Python · By jinzhezenggroup

Prepares, validates and runs DP-GEN simplify jobs that thin out repeated or redundant DeepMD datasets, generating param.json and machine.json for local or scheduler runs.

jinzhezenggroup/computational-chemistry-agent-skills

Generates 3D molecular conformers from SMILES strings or files with RDKit, keeps the lowest-energy one per molecule, and falls back to 2D coordinates when embedding fails.

jinzhezenggroup/computational-chemistry-agent-skills

Computes RDKit physicochemical descriptors and molecular fingerprints from SMILES through a uv-run CLI script that skips and logs invalid molecules.

jinzhezenggroup/computational-chemistry-agent-skills

Prepare and explain xTB semiempirical quantum-chemistry workflows for single-point energy, forces, charges, dipole, geometry optimization, and molecular dynamics.

jinzhezenggroup/computational-chemistry-agent-skills

Write, review, and run high-level xTBloom Python GFN2-xTB inference with Calculator, Structure, and BatchCalculator, including single systems, repeated geometry updates, heterogeneous ragged…

jinzhezenggroup/computational-chemistry-agent-skills

Run Python inference with DeePMD-kit models using the DeepPot API.

jinzhezenggroup/computational-chemistry-agent-skills

Use dpdata Python Driver plugins to label systems (energies/forces/virials) via System.predict(), list available drivers, and build Driver objects (ase/deepmd/gaussian/sqm/hybrid).

jinzhezenggroup/computational-chemistry-agent-skills

Minimize geometries with dpdata minimizer plugins via System.minimize(), including how minimizers relate to drivers (ASEMinimizer needs a dpdata Driver) and how to list supported minimizers (ase/sqm).

jinzhezenggroup/computational-chemistry-agent-skills