Algorithms

One page per ported algorithm. Template for every page:

Diagrams live in docs/public/diagrams/ (29 SVG, one shared style, animated with SMIL and static under prefers-reduced-motion). Every page that describes a procedure or a geometry embeds one. The inventory and decision pages (Golden data, External validation, Algorithm coverage, Dependency map, sci-form reuse, ML backend, Modules, Symmetry backend) are tables and records of decisions and have no algorithm to draw.

Pages are added with the feature that introduces them:

Lattice conventions (Task 1.2.5)
Limits model (Task 1.3)
P1 expansion with provenance (Task 1.6)
Supercells and origin shifts (Task 1.7)
Slab construction (Task 1.8)
Cartesian transforms and ellipsoids (Task 1.9)
Periodic neighbor search (Task 1.10)
Bond perception (Task 1.11)
Primitive rings (Task 1.12)
Functional groups (Task 1.13)
Measures (Task 1.14)
CIF parsing (Task 1.15)
POSCAR and XYZ (Task 1.16)
Symmetry detection (Task 2.1)
Agent session and diagnostics (Task 8.1)
Analysis: patterns, peaks, grids and nets (Task 5.1-5.9)
Builders: molecules, polymers and carbon (Task 6.1-6.9)
MOF builder (Task 6.12-6.16)
Powder pipeline (Task 7.5-7.10)
Modules, jobs and reports (Task 3.13, 5.10)
Algorithm coverage (Task 8.7.2)
UFF and UFF4MOF (Task 4.2)
Charges and electrostatics (Task 4.3)
Optimization, scans and EOS (Task 4.4-4.5)
Vibrations and thermodynamics (Task 4.8)
Powder indexing (Task 7.5)
Pawley fit (Task 7.6)
Le Bail extraction (Task 7.6)
Rietveld refinement (Task 7.8)
External validation (Task 0.9)
Nets and RCSR identification (Task 5.6)
Extinction screening (Task 7.10)
Machine-learning backend (Task 4.11)
Symmetry backend: moyo (Task 0.3.5)
Validation and tolerances (Task 0.9.4)
Golden data (Task 0.9.3)
sci-form reuse (Task 0.4)
Disordered carbons (Task 6.8)
Dependency replacement map (Task 0.10)

The neighbor-search page records the linked-cell index and the scaling benchmark in Phase 1.

Algorithms ​