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- GpawGenerate and manage GPAW Python-based DFT calculations. Use when the user requests GPAW, Python DFT, real-space grid DFT, or LCAO-DFT with ASE integration.Votes: 0GitHub stars: 204
- GibbsUse when the user asks for Gibbs free energy, zero-point energy (ZPE), thermal corrections, or thermodynamic properties from DFT + frequency data.Votes: 0GitHub stars: 204
- GaussianGenerate and manage Gaussian calculations. Use when the user requests Gaussian, G16, GJF files, or needs hybrid functionals (B3LYP), MP2, CCSD(T), or molecular quantum chemistry with Gaussian basis sets.Votes: 0GitHub stars: 204
- Energy DiagramUse when the user asks to generate a reaction energy diagram, free energy profile, potential energy surface plot, or pathway comparison diagram for catalysis or reaction mechanism studies.Votes: 0GitHub stars: 204
- DpdataConvert between computational chemistry data formats using dpdata. Handles VASP, QE, CP2K, Gaussian, LAMMPS, and DeePMD formats. Essential for preparing ML potential training data.Votes: 0GitHub stars: 204
- Dos AnalysisUse when the user asks about density of states (DOS), projected DOS (PDOS), d-band center, spin-resolved DOS, or electronic structure analysis from completed DFT calculations.Votes: 0GitHub stars: 204
- DftbplusGenerate and manage DFTB+ calculations. Use when the user requests DFTB+, tight-binding DFT, SCC-DFTB, or needs fast approximate DFT for large systems or MD.Votes: 0GitHub stars: 204
- Deepmd InferenceRun DeePMD-kit inference to predict energies, forces, and stresses using a trained DP model. Also covers model evaluation and testing.Votes: 0GitHub stars: 204
- Cp2k StaticCP2K single point energy calculation. Uses GTH pseudopotentials, Gaussian-plane-wave (GPW) method, and DZVP basis sets for periodic DFT.Votes: 0GitHub stars: 204
- Cp2k RelaxCP2K geometry optimization. Handles bulk, slab, and molecular systems with GPW method. Efficient for large systems (200+ atoms).Votes: 0GitHub stars: 204
- Convergence TestUse when the user asks to test ENCUT convergence, k-point convergence, or any parameter sweep to determine converged computational settings.Votes: 0GitHub stars: 204
- Co2rrUse when the user asks about CO2 reduction reaction (CO2RR), CO2 electroreduction intermediates, Faradaic efficiency, or selectivity toward CO, methanol, methane, formic acid, etc.Votes: 0GitHub stars: 204
- Charge AnalysisUse when the user asks about Bader charge analysis, charge transfer, oxidation states from DFT, or electron density partitioning.Votes: 0GitHub stars: 204
- Adsorption EnergyUse when the user asks for adsorption energy, binding energy, or wants to compare how strongly a molecule binds to a surface.Votes: 0GitHub stars: 204
- AbinitGenerate and manage ABINIT DFT calculations. Use when the user requests ABINIT, or needs DFPT phonons, GW calculations, or BSE optical spectra.Votes: 0GitHub stars: 204
- Rfdb Stale Node CleanupRecover from stale RFDB nodes that survive `commit_batch` cleanup despite having their `file` field listed in `changed_files`. Use when: (1) re-running an enricher/orchestrator step but old data with the same file field stays in the graph, (2) `commit_batch(changed_files=[X], ...)` reports success but a query later still returns nodes with `file = X`, (3) you re-pointed structural nodes (e.g., DIRECTORY/FILE) from a synthetic file path to real file paths and the old synthetic-path nodes won't...Votes: 0GitHub stars: 36
- Grafema Uri Semantic Id ParsingFix silent failures when parsing Grafema semantic IDs that are in URI format instead of legacy arrow format. Use when: (1) code splits semantic IDs by "->" but gets the whole string back because IDs are grafema:// URIs, (2) file path extraction from semantic IDs returns empty or wrong values, (3) derived edges (DEPENDS_ON, etc.) produce 0 results despite source edges existing, (4) any code that processes semantic IDs after the analysis pipeline's to_uri_format() has run. The grafema:// URI fo...Votes: 0GitHub stars: 36
- Grafema Test Backend UsageFix node query issues in Grafema tests when nodes have numeric IDs instead of human-readable IDs, or when `type` field is undefined. Use when: (1) queryNodes returns nodes with numeric IDs like "52710336597754872375318185843222727675" instead of semantic IDs like "net:request#__network__", (2) node.type is undefined but node.nodeType has a value, (3) metadata is a JSON string instead of parsed object, (4) tests fail with "Cannot read property 'length' of undefined" after queryNodes. Covers RF...Votes: 0GitHub stars: 36
- Grafema Batch Plugin DevelopmentHow to write a Grafema batch-mode plugin that reads the graph and filesystem, then writes new edges/nodes directly to RFDB. Use when: (1) need to add project-specific edges that generic analyzers can't produce, (2) need to read config files (JSON/YAML) and trace values into code, (3) implementing framework-specific resolvers (Django settings, Express routes, pipeline configs). Covers: grafema.config.yaml plugin config, RFDB field naming (src/dst NOT source/target), addEdges/addNodes API, RFDB...Votes: 0GitHub stars: 36
- Gap LoopCyclical dogfooding loop: test AI-AGENT-STORIES.md against the live graph, discover new stories, analyze gaps, fix root causes, re-test, write report. Use when: (1) user says "/gap-loop", (2) periodic dogfooding session, (3) after a release or major feature to re-validate stories, (4) before sprint planning to prioritize product gaps.Votes: 0GitHub stars: 36
- Dataflow Gauntlet MethodologySystematic methodology for achieving 100% backward dataflow reachability in a new language. Create gauntlet fixture, write trace, diagnose gaps, fix analyzer/algorithm, iterate to 100%. Language-agnostic process. Use when: (1) adding a new language to Grafema, (2) auditing dataflow coverage for existing language, (3) user says "/dataflow-gauntlet".Votes: 0GitHub stars: 36
- Code Server Playwright AutomationFix Playwright automation failures against code-server (VS Code in browser). Use when: (1) trust dialog blocks all clicks — "monaco-dialog-modal-block intercepts pointer events", (2) button:has-text() finds wrong buttons behind modal dialog, (3) keyboard shortcuts don't work — Meta vs Control inconsistency, (4) VS Code extension activity bar icon not found by aria-label, (5) panels show placeholder text despite extension being "Connected". Covers trust dialog dismissal, keyboard shortcut hybr...Votes: 0GitHub stars: 36
- Code AnalysisAnalyze code systematically: clone repos, inspect JARs, search documentation, reverse-engineer binaries. Triggers: analyzing unknown codebases, finding API endpoints, understanding compiled code, security auditing.Votes: 0GitHub stars: 8
- Wardrobe Receipt CatalogerScan Gmail for clothing purchase receipts, extract item details (brand, product, color, size, price, purchase date), download product images, then catalog each item in the Logseq wiki: update Wardrobe.md in the correct section, create/update brand pages, and link to the product page, Internet Archive snapshot, and original receipt email. TRIGGER when the user wants to sync recent clothing purchases to their wiki, catalog new wardrobe items from email receipts, or audit what they've bought.Votes: 0GitHub stars: 8