ReleaseNotes.txt

************************
*** PMFvXXXX
*** 
************************

### Utilities

- subsetMeshFromDEM

  - Generate automatically a subsetMesh using two DEM files, respectively for
    the top and the bottom of the aquifer:

    subsetMeshFromDEM /patch/to/file/top.xyz /patch/to/file/bottom.xyz

    two patches are automatically generated: top and bottom.

- setFieldsFromXY

  - utility now generate a mapping file (.map) linking mesh cells to XY points.
  If .map file is present, utility check that number of cells corresponds to the
  mesh and that number of points corresponds to the interpolation. This allows
  the re-use of similar interpolation with reduced cost. Works both for serial
  and parallel runs.

### Bug

- groundwaterTransport2DFoam

  - fix dryCells (C=0 and dC/dt=0)

************************
*** PMFv2107.1
*** Minor fixes for PMFv2107
************************

### Libraries

- numericalMethods

  - timestepManager: new class managing derivative computations (1s, 2nd
  and 3rd order) and timestepping based on truncation error.
  This allows to simplify the code of the solvers by implementing common
  functions in this new class

- porousBoundaryConditions

  - fixedHeadPressure/fixedHeadPressureSTL BCs have been deleted. They can be
  replaced by usual fixedValue while initialize values with the utility
  setBoundaryWaterLevel

### Solvers

- steadyGroundwaterFoam

  - seepage has been added (similar to transient solver groundwaterFoam)

- groundwater solvers

  - number of seepage cells is only displayed for serial simulation (parallel
  simulations give wrong value in terminal due to domain decomposition)

### Tutorials

- darcyFoam

  - fix input folder (0 -> 0.org) to avoid paraview visualizations

### utilities

- setBoundaryWaterLevel

  - replace setBoundaryHeadPressure as it can be used for potential or h
  - version option (2D/3D) has been replaced by field option (h/potential)

### Bug Fix

- groundwaterFoam/groundwater2DFoam: set deltah/dpotential=0 for seepage cells

- steadyGroundwaterFoam: set residual=0 for seepage cells

- pcVanGenuchten: fix Se computation when -VSMALL < h < 0

- set derivative=0 (1st/2nd/3rd order) for dry cells.

************************
*** PMFv2107
*** Bug Fix + tools folder 
************************

### General

- MNT (Modèle Numérique de Terrain) has been replaced by DEM (Digital
  Elevation Model) for file name, field name, comments...

### Tools

- new folder containing external tools (python/bash scripts) for the toolbox

- pmf_csvToEvent

  - python script to convert csv file extracted from simulations into event
  file. It can be used to recover 1D column unsaturated fluxes for example to
  inject in 2D watershed model. For usage, execute:

  python pmf_csvToEvent.py --help

### Tutorials

- Global

  - scripts are now compatible with python 3.

### Bug fixes

- Time-step management when (eventTimeTracking=false) has been fixed

************************
*** PMFv2102
*** Newton Algorithm for unsaturated solvers (groundwater)
************************

### Compilation

- Toolbox now accepts parallel compilation, run :

  ./Allwmake -jX

  with X the number of processors

### Solvers

- Global

  - output event value are not explictly computed but constructed by
  interpolation to avoid time step instabilities. Time interpolated fields are
  also used for CSV outputs.

- groundwaterFoam/groundwaterTransportFoam

  - pressure head equation can be solved using Newton algorithm to handle
  strong non linearities. Convergence is faster than Picard's algorithm and can
  handle complex cases where Picard does not converge, for example flow close
  to the saturated point.
  - pressure head equation is first solved using Picard formulation until the
  Picard tolerance is reached (specified in system/fvSolution) and then equation
  is solver using Newton method until the Newton tolerance.
  - the equations residual is now signed and under-relaxation occurs only when
  residual increases without changing sign.
  - timestep is managed using time scheme for truncation error. Only the Euler
  timescheme is currently handled for the pressure head equation but 2nd order
  schemes can be used for C equation (see tutorials).

- stationaryGroundwaterFoam

  - convergence and time control is now based on hEqn residual.
  - additional under-relaxation has been added (based on residual decrease)
  to improve convergence rate.
  - seepage option is now independant from fixedPotentialList and is activated
  in transportProperties as:
     seepage yes;

- groundwater2DFoam/groundwater2DTransportFoam

  - add waterSourceEventFile options to 2D solvers to force localized volumetric
  in 2D solvers (same usage as groundwaterFoam/groundwaterTransportFoam)  

### Utilities

- setBoundaryHeadPressure

  - add uniform potential option for 2D solvers (potential field)

- setFieldsFromXY

  - user can specify the number of points for interpolation (default = 3):
    1 => use closest point value
    0 => use number of neighbour faces for each cell

### Libraries

- numericalMethods

  - new Jacobian Matrix class for handling FD Newton algorithm (finite
  difference method, for debugging only)

### Bug fixes

- solved ambiguous calls for compatibility with CLANG and OSX
- fix dimensions in ToddNo.H
- fix interpolation functions for event value computation
- 3rd time derivative computed on potential (instead of hwater) to avoid
instabilities when hwater tends to 0
- fix retard coefficient for unsaturated (depends on saturation flow)
- fix flow/balance computation in 2D solvers
- handle correctly dry cells for stationaryGroundwater2DFoam solver
- fix deltat reduction for Picard loop groundwaterTransportFoam
- fix C flux computation in CSV (groundwaterTransportFoam)
- add FatalError when timestep is fixed and Picard/Newton does not converge

************************
*** PMFv1912
*** Multi-species transport and timestep management
************************

### Solvers

- Global:

  -patchEvent are now automatically read by solvers inside fields file
  -keyword "eventTimeTracking" is used to constraint the solver to
  explictly compute solution at event time (source/patch events)

- groundwaterFoam

  - The non-convergence of the Picard's algorithm now forces the solver to
  recompute the time iteration reducing the time step
  - add specific storage term (Ss) to the Richards' formulation
  - adding by default the mass-conservative terms to head pressure equation
  (mixed-formulation). The old head-pressure formulation can be now obtained
  adding "massConservative false;" in transportProperties

- groundwater2DFoam

  - solver adapted to handle uniform or non-uniform infiltration event (also
  accept non-conformal mesh event => consider as uniform infiltration)
  - time-stepping is now based on the truncation error (see the notes for
  porousScalarTransportFoam)

- porousScalarTransportFoam
  
  - support for multiple transported species in a single case. Species are
  listed in a "species" wordList in the transportProperties dictionary. 
  Each species can have its own porousTransport parameters and dispersion
  model. These are found in sub-dictionaries of transportProperties, each 
  named the same as a species. The change is backward compatible (the absence
  of a list of species is taken to mean a single species with name "C", and
  species without their own sub-dictionaries have their properties read
  directly from transportProperties). This support has also been extended to 
  all transport solvers in the toolbox
  - epsTotal now defaults to 1
  - eps can now be passed either as a scalar or as a field
  - time-stepping is based on the truncation error related ot the time scheme
  used (Euler, backward or CrankNicolson) and specified by the "truncationError"
  keyword in system/controlDict. The relative numerical error is computed using
  dC3/dt3 or dC2/dt2 (depending on the time-scheme) and maintained below the
  user-defined value

- porousScalarTransport2DFoam

  - support for multiple transported species in a single case (see the notes
  for porousScalarTransportFoam)
  - epsTotal now defaults to 1
  - eps can now be passed either as a scalar or as a field
  - time-stepping is now based on the truncation error (see the notes for
  porousScalarTransportFoam)
  
- groundwaterTransportFoam

  - The non-convergence of the Picard's algorithm now forces the solver to
  recompute the time iteration reducing the time step
  - CSV output fixed
  - add specific storage term (Ss) to the Richards' formulation
  - adding by default the mass-conservative terms to head pressure equation
  (mixed-formulation). The old head-pressure formulation can be now obtained
  adding "massConservative false;" in transportProperties
  - support for multiple transported species in a single case (see the notes
  for porousScalarTransportFoam)
  - epsTotal now defaults to 1
  - eps can now be passed either as a scalar or as a field
  - time-stepping is now based on the truncation error for the species
   (see the notes for porousScalarTransportFoam)

- groundwaterTransport2DFoam

  - new solver coupling 2D water modeling (groundwater2DFoam) with 2D scalar
  transport (porousScalarTransport2DFoam)
  - support for multiple transported species in a single case (see the notes
  for porousScalarTransportFoam)
  - epsTotal now defaults to 1
  - time-stepping is now based on the truncation error for the species and
  hwater variations (see the notes for porousScalarTransportFoam)

### Libraries

- toolsGIS

  - uniformInfiltrationEventFile replaced by infiltrationEventFile
  infiltration for groundwater2DFoam can be uniform or non-uniform (value
  specified at each time for each cell in event file)

- eventFile

  - now accepts two successive identical dates with different values for
  imposing step variation.

- eventFlux

  - now accept zero flux field (phi=0)
  - FatalError is handle if fixed flux > 0 and phi = 0
  - new static function through wich solvers can designate a list to be
  populated with non-owning pointers to patchEventFiles associated with
  instances of this BC. This scheme replaces the previous method which used an
  IODictionary to communicate with solvers. If no list is passed, any
  eventFlux condition with an event file will trigger a fatal error.

- eventInfiltration

  - new static function through wich solvers can designate a list to be
  populated with non-owning pointers to patchEventFiles associated with
  instances of this BC. This scheme replaces the previous method which used an
  IODictionary to communicate with solvers. If no list is passed, any
  eventInfiltration condition with an event file will trigger a fatal error.

- porousModels

  - relativePermeabilityModel/capillarityModel has new function Se() which
  return effective saturation.

- multiscalarMixture

  - new class developed to support multiple species in transport solvers.
  Objects of this class can read the properties for all species in a case,
  and also contain their concentration fields. They also do most of the work
  required to support species source events ("eventFileTracerSource" entries); 
  however, time tracking cannot be handled internally by this class and 
  therefore solvers that support this type of events have to, on construction,
  refer to a list that will be populated with non-owning pointers to any event
  files that are found (otherwise the solver will be deemed incompatible with 
  this type of events and the presence of any "eventFileTracerSource" entry 
  will raise a fatal error).


### Tutorials

- fix event keywords in several tutorials

- cleaning configuration files removing useless keywords/dictionaries

- new 1D_eventFlux test case for time scheme efficiency comparison (Euler,
  backward, CrankNicolson)

************************
*** PMFv1906
*** Event file generalization + seepage/forcing term for 2D solvers
************************

### Solvers

- Global :

  - Event file can be specified in transportProperties to force the solver
    to compute solution at given date time.
    eventFileSource for volumetric/mass event :
    eventFilePatch for infiltration/fixed flux event on BC
    eventFileOutput to specify write times

  - solvers with injection/extraction terms are now conservative using Euler
  or backward time-scheme (Crank-Nicholson still not supported)

  - All injection terms in event should be negative (as for boundaries) and
  extraction terms should be positive (as for outlet boundary fluxes)

- groundwater2DFoam

  - solver accepts dry cells (display WARNING when adding water)

- groundwaterFoam

  - seepage function is available (generates seepageTerm field)
  - potentialMNT field is modified if < z0

- impesFoam/anisoImpesFoam

  - generalization of the "event" use wellbore dictionary/function is obsolete

- porousScalarTransportFoam

  - water content (theta) can be given instead of saturation (Sphase) to allow
  the direct use of pre-computed stationaryGroundwaterFoam computations
  - timestep is now controlled by porous- Courant number
  
- porousScalarTransport2DFoam

  - retard coefficient fixed
  - seepage outlet handled (requires seepageTerm field)
  - fatal error added when hwater field is negative
  - solver requires for initialization hwater or potential/z0

- stationaryGroundwater2DFoam

  - seepage function is available (generates seepageTerm field)
  - potentialMNT field is modified if < z0

### Libraries

- porousBoundaryConditions

  - eventInfiltration
    new BC to impose event variable velocity in impesFoam, anisoImpesFoam
    and groundwaterFoam. Patch event file is directly given in the BC
    dictionary using the keyword "eventFile" (as for fixedFlux)

  - eventFlux
    replace old fixedFlux BC for porousScalarTransportFoam

- porousModels

  - alphaDispersion model fixed

- toolsGIS

  - event files generalized to all solvers
  - value at given time is interpolated using given event values
  - event values before first event time and after last event time is equal to 0
  - keyword event differenciation : 
    - source event for injection/extraction terms in the domains
    - patch event for tracer injection (porousScalarTransportFoam)
    - infiltration event for uniform infiltration (groundwater2DFoam)
    - output event to specify write times

************************
*** V1901
*** Hydrology module release
************************

### Wiki

- A wiki has been initialised for some solvers and utilities on github

  https://github.com/phorgue/porousMultiphaseFoam/wiki

### Solvers

- groundwater2DFoam

  - water bilan added (with stationary option to stop run)
  - dhmax is relative to the max of hwater field
  - potentialEqn is solved instead of hwater equation (identical to stationary)

- porousScalarTransportFoam

  - mass balance added for C tracer for each non-wall patch and injection
  wellbores. Results are displayed in terminal and CSV file (see tutorials)

- porousScalarTransport2DFoam

  - passive scalar transport for pre-calulated 2D flux field with
  groundwater2DFoam

- stationaryGroundwater2DFoam

  - "stationary" version of groundwater2DFoam
  - fixedPotentialList added in transportProperties (optional)
  - forcing potential mode is added with two possible modes :
    - fixedValue : use values given in fixedPotentialList
    - fixedMNT : use bilinear interpolated value using fileMNT given 

- stationaryGroundwaterFoam

  - "stationary" version of groundwaterFoam (Richards's equation)

### Tutorials

- groundwater2DFoam

  - updated to be similar to the stationary case

- stationaryGroundwater2DFoam

  - new tutorial relative to the new solver (use forcingPotential option)

- stationaryGroundwaterFoam

  - new tutorial relative to the new solver

- porousScalarTransportFoam

  - new tutorial case to validate the new BC fixedFlux

### Libraries

- toolsGIS

  - new library containing classes for GIS manipulation
  - first class is MNT file used to read xyz file and performed
    bilinear interpolation
  - second class is eventFile to specify spatiallized time-varying source term
    for groundwater(2D)Foam and porousScalar(2D)Foam solvers

- porousBoundaryConditions

  - new boundary condition "fixedFlux" to impose a user-defined fixed flux
  for a given specie C. Dispersion is set to 0 along this boundary to respect
  mass conservation and ensure that fixed flux is correctly computed
  "event table" can be given in BC for time-dependent fixed flux

### Utilities

- setFieldsFromMNT

  - new utility to initialize fields using MNTfile class with bilinear
  interpolation

- setFieldsFromXY

  - new option to add offset to interpolated value (also in setFieldsFromMNT)

************************
*** V1809
*** New solvers : groundwater2DFoam + groundwaterTransportFoam
************************

### Solvers

- groundwaterFoam

  - wellbore added to handle injection/extraction
  
- impesFoam/anisoImpesFoam/groundwaterFoam

  - wellboreProperies is a subDict of transportProperties
  - Winj/Wext (wellbore positions) are moved from 0/ to constant/

- porousScalarTransportFoam

  - retard coefficient "R" added
  - new time-stepping (using dCmax absolute and relative)

- groundwater2DFoam

  - new solver for 2D groundwater flow modeling (Dupuit's hypothesis)

- groundwaterTransportFoam

  - new solver coupling groundwaterFoam and porousScalarTransportFoam
  the C component is transported in fluid phase with variable saturation

### Libraries

- dispersionModels

  - alphaL/alphaT can be heterogeneous (volScalarField) in the

### Tutorials

- impesFoam/anisoImpesFoam

  - updated (wellboreProperties removed)

- groundwater2DFoam

  - 2 test case for solver validation

### Utilities

- setFieldsFromXY (replace setPermeabilityFieldFromXY)

  - can be used to initialize any volScalarFields from a rectangularMatrix
    (x | y | value) with linear interpolation between 3 closest points

************************
*** V1.6.0 (2018-05)
*** New model kr/pc Ippisch-Vogel-Bastian
************************

### Solvers

- groundwaterFoam

  - new time step managing (timeStep in controlDict) :
    - "Picard" is based on the number of Picard's iteration (old method)
    - "dthetadT" is based on the saturation variation at the previous time step 

- darcyFoam

  - moved to utility folder (now compute pressure field in the time folder with
  time iteration)

### Libraries

- capillary and relative permeability model

  - new Ippisch model (example in the tutorials/groundwaterFoam/realCase)

- boundary condtions for Head pressure (currently, gravity should be along the
  Z-axis). Computation are made at each time step, we recommend the use of the
  setBoundaryHeadPressure function

  - fixedHeadPressure : potential can be fixed (h is computed as potential - z
    coordinate of the face)
    if hUnsaturated is given, potential equal to this value in for all faces
    with z > potential.
    else h is computed as for the saturated zone.

  - fixedHeadPressureSTL : potential on the boundary is computed using an STL
  file.

### Utilities

- new folder including utility function for the porousMultiphaseFoam toolbox

  - darcyFoam : It compute pressure and flux field for a given phase at a given
    time (overwriting
    the files in current time step).
    phase used for the computation can be specified with the -phase option ("a"
    by default)

  - setBoundaryHeadPressure : initialize head pressure boundary condition using
  fixed value (as fixedHeadPressure BC) or STL file (as fixedHeadPressureSTL)

  - setPermeabilityFieldFromXY : initialize a permeability from table
  (x | y | K)

************************
*** V1.5.1 (2018-02)
*** Bug fixes on groundwaterFoam
************************

### Libraries

- capillarity and relative permeability models

  - parameters for each model are now displayed in log file (the uniform value
    or "read file")

### Bug Fixes

- pcVanGenuchten

  - initialisation no longer calls correct() function to avoid numerical issues
    using groundwaterFoam (the functions correct() or correctAndSb() are
    directly called in the solvers)

  - it is now possible to set up h=0 using groundwaterFoam

**********************
*** V1.5 (2017-09)
*** Scalar transport with dispersion coefficients
**********************

### Solvers

- porousScalarTransportFoam

  - passive scalar transport solver in porous media with dispersion coefficient

### Libraries

- dispersionModels

  - models to compute the effective diffusion (or dispersion) in porous media
  (model with alphaT and alphaL is available).

### Bug fixes

- OpenFOAM 5.0 compatibility fixed

************************
*** V1.4.1 (2017-08)
*** Bug fixes and toolbox cleaning
************************

### Toolbox cleaning (indent fixed)

### Bug fixes

- darcyFoam

  - Ua field is correctly written

- impesFoam

  - capillary term correctly computed
    ("fvc::interpolate(fvc:grad(Sb))" ==> "fvc:snGrad(Sb)")

- incompressiblePhase

  - test on phi header has been removed (useless and incompatibility with
    OpenFOAM 5.0)

**********************
*** V1.4 (2017-02)
*** New solver for one-phase flow : darcyFoam
**********************

### Toolbox re-organization

### Solvers

- darcyFoam (new solver)

  - one phase flow solver similar to porousSimpleFoam but using the
    porousMultiphaseFoam toolbox's parameters.

### Bug Fixes

- anisoImpesFoam/impesFoam/groundwaterFoam

  - solver now update  phia or phib in SEqn.H only if Ua or Ub are fixedValue
    boundary conditions to avoid numerical instabilities (bug partially fixed
    in V1.3.1).


************************
*** V1.3.1 (2017-02)
*** Parallel computation fixed
************************

### Bug Fixes

- anisoImpesFoam/impesFoam/groundwaterFoam

  - solvers does not update phia/phib in SEqn.H if boundary is a processor
    patch in order to avoid numerical instabilities.

**********************
*** V1.3 (2016-09)
*** New Stability numbers and python script for tutorials execution 
**********************

### Compatibility fixed for OpenFOAM 4.0

### Solvers

- impesFoam

  - three stability numbers are now available : Coats, Todd and Courant
    (see doc for more informations)

- anisoImpesFoam

  - still two stability numbers (Coats and Courant) but minor changes to respect
    coding style (with impesFoam)

### Tutorials

- impesFoam

  - capillary cases modified to use the new Todd's number condition
    
- python scripts

  - runTutorials.py runs each tutorials from with end signal to check backward
    compatibility. Messages are [ OK ] or [ Error OpenFOAM ] or [ Error C++ ]

  - cleanTutorials.py cleans test cases from tutorialsList.py

**********************
*** V1.2 (2016-05)
*** Relative permeability and capillary pressure laws can be heterogenous
**********************

### Libraries

- capillarityModels

  - models now reads "constant/porousModels" folder to find parameters fields
    which can be heteroegenous. Switch to the transportProperties dictionary if
    file is not found.

- relativePermeabilityModels

  - similar to capillarityModels

### Tutorials

- impesFoam-tutorials

  - BuckleyLeverett/BrooksAndCorey case updated to use volScalarField
    parameters instead of transport properties

- groundwaterFoam-tutorials

  - 1Dinfiltration case updated to use volScalarField parameters instead of
    transport properties
	
### Bug Fixes

- impesFoam/anisoImpesFoam/groundwaterFoam

  - error between timestep used and timestep displayed
  - velocity BC updated before SEqn.H (or hEqn.H) for time-dependent conditions

- groundwaterFoam

  - change writeOpt for phitheta (useless field, only phi is used)

**********************
*** V1.1 (2015-09)
*** New solver for groundwater flows (Richards' equation)
**********************

### Solvers

- groundwaterFoam (new solver)

  - solver added for solving Richards' equation (unsaturated soils)

- impesFoam/anisoImpesFoam

  - wellbore positions are optional
  - displays only the CFL chosen (Coats / Courant Number)
	
### Libraries

- capillarityModels

  - new functions for groundwaterFoam added in the pcVanGenuchen class
    (pcLinear and pcBrooksAndCorey does not work with groundwaterFoam)

### Tutorials

- groundWaterFoam-tutorials

  - validation case (1Dinfiltration) and example (realCase) added

### Bug Fixes

- impesFoam/anisoImpesFoam

  - parallel computation of min/max added

- porousBoundaryConditions

  - effective saturation corrected for Dirichlet boundary conditions

**********************
*** V1.0 (2014-10)
*** 1st release of the toolbox, two solvers two-phase flow in porous media
**********************

### Solvers 

- impesFoam (new solver)

  - two-phase flow solvers for isotropic porous medium
    (permeability K is volScalarField)

- anisoImpesFoam (new solver)

  - two-phase flow solvers for anisotropic porous medium
  (permeability K is volTensorField)

### Libraries

- capillarityModels

  - usual capillary models for impesFoam/anisoImpesFoam (Brooks and Corey,
    Van Genuchten, Linear)

- phaseModels

  - incompressible phase model for poroous media flows (constant density and
    viscosity)

- relativePermeabilityModels

  - usual relative permeability laws for impesFoam/anisoImpesFoam (Brooks and
    Corey, Van Genuchten)