{"id":"glossary","title":"Glossary","subtitle":"Terminology index for materials science, MD, DFT, and MLIPs.","category":"foundations","tags":["glossary","reference"],"source":"articles/GLOSSARY.md","lang":"en","words":652,"readMinutes":3,"toc":[{"depth":2,"text":"Materials Science Terms","id":"materials-science-terms"},{"depth":3,"text":"Potentials & Force Fields","id":"potentials-force-fields"},{"depth":3,"text":"Simulation Methods","id":"simulation-methods"},{"depth":3,"text":"Analysis","id":"analysis"},{"depth":3,"text":"Benchmarks","id":"benchmarks"},{"depth":2,"text":"LAMMPS Ecosystem","id":"lammps-ecosystem"},{"depth":2,"text":"glim Tech Stack","id":"glim-tech-stack"},{"depth":3,"text":"Web & Graphics","id":"web-graphics"},{"depth":3,"text":"Rendering Techniques","id":"rendering-techniques"},{"depth":3,"text":"Parsing","id":"parsing"},{"depth":2,"text":"glim Project Structure","id":"glim-project-structure"},{"depth":2,"text":"File Extensions","id":"file-extensions"}],"html":"<h1 id=\"glim-glossary\">glim Glossary</h1><p>Terminology index for glim research and development. Organized by domain.</p>\n<hr>\n<h2 id=\"materials-science-terms\">Materials Science Terms</h2><h3 id=\"potentials-amp-force-fields\">Potentials &amp; Force Fields</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>EAM</strong> (Embedded Atom Method)</td>\n<td data-label=\"Definition\">Many-body potential commonly used for metals. Embedding function + pair terms.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>MEAM</strong> (Modified EAM)</td>\n<td data-label=\"Definition\">Extension of EAM with angular dependencies.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>ReaxFF</strong> (Reactive Force Field)</td>\n<td data-label=\"Definition\">Bond-order potential for reactive MD, handles bond formation/breaking.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Tersoff</strong></td>\n<td data-label=\"Definition\">Bond-order potential for covalent materials (Si, C, Ge).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>LAMMPS</strong></td>\n<td data-label=\"Definition\">Large-scale Atomic/Molecular Massively Parallel Simulator — MD code.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>MLIP</strong> (Machine Learning Interatomic Potential)</td>\n<td data-label=\"Definition\">Neural network potentials (DeePMD, MACE, NequIP) trained on DFT data.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>DeePMD</strong></td>\n<td data-label=\"Definition\">Deep learning potential with embedding networks.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>MACE</strong></td>\n<td data-label=\"Definition\">Equivariant message-passing neural network potential.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>NequIP</strong></td>\n<td data-label=\"Definition\">Neural Equivariant Interatomic Potentials.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>FitSNAP</strong></td>\n<td data-label=\"Definition\">Fitting SNAP potentials — spectral neighbor analysis potential.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>SNAP</strong></td>\n<td data-label=\"Definition\">Spectral Neighbor Analysis Potential.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>ACE</strong> (Atomic Cluster Expansion)</td>\n<td data-label=\"Definition\">Framework for efficient atomic descriptors.</td>\n</tr>\n</tbody></table></div><h3 id=\"simulation-methods\">Simulation Methods</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>DFT</strong> (Density Functional Theory)</td>\n<td data-label=\"Definition\">Quantum mechanical method for electronic structure.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>MD</strong> (Molecular Dynamics)</td>\n<td data-label=\"Definition\">Classical particle simulation using force fields.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>PIMD</strong> (Path Integral MD)</td>\n<td data-label=\"Definition\">Quantum dynamics using ring polymers.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>MC</strong> (Monte Carlo)</td>\n<td data-label=\"Definition\">Stochastic sampling method.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>PBC</strong> (Periodic Boundary Conditions)</td>\n<td data-label=\"Definition\">Replicates simulation box infinitely.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>NVE</strong></td>\n<td data-label=\"Definition\">Microcanonical ensemble (constant N, V, E).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>NVT</strong></td>\n<td data-label=\"Definition\">Canonical ensemble (constant N, V, T).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>NPT</strong></td>\n<td data-label=\"Definition\">Isobaric-isothermal ensemble (constant N, P, T).</td>\n</tr>\n</tbody></table></div><h3 id=\"analysis\">Analysis</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>RDF</strong> (Radial Distribution Function)</td>\n<td data-label=\"Definition\">g(r) — probability density of finding atoms at distance r.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>MSD</strong> (Mean Squared Displacement)</td>\n<td data-label=\"Definition\">&lt;Δr²(t)&gt; — measures diffusion.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Coordination Number</strong></td>\n<td data-label=\"Definition\">Number of nearest neighbors within cutoff.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Stress Tensor</strong></td>\n<td data-label=\"Definition\">3×3 matrix describing forces per unit area.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>OVITO</strong></td>\n<td data-label=\"Definition\">Visualization and analysis tool for MD (paid Pro version).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>VMD</strong></td>\n<td data-label=\"Definition\">Visual Molecular Dynamics — older visualization tool.</td>\n</tr>\n</tbody></table></div><h3 id=\"benchmarks\">Benchmarks</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>Delta Codes</strong></td>\n<td data-label=\"Definition\">DFT benchmark comparing total energies across elemental crystals.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Δ-factor</strong></td>\n<td data-label=\"Definition\">RMS energy difference per atom vs. reference (target: &lt;1 meV/atom).</td>\n</tr>\n</tbody></table></div><hr>\n<h2 id=\"lammps-ecosystem\">LAMMPS Ecosystem</h2><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>dump file</strong></td>\n<td data-label=\"Definition\">LAMMPS output containing atomic positions per timestep.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>lammpstrj</strong></td>\n<td data-label=\"Definition\">Common dump file extension.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>log file</strong></td>\n<td data-label=\"Definition\">LAMMPS output containing thermodynamic data (temp, energy, etc.).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>data file</strong></td>\n<td data-label=\"Definition\">LAMMPS input file with initial configuration + topology.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>thermo</strong></td>\n<td data-label=\"Definition\">Thermodynamic output (Temperature, Energy, Pressure, etc.).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>KOKKOS</strong></td>\n<td data-label=\"Definition\">Performance portability library for GPUs/HPs in LAMMPS.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>pair_style</strong></td>\n<td data-label=\"Definition\">LAMMPS command specifying interaction potential.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>fix</strong></td>\n<td data-label=\"Definition\">LAMMPS command for perturbations, thermostats, etc.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>compute</strong></td>\n<td data-label=\"Definition\">LAMMPS command for calculating properties.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>OpenKIM</strong></td>\n<td data-label=\"Definition\">Open Knowledgebase of Interatomic Models.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Pizza.py</strong></td>\n<td data-label=\"Definition\">Python toolkit for LAMMPS analysis (older).</td>\n</tr>\n</tbody></table></div><hr>\n<h2 id=\"glim-tech-stack\">glim Tech Stack</h2><h3 id=\"web-amp-graphics\">Web &amp; Graphics</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>WebGPU</strong></td>\n<td data-label=\"Definition\">Next-gen web graphics API with compute shaders.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>WebGL</strong></td>\n<td data-label=\"Definition\">Current web graphics API (no compute shaders).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>WASM</strong> (WebAssembly)</td>\n<td data-label=\"Definition\">Binary format runnable in browsers at near-native speed.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>wgsl</strong></td>\n<td data-label=\"Definition\">WebGPU Shading Language.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>R3F</strong> (React Three Fiber)</td>\n<td data-label=\"Definition\">React renderer for Three.js.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Three.js</strong></td>\n<td data-label=\"Definition\">JavaScript 3D library.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Zustand</strong></td>\n<td data-label=\"Definition\">Lightweight React state management.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Vite</strong></td>\n<td data-label=\"Definition\">Fast JavaScript build tool.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Turbo</strong> (Turborepo)</td>\n<td data-label=\"Definition\">Monorepo build orchestration.</td>\n</tr>\n</tbody></table></div><h3 id=\"rendering-techniques\">Rendering Techniques</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>Impostor spheres</strong></td>\n<td data-label=\"Definition\">Render each atom as a quad; fragment shader raycasts sphere.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>InstancedMesh</strong></td>\n<td data-label=\"Definition\">Single draw call for many identical geometries.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Indirect draw</strong></td>\n<td data-label=\"Definition\">GPU builds draw buffer; single draw call regardless of atom count.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Frustum culling</strong></td>\n<td data-label=\"Definition\">Skip rendering atoms outside camera view.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>SSAO</strong> (Screen Space Ambient Occlusion)</td>\n<td data-label=\"Definition\">Post-process darkening for depth perception.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>DOF</strong> (Depth of Field)</td>\n<td data-label=\"Definition\">Blur based on distance from focus plane.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Bloom</strong></td>\n<td data-label=\"Definition\">Glow effect for bright areas.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Tone mapping</strong></td>\n<td data-label=\"Definition\">Map HDR colors to display range (ACES filmic).</td>\n</tr>\n</tbody></table></div><h3 id=\"parsing\">Parsing</h3><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>wasm-pack</strong></td>\n<td data-label=\"Definition\">Build Rust → WASM with JS bindings.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>wasm-bindgen</strong></td>\n<td data-label=\"Definition\">Generate JS bindings from Rust.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Web Worker</strong></td>\n<td data-label=\"Definition\">Background thread for parsing without blocking UI.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>Streaming parser</strong></td>\n<td data-label=\"Definition\">Process data incrementally without loading all into memory.</td>\n</tr>\n</tbody></table></div><hr>\n<h2 id=\"glim-project-structure\">glim Project Structure</h2><div class=\"table-wrap\"><table><thead><tr>\n<th>Term</th>\n<th>Definition</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Term\"><strong>glimPSE</strong></td>\n<td data-label=\"Definition\">WebGPU-powered LAMMPS visualization web app (current focus).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>glimPSE</strong></td>\n<td data-label=\"Definition\">The monorepo in <code>atlas/glimPSE/</code>.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>@glim/core</strong></td>\n<td data-label=\"Definition\">Shared types package.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>@glim/parsers</strong></td>\n<td data-label=\"Definition\">File parsing package (dump, log, data).</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>@glim/scene</strong></td>\n<td data-label=\"Definition\">R3F scene components package.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>@glim/renderer</strong></td>\n<td data-label=\"Definition\">Low-level WebGPU pipeline package.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>@glim/ui</strong></td>\n<td data-label=\"Definition\">App shell and panels package.</td>\n</tr>\n<tr>\n<td data-label=\"Term\"><strong>@glim/web</strong></td>\n<td data-label=\"Definition\">Vite app entry point.</td>\n</tr>\n</tbody></table></div><hr>\n<h2 id=\"file-extensions\">File Extensions</h2><div class=\"table-wrap\"><table><thead><tr>\n<th>Extension</th>\n<th>File Type</th>\n</tr>\n</thead><tbody><tr>\n<td data-label=\"Extension\"><code>.lammpstrj</code></td>\n<td data-label=\"File Type\">LAMMPS dump file (text trajectory)</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.dump</code></td>\n<td data-label=\"File Type\">Alternative dump file extension</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.log</code></td>\n<td data-label=\"File Type\">LAMMPS log/thermo file</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.data</code></td>\n<td data-label=\"File Type\">LAMMPS data file (initial config)</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.lmp</code></td>\n<td data-label=\"File Type\">Alternative LAMMPS data extension</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.wgsl</code></td>\n<td data-label=\"File Type\">WebGPU Shading Language</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.tsx</code></td>\n<td data-label=\"File Type\">TypeScript React component</td>\n</tr>\n<tr>\n<td data-label=\"Extension\"><code>.rs</code></td>\n<td data-label=\"File Type\">Rust source file</td>\n</tr>\n</tbody></table></div><hr>\n<p><em>See docs/navigation.md for codebase navigation. See docs/research-index.md for research document index.</em>\na</p>\n"}