Validate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor runtime logs for residual growth, NaN/Inf, and adaptive dt collapse, and perform post-flight validation of results (physical bounds, mass/energy conservation, convergence). Diagnose failed simulations with probable-cause analysis and recommended fixes. Use when preparing to launch a simulation, checking whether a running job is healthy, verifying that finished results are trustworthy, or debugging a crash or blow-up, even if the user only says "my simulation crashed" or "can I trust these results."
Installation
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Validate simulations across three stages — run pre-flight checks on configuration files (parameter ranges, required fields, disk space), monitor runtime logs for residual growth, NaN/Inf, and adaptive dt collapse, and perform post-flight validation of results (physical bounds, mass/energy conservation, convergence). Diagnose failed simulations with probable-cause analysis and recommended fixes. Use when preparing to launch a simulation, checking whether a running job is healthy, verifying that finished results are trustworthy, or debugging a crash or blow-up, even if the user only says "my simulation crashed" or "can I trust these results."
allowed-tools
Read, Bash, Write, Grep, Glob
metadata
{"author":"HeshamFS","version":"1.2.2","security_tier":"high","security_reviewed":true,"tested_with":["claude-code"],"last_evaluated":"2026-06-24","eval_cases":5,"last_reviewed":"2026-06-23","standards":["Courant-Friedrichs-Lewy (CFL) stability condition (Courant, Friedrichs & Lewy, 1928)","von Neumann stability analysis (diffusion-Fourier number limit dt <= dx^2/(2*D*dim))","IEEE 754 floating-point arithmetic (NaN / Inf / overflow detection)","Variational / gradient-flow energy dissipation for Allen-Cahn and Cahn-Hilliard phase-field models","Conservation laws (mass / energy / momentum drift checks)"]}
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:
Input
Description
Example
Config file
Simulation configuration (JSON/YAML)
simulation.json
Log file
Runtime output log
simulation.log
Metrics file
Post-run metrics (JSON)
results.json
Required params
Parameters that must exist
dt,dx,kappa
Valid ranges
Parameter bounds
dt:1e-6:1e-2
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? → Results are valid
Choosing Validation Thresholds
Metric
Conservative
Standard
Relaxed
Mass tolerance
1e-6
1e-3
1e-2
Residual growth
2x
10x
100x
dt reduction
10x
100x
1000x
Script Outputs (JSON Fields)
Script
Output Fields
scripts/preflight_checker.py
report.status, report.blockers, report.warnings
scripts/runtime_monitor.py
alerts, residual_stats, dt_stats (alerts include NaN/Inf/overflow detection, residual growth, and dt collapse)
scripts/result_validator.py
checks, confidence_score, failed_checks, status (PASS / FAIL / INSUFFICIENT_DATA); confidence_score is null when no check ran
scripts/failure_diagnoser.py
probable_causes, recommended_fixes
Three-Stage Validation Protocol
Stage 1: Pre-flight (Before Simulation)
Run scripts/preflight_checker.py --config simulation.json
BLOCK status: Stop immediately, fix all blocker issues
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.
All validation checks passed → proceed with confidence
0.75+
Most checks passed, minor issues
0.5-0.75
Significant issues, review carefully
< 0.5
Major problems, do not trust results
null (status INSUFFICIENT_DATA)
No recognized metrics fields; no check ran — NOT a pass. Inspect the metrics file.
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
Pattern in Log
Likely Cause
Recommended Fix
NaN, Inf, overflow
Numerical instability
Reduce dt, increase damping
max iterations, did not converge
Solver failure
Tune preconditioner, tolerances
out of memory
Memory exhaustion
Reduce mesh, enable out-of-core
dt reduced
Adaptive stepping triggered
May be okay if controlled
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
Tempting shortcut
Why it's wrong / what to do
"Preflight passed, so the run is numerically stable."
preflight_checker.py checks required keys, ranges, output-dir writability, and disk space only. It does NOT compute CFL/Fourier. Gate stability with cfl_checker.py separately.
"result_validator printed a confidence score, so results are good."
An empty or unrecognized metrics file returns confidence_score: null and status INSUFFICIENT_DATA — that is "no check ran", not a pass. Verify recognized fields are present and status == PASS.
"Energy ends lower than it started, so the dissipative run is fine."
The default energy_net_decrease only compares first vs last and misses mid-run spikes. For gradient-flow models use --variational to enforce the strict monotone energy_monotone check.
"I asked for bounds and didn't get a bounds_satisfied: false, so bounds hold."
If field_min/field_max are absent the validator emits bounds_unverifiable (a FAILED check), never a vacuous pass. Ensure the metrics file actually carries the field extrema.
"The simulation finished without crashing, so the results are trustworthy."
Run completion is not correctness. Verify mass conservation, energy behavior, physical bounds, and a clean runtime_monitor alert list before using results.
"dt got smaller during the run, so the solver is failing."
runtime_monitor dt-collapse is direction-aware (running-max vs current) and only alerts past --dt-drop; a controlled adaptive ramp is expected. Check the actual dt_stats and whether an alert fired.
"I'll just use the default thresholds."
Defaults (--mass-tol 1e-3, --residual-growth 10, --dt-drop 100) are the Standard column; a conservation-critical problem needs the Conservative tolerances. Pick thresholds for the physics, then record them.
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
v1.2.2 (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
