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Runs the six structural checks on a converted SAGE LHaloTree HDF5 file. Use after any conversion run — test or full — to verify the output file is structurally correct before proceeding.
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
SOC 職業分類に基づく
Guides drafting or adapting a format-specific conversion driver for the SAGE merger tree converter. Use when no existing driver matches the input format and a new driver must be written in assets/ before the test conversion can run.
Provides field-level guidance for mapping input merger tree fields to the SAGE LHaloTree schema (HDF5 or binary). Use during web discovery or KDB entry creation when individual field mappings, unit conversions, or pointer reconstruction decisions need to be made.
Independently verifies the semantic validation plots and plotting code against the mandatory checklist. Use after semantic-validation generates the seven plots, before presenting results to the user. Operates independently - does not rely on the main agent's assessment.
Generates the seven mandatory semantic validation plots of the converted output merger trees. Use after a full conversion run in Stage 3 to assess whether the converted trees are physically plausible.
Adds a new format driver and schema mapping JSON to the KDB after a successful conversion of a previously unknown format. Use in Stage 4 when the input format was not found in the KDB at session start.
Updates an existing KDB schema mapping JSON with new information discovered during a conversion session. Use in Stage 4 when the input format was found in the KDB but the session revealed missing or incorrect information in the existing entry.
| name | syntactic-validation |
| description | Runs the six structural checks on a converted SAGE LHaloTree HDF5 file. Use after any conversion run — test or full — to verify the output file is structurally correct before proceeding. |
If the Stage 2 preamble has not already been output this session (i.e., driver-authoring was not read first), output the following verbatim now:
Stage 2 — Test Engine
I'll run a test conversion on ~100 trees and validate the output structurally.
1. Driver check
- exists -> proceed to step 2
- missing -> author driver -> proceed to step 2
2. Test conversion (~100 trees)
3. Syntactic validation (6 checks)
4. Functional validation
- SAGE binary set -> run SAGE dry-run
- not set -> skip
5. [G2] Confirm test validation
Determine the output format from the conversion run, then follow the appropriate path:
lhalo_hdf5 output (file ends in .hdf5): run all six checks below via run_syntactic_checks.py. Continue reading this skill.
lhalo_binary output (no .hdf5 extension, e.g. test_<base>_STC.0): run the binary check script instead and skip the six HDF5 checks:
$PYTHON_BIN .ai/skills/syntactic-validation/scripts/run_binary_checks.py \
--file <output_binary_path> \
--n-snapshots <N>
The binary script implements five checks: file_readable, header_consistency, file_size_consistency, first_tree_pointers, first_tree_snapnums. It exits with code 0 if all five pass. Record the result and proceed to Gate G2 once all five checks PASS.
Two path prefixes are used in this skill:
.ai/skills/syntactic-validation/references/<file> — files in this skill's own references/ subfolder.reference/<file> (project root) — files in the project-root reference/ directory (e.g. reference/sage_lhalotree_hdf5_schema.md).Run all six checks in order. Each check produces an explicit PASS or FAIL.
There are no partial passes. Record each result in assets/validation_log.md.
Run the deterministic script first:
$PYTHON_BIN .ai/skills/syntactic-validation/scripts/run_syntactic_checks.py \
--file <output_hdf5_path> \
--n-snapshots <N>
The script implements checks 2–6. Check 1 (file integrity) is done manually as described below. The script exits with code 0 if all checks pass, non-zero otherwise.
See .ai/skills/syntactic-validation/references/check_procedures.md for the full pass conditions and expected output
for each check. See .ai/skills/syntactic-validation/references/h5py_patterns.md for Python code patterns.
Applies to lhalo_hdf5 only. For lhalo_binary, use run_binary_checks.py (see Format Dispatch above).
Method: Run h5dump -n <file>. If h5dump is not available, fall back to
opening the file with $PYTHON_BIN -c "import h5py; h5py.File('<file>', 'r').close()".
PASS: The file opens without error and the root groups are listed. FAIL: Any error opening the file (corrupt, incomplete, wrong format).
Method: Compare all datasets in each Tree<X>/ group against the mandatory
field list in reference/sage_lhalotree_hdf5_schema.md (project root). Also verify:
Header/TreeNHalos exists as a dataset (not an attribute).len(Header/TreeNHalos) == Header.attrs["NtreesPerFile"].sum(Header/TreeNHalos) == Header.attrs["NhalosPerFile"].PASS: All mandatory fields present in every tree group; no undocumented extra
fields; TreeNHalos length and sum match header attributes.
FAIL: Any mandatory field missing, any undocumented field present, or any
header attribute inconsistency.
Mandatory fields: Descendant, FirstProgenitor, NextProgenitor,
FirstHaloInFOFGroup, NextHaloInFOFGroup, SubhaloLen, Group_M_Crit200,
SubhaloVMax, SubhaloIDMostBound, SnapNum, SubhaloPos, SubhaloVel, SubhaloSpin.
Method: For every halo in every tree, verify:
FirstProgenitor[i] is -1 or in [0, N-1].NextProgenitor[i] is -1 or in [0, N-1].Descendant[i] is -1 or in [0, N-1].FirstProgenitor[i] != -1: SnapNum[FirstProgenitor[i]] < SnapNum[i].NextProgenitor[i] != -1: SnapNum[NextProgenitor[i]] < SnapNum[i] (same
snapshot as FirstProgenitor's snapshot is also acceptable if it is strictly
less than i's snapshot).Descendant[i] != -1: SnapNum[Descendant[i]] > SnapNum[i].PASS: All constraints satisfied for every halo in every tree. FAIL: Any out-of-range index or any snapshot ordering violation.
Method: For every halo in every tree, verify:
FirstHaloInFOFGroup[i] is -1 or in [0, N-1].NextHaloInFOFGroup[i] is -1 or in [0, N-1].FirstHaloInFOFGroup[i] != -1: SnapNum[FirstHaloInFOFGroup[i]] == SnapNum[i].NextHaloInFOFGroup[i] != -1: SnapNum[NextHaloInFOFGroup[i]] == SnapNum[i].PASS: All constraints satisfied. FAIL: Any out-of-range index or any cross-snapshot spatial link.
Method: For every halo in every tree, verify SnapNum[i] is in
[0, n_snapshots - 1] where n_snapshots is provided via --n-snapshots.
If --n-snapshots is not known, use max(SnapNum) over all trees as a lower bound
and report a note that the upper bound was not verified.
PASS: All SnapNum values are non-negative integers within the valid range.
FAIL: Any SnapNum value is negative or exceeds n_snapshots - 1.
Method: For every halo in every tree, verify:
Group_M_Crit200[i] is in [0.0, 1e6] (units: 10¹⁰ M☉/h).|SubhaloVel[i]| is in [0, 10000] km/s (physically reasonable upper bound).|SubhaloVMax[i]| is in [0, 10000] km/s.SubhaloPos[i, :] values are finite (not NaN or Inf).Group_M_Crit200[i] is finite (not NaN or Inf).PASS: All values within physically reasonable bounds; no NaN or Inf. FAIL: Any value outside bounds or any NaN/Inf.
assets/drivers/<format_id>.py.