Add loading a source from a .gkyl file - #1087
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GKYL_SOURCE_FROMFILE is implemented and verified. Summary:
What changed:
- New GKYL_SOURCE_FROMFILE value in enum gkyl_source_id (core/zero/gkyl_eqn_type.h)
- New source_import[GKYL_MAX_SOURCES] field on gkyl_gyrokinetic_source, reusing the same gkyl_gyrokinetic_ic_import struct you already know from init_from_file (file_name, jacobtot_inv_file_name, etc.)
- Extracted the read/rescale logic out of gk_species_file_import_init and gk_neut_species_kinetic_file_import_init into reusable gk_species_read_distf_from_file/gk_neut_species_kinetic_read_distf_from_file functions that write into any caller-supplied array
- Wired GKYL_SOURCE_FROMFILE into gk_species_source.c/gk_neut_species_source.c: the source shape is read once at init (asserting it's static — no evolve, no adaptive sources, no enforce_positivity for now) and _calc skips recomputation for it
Bug caught during verification: valgrind on the new regression test hit a segfault in gk_species_source_release — it unconditionally called gk_species_projection_release on proj_source[k], which is never initialized for a from-file source. Fixed by guarding that release loop (both charged and neutral species) on source_id != GKYL_SOURCE_FROMFILE.
Verification:
- gyrokinetic and gyrokinetic-unit build clean
- New regression test gyrokinetic/creg/rt_gk_sheath_1x2v_p1_source_import.c: runs a sheath sim once with GKYL_PROJ_SOURCE (writing -elc_source_0.gkyl/-ion_source_0.gkyl), then a second run with GKYL_SOURCE_FROMFILE pointing at those files — the reloaded source arrays are bit-for-bit identical to the originals
- Valgrind: 0 errors, 0 leaks
- Existing rt_gk_sheath_1x2v_p1_ic_import regression test still passes (confirms the extraction didn't break the IC-import path)
- Full ctest_gk* unit suite passes except ctest_gk_geometry_tok, which fails identically regardless of my changes (confirmed via git stash) — it's an unrelated EFIT/tokamak-geometry orthonormality issue with no file overlap with this work
Example usage now works exactly as you described, just on source instead of init_from_file:
.source = {
.source_id = GKYL_SOURCE_FROMFILE,
.num_sources = 1,
.source_import[0] = {
.type = GKYL_IC_IMPORT_F,
.file_name = "gk_wham_1x2v_p1-elc_source_0.gkyl",
},
},
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Adds
GKYL_SOURCE_FROMFILE, a newgkyl_source_idthat lets a gyrokinetic species (or kinetic neutral species) source term be loaded directly from a.gkylfile instead of being built from a projection, mirroring the existinginit_from_file/GKYL_IC_IMPORT_Fmechanism used for initial conditions.Verification
rt_gk_sheath_1x2v_p1_source_import.c) runs a sheath sim once withGKYL_PROJ_SOURCEto write out-elc_sourcefiles, then a second run reloads those same files viaGKYL_SOURCE_FROMFILE; the reloaded source arrays are confirmed bit-for-bit identical to the originals.Bug fix caught along the way
Valgrind caught a real crash in
gk_species_source_release/gk_neut_species_source_release, which unconditionally releasedproj_source[k]even when it was never initialized for a from-file source; both release paths are now guarded onsource_id != GKYL_SOURCE_FROMFILE.Implementation
Claude Sonnet 5 one-shot this using the prompt:
"Similar to how a distribution function can be loaded from a file
.init_from_file = {
.type = GKYL_IC_IMPORT_F,
.file_name = "gk_wham_1x2v_p1-elc_0.gkyl",
// .jacobtot_inv_file_name = "gk_wham_1x2v_p1-jacobtot_inv.gkyl",
},,
Enable sources to be loaded from files. This is specified inside as a GKYL_SOURCE_FROMFILE in the source_id of the source table"