Data Structures

Here are the data structures with brief descriptions:

[detail level 12]

►Nceps	A namespace for all utility methods
CFunction	Function caller : abstract base, only contains an variadic operator()
CResultOfImpl	Simply to indicate that ResultOfImpl will be a template to be specialized
CResultOfImpl< Function< _Res(_Args...)> >	Used to get the return type of a Function struct
CResultOfImpl< _DerivedFn< _Signature > >	Used to get the return type of a function
CFunction< _Res(_Args...)>	Base Function type for ceps. It's an abstract class which contains only a variadic operator parenthesis. Specialized to signature _Res(_Args...)
CMemberFunction	Just to say that MemberFunction will be templated
CMemberFunction< _Class, _Res(_Class::*)(_Args...)>	A struct that can be used to convert member functions into ceps::Function
CMemberFunction< _Class *, _Res(_Class::*)(_Args...)>	A struct that can be used to convert member functions into ceps::Function pointer specialization
CConstantFunction	Specialization of ceps::Function that returns constant values
CConstantFunction< _Res(_Args...)>	Specialization of ceps::Function that returns constant values
CPiecewiseFunction	Specialization of ceps::Function with several constant values
CPiecewiseFunction< _N, _Object, _Res(_Args...)>	Specialization of ceps::Function with several constant values
CResultOfOperationStruct
CResultOfOperationStruct<'+', _T1, _T2 >	Gives the type of result of addition
CResultOfOperationStruct<'-', _T1, _T2 >	Gives the type of result of substraction
CResultOfOperationStruct<' *', _T1, _T2 >	Gives the type of result of multiplication
CResultOfOperationStruct<'/', _T1, _T2 >	Gives the type of result of division
CFunctionOperation	The product of two functions, a function mult(_Res1,_Res2) must be implemented to be able to deduce the type of the product
CHoldsAttributes	An abstract class from which all objects that contain region attributes should derive
CHoldsBoundary	Abstract class to describe if an entity is on a boundary or not Objects that can be located in a mesh should inherit from this class
CHoldsCells	An abstract class for objects that regroup pointers to cells (eg a mesh, a finite elements discretization, a finite volume discretization)
CHoldsDimension	Abstract class for objects that have a dimensionality (0D to 3D)
CHoldsGeomObject	For objects that have pointers to either a node or a cell
CHoldsGlobalIndex	Abstract class for objects that have a global index
CHoldsNodes
CHoldsProcIds	Abstract class for objects that contain a CPU Id
CAbstractAssembler	Common elements for linear system assembly
CAbstractDiscretization	Abstract Class for all numerical method (FE, FD, FV etc)
CAbstractIonicModel	Represents a ionic model for a group of cells, i.e. multiple systems of ODEs
CAbstractOdeSolver	Solves ODE systems
►CAbstractPacemakerProblem	Common elements of problems with a pacemaker
CPowerSupply	Function supply(t)
CAbstractPacemakerSolver	Solves pacemaker bidomain problem with FBE, SBDF RK or CN schemes
CAbstractPdeProblem	Base class for creating PDEs to solve
CAbstractPdeSolver	Base class for PDE solving
CAbstractSelector
CAbstractStaticPdeProblem	Astract Problem which does not depend on time
CAbstractStaticPdeSolver	Base class for solving PDE with no time dependance
CAbstractTimedPdeProblem	Astract Problem which does depend on time
CAbstractTimedPdeSolver	Base class for solving PDE with time dependance
CActivationTracker	Class managing computations from potential to outputs
CAP95	Aliev-Panfilov ionic model
CArraySAFunc	Functor that gets its result from an array
CAttributesSelector
►CBidomainProblem	Bidomain equation main class
CUnknownsName	Name of unknowns in a struct
CBidomainSolver	Solves bidomain problem with FBE, SBDF RK or CN schemes
►CBilayerMonodomainProblem	Two coupled monodomains
CUnknownsName	Name of unknowns in a struct
CBilayerMonodomainSolver	Monodomain solver on two atrial layers
CBoundaryCondition	Boundary condition
CBoundaryConditionManager	Boundary condition to manage Dirichlet, Neumann and Robin conditions
CBoundarySelector
CBR77	Beeler Reuter (1977) ionic model
CBR77Modified	Beeler Reuter model with bounded iNa current to avoid diverging solution because of
►CCardiacProblem	A abstract class that regroups common parameters of cardiac problems
CFiberAligner	A functor that aligns conductivities along the fibers directions
CUnknownsName	Name of unknowns in a struct
CCardiacSolver	Solves cardiac problems, that all share the same structure
CCepsException
CCepsHash3	A triple hash to be used for coordinates (multiplied *10^12 then truncated)
CCepsMathOperation	Ceps math operator functor, holds (+,-,*,/) definitions depending on mathematical definitions, so some definitions are missing
CCepsMathOperation< CepsMathScalar, CepsMathScalar >	Define operations between CepsMathScalar and CepsMathScalar available: plus, minus, mult and div
CCepsMathOperation< CepsMathScalar, CepsMathTensor >	Define operations between CepsMathScalar and CepsMathTensor available: plus, minus and mult
CCepsMathOperation< CepsMathScalar, CepsMathVertex >	Define operations between CepsMathScalar and CepsMathVertex available: plus, minus and mult
CCepsMathOperation< CepsMathTensor, CepsMathScalar >	Define operations between CepsMathTensor and CepsMathScalar available: plus, minus, mult and div
CCepsMathOperation< CepsMathTensor, CepsMathTensor >	Define operations between CepsMathTensor and CepsMathTensor available: plus, minus and mult
CCepsMathOperation< CepsMathTensor, CepsMathVertex >	Define operations between CepsMathTensor and CepsMathVertex available: only mult
CCepsMathOperation< CepsMathVertex, CepsMathScalar >	Define operations between CepsMathVertex and CepsMathScalar available: plus, minus, mult and div
CCepsMathOperation< CepsMathVertex, CepsMathTensor >	Define operations between CepsMathVertex and CepsMathTensor available: only mult
CCepsMathOperation< CepsMathVertex, CepsMathVertex >	Define operations between CepsMathVertex and CepsMathVertex available: plus, minus and mult
CCepsObject	Base class for other (big) CEPS classes. All classes can get a pointer to this base class and also contain a Profiler
CCepsStandardArgs	Structure used to pass arguments to SAFunc (see pde directory) The flags of the SAFunc allows extraction of the correct argument from this structured type
CCepsVertex
►CCLMonodomainProblem
CUfunc	Simply f(u) = u with u from vector
CUnknownsName	Name of unknowns in a struct
CCoeffInterpolatorSAFunc	Functions with result that is deduced from a coefficient and an interpolation map
CCoeffReader	Reader used to import point or cell data from files
CCompactSupportFunction	The support compact functions themselves
CConstantSAFunc	================================================================================================ Derivation of SAFunc for constants (no dependance in time or space)
CConvergenceStudy	Generic class that regroups common elements of convergence studies
CCoupledNodesReader	A derived class of FileReader that is used when reading coupled Nodes files
CCRN98	Courtemanche-Ramirez-Nattel ionic model
CCstPiecewiseSAFunc	================================================================================================ Functions defined by region, or by unknown (piecewise), with constant pieces
CCustomSelector
CDegreeOfFreedom	A degree of freedom for any kind of problem The dof can be associated to a geometrical element or not. Each dof is tied to a single PDE unknown, has one global index, and can have one attribute
CDicoFuncTimeSelector	A simple SA func that extracts time from arguments, will be added to the dictionary upon creation
CDirichletAnodeCathodeProblem	Poisson equation with Dirichlet 1 on anode, 0 on cathode. Neumann elsewhere. Functional tensorial conductivity
CDirichletAnodeCathodeSolver	DirichletAnodeCathode solver with custom stiffness tensor
CDistributedFactory
CDistributedHaloVector	Extended distributed vectors
CDistributedInfos	A class that manages data that is distributed between processors, not only real values (as in DistributedVector or DistributedMatrix)
CDistributedMatrix	Sparse matrix distributed between process
CDistributedVector	Structure to hold spatially dependant data and distribute it between process
CElectrodeBase	Base class for electrode objects. This one just holds attributes and size, and has very few options
CExcitationSpatialFunction	ExcitationSpatialFunction inherited from ceps::Function
CExcitationTimeFunction	ExcitationTimeFunction inherited from ceps::Function
CExplicitEulerOdeSolver	First order Explicit Euler, aka RK1 or FBE or ..
CExponentialAdamsBashforthOdeSolver	Numerical integration of using EAB methods
►CExtendedBidomainProblem	Bidomain equation with extracardiac medium main class
CUnknownsName	Name of unknowns in a struct
CExtendedBidomainSolver	Solves bidomain extended problem with FBE, SBDF RK or CN schemes
CFBEOdeSolver	Numerical integration of ODE using semi implicit Euler method
CFctPiecewiseSAFunc	================================================================================================ Functions defined by region, or by unknown (piecewise), with functional pieces
►CFEAssembler	A base class made for Finite Element assembler
CIntegrationTools	Integration tools which contains quadrature rule, and values of the basis functions and basis functions gradients evaluated at quadrature points
CFEBase	Abstract class for finite elements
CFEBidomainAssembler	Linear system builder for the bidomain equation
CFEBilayerMonodomainAssembler	Matrix builder for monodomain equation on two coupled layers
CFECardiacBCAssembler	Class to fill linear systems with coefficients linked to boundary conditions
CFECardiacParameters	Common elements of cardiac assemblers
CFEDivKGradAssembler	Assembles the stiffness matrix for a given k-simplexes geometry
CFEDivKGradBCAssembler	Class to fill linear systems with coefficients linked to boundary conditions
CFEExtendedBidomainAssembler	Linear system builder for the bidomain extended equation
CFEHeatAssembler	Assembles the heat problem matrix for a given set of finite elements. here the diffusion coefficient is dependant of time and/or space
CFEIntegrator	Computes the integral of a quantity on the whole domain or subdomains, using a FE matrix
CFEMassAssembler	Assembles the mass matrix for a given k-simplexes geometry
CFEMonodomainAssembler	Matrix building routines for the monodomain equation
CFEMonodomainIntraAssembler	Matrix building routines for the monodomain equation
CFENode	A nodal point on a finite element. It is different from a geom node as it may have different properties. Also, there is not necessarily a match between geom nodes from the mesh and FE nodal points
CFENullMeanConstraintAssembler	A class that adds a 0 mean constraint to an already existing assembler
CFEPacemakerBidomainAssembler
CFEPacemakerPoissonAssembler
CFEStaticSolver	Solve a static problem using Finite Elements. Based on finite elements assemblers
CFETimedSolver	Solve a timed problem using Finite Elements. Implemented numerical schemes: SBDF (1 (FBEuler),2,3,4) RK
CField	A Field is an object wrapped around a SAFunc functor, defined on at least one domain
CFileInterpolatorSAFunc	Functor that uses data from a collection of files to return a value at position x and time t
CFileReader	Base class that regroups common reader functionalities
CFileWriter	Enables the writing of files
CFiniteElements	Holds all finite elements corresponding to each geometrical element
CFlags	Management of run options
CFluxAnodeCathodeProblem	Poisson equation with Neumann 1 on anode, -1 on cathode. Neumann 0 elsewhere. Functional tensorial conductivity
CFluxAnodeCathodeSolver	Solver for a Poisson equation with Neumann BC (using 0 mean constraint)
CFunctionDictionary	FunctionDictionary that holds functions which can be used to define source terms, boundary conditions or physical coefficients
CGaussianQuadrature	Gaussian quadrature for Pk simplex
CGeomCell	Abstract class for geometrical cell. On top of index and attributes managament, the cell has information on the deformation from reference element to actual cell (jacobian of deformation)
CGeomCellJunction	Meta-cell for connections between meshes
CGeometry	Encapsulates all the geometrical data
CGeometryPartitioner	Class is used to compute a geometry (multiple meshes) partitioning
CGeometryReader	Regroups all geometrical data readers and prepare for partitionning
CGeomNode	Base class for nodes used in meshes
CGeomSimplex	K-simplex geometrical element
CGmshMeshReader	Reader for gmsh (.msh) files. For now, only version 2 of the msh format is implemented
CHeatProblem	Heat PDE, single unknown, constant diffusion coeff 1, homogeneous Neumann (no BC defined)
CHeatSolver	Solve heat equation
CHoldsAnodeCathode	An abstract class for objects (problems) that have an anode and a cathode The template argument must be or derive from ElectrodeBase
CInputParameters	Reads and stores simulation configuration
CIonicSolver	Groups two ODE solvers for ionic variables and interacts with cardiac problem
CLaplacianProblem	Laplacian PDE, single unknown, constant stiffness coefficient
CLaplacianSolver	Solve laplacian equation with backward Euler, constant time step, using Finite Elements
CLinearSystem	Linear system Ax=b to be solved
CLocalGlobalMapping	A map destined for things that have (or could have) a global index and must be distributed amongst CPUs. The class manages the local to global indices mapping, and back
CMeditGeometryWriter	Convert a Geometry to a mesh file readable by the Medit viewer
CMeditMeshReader	Reader for medit (.mesh) files
CMeditSolutionWriter	Outputs a solution vector to medit format
CMesh	Geometrical information of 1,2 or 3D distributed cells
CMeshReader	Abstract base class that encapsulates primary functionalities of each mesh reader
►CMonodomainProblem	Defines and solve the monodomain problem, see models page of user doc
CUnknownsName	Name of unknowns in a struct
CMonodomainSolver	Solves the monodomain problem with FBE, SBDF RK or CN schemes
CMonomial	A class that describes a monomial of N variables It contains exponents and coefficients for each dimension of variables
CMpiType	Used to retrieve the MPI "type" in function of the true type
CMS03	Mitchell-Schaeffer ionic model
CMS03Modified	Mitchell-Schaeffer ionic model, with modification to keep ionic current bounded
CNodeCoupling	Meta-cell for connections between meshes
COperatorSAFunc	Operation on two SA Funcs
CORdmD16	O'Hara - Rudy CiPA v1.0 (2017) ionic model
►CPacemakerBidomainProblem	Bidomain equation with extracardiac medium and connected to a pacemaker main class
CPowerSupply	Power source function
CUnknownsName	Struct for all names of unknowns
CPacemakerBidomainSolver	Solves pacemaker bidomain problem with FBE, SBDF RK or CN schemes
►CPacemakerPoissonProblem	Bidomain equation with extracardiac medium and connected to a pacemaker main class
CPowerSupply	Power source function
CUnknownsName	Struct for all names of unknowns
CPacemakerPoissonSolver	Solves pacemaker poisson problem with FBE, SBDF RK or CN schemes
CParallelRCElectrode
CPdeErrorCalculator	Utility to measure distance with respect to analytic solution or given vectors
CPolynomial	A class to represent polynomials, as a collection of Monomial and coefficients
CProfiler	A Chronometer used to measure execution of blocks of code, plus some methods to get current memory usage of the process
CPtscotchPartitioner	Geometry partitioning with PtScotch
CReferenceFE	Base class for reference finite elements
CRungeKuttaOdeSolver	Numerical integration of using RK explicit methods
CRushLarsenOdeSolver	Numerical integration of using Rush Larsen methods
CSAFunc	A SAFunc is a ceps::Function that uses CepsStandardArgs as argument of call operator (), hence the name. Moreover, an object is stored as ptr in the class. This object can be used to evaluate the result
CSBDFOdeSolver	Numerical integration of using Stiff Backward Differentiation methods
CSolVecSAFunc	A SAFunc which gets its values from a distributed vector of values on degrees of freedom
CSourceTerm	Source term, essentially a ScalarField
CSourceTermManager	Source term manager to create and manage SourceTerm objects
CSphereSelector
CTetgenMeshReader	Parser for tetgen .ele .node ... files
CTimeIntegrator	A class that computes the integral over time of a pointed scalar. The integral is computed each time the update() method is called. Time step has to be constant. NewtonCotes methods of order 1,2,3,4,6,7,8,9,10 are implemented
CTimeOnlySAFunc	================================================================================================ Derivation of SAFunc for constants (no dependance in space) but dependance in time
CTimeStepper	A simple time stepper used in dynamic linear solvers
CTimeWriter
CTTP06	Ten-Tusscher Panvilov ionic model (3 variants)
CUnknown	A class used to defined an unknown of a PDE problem The unknown can be defined on a specific region, or can be 0D. If defined on a region, it can be localized either on cells or points of the mesh (point by default). Each unknown has an ID (int), and a name (str)
CUnknownInteraction	Data describing how two unknowns are coupled
CVariableTimeStepper	FIXME Variable ?
CVtkMeshReader	This class enables reading of vtk dataset files
CVtkWriter	A class that enables the output of binary parallel VTK format files