ai-modcon/genesis-skills/gs2

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):

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