Memory test PR

CLAUDE.md

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+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+Sirocco (Simulating Ionization and Radiation in Outflows Created by Compact Objects) is a Monte Carlo radiative transfer code using the Sobolev approximation. It simulates winds and outflows in systems like cataclysmic variables, AGN, X-ray binaries, and young stellar objects. Formerly known as "Python" (renamed October 2024).
+
+## Build Commands
+
+**Environment setup** (required before building):
+```bash
+export SIROCCO=/path/to/Sirocco
+```
+
+**First-time full build** (compiles GSL, CUnit, then Sirocco):
+```bash
+./configure        # detects compilers (mpicc/gcc) and optional CUDA
+make install       # builds GSL 2.6, CUnit 3.2.7, and all source
+```
+
+**Recompile source only** (after initial install):
+```bash
+cd source && make CC=mpicc sirocco       # main program
+cd source && make CC=mpicc all           # all targets + indent check
+cd source && make D sirocco              # debug/profiling build (-g -pg)
+cd source && make CC=gcc sirocco         # compile without MPI
+cd source && make INDENT=no sirocco      # skip auto-indentation
+```
+
+**Other build targets** (all from `source/`):
+- `make swind` — spectral wind analysis
+- `make windsave2table` — convert wind saves to ASCII tables
+- `make windsave2fits` — convert wind saves to FITS (requires cfitsio)
+- `make rad_hydro_files`, `make modify_wind`, `make inspect_wind` — wind utilities
+- `make sirocco_optd` — optical depth calculations
+
+**Clean build artifacts**:
+```bash
+cd source && make clean
+```
+
+**Unit tests** (requires CUnit + cmake):
+```bash
+make check                    # from top-level
+cd source && make check       # from source directory
+```
+
+**Running Sirocco**:
+```bash
+$SIROCCO/bin/Setup_Sirocco_Dir              # set up working directory with symlinks
+sirocco parameter_file.pf                    # serial
+sirocco -i root                              # interactive mode (creates parameter file)
+mpirun -n 4 sirocco parameter_file.pf       # parallel with MPI
+```
+
+## Architecture
+
+### Language and Compilation
+- C (gnu99 standard), ~130 source files in `source/`
+- Default compiler: `mpicc` (sets `-DMPI_ON`); falls back to gcc/clang
+- Optional CUDA support via `--with-cuda` configure flag (matrix operations on GPU)
+- Dependencies: GSL 2.6 (bundled in `software/`), CUnit 3.2.7 (bundled)
+- Auto-indentation enforced on commit via `py_progs/run_indent.py` using GNU indent
+
+### Key Source Files
+- `source/sirocco.c` — main entry point, orchestrates ionization and spectrum cycles
+- `source/sirocco.h` (~98KB) — central header with all major data structures (`PlasmaPtr`, `WindPtr`, `PhotPtr`, domain geometry structs)
+- `source/atomic.h` (~31KB) — atomic data structures (ions, lines, levels, cross-sections)
+- `source/templates.h` — auto-generated function prototypes (via `cproto`)
+- `source/version.h` — auto-generated at build time from git hash
+
+### Core Code Organization (in `source/`)
+- **Wind models**: `define_wind.c`, `wind.c`, `wind2d.c`, `spherical.c`, `cylindrical.c`, `rtheta.c`, `sv.c` (Shlosman-Vitello), `knigge.c`, `homologous.c`, `corona.c`, `shell_wind.c`, `hydro_import.c`
+- **Photon transport**: `trans_phot.c`, `photon2d.c`, `photon_gen.c`, `extract.c`, `paths.c`, `phot_util.c`
+- **Radiation & spectra**: `radiation.c`, `spectra.c`, `bands.c`, `continuum.c`, `brem.c`, `compton.c`, `emission.c`
+- **Ionization**: `ionization.c`, `direct_ion.c`, `saha.c`, `charge_exchange.c`, `partition.c`, `levels.c`, `recomb.c`
+- **Macro-atom**: `matom.c`, `matom_diag.c`, `macro_gov.c`, `macro_gen_f.c`, `macro_accelerate.c`, `estimators_macro.c`
+- **Line transfer**: `lines.c`, `resonance.c` (`resonate.c`), `dielectronic.c`
+- **Disk**: `disk.c`, `disk_init.c`, `disk_photon_gen.c`
+- **Setup/config**: `setup.c`, `setup_domains.c`, `setup_disk.c`, `setup_star_bh.c`, `setup_line_transfer.c`, `parse.c`, `rdpar.c`
+- **MPI communication**: `communicate_plasma.c`, `communicate_wind.c`, `communicate_macro.c`, `communicate_spectra.c`, `para_update.c`
+- **I/O**: `windsave.c`, `windsave2table_sub.c`, `xlog.c`, `diag.c`
+- **Math utilities**: `recipes.c`, `random.c`, `cdf.c`, `vvector.c`, `matrix_cpu.c`, `matrix_gpu.cu`
+- **Frame transformations**: `frame.c`
+
+### Data Directories
+- `xdata/` — atomic data files read at runtime (referenced via `Atomic_data` parameter)
+- `xmod/` — model grids and spectra for disk/stellar models
+- `examples/` — parameter files (`.pf`) organized by type: `basic/`, `extended/`, `regress/`, `gh-workflow/`
+
+### Python Utilities (`py_progs/`)
+Support scripts for data processing, visualization, and code maintenance:
+- `run_indent.py` — enforces GNU indent code style on changed C files
+- `MakeMacro.py` — generates macro-atom data from Chianti/Topbase databases
+- `plot_spec.py`, `plot_wind.py`, `plot_tot.py` — visualization
+- `hydro_2_python.py` — parse hydro simulation output for use with Sirocco's hydro import facility
+- `import_model.py` — unified import-file generator for all coordinate systems (spherical, cylindrical, polar, cyl3d, sph3d)
+- `balmer_decrement.py` — physics validation test
+- `regression.py` — regression testing utilities
+
+### Testing
+- **Unit tests**: CUnit-based in `source/tests/` (test_matrix, test_compton, test_define_wind, test_run_mode, test_translate)
+- **Integration tests**: GitHub Actions workflow (`.github/workflows/build.yml`) runs multiple example parameter files (CV, AGN, XRB, SN models) on pushes to dev/main
+- **Regression tests**: Examples in `examples/regress/`
+
+### Build System Notes
+- `Makefile.in` is the top-level template (not auto-generated by autoconf — `configure` is a hand-written shell script)
+- `source/Makefile` handles all C compilation, prototype generation, and indentation
+- `source/tests/Makefile` includes the main source Makefile and links all Sirocco source for unit tests
+- `get_models.c` cannot be included in `sirocco_source` list (prototype generation issue) but is added separately to object lists
+- `make prototypes` regenerates `templates.h`, `log.h`, `atomic_proto.h`, `math_proto.h` via `cproto`
+
+## Dependencies
+- GSL 2.6 (bundled in `software/`)
+- CUnit 3.2.7 (bundled in `software/`, requires CMake)
+- MPI: OpenMPI or MPICH (`mpicc`)
+- Optional: cfitsio (for FITS output via `windsave2fits`)
+- Optional: CUDA (for GPU matrix operations via `--with-cuda`)
+
+## Parameter Files
+
+Sirocco uses `.pf` parameter files with key-value pairs:
+```
+System_type(star,cv,bh,agn,previous)       cv
+Central_object.mass(msol)                   0.8
+Wind.type(SV,star,hydro,corona,...)         sv
+Photons_per_cycle                           100000
+```
+Example files are in `examples/basic/`, `examples/extended/`, and `examples/gh-workflow/`.
+
+## Documentation
+- Full docs: https://sirocco-rt.readthedocs.io
+- Model spectra (optional): clone `https://github.com/sirocco-rt/xmod` into `xmod/`
+
+## Claude Code Rules
+- **Never change the version number** in `source/version.h` or `source/Makefile` without explicit user instruction. Always ask before touching these.
+- **Never create two files whose names differ only in case** (e.g. `macro2simple.py` and `Macro2Simple.py`). macOS uses a case-insensitive filesystem and will treat them as the same file, causing one to silently overwrite the other on any Mac clone or pull.
+
+## Coding Conventions
+- GNU indent style enforced automatically on changed files during build (unless `INDENT=no`)
+- ANSI C with gnu99 standard
+- MPI code guarded by `#ifdef MPI_ON` preprocessor directives
+- CUDA code guarded by `#ifdef CUDA_ON`
+- Logging via `xlog.c` functions (Log, Error, Debug)