q734738781
80 verified skills428 total stars
cp2k-aimd-preparation
Use this skill for source-grounded CP2K AIMD preparation, restart staging, generic execution handoff through cp2k_execute, and run-health inspection.
data-ai9
scan-to-ts
Use this skill for a bounded molecular reaction-coordinate workflow that starts from a relaxed scan, identifies a TS-side guess, and refines it with ORCA OptTS.
development7
surface-and-termination-screening
Use this skill for turning one relaxed bulk reference into a controlled slab/termination screening set, including slab generation, freezing policy, optional lateral expansion, and standardized VASP ranking runs.
tools7
neb-calculation
Use this skill for the execution stage of NEB and dimer workflows, especially the detailed run protocol for plain-NEB to CI-NEB refinement or NEB/frequency/dimer refinement.
testing7
nmr-ensemble-workup
Use this skill for a bounded flexible-molecule NMR workflow that requires conformer generation, xTB cleanup, ORCA NMR execution, and evidence handoff for later Boltzmann aggregation.
tools7
phonon-displacement-workflow
Use this skill for finite-displacement phonon force-collection setup when the immediate task is to generate supercell displacements, prepare force jobs, and collect consistent VASP outputs for later phonon fitting.
content-media7
md-diffusion-analysis
Use this skill for VASP MD execution and post-analysis when the goal is trajectory-based MSD/RDF/diffusion evidence rather than a generic VASP run log. MACE MD belongs to dynamics_worker.
development7
vasp-batch-execution
Use this skill for dispatching prepared VASP jobs with remote_submission or remote_submission_batch, choosing valid stage layouts, and collecting clean failure evidence.
data-ai7
band-and-dos-analysis
Use this skill for post-relax bulk electronic-structure workflows when the goal is a clean DOS or band-path-ready calculation sequence with explicit KPOINTS provenance and result summaries.
development7
bulk-relax-and-reference
Use this skill for bulk-reference preparation and analysis when a workflow needs a relaxed bulk baseline, symmetry-inequivalent site ledger, and optional band/DOS follow-up from one consistent starting structure.
research7
conformer-search-and-preopt
Use this skill for one molecular conformer-search episode that starts from a SMILES string or one seed structure, expands into a conformer ensemble, prunes it, and produces xTB-optimized candidates for downstream ORCA work.
tools7
elastic-property-workup
Use this skill for finite-strain elastic workflows when the immediate goal is to generate a controlled strain set, run the corresponding VASP calculations, and collect the stress/energy outputs needed for later fitting.
development7
defect-and-dopant-screening
Use this skill for first-pass vacancy, substitution, and explicit interstitial candidate generation plus standardized VASP screening, without pretending to solve formation energies or charge corrections in one step.
development7
xtb-screen-and-prune
Use this skill for bounded xTB screening, optimization, Hessian checking, and ensemble pruning when the main objective is to cheaply rank or clean up molecular candidates before higher-level calculations.
testing7
orca-optfreq-thermochemistry
Use this skill for bounded ORCA molecular optimization, frequency, opt+freq thermochemistry, TDDFT, or NMR preparation/execution/analysis after the molecular structure set is already chosen.
research7
nebts-and-irc
Use this skill for bounded molecular NEB-TS and IRC workflows in ORCA when the task already has explicit reactant/product or TS-side starting structures.
development7
lammps-preparation
Use this skill for source-grounded LAMMPS force-field validation and preparation of minimization, MD, and restart stages.
tools7
mace-finetuning-and-benchmark
Use this skill for remote MACE fine-tuning/training plus held-out evaluation using the validated reference-script conventions, especially the `mace-mh-1 + omat_pbe` replay-style path with explicit E0 and replay controls.
testing7
lammps-minimization
Use this skill for LAMMPS force-field minimization stages and generic minimization log inspection.
tools7
mace-md-sampling
Use this skill for MACE-backed ASE MD sampling, thermal stability checks, trajectory generation, and trajectory-health analysis through the managed mace_md_dir remote task.
testing7
cp2k-dft-preparation
Use this skill for source-grounded CP2K conventional DFT preparation in materials workflows: single-point, fixed-cell geometry optimization, cell optimization, frequency, and DOS-style stages.
tools7
cp2k-vibrational-analysis
Use this skill for CP2K vibrational-analysis preparation and task-specific thermochemistry parsing after an accepted stationary point.
testing7
mace-screening-and-relaxation
Use this skill for MACE-based rapid screening, relaxation, single-point ranking, and candidate pruning before DFT. MACE MD sampling belongs to dynamics_worker.
development7
dpdispatcher-remote-receipts
Use this skill when a DPDispatcher-backed managed execution tool reports remote_context_id, submission_hash, receipt_rel, DPDispatcherDispatchError, network transport failures, or possible orphan remote jobs; it guides minimal receipt inspection and controlled recovery through execute without registering a new control tool.
tools7
remote-stage-layouts
Use this skill before calling low-level remote_submission or remote_submission_batch; it defines the stage-directory layout for registered DPDispatcher task_name templates.
tools7
adsorption-screening
Use this skill for adsorption-candidate generation, execution, and first-pass ranking when screening one adsorbate across one slab family with reproducible site provenance and thermochemistry-ready metadata.
testing7
active-learning-relabel-loop
Use this skill for candidate ranking and relabel-loop bookkeeping when the task is to select the next structures for expensive reference calculations from a structure pool or curated dataset.
data-ai7
trajectory-analysis
Use this skill for generic CP2K/LAMMPS trajectory and run-health checks and for deciding when task-specific trajectory parsing is required.
testing7
mace-dataset-curation
Use this skill for turning VASP result trees into extxyz training datasets that follow the validated reference-script conventions for REF labels, optional head/config_type tags, and fixed split artifacts before MACE training.
testing7
cp2k-pathway-calculations
Use this skill for source-grounded CP2K NEB and dimer path-refinement preparation through the single cp2k_prepare tool.
tools7
cp2k-run-analysis
Use this skill for generic CP2K run-health analysis after cp2k_execute, without replacing property-specific parsers.
testing7
cp2k-aimd-restart
Use this skill to continue CP2K AIMD from existing result directories without losing restart context or overwriting previous outputs.
data-ai7
cp2k-electronic-properties
Use this skill for CP2K DOS/PDOS, band-style, and population-analysis follow-up planning where parsing is task-specific and should usually be scripted.
testing7
lammps-restart
Use this skill to continue LAMMPS stages from restart files while preserving prior stage context.
tools7
lammps-md-execution
Use this skill for LAMMPS NVE/NVT/NPT/annealing preparation, execution, restart output, and generic MD health analysis.
research7
nature-response
Draft, audit, or revise point-by-point reviewer response letters for Nature-family manuscript revisions. Use when the user provides reviewer comments, editor decision letters, revision notes, response drafts, or asks how to respond to major/minor revision requests, rebuttal letters, response to reviewers, peer-review reports, 审稿意见回复, 逐点回复, 修回信, 大修回复, 小修回复, or 如何回复 reviewer.
testing5
structure-visual-inspection
Use this skill when a task needs visual inspection of atomic structures, adsorption geometries, slab-site context, or image-based sanity checks before or alongside numerical analysis.
testing5
adsorption-site-screening
Use this skill for adsorption-site enumeration and adsorbate placement workflows, including candidate screening setup and batch structure generation.
tools5
neb-prepare
Use this skill for NEB and dimer preparation work: validate endpoint pairs, choose image counts, build image trees, prepare VASP NEB roots, and prepare dimer-ready inputs or raw mode guesses.
development5
adsorbate-and-intermediate-generation
Use this skill for generating adsorbates and reaction intermediates, standardizing molecular inputs, and preparing structures for adsorption placement.
development5
paper-writer
Medical/scientific paper writing workflow skill. Manages the full pipeline from literature search to submission-ready manuscript. Creates and manages a project directory with IMRAD-format section files, literature matrix, reference management, and quality checklists. Supports both English and Japanese papers. Triggers: 'write paper', 'paper-write', 'start manuscript', '論文を書く', '論文執筆', '論文プロジェクト', 'manuscript', 'research paper', '原稿作成'.
development5
literature-grounding
Use this skill when the user asks for papers, prior work, benchmark conventions, prior-art mapping, or other explicit evidence grounding from published work, including heterogeneous-catalysis method benchmarks.
testing5
slab-construction-and-surface-modeling
Use this skill for slab construction, vacuum and layer choices, surface supercell setup, and atom-fixing strategy in heterogeneous catalysis workflows.
data-ai5
neb-analysis
Use this skill for NEB post-analysis: barrier extraction, profile interpretation, endpoint-energy pitfalls, and common QC checks after a pathway run finishes.
testing5
materials-discovery-and-bulk-selection
Use this skill for materials discovery and bulk structure selection before slab construction, including database query strategy, candidate filtering, and export readiness.
data-ai5
achemso-latex-manuscript
Write ACS-style manuscript sections against the local achemso LaTeX template, using deterministic template edits and preserving BibTeX structure.
documentation5
vasp-input-preparation
Use this skill for preparing canonical VASP relax/static/frequency/DOS/MD input sets, choosing the correct regime and preset, handling INCAR patch-policy edge cases, explicit slab-frequency setup, and producing execution-ready folder layouts before dispatch.
testing5
thermo-free-energy-and-reporting
Use this skill for thermodynamic and free-energy post-processing, result normalization, explicit adsorbate-only frequency-job SOP, and concise reporting standards for catalyst comparison.
testing5
citation-management
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
development5
scientific-visualization
Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars, colorblind-safe palettes, and specific journal formatting (Nature, Science, Cell). Orchestrates matplotlib/seaborn/plotly with publication styles. For quick exploration use seaborn or plotly directly.
development5
scientific-writing
Core skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points). Use two-stage process with (1) section outlines with key points using research-lookup then (2) convert to flowing prose. IMRAD structure, citations (APA/AMA/Vancouver), figures/tables, reporting guidelines (CONSORT/STROBE/PRISMA), for research papers and journal submissions.
tools5
nature-reader
Build full-text bilingual, figure-aware, source-grounded Markdown reading files for journal or conference papers from PDF, DOI, arXiv, publisher HTML, or pasted text. Use whenever the user asks to translate an entire paper, make a complete markdown reader, preserve figure or table placement near the relevant prose, or keep exact source anchors for every block. Do not use this for summaries, bullet-keyword notes, or citation-only tasks.
development5
venue-templates
Access comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE, ACM), academic conferences (NeurIPS, ICML, CVPR, CHI), research posters, and grant proposals (NSF, NIH, DOE, DARPA). This skill should be used when preparing manuscripts for journal submission, conference papers, research posters, or grant proposals and need venue-specific formatting requirements and templates.
development5
nature-data
Prepare, audit, or revise Nature-ready Data Availability statements, data repository plans, dataset citations, and FAIR metadata checklists for manuscripts. Use when the user asks about Nature data availability, research data sharing, repository selection, accession numbers, restricted or sensitive data, source data, supplementary datasets, DataCite-style dataset references, FAIR metadata for academic publication, or Chinese-to-English data availability wording for Chinese-speaking authors preparing Nature-family submissions.
testing5
nature-polishing
Polish, restructure, or translate academic prose into Nature-leaning English using the paper-architecture and writing-strategy principles from Scientific English Writing & Communication, with phrase-level support from Academic Phrasebank. Use whenever the user asks to polish a manuscript paragraph, abstract, introduction, results, discussion, conclusion, title, methods section, or Chinese academic draft for publication-quality English.
testing5
nature-figure
Submission-grade Nature/high-impact journal figure workflow for Python or R. Use whenever the user asks to create, revise, audit, or polish manuscript figures, multi-panel scientific plots, or journal-ready SVG/PDF/TIFF outputs, especially for Nature-family or other high-impact journals. Before plotting, define the figure's conclusion, evidence logic, export needs, and review risks. If the user has not chosen Python or R, ask "Python or R?" and stop. Use only the selected backend for figure generation, previewing, exporting, and QA. Supports matplotlib/seaborn and ggplot2/patchwork/ComplexHeatmap. Not for dashboards or Illustrator/Figma-first infographics.
development5
nature-citation
Add strict Nature/CNS citations to manuscript text by splitting long passages into citable segments, searching only accepted flagship and subjournal titles from Nature Portfolio, the AAAS Science family, and Cell Press, filtering by publication time range, and exporting one reference-manager-ready output by default. Use this skill whenever the user asks to input text and automatically get references, add citations to a paragraph/manuscript, find Nature-series or CNS support for statements, create text-to-reference correspondence, "分段引用", "自动给出引用", "Nature系列引用", "CNS及子刊", "支撑文献", "补引用", "找引用", or export EndNote/RIS/ENW/Zotero RDF.
testing5
nature-paper2ppt
Build a complete but efficient Nature-style Chinese PPTX presentation from a scientific paper, preprint, PDF, article text, abstract, figure legends, or reading notes. Use this skill whenever the user asks to make slides/PPT/PPTX for journal club, group meeting, paper sharing, thesis seminar, lab meeting, department report, or academic presentation from a research paper, not only medical papers. It identifies the paper type and argument, selects only the figures needed for the story, writes Chinese slide content and speaker notes, creates the actual .pptx deck, and performs lightweight verification with cross-platform Python tooling by default.
tools5
figure-design-and-captioning
Design evidence-carrying figures and captions from research outputs, with reproducible script and data references.
testing3
transition-state-neb
Use this skill for transition-state and NEB workflows, including image generation, NEB VASP input setup, official VASP improved-dimer preparation, reaction-mode guessing, and execution/evidence checks for pathway calculations.
development3
thermo-free-energy-and-reporting
Use this skill for thermodynamic and free-energy post-processing, result normalization, explicit adsorbate-only frequency-job SOP, and concise reporting standards for catalyst comparison.
testing3
reaction-neb-analysis
Use this skill for end-to-end NEB pathway setup, execution, and post-analysis when a reaction coordinate needs a barrier estimate and image-profile artifacts rather than just an image tree.
development3
literature-grounding
Use this skill when the user asks for papers, prior work, benchmark conventions, prior-art mapping, or other explicit evidence grounding from published work, including heterogeneous-catalysis method benchmarks.
testing3
vasp-batch-execution
Use this skill for dispatching prepared VASP jobs with vasp_execute_batch, choosing valid input/output layouts, avoiding nested or overlapping calc trees, and collecting clean failure evidence.
data-ai3
surface-and-termination-screening
Use this skill for turning one relaxed bulk reference into a controlled slab/termination screening set, including slab generation, freezing policy, optional lateral expansion, and standardized VASP ranking runs.
tools3
slab-construction-and-surface-modeling
Use this skill for slab construction, vacuum and layer choices, surface supercell setup, and atom-fixing strategy in heterogeneous catalysis workflows.
data-ai3
phonon-displacement-workflow
Use this skill for finite-displacement phonon force-collection setup when the immediate task is to generate supercell displacements, prepare force jobs, and collect consistent VASP outputs for later phonon fitting.
content-media3
materials-discovery-and-bulk-selection
Use this skill for materials discovery and bulk structure selection before slab construction, including database query strategy, candidate filtering, and export readiness.
data-ai3
mace-screening-and-relaxation
Use this skill for MACE-based rapid screening and relaxation loops before DFT, including candidate pruning and handoff criteria.
development3
elastic-property-workup
Use this skill for finite-strain elastic workflows when the immediate goal is to generate a controlled strain set, run the corresponding VASP calculations, and collect the stress/energy outputs needed for later fitting.
development3
bulk-relax-and-reference
Use this skill for bulk-reference preparation and analysis when a workflow needs a relaxed bulk baseline, symmetry-inequivalent site ledger, and optional band/DOS follow-up from one consistent starting structure.
research3
band-and-dos-analysis
Use this skill for post-relax bulk electronic-structure workflows when the goal is a clean DOS or band-path-ready calculation sequence with explicit KPOINTS provenance and result summaries.
development3
defect-and-dopant-screening
Use this skill for first-pass vacancy, substitution, and explicit interstitial candidate generation plus standardized VASP screening, without pretending to solve formation energies or charge corrections in one step.
development3
md-diffusion-analysis
Use this skill for MD execution and post-analysis when the goal is trajectory-based MSD/RDF/diffusion evidence rather than a generic VASP run log.
development3
structure-visual-inspection
Use this skill when a task needs visual inspection of atomic structures, adsorption geometries, slab-site context, or image-based sanity checks before or alongside numerical analysis.
testing3
vasp-input-preparation
Use this skill for preparing canonical VASP relax/static/frequency/DOS/MD input sets, choosing the correct regime and preset, handling INCAR patch-policy edge cases, explicit slab-frequency setup, and producing execution-ready folder layouts before dispatch.
testing3
results-and-discussion-writing
Write Results and Discussion sections that separate observations from interpretation and preserve uncertainty.
documentation3
adsorption-screening
Use this skill for adsorption-candidate generation, execution, and first-pass ranking when screening one adsorbate across one slab family with reproducible site provenance and thermochemistry-ready metadata.
testing3
adsorbate-and-intermediate-generation
Use this skill for generating adsorbates and reaction intermediates, standardizing molecular inputs, and preparing structures for adsorption placement.
development3
adsorption-site-screening
Use this skill for adsorption-site enumeration and adsorbate placement workflows, including candidate screening setup and batch structure generation.
tools3