Struct ModelStateDerived¶
Defined in File model_state.h
Struct Documentation¶
-
struct
amici
::
ModelStateDerived
¶ Storage for
amici::Model
quantities computed based onamici::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
xnx_solver
)
-
SUNMatrixWrapper
dxdotdp_full
¶ Temporary storage of
dxdotdp_full
data across functions (Python only) (dimension:nplist
xnx_solver
, nnz: dynamic, typeCSC_MAT
)
-
SUNMatrixWrapper
dxdotdp_explicit
¶ Temporary storage of
dxdotdp_explicit
data across functions (Python only) (dimension:nplist
xnx_solver
, nnz:ndxdotdp_explicit
, typeCSC_MAT
)
-
SUNMatrixWrapper
dxdotdp_implicit
¶ Temporary storage of
dxdotdp_implicit
data across functions, Python-only (dimension:nplist
xnx_solver
, nnz: dynamic, typeCSC_MAT
)
-
SUNMatrixWrapper
dxdotdx_explicit
¶ Temporary storage of
dxdotdx_explicit
data across functions (Python only) (dimension:nplist
xnx_solver
, nnz:nxdotdotdx_explicit
, typeCSC_MAT
)
-
SUNMatrixWrapper
dxdotdx_implicit
¶ Temporary storage of
dxdotdx_implicit
data across functions, Python-only (dimension:nplist
xnx_solver
, nnz: dynamic, typeCSC_MAT
)
-
AmiVectorArray
dxdotdp
= {0, 0}¶ Temporary storage of
dxdotdp
data across functions, Matlab only (dimension:nplist
xnx_solver
, row-major)
-
std::vector<SUNMatrixWrapper>
dJydy_
¶ Sparse observable derivative of data likelihood, only used if
pythonGenerated
==true
(dimensionnytrue
,nJ
xny
, row-major)
-
std::vector<realtype>
dJydy_matlab_
¶ Observable derivative of data likelihood, only used if
pythonGenerated
==false
(dimensionnJ
xny
xnytrue
, 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
xnx_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
xnx_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
xnx_solver
, row-major)
-
std::vector<realtype>
drzdp_
¶ parameter derivative of event regularization variable (dimension: nz x nplist, row-major)
-
std::vector<realtype>
dydx_
¶ state derivative of time-resolved observable (dimension:
nx_solver
xny
, row-major)
-
std::vector<realtype>
sx_
¶ temporary storage for flattened sx, (dimension:
nx_solver
xnplist
, row-major)
-
std::vector<realtype>
dsigmaydp_
¶ temporary storage for parameter derivative of data standard deviation, (dimension: ny x nplist, row-major)
-
std::vector<realtype>
dsigmazdp_
¶ temporary storage for parameter derivative of event standard deviation, (dimension: nz x nplist, row-major)
-
std::vector<realtype>
deltasx_
¶ temporary storage for change in sx after event (dimension:
nx_solver
xnplist
, row-major)
-
std::vector<realtype>
deltaxB_
¶ temporary storage for change in xB after event (dimension:
nx_solver
)
-