SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers coarse-grained (CG) molecular dynamics: mapping atomistic structures to CG bead representations, parameterizing CG force fields (Martini 3, iterative Boltzmann inversion, force matching), running CG simulations in GROMACS and LAMMPS, backmapping CG configurations to atomistic resolution, and…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers enhanced sampling methods for atomistic MD simulations where rare events, large free-energy barriers, or slow conformational transitions prevent standard MD from converging on accessible timescales. It addresses collective variable (CV) selection and validation; umbrella sampling with WHAM/MBAR…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers quantitative free-energy calculations from molecular dynamics: alchemical methods (free energy perturbation, thermodynamic integration, BAR, MBAR), potential of mean force from umbrella sampling, absolute and relative binding/hydration/solvation free energies, thermodynamic cycles, lambda schedules…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers end-to-end molecular dynamics simulations using GROMACS: topology construction and the .top/.itp hierarchy, .mdp parameter anatomy for energy minimization, NVT, NPT, and production runs, the grompp → mdrun → analysis pipeline, cutoff and PME setup, thermostat and barostat selection, constraint…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers end-to-end molecular dynamics simulations using LAMMPS (Large-scale Atomic/Massively Parallel Simulator): input script anatomy, force-field selection and deployment, ensemble control, equilibration protocol, production runs, restart logic, and parallel execution. LAMMPS is the dominant open-source MD…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers quantitative post-processing of atomistic molecular dynamics trajectories: loading and preprocessing trajectories from LAMMPS, GROMACS, or ASE; computing structural observables (RDF, coordination numbers, angular distributions, bond orientational order, common-neighbor analysis, centrosymmetry…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers the systematic process of bringing an atomistic simulation from its initial (often artificial) configuration to a state representative of the target thermodynamic ensemble before collecting production statistics. It addresses ensemble selection, thermostat and barostat time constants, timestep…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers selection, validation, and deployment of interatomic force fields for molecular dynamics: the physical basis and transferability limits of every major functional form (EAM, MEAM, Tersoff, Stillinger-Weber, Buckingham, COMB, ReaxFF, AMBER, CHARMM, OPLS, GROMOS, and ML potentials); parameter-file…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers reactive molecular dynamics (reactive MD) using LAMMPS with the ReaxFF and COMB force fields: force-field selection and parameter provenance, charge equilibration (QEq) setup and diagnostics, timestep and thermostat selection for reactive systems, thermal protocols for reaction sampling, reaction…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers molecular datasets for chemistry and molecular machine learning: selecting appropriate sources, preserving identifiers and metadata, standardizing molecular records, deduplicating structures, harmonizing units and labels, creating leakage-aware splits, auditing provenance and licenses, and preparing…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers molecular featurization for chemistry and molecular machine learning: parsing SMILES, SMARTS, InChI, SDF, and MOL2-like records; RDKit sanitization and standardization; fingerprints such as Morgan/ECFP, MACCS, atom-pair, torsion, pharmacophore, and topological fingerprints; physicochemical…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers molecular line notations for cheminformatics and molecular machine learning: parsing and validating SMILES; canonical, non-canonical, and isomeric SMILES; stereochemistry handling; aromaticity perception; RDKit sanitization; molecule standardization, salt/fragment handling, neutralization, and…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers end-to-end quantum chemistry workflows for molecules, reactions, and molecular materials: structure preparation and standardization; geometry optimization; frequency analysis and thermochemistry; transition-state search and reaction-profile construction; method and basis-set selection and…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
Select, calibrate, implement, and validate creep deformation and rupture models for materials and components under sustained thermomechanical loading. The workflow separates rate prediction, transient deformation, stress redistribution, damage evolution, and rupture so that a secondary-creep fit is not mistaken for a…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers crystal plasticity and crystal plasticity finite element (CPFE) modeling of metals: orientation representations and conventions, slip-system definitions for FCC/BCC/HCP, resolved shear stress and Schmid factors, the multiplicative decomposition F = Fe Fp, rate-dependent and rate-independent flow…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
Build, calibrate, and validate fatigue assessments for metallic materials and components. Select among stress-life, strain-life, local-strain, multiaxial critical-plane, defect-sensitive, crystal-plasticity, and fracture-mechanics methods according to the physical stage being predicted and the available evidence.
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers finite element modeling for materials, chemistry, mechanics, transport, and coupled multiphysics problems: weak-form construction, boundary and initial conditions, mesh generation, element choice, solver selection, parameter calibration, convergence studies, validation, uncertainty analysis, and…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
Select, construct, and validate fracture-mechanics assessments for cracked materials and components. The workflow distinguishes strength, damage, fracture initiation, stable crack propagation, and unstable fracture, then connects analytical LEFM checks with finite-element, elastic-plastic, cohesive-zone, phase-field…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers computational and data-driven workflows for battery materials discovery and characterization: voltage profiles, redox couples, intercalation thermodynamics, phase stability, ion migration barriers, defect chemistry, ionic conductivity, electrochemical stability windows, surface and interface…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers corrosion and electrochemistry workflows for materials degradation and surface reactions: electrode potentials, reference electrodes, polarization curves, impedance, passivation, pitting, galvanic coupling, Pourbaix diagrams, transport modeling, surface chemistry, parameter calibration, uncertainty…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
AiiDA (Automated Interactive Infrastructure and Database for Computational Science) is a Python-based, provenance-first workflow engine for computational materials science. It manages the complete lifecycle of calculations: input generation, remote HPC job submission via SSH, output retrieval and parsing, automatic…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers end-to-end DFT, AIMD, and atomistic simulation workflows using CP2K, from input file construction through convergence testing, geometry optimization, and ab initio molecular dynamics. CP2K uses the Gaussian and Plane Waves (GPW) method, which combines a Gaussian-type orbital (GTO) basis with an…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers systematic convergence testing for plane-wave DFT calculations: cutoff energy (ENCUT / ecutwfc), k-point mesh density, smearing scheme and width, and SCF thresholds. Convergence requirements change significantly depending on the property of interest, the code, and the downstream use of the data.…
SFETNI/Deep-Matter-Chem-Skills
Skill Claude CodeCodex
This skill covers the systematic generation of DFT-labeled datasets for training machine-learned interatomic potentials: configuration-space coverage strategy, single-point labeling with VASP and Quantum ESPRESSO, label consistency enforcement (energies, forces, stresses, units, PBC), isolated atom reference energy…