AI-ModConAI-ModCon/genesis-skills/skills/plasma-sim-skills/gs2/SKILL.md

gs2

Skill30 starsChanged 51 days agoBSD-2-ClauseView on GitHub

Gyrokinetics simulation code GS2. Use when installing GS2, writing or modifying GS2 input namelists, configuring species/grid/field/collision parameters, or launching GS2 runs on local machines or HPC clusters.

In this repository30 other files it gives its agents.
- skills/academy/agents.mdAGENTS.md
- academySkill
- amsc-data-movement-apiSkill
- amsc-magSkill
- amsc-python-clientSkill
- globus-computeSkill
- i2-apiSkill
- iri-apiSkill
- skill-explorerSkill
- croissant-validatorSkill
- datacard-generatorSkill
- hdmf-schema-builderSkill
- skill-creatorSkill
- well-convertSkill
- card-eval-updaterSkill
- agentic-vulnerabilities-scanSkill
- ai-fingerprintSkill
- battleprintSkill
- fingerprintingSkill
- uncertainty-quantificationSkill
- uq-metrics-evaluatorSkill
- skill-searchSkill
- auroraSkill
- frontierSkill
- pbsSkill
- perlmutterSkill
- slurmSkill
- literature-searchSkill
- multi-agent-systemsSkill
- gkeyllSkill

The file

We split this skill into the rules it gives an agent

2 rules. About 0 are common, 1 is distinctive, and 1 is very specific to this project.

≈0
Common · estimate
Many files like this have a rule of this kind.
≈1
Distinctive · estimate
This author's own choices. Worth a look.
1
Very specific
Tied to their project's names, files or tools. Probably skip.

Common
Distinctive
Very specific

Very specific:
If your HPC system is not in Makefiles/, create a new Makefile.$GK_SYSTEM.
line 26
Distinctive:
Start from an existing example rather than writing from scratch:
line 53

≈ “Common” is an estimate: at least 1 in 5 of the 350,495 skill files we read have a rule of the same kind, not the same words. “Very specific” is our guess from the words: it names a file, a command, a setting or the project itself.

Keep what fits and drop the rest. Your version, ready for your agents.

Files

SKILL.md

GS2 — Gyrokinetics Simulation Code

GS2 is an Eulerian gyrokinetic flux-tube code for studying low-frequency turbulence and instabilities in magnetized plasmas. It solves the nonlinear gyrokinetic equation for multiple species with optional electromagnetic fields.

Installation

# Clone with all submodules
git clone --recurse-submodules https://bitbucket.org/gyrokinetics/gs2.git
cd gs2

# Set the system name (see references/installation.md for supported systems)
export GK_SYSTEM=your_system_name

# Build
make -I Makefiles

If your HPC system is not in Makefiles/, create a new Makefile.$GK_SYSTEM. See references/installation.md for dependencies, supported systems, and build flags.

Input File Basics

GS2 uses Fortran namelist format (.in files):

&namelist_name
  parameter = value   ! inline comments allowed
/

Key namelists (order in file does not matter):

Namelist	Purpose
`knobs`	Timestep, beta, run duration
`species_parameters_N`	Per-species mass, charge, temperature, density
`theta_grid_knobs`	Magnetic geometry / poloidal grid
`fields_knobs`	Field equation algorithm
`dist_fn_knobs`	Distribution function evolution
`collisions_knobs`	Collision operator
`kt_grids_knobs`	Perpendicular wavenumber grid type
`init_g_knobs`	Initial condition for distribution function
`gs2_diagnostics_knobs`	Output frequency and diagnostics
`hyper_knobs`	Hyperviscosity/hyperresistivity

Start from an existing example rather than writing from scratch:

ls tests/linear_tests/cyclone_itg_collisional/

See references/namelists.md for parameter details.

Running Simulations

# Validate input before running
gs2 --check-input run.in

# Serial run
gs2 run.in

# MPI parallel run
mpirun -np 128 gs2 run.in

# Restart from checkpoint
mpirun -np 128 gs2 run.in --restart

Output goes to run.out (text) and run.nc (NetCDF diagnostics).

See references/running.md for MPI decomposition strategies, HPC job scripts, convergence checks, and restart workflow.

Quick Reference

gs2 --help          # list all command-line options
gs2 --check-input   # validate namelists without running

Common build flags:

make -I Makefiles DEBUG=on       # debug build
make -I Makefiles USE_MPI=on     # explicit MPI enable

Additional Resources

Installation details
Namelist parameter reference
Running and HPC workflow
GS2 docs: https://gyrokinetics.gitlab.io/gs2/
Namelist reference: https://gyrokinetics.gitlab.io/gs2/page/namelists/index.html
Source: https://bitbucket.org/gyrokinetics/gs2

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