Simulation Validator

Goal

Provide a three-stage validation protocol: pre-flight checks, runtime monitoring, and post-flight validation for materials simulations.

Requirements

• Python 3.10+
• No external dependencies (uses Python standard library only)
• Works on Linux, macOS, and Windows

Inputs to Gather

Before running validation scripts, collect from the user:

Decision Guidance

When to Run Each Stage

Is simulation about to start?
├── YES → Run Stage 1: preflight_checker.py
│         └── BLOCK status? → Fix issues, do NOT run simulation
│         └── WARN status? → Review warnings, document if accepted
│         └── PASS status? → Proceed to run simulation
│
Is simulation running?
├── YES → Run Stage 2: runtime_monitor.py (periodically)
│         └── Alerts? → Consider stopping, check parameters
│
Has simulation finished?
├── YES → Run Stage 3: result_validator.py
│         └── Failed checks? → Do NOT use results
│                            → Run failure_diagnoser.py
│         └── All passed? → Selected metric checks passed; physical validity still needs model-specific evidence

Choosing Validation Thresholds

Script Outputs (JSON Fields)

Three-Stage Validation Protocol

Stage 1: Pre-flight (Before Simulation)

1. Run scripts/preflight_checker.py --config simulation.json
2. BLOCK status: Stop immediately, fix all blocker issues
3. WARN status: Review warnings, document accepted risks
4. PASS status: Proceed to simulation

Note: preflight_checker.py validates required keys, numeric ranges, output-directory access, and disk space. It does not evaluate numerical stability (CFL / diffusion-Fourier). For explicit stability gating use skills/core-numerical/numerical-stability/scripts/cfl_checker.py.

python3 scripts/preflight_checker.py \
    --config simulation.json \
    --required dt,dx,kappa \
    --ranges "dt:1e-6:1e-2,dx:1e-4:1e-1" \
    --min-free-gb 1.0 \
    --json

Stage 2: Runtime (During Simulation)

1. Run scripts/runtime_monitor.py --log simulation.log periodically
2. Configure alert thresholds based on problem type
3. Stop simulation if critical alerts appear

python3 scripts/runtime_monitor.py \
    --log simulation.log \
    --residual-growth 10.0 \
    --dt-drop 100.0 \
    --json

Stage 3: Post-flight (After Simulation)

1. Run scripts/result_validator.py --metrics results.json
2. All checks PASS: Results are valid for analysis
3. Any check FAIL: Do NOT use results, diagnose failure

python3 scripts/result_validator.py \
    --metrics results.json \
    --bound-min 0.0 \
    --bound-max 1.0 \
    --mass-tol 1e-3 \
    --json

For variational / gradient-flow models (Allen-Cahn, Cahn-Hilliard), add --variational to enforce a strict monotone non-increasing energy check.

Failure Diagnosis

When validation fails:

python3 scripts/failure_diagnoser.py --log simulation.log --json

Conversational Workflow Example

User: My phase field simulation crashed after 1000 steps. Can you help me figure out why?

Agent workflow:

1. First, check the log for obvious errors:

   python3 scripts/failure_diagnoser.py --log simulation.log --json

2. If diagnosis suggests numerical blow-up, check runtime stats:

   python3 scripts/runtime_monitor.py --log simulation.log --json

3. Recommend fixes based on findings:
   • If residual grew rapidly → reduce time step
   • If dt collapsed → check stability conditions
   • If NaN detected → check initial conditions

Error Handling

Interpretation Guidance

Status Meanings

Confidence Score Interpretation

A requested bound (--bound-min/--bound-max) with no matching field_min/field_max in the metrics is reported as a failed bounds_unverifiable check, never a vacuous pass. For variational/gradient-flow runs, pass --variational (or set "energy_variational": true in the metrics) to enforce a strict monotone non-increasing energy check (energy_monotone); otherwise a weaker energy_net_decrease check is used, which does not detect mid-run spikes.

Common Failure Patterns

Verification checklist

Do not trust a validation verdict until each applicable item below is satisfied with the concrete artifact named. Record these in your summary to the user.

• Ran result_validator.py --json and confirmed results.status is PASS (not INSUFFICIENT_DATA) AND results.confidence_score == 1.0; a null score or INSUFFICIENT_DATA means no check ran — treat as unverified, not as a pass.
• Listed results.checks and confirmed every requested check actually appears (e.g. mass_conserved, bounds_satisfied, no_nan, and energy_monotone/energy_net_decrease); confirmed results.failed_checks is empty and contains no bounds_unverifiable entry (which means a requested bound had no field_min/field_max to compare against).
• For variational/gradient-flow models (Allen-Cahn, Cahn-Hilliard), passed --variational (or set "energy_variational": true) so energy_monotone is enforced; recorded that the weaker energy_net_decrease was NOT relied on, since it cannot detect mid-run energy spikes.
• Recorded the mass drift tolerance used (--mass-tol, default 1e-3) and confirmed it matches the Conservative/Standard/Relaxed column appropriate to the run; did not silently accept the default for a tight-conservation problem.
• Ran runtime_monitor.py --json and recorded residual_stats (min/max/last) and dt_stats; confirmed there are no alerts for NaN/Inf/overflow, residual growth above --residual-growth, or dt collapse below --dt-drop.
• Confirmed numerical stability was gated separately via core-numerical/numerical-stability/scripts/cfl_checker.py (CFL/Fourier limit) — preflight_checker.py does NOT evaluate CFL/Fourier and a PASS preflight says nothing about temporal/spatial stability.
• On any FAIL or alert, ran failure_diagnoser.py --json and recorded the probable_causes/recommended_fixes, rather than reusing the results.

Common pitfalls & rationalizations

Security

Input Validation

• Config file paths are validated for existence before parsing; non-existent paths produce clear errors (exit code 2)
• --required parameter names are validated against a safe-character allowlist (^[A-Za-z0-9_.-]+$); names with shell metacharacters are rejected
• --ranges entries are parsed as name:min:max with finite numeric bounds enforced and max > min required
• --min-free-gb is validated as a finite positive number (negatives, zero, nan, inf rejected)
• --residual-growth and --dt-drop thresholds are validated as finite positive numbers
• --bound-min and --bound-max are validated as finite numbers (nan/inf rejected), and --bound-max > --bound-min is enforced; --mass-tol is validated as a finite positive number
• Invalid input exits with code 2 and an explanatory message

File Access

• preflight_checker.py reads a single user-specified config file (JSON/YAML) and checks disk space on the volume hosting the resolved output directory
• runtime_monitor.py reads a single log file specified by --log; log files are size-limited (500 MB max) and rejected before parsing if larger
• result_validator.py reads a single metrics file (JSON) specified by --metrics
• failure_diagnoser.py reads a single log file specified by --log; log files are size-limited (500 MB max) before parsing
• No scripts write to the filesystem; all output goes to stdout

Tool Restrictions

• Read: Used to inspect script source, references, config files, and simulation logs
• Bash: Used to execute the four Python validation scripts (preflight_checker.py, runtime_monitor.py, result_validator.py, failure_diagnoser.py) with explicit argument lists
• Write: Used to save validation reports; writes are scoped to the user's working directory
• Grep/Glob: Used to locate log files, config files, and search references

Safety Measures

• No eval(), exec(), or dynamic code generation
• All subprocess calls use explicit argument lists (no shell=True)
• failure_diagnoser.py uses hardcoded, pre-compiled diagnostic regex patterns; runtime_monitor.py accepts optional --residual-pattern / --dt-pattern overrides that are compiled with re.compile (no eval) and applied only to the user's own log
• Diagnostic strings emitted in output are drawn from the skill's fixed cause/fix table, not interpolated from raw log content

Limitations

• Not a real-time monitor: Scripts analyze logs after-the-fact
• Regex-based: Log parsing depends on pattern matching; may miss unusual formats
• No automatic fixes: Scripts diagnose but don't modify simulations

References

• references/validation_protocol.md - Detailed checklist and criteria
• references/log_patterns.md - Common failure signatures and regex patterns

Version History

• v1.2.3 (2026-10-19): Reject invalid or incomplete metrics and distinguish the check-pass fraction from physical or statistical confidence.
• v1.2.2 (2026-06-24): Added a Verification checklist (evidence-based, tied to the four scripts' JSON outputs) and a Common pitfalls & rationalizations table to harden agent interpretation of validation verdicts.
• v1.2.0 (2026-06-23): Corrected diagnostic regexes (no false convergence/blow-up on healthy logs), direction-aware dt-collapse detection, NaN/Inf scan in runtime monitor, strict variational energy check, non-vacuous bounds/confidence, config-relative output-dir + correct-volume disk check, and implemented the documented input-validation/file-size safeguards
• v1.1.0 (2024-12-24): Enhanced documentation, decision guidance, Windows compatibility
• v1.0.0: Initial release with 4 validation scripts

Numerical and evidence limits

The confidence_score field is retained for compatibility and is the fraction of selected checks passed. It is not a statistical confidence level or probability of physical correctness. Energy checks require at least two finite samples. Passing supplied metrics does not validate the governing model, units, boundary conditions or solver execution.