Fix _rerun.csv file handling so rerun can re-read its labels#17
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The streamfunction flux arrays and their per-zone loops were hard-coded to a fixed 21 kill zones, and the kill-zone (10) and tracer (10) capacities were scattered as bare literals across many files (including per-project kill_zones.F90). This generalizes those limits and sizes the streamfunction allocation to the zones a run actually uses. - Add named capacity constants in mod_precdef: MAXGEOZONES, MAXTRACERS, and MAXZONES = 1 + MAXTRACERS + MAXGEOZONES, used to dimension the kill-zone and tracer configuration arrays. - Compute maxlbas (the actual streamfunction zone count) from the run: namelist geographic zones + subdomain wall zones + tracer kill zones, finalised in init_subdomain once exitType and all zones are known. The flux arrays (offline) and the compute_stream loop now size to maxlbas instead of a fixed 21. - Derive runtime loop bounds and the subdomain "last 4" wall slots from SIZE() of the arrays, removing the hard-coded slot numbers (7-10) in mod_subdomain and the 1,10 loops in kill_zones.F90 (x5), mod_diffusion, and mod_init. - Initialise ienw/iene/jens/jenn to 0 so undefined slots are well-defined. Fixes a latent out-of-bounds when the configured zone count differs from 21, and an under-allocation when an exitType=2 run uses a subdomain (which promotes exitType to 3 and adds geographic walls). Behaviour is otherwise unchanged: streamfunction output now contains the actual number of zone blocks, verified byte-identical to the previous output for the real zones. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
`./runtracmass rerun` could not re-read the trajectory labels it needs, due to two issues in the rerun file path (both independent of streamfunctions): - The output-file prefix default (outDataFile = 'TRACMASS' when empty) was applied only inside open_outfiles, which runs AFTER read_rerun. So read_rerun looked for '_rerun.csv' instead of 'TRACMASS_rerun.csv' and reported "No rerun file", leaving every trajectory label unset. Apply the default in init_namelist, before it is first used. - _rerun.csv is written comma-separated but read_rerun parsed it with a fixed "(I8,I3,I10)" format, mis-reading lbas. Use list-directed input. With both fixes a rerun pass correctly re-seeds and re-integrates the labelled trajectories (verified: exit positions identical to a normal run). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This was referenced Jun 23, 2026
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Summary
Two independent fixes to the
./runtracmass rerunfile-handling path. As-is, a rerun pass cannot re-read the trajectory labels (lbas) it needs, so it silently deactivates/mislabels every trajectory.The bugs
outDataFiledefaults to'TRACMASS'only insideopen_outfiles, which runs afterread_rerun. Soread_rerunlooked for_rerun.csvinstead ofTRACMASS_rerun.csv→ "No rerun file" → every trajectory label left unset. Fixed by applying the default ininit_namelist, before first use._rerun.csvis written comma-separated ((I8,',',I3,',',I10)) butread_rerunparsed it with(I8,I3,I10), mis-readinglbas. Fixed with list-directed input.Effect
Without these, a rerun pass reports
0 exitedand writes an empty_run.csv— it never re-integrates the labelled trajectories. (Offline never noticed because it ignores the re-integration and re-reads the trajectory files from disk.) With the fixes, a rerun pass correctly re-seeds and re-integrates the labelled trajectories — verified: exit positions are identical to a normal run.Also fixes a crash in offline rerun
As a side effect, this resolves a crash in offline rerun (
./runtracmass rerunwithl_offline=.TRUE.). Onmain, the broken file handling leaves every trajectory deactivated, producing inconsistent_ini/_rerunfiles; the offline postprocess then reads anntracbeyond what it allocated and crashes:With
read_rerunworking, the files are consistent and the crash no longer occurs. (A separate, narrower robustness gap remains — the postprocess indexestraj_out(ntrac1)without a bounds check, so a genuinely inconsistent/stale_rerun.csvcould still crash ungracefully — but that is independent of this PR.)Testing
Theoretical project, gfortran
-fbounds-check: clean build; a rerun pass now reports the same terminations as the original run and reproduces identical trajectory exit positions; offline rerun completes without the out-of-bounds crash.🤖 Generated with Claude Code
Addresses #19.