Agent Skills for computational materials science -- numerical stability, solvers, meshing, convergence, and simulation workflows.
Install
npx skills add HeshamFS/materials-simulation-skillsgh skill install HeshamFS/materials-simulation-skillsgit clone --depth 1 https://github.com/HeshamFS/materials-simulation-skillsSkills in this collection
- Benchmark And Mms PlannerHesham SalamaPlan verification and validation campaigns for simulation codes using manufactured solutions, canonical benchmark problems, grid/time refinement, uncertainty propagation, and pass/fail acceptance criteria. Use when an agent needs to prove a solver, model, or result is trustworthy rather than only plausible.
- Convergence StudyHesham SalamaPerform spatial and temporal convergence analysis for solution verification — compute observed convergence orders from grid or timestep refinement studies, apply Richardson extrapolation to estimate discretization error, and calculate the Grid Convergence Index (GCI) per ASME V&V 20 standards.
- Differentiation SchemesHesham SalamaSelect and apply numerical differentiation schemes for PDE and ODE discretization — generate finite-difference stencils at arbitrary order and accuracy, choose between central, upwind, compact (Pade), and spectral methods, handle boundary stencils, and estimate truncation error scaling.
- Fair Simulation PackagerHesham SalamaCreate FAIR-minded reproducibility bundles for materials simulations by collecting input/output file inventories, hashes, units, engine versions, structure identifiers, provenance, and NOMAD/OPTIMADE/Materials Project friendly metadata. Use before publishing, sharing, archiving, or handing simulation results to another agent.
- Hpc Runtime DoctorHesham SalamaDiagnose HPC runtime and scheduler problems for materials simulations, including MPI/OpenMP/GPU layout, modules, CUDA/Kokkos hints, scratch paths, walltime, job arrays, restart strategy, scheduler portability, and resource mismatch. Use when an ALREADY-SUBMITTED job failed, ran slowly, got killed, or behaved differently on a cluster than on a workstation.
- Linear SolversHesham SalamaSelect and configure linear solvers for Ax=b systems arising in numerical simulations — choose between direct (LU, Cholesky) and iterative (CG, GMRES, BiCGSTAB, MINRES) methods, analyze sparsity patterns and matrix conditioning, recommend preconditioners (AMG, ILU, IC), apply row/column scaling, and diagnose convergence stagnation from residual histories.
- Md Analysis PlannerHesham SalamaPlan molecular dynamics post-processing for materials simulations, including RDF, MSD and diffusion, VACF/VDOS, coordination numbers, bond-angle distributions, stress-strain curves, equilibration detection, PBC unwrapping, and trajectory format choices. Use before writing MD analysis scripts or trusting trajectory-derived results.
- Mesh GenerationHesham SalamaPlan and evaluate mesh generation for numerical simulations — estimate grid resolution from physics scales (interface width, boundary layers, wavelengths), check aspect ratios and skewness against quality thresholds, choose between structured, unstructured, and adaptive mesh refinement strategies, and compute grid sizing for 1D/2D/3D domains.
- Nonlinear SolversHesham SalamaSelect and configure nonlinear solvers for root-finding f(x)=0, optimization min F(x), and least-squares problems — choose among Newton, Newton-Krylov, quasi-Newton (BFGS, L-BFGS), Broyden, Anderson acceleration, and Levenberg-Marquardt methods, configure line search or trust-region globalization, diagnose convergence rate (quadratic, linear, stagnated), and assess Jacobian quality and…
- Numerical IntegrationHeshamFSSelect and configure time integration methods for ODE/PDE simulations. Use when choosing explicit/implicit schemes, setting error tolerances, adapting time steps, diagnosing integration accuracy, planning IMEX splitting, or handling stiff/non-stiff coupled systems.
- Numerical StabilityHesham SalamaAnalyze numerical stability for time-dependent PDE simulations — check CFL and Fourier criteria, perform von Neumann stability analysis, detect stiffness, evaluate matrix conditioning, and recommend explicit vs implicit time-stepping schemes.
- Ontology ExplorerHesham SalamaParse, navigate, and query materials science ontology structures — browse class hierarchies, inspect individual classes and their properties, look up object and data property definitions with domain/range, search for ontology terms by keyword, and parse or summarize raw OWL/XML files. Currently supports CMSO and ASMO; the broader OCDO ecosystem (CDCO, PODO, PLDO, LDO) is planned.
- Ontology MapperHesham SalamaMap materials science terms, crystal structures, and sample descriptions to standardized ontology classes and properties — resolve natural-language concepts to ontology entries with confidence scores, translate Bravais lattice types, space groups, and lattice constants into ontology-compliant annotations, and produce full sample metadata from structured descriptions.
- Ontology ValidatorHesham SalamaValidate material sample annotations against ontology constraints — check that class names and property names exist in the ontology, verify domain and range consistency for object property relationships, assess annotation completeness (required, recommended, and optional properties), and flag unknown or misspelled terms.
- Parameter OptimizationHesham SalamaExplore and optimize simulation parameters via design of experiments (DOE), sensitivity analysis, and optimizer selection — generate Latin Hypercube, quasi-random, or factorial sample plans, rank parameter influence with sensitivity scores, recommend Bayesian optimization, CMA-ES, or gradient- based methods based on dimension and budget, and fit surrogate models for expensive evaluations.
- Performance ProfilingHesham SalamaIdentify computational bottlenecks, analyze parallel scaling, estimate memory requirements, and generate optimization recommendations for materials simulations — parse timing logs to find dominant phases (solver, assembly, I/O), evaluate strong and weak scaling efficiency, profile memory from mesh and field parameters, and detect bottlenecks with actionable fix suggestions.
- Post ProcessingHesham SalamaExtract, analyze, and summarize simulation output data — pull spatial fields at specific timesteps, compute time-series trends and detect steady state, extract line profiles through the domain, generate statistical summaries and distributions, calculate derived quantities (gradients, fluxes, volume fractions, interface area), compare results against analytical solutions or experimental data, and…
- Simulation Failure TriageHesham SalamaFirst-response triage for cross-code (LAMMPS/VASP/QE/MOOSE) simulation failures: classifies the failure signature (nonconvergence, NaN/Inf, exploding energy, unstable timestep, pressure blow-up, missing potentials/pseudopotentials, memory exhaustion, process crash/segfault, corrupted output, incomplete runs) and proposes a SAFE one-change-at-a-time RETRY LADDER with explicit STOP CONDITIONS…
- Simulation OrchestratorHesham SalamaOrchestrate multi-simulation campaigns — generate parameter sweep configurations (grid, linspace, or Latin Hypercube sampling), initialize and track batch job campaigns, monitor job completion status, and aggregate results with summary statistics across all runs.
- Simulation ValidatorHesham SalamaValidate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor runtime logs for residual growth, NaN/Inf, and adaptive dt collapse, and perform post-flight validation of results (physical bounds, mass/energy conservation, convergence). Diagnose failed simulations with probable-cause analysis and recommended fixes.
- Skill EvaluatorHesham SalamaRigorously evaluate an Agent Skill end-to-end across ANY coding-agent CLI — verify its scripts emit the documented numbers (deterministic checks), test whether its description triggers on the right prompts, and measure whether an agent following the SKILL.md beats a no-skill baseline (with/without pass-rate delta, mean ± stddev, benchmarked).
- Slurm Job Script GeneratorHesham SalamaGenerate correct, copy-pasteable SLURM sbatch job scripts and sanity-check HPC resource requests — configure nodes, MPI tasks, OpenMP threads, memory (per-node or per-cpu), GPUs, walltime, partitions, modules, and environment variables, with automatic detection of conflicting directives and oversubscription.
- Time SteppingHesham SalamaPlan and control time-step policies for transient simulations — couple CFL and physics-based stability limits with adaptive stepping, ramp initial transients through sharp gradients or phase changes, schedule output intervals and checkpoint cadence, and plan restart strategies for long-running jobs.
- Workflow Engine MapperHesham SalamaMap computational materials tasks onto workflow engines such as atomate2, jobflow, AiiDA, pyiron, or a simple one-off script. Use when deciding how to structure a reproducible campaign, DAG, restart strategy, provenance record, storage layout, or migration path from ad hoc scripts to managed workflows.