MoonBit Marine Biogeochemical Box Model Engine: Configurable NPZD, oxygen depletion, and carbon cycle simulation framework.

marine

biogeochemistry

box-model

carbon-cycle

npzd

simulation

moon add lqlnvj/moonbit-biogeochem@0.1.1

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Author

lqlnvj

Version

0.1.1

License

Apache-2.0

Repository

github.com/lqlnvj/moonbit-biogeochem

Last updated

4 hours ago

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README

#MoonBit Marine Biogeochemical Box Model Engine

moonbit-biogeochem is a configurable marine biogeochemical simulation engine written in MoonBit. It provides reusable state and forcing types, reaction and carbonate chemistry utilities, ODE solvers, ecological model families, diagnostics, grid extensions, data-assimilation interfaces, and report exporters.

#Capabilities

Ecological and geochemical models: NPZD, NPZD+D, oxygen depletion, carbonate chemistry, iron limitation, diatom–silicon competition, and microbial-loop dynamics.
Numerical integration: Forward Euler, implicit Euler, trapezoidal predictor–corrector, Adams–Bashforth 2/3, RK4, and adaptive RKF45.
Diagnostics: trajectory validation, time-series statistics, threshold crossings, duration metrics, scenario validation, Redfield audits, and water-column stability checks.
Sensitivity and uncertainty analysis: parameter sweeps, finite-difference sensitivity, Sobol indices, Monte Carlo sampling, and carbon-pump metrics.
Extensions: one-dimensional vertical water columns, advection–diffusion–reaction stepping, sediment diagenesis, nudging, EnKF interfaces, and declarative builders.
Export and presentation: CSV, JSON, Markdown, JUnit XML, ASCII plots, heatmaps, and Mermaid diagrams.

#Architecture

flowchart TD
    A[src/types] --> B[src/core]
    B --> C[src/solver]
    C --> D[src/models]
    D --> E[src/analysis]
    D --> F[src/extensions]
    D & E & F --> G[src/exporter]
    G --> H[cmd/main]

#Repository layout

Path	Purpose
src/types	Physical units, state vectors, parameters, light attenuation, and environmental forcing.
src/core	Reaction kinetics, Redfield stoichiometry, gas transfer, and seawater thermodynamics.
src/solver	ODE solvers, adaptive stepping, and trajectory integrity validation.
src/models	Ecological, oxygen, carbonate, iron, silicon, and microbial-loop model families.
src/analysis	Sweeps, sensitivity, uncertainty quantification, trajectory metrics, and scenario checks.
src/extensions	Water-column transport, sediment processes, assimilation interfaces, and builders.
src/exporter	Serializers, reports, plots, and diagram exporters.
cmd/main	Interactive demonstration of the main simulation workflow.
cmd/benchmark	Deterministic native workloads used for repeatable performance measurements.
scripts	Source accounting and benchmark runners.

#Quick start

Install the current MoonBit toolchain with the official installer, then run:

moon check
moon test
moon run cmd/main --target native --release

#Library example

let model = @models.create_npzd_model(15.0, 0.5, 0.1, 0.2)
let env_fn = fn(t) { @types.EnvironmentForcing::seasonal_forcing(t, 45.0) }
let trajectory = @solver.solve_rk4(model, 30.0, 0.5, env_fn).unwrap()
let series = trajectory.get_time_series("P").unwrap()
let plot = @exporter.render_ascii_plot(series, "Phytoplankton (mmol N/m^3)", 30, 6)
println(plot)

#Validation and diagnostics

Trajectories, model scenarios, and vertical columns expose checked entry points for dimensions, finite values, monotonic time, physical bounds, and transport stability. These checks are useful at data-ingestion boundaries and before expensive simulations.

let validation = trajectory.validate()
let summary = @analysis.summarize_trajectory(trajectory).unwrap()
println(summary.duration.to_string())

#Benchmarking and source accounting

The benchmark is deterministic and runs native NPZD and coupled-carbon workloads. Use the PowerShell helper to collect repeated wall-clock measurements and retain the raw output:

pwsh -NoProfile -File scripts/run-benchmark.ps1 -Runs 5

The checked-in benchmark report records the toolchain, platform, workload outputs, and five-run timing summary. It is a reference measurement rather than a cross-machine performance guarantee.

Source accounting is reproducible and excludes _build artifacts. Production and test files are counted separately:

pwsh -NoProfile -File scripts/measure-source.ps1

At this revision the command reports 5,330 production MoonBit lines and 808 test lines. The command should be used for later revisions instead of relying on a stale badge or manual estimate.

#Development and testing

MoonBit package interfaces are generated by the toolchain; do not edit pkg.generated.mbti files by hand.

moon fmt
moon info
moon check --target all --deny-warn
moon test --target all --deny-warn
moon fmt --check

Coverage can be collected locally with:

moon test --enable-coverage
moon coverage report -f summary
moon coverage analyze

Pull requests are checked on Ubuntu, macOS, and Windows. CI installs MoonBit through the official stable-channel installers, checks all supported targets, runs the full test suite, and verifies generated interface information.

#Contributing

Keep each package focused, place black-box tests in files ending with _test.mbt, and use _wbtest.mbt for white-box tests. Format changes with moon fmt, refresh interfaces with moon info, and include a focused regression test for behavior changes. See CONTRIBUTING.md for repository conventions.

#License

This project is licensed under the Apache License 2.0. See LICENSE for details.

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