Changes

v3.0 Planned (pending some improvements in LinearSolve)

• Remove VoronoiFVM solver strategies
• Stop re-exporting ForwardDiff.value
• Try to remove type piracies
• Remove params from edge, node structs (appearantly never used)

v2.5.0 November 17, 2024

• update show methods for physics, grid

v2.4.0 November 11, 2024

• Use precs based linear solver API, see https://github.com/SciML/LinearSolve.jl/pull/514 with ExtendableSparse 1.6
• Deprecate VoronoiFVM solver strategies

v2.3.0 November 5, 2024

• Allow to use result of time embedding a steady state for impedance
• Move to WIAS-PDELib org

v2.2.0 October 30, 2024

• Add params to SystemState, allow to pass params to ODEProblem
• Fix use of end results of time evolution as steady state for impedance calculations
• new internal solutionarray method.

October 28, 2024

Moved repositiory from https://github.com/j-fu/VoronoiFVM.jl to https://github.com/WIAS-PDELib/VoronoiFVM.jl. WIAS-PDELib is a github organization created to collectively manage the Julia packages developed under the lead of the WIAS Numerical Mathematics and Scientific Computing research group. According to the github docs on repository transfer, all links to the previous repository location are automatically redirected to the new location, and all relationships with forks stay intact.

v2.1.0 October 23, 2024

• Features:
  • Add VoronoiFVMExtendableFEMBaseExt extension allowing to use velocity fields caculated with ExtendableFEM in convection-diffusion problems

v2.0.2 October 12, 2024

• Bugfixes
  • replace internally used values and vec methods by new dofs
  • fix #119, update Example115, Example120, test sparse unknown storage & ODE solver
  • directly re-export ForwardDiff.value, dont type-pirate a new method

v2.0.1 October 7, 2024

• Bugfixes
  • fix case where the last element of a time solution is used as initial value for a next solve

v2.0.0 September 12, 2024

Breaking:

• Removed deprecated solve methods:

    solve(inival, system::VoronoiFVM.AbstractSystem, lambdas;kwargs...)
    solve(inival, system::VoronoiFVM.AbstractSystem; kwargs...)
    solve!(solution,inival, system::VoronoiFVM.AbstractSystem; kwargs...)

• History is now a field of the solution but not system, to be accessed with $history(solution)$, instead of $history(system)$ both for stationary and transient solutions
• VoronoiFVM.Physics callbacks (flux, storage, etc.) need a data argument, even if data is not provided during $Physics$ or $System$ construction

Added

• Introduced $SystemState$ which contains entries (matrix, residuals, data) which before were part of $System$. One can have different states with different data for the same system.
• Introduced solve!(state::SystemState; kwargs...) method
• Stationary solutions now contain a history entry and are subtypes of VoronoiFVM.AbstractSolutionArray
• Changelog now in package root

Modified

• Sparse solver default for Float64 in all space dimensions is now UMFPACKFactorization. For all other number types it is SparspakFactorization. Before it was KLU for 1D, Sparspak for 2D an UMFPACK for 3D.

v1.25.0, Sept 9, 2024

• VoronoiFVM.Physics callbacks (flux, storage, etc.) without data argument are now deprecated

v1.24.0 August 20, 2024

• Bernoulli function using expm1 (thanks @tcaduser !)

v1.23.0 August 2, 2024

• Add integrate(sys,solution) method

v1.22.0 July 17, 2024

• Multithreaded assembly

v1.21.0 July 1, 2024

• Introduce nondelaunay method for checking Delaunay properties of grid

v1.20.0 April 26 2024

• Drop Julia 1.6 support, improve package quality (partial Aqua tests, explicit imports)

v1.19.0 Feb 01 2024

• Enable equation block preconditioning for sparse unknown storage

v1.18.0 Feb 01 2024

• Re-shoring of OrdinaryDiffEq interface, no need of VoronoiFVMDiffEq.jl anymore It appeared that it is sufficient to depend on SciMLBase for this, and all tests can be done with OrdinaryDiffEq.jl

v1.17.1 Jan 30, 2024

• Bugfix for boundary node factors
• Bugfix with types for RecursiveArrayTools

v1.16.0 Dec 15, 2023

• Bugfix for assembly of outflow bc
• Bugfix for matrixtype=:banded
• Updated plothistory:

v1.15.0 Dec 1, 2023

• Adjusted time/embedding stepping scheme, added num_final_steps to VoronoiFVM.SolverControl. This may lead to sligthly different results when solving time dependent problems. Some unit test values have been adapted. Before, accidentally, very small time steps at the end of an evolution were possible.

v1.14.0 Nov 27, 2023

• Add Δu_max_factor and Δt_decrease to VoronoiFVM.SolverControl. Before (with values 2.0 and 0.5, respectively) the were fixed. New Δu_max_factor=1.2 default.
• Add history to VoronoiFVM.TransientSolution, prepare deprecation of system.history
• Add plothistory method

v1.13.0 July 24, 2023

• Add nodevolumes method

v1.12.0 July 22, 2023

• Add functionality for outflow boundary conditions

v1.11.0 July 17, 2023

• Add calc_divergences method for checking velocity field divergences
• Fix form factor calculation and velocity projecion for unstructructured grids and cylindrical symmetry

v1.10.0 July 11, 2023

• Use AbstractTransientSolution in gridvisualize stuff

v1.9.0 June 27, 2023

• With control.handle_exceptions=true, in case of a failing step, time stepping and embeding now returns the solution calculated so far instead of throwing an error

v1.8.0 June 20, 2023

• LinearSolve 2.x

v1.7.0 May 17, 2023

• Discrete Sobolev norms

v1.6.0 May 12, 2023

• Rework linear solver strategies - prevent combinatorial explosion. E.g. gmres_iluzero is now GMRESIteration(ILUZeroPreconditioner()) etc.

v1.5.0 May 9, 2023

• Introduced solver strategies like gmres_iluzero(), direct_umfpack() etc. See documentation of the module VoronoiFVM.SolverStrategies. More to come.
• edgewise assembly - faster in particular for 3D
• Plan: edgewise assembly seems to be non-breaking, if this is confirmed, will be made default in 1.6 or (if it appears to be breaking for some) in 2.0.

v1.4.0 May 3, 2023

• equation-block preconditioning support with the help of ExtendableSparse.jl

v1.3.0 April 13, 2023

• inplace_linsolve! for dense linear system solution in flux functions
• Mixture flow example 510

v1.2.0 March 17, 2023

• Initialization of quantities, create unknowns using Base.map

v1.1.0 Feb 22, 2023

• Edge reactions, Joule heating

v1.0.0 Feb 22, 2023

• full LinearSolve compatibility

v0.19.0 Jan 31, 2023

This is a breaking release. Implementations using default solver settings should continue to work without modifications, albeit possibly showing deprecation and allocation warnings. Really breaking is control of iterative linear solvers and allocation checks.

Breaking

• Make solve a method of CommonSolve.solve (and re-export it).
• Rely on LinearSolve.jl for linear system solution including control of iterative solvers.
• New verbosity handling. verbose can now be a Bool or a String of flag characters, allowing for control of different output categories. I would love to do this via logging, but there is still a long way to go IMHO
• Allocation check is active by default with warnings instead of throwing an error. These warnings can be muted by passing a verbose string without 'a'. This is now the only control in this respect. All check_allocs methods/kwargs, control via environment variables have been removed.
• Deprecation warnings can be switched off by passing a verbose string without 'd'.
• Improve iteration logging etc., allow for logging of linear iterations ('l' flag character)

Deprecations

• Deprecated all VoronoiFVM.solve methods with signatures others than solve(system; kwargs...) which renders them incompatible to the philosophy of `CommonSolve. Updated examples accordingly.
• Deprecated the following entries of SolverControl/solve kwargs: :tol_absolute => :abstol, :tol_relative => :reltol, :damp => :damp_initial, :damp_grow => :damp_growth :max_iterations => e:maxiters :tol_linear => :reltol_linear :max_lureuse =>
• NewtonControl

v0.18.8 - 0.18.10 Dec 11, 2022 - Jan 5, 2023

• Internal restructuring: remove @create_physics_wrappers macro, reduce boilerplate in assembly, wrap repeating pattenrns into functions. The price in the moment is a bit of a slowdown of assembly.
• Fix parameter dependency handling (now we can get parameter derivative without solving in dual numbers; see the runh() example in Example430. However in the moment the advantatge is not very clear, so this is on hold...

v0.18.7 Dec 7, 2022

• bump gridvisualize compat

v0.18.6 Dec 3, 2022

• enable non-diagonal mass matrices for VoronoiFVMDiffEq

v0.18.5 Nov 30, 2022

• ready for Julia 1.9, re-enable CI on nighly

v0.18.4 Nov 29, 2022

• Add API methods used by VoronoiFVMDiffEq.jl

v0.18.3 Oct 18 2022

• Removed some allocations

v0.18.2 Oct 13 2022

• Emerging capability of differencing wrt. parameters (experimental, see example 430)
• Allow iterative methods from Krylov.jl
• Proper Dirichlet initialization with bcondition
• Allow for more general matrix structures (banded, tridiagonal, multidiagonal)

v0.18.1 September 25 2022

• Working spherical symmetry case

v0.18 September 12 2022

• Remove DifferentialEquations interface (move this to a glue package)

The current method of activating it through require is too brittle with respect to versioning.

v0.17.1 August 20 2022

• Fix DifferentialEquations interface, start transition to LinearSolve

v0.17.0 July 1 2022

• ensure not to assemble data for species where they are not enabled This change should be breaking only for incorrect code where physics callbacks write into degrees of freedom which are not enabled

v0.16.5 June 30, 2022

• add iteration to solver options, allow to choose :cg, :bicgstab.
• allow setting penalty with boundary_dirichlet!

v0.16.4 May 25, 2022

• fix x-t plots

v0.16.3 March 18, 2022

• Linearization API
• relax some type constraints

v0.16.2 Feb 18, 2022

• ExtendableGrids 0.9

v0.16.1 Feb 17, 2022

• fix quantity postprocessing
• define unknown access for abstract vectors instead of vectors
• pass rhs/unknowns wrappers in postprocessing methods
• integrals as a wrapper type with proper quantity handling

v0.16.0 Feb 13, 2022

• Expose ODEProblem (and possibly ODEFunc) from VoronoiFVM.System.
• Breaking: Remove solve wrapper for DifferentialEquations.solve, instead recommend to call that directly
• Breaking: Handle DifferentialEquations.jl via Requires.jl.

v0.15.1 Jan 15, 2022

• Documentation fixes
• Fix OrdinaryDiffEq interface
• added example for current calculation with Quantities
• Fixed type instabilities in quantities interface

v0.15.0 Jan 1, 2022

• Breaking: History is not anymore returned by solve, instead it can be accessed via history after the solution.
• Cleaned API:
  • VoronoiFVM.solve(system::VoronoiFVM.AbstractSystem; kwargs...) is now the main method of solve which allows to access stationary, transient, embedding and DifferentialEquations based solvers.
  • Joint implementation for implicit Euler timestepping and parameter embedding
  • Handle more kwargs via SolverControl (e.g. log)
  • Use Parameters.jl in struct definition
  • Add history types NewtonSolverHistory, TransientSolverHistory
  • detailed and summary methods for both history types
  • Nonlinear solver example notebook (under development): nonlinear-solvers.jl
• OrdinaryDiffEq solver now in CI
• scalarplot for 1D transient solutions
• Sparsity detection via Symbolics.jl instead of the sunsetted SparsityDetection.jl

v0.14.0 Dec 24, 2021

Backward compatible, hopefully nonbreaking API simplification

• Boundary conditions are now specified in breaction. Advantages:
  • easy x/t dependency
  • unified (upcoming) interface for parameters
  • unified handling of standard and nonstandard boundary conditions
  • simpler documentation
• Made NewtonControl alias of SolverControl, continue to work with SolverControl
• System constructor now directly takes physics callback functions, no need anymore to work with extra physics struct
• solve() now takes "SolverControl" parameters as kwargs,no need anymore to work with extra NewtonControl/SolverControl struct
• Notebooks as part of documentation and CI
• See also the pluto notebook api-update.jl

v0.13.2 Oct 29, 2021

• Bernoulli function overhaul

v0.13.1

• sorted things with ExtendableGrids
• nodal flux reconstruction (e.g. for visualization)

v0.13.0, Oct 13, 2021

• various bug fixes, explicit numbering of edge nodes

v0.12.3, July 7, 2021

• Add quantity id
• Document quantities

v0.12.2, July 7, 2021

Introduce the notion of quantities which can be continuous or discontinuous at interfaces.

• Quantity handling is implemented on top of species handling
• Unknowns u and rhs y now passed to callbacks as wrapper types, and can be indexed by quantity or by species numbers. Moreover, this will allow to abstract parameters, gradients etc. in future versions.

v0.12.0, July 2 2021

• By default, the u parameter in flux callbacks is now a nspec x 2 array
• unknowns(edge,u), viewK, viewL are obsolete, they still work for backward compatibility
• physics.num_species is now meaningless, num_species is automatically detected.
• SparseSystem and DenseSystem are now type aliases of a parametrized type instead of two independent subtypes of System

v0.11.8

• increase chunk size threshold to match argument length in calls to vectormodejacobian

v0.11.7

• First attempts on surface flux

v0.11.1, April 13, 2021

• Assembly loops cleaned from type instabilities
• Optionally check for allocations due to type instabilities introduced in physics callbacks. See check_allocs! for more information.

v0.11, April 12, 2021

• Depending on Julia 1.5 now
• Lineaer solvers now based on factorize! from ExtendableSparse 0.5
• Documentation overhaul
• Re-checking impedance calculation

v0.10.13 April 1, 2021

• Outflow boundary conditions

v0.10.8 March 22, 2021

• TransientSolution structure, transient solve
• Solve compatible with DifferentialEquations.jl

v0.10.3 Feb 11, 2021

• Introduce non-mutating solve
• Optionally record history if log kw is true in solve.

v0.10.0 Jan 9 2021

• Moving visualization to the package GridVisualize.jl, emerging from the visualization methods in ExtendableGrids

v0.9.0 Dec 21 2020

• Add the possibility to interface with DifferentialEquations.jl
• Breaking: The API change to passing the unknowns to the an edge callback as a matrix turned out to be a dead end in the strategic sense. In order to extend functionality, we need to be able to pass more data to which we can apply differetiation. Particular plans involve bifurcation parameters and reconstructed gradients. So we return to the viewK/viewL pattern we had before. However, these are now aliases:
  • viewK(edge,u)=unknowns(edge,u,1)
  • viewL(edge,u)=unknowns(edge,u,2)
  In order to ease refactoring in the case where models have been implemented with Matrix access to the unknowns, unknowns(edge,u) returns a matrix of the edge unknowns. For refactoring, just rewrite e.g.

    function flux(y,u,edge)
        for ispec=1:nspec
            y[ispec]=u[ispec,1]-u[ispec,2]
        end
    end

to

    function flux(y,u0,edge)
        u=unknowns(edge,u0)
        for ispec=1:nspec
            y[ispec]=u[ispec,1]-u[ispec,2]
        end
    end

v0.8.5 Sep 1 2020

• allow any object in Physics.data (thanks Jan Weidner)
• add generic operator for non-canonical problem structures

v0.8.4 July 25 2020

• Update ExtendableGrids + ExtendableSparse

v0.8.3 June 25 2020

• Replace splatting by dispatch on availability of data record

v0.8.2 May 15 2020

• Form factors are now pre-calculated and stored
• Introduced update_grid! for triggering re-calculation if coordinates have changed

v0.8.1 May 2 2020

• Introduce evolve! : time solver with automatic timestep control

v0.8 Apr 28, 2020

• Replaced VoronoiFVM grid module by ExtendableGrids.jl
• Moved grid generation, modification, plotting over to ExtendableGrids
• Necessary changes in codes using VoronoiFVM:
  • Replace grid.coord by coord obtained via coord=coordinates(grid) or coord=grid[Coordinates] after importing ExtendableGrids
  • Replace VoronoiFVM.plot by ExtendableGrids.plot.
  • In the plot method, Plotter is now a keyword argument
  • VoronoiFVM.Grid() now returns a ExtendableGrids.ExtendableGrid, in fact it is just an alias to ExtendableGrids.simplexgrid
  • For using any methods on grids like cellmask! one needs to use ExtendableGrids
  • Subgrids now are of the same type ExtendableGrids, views are currently defined for vectors only.

v0.7 Feb 28 2020

• API modification:

  • Breaking:

    • data parameter passed to physics callbacks only if Physics object is created with data parameter.

      This makes the API more consistent in the case that parameters are just taken from the closure (the scope where the physics functions are defined) and no data object has been created.

    • Replace node.coord[i] by node[i].

    • Replace edge.coordK[i] by edge[i,1].

    • Replace edge.coordL[i] by edge[i,2].

      This now directly accesses the coordinate field of the grid and avoids copying of the coordinates

  • Backward compatible:

    • No need for viewK and viewL in edge callbacks (they also make trouble with allocations...)
      • Replace uk[i] by u[i,1]
      • Replace ul[i] by u[i,2]
    • Replace VoronoiFVM.DenseSystem(...) by VoronoiFVM.System(..., unknown_storage=:dense)
    • Replace VoronoiFVM.SparseSystem(...) by VoronoiFVM.System(..., unknown_storage=:sparse)

• No allocations anymore in assembly loop:

  • Replaced ElasticArray in Grid by normal one - this was the largest regression
  • Return nothing from mutating methods to avoid some allocations
  • Indexing in formfactors.jl with Int

v0.6.5 Jan 25 2020

• use updateindex! for matrix, depend on ExtendableSparse 0.2.6

v0.6.4 2020-01-20

• Rearranged + commented boundary assembly loop
• Reworked + renamed some examples
• Document that unknowns doesn't initialize values.

v0.6.3 2019-12-21

remove xcolptrs call Update dependency on ExtendableSparse

v0.6.2 2019-12-20

Updated dependency list (Triangulate ^0.4.0)

v0.6.1, 2019-12-17

• return "plotted" for being able to place colormap
• require Triangulate >= 0.3.0

v0.6.0, Dec 15 2019

• Removed Triangle submodule, depend on new Triangulate.jl Triangle wrapper
• link to source code in examples
• boundary_dirichlet! etc methods for setting boundary conditions

v0.5.6 Dec 5 2019

• Bug fixes
• check triangle input for min 3 points
• check triangle edgelist for C_NULL
• voronoi plot

v0.5.5 Dec 4 2019

• (Temporary) Copy of TriangleRaw as Triangle submodule. To be replaced by dependency on evisioned package

v0.5.4 Dec 3 2019

• Re-enabled ElasticArrays in grid structure (for the time being)
• Added potkink example: this adds an inner boundary

v0.5.3 Dec 1 2019

• triangle in optional submodule
• Modified API for plotting
  • Removed formal dependency on Plots and PyPlot
  • Use Plotter module as first parameter to plot methods - replaces fvmplot and fvmpyplot functions. Use VoronoiFVM.plot(PyPlot,...) resp. VoronoiFVM.plot(Plots,...)
  • No more complaints when package is used in environment with plots or pyplot installed
• Modified API for impedance

v0.5.2 Nov 19, 2019

• Reorganized grid stuff
• Included triangle (after Ideas from TriangleMesh.jl)

v0.5.1 Nov 13, 2019

• Fixed performance regression: AbstractArrays for Grid components were slow.
• Added handling of cylindrical coordinates

V0.5, November 10, 2019

• Velocity projections
• Added edge handling to grid struct

V0.4.2, November 6, 2019

• Replaced PyPlot by Plots
• Better and more examples

V0.4, July 12, 2019

• Registered with Julia ecosystem
• Enhance Newton solver by embedding, exception handling
• Replace SparseMatrixCSC with ExtendableSparseMatrix
• fixed allocation issues in assembly
• assured that users get allocation stuff right via typed functions in physics structure
• more julianic API

V0.3, April 9 2019

• Renamed from TwoPointFluxFVM to VoronoiFVM
• Complete rewrite of assembly allowing sparse or dense matrix to store degree of freedom information
  • Solution is a nnodes x nspecies sparse or dense matrix
  • The wonderful array interface of Julia still provides slicing etc in order to access species without need to write any bulk_solution stuff or whatever when using the sparse variant
• Re-export value() for debugging in physics functions
• Test function handling for flux calculation
• First working steps to impedance handling
• Abolished Graph in favor of Grid, Graph was premature optimization...

V0.2, Feb 20, 2019

• Changed signature of all callback functions: This also allows to pass user defined arrays etc. to the callback functions. In particular, velocity vectors can be passed this way.

  • Besides of flux!(), they now all have node::VoronoiFVM.Node as a second argument.

  • flux!() has edge::VoronoiFVM.Edge as a second argument

  • the x argument in source!() is omitted, the same data are now found in node.coord

• New method edgelength(edge::VoronoiFVM.Edge)

V0.1, Dec. 2018

• Initial release