{"id":"8da77de7-465d-4e04-ac86-00c20b8d6a19","shortId":"dsHgx2","kind":"skill","title":"lammps-workflows","tagline":"Use when the task involves LAMMPS atomistic simulation workflows, including input script creation, minimize, NVT, NPT, and restart setups, force-field and data-file checks, log.lammps review, restart handling, and scheduler scripts.","description":"# LAMMPS Workflows\n\nThis skill handles practical LAMMPS setup, review, and restart tasks. Use it when the request is about `LAMMPS`, `in.lammps`, `log.lammps`, force-field wiring, data files, or thermostat and barostat workflows.\n\n## When to use\n\nUse this skill when the request mentions or implies:\n\n- `LAMMPS`, `in.lammps`, `log.lammps`, `read_data`, `pair_style`, `pair_coeff`, `thermo`\n- minimization, equilibration, `NVT`, `NPT`, restart files, or scheduler scripts\n- classical MD or atomistic simulation setup, not plane-wave DFT\n\n## Operating stance\n\nPrioritize missing information in this order:\n\n1. simulation intent: minimize, NVT, NPT, or restart\n2. units, atom style, and force-field family\n3. structure source: `read_data`, `read_restart`, or generated structure\n4. temperature, pressure, timestep, and run length\n5. scheduler and MPI or OpenMP layout\n\nNever silently invent:\n\n- a force field for a chemistry-sensitive system\n- unit systems or atom styles without saying so\n- whether long-range electrostatics, constraints, or special fixes are required\n- whether a restart file is compatible with changed force-field definitions\n\n## Workflow\n\n### 1. Classify the request\n\n- **Setup**: create or edit `in.lammps`, run scripts, and a stage layout.\n- **Review**: inspect an existing LAMMPS directory and summarize status.\n- **Recovery**: diagnose input, force-field, or runtime issues and propose the smallest safe correction.\n\n### 2. Gather the minimum viable context\n\nBefore recommending code-specific changes, establish:\n\n- the intended force field and any required potential files\n- the units and atom style\n- the structure source and whether the box topology is already valid\n- the target ensemble and physical conditions\n- the scheduler environment\n\n### 3. Use the bundled helpers\n\n- `scripts/make_lammps_inputs.py`\n  Generate conservative minimization, NVT, NPT, or restart input skeletons.\n- `scripts/check_lammps_job.py`\n  Check a LAMMPS directory for missing input, data, or potential-file references.\n- `scripts/summarize_lammps_log.py`\n  Summarize `log.lammps` or a run directory using thermo-block heuristics.\n- `scripts/recommend_lammps_recovery.py`\n  Turn broken or unstable LAMMPS runs into concrete recovery guidance.\n- `scripts/export_status_report.py`\n  Export a shareable markdown status report from a LAMMPS working directory.\n- `scripts/export_input_suggestions.py`\n  Export conservative LAMMPS input suggestion snippets based on detected recovery patterns.\n\n### 4. Load focused references only when needed\n\n- LAMMPS workflow guidance: `references/lammps.md`\n- force-field and data-file risks: `references/force-fields.md`\n- failure handling: `references/failure-modes.md`\n- scheduler considerations: `references/schedulers.md`\n\n### 5. Deliver an auditable answer\n\nWhenever you recommend a LAMMPS change, include:\n\n- the intended ensemble and units\n- the assumed force field or potential family\n- any unresolved input-file or chemistry decisions the user still needs to confirm\n- what outputs should be checked after the next run\n\n## Guardrails\n\n- A well-formed `in.lammps` file is not enough if the force field is wrong.\n- Do not treat minimize, NVT, and NPT as interchangeable; explain why the chosen ensemble matches the goal.\n- If a referenced data or potential file is missing, say so directly.\n\n## Quality bar\n\n- Keep workflow advice tied to the actual ensemble and force-field assumptions.\n- Separate syntax issues from model-quality issues.\n- If the current input still contains placeholders, call that out 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chars)","verified":false,"liveness":"unknown","lastLivenessCheck":null,"agentReviews":{"count":0,"score_avg":null,"cost_usd_avg":null,"success_rate":null,"latency_p50_ms":null,"narrative_summary":null,"summary_updated_at":null},"enrichmentModel":"deterministic:skill-github:v1","enrichmentVersion":1,"enrichedAt":"2026-05-18T19:08:07.646Z","embedding":null,"createdAt":"2026-05-12T07:07:06.333Z","updatedAt":"2026-05-18T19:08:07.646Z","lastSeenAt":"2026-05-18T19:08:07.646Z","tsv":"'1':121,206 '2':129,245 '3':138,292 '4':148,368 '5':155,394 'actual':494 'advic':490 'alreadi':281 'answer':398 'assum':412 'assumpt':500 'atom':131,177,270 'atomist':10,105 'audit':397 'bar':487 'barostat':69 'base':363 'block':331 'box':278 'broken':335 'bundl':295 'call':516 'chang':200,256,404 'check':30,308,436 'chemistri':171,424 'chemistry-sensit':170 'chosen':469 'classic':102 'classifi':207 'code':254 'code-specif':253 'coeff':91 'compat':198 'concret':341 'condit':288 'confirm':431 'conserv':299,358 'consider':392 'constraint':187 'contain':514 'context':250 'correct':244 'creat':211 'creation':16 'current':511 'data':28,64,87,142,315,384,477 'data-fil':27,383 'decis':425 'definit':204 'deliv':395 'detect':365 'dft':112 'diagnos':231 'direct':485 'directori':226,311,327,355 'edit':213 'electrostat':186 'enough':450 'ensembl':285,408,470,495 'environ':291 'equilibr':94 'establish':257 'exist':224 'explain':466 'explicit':519 'export':345,357 'failur':388 'famili':137,417 'field':25,62,136,167,203,235,261,381,414,454,499 'file':29,65,98,196,266,319,385,422,447,480 'fix':190 'focus':370 'forc':24,61,135,166,202,234,260,380,413,453,498 'force-field':23,60,134,201,233,379,497 'form':445 'gather':246 'generat':146,298 'goal':473 'guardrail':441 'guidanc':343,377 'handl':34,42,389 'helper':296 'heurist':332 'impli':82 'in.lammps':58,84,214,446 'includ':13,405 'inform':117 'input':14,232,305,314,360,421,512 'input-fil':420 'inspect':222 'intend':259,407 'intent':123 'interchang':465 'invent':164 'involv':8 'issu':238,503,508 'keep':488 'lammp':2,9,38,44,57,83,225,310,338,353,359,375,403 'lammps-workflow':1 'layout':161,220 'length':154 'load':369 'log.lammps':31,59,85,323 'long':184 'long-rang':183 'markdown':348 'match':471 'md':103 'mention':80 'minim':17,93,124,300,460 'minimum':248 'miss':116,313,482 'model':506 'model-qu':505 'mpi':158 'need':374,429 'never':162 'next':439 'npt':19,96,126,302,463 'nvt':18,95,125,301,461 'openmp':160 'oper':113 'order':120 'output':433 'pair':88,90 'pattern':367 'physic':287 'placehold':515 'plane':110 'plane-wav':109 'potenti':265,318,416,479 'potential-fil':317 'practic':43 'pressur':150 'priorit':115 'propos':240 'qualiti':486,507 'rang':185 'read':86,141,143 'recommend':252,401 'recoveri':230,342,366 'refer':320,371 'referenc':476 'references/failure-modes.md':390 'references/force-fields.md':387 'references/lammps.md':378 'references/schedulers.md':393 'report':350 'request':54,79,209 'requir':192,264 'restart':21,33,48,97,128,144,195,304 'review':32,46,221 'risk':386 'run':153,215,326,339,440 'runtim':237 'safe':243 'say':180,483 'schedul':36,100,156,290,391 'script':15,37,101,216 'scripts/check_lammps_job.py':307 'scripts/export_input_suggestions.py':356 'scripts/export_status_report.py':344 'scripts/make_lammps_inputs.py':297 'scripts/recommend_lammps_recovery.py':333 'scripts/summarize_lammps_log.py':321 'sensit':172 'separ':501 'setup':22,45,107,210 'shareabl':347 'silent':163 'simul':11,106,122 'skeleton':306 'skill':41,76 'skill-lammps-workflows' 'smallest':242 'snippet':362 'sourc':140,274 'source-chatmaterials' 'special':189 'specif':255 'stage':219 'stanc':114 'status':229,349 'still':428,513 'structur':139,147,273 'style':89,132,178,271 'suggest':361 'summar':228,322 'syntax':502 'system':173,175 'target':284 'task':7,49 'temperatur':149 'thermo':92,330 'thermo-block':329 'thermostat':67 'tie':491 'timestep':151 'topic-agent-skills' 'topic-chatmaterials' 'topic-lammps' 'topic-materials-science' 'topic-molecular-dynamics' 'topic-skills' 'topic-workflows' 'topolog':279 'treat':459 'turn':334 'unit':130,174,268,410 'unresolv':419 'unstabl':337 'use':4,50,73,74,293,328 'user':427 'valid':282 'viabl':249 'wave':111 'well':444 'well-form':443 'whenev':399 'whether':182,193,276 'wire':63 'without':179 'work':354 'workflow':3,12,39,70,205,376,489 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