Simulation Validator

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)

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:

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

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

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

1. 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

| Error | Cause | Resolution | |-------|-------|------------| | Config not found | File path invalid | Verify config path exists | | Non-numeric value | Parameter is not a number | Fix config file format | | out of range | Parameter outside bounds | Adjust parameter or bounds | | Output directory not writable | Permission issue | Check directory permissions | | Insufficient disk space at | Disk nearly full on the output volume | Free up space or reduce output | | Invalid parameter name | --required name has disallowed characters | Use only letters, digits, _, ., - | | range max ... must be greater than min | Inverted/degenerate --ranges or bounds | Ensure max > min | | must be a finite positive number | nan/inf/negative threshold supplied | Pass a finite positive value | | Log file too large | Log exceeds the 500 MB parse cap | Truncate or pre-filter the log |

Interpretation Guidance

Status Meanings

| Status | Meaning | Action | |--------|---------|--------| | PASS | All checks passed | Proceed with confidence | | WARN | Non-critical issues found | Review and document | | BLOCK | Critical issues found | Must fix before proceeding |

Confidence Score Interpretation

| Score | Meaning | |-------|---------| | 1.0 | All validation checks passed → proceed with confidence | | 0.75+ | Most checks passed, minor issues | | 0.5-0.75 | Significant issues, review carefully | | 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
• v1.0.0: Initial release with 4 validation scripts

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

• Author: HeshamFS
• Source: HeshamFS/materials-simulation-skills
• License: Apache-2.0

Install and usage instructions live in the source repository linked above.