScript library for solving initial value problem ([IVP](https://en.wikipedia.org/wiki/Initial_value_problem)) for ordinary differential equations ([ODEs](https://en.wikipedia.org/wiki/Ordinary_differential_equation)) using numerical methods. The primary solver is [LSODA](https://doi.org/10.1137/0904010) — a variable-order method that automatically detects stiffness and switches between Adams (non-stiff) and BDF (stiff) formulations.
 
 ## Features
 
 * Solving both [stiff](https://en.wikipedia.org/wiki/Stiff_equation) and non-stiff equations
 * Fast computations
-* A set of Rosenbrock–Wanner-type methods:
+* Automatic stiffness-detecting method:
+  * [LSODA](https://doi.org/10.1137/0904010) - variable-order Nordsieck-based solver with automatic switching between Adams (non-stiff) and BDF (stiff) methods ([Petzold, 1983](https://doi.org/10.1137/0904010); [Hindmarsh, 1983](https://computing.llnl.gov/sites/default/files/ODEPACK_pub1_u88007.pdf)). Ported to TypeScript from the C library [liblsoda](https://github.com/sdwfrost/liblsoda)
+* Implicit methods (for stiff ODEs) - Rosenbrock–Wanner type:
   * The modified Rosenbrock triple ([MRT](https://doi.org/10.1137/S1064827594276424))
   * The [ROS3PRw](https://doi.org/10.1016/j.cam.2015.03.010) method
   * The [ROS34PRw](https://doi.org/10.1016/j.cam.2015.03.010) method
+* Explicit methods (for non-stiff ODEs):
+  * Runge-Kutta type:
+    * The Bogacki-Shampine 3(2) method ([RK3](https://en.wikipedia.org/wiki/Bogacki%E2%80%93Shampine_method))
+    * The Runge-Kutta-Fehlberg method ([RK4](https://en.wikipedia.org/wiki/Runge%E2%80%93Kutta%E2%80%93Fehlberg_method))
+    * The Dormand-Prince 5(4) method ([RKDP](https://en.wikipedia.org/wiki/Dormand%E2%80%93Prince_method))
+  * Adams-Bashforth type:
+    * The predictor-corrector method of order 4 ([AB4](https://en.wikipedia.org/wiki/Linear_multistep_method))
+    * The predictor-corrector method of order 5 ([AB5](https://en.wikipedia.org/wiki/Linear_multistep_method))
 * Scripting:
   * declarative specification of models
   * auto-generated JavaScript code
@@ -61,10 +77,23 @@ on the segment $[t_0, t_1]$ with the step $h$:
 
 1. Import `ODEs` and a desired numerical method:
 
+   Automatic method:
+   * `lsoda` - [LSODA](https://doi.org/10.1137/0904010) variable-order solver with automatic switching between Adams (non-stiff) and BDF (stiff)
+
+   Implicit methods (for stiff ODEs):
    * `mrt` - the [MRT](https://doi.org/10.1137/S1064827594276424) method
    * `ros3prw`- the [ROS3PRw](https://doi.org/10.1016/j.cam.2015.03.010) method
    * `ros34prw` - the [ROS34PRw](https://doi.org/10.1016/j.cam.2015.03.010) method
 
+   Explicit methods (for non-stiff ODEs) — Runge-Kutta type:
+   * `rk3` - the Bogacki-Shampine 3(2) method
+   * `rk4` - the Runge-Kutta-Fehlberg 4(5) method
+   * `rkdp` - the Dormand-Prince 5(4) method
+
+   Explicit methods (for non-stiff ODEs) — Adams-Bashforth type:
+   * `ab4` - the predictor-corrector method of order 4
+   * `ab5` - the predictor-corrector method of order 5
+
 2. Specify `ODEs` object that defines a problem:
 
    * `name` - name of a model
@@ -97,10 +126,10 @@ x(0) = 1 \\
 y(0) = -1
 \end{cases}$$
 
-To solve it on the segment $[0, 2]$ with the step $0.01$ using the [MRT](https://doi.org/10.1137/S1064827594276424) method with the tolerance $10^{-7}$, we start with imports:
+To solve it on the segment $[0, 2]$ with the step $0.01$ using [LSODA](https://doi.org/10.1137/0904010) with the tolerance $10^{-7}$, we start with imports:
 
 ```typescript
-import {ODEs, mrt} from 'diff-grok';
+import {ODEs, lsoda} from 'diff-grok';
 ```
 
 Next, we create
@@ -127,7 +156,7 @@ const task: ODEs = {
 Finally, we call the specified numerical method to solve `task`:
 
 ```typescript
-const solution = mrt(task);
+const solution = lsoda(task);
 ```
 
 Currently, `solution` contains:
@@ -167,38 +196,70 @@ The following [classic problems](https://archimede.uniba.it/~testset/testsetivps
   * describes a chemical reaction part of the air pollution model designed at The Dutch National Institute of Public Health and Environmental Protection
   * [pollution.ts](./src/examples/pollution.ts)
 
-The MRT, ROS3PRw and ROS34PRw methods demonstrate the following time performance (AMD Ryzen 5 5600H 3.30 GHz CPU):
+The LSODA, MRT, ROS3PRw and ROS34PRw methods demonstrate the following time performance (AMD Ryzen 5 5600H 3.30 GHz CPU):
 
-|Problem|Segment|Points|Tolerance|MRT, ms|ROS3PRw, ms|ROS34PRw, ms|
-|-|-|-|-|-|-|-|
-|[Rober](https://archimede.uniba.it/~testset/report/rober.pdf)|[0, 10E+11]|40K|1E-7|103|446|285|
-|[HIRES](https://archimede.uniba.it/~testset/report/hires.pdf)|[0, 321.8122]|32K|1E-10|222|362|215|
-|[VDPOL](https://archimede.uniba.it/~testset/report/vdpol.pdf)|[0, 2000]|20K|1E-12|963|1576|760|
-|[OREGO](https://archimede.uniba.it/~testset/report/orego.pdf)|[0, 360]|36K|1E-8|381|483|199|
-|[E5](https://archimede.uniba.it/~testset/report/e5.pdf)|[0, 10E+13]|40K|1E-6|14|17|8|
-|[Pollution](https://archimede.uniba.it/~testset/report/pollu.pdf)|[0, 60]|30K|1E-6|36|50|23|
+|Problem|Segment|Points|Tolerance|LSODA, ms|MRT, ms|ROS3PRw, ms|ROS34PRw, ms|
+|-|-|-|-|-|-|-|-|
+|[Rober](https://archimede.uniba.it/~testset/report/rober.pdf)|[0, 10E+11]|40K|1E-7|67|175|446|285|
+|[HIRES](https://archimede.uniba.it/~testset/report/hires.pdf)|[0, 321.8122]|32K|1E-10|125|122|362|215|
+|[VDPOL](https://archimede.uniba.it/~testset/report/vdpol.pdf)|[0, 2000]|20K|1E-12|268|492|1576|760|
+|[OREGO](https://archimede.uniba.it/~testset/report/orego.pdf)|[0, 360]|36K|1E-8|76|205|483|199|
+|[E5](https://archimede.uniba.it/~testset/report/e5.pdf)|[0, 10E+13]|40K|1E-6|7|6|17|8|
+|[Pollution](https://archimede.uniba.it/~testset/report/pollu.pdf)|[0, 60]|30K|1E-6|12|18|50|23|
 
 Maximum absolute deviations (MADs) from the reference solutions obtained using SciPy (Radau) are summarized in the table below:
 
-|Problem|MRT|ROS3PRw|ROS34PRw|
-|-|-|-|-|
-|[Rober](https://archimede.uniba.it/~testset/report/rober.pdf)|1.87e-8|1.88e-8|1.88e-8|
-|[HIRES](https://archimede.uniba.it/~testset/report/hires.pdf)|4.80e-11|1.05e-14|2.87e-14|
-|[VDPOL](https://archimede.uniba.it/~testset/report/vdpol.pdf)|5.12e-4|5.12e-4|5.12e-4|
-|[OREGO](https://archimede.uniba.it/~testset/report/orego.pdf)|3.05e-5|3.45e-7|2.31e-6|
-|[E5](https://archimede.uniba.it/~testset/report/e5.pdf)|1.12e-19| 1.33e-19|3.40e-17|
-|[Pollution](https://archimede.uniba.it/~testset/report/pollu.pdf)|4.06e-10|9.16e-12|1.58e-10|
+|Problem|LSODA|MRT|ROS3PRw|ROS34PRw|
+|-|-|-|-|-|
+|[Rober](https://archimede.uniba.it/~testset/report/rober.pdf)|1.87e-8|1.87e-8|1.88e-8|1.88e-8|
+|[HIRES](https://archimede.uniba.it/~testset/report/hires.pdf)|1.51e-11|4.80e-11|1.05e-14|2.87e-14|
+|[VDPOL](https://archimede.uniba.it/~testset/report/vdpol.pdf)|5.12e-4|5.12e-4|5.12e-4|5.12e-4|
+|[OREGO](https://archimede.uniba.it/~testset/report/orego.pdf)|3.84e-6|3.05e-5|3.45e-7|2.31e-6|
+|[E5](https://archimede.uniba.it/~testset/report/e5.pdf)|3.02e-19|1.12e-19| 1.33e-19|3.40e-17|
+|[Pollution](https://archimede.uniba.it/~testset/report/pollu.pdf)|1.23e-10|4.06e-10|9.16e-12|1.58e-10|
 
 Run [check-methods.ts](./src/examples/check-methods.ts) to reproduce these results (see [here](#examples) how to run scripts standalone).
 
 The following charts compare the Diff Grok and Radau solutions for the **van der Pol** system:
 
-![Pollution](images/VDPOL.png)
+![VDPOL](images/VDPOL.png)
 
 The following graphs present a comparison of the Diff Grok and Radau solutions for the **Pollution** model, highlighting a portion of the functions:
 
 ![Pollution](images/POLL.png)
 
+<details>
+<summary><strong>Gallery</strong></summary>
+
+**VDPOL**
+
+![VDPOL](images/VDP0L.png)
+
+**HIRES**
+
+![HIRES](images/HIRES.png)
+
+**E5**
+
+![E5](images/E5.png)
+
+**POLL**
+
+![POLL](images/POLL-full.png)
+
+**OREGO**
+
+![OREGO](images/OREGO.png)
+
+**Rober**
+
+![ROBER](images/ROBER.png)
+
+</details>
+
+<details>
+<summary><strong>Run benchmarks</strong></summary>
+
 Run benchmark models and find the reference solutions via the following links to the [Datagrok](https://public.datagrok.ai) platform:
 
 |Problem|Diff Grok|Radau|
@@ -212,6 +273,8 @@ Run benchmark models and find the reference solutions via the following links to
 
 In the file [print-benchmark.ts](./src/examples/print-benchmark.ts), you can find standalone functions that print the solutions of these problems to the console, as well as Python scripts for computing the solutions using SciPy.
 
+</details>
+
 ## Scripting
 
 The library provides tools for declarative specifying models defined by IVPs. This feature enables a development of "no-code" modeling tools seamlessly integrated with the [Datagrok](https://datagrok.ai) platform.
@@ -522,7 +585,7 @@ Diff Grok contains a set of examples located in the folder [src/examples](./src/
 
 |File|Features|
 |-|-|
-|[basic-use.ts](./src/examples/basic-use.ts)|Minimal "Hello World" example. Illustrates the use of the [MRT](https://doi.org/10.1137/S1064827594276424) method.|
+|[basic-use.ts](./src/examples/basic-use.ts)|Minimal "Hello World" example. Illustrates the use of the [LSODA](https://doi.org/10.1137/0904010) method.|
 |[check-methods.ts](./src/examples/check-methods.ts)| Checks the [performance](#performance) of numerical methods.|
 |[corr-probs.ts](./src/examples/corr-probs.ts)|Solves a set of problems with exact solutions and evaluate the deviation.|
 |[cyclic-model.ts](./src/examples/cyclic-model.ts)| Considers pharmacokinetic-pharmacodynamic (PK-PD) simulation and shows how to apply pipelines and cyclic models.|
@@ -530,6 +593,9 @@ Diff Grok contains a set of examples located in the folder [src/examples](./src/
 |[pipeline-use.ts](./src/examples/pipeline-use.ts)|Considers modeling queues and shows shows how to apply pipelines and models with customized outputs.|
 |[scripting.ts](./src/examples/scripting.ts)|Shows how to generate JS-script from Diff Grok model.|
 
+<details>
+<summary><strong>Run examples</strong></summary>
+
 To run examples standalone:
 
 1. Install TypeScript locally. If your project does not already include TypeScript:
@@ -567,6 +633,16 @@ tsc src/examples/basic-use.ts
 node src/examples/basic-use.js
 ```
 
+</details>
+
+## References
+
+* L. Petzold, "Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations," *SIAM J. Sci. Stat. Comput.*, 4(1), 136–148, 1983. [doi:10.1137/0904010](https://doi.org/10.1137/0904010)
+* A. C. Hindmarsh, "ODEPACK, A Systematized Collection of ODE Solvers," *Scientific Computing*, R. S. Stepleman et al. (eds.), North-Holland, Amsterdam, pp. 55–64, 1983. [link](https://computing.llnl.gov/sites/default/files/ODEPACK_pub1_u88007.pdf)
+* The LSODA solver is ported to TypeScript from the C library [liblsoda](https://github.com/sdwfrost/liblsoda)
+* T. Rang and L. Angermann, "New Rosenbrock W-Methods of Order 3 for Partial Differential Algebraic Equations of Index 1," *BIT Numer. Math.*, 45, 761–787, 2005. [doi:10.1007/s10543-005-0035-y](https://doi.org/10.1016/j.cam.2015.03.010)
+* E. Hairer and G. Wanner, *Solving Ordinary Differential Equations II: Stiff and Differential-Algebraic Problems*, Springer, 1996. [doi:10.1137/S1064827594276424](https://doi.org/10.1137/S1064827594276424)
+
 ## Contributing
 
 We welcome contributions of all kinds - bug reports, feature requests, documentation updates, and pull requests.

package/index.js

@@ -1,4 +1,4 @@
-export { mrt, ros3prw, ros34prw, CallbackAction, DEFAULT_OPTIONS, getCallback, Callback, IterCheckerCallback, TimeCheckerCallback } from './src/solver-tools';
+export { mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda, CallbackAction, DEFAULT_OPTIONS, getCallback, Callback, IterCheckerCallback, TimeCheckerCallback } from './src/solver-tools';
 export { perfProbs, corrProbs, refPoints, printRobertson, printHires, printOrego, printE5, printVdpol, printPollution } from './src/examples';
 export { DF_NAME, CONTROL_EXPR, MAX_LINE_CHART, getIVP, getScriptLines, getScriptParams, getJScode, SCRIPTING, BRACE_OPEN, BRACE_CLOSE, BRACKET_OPEN, BRACKET_CLOSE, ANNOT_SEPAR, CONTROL_SEP, STAGE_COL_NAME, ARG_INPUT_KEYS, DEFAULT_SOLVER_SETTINGS, ModelError, getFunc4worker } from './src/scripting-tools';
 export { getIvp2WebWorker, solveIvp } from './src/worker-tools';

package/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAa,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,cAAc,EAAE,eAAe,EACzE,WAAW,EAAgB,QAAQ,EAAE,mBAAmB,EAAE,mBAAmB,EAAC,MAAM,oBAAoB,CAAC;AAE3G,OAAO,EAAC,SAAS,EAAE,SAAS,EAAe,SAAS,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,EAC1F,OAAO,EAAE,UAAU,EAAE,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAE7D,OAAO,EAAC,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,EAAE,cAAc,EAAE,eAAe,EAAE,SAAS,EAC3E,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE,WAAW,EAChG,WAAW,EAAE,cAAc,EAAE,cAAc,EAAE,uBAAuB,EAAE,UAAU,EAChF,cAAc,EAA4B,MAAM,uBAAuB,CAAC;AAE1E,OAAO,EAAgB,gBAAgB,EAAE,QAAQ,EAAC,MAAM,oBAAoB,CAAC;AAE7E,OAAO,EAAoB,aAAa,EAAE,aAAa,EAAE,cAAc,EAAE,eAAe,EACtF,yBAAyB,EAAE,cAAc,EAAE,kBAAkB,EAAE,0BAA0B,EACzF,2BAA2B,EAAC,MAAM,gBAAgB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAa,GAAG,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,KAAK,EACzE,cAAc,EAAE,eAAe,EAC/B,WAAW,EAAgB,QAAQ,EAAE,mBAAmB,EAAE,mBAAmB,EAAC,MAAM,oBAAoB,CAAC;AAE3G,OAAO,EAAC,SAAS,EAAE,SAAS,EAAe,SAAS,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,EAC1F,OAAO,EAAE,UAAU,EAAE,cAAc,EAAC,MAAM,gBAAgB,CAAC;AAE7D,OAAO,EAAC,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,EAAE,cAAc,EAAE,eAAe,EAAE,SAAS,EAC3E,SAAS,EAAE,UAAU,EAAE,WAAW,EAAE,YAAY,EAAE,aAAa,EAAE,WAAW,EAChG,WAAW,EAAE,cAAc,EAAE,cAAc,EAAE,uBAAuB,EAAE,UAAU,EAChF,cAAc,EAA4B,MAAM,uBAAuB,CAAC;AAE1E,OAAO,EAAgB,gBAAgB,EAAE,QAAQ,EAAC,MAAM,oBAAoB,CAAC;AAE7E,OAAO,EAAoB,aAAa,EAAE,aAAa,EAAE,cAAc,EAAE,eAAe,EACtF,yBAAyB,EAAE,cAAc,EAAE,kBAAkB,EAAE,0BAA0B,EACzF,2BAA2B,EAAC,MAAM,gBAAgB,CAAC"}

package/index.ts

@@ -1,4 +1,5 @@
-export {Func, ODEs, mrt, ros3prw, ros34prw, CallbackAction, DEFAULT_OPTIONS, SolverOptions,
+export {Func, ODEs, mrt, ros3prw, ros34prw, rk4, ab5, ab4, rkdp, rk3, lsoda,
+  CallbackAction, DEFAULT_OPTIONS, SolverOptions,
   getCallback, SolverMethod, Callback, IterCheckerCallback, TimeCheckerCallback} from './src/solver-tools';
 
 export {perfProbs, corrProbs, CorrProblem, refPoints, printRobertson, printHires, printOrego,

package/jest.config.js

@@ -2,6 +2,7 @@
 module.exports = {
   preset: 'ts-jest',
   testEnvironment: 'node',
+  moduleFileExtensions: ['ts', 'tsx', 'js', 'jsx', 'json', 'node'],
   roots: ['<rootDir>/src'],
   testMatch: ['**/__tests__/**/*.ts', '**/?(*.)+(spec|test).ts'],
   collectCoverageFrom: [

package/package.json

@@ -8,7 +8,7 @@
     "access": "public"
   },
   "license": "MIT",
-  "version": "1.0.10",
+  "version": "1.1.0",
   "description": "Tools for solving initial value problem for ordinary differential equations",
   "keywords": [
     "initial value problem",

package/src/examples/bioreactor.js

@@ -0,0 +1,125 @@
+/** Example. Solve the following initial value problem
+
+      dx / dt = x + y - t
+      dy / dt = x * y + t
+      x(0) = 1
+      y(0) = -1
+
+    on [0, 2] with the step 0.01.
+ */
+import { lsoda } from '../../index';
+// constants
+const VLinit = 7.2;
+const VTV = 10;
+const speed = 400;
+const diam = 6;
+const power = 2.1;
+const pH = 7.4;
+const k1red = 0.05604;
+const k1ox = 0.0108;
+const k2Fd = 1.35;
+const k2Fa = 110400000;
+const k2Kd = 0.04038;
+const k2Ka = 120000000;
+const k3FKa = 181200000;
+const k3FKd = 0.01188;
+const k4ox = 0.0108;
+const k4red = 0.05604;
+const ktox = 0.005;
+const krcyst = 0;
+const pO2sat = 100;
+const pKa2MEA = 8.18;
+const H = 1.072069378;
+const R = 0.082;
+const _t0 = 0;
+const _t1 = 1000;
+const _h = 1;
+const FFox = 0.2;
+const KKox = 0.2;
+const FFred = 0.1;
+const KKred = 0.1;
+const Ffree = 0;
+const Kfree = 0;
+const FKred = 0;
+const FKox = 0;
+const MEAthiol = 15;
+const CO2 = 0.12;
+const yO2P = 0.209;
+const CYST = 0;
+const VL = 7.2;
+const qin = 1;
+const yO2in = 0.21;
+const T = 300;
+const P = 1;
+const switchTime = 135;
+// the problem definition
+const task = {
+    name: 'Bioreactor',
+    arg: { name: 't', start: _t0, finish: _t1, step: _h },
+    initial: [FFox, KKox, FFred, KKred, Ffree, Kfree, FKred, FKox, MEAthiol, CO2, yO2P, CYST, VL],
+    func: (t, _y, _output) => {
+        // extract function values
+        const FFox = _y[0];
+        const KKox = _y[1];
+        const FFred = _y[2];
+        const KKred = _y[3];
+        const Ffree = _y[4];
+        const Kfree = _y[5];
+        const FKred = _y[6];
+        const FKox = _y[7];
+        const MEAthiol = _y[8];
+        const CO2 = _y[9];
+        const yO2P = _y[10];
+        const CYST = _y[11];
+        const VL = _y[12];
+        // evaluate expressions
+        const KF = pow(VL, -0.65) * 0.065 * pow(Math.pow(speed, 3) * Math.pow(diam, 5) * power / 2.16e12, 0.361);
+        const MA = MEAthiol * pow(10, pH - pKa2MEA);
+        const qout = qin - KF * (yO2P * H - CO2) * VL * R * T / (P * 1000);
+        const OTR = KF * (yO2P * H - CO2);
+        const Fin = t < switchTime ? 0 : 0.025;
+        const Fper = t < switchTime ? 0.025 : Fin;
+        const E0 = VLinit / VL;
+        const E1 = Math.pow((MA * E0), 2);
+        const E11 = k1red * FFox * E0 * E1;
+        const E12 = k1ox * FFred * E0;
+        const E31 = k2Fd * FFred * E0;
+        const E32 = k2Fa * Math.pow((Ffree * E0), 2) * E1;
+        const E21 = k1red * KKox * E0 * E1;
+        const E22 = k1ox * KKred * E0;
+        const E41 = k2Kd * KKred * E0;
+        const E42 = k2Ka * Math.pow((Kfree * E0), 2) * E1;
+        const E51 = k3FKa * Ffree * E0 * Kfree * E0;
+        const E52 = k3FKd * FKred * E0;
+        const E61 = k4ox * FKred * E0 * Math.pow((CYST * E0), 2);
+        const E62 = k4red * FKox * E0 * E1;
+        const E70 = E0 * CO2;
+        const E71 = Math.pow((MEAthiol * E0), 2);
+        const E72 = (E70 >= 0) ? sqrt(E70) : 0;
+        // compute output
+        _output[0] = -E11 + E12;
+        _output[1] = -E21 + E22;
+        _output[2] = E11 - E12 - E31 + E32;
+        _output[3] = E21 - E22 - E41 + E42;
+        _output[4] = 2 * (E31 - E32) - E51 + E52;
+        _output[5] = 2 * (E41 - E42) - E51 + E52;
+        _output[6] = E51 - E52 - E61 + E62;
+        _output[7] = E61 - E62;
+        _output[8] = 2 * (-E11 + E12 - E21 + E22 + E31 + E41 - E32 - E42 - E62 - ktox * E71 * E72) -
+            (MEAthiol + MA) * (Fin + Fper) / VL;
+        _output[9] = (Fin * pO2sat * 0.0022 - 2 * Fper * CO2) / VL + OTR - 0.5 * ktox * E71 * E72;
+        _output[10] = -OTR * (VL / (VTV - VL)) * R * T * P + yO2in * qin - yO2P * qout;
+        _output[11] = ktox * E71 * E72 - krcyst * CYST * E0 - (Fin + Fper) * CYST / VL;
+        _output[12] = Fin - Fper;
+    },
+    tolerance: 0.00005,
+    solutionColNames: ['FFox', 'KKox', 'FFred', 'KKred', 'Ffree', 'Kfree', 'FKred',
+        'FKox', 'MEAthiol', 'CO2', 'yO2P', 'CYST', 'VL'],
+};
+// used Math-functions
+const pow = (x, y) => Math.pow(x, y);
+const tan = (x) => Math.tan(x);
+const sqrt = (x) => Math.sqrt(x);
+const exp = (x) => Math.exp(x);
+const solution = lsoda(task);
+//# sourceMappingURL=bioreactor.js.map

package/src/examples/bioreactor.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bioreactor.js","sourceRoot":"","sources":["bioreactor.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAO,KAAK,EAAM,MAAM,aAAa,CAAC;AAE7C,YAAY;AACZ,MAAM,MAAM,GAAG,GAAG,CAAC;AACnB,MAAM,GAAG,GAAG,EAAE,CAAC;AACf,MAAM,KAAK,GAAG,GAAG,CAAC;AAClB,MAAM,IAAI,GAAG,CAAC,CAAC;AACf,MAAM,KAAK,GAAG,GAAG,CAAC;AAClB,MAAM,EAAE,GAAG,GAAG,CAAC;AACf,MAAM,KAAK,GAAG,OAAO,CAAC;AACtB,MAAM,IAAI,GAAG,MAAM,CAAC;AACpB,MAAM,IAAI,GAAG,IAAI,CAAC;AAClB,MAAM,IAAI,GAAG,SAAS,CAAC;AACvB,MAAM,IAAI,GAAG,OAAO,CAAC;AACrB,MAAM,IAAI,GAAG,SAAS,CAAC;AACvB,MAAM,KAAK,GAAG,SAAS,CAAC;AACxB,MAAM,KAAK,GAAG,OAAO,CAAC;AACtB,MAAM,IAAI,GAAG,MAAM,CAAC;AACpB,MAAM,KAAK,GAAG,OAAO,CAAC;AACtB,MAAM,IAAI,GAAG,KAAK,CAAC;AACnB,MAAM,MAAM,GAAG,CAAC,CAAC;AACjB,MAAM,MAAM,GAAG,GAAG,CAAC;AACnB,MAAM,OAAO,GAAG,IAAI,CAAC;AACrB,MAAM,CAAC,GAAG,WAAW,CAAC;AACtB,MAAM,CAAC,GAAG,KAAK,CAAC;AAEhB,MAAM,GAAG,GAAG,CAAC,CAAC;AACd,MAAM,GAAG,GAAG,IAAI,CAAC;AACjB,MAAM,EAAE,GAAG,CAAC,CAAC;AACb,MAAM,IAAI,GAAG,GAAG,CAAC;AACjB,MAAM,IAAI,GAAG,GAAG,CAAC;AACjB,MAAM,KAAK,GAAG,GAAG,CAAC;AAClB,MAAM,KAAK,GAAG,GAAG,CAAC;AAClB,MAAM,KAAK,GAAG,CAAC,CAAC;AAChB,MAAM,KAAK,GAAG,CAAC,CAAC;AAChB,MAAM,KAAK,GAAG,CAAC,CAAC;AAChB,MAAM,IAAI,GAAG,CAAC,CAAC;AACf,MAAM,QAAQ,GAAG,EAAE,CAAC;AACpB,MAAM,GAAG,GAAG,IAAI,CAAC;AACjB,MAAM,IAAI,GAAG,KAAK,CAAC;AACnB,MAAM,IAAI,GAAG,CAAC,CAAC;AACf,MAAM,EAAE,GAAG,GAAG,CAAC;AACf,MAAM,GAAG,GAAG,CAAC,CAAC;AACd,MAAM,KAAK,GAAG,IAAI,CAAC;AACnB,MAAM,CAAC,GAAG,GAAG,CAAC;AACd,MAAM,CAAC,GAAG,CAAC,CAAC;AACZ,MAAM,UAAU,GAAG,GAAG,CAAC;AAEvB,yBAAyB;AACzB,MAAM,IAAI,GAAG;IACX,IAAI,EAAE,YAAY;IAClB,GAAG,EAAE,EAAC,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,EAAE,EAAC;IACnD,OAAO,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;IAC7F,IAAI,EAAE,CAAC,CAAS,EAAE,EAAgB,EAAE,OAAqB,EAAE,EAAE;QAC3D,0BAA0B;QAC1B,MAAM,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACnB,MAAM,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACnB,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACpB,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACpB,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACpB,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACpB,MAAM,KAAK,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACpB,MAAM,IAAI,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACnB,MAAM,QAAQ,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;QAClB,MAAM,IAAI,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC;QACpB,MAAM,IAAI,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC;QACpB,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAC;QAElB,uBAAuB;QACvB,MAAM,EAAE,GAAG,GAAG,CAAC,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,KAAK,GAAG,GAAG,CAAC,SAAA,KAAK,EAAE,CAAC,CAAA,GAAG,SAAA,IAAI,EAAE,CAAC,CAAA,GAAG,KAAK,GAAG,OAAO,EAAE,KAAK,CAAC,CAAC;QACrF,MAAM,EAAE,GAAG,QAAQ,GAAG,GAAG,CAAC,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC,CAAC;QAC5C,MAAM,IAAI,GAAG,GAAG,GAAG,EAAE,GAAG,CAAC,IAAI,GAAG,CAAC,GAAG,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC;QACnE,MAAM,GAAG,GAAG,EAAE,GAAG,CAAC,IAAI,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC;QAClC,MAAM,GAAG,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;QACvC,MAAM,IAAI,GAAG,CAAC,GAAG,UAAU,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC;QAC1C,MAAM,EAAE,GAAG,MAAM,GAAG,EAAE,CAAC;QACvB,MAAM,EAAE,GAAG,SAAA,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,CAAC;QACxB,MAAM,GAAG,GAAG,KAAK,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,CAAC;QACnC,MAAM,GAAG,GAAG,IAAI,GAAG,KAAK,GAAG,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,IAAI,GAAG,KAAK,GAAG,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,IAAI,GAAG,SAAA,CAAC,KAAK,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,GAAG,EAAE,CAAC;QACxC,MAAM,GAAG,GAAG,KAAK,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,CAAC;QACnC,MAAM,GAAG,GAAG,IAAI,GAAG,KAAK,GAAG,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,IAAI,GAAG,KAAK,GAAG,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,IAAI,GAAG,SAAA,CAAC,KAAK,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,GAAG,EAAE,CAAC;QACxC,MAAM,GAAG,GAAG,KAAK,GAAG,KAAK,GAAG,EAAE,GAAG,KAAK,GAAG,EAAE,CAAC;QAC5C,MAAM,GAAG,GAAG,KAAK,GAAG,KAAK,GAAG,EAAE,CAAC;QAC/B,MAAM,GAAG,GAAG,IAAI,GAAG,KAAK,GAAG,EAAE,GAAG,SAAA,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,CAAC;QAC/C,MAAM,GAAG,GAAG,KAAK,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,CAAC;QACnC,MAAM,GAAG,GAAG,EAAE,GAAG,GAAG,CAAC;QACrB,MAAM,GAAG,GAAG,SAAA,CAAC,QAAQ,GAAG,EAAE,CAAC,EAAE,CAAC,CAAA,CAAC;QAC/B,MAAM,GAAG,GAAG,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAEvC,iBAAiB;QACjB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC;QACxB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC;QACxB,OAAO,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;QACnC,OAAO,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;QACnC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC,GAAG,GAAG,GAAG,GAAG,CAAC;QACzC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,CAAC,GAAG,GAAG,GAAG,GAAG,CAAC;QACzC,OAAO,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;QACnC,OAAO,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,GAAG,CAAC;QACvB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,IAAI,GAAG,GAAG,GAAG,GAAG,CAAC;YACxF,CAAC,QAAQ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QACtC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,GAAG,MAAM,GAAG,MAAM,GAAG,CAAC,GAAG,IAAI,GAAG,GAAG,CAAC,GAAG,EAAE,GAAG,GAAG,GAAG,GAAG,GAAG,IAAI,GAAG,GAAG,GAAG,GAAG,CAAC;QAC1F,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,GAAG,CAAC,EAAE,GAAG,CAAC,GAAG,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,KAAK,GAAG,GAAG,GAAG,IAAI,GAAG,IAAI,CAAC;QAC/E,OAAO,CAAC,EAAE,CAAC,GAAG,IAAI,GAAG,GAAG,GAAG,GAAG,GAAG,MAAM,GAAG,IAAI,GAAG,EAAE,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;QAC/E,OAAO,CAAC,EAAE,CAAC,GAAG,GAAG,GAAG,IAAI,CAAC;IAC3B,CAAC;IACD,SAAS,EAAE,OAAO;IAClB,gBAAgB,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO,EAAE,OAAO;QAC5E,MAAM,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,IAAI,CAAC;CACnD,CAAC;AAEF,sBAAsB;AACtB,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;AACrD,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;AACvC,MAAM,IAAI,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AACzC,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;AAEvC,MAAM,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC"}

package/src/examples/bioreactor.ts

@@ -0,0 +1,132 @@
+/** Example. Solve the following initial value problem
+
+      dx / dt = x + y - t
+      dy / dt = x * y + t
+      x(0) = 1
+      y(0) = -1
+
+    on [0, 2] with the step 0.01.
+ */
+
+import {ODEs, lsoda, mrt} from '../../index';
+
+// constants
+const VLinit = 7.2;
+const VTV = 10;
+const speed = 400;
+const diam = 6;
+const power = 2.1;
+const pH = 7.4;
+const k1red = 0.05604;
+const k1ox = 0.0108;
+const k2Fd = 1.35;
+const k2Fa = 110400000;
+const k2Kd = 0.04038;
+const k2Ka = 120000000;
+const k3FKa = 181200000;
+const k3FKd = 0.01188;
+const k4ox = 0.0108;
+const k4red = 0.05604;
+const ktox = 0.005;
+const krcyst = 0;
+const pO2sat = 100;
+const pKa2MEA = 8.18;
+const H = 1.072069378;
+const R = 0.082;
+
+const _t0 = 0;
+const _t1 = 1000;
+const _h = 1;
+const FFox = 0.2;
+const KKox = 0.2;
+const FFred = 0.1;
+const KKred = 0.1;
+const Ffree = 0;
+const Kfree = 0;
+const FKred = 0;
+const FKox = 0;
+const MEAthiol = 15;
+const CO2 = 0.12;
+const yO2P = 0.209;
+const CYST = 0;
+const VL = 7.2;
+const qin = 1;
+const yO2in = 0.21;
+const T = 300;
+const P = 1;
+const switchTime = 135;
+
+// the problem definition
+const task = {
+  name: 'Bioreactor',
+  arg: {name: 't', start: _t0, finish: _t1, step: _h},
+  initial: [FFox, KKox, FFred, KKred, Ffree, Kfree, FKred, FKox, MEAthiol, CO2, yO2P, CYST, VL],
+  func: (t: number, _y: Float64Array, _output: Float64Array) => {
+    // extract function values
+    const FFox = _y[0];
+    const KKox = _y[1];
+    const FFred = _y[2];
+    const KKred = _y[3];
+    const Ffree = _y[4];
+    const Kfree = _y[5];
+    const FKred = _y[6];
+    const FKox = _y[7];
+    const MEAthiol = _y[8];
+    const CO2 = _y[9];
+    const yO2P = _y[10];
+    const CYST = _y[11];
+    const VL = _y[12];
+
+    // evaluate expressions
+    const KF = pow(VL, -0.65) * 0.065 * pow(speed**3 * diam**5 * power / 2.16e12, 0.361);
+    const MA = MEAthiol * pow(10, pH - pKa2MEA);
+    const qout = qin - KF * (yO2P * H - CO2) * VL * R * T / (P * 1000);
+    const OTR = KF * (yO2P * H - CO2);
+    const Fin = t < switchTime ? 0 : 0.025;
+    const Fper = t < switchTime ? 0.025 : Fin;
+    const E0 = VLinit / VL;
+    const E1 = (MA * E0)**2;
+    const E11 = k1red * FFox * E0 * E1;
+    const E12 = k1ox * FFred * E0;
+    const E31 = k2Fd * FFred * E0;
+    const E32 = k2Fa * (Ffree * E0)**2 * E1;
+    const E21 = k1red * KKox * E0 * E1;
+    const E22 = k1ox * KKred * E0;
+    const E41 = k2Kd * KKred * E0;
+    const E42 = k2Ka * (Kfree * E0)**2 * E1;
+    const E51 = k3FKa * Ffree * E0 * Kfree * E0;
+    const E52 = k3FKd * FKred * E0;
+    const E61 = k4ox * FKred * E0 * (CYST * E0)**2;
+    const E62 = k4red * FKox * E0 * E1;
+    const E70 = E0 * CO2;
+    const E71 = (MEAthiol * E0)**2;
+    const E72 = (E70 >= 0) ? sqrt(E70) : 0;
+
+    // compute output
+    _output[0] = -E11 + E12;
+    _output[1] = -E21 + E22;
+    _output[2] = E11 - E12 - E31 + E32;
+    _output[3] = E21 - E22 - E41 + E42;
+    _output[4] = 2 * (E31 - E32) - E51 + E52;
+    _output[5] = 2 * (E41 - E42) - E51 + E52;
+    _output[6] = E51 - E52 - E61 + E62;
+    _output[7] = E61 - E62;
+    _output[8] = 2 * (-E11 + E12 - E21 + E22 + E31 + E41 - E32 - E42 - E62 - ktox * E71 * E72) -
+      (MEAthiol + MA) * (Fin + Fper) / VL;
+    _output[9] = (Fin * pO2sat * 0.0022 - 2 * Fper * CO2) / VL + OTR - 0.5 * ktox * E71 * E72;
+    _output[10] = -OTR * (VL / (VTV - VL)) * R * T * P + yO2in * qin - yO2P * qout;
+    _output[11] = ktox * E71 * E72 - krcyst * CYST * E0 - (Fin + Fper) * CYST / VL;
+    _output[12] = Fin - Fper;
+  },
+  tolerance: 0.00005,
+  solutionColNames: ['FFox', 'KKox', 'FFred', 'KKred', 'Ffree', 'Kfree', 'FKred',
+    'FKox', 'MEAthiol', 'CO2', 'yO2P', 'CYST', 'VL'],
+};
+
+// used Math-functions
+const pow = (x: number, y: number) => Math.pow(x, y);
+const tan = (x: number) => Math.tan(x);
+const sqrt = (x: number) => Math.sqrt(x);
+const exp = (x: number) => Math.exp(x);
+
+const solution = lsoda(task);