Module chemistry_modeling

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Chemistry Modeling Library - Molecular Simulation and Chemical Analysis

This module provides high-performance chemistry modeling operations leveraging Phase 2 enhancements:

NVMe Computational Storage (CSD) for hardware-accelerated molecular computations
Linear Algebra Library for quantum chemistry calculations
Hardware-Sympathetic Storage (ZNS) for zero-copy molecular data
Statistical Computing Library for molecular dynamics analysis

Modules§

basis_set: Basis Set and Spatial Discretization Engine for Quantum Chemistry Basis Set & Spatial Discretization (Task H)
dft: Density Functional Theory (DFT) Integration Density Functional Theory (DFT) Integration
integrals: Analytical Integral Engine for Quantum Chemistry Analytical Integral Engine for Quantum Chemistry
molecular_dynamics: Real molecular-dynamics engine (Lennard-Jones force field + velocity-Verlet integrator) backing run_molecular_dynamics. Split into its own library submodule (PROJECT RULE §11) so the genuine numerical core is reviewable on its own and carries its own correctness tests. Real molecular dynamics — Lennard-Jones force field + velocity-Verlet integrator.
scf: Self-Consistent Field (SCF) Iterative Driver Self-Consistent Field (SCF) Iterative Driver

Structs§

AdaptiveParameters: Adaptive parameters
AngleCalculator: Angle calculator
AngleCalculatorParameters: Angle calculator parameters
AngleParameter: Angle parameters
ArrheniusParameters: Arrhenius parameters
Atom: Atom representation
BasisFunction: Basis functions
BasisSet: Basis sets
Bond: Bond representation
BondCalculator: Bond calculator
BondCalculatorParameters: Bond calculator parameters
BondParameter: Bond parameters
BondedInteractions: Bonded interactions
BoundaryCondition: Boundary conditions
BoundaryConditions: Boundary conditions
Buckingham: Buckingham potential
ChemistryModelingLibrary: Chemistry Modeling Library Manager
ChemistryOperationResult: Chemistry operation result
ChemistryPerformanceMetrics: Chemistry library performance summary metrics
ChemistryPerformanceMonitor: Chemistry performance monitor
ConstraintHandler: Constraint handler
ConstraintParameters: Constraint parameters
ConvergenceInfo: Convergence information
Coulomb: Coulomb potential
DescriptorCalculator: Descriptor calculator
DipoleMoment: Dipole moment
ElectronicEnergy: Electronic energy
EnergyCalculator: Energy calculator
EnergyConservation: Energy conservation
EnergyPoint: Energy points
EnergyProfile: Energy profile
EnsembleManager: Ensemble manager
EnsembleTransition: Ensemble transitions
EquilibriumCalculator: Equilibrium calculator
EquilibriumConditions: Equilibrium conditions
EquilibriumConstant: Equilibrium constant
EwaldSummation: Ewald summation
FallOffParameters: Fall-off parameters
ForceField: Force fields
ForceFieldCalculator: Force field calculator
ForceFieldParameters: Force field parameters
FrameEnergy: Frame energy
GibbsEnergy: Gibbs energy
ImproperCalculator: Improper calculator
ImproperCalculatorParameters: Improper calculator parameters
IntegratorParameters: Integrator parameters
InteractionCalculator: Interaction calculator
KineticEnergy: Kinetic energy
KineticsCalculator: Kinetics calculator
KineticsResults: Kinetics analysis results
LennardJones: Lennard-Jones potential
LongRangeInteractions: Long-range interactions
MLModel: Machine learning models
MLModelParameters: ML model parameters
MinimumImage: Minimum image convention
ModelPerformance: Model performance
ModifiedArrheniusParameters: Modified Arrhenius parameters
MolecularDescriptors: Molecular descriptors
MolecularIntegrator: Molecular integrator
MolecularProperties: Molecular properties
MolecularSimulator: Molecular simulator for molecular dynamics simulations
Molecule: Molecule representation
MullikenCharges: Mulliken charges
NonbondedInteractions: Nonbonded interactions
NonbondedParameter: Nonbonded parameters
NuclearEnergy: Nuclear energy
ParticleMesh: Particle mesh
Phase: Phases
PhaseBoundary: Phase boundaries
PhaseCalculator: Phase calculator
PhaseDiagram: Phase diagrams
PhaseEquilibrium: Phase equilibria
PhaseTransition: Phase transitions
Polarizability: Polarizability
PotentialEnergy: Potential energy
PredictedProperties: Predicted molecular properties
PressureDependence: Pressure dependence
PropertyMetrics: Property metrics
PropertyModel: Property models
PropertyModelParameters: Property model parameters
PropertyPredictor: Property predictor for molecular property prediction
QuantumCalculator: Quantum calculator for quantum chemistry calculations
QuantumDescriptors: Quantum descriptors
QuantumEnergyCalculator: Quantum energy calculator
QuantumMetrics: Quantum metrics
QuantumProperties: Quantum chemistry properties
QuantumPropertyCalculator: Quantum property calculator
QuantumTotalEnergy: Quantum total energy
RateConstant: Rate constants
RateLaw: Rate laws
RateLawParameters: Rate law parameters
Reaction: Reactions
ReactionAnalyzer: Reaction analyzer for chemical reaction analysis
ReactionConditions: Reaction conditions for chemistry simulations
ReactionField: Reaction field
ReactionMechanism: Reaction mechanisms
ReactionMetrics: Reaction metrics
ReactionNetwork: Reaction network
ReactionPathway: Reaction pathways
ReactionQuotient: Reaction quotient
ReactionStep: Reaction steps
ReferenceConditions: Reference conditions
ReferenceData: Reference data
SCFParameters: SCF parameters
SamplingMethod: Sampling methods
SamplingParameters: Sampling parameters
SimulationConfig: Simulation configuration
SimulationEngine: Simulation engine
SimulationFrame: Simulation frame
SimulationMetrics: Simulation metrics
SimulationTrajectory: Simulation trajectory
Species: Species
SpeciesProperties: Species properties
StabilityAnalysis: Stability analysis
StructuralProperties: Exact structural / mass properties of a molecule (see the methods on [ChemistryModelingLibrary]). Every field is computed from a closed-form definition over atomic data and geometry, not an approximation or fit.
TemperatureController: Temperature controller
TemperatureDependence: Temperature dependence
TemperatureFluctuation: Temperature fluctuation
TemperatureProfile: Temperature profile
ThermodynamicData: Thermodynamic data
ThermodynamicsCalculator: Thermodynamics calculator
ThermostatParameters: Thermostat parameters
TimeStepControl: Time step control
TopologicalDescriptors: Topological descriptors
TorsionCalculator: Torsion calculator
TorsionCalculatorParameters: Torsion calculator parameters
TorsionParameter: Torsion parameters
TotalEnergy: Total energy
TrainingData: Training data
TrajectoryProperties: Trajectory properties
UBParameters: UB parameters
WavefunctionCalculator: Wavefunction calculator

Enums§

AngleCalculatorType: Angle calculator types
BasisFunctionType: Basis function types
BasisSetType: Basis set types
BondCalculatorType: Bond calculator types
BoundaryType: Boundary types
ChemistryError: Chemistry error types
ConstraintAlgorithm: Constraint algorithms
Ensemble: Ensembles
ForceFieldType: Force field types
ImproperCalculatorType: Improper calculator types
IntegratorType: Integrator types
MLModelType: ML model types
PhaseBoundaryType: Phase boundary types
PhaseType: Phase types
PropertyModelType: Property model types
PropertyType: Property types
QuantumMethodType: Quantum method types
RateLawType: Rate law types
ReactionType: Reaction types
SamplingMethodType: Sampling method types
SimulationType: Simulation types
StabilityAnalysisMethod: Stability analysis methods
TemperatureControlMethod: Temperature control methods
TemperatureProfileType: Temperature profile types
TimeStepControlType: Time step control types
TorsionCalculatorType: Torsion calculator types
TransitionMethod: Transition methods
TransitionType: Transition types

Functions§

standard_atomic_weight: IUPAC standard atomic weight (amu) for common elements. Conventional values (IUPAC 2021). Returns None for elements outside the table so callers can fall back to a declared per-atom mass rather than receive a fabricated one.

Module chemistry_modeling

Module chemistry_modeling Copy item path

Modules§

Structs§

Enums§

Functions§

Module chemistry_modeling