Struct ModelStateDerived¶

Defined in File model_state.h

Struct Documentation¶

struct amici::ModelStateDerived¶

Storage for amici::Model quantities computed based on amici::ModelState for a specific timepoint.

Serves as workspace for a model simulation to avoid repeated reallocation.

Public Functions

ModelStateDerived() = default¶

ModelStateDerived(ModelDimensions const &dim)¶

Constructor from model dimensions.

Parameters

dim: Model dimensions

Public Members

SUNMatrixWrapper J_¶: Sparse Jacobian (dimension: amici::Model::nnz)

SUNMatrixWrapper JB_¶: Sparse Backwards Jacobian (dimension: amici::Model::nnz)

SUNMatrixWrapper dxdotdw_¶: Sparse dxdotdw temporary storage (dimension: ndxdotdw)

SUNMatrixWrapper dwdx_¶: Sparse dwdx temporary storage (dimension: ndwdx)

SUNMatrixWrapper dwdp_¶: Sparse dwdp temporary storage (dimension: ndwdp)

SUNMatrixWrapper M_¶: Dense Mass matrix (dimension: nx_solver x nx_solver)

SUNMatrixWrapper dxdotdp_full¶: Temporary storage of dxdotdp_full data across functions (Python only) (dimension: nplist x nx_solver, nnz: dynamic, type CSC_MAT)

SUNMatrixWrapper dxdotdp_explicit¶: Temporary storage of dxdotdp_explicit data across functions (Python only) (dimension: nplist x nx_solver, nnz: ndxdotdp_explicit, type CSC_MAT)

SUNMatrixWrapper dxdotdp_implicit¶: Temporary storage of dxdotdp_implicit data across functions, Python-only (dimension: nplist x nx_solver, nnz: dynamic, type CSC_MAT)

SUNMatrixWrapper dxdotdx_explicit¶: Temporary storage of dxdotdx_explicit data across functions (Python only) (dimension: nplist x nx_solver, nnz: nxdotdotdx_explicit, type CSC_MAT)

SUNMatrixWrapper dxdotdx_implicit¶: Temporary storage of dxdotdx_implicit data across functions, Python-only (dimension: nplist x nx_solver, nnz: dynamic, type CSC_MAT)

AmiVectorArray dxdotdp = {0, 0}¶: Temporary storage of dxdotdp data across functions, Matlab only (dimension: nplist x nx_solver , row-major)

std::vector<SUNMatrixWrapper> dJydy_¶: Sparse observable derivative of data likelihood, only used if pythonGenerated == true (dimension nytrue, nJ x ny, row-major)

std::vector<realtype> dJydy_matlab_¶: Observable derivative of data likelihood, only used if pythonGenerated == false (dimension nJ x ny x nytrue , row-major)

std::vector<realtype> dJydsigma_¶: Observable sigma derivative of data likelihood (dimension nJ x ny x nytrue, row-major)

std::vector<realtype> dJydx_¶: State derivative of data likelihood (dimension nJ x nx_solver, row-major)

std::vector<realtype> dJydp_¶: Parameter derivative of data likelihood for current timepoint (dimension: nJ x nplist, row-major)

std::vector<realtype> dJzdz_¶: event output derivative of event likelihood (dimension nJ x nz x nztrue, row-major)

std::vector<realtype> dJzdsigma_¶: event sigma derivative of event likelihood (dimension nJ x nz x nztrue, row-major)

std::vector<realtype> dJrzdz_¶: event output derivative of event likelihood at final timepoint (dimension nJ x nz x nztrue, row-major)

std::vector<realtype> dJrzdsigma_¶: event sigma derivative of event likelihood at final timepoint (dimension nJ x nz x nztrue, row-major)

std::vector<realtype> dJzdx_¶: state derivative of event likelihood (dimension nJ x nx_solver, row-major)

std::vector<realtype> dJzdp_¶: parameter derivative of event likelihood for current timepoint (dimension: nJ x nplist x, row-major)

std::vector<realtype> dzdx_¶: state derivative of event output (dimension: nz x nx_solver, row-major)

std::vector<realtype> dzdp_¶: parameter derivative of event output (dimension: nz x nplist, row-major)

std::vector<realtype> drzdx_¶: state derivative of event regularization variable (dimension: nz x nx_solver, row-major)

std::vector<realtype> drzdp_¶: parameter derivative of event regularization variable (dimension: nz x nplist, row-major)

std::vector<realtype> dydp_¶: parameter derivative of observable (dimension: ny x nplist, row-major)

std::vector<realtype> dydx_¶: state derivative of time-resolved observable (dimension: nx_solver x ny, row-major)

std::vector<realtype> w_¶: temporary storage of w data across functions (dimension: nw)

std::vector<realtype> sx_¶: temporary storage for flattened sx, (dimension: nx_solver x nplist, row-major)

std::vector<realtype> x_rdata_¶: temporary storage for x_rdata (dimension: nx_rdata)

std::vector<realtype> sx_rdata_¶: temporary storage for sx_rdata slice (dimension: nx_rdata)

std::vector<realtype> y_¶: temporary storage for time-resolved observable (dimension: ny)

std::vector<realtype> sigmay_¶: data standard deviation for current timepoint (dimension: ny)

std::vector<realtype> dsigmaydp_¶: temporary storage for parameter derivative of data standard deviation, (dimension: ny x nplist, row-major)

std::vector<realtype> z_¶: temporary storage for event-resolved observable (dimension: nz)

std::vector<realtype> rz_¶: temporary storage for event regularization (dimension: nz)

std::vector<realtype> sigmaz_¶: temporary storage for event standard deviation (dimension: nz)

std::vector<realtype> dsigmazdp_¶: temporary storage for parameter derivative of event standard deviation, (dimension: nz x nplist, row-major)

std::vector<realtype> deltax_¶: temporary storage for change in x after event (dimension: nx_solver)

std::vector<realtype> deltasx_¶: temporary storage for change in sx after event (dimension: nx_solver x nplist, row-major)

std::vector<realtype> deltaxB_¶: temporary storage for change in xB after event (dimension: nx_solver)

std::vector<realtype> deltaqB_¶: temporary storage for change in qB after event (dimension: nJ x nplist, row-major)

AmiVector x_pos_tmp_ = {0}¶: temporary storage of positified state variables according to stateIsNonNegative (dimension: nx_solver)