neko-simulation-setup

name	neko-simulation-setup
description	Help set up, explain, or modify Neko CFD simulation cases, including case files, meshes, and optional user files.

Neko Simulation Setup

Use this skill when helping with a concrete Neko simulation case, advising on simulation settings, explaining an existing case setup, or creating the files needed to run a case.

Core Workflow

• Treat each simulation as a separate case folder.
• The goal is to produce:
  • A computational mesh file, if not already provided by the user.
  • A JSON configuration file, usually .case or .json, referred to as the case file.
  • A Fortran user file, only when the setup really needs custom behavior.
• Prefer starting from an existing example instead of creating a case from scratch. Read examples/README.md, then the relevant example README.md.
• Ask the user whether a particular example is a good starting point when this is not already clear.
• Prompt for missing CFD-specific details. Avoid relying on educated guesses for physical setup, boundary conditions, mesh resolution, or solver choices. When making assumptions, state them explicitly.

Case File

• Use doc/pages/user-guide/case-file.md as the definitive reference for case file contents, and acknowledge that you got access to this file.
• The doc/schema folder contains JSON schema files that define the structure of case files. Use these to validate generated case files. You can use the contrib/validate_case_schema.py script to that end.
• Name generated case files after the case folder, using .json unless the user specifically asks for .case.
• Pretty-format generated JSON.

Mesh File

• Read doc/pages/user-guide/meshing.md before advising on or creating meshes.
• Handle meshes according to the available source:
  • If the user provides .nmsh, use it directly.
  • If the user provides .re2, convert it to .nmsh with rea2nbin.
  • If the user provides another format, help convert it first to .re2 and then to .nmsh, using the meshing guide.
  • If there is no mesh and the geometry is a box, generate it with genmeshbox.
    • Before using genmeshbox, study contrib/genmeshbox/genmeshbox.f90 closely enough to understand its inputs and behavior.
    • For non-uniform box meshes, generate edge-location files when needed, because genmeshbox reads non-uniform element distributions from files.
  • Always run mesh_checker on any generated or existing .nmsh file and make sure it reports no errors.

User File

• Read doc/pages/user-guide/user-file.md before creating or changing a user file.
• Create a user file only when the case cannot be expressed cleanly through the case file.
• Name the user file after the case folder with a .f90 extension.
• Look at examples/programming/README.md and the documented .f90 examples there before writing custom user-file logic. Other examples may also contain relevant user files.
• Follow doc/pages/developer-guide/code-style.md for Fortran style.
• Use doc/pages/developer-guide/important_types.md and the corresponding source files under src when working with important Neko types.
• Be generous with explanatory comments in generated user files.
• Run makeneko on any generated user file and make sure it compiles.

Completion Checks

• Confirm the case folder contains the expected case file, mesh file, and any necessary user file.
• Confirm generated JSON is formatted and named consistently.
• Confirm mesh_checker passed for the .nmsh mesh.
• Confirm makeneko passed when a user file was created or modified.
• If any check cannot be run locally, clearly tell the user what remains to be run and why.