@researai/deepscientist 1.5.17 → 1.6.0

package/src/skills/science/references/domain-index.md

@@ -0,0 +1,422 @@
+# Science Package Domain Index
+
+This generated index groups FermiLink skilled-scipkg package cards for DeepScientist routing.
+Package cards are knowledge pointers only; run package checks before computed work.
+
+- Package count: `169`
+- Upstream commit: `93f089a333a43089fb1a08a73c37d05fd6683214`
+
+## Domains
+
+### Astronomy Astrophysics
+
+- [`amuse`](packages/amuse.md): AMUSE Astrophysical Simulation Environment
+- [`astropy`](packages/astropy.md): Astropy Astronomy Core Library
+- [`astroquery`](packages/astroquery.md): Astroquery Astronomical Data Access
+- [`batman`](packages/batman.md): BATMAN Exoplanet Transit Light-Curve Modeler
+- [`ccdproc`](packages/ccdproc.md): CCDProc CCD Image Reduction
+- [`celerite2`](packages/celerite2.md): celerite2 Gaussian Process Toolkit
+- [`enzo-e`](packages/enzo-e.md): Enzo-E Exascale Astrophysics Simulator
+- [`exoplanet`](packages/exoplanet.md): exoplanet Bayesian Exoplanet Inference Toolkit
+- [`lightkurve`](packages/lightkurve.md): Lightkurve Kepler and TESS Light-Curve Analysis
+- [`photutils`](packages/photutils.md): Photutils Astronomical Photometry Toolkit
+- [`pynbody`](packages/pynbody.md): Pynbody Astrophysical Simulation Analysis
+- [`specutils`](packages/specutils.md): Specutils Astronomical Spectroscopy
+- [`starry`](packages/starry.md): starry stellar and exoplanet mapper
+- [`swift`](packages/swift.md): SWIFT Astrophysical Simulation Engine
+
+### Bioinformatics
+
+- [`anndata`](packages/anndata.md): AnnData Annotated Data Matrices
+- [`biopython`](packages/biopython.md): Biopython
+- [`datamol`](packages/datamol.md): Datamol Molecular Processing Toolkit
+- [`deepchem`](packages/deepchem.md): DeepChem Molecular Machine Learning Toolkit
+- [`gwaslab`](packages/gwaslab.md): GWASLab Summary Statistics Toolkit
+- [`hail`](packages/hail.md): Hail Genomics Analytics
+- [`limix`](packages/limix.md): LIMIX Genomic Linear Mixed Models
+- [`nextflow`](packages/nextflow.md): Nextflow Scientific Workflow Engine
+- [`openbabel`](packages/openbabel.md): Open Babel
+- [`openff-toolkit`](packages/openff-toolkit.md): Open Force Field Toolkit
+- [`plink-ng`](packages/plink-ng.md): PLINK 2 Genome Association Toolkit
+- [`pysam`](packages/pysam.md): Pysam Genomics I/O
+- [`rdkit`](packages/rdkit.md): RDKit Cheminformatics Toolkit
+- [`scanpy`](packages/scanpy.md): Scanpy Single-Cell Toolkit
+- [`scikit-allel`](packages/scikit-allel.md): scikit-allel Population Genetics
+- [`scikit-bio`](packages/scikit-bio.md): scikit-bio Bioinformatics Library
+- [`scvi-tools`](packages/scvi-tools.md): scvi-tools Single-Cell Probabilistic Modeling
+- [`snakemake`](packages/snakemake.md): Snakemake Workflow Manager
+- [`squidpy`](packages/squidpy.md): Squidpy Spatial Omics Analysis
+- [`tvb-root`](packages/tvb-root.md): The Virtual Brain Core
+
+### Computational Chemistry
+
+- [`custodian`](packages/custodian.md): Custodian JIT Simulation Job Manager
+- [`datamol`](packages/datamol.md): Datamol Molecular Processing Toolkit
+- [`deepchem`](packages/deepchem.md): DeepChem Molecular Machine Learning Toolkit
+- [`gromacs`](packages/gromacs.md): GROMACS Molecular Dynamics
+- [`nwchem`](packages/nwchem.md): NWChem Computational Chemistry
+- [`openbabel`](packages/openbabel.md): Open Babel
+- [`openff-toolkit`](packages/openff-toolkit.md): Open Force Field Toolkit
+- [`openmm`](packages/openmm.md): OpenMM Molecular Dynamics Toolkit
+- [`packmol`](packages/packmol.md): Packmol Molecular Configuration Builder
+- [`psi4`](packages/psi4.md): Psi4 Quantum Chemistry
+- [`pyscf`](packages/pyscf.md): PySCF Quantum Chemistry
+- [`rdkit`](packages/rdkit.md): RDKit Cheminformatics Toolkit
+- [`xtb`](packages/xtb.md): xTB Extended Tight-Binding Quantum Chemistry
+
+### Computational Fluid Dynamics
+
+- [`amuse`](packages/amuse.md): AMUSE Astrophysical Simulation Environment
+- [`dealii`](packages/dealii.md): deal.II Finite Element Library
+- [`devito`](packages/devito.md): Devito Stencil Compiler
+- [`dolfinx`](packages/dolfinx.md): DOLFINx
+- [`elmerfem`](packages/elmerfem.md): Elmer FEM
+- [`enzo-e`](packages/enzo-e.md): Enzo-E Exascale Astrophysics Simulator
+- [`espresso`](packages/espresso.md): ESPResSo Soft-Matter Molecular Dynamics
+- [`kratos`](packages/kratos.md): Kratos Multiphysics
+- [`mfem`](packages/mfem.md): MFEM Finite Element Library
+- [`mitgcm`](packages/mitgcm.md): MIT General Circulation Model (MITgcm)
+- [`moose`](packages/moose.md): MOOSE Multiphysics Framework
+- [`nekrs`](packages/nekrs.md): nekRS CFD Solver
+- [`openfoam-dev`](packages/openfoam-dev.md): OpenFOAM-dev CFD Platform
+- [`palabos`](packages/palabos.md): Palabos Lattice Boltzmann CFD
+- [`pyfr`](packages/pyfr.md): PyFR High-Order CFD Solver
+- [`pynbody`](packages/pynbody.md): Pynbody Astrophysical Simulation Analysis
+- [`seissol`](packages/seissol.md): SeisSol Earthquake Wave Simulator
+- [`sfepy`](packages/sfepy.md): SfePy Finite Element PDE Solver
+- [`su2`](packages/su2.md): SU2 Open-Source CFD Suite
+- [`swift`](packages/swift.md): SWIFT Astrophysical Simulation Engine
+
+### Computational Neuroscience
+
+- [`arbor`](packages/arbor.md): Arbor Neural Simulation Library
+- [`brian2`](packages/brian2.md): Brian2 Spiking Neural Network Simulator
+- [`nest-simulator`](packages/nest-simulator.md): NEST Spiking Neural Network Simulator
+- [`neuron`](packages/neuron.md): NEURON Neural Simulator
+- [`tvb-root`](packages/tvb-root.md): The Virtual Brain Core
+
+### Computational Science
+
+- [`arc`](packages/arc.md): ARC Alkali Rydberg Calculator
+- [`atomsmltr`](packages/atomsmltr.md): atomSmltr Laser Cooling and Trapping Simulator
+- [`cantera`](packages/cantera.md): Cantera Chemical Kinetics and Combustion
+- [`cellrank`](packages/cellrank.md): CellRank Single-Cell Fate Mapping
+- [`chempy`](packages/chempy.md): ChemPy Chemical Modeling Toolkit
+- [`cirq`](packages/cirq.md): Cirq Quantum Circuit Framework
+- [`dumux`](packages/dumux.md): DuMux Porous Media Simulator
+- [`kadanoffbaym-jl`](packages/kadanoffbaym-jl.md): KadanoffBaym.jl
+- [`modflow6`](packages/modflow6.md): MODFLOW 6 Groundwater Model
+- [`mom6`](packages/mom6.md): MOM6 Modular Ocean Model
+- [`mpas-model`](packages/mpas-model.md): MPAS Model for Prediction Across Scales
+- [`mumax3`](packages/mumax3.md): MuMax3 Micromagnetic Simulator
+- [`nessi`](packages/nessi.md): NESSi Non-Equilibrium Systems Simulation
+- [`openmoc`](packages/openmoc.md): OpenMOC Reactor Physics Solver
+- [`opm-simulators`](packages/opm-simulators.md): OPM Flow Reservoir Simulator
+- [`oqupy`](packages/oqupy.md): OQuPy
+- [`perceval`](packages/perceval.md): Perceval Photonic Quantum Toolkit
+- [`pylcp`](packages/pylcp.md): PyLCP Laser Cooling Physics
+- [`qibo`](packages/qibo.md): Qibo Quantum Simulation and Control
+- [`qiskit`](packages/qiskit.md): Qiskit Quantum SDK
+- [`quantumoptics-jl`](packages/quantumoptics-jl.md): QuantumOptics.jl Quantum Dynamics Simulator
+- [`quimb`](packages/quimb.md): Quimb Quantum Tensor Networks
+- [`qulacs`](packages/qulacs.md): Qulacs Quantum Circuit Simulator
+- [`qutip`](packages/qutip.md): QuTiP Quantum Toolbox
+- [`rmg-py`](packages/rmg-py.md): RMG-Py Reaction Mechanism Generator
+- [`scqubits`](packages/scqubits.md): scqubits superconducting qubit simulator
+- [`sunny-jl`](packages/sunny-jl.md): Sunny.jl Magnetic Materials Modeling
+- [`sw4`](packages/sw4.md): SW4 Seismic Waves Solver
+- [`tdnegf`](packages/tdnegf.md): TDNEGF Hybrid Quantum Transport
+- [`tenpy`](packages/tenpy.md): TeNPy Tensor Network Python
+- [`wrf`](packages/wrf.md): WRF Weather Forecasting Model
+- [`yt`](packages/yt.md): yt Volumetric Simulation Analysis
+
+### Electromagnetics
+
+- [`elmerfem`](packages/elmerfem.md): Elmer FEM
+- [`fdtdbath-meep`](packages/fdtdbath-meep.md): Modified Meep FDTD Electromagnetics Simulator for FDTD-Bath approach of condensed-phase polaritonics
+- [`gprmax`](packages/gprmax.md): gprMax Ground Penetrating Radar Simulator
+- [`maxwelllink`](packages/maxwelllink.md): MaxwellLink Light-Matter Co-Simulation
+- [`meep`](packages/meep.md): Meep Electromagnetic FDTD Simulator
+- [`openems`](packages/openems.md): openEMS Electromagnetic Solver
+- [`picongpu`](packages/picongpu.md): PIConGPU
+- [`psc`](packages/psc.md): PSC Particle-in-Cell Plasma Simulator
+- [`scuff-em`](packages/scuff-em.md): SCUFF-EM Electromagnetic BEM Suite
+- [`smilei`](packages/smilei.md): Smilei Plasma PIC Simulator
+- [`strawberryfields`](packages/strawberryfields.md): Strawberry Fields Continuous-Variable Quantum Toolkit
+- [`warpx`](packages/warpx.md): WarpX PIC Plasma Simulator
+
+### Finite Element Engineering
+
+- [`calculix`](packages/calculix.md): CalculiX Finite Element Program
+- [`coffea`](packages/coffea.md): Coffea Collider HEP Analysis Framework
+- [`dealii`](packages/dealii.md): deal.II Finite Element Library
+- [`dolfinx`](packages/dolfinx.md): DOLFINx
+- [`elmerfem`](packages/elmerfem.md): Elmer FEM
+- [`geosx`](packages/geosx.md): GEOSX Subsurface Multiphysics Framework
+- [`itensor`](packages/itensor.md): ITensor Tensor Network Library
+- [`kratos`](packages/kratos.md): Kratos Multiphysics
+- [`mfem`](packages/mfem.md): MFEM Finite Element Library
+- [`moose`](packages/moose.md): MOOSE Multiphysics Framework
+- [`opensees`](packages/opensees.md): OpenSees Earthquake Engineering Simulator
+- [`pylith`](packages/pylith.md): PyLith Tectonic Deformation Simulator
+- [`sfepy`](packages/sfepy.md): SfePy Finite Element PDE Solver
+- [`squidpy`](packages/squidpy.md): Squidpy Spatial Omics Analysis
+- [`wannier_tools`](packages/wannier_tools.md): WannierTools Topological Materials Toolkit
+
+### High Energy Physics
+
+- [`acts`](packages/acts.md): ACTS Common Tracking Software
+- [`awkward`](packages/awkward.md): Awkward Array
+- [`coffea`](packages/coffea.md): Coffea Collider HEP Analysis Framework
+- [`dd4hep`](packages/dd4hep.md): DD4hep Detector Description Toolkit
+- [`delphes`](packages/delphes.md): Delphes Fast Collider Simulation
+- [`fairroot`](packages/fairroot.md): FairRoot Particle Physics Framework
+- [`geant4`](packages/geant4.md): Geant4 Particle-Matter Simulation Toolkit
+- [`hoomd-blue`](packages/hoomd-blue.md): HOOMD-blue Particle Simulation
+- [`mcdc`](packages/mcdc.md): MC/DC Neutron Transport
+- [`molecool`](packages/molecool.md): MoleCool Molecular Laser Cooling Simulator
+- [`netket`](packages/netket.md): NetKet Quantum Many-Body ML
+- [`openmc`](packages/openmc.md): OpenMC Monte Carlo Particle Transport
+- [`pyhf`](packages/pyhf.md): pyhf HistFactory Inference Toolkit
+- [`root`](packages/root.md): CERN ROOT Data Analysis Framework
+- [`uproot5`](packages/uproot5.md): Uproot5 ROOT I/O
+
+### Materials Science
+
+- [`abinit`](packages/abinit.md): ABINIT Electronic-Structure Suite
+- [`alamode`](packages/alamode.md): ALAMODE Lattice Thermal Transport
+- [`atomate2`](packages/atomate2.md): Atomate2 Materials Workflow Library
+- [`custodian`](packages/custodian.md): Custodian JIT Simulation Job Manager
+- [`deepchem`](packages/deepchem.md): DeepChem Molecular Machine Learning Toolkit
+- [`dftk-jl`](packages/dftk-jl.md): DFTK.jl Density-Functional Toolkit
+- [`elk`](packages/elk.md): Elk All-Electron DFT Code
+- [`hiphive`](packages/hiphive.md): hiphive Force-Constant Modeling
+- [`jdftx`](packages/jdftx.md): JDFTx
+- [`jobflow`](packages/jobflow.md): Jobflow Computational Workflow Library
+- [`lammps`](packages/lammps.md): LAMMPS Molecular Dynamics
+- [`openmx`](packages/openmx.md): OpenMX Materials DFT Package
+- [`phono3py`](packages/phono3py.md): Phono3py
+- [`phonopy`](packages/phonopy.md): Phonopy Phonon Lattice Dynamics
+- [`pyiron_base`](packages/pyiron_base.md): pyiron Base Workflow Core
+- [`pyscf`](packages/pyscf.md): PySCF Quantum Chemistry
+- [`q-e`](packages/q-e.md): Quantum ESPRESSO
+- [`sisl`](packages/sisl.md): sisl Electronic Structure Toolkit
+- [`spglib`](packages/spglib.md): Spglib Crystal Symmetry Toolkit
+- [`vampire`](packages/vampire.md): VAMPIRE Atomistic Spin Dynamics Simulator
+
+### Molecular Dynamics
+
+- [`cavity-md-ipi`](packages/cavity-md-ipi.md): CavMD: Cavity Molecular Dynamics
+- [`cp2k`](packages/cp2k.md): CP2K Quantum Chemistry Suite
+- [`dftb`](packages/dftb.md): DFTB+ Atomistic Simulator
+- [`espresso`](packages/espresso.md): ESPResSo Soft-Matter Molecular Dynamics
+- [`gromacs`](packages/gromacs.md): GROMACS Molecular Dynamics
+- [`hoomd-blue`](packages/hoomd-blue.md): HOOMD-blue Particle Simulation
+- [`lammps`](packages/lammps.md): LAMMPS Molecular Dynamics
+- [`maxwelllink`](packages/maxwelllink.md): MaxwellLink Light-Matter Co-Simulation
+- [`molecool`](packages/molecool.md): MoleCool Molecular Laser Cooling Simulator
+- [`nwchem`](packages/nwchem.md): NWChem Computational Chemistry
+- [`openmm`](packages/openmm.md): OpenMM Molecular Dynamics Toolkit
+- [`packmol`](packages/packmol.md): Packmol Molecular Configuration Builder
+- [`q-e`](packages/q-e.md): Quantum ESPRESSO
+- [`vampire`](packages/vampire.md): VAMPIRE Atomistic Spin Dynamics Simulator
+
+### Plasma Particle Simulation
+
+- [`fbpic`](packages/fbpic.md): FBPIC Spectral Quasi-3D PIC
+- [`kwant`](packages/kwant.md): Kwant Quantum Transport Toolkit
+- [`picongpu`](packages/picongpu.md): PIConGPU
+- [`psc`](packages/psc.md): PSC Particle-in-Cell Plasma Simulator
+- [`smilei`](packages/smilei.md): Smilei Plasma PIC Simulator
+- [`tkwant`](packages/tkwant.md): Tkwant Time-Dependent Quantum Transport
+- [`warpx`](packages/warpx.md): WarpX PIC Plasma Simulator
+
+### Quantum Chemistry
+
+- [`abinit`](packages/abinit.md): ABINIT Electronic-Structure Suite
+- [`atomate2`](packages/atomate2.md): Atomate2 Materials Workflow Library
+- [`cp2k`](packages/cp2k.md): CP2K Quantum Chemistry Suite
+- [`custodian`](packages/custodian.md): Custodian JIT Simulation Job Manager
+- [`deepchem`](packages/deepchem.md): DeepChem Molecular Machine Learning Toolkit
+- [`dftb`](packages/dftb.md): DFTB+ Atomistic Simulator
+- [`dftd4`](packages/dftd4.md): DFT-D4 Dispersion Correction
+- [`dftk-jl`](packages/dftk-jl.md): DFTK.jl Density-Functional Toolkit
+- [`elk`](packages/elk.md): Elk All-Electron DFT Code
+- [`jdftx`](packages/jdftx.md): JDFTx
+- [`kite`](packages/kite.md): KITE Quantum Transport Suite
+- [`kwant`](packages/kwant.md): Kwant Quantum Transport Toolkit
+- [`nwchem`](packages/nwchem.md): NWChem Computational Chemistry
+- [`openmx`](packages/openmx.md): OpenMX Materials DFT Package
+- [`pennylane`](packages/pennylane.md): PennyLane
+- [`psi4`](packages/psi4.md): Psi4 Quantum Chemistry
+- [`pybinding`](packages/pybinding.md): Pybinding Tight Binding Toolkit
+- [`pyscf`](packages/pyscf.md): PySCF Quantum Chemistry
+- [`q-e`](packages/q-e.md): Quantum ESPRESSO
+- [`quantica-jl`](packages/quantica-jl.md): Quantica.jl Lattice Quantum Systems
+- [`sisl`](packages/sisl.md): sisl Electronic Structure Toolkit
+- [`tkwant`](packages/tkwant.md): Tkwant Time-Dependent Quantum Transport
+- [`wannier_tools`](packages/wannier_tools.md): WannierTools Topological Materials Toolkit
+- [`xtb`](packages/xtb.md): xTB Extended Tight-Binding Quantum Chemistry
+
+### Robotics Physics
+
+- [`bullet3`](packages/bullet3.md): Bullet Physics SDK (bullet3)
+- [`dart`](packages/dart.md): DART Robotics Dynamics Engine
+- [`drake`](packages/drake.md): Drake Robotics Toolkit
+- [`gz-sim`](packages/gz-sim.md): Gazebo Sim (gz-sim)
+- [`mujoco`](packages/mujoco.md): MuJoCo Physics Simulator
+- [`swift`](packages/swift.md): SWIFT Astrophysical Simulation Engine
+
+### Workflow Provenance
+
+- [`acts`](packages/acts.md): ACTS Common Tracking Software
+- [`aiida-core`](packages/aiida-core.md): AiiDA Core Workflow Engine
+- [`amuse`](packages/amuse.md): AMUSE Astrophysical Simulation Environment
+- [`anndata`](packages/anndata.md): AnnData Annotated Data Matrices
+- [`arbor`](packages/arbor.md): Arbor Neural Simulation Library
+- [`astropy`](packages/astropy.md): Astropy Astronomy Core Library
+- [`atomate2`](packages/atomate2.md): Atomate2 Materials Workflow Library
+- [`bloqade`](packages/bloqade.md): Bloqade Neutral Atom Quantum SDK
+- [`bullet3`](packages/bullet3.md): Bullet Physics SDK (bullet3)
+- [`calculix`](packages/calculix.md): CalculiX Finite Element Program
+- [`cavity-md-ipi`](packages/cavity-md-ipi.md): CavMD: Cavity Molecular Dynamics
+- [`celerite2`](packages/celerite2.md): celerite2 Gaussian Process Toolkit
+- [`cesm`](packages/cesm.md): CESM (Community Earth System Model)
+- [`chemicals`](packages/chemicals.md): Chemicals Thermophysical Data Library
+- [`custodian`](packages/custodian.md): Custodian JIT Simulation Job Manager
+- [`datamol`](packages/datamol.md): Datamol Molecular Processing Toolkit
+- [`dealii`](packages/dealii.md): deal.II Finite Element Library
+- [`devito`](packages/devito.md): Devito Stencil Compiler
+- [`dolfinx`](packages/dolfinx.md): DOLFINx
+- [`enzo-e`](packages/enzo-e.md): Enzo-E Exascale Astrophysics Simulator
+- [`espresso`](packages/espresso.md): ESPResSo Soft-Matter Molecular Dynamics
+- [`exoplanet`](packages/exoplanet.md): exoplanet Bayesian Exoplanet Inference Toolkit
+- [`geosx`](packages/geosx.md): GEOSX Subsurface Multiphysics Framework
+- [`gromacs`](packages/gromacs.md): GROMACS Molecular Dynamics
+- [`hiphive`](packages/hiphive.md): hiphive Force-Constant Modeling
+- [`itensors-jl`](packages/itensors-jl.md): ITensors.jl Tensor Network Library
+- [`jobflow`](packages/jobflow.md): Jobflow Computational Workflow Library
+- [`kite`](packages/kite.md): KITE Quantum Transport Suite
+- [`kratos`](packages/kratos.md): Kratos Multiphysics
+- [`lammps`](packages/lammps.md): LAMMPS Molecular Dynamics
+- [`limix`](packages/limix.md): LIMIX Genomic Linear Mixed Models
+- [`maxwelllink`](packages/maxwelllink.md): MaxwellLink Light-Matter Co-Simulation
+- [`mfem`](packages/mfem.md): MFEM Finite Element Library
+- [`moose`](packages/moose.md): MOOSE Multiphysics Framework
+- [`nekrs`](packages/nekrs.md): nekRS CFD Solver
+- [`nextflow`](packages/nextflow.md): Nextflow Scientific Workflow Engine
+- [`nwchem`](packages/nwchem.md): NWChem Computational Chemistry
+- [`openems`](packages/openems.md): openEMS Electromagnetic Solver
+- [`openff-toolkit`](packages/openff-toolkit.md): Open Force Field Toolkit
+- [`openfoam-dev`](packages/openfoam-dev.md): OpenFOAM-dev CFD Platform
+- [`openmx`](packages/openmx.md): OpenMX Materials DFT Package
+- [`opensn`](packages/opensn.md): OpenSn Linear Boltzmann Solver
+- [`palabos`](packages/palabos.md): Palabos Lattice Boltzmann CFD
+- [`parflow`](packages/parflow.md): ParFlow Watershed Flow Model
+- [`pennylane`](packages/pennylane.md): PennyLane
+- [`phonopy`](packages/phonopy.md): Phonopy Phonon Lattice Dynamics
+- [`picongpu`](packages/picongpu.md): PIConGPU
+- [`plink-ng`](packages/plink-ng.md): PLINK 2 Genome Association Toolkit
+- [`precice`](packages/precice.md): preCICE Coupling Library
+- [`psc`](packages/psc.md): PSC Particle-in-Cell Plasma Simulator
+- [`psi4`](packages/psi4.md): Psi4 Quantum Chemistry
+- [`pyiron_base`](packages/pyiron_base.md): pyiron Base Workflow Core
+- [`pysam`](packages/pysam.md): Pysam Genomics I/O
+- [`pyscf`](packages/pyscf.md): PySCF Quantum Chemistry
+- [`rdkit`](packages/rdkit.md): RDKit Cheminformatics Toolkit
+- [`root`](packages/root.md): CERN ROOT Data Analysis Framework
+- [`scikit-allel`](packages/scikit-allel.md): scikit-allel Population Genetics
+- [`sisl`](packages/sisl.md): sisl Electronic Structure Toolkit
+- [`smilei`](packages/smilei.md): Smilei Plasma PIC Simulator
+- [`snakemake`](packages/snakemake.md): Snakemake Workflow Manager
+- [`specfem3d-globe`](packages/specfem3d-globe.md): SPECFEM3D Globe
+- [`specutils`](packages/specutils.md): Specutils Astronomical Spectroscopy
+- [`spglib`](packages/spglib.md): Spglib Crystal Symmetry Toolkit
+- [`swift`](packages/swift.md): SWIFT Astrophysical Simulation Engine
+- [`thermo`](packages/thermo.md): Thermo Chemical Engineering Thermodynamics
+- [`tvb-root`](packages/tvb-root.md): The Virtual Brain Core
+- [`uproot5`](packages/uproot5.md): Uproot5 ROOT I/O
+- [`warpx`](packages/warpx.md): WarpX PIC Plasma Simulator
+
+## Common Tags
+
+- `hpc`: 28
+- `electronic-structure`: 17
+- `computational-physics`: 16
+- `simulation`: 14
+- `materials-science`: 13
+- `multiphysics`: 12
+- `bioinformatics`: 11
+- `astronomy`: 10
+- `molecular-dynamics`: 10
+- `computational-chemistry`: 10
+- `finite-element`: 9
+- `quantum-chemistry`: 9
+- `pde`: 9
+- `tight-binding`: 9
+- `electromagnetics`: 9
+- `genomics`: 8
+- `dft`: 7
+- `cfd`: 7
+- `astrophysics`: 6
+- `hep`: 6
+- `materials-simulation`: 6
+- `quantum-transport`: 6
+- `condensed-matter`: 6
+- `computational-neuroscience`: 5
+- `quantum-optics`: 5
+- `quantum-computing`: 5
+- `robotics`: 5
+- `cheminformatics`: 5
+- `julia`: 5
+- `plasma-physics`: 5
+- `particle-in-cell`: 5
+- `monte-carlo`: 5
+- `quantum-simulation`: 5
+- `cpp`: 4
+- `workflow`: 4
+- `phonons`: 4
+- `lattice-dynamics`: 4
+- `hydrodynamics`: 4
+- `cosmology`: 4
+- `exoplanets`: 4
+- `time-series`: 4
+- `structural-mechanics`: 4
+- `quantum`: 4
+- `amr`: 4
+- `fdtd`: 4
+- `gwas`: 4
+- `tensor-networks`: 4
+- `gpu`: 4
+- `open-quantum-systems`: 4
+- `seismology`: 4
+- `reproducibility`: 3
+- `single-cell`: 3
+- `atomic-physics`: 3
+- `high-throughput`: 3
+- `laser-cooling`: 3
+- `numerical-simulation`: 3
+- `computational-biology`: 3
+- `chemical-kinetics`: 3
+- `thermodynamics`: 3
+- `climate-modeling`: 3
+- `earth-system`: 3
+- `quantum-circuits`: 3
+- `solid-state`: 3
+- `detector-simulation`: 3
+- `root`: 3
+- `atomistic-simulation`: 3
+- `density-functional-theory`: 3
+- `particle-physics`: 3
+- `photonics`: 3
+- `radiation-transport`: 3
+- `geophysics`: 3
+- `quantum-many-body`: 3
+- `many-body`: 3
+- `quantum-dynamics`: 3
+- `neutron-transport`: 3
+- `reactor-physics`: 3
+- `quantum-physics`: 3
+- `ab-initio`: 3
+- `molecular-modeling`: 3
+- `dfpt`: 2

package/src/skills/science/references/hpc-via-bash-exec.md

@@ -0,0 +1,42 @@
+# HPC Via `bash_exec`
+
+DeepScientist does not embed an HPC scheduler. The agent operates HPC through
+`bash_exec(...)` just like any other terminal action.
+
+## Pattern
+
+1. Verify remote access or local scheduler availability.
+2. Write a small job script or command file in the workspace.
+3. Submit through `bash_exec(...)`, for example `ssh cluster sbatch job.sh`.
+4. Capture job id, queue state, and log paths.
+5. Record a science node with `status="queued"` or `status="running"`.
+6. Monitor with low-frequency `bash_exec` reads:
+   - `squeue` / `sacct`
+   - `tail` or `sed -n` on logs
+   - file existence and output JSON checks
+7. On completion, record a success/failed update and validation node.
+
+## Evidence Fields
+
+Use `metadata` for scheduler facts:
+
+```python
+artifact.science(
+    action="record_node",
+    node_type="science.computational_run",
+    node_id="run_lammps_water_viscosity",
+    status="queued",
+    package_id="lammps",
+    input_paths=["simulations/inputs/water_viscosity.in"],
+    log_paths=["simulations/logs/water_viscosity.slurm.out"],
+    metadata={"scheduler": "slurm", "job_id": "123456"},
+)
+```
+
+## Cautions
+
+- Do not claim a queued job has produced results.
+- Do not infer global completion from a truncated log window.
+- Do not poll rapidly for multi-hour jobs. Use durable job ids and saved logs.
+- If the cluster requires modules, licenses, or allocations, treat missing
+  setup as a blocker and record the failed/blocked package check.

package/src/skills/science/references/package-check-playbook.md

@@ -0,0 +1,64 @@
+# Package Check Playbook
+
+Package knowledge and solver installation are separate.
+
+Before any computed result:
+
+1. Check import or executable existence.
+2. Capture version and important backend details.
+3. Run a minimal smoke test when the package supports it.
+4. Save the check result to a durable file, usually under
+   `validation/environment/`.
+5. Record a `science.package_check` node.
+
+## Python Package Pattern
+
+Use `bash_exec(...)` to run a short script that writes JSON:
+
+```bash
+python - <<'PY'
+import json, pathlib
+result = {"package_id": "pyscf", "import": "failed", "version": None, "smoke": "not_run"}
+try:
+    import pyscf
+    result["import"] = "passed"
+    result["version"] = getattr(pyscf, "__version__", None)
+    result["smoke"] = "passed"
+except Exception as exc:
+    result["error"] = repr(exc)
+pathlib.Path("validation/environment").mkdir(parents=True, exist_ok=True)
+pathlib.Path("validation/environment/pyscf_doctor.json").write_text(json.dumps(result, indent=2), encoding="utf-8")
+PY
+```
+
+Then record:
+
+```python
+artifact.science(
+    action="record_node",
+    node_type="science.package_check",
+    node_id="pkg_pyscf_check",
+    status="passed",
+    package_id="pyscf",
+    evidence_paths=["validation/environment/pyscf_doctor.json"],
+)
+```
+
+## CLI Solver Pattern
+
+Check:
+
+- executable path
+- version output
+- module/environment state if on HPC
+- a minimal dry run or example input if available
+
+Record failed checks too when they explain a blocker. Use `status="failed"` or
+`status="blocked"` and include the log path.
+
+## Interpretation
+
+- `passed` means the current environment can run at least the smoke path.
+- `failed` means the package was attempted and did not work.
+- `blocked` means the agent could not check because credentials, data, modules,
+  license, network, or user confirmation are missing.