Struct ChemistryModelingLibrary 

pub struct ChemistryModelingLibrary { /* private fields */ }

Chemistry Modeling Library Manager

Implementations

impl ChemistryModelingLibrary

pub fn new() -> Self

Create new chemistry modeling library

pub fn attach_dependencies( &mut self, linear_algebra: Arc<Mutex<LinearAlgebraLibrary>>, statistical_computing: Arc<Mutex<StatisticalComputingLibrary>>, csd_manager: Arc<Mutex<CsdManager>>, zns_manager: Arc<Mutex<ZnsZoneManager>>, )

Attach the Phase 2 cross-library dependencies (linear algebra, statistical computing, CSD computational storage, ZNS zero-copy storage). This is the wiring point called after new once the caller has constructed the shared library handles. Sub-components read them through this library.

pub fn initialize(&mut self) -> Result<(), ChemistryError>

Initialize the library

pub fn run_molecular_dynamics( &mut self, config: SimulationConfig, molecule: Molecule, ) -> Result<ChemistryOperationResult<SimulationTrajectory>, ChemistryError>

Run molecular dynamics simulation

pub fn calculate_quantum_properties( &mut self, molecule: Molecule, method: QuantumMethodType, ) -> Result<ChemistryOperationResult<QuantumProperties>, ChemistryError>

Calculate quantum properties

pub fn analyze_reaction_kinetics( &mut self, reaction: Reaction, conditions: ReactionConditions, ) -> Result<ChemistryOperationResult<KineticsResults>, ChemistryError>

Analyze reaction kinetics

pub fn predict_properties( &mut self, molecule: Molecule, properties: Vec<PropertyType>, ) -> Result<ChemistryOperationResult<PredictedProperties>, ChemistryError>

Predict molecular properties

pub fn get_performance_stats(&self) -> ChemistryPerformanceMetrics

Get performance statistics

pub fn list_force_fields(&self) -> Vec<String>

List available force fields

pub fn get_molecule_info(&self, molecule_id: &str) -> Option<Molecule>

Get molecule information

pub fn molecular_mass(&self, molecule: &Molecule) -> f64

Total molecular mass in amu, summed from IUPAC standard atomic weights by element (falling back to the atom’s own declared mass when the element is outside the built-in table). Reproducible and independent of whatever per-atom mass the caller happened to set.

pub fn molecular_formula(&self, molecule: &Molecule) -> String

Molecular formula in Hill notation: carbon first, then hydrogen, then all remaining elements in alphabetical order, each with its count (count of 1 omitted). E.g. water → H2O, methane → CH4, ethanol → C2H6O.

pub fn nuclear_repulsion_energy( &self, molecule: &Molecule, ) -> Result<f64, ChemistryError>

Nuclear repulsion energy E_nn = Σ_{i<j} Z_i·Z_j / r_ij.

This is the exact classical Coulomb repulsion between the point nuclei; it is returned in atomic units (Hartree) when the atom coordinates are in bohr. A single atom (or none) has no nuclear pairs and returns 0.0. Refuses (rather than inventing a value) when any atom has a zero nuclear charge, a malformed coordinate vector, or two nuclei coincide.

pub fn bond_length( &self, molecule: &Molecule, i: usize, j: usize, ) -> Result<f64, ChemistryError>

Bond length (Euclidean distance) between atoms i and j, in the same length unit as the coordinates.

pub fn bond_angle( &self, molecule: &Molecule, i: usize, j: usize, k: usize, ) -> Result<f64, ChemistryError>

Bond angle i–j–k in radians, with j the vertex. Computed from the exact dot-product definition θ = acos((u·v)/(|u||v|)), u = r_i−r_j, v = r_k−r_j.

pub fn center_of_mass( &self, molecule: &Molecule, ) -> Result<[f64; 3], ChemistryError>

Center of mass, mass-weighted by standard atomic weights (falling back to the atom’s declared mass). Same length unit as the coordinates.

pub fn principal_moments_of_inertia( &self, molecule: &Molecule, ) -> Result<[f64; 3], ChemistryError>

Principal moments of inertia (ascending), in amu·(length unit)². Builds the exact inertia tensor about the center of mass and diagonalizes it with the tested scf::jacobi_diagonalization (real symmetric 3×3).

pub fn structural_properties( &self, molecule: &Molecule, ) -> Result<StructuralProperties, ChemistryError>

Aggregate the exact structural / mass properties into one result. The nuclear repulsion energy is only meaningful when the coordinates are in bohr; it is included here as Some when computable and None (with the reason discarded) when the geometry cannot support it.