Internal API

Besides of the interface methods for VoronoiFVMDiffEq, these are not exported and therefore should not be used outside of the package

Wrapping evaluators for physics callbacks

VoronoiFVM.ResEvaluator — Type
struct ResEvaluator{Tv<:Number, Func<:Function, G} <: VoronoiFVM.AbstractEvaluator

Evaluator for functions from physics. Allows to call different types of physic functions (flux, reaction, source) an provides a common interface to different function formats (with data, without data etc.)

  • fwrap::Function: wrapper function in Format ready for Diffetential equations

  • y::Vector{Tv} where Tv<:Number: pre-allocated result

  • geom::Any: Geometry object # geometry (node, edge...)

  • nspec::Int64: number of species

  • isnontrivial::Bool: Is the function not one of nofunc ot nofunc2

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VoronoiFVM.ResEvaluator — Method
 ResEvaluator(physics,symb,uproto,geom,nspec)

Constructor for ResEvaluator

  • physics Physics object
  • symb: symbol naming one of the functions in physics to be wrapped.
  • uproto: solution vector prototype,
  • geom: node, edge...
  • nspec: number of species
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VoronoiFVM.evaluate! — Method
evaluate!(e::VoronoiFVM.ResEvaluator)

Call function in evaluator, store result in predefined memory.

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VoronoiFVM.evaluate! — Method
evaluate!(e::VoronoiFVM.ResEvaluator, u)

Call function in evaluator, store result in predefined memory.

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VoronoiFVM.res — Method
res(
    e::VoronoiFVM.ResEvaluator
) -> Vector{Tv} where Tv<:Number

Retrieve evaluation result

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VoronoiFVM.ResJacEvaluator — Type
struct ResJacEvaluator{Tv<:Number, Func<:Function, Cfg, Res, G} <: VoronoiFVM.AbstractEvaluator

Evaluator for functions from physics and their Jacobians. Allows to call different types of physic functions (flux, reaction, source) an provides a common interface to different function formats (with data, without data etc.)

  • fwrap::Function: wrapper function in Format ready for Differential equations

  • config::Any: ForwardDiff.JacobianConfig

  • result::Any: DiffResults.JacobianResult

  • y::Vector{Tv} where Tv<:Number: pre-allocated result

  • geom::Any: Geometry object # geometry (node, edge...)

  • nspec::Int64: number of species

  • isnontrivial::Bool: Is the function not one of nofunc ot nofunc2

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VoronoiFVM.ResJacEvaluator — Method
ResJacEvaluator(physics, symb, uproto, geom, nspec)

Constructor for ResJEvaluator

  • physics Physics object
  • symb: symbol naming one of the functions in physics to be wrapped.
  • uproto: solution vector prototype,
  • geom: node, edge...
  • nspec: number of species
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VoronoiFVM.evaluate! — Method
evaluate!(e::VoronoiFVM.ResJacEvaluator, u)

Call function in evaluator, store result and jacobian in predefined memory.

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VoronoiFVM.isnontrivial — Function
isnontrivial(e::VoronoiFVM.AbstractEvaluator) -> Any

Does calling the evaluator giva nontrivial (nonzero) result?

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Global node and edge assembly loops

VoronoiFVM.CellwiseAssemblyData — Type
struct CellwiseAssemblyData{Tv, Ti} <: VoronoiFVM.AbstractAssemblyData{Tv, Ti}

Data for cellwise assembly.

  • nodefactors::Matrix: Precomputed geometry factors for cell nodes. This is a ncells x nnodes_per_cell full matrix.
  • edgefactors::Matrix: Precomputed geometry factors for cell edges This is a ncells x nedge_per_cell full matrix.
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VoronoiFVM.EdgewiseAssemblyData — Type
struct EdgewiseAssemblyData{Tv, Ti} <: VoronoiFVM.AbstractAssemblyData{Tv, Ti}
  • nodefactors::SparseArrays.SparseMatrixCSC{Tv, Ti} where {Tv, Ti}: Precomputed geometry factors for nodes. This is a nnodes x nregions sparse matrix.
  • edgefactors::SparseArrays.SparseMatrixCSC{Tv, Ti} where {Tv, Ti}: Precomputed geometry factors for edges This is a nedges x nregions sparse matrix.
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VoronoiFVM._fill! — Function
_fill!(node, asmdata, inode, icell)

Fill node with the help of assemblydata.

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_fill!(node, asmdata, ibnode, ibface)

Fill boundary node with the help of assemblydata.

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_fill!(edge, asmdata, iedge, icell)

Fill edge with the help of assemblydata.

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_fill!(bedge, asmdata, ibedge, ibface)

Fill boundary edge with the help of assemblydata.

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_fill!(node, asmdata, k, inode)

Fill node with the help of assemblydata.

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_fill!(edge, asmdata, k, iedge)

Fill edge with the help of assemblydata.

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Local node and edge assembly loops

Local assembly methods organize the assembly of data to those degrees of freedom (dofs) which are defined for a given node or edge. E.g. for an node residual for nspec defined species, only those entries need to be assembled into the global residual vector which correspond to actually defined degrees of freedom.

Similarly for nspec x nspec node Jacobian, an for the nparam x nspec parameter derivatives.

These local assembly methods organize the correct loops and call back to the concrete assembly methods passed to them. These receive global degrees of freedom and the local species numbers to be handled. The callbacks can be used as well for other purposes than assembly

VoronoiFVM.assemble_res_jac — Function
assemble_res_jac(node, system, asm_res, asm_jac, asm_param)

Assemble residual and jacobian for node functions. Parameters:

  • system: System to be worked with

  • node: node

  • asm_jac(idof,jdof,ispec,jspec): e.g. assemble entry ispec,jspec of local jacobian into entry idof,jdof of global matrix

  • asm_param(idof,ispec,iparam) shall assemble parameter derivatives

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assemble_res_jac(bnode, system, asm_res, asm_jac, asm_param)

Assemble residual and jacobian for boundary node functions. See assemble_res_jac for more explanations.

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assemble_res_jac(edge, system, asm_res, asm_jac, asm_param)

Assemble residual and jacobian for edge (flux) functions. Parameters:

  • system: System to be worked with
  • edge: edge
  • asm_res(idofK,idofL,ispec): e.g. assemble local ispec to global degrees of freedom in unknowns
  • asm_jac(idofK,jdofK,idofL,jdofL,ispec,jspec): e.g. assemble entry ispec,jspec of local jacobian into entry four entries defined by idofK and idofL of global matrix
  • asm_param(idofK,idofL,ispec,iparam) shall assemble parameter derivatives
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assemble_res_jac(bedge, system, asm_res, asm_jac, asm_param)

Assemble residual and jacobian for boundary edge (flux) functions. See assemble_res_jac for more explanations.

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VoronoiFVM.assemble_res — Function
assemble_res(node, system, asm_res)

Assemble residual for node functions. See assemble_res_jac for more explanations.

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assemble_res(bnode, system, asm_res)

Assemble residual for boundary node functions. See assemble_res_jac for more explanations.

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assemble_res(edge, system, asm_res)

Assemble residual for edge (flux) functions. See assemble_res_jac for more explanations.

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assemble_res(bedge, system, asm_res)

Assemble residual for boundary edge (flux) functions. See assemble_res_jac for more explanations.

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Degree of Freedom management

We distinguish

  • active degrees of freedom: these are the actual degrees of freedom
  • degrees of freedom (dof) potential degrees of freedom - the may be active dofs or dummy ones With sparse arrays there are no dummy ones, with dense arrays dummy are maske in the node_dof field
  • species: each degree of freedom has associated the species it represents and the node index where it is localized
VoronoiFVM.getnodedof — Function
getnodedof(system,ispec,inode)

Get active or dummy degree of freedom associated with node and species

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Abstract geometry data

VoronoiFVM.AbstractNode — Type
abstract type AbstractNode{Tc<:Number, Tp<:Number, Ti<:Integer} <: VoronoiFVM.AbstractGeometryItem{Tc<:Number, Tp<:Number, Ti<:Integer}

Abstract type for nodes.

node[idim] gives the the corresponding coordinate.

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VoronoiFVM.AbstractNodeData — Type
abstract type AbstractNodeData{Tv<:Number} <: AbstractArray{Tv<:Number, 1}

Abstract type for data on nodes. u[ispec] accesses value of species at this node.

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VoronoiFVM.AbstractEdge — Type
abstract type AbstractEdge{Tv<:Number, Tp<:Number, Ti<:Integer} <: VoronoiFVM.AbstractGeometryItem{Tv<:Number, Tp<:Number, Ti<:Integer}

Abstract type for edges

edge[idim,inode] gives coordinate of node.

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VoronoiFVM.AbstractEdgeData — Type
abstract type AbstractEdgeData{Tv<:Number} <: AbstractArray{Tv<:Number, 2}

Abstract type for data on edges. u[ispec,inode] accesses value of species at corresponding node.

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Global assembly & helpers

VoronoiFVM.eval_and_assemble — Function
eval_and_assemble(
    system,
    U,
    UOld,
    F,
    time,
    tstep,
    λ,
    params;
    edge_cutoff
)

Main assembly method.

Evaluate solution with result in right hand side F and assemble Jacobi matrix into system.matrix.

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VoronoiFVM._add — Function
_add(U::Array{Tv, 2}, idof, val) -> Any

Add residual value into global degree of freedom

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_add(U::VoronoiFVM.SparseSolutionArray, idof, val) -> Any

Add residual value into global degree of freedom

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Interface methods for VoronoiFVMDiffEq.jl

VoronoiFVM._eval_res_jac! — Function
_eval_res_jac!(sys, u, t)

Evaluate functiaon and Jacobian at u if they have not been evaluated before at u. See https://github.com/SciML/DifferentialEquations.jl/issues/521 for discussion of another way to do this.

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VoronoiFVM.mass_matrix — Function
mass_matrix(system)

Calculate the mass matrix for use with ODEFunction. Return a Diagonal matrix if it occurs to be diagonal, otherwise return a SparseMatrixCSC.

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VoronoiFVM.prepare_diffeq! — Function
prepare_diffeq!(sys, jacval, tjac)

Prepare system for use with VoronoiFVMDiffEq.

  • jacval: value at which to evaluate jacobian to obtatin prototype
  • tjac: time moment for jacobian

Returns a prototype for the jacobian.

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