abinit
FreeGenerate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
The English summary is being prepared. Showing the original description.
Run and resume the CatGo md-orchestration poll loop — delegate each poll to a subagent (keep main context lean), verify convergence by force, auto-advance each converged species per-species (pipeline, not barrier), and resume a campaign from disk after context compaction / new session. Use when driving or resuming a campaign's job-watch loop. Pairs with catgo-campaign.
The English summary is being prepared. Showing the original description.
Run score Not tested
See how to installReview the instructions the agent will receive before you install.
TL;DR: Human-triggered ~10-min loop. Delegate each poll to a subagent (compact summary back). Verify convergence by force. Auto-advance each converged species to its next step (per species, not a barrier). State is on disk → any agent resumes.
Do NOT run poll/verify inline. Dispatch ONE subagent (opus) to run steps 1-3 (poll, ssh-read OUTCAR, verify, write result.md/STATUS/LESSONS) and return a compact summary only (one line per calc; no raw OUTCAR/OSZICAR/ssh dumps) — over a long run the verbose output would fill the main context toward 1M. Gates stay in the main agent (input-file gate, checkpoints): the subagent reports, the main agent shows the user + acts. The subagent must not submit/cancel jobs or touch the :8000 backend.
plan.md + active STATUS.md (keep working context lean).python poll.py --project <dir> --ssh <alias> — updates STATUS: queued via squeue;
once a job leaves the queue, sacct gives the terminal verdict (COMPLETED→DONE;
FAILED/TIMEOUT/OUT_OF_MEMORY/CANCELLED→FAILED; exit_code recorded).FORCES: max atom < |EDIFFG| (force, NOT
dE; the "kinetic energy error for atom" EATOM line is benign). Write energy_eV +
max_force_eVA into result.md; on real failure (DONE-but-unconverged, or FAILED)
record cause + fix in LESSONS.md.submit_calc.py.
⛔ INPUT-FILE GATE (hard rule): "auto-advance" means auto-PREP, NOT auto-submit. Sync the
converged CONTCAR and the next-step INCAR to the LOCAL folder, tell the user the exact LOCAL
paths of INCAR + CONTCAR, and WAIT — the user checks/edits the files on disk. Submit ONLY after
the user confirms. Do NOT push to the CatGO viewer as a substitute, and NEVER auto-submit. (YOLO waives.)python aggregate.py --project <dir> --plot → summary → checkpoint.python make_report.py --project <dir> --occasion groupmeeting.State lives ON DISK, not in context — a campaign survives compaction, a new session, or a different agent. To resume with zero conversation history:
catgo-campaign skill; identify the project dir.README.md → plan.md (+ each calc/<stage>/plan.md) → cluster.md →
every calc/**/STATUS.md → result.md files → LESSONS.md = done / running / next.ScheduleWakeup dies with the session. For a campaign that must advance without you, register a cron routine that wakes a fresh agent on a schedule to poll the project (it resumes from disk). Otherwise the user says "resume <project>" in a new session.
No reviews yet. Tell others what you thought.
No login needed. Share how it worked for you, ask a question, or note where it did not run.
No comments yet. Be the first to write one.
Generate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.
The English summary is being prepared. Showing the original description.
Use when the user asks to place an adsorbate molecule on a surface, find adsorption sites, or set up a surface+adsorbate model for DFT.
The English summary is being prepared. Showing the original description.
Use when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.
The English summary is being prepared. Showing the original description.
Use when the user asks to analyze computational results: Gibbs free energy, OER/HER/CO2RR overpotentials, adsorption energy, convergence tests, DOS/d-band analysis, or Bader charge analysis.
The English summary is being prepared. Showing the original description.
Use AmberTools antechamber for molecular force field parameterization. Generates GAFF/GAFF2 parameters and AM1-BCC or RESP charges for use in AMBER or LAMMPS classical MD simulations.
The English summary is being prepared. Showing the original description.
One-shot recipes for adding, deleting, moving, and replacing individual atoms in the active CatGo viewer structure. Use whenever the user asks to "add an atom", "delete atoms", "remove this atom", "move atom N", "replace H with Li", or any single-atom edit — including "add a hydrogen on top of atom 12" / "delete atoms 5–9" / "swap the oxygen at site 3 for fluorine". Skips the discovery loop (no need to list structure tools or check adsorption sites first); goes straight to the matching `catgo_structure` action. Triggers in Chinese on 加原子, 删原子, 减原子, 移动原子, 替换原子, 增加氢, 删除氧, 把 ... 换成 ....
The English summary is being prepared. Showing the original description.