Agent skill
time-stepping
Plan and control time-step policies for simulations. Use when coupling CFL/physics limits with adaptive stepping, ramping initial transients, scheduling outputs/checkpoints, or planning restart strategies for long runs.
Install this agent skill to your Project
npx add-skill https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/time-stepping
SKILL.md
Time Stepping
Goal
Provide a reliable workflow for choosing, ramping, and monitoring time steps plus output/checkpoint cadence.
Requirements
- Python 3.8+
- No external dependencies (uses stdlib)
Inputs to Gather
| Input | Description | Example |
|---|---|---|
| Stability limits | CFL/Fourier/reaction limits | dt_max = 1e-4 |
| Target dt | Desired time step | 1e-5 |
| Total run time | Simulation duration | 10 s |
| Output interval | Time between outputs | 0.1 s |
| Checkpoint cost | Time to write checkpoint | 120 s |
Decision Guidance
Time Step Selection
Is stability limit known?
├── YES → Use min(dt_target, dt_limit × safety)
└── NO → Start conservative, increase adaptively
Need ramping for startup?
├── YES → Start at dt_init, ramp to dt_target over N steps
└── NO → Use dt_target from start
Ramping Strategy
| Problem Type | Ramp Steps | Initial dt |
|---|---|---|
| Smooth IC | None needed | Full dt |
| Sharp gradients | 5-10 | 0.1 × dt |
| Phase change | 10-20 | 0.01 × dt |
| Cold start | 10-50 | 0.001 × dt |
Script Outputs (JSON Fields)
| Script | Key Outputs |
|---|---|
scripts/timestep_planner.py |
dt_limit, dt_recommended, ramp_schedule |
scripts/output_schedule.py |
output_times, interval, count |
scripts/checkpoint_planner.py |
checkpoint_interval, checkpoints, overhead_fraction |
Workflow
- Get stability limits - Use numerical-stability skill
- Plan time stepping - Run
scripts/timestep_planner.py - Schedule outputs - Run
scripts/output_schedule.py - Plan checkpoints - Run
scripts/checkpoint_planner.py - Monitor during run - Adjust dt if limits change
Conversational Workflow Example
User: I'm running a 10-hour phase-field simulation. How often should I checkpoint?
Agent workflow:
- Plan checkpoints based on acceptable lost work:
bash
python3 scripts/checkpoint_planner.py --run-time 36000 --checkpoint-cost 120 --max-lost-time 1800 --json - Interpret: Checkpoint every 30 minutes, overhead ~0.7%, max 30 min lost work on crash.
Pre-Run Checklist
- Confirm dt limits from stability analysis
- Define ramping strategy for transient startup
- Choose output interval consistent with physics time scales
- Plan checkpoints based on restart risk
- Re-evaluate dt after parameter changes
CLI Examples
# Plan time stepping with ramping
python3 scripts/timestep_planner.py --dt-target 1e-4 --dt-limit 2e-4 --safety 0.8 --ramp-steps 10 --json
# Schedule output times
python3 scripts/output_schedule.py --t-start 0 --t-end 10 --interval 0.1 --json
# Plan checkpoints for long run
python3 scripts/checkpoint_planner.py --run-time 36000 --checkpoint-cost 120 --max-lost-time 1800 --json
Error Handling
| Error | Cause | Resolution |
|---|---|---|
dt-target must be positive |
Invalid time step | Use positive value |
t-end must be > t-start |
Invalid time range | Check time bounds |
checkpoint-cost must be < run-time |
Checkpoint too expensive | Reduce checkpoint size |
Interpretation Guidance
dt Behavior
| Observation | Meaning | Action |
|---|---|---|
| dt stable at target | Good | Continue |
| dt shrinking | Stability issue | Check CFL, reduce target |
| dt oscillating | Borderline stability | Add safety factor |
Checkpoint Overhead
| Overhead | Acceptability |
|---|---|
| < 1% | Excellent |
| 1-5% | Good |
| 5-10% | Acceptable |
| > 10% | Too frequent, increase interval |
Limitations
- Not adaptive control: Plans static schedules, not runtime adaptation
- Assumes constant physics: If parameters change, re-plan
References
references/cfl_coupling.md- Combining multiple stability limitsreferences/ramping_strategies.md- Startup policiesreferences/output_checkpoint_guidelines.md- Cadence rules
Version History
- v1.1.0 (2024-12-24): Enhanced documentation, decision guidance, examples
- v1.0.0: Initial release with 3 planning scripts
Recommended Agent Skills
Expand your agent's capabilities with these related and highly-rated skills.
vcf-annotator
Annotate VCF variants with VEP, ClinVar, gnomAD frequencies, and ancestry-aware context. Generates prioritised variant reports.
chemist-analyst
Analyzes events through chemistry lens using molecular structure, reaction mechanisms, thermodynamics, kinetics, and analytical techniques (spectroscopy, chromatography, mass spectrometry). Provides insights on chemical processes, material properties, reaction pathways, synthesis, and analytical methods. Use when: Chemical reactions, material analysis, synthesis planning, process optimization, environmental chemistry. Evaluates: Molecular structure, reaction mechanisms, yield, selectivity, safety, environmental impact.
bio-alignment-io
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
sleep-analyzer
分析睡眠数据、识别睡眠模式、评估睡眠质量,并提供个性化睡眠改善建议。支持与其他健康数据的关联分析。
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
bio-hi-c-analysis-matrix-operations
Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.
Didn't find tool you were looking for?