Valenx

A native, open-source desktop simulation suite — written in Rust, no browser, no subscription, no vendor lock-in. One app spanning: engineering — aerospace (launch-vehicle ascent, orbital mechanics, re-entry), CFD, FEA, electromagnetics, multibody dynamics, thermal, battery, and a parametric CAD/CAM suite; chemistry & materials — molecular dynamics, quantum chemistry, reaction dynamics, and cheminformatics; and computational biology — genomics, sequence alignment, phylogenetics, population genetics, protein structure & design, RNA/mRNA design, CRISPR gene-editing, cryo-EM, and systems biology; and neuroengineering — neural-interface / BCI stimulation (extracellular fields, Hodgkin–Huxley cable models, bioheat). Native Rust solvers plus 141 open-source tool integrations.

Status: 0.1.0-alpha.1 — pre-release. The workflow loop is usable end-to-end (load project, click a case, Prepare, Run, inspect results) but real-world testing is just beginning. Expect sharp edges; please file issues.

What it does

Valenx unifies a stack of open-source simulation tools behind one Rust-native desktop shell so you can:

• Run CFD / FEA / EM / battery / multibody simulations from one UI (OpenFOAM, SU2, CalculiX, Code_Aster, Elmer, OpenRadioss, openEMS, Meep, PyBaMM, MuJoCo, preCICE, …)
• Drive molecular dynamics (GROMACS, LAMMPS, OpenMM, NAMD, AmberTools, HOOMD-blue)
• Predict protein structure (AlphaFold 2/3, ESMFold, OpenFold, RoseTTAFold, OmegaFold, ColabFold)
• Design proteins (RFdiffusion, ProteinMPNN, ESM-IF, Chroma, RFantibody, ESM3)
• Design CRISPR guides + analyze edit outcomes (CHOPCHOP, CRISPOR, Cas-OFFinder, inDelphi, FORECasT, BE-Designer, PrimeDesign)
• Fold RNA + design mRNA vaccines (ViennaRNA, NUPACK, mfold, LinearFold, DNA Chisel, LinearDesign)
• Reconstruct cryo-EM volumes (RELION, EMAN2, CTFFIND)
• Pipe everything through reproducible workflows (Snakemake, Nextflow, Cromwell, cwltool)

The idea: native Rust engines for the core science, one app, your laptop — plus optional adapters to 141 external tools when you want them. No cloud, no API keys, your data never leaves your machine.

Native engines — included, nothing to install

A large part of Valenx runs without any external tool — native in-house Rust solvers ship inside the app and work out of the box:

• Computational biology — a 14-panel Genetics Workbench: sequence analysis, pairwise + multiple alignment, phylogenetics, population genetics, RNA secondary structure, RNA/mRNA design, molecular dynamics, cheminformatics, macromolecular structure (PDB/mmCIF, DSSP, superposition), quantum chemistry (Hartree–Fock / MP2 / Kohn–Sham DFT), genomics, systems biology, docking, and CRISPR / gene-edit design — all native (valenx-bioseq, valenx-align, valenx-phylo, valenx-rnastruct, valenx-md, valenx-qchem, …).
• Aerospace / GN&C — a launch-vehicle + orbital engine: multi-stage gravity-turn ascent to orbit, 3-D orbital mechanics with J2 oblateness, a 6-DOF rigid-body attitude core, and impulsive maneuvers (Hohmann, bi-elliptic, plane-change, Lambert rendezvous) — validated against textbook/analytic results (valenx-astro; see Validation).
• Fluids & structures — a 3-D external-aerodynamics wind-tunnel workbench and 2-D CFD with Menter k-ω SST turbulence, plus finite-element analysis (8 native solvers: static, modal, thermal, nonlinear, plasticity, beam, buckling, transient dynamics).
• CAD / CAM / CAE — a geometry kernel (primitives, booleans, fillets, NURBS surfaces), a parametric feature-tree history, CAM toolpaths + G-code post-processing, technical drafting (DXF / SVG / PDF), assemblies with interference detection, architectural / structural modelling (IFC4, Eurocode), surface modelling (NURBS fitting + blends), and JT / STEP-AP242 / IGES interop.
• Engineering design workbenches — a growing set of native parametric design calculators, each a right-side panel (View menu) with a form → compute → readout and, where the geometry suits it, a live wireframe preview: helical springs (spring index, axial stiffness, Wahl factor, developed wire length + a 3-D helix preview), involute gears (pitch / base / addendum / dedendum diameters, mesh ratio + a tooth-profile preview), piping (NPS bore, flow + metal area, wetted + external surface), structural frames (section area + perimeter), sheet-metal bends (bend allowance / deduction), fasteners (ISO 4017 bolt dimensions), collision (AABB volume / surface / overlap), geodesics (haversine + rhumb distance, bearings, cross-track), and field statistics — all closed-form and computed in-process (valenx-springs, valenx-gears, valenx-frames, …). These are research-grade design readouts, not a commercial parametric-modelling replacement (the roadmap targets FreeCAD-class parity, not Fusion 360 / SolidWorks).
• Reaction dynamics & graphics — a reaction-dynamics / AIMD simulator (velocity-Verlet on quantum-chemistry forces) and a physically-based path tracer (light-tree importance sampling, bidirectional path tracing, subsurface scattering).
• Neuroengineering / BCI — a neural-interface stimulation and recording suite (valenx-neuro): an implanted electrode's extracellular FEM field (reusing the FEA solver), Hodgkin–Huxley cable axons, the Rattay activating function coupling the two (an electrode recruits nearby neurons), bioheat tissue heating, and electrode–tissue impedance, plus an unconditionally-stable implicit cable solver, myelinated saltatory fibers (conduction velocity matched to the empirical 6·D rule), strength–duration curves, an anisotropic-tensor FEM field, and multi-contact current steering, and extracellular recording (the forward-EAP read-out model) — each validated against a textbook or closed-form result (see Validation).

The external tools below are optional — reach for them when you want a reference implementation, a GPU/ML model, or a domain not yet native. A few domains are still external-only and on the roadmap: a native electromagnetics solver, native unstructured meshing, and large-scale 3-D / industrial CFD. Contributors welcome — AI-assisted included (see CONTRIBUTING.md + AGENTS.md).

Validation

Native solvers are checked against published references or analytic results — the figures below are reproduced by the test suite, not asserted. Full detail — every per-crate validation suite and the ~200 bugs surfaced and fixed by running them — lives in docs/VALIDATION.md.

Solver	Benchmark / reference	Result
Orbital — valenx-astro	LEO→GEO Hohmann Δv vs textbook ~3.9 km/s	3,892 m/s total (2,425 + 1,467), ToF 5.27 h — test
Orbital — valenx-astro	J2 secular nodal regression vs closed-form rate	within 5% of the analytic dΩ/dt; a, i secularly unchanged — test
CFD — valenx-cfd-native	Lid-driven cavity vs Ghia, Ghia & Shin 1982	centerline MAE 0.035 / 0.016 / 0.024 at Re 100 / 400 / 1000
CFD — valenx-cfd-native	Poiseuille channel vs analytic	u_max 1.4949 vs 1.5000 (0.34% error)
CFD — valenx-cfd-native	Backward-facing step vs Armaly / Gartling	reattachment x_r/h ≈ 4.5, inside the published envelope
FEA — valenx-fem	Constant-strain patch test	satisfied to ~1e-9; Hex8 90% / Tet10 112% of the Euler–Bernoulli tip
MD — valenx-md	Argon NVE energy conservation	std-to-mean < 1%, no secular drift; lattice sum < 0.5% vs analytic
Quantum chem — valenx-qchem	Hydrogen atom, exact Kohn–Sham	reproduces −0.212742 Ha; LDA → uniform-gas and PBE → LDA limits hold
Docking — valenx-dock-screen	1HVR / 3PTB / 1STP redocking	RMSD 0.305 / 0.263 / 0.139 Å (mean 0.236), 100% < 2 Å
Neuro — valenx-neuro	Hodgkin–Huxley axon	textbook action potential (~100 mV overshoot, threshold, refractory) + propagating cable
Neuro — valenx-neuro	field + activating function	point source φ = I/(4πσr); cathodic depolarizes, anodic hyperpolarizes (Rattay)
Neuro — valenx-neuro	electrode recruitment	threshold rises with electrode–fiber distance; recruitment monotone in current
Neuro — valenx-neuro	bioheat + impedance	ΔT = Q/(4πk r); electrode access resistance R = 1/(4σa)
Neuro — valenx-neuro	implicit cable + myelinated fiber	unconditionally-stable implicit solver (stable at 100 µm, fixes the v1 RK4 limit); myelinated CV ≈ 6·D within ~6% (57 / 113 m/s at 10 / 20 µm), ∝ D not √D
Neuro — valenx-neuro	strength–duration	rheobase + chronaxie 1.65 ms (≈ ½ membrane τ); Lapicque constant-charge law holds to < 1% at short widths
Neuro — valenx-neuro	anisotropic FEM + steering	tensor-σ point source matches the closed-form anisotropic Green's function within ~10%; multi-contact current steering shifts the focus
Neuro — valenx-neuro	extracellular recording (forward-EAP)	biphasic spike with a dominant-negative (sink) phase; amplitude falls off with electrode distance; membrane currents conserve charge (Σ ≈ 0)

Install

0.1.0-alpha.1 builds from source today — pre-built installers aren't published yet. Building is one command (Build from source, just below) and is the supported path for the alpha. The signed packages below are the planned 1.0 distribution; they'll appear on Releases as they're cut.

Platform	Planned package
Windows	Valenx-<ver>-x86_64.msi
macOS	Valenx-<ver>.dmg
Linux (Debian/Ubuntu)	valenx_<ver>_amd64.deb
Linux (Fedora/RHEL/openSUSE)	valenx-<ver>.x86_64.rpm

Full installer guide with per-OS pinning recipes: docs/INSTALLER.md.

Build from source

# Linux / macOS
git clone https://github.com/nochallenge/valenx
cd valenx
cargo build --release -p valenx-app
./target/release/valenx

# Windows (PowerShell)
git clone https://github.com/nochallenge/valenx
cd valenx
cargo build --release -p valenx-app
.\target\release\valenx.exe

Requires Rust 1.88+. See CONTRIBUTING.md for full dev setup.

Documentation

• QUICKSTART.md — five-minute walkthrough
• docs/INSTALLER.md — install + pin to dock/taskbar
• STATUS.md — what's done, scaffolded, documentation-only
• ARCHITECTURE.md — how the pieces fit together
• ROADMAP.md — 20-year plan
• CHANGELOG.md — release history
• docs/CI.md — CI policy (manual-trigger only; here's why)
• CONTRIBUTING.md — how to contribute + dev setup
• SECURITY.md — vulnerability disclosure
• CODE_OF_CONDUCT.md — Contributor Covenant v2.1
• POLICIES.md — SemVer, deprecation, MSRV, dependency rules
• rfcs/ — RFC process + accepted proposals

What's actually working

Live adapters	141 fully live with real prepare/run/collect across CFD / FEA / EM / chemistry / MD / battery / multibody / coupling + a 123-adapter biology stack (structure prediction, alignment, variant calling, single-cell, workflow managers, viewers, cheminformatics, quantum chemistry, protein design, RNA structure, phylogenetics, CRISPR, cryo-EM, microscopy, mRNA design, and more)
Tests	10,000+ passing, 0 failed, 0 clippy warnings, 0 rustdoc warnings (workspace-wide)
Workflow loop	load project → click case → Run / Prepare / Open workdir / Run-from-prepared, all live
Sweeps + export	grid / Latin-hypercube / gradient-descent optimisers, materialise → run (sync or threaded) → assemble dataset (csv / npy / npz / manifest.json)
Mesh quality	Equiangle skewness · cell-face orthogonality · aspect-ratio + skewness histograms · cell-face + edge adjacency. Surfaced in the GUI Quality panel and via the headless valenx-mesh-info CLI (text / JSON / --check METRIC=THRESHOLD for CI gates)
HPC	valenx-executor-slurm does end-to-end remote-cluster submission: rsync staging + ssh-dispatched sbatch / squeue / sacct / scancel, sacct fallback for terminal state, GPU (--gres) + multi-rank srun, post-completion fetch_results
Visual results	OpenFOAM + Elmer + CalculiX + SU2 populate Results.fields with parsed .vtu / .vtk legacy / .frd / appended-binary data; auto-routed via vtk_dispatch. Vector + tensor fields render as magnitude / Frobenius norm. Viewport paints filled triangles + wireframe by field value with colour-bar legend + time-scrubbing
Compliance	RBAC (3 roles + per-project override) + append-only audit log with SHA-256 chain. valenx-audit verify and valenx-audit tail CLIs for offline integrity checks + headless inspection
CLI tooling	valenx-init scaffolds a project. valenx-validate runs a structural pre-flight on a project bundle. valenx-results inspects the results.json sidecar a finished run leaves on disk. valenx-report writes a self-contained HTML report and/or a flat scalar history CSV from a finished run. All four are exit-code-driven; the inspectors offer JSON output for downstream CI tooling

Supported solvers

Beyond its native engines, Valenx integrates 141 external open-source tools as optional adapters — for reference implementations, GPU/ML models, and domains not yet native. Each tool below is wrapped by a Valenx adapter crate (crates/valenx-adapters/<domain>/valenx-adapter-<tool>) that handles probing, case preparation, subprocess execution, and result collection. You install only the ones you actually use.

CFD / FEA / EM / multiphysics OpenFOAM, SU2, gmsh, Netgen, FreeCAD, CalculiX, Elmer, Code_Aster, OpenRadioss, Cantera, openEMS, Meep, PyBaMM, MuJoCo, preCICE.

Molecular dynamics GROMACS, LAMMPS, OpenMM, NAMD, AmberTools sander, HOOMD-blue. Trajectory analysis: MDAnalysis, MDTraj, PLUMED, ProDy, cpptraj.

Protein structure prediction + design AlphaFold 2, AlphaFold 3, ESMFold, OpenFold, RoseTTAFold, OmegaFold, ColabFold, FoldSeek. Design: RFdiffusion, ProteinMPNN, ESM-IF, Chroma, RFantibody, ESM3, ESM Cambrian.

Sequence alignment + search + variant calling BWA, minimap2, Bowtie2, HISAT2, STAR, MMseqs2, DIAMOND, BLAST+, MAFFT, MUSCLE, Clustal Omega, T-Coffee, HMMER, samtools, bcftools, GATK HaplotypeCaller, DeepVariant.

Transcript quantification + single-cell Salmon, Kallisto, Scanpy, scVI, Seurat, AnnData.

Cheminformatics + quantum chemistry RDKit, DeepChem, Open Babel, Avogadro 2, Psi4, NWChem, xTB.

Molecular docking + viewers AutoDock Vina, AutoDock 4. PyMOL, VMD, ChimeraX, IGV, Mol*, NGL.

CRISPR design + edit-outcome prediction CHOPCHOP, CRISPOR, Cas-OFFinder. Base/prime: BE-Designer, BE-Hive, PrimeDesign, pegFinder. Outcomes: inDelphi, FORECasT, AlphaMissense, CRISPRitz.

RNA structure + mRNA design ViennaRNA, RNAstructure, NUPACK, mfold, EternaFold, LinearFold. mRNA: DNA Chisel, LinearDesign, iCodon. Tertiary: SimRNA.

Cryo-EM + microscopy RELION, EMAN2, CTFFIND. Bioimage: Fiji, CellProfiler, Ilastik.

Phylogenetics + population genetics IQ-TREE, RAxML-NG, FastTree, BEAST 2, MrBayes. PopGen: SLiM, msprime, tskit.

Systems / synthetic biology COPASI, BioNetGen, PhysiCell, Smoldyn, MCell. SynBio: pySBOL, j5, Cello, pydna, Jalview.

Sequencing read simulators + Rosetta family ART, wgsim, Badread. Rosetta, PyRosetta.

DNA structural geometry + pharmacokinetics X3DNA, Curves+, DSSR. PK-Sim.

Workflow managers Snakemake, Nextflow, planemo, Cromwell, cwltool.

Several upstream tools ship under academic / non-commercial terms (AlphaFold 3, NAMD, VMD, CTFFIND, Rosetta, ViennaRNA, NUPACK, mfold, AlphaMissense, X3DNA family, Curves+). Valenx surfaces these via mandatory "academic"-keyworded probe warnings — you choose whether to install the binary based on your use case.

Full per-tool status and capability matrix: STATUS.md.

Design principles

1. Native desktop app. No browser. No localhost. Downloads like FreeCAD, runs like FreeCAD.
2. Open source, dual MIT / Apache-2.0. Free forever, commercial friendly, ecosystem-standard.
3. Rust first. Safe, fast, modern tooling.
4. Bundle existing solvers. Reuse decades of validated physics. Don't rewrite what already works.
5. Replace where it matters. The UX, the integration, the workflow — that's what we build new.

License

Dual-licensed under either of:

• MIT License (LICENSE-MIT)
• Apache License, Version 2.0 (LICENSE-APACHE)

at your option.

This is the Rust ecosystem standard — the same dual layout used by rustc, Tokio, Serde, Bevy, and most of the Rust crate ecosystem.

Contribution

Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in Valenx by you, as defined in the Apache-2.0 license, shall be dual-licensed as above, without any additional terms or conditions.

See CONTRIBUTING.md for guidelines.

Contribute

We're pre-alpha. If you want to help — shell scaffolding, adapters, physics solvers, documentation — start here:

• Read CONTRIBUTING.md for dev setup and workflow
• Big ideas → file an RFC (see rfcs/README.md)
• Small fixes → open a PR directly
• Security issues → SECURITY.md (please don't file public issues)
• Be respectful → CODE_OF_CONDUCT.md