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glim Glossary
Terminology index for glim research and development. Organized by domain.
Materials Science Terms
Potentials & Force Fields
| Term |
Definition |
| EAM (Embedded Atom Method) |
Many-body potential commonly used for metals. Embedding function + pair terms. |
| MEAM (Modified EAM) |
Extension of EAM with angular dependencies. |
| ReaxFF (Reactive Force Field) |
Bond-order potential for reactive MD, handles bond formation/breaking. |
| Tersoff |
Bond-order potential for covalent materials (Si, C, Ge). |
| LAMMPS |
Large-scale Atomic/Molecular Massively Parallel Simulator — MD code. |
| MLIP (Machine Learning Interatomic Potential) |
Neural network potentials (DeePMD, MACE, NequIP) trained on DFT data. |
| DeePMD |
Deep learning potential with embedding networks. |
| MACE |
Equivariant message-passing neural network potential. |
| NequIP |
Neural Equivariant Interatomic Potentials. |
| FitSNAP |
Fitting SNAP potentials — spectral neighbor analysis potential. |
| SNAP |
Spectral Neighbor Analysis Potential. |
| ACE (Atomic Cluster Expansion) |
Framework for efficient atomic descriptors. |
Simulation Methods
| Term |
Definition |
| DFT (Density Functional Theory) |
Quantum mechanical method for electronic structure. |
| MD (Molecular Dynamics) |
Classical particle simulation using force fields. |
| PIMD (Path Integral MD) |
Quantum dynamics using ring polymers. |
| MC (Monte Carlo) |
Stochastic sampling method. |
| PBC (Periodic Boundary Conditions) |
Replicates simulation box infinitely. |
| NVE |
Microcanonical ensemble (constant N, V, E). |
| NVT |
Canonical ensemble (constant N, V, T). |
| NPT |
Isobaric-isothermal ensemble (constant N, P, T). |
Analysis
| Term |
Definition |
| RDF (Radial Distribution Function) |
g(r) — probability density of finding atoms at distance r. |
| MSD (Mean Squared Displacement) |
<Δr²(t)> — measures diffusion. |
| Coordination Number |
Number of nearest neighbors within cutoff. |
| Stress Tensor |
3×3 matrix describing forces per unit area. |
| OVITO |
Visualization and analysis tool for MD (paid Pro version). |
| VMD |
Visual Molecular Dynamics — older visualization tool. |
Benchmarks
| Term |
Definition |
| Delta Codes |
DFT benchmark comparing total energies across elemental crystals. |
| Δ-factor |
RMS energy difference per atom vs. reference (target: <1 meV/atom). |
LAMMPS Ecosystem
| Term |
Definition |
| dump file |
LAMMPS output containing atomic positions per timestep. |
| lammpstrj |
Common dump file extension. |
| log file |
LAMMPS output containing thermodynamic data (temp, energy, etc.). |
| data file |
LAMMPS input file with initial configuration + topology. |
| thermo |
Thermodynamic output (Temperature, Energy, Pressure, etc.). |
| KOKKOS |
Performance portability library for GPUs/HPs in LAMMPS. |
| pair_style |
LAMMPS command specifying interaction potential. |
| fix |
LAMMPS command for perturbations, thermostats, etc. |
| compute |
LAMMPS command for calculating properties. |
| OpenKIM |
Open Knowledgebase of Interatomic Models. |
| Pizza.py |
Python toolkit for LAMMPS analysis (older). |
glim Tech Stack
Web & Graphics
| Term |
Definition |
| WebGPU |
Next-gen web graphics API with compute shaders. |
| WebGL |
Current web graphics API (no compute shaders). |
| WASM (WebAssembly) |
Binary format runnable in browsers at near-native speed. |
| wgsl |
WebGPU Shading Language. |
| R3F (React Three Fiber) |
React renderer for Three.js. |
| Three.js |
JavaScript 3D library. |
| Zustand |
Lightweight React state management. |
| Vite |
Fast JavaScript build tool. |
| Turbo (Turborepo) |
Monorepo build orchestration. |
Rendering Techniques
| Term |
Definition |
| Impostor spheres |
Render each atom as a quad; fragment shader raycasts sphere. |
| InstancedMesh |
Single draw call for many identical geometries. |
| Indirect draw |
GPU builds draw buffer; single draw call regardless of atom count. |
| Frustum culling |
Skip rendering atoms outside camera view. |
| SSAO (Screen Space Ambient Occlusion) |
Post-process darkening for depth perception. |
| DOF (Depth of Field) |
Blur based on distance from focus plane. |
| Bloom |
Glow effect for bright areas. |
| Tone mapping |
Map HDR colors to display range (ACES filmic). |
Parsing
| Term |
Definition |
| wasm-pack |
Build Rust → WASM with JS bindings. |
| wasm-bindgen |
Generate JS bindings from Rust. |
| Web Worker |
Background thread for parsing without blocking UI. |
| Streaming parser |
Process data incrementally without loading all into memory. |
glim Project Structure
| Term |
Definition |
| glimPSE |
WebGPU-powered LAMMPS visualization web app (current focus). |
| glimPSE |
The monorepo in atlas/glimPSE/. |
| @glim/core |
Shared types package. |
| @glim/parsers |
File parsing package (dump, log, data). |
| @glim/scene |
R3F scene components package. |
| @glim/renderer |
Low-level WebGPU pipeline package. |
| @glim/ui |
App shell and panels package. |
| @glim/web |
Vite app entry point. |
File Extensions
| Extension |
File Type |
.lammpstrj |
LAMMPS dump file (text trajectory) |
.dump |
Alternative dump file extension |
.log |
LAMMPS log/thermo file |
.data |
LAMMPS data file (initial config) |
.lmp |
Alternative LAMMPS data extension |
.wgsl |
WebGPU Shading Language |
.tsx |
TypeScript React component |
.rs |
Rust source file |
See docs/navigation.md for codebase navigation. See docs/research-index.md for research document index.
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