hpc-fenics

# HPC FEniCS Treat FEniCS as a family with two main stacks: classic FEniCS and DOLFINx. ## Start 1. Read `references/runtime-selection.md` first. 2. Read `references/dolfinx-boundary-workflow.md` when targeting DOLFINx boundary conditions. 3. Read `references/ufl-and-solver-patterns.md` when translating PDEs, choosing spaces, or building forms. 4. Read `references/pde-template-cookbook.md` when mapping common PDE classes to known formulation patterns. 5. Read `references/time-dependent-and-nonlinear-patterns.md` when building transient or nonlinear solvers. 6. Read `references/implementation-skeletons.md` when you need a concrete script shape for classic FEniCS or DOLFINx. 7. Read `references/petsc-solver-playbook.md` when choosing linear, nonlinear, or block solver settings. 8. Read `references/mixed-problems-and-output.md` when working with mixed spaces, XDMF, or post-processing. 9. Read `references/cluster-execution-playbook.md` when staging a FEniCS or DOLFINx script for scheduler-backed cluster execution. 10. Read `references/boundary-io-and-errors.md` when repairing runtime failures or resolving IO issues. ## Work sequence 1. Choose one stack and stay consistent: - classic FEniCS: `fenics` or `dolfin` - modern stack: `dolfinx` 2. Translate the PDE into the correct weak form before writing code. 3. Match unknown type and space: - scalar field -> scalar space - vector field -> vector space - mixed formulation -> mixed space with explicit subspace handling 4. For linear problems, use `TrialFunction` and `TestFunction`. 5. For nonlinear problems, use a `Function` for the unknown and solve a residual form. 6. Write outputs in a format the expected post-processor can open, usually XDMF for mesh-coupled fields. ## Guardrails - Do not mix classic FEniCS imports with DOLFINx APIs in one script. - Do not use `TrialFunction` for a nonlinear unknown. - Do not guess a boundary condition if the PDE is under-constrained; say what is missing. - Do not ignore shape and rank mismatches in UFL expressions. ## Additional References Load these on demand: - `references/gmsh-meshtags-and-refinement.md` for imported meshes, physical groups, markers, and refinement transfer - `references/io-visualization-and-writers.md` for XDMF, VTK, VTX, and visualization-safe output - `references/parallel-and-mpi-caveats.md` for ownership, boundary marking, and parallel consistency - `references/space-boundary-output-matrix.md` for function-space, boundary-condition, and writer-selection matrices - `references/cluster-execution-playbook.md` for MPI launch, environment pinning, and cluster-side IO planning ## Reusable Templates Use `assets/templates/` when a concrete script scaffold is needed, especially: - `poisson_dolfinx.py` - `transient_diffusion_dolfinx.py` - `fenics-dolfinx-slurm.sh` ## Outputs Report: - chosen stack and version family if known - PDE form and space selection - boundary conditions applied - expected output files - the exact failure class if the script is being repaired