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MagShockZ

Analysis code for the Magnetized Collisionless Shocks on Z (MagShockZ) experiment. It converts FLASH MHD output into initialized OSIRIS PIC input decks, drives WarpX hybrid and full-PIC piston runs off the same data, and analyses all three. Most work runs on NERSC Perlmutter.

Quick start

conda activate analysis
pip install -e .                    # editable; also do this in the osiris2 env

python scripts/osiris_overview.py --config config/perlmutter_1.3.1d.yaml

import magshockz then works from a script, a notebook, a REPL or an sbatch file with no path manipulation:

from magshockz.common import run_spec, piston_profile
from magshockz.init.warpx import units

Documentation

docs/user_guide.md is the place to start — every command, both environments, the shared flags.

document covers
docs/user_guide.md every command, both environments, the shared flags
docs/osiris_pipeline.md run specs, RunSpec resolution, deck generation, collisions
docs/flash_analysis.md FLASH config resolution, results directories, experimental streak images
docs/warpx_pipeline.md both WarpX schemas; the heater deck's constraints
docs/physics_notes.md OSIRIS normalized units, the FLASH sqrt(4π), the PyYAML 1.1 float trap

CLAUDE.md is the guidance file for Claude Code: layout, architecture and code style. It is not a substitute for the above.

Layout

magshockz/            the installable package -- all pure, testable logic
  common/             used by two or more codes
  init/{osiris,warpx} deck generation and validation
  analysis/{flash,osiris,warpx}
scripts/              thin CLI wrappers, flat, prefixed by code (flash_/osiris_/warpx_/paper_)
runs/                 run specs: the inputs that DEFINE a run (*.run.yaml, *.warpx.yaml)
config/               analysis configs: how to ANALYSE a run
init_warpx/           WarpX sbatch + build scripts
notebooks/            exploratory notebooks
tests/                pytest suite
docs/                 the documentation above
input_files/          generated run trees (gitignored, regenerable)

Each run's parameters live once, in a run.yaml in the run's own directory; analysis reads them back through magshockz/common/run_spec.py::RunSpec rather than re-copying them into analysis configs.

Environments

Two conda environments, used for disjoint stages — do not mix them:

  • osiris2 — FLASH→OSIRIS deck generation. The converter is the standalone flash2osiris package.
  • analysis — OSIRIS/WarpX/FLASH analysis; has pyVisOS (osh5io/osh5def/osh5vis), osiris_utils, yt and unyt.

Tests

pytest                                        # full suite
pytest --cov=magshockz --cov-report=term-missing

CI installs the package and runs the same suite. The OSIRIS stack is not pip-installable, so tests/conftest.py stubs it when absent and runs against the real one on Perlmutter.