PMFv1912 : Multi-species transport and timestep managing

.gitignore

@@ -2,6 +2,7 @@
 *.dep
 *~
 *.pyc
+\#*
 linux64GccDPOpt/
 linux64GccDPInt32Opt/
 lnInclude/

Allwmake

@@ -2,18 +2,21 @@
 cd ${0%/*} || exit 1    # run from this directory
 set -x
 
-# Compiling libraries 
+# Compiling libraries
+wmake libraries/numericalMethods
 wmake libraries/porousModels
 wmake libraries/toolsGIS
 wmake libraries/porousBoundaryConditions
+
 # Compiling solvers 
 wmake solvers/impesFoam
 wmake solvers/anisoImpesFoam
 wmake solvers/groundwaterFoam
 wmake solvers/porousScalarTransportFoam
 wmake solvers/porousScalarTransport2DFoam
 wmake solvers/groundwater2DFoam
-#wmake solvers/groundwaterTransportFoam
+wmake solvers/groundwaterTransport2DFoam
+wmake solvers/groundwaterTransportFoam
 wmake solvers/stationaryGroundwater2DFoam
 wmake solvers/stationaryGroundwaterFoam
 

ListOfContributors.txt

@@ -0,0 +1,12 @@
+# Developers
+Pierre Horgue (phorgue@imft.fr)
+Jacques Franc
+Gabriel Gerlero
+
+# Bug track/fix and beta tester
+avlmachado (github)
+Mohammed Elwardi Fadeli
+Romain Guibert
+Lachlan Mason
+François Renard
+Cyprien Soulaine

README

@@ -1,64 +1,72 @@
-**************************************************************************
-************* PorousMultiphaseFoam (PMF) for OpenFOAM ********************
-**************************************************************************
-
-* General Informations
-
-- The current branches (last version of the toolbox)
-
-  - branch "openfoam-v1812" > PMFv1906
-  - branch "openfoam-v6"    > PMFv1906
-
-- Old branches not updated
-
-   - branch "openfoam-v5"     > PMFv1809
-   - branch "foam-extend-4.0" >	PMFv1809
-   - branch "openfoam-v1806"  > PMFv1809
-   - branch "openfoam-v1712"  > PMFv1805
-
-- Older version (no branches)
-
-    - OpenFOAM 4.0	PMFv1.4.1
-    - OpenFOAM 3.0	PMFv1.2
-
-  - version no supported:
-    - OpenFOAM 2.4 and older
-    - foam-extend 3.2 and older
-    - OpenFOAM v1706 and older
-
-- This toolbox needs only a standard OpenFOAM installation (see www.openfoam.org
-  or openfoam.com)
-
-- Please cite the related paper in the "doc" folder if you are using this toolbox.
-
-- Read the COPYING_OPENFOAM file for information about OpenFOAM and this toolbox Copyrights.
-
-* Installation instructions : 
-
-- First, source the OpenFOAM configuration file, i.e. (example for ubuntu version) : 
-   source /opt/openfoamv6/etc/bashrc
-
-- then in the "porousMultiphaseFoam" directory, run :
-
-	./Allwmake
-
-  to install the package.
-
-- Dynamic libraries, "libporousBoundaryConditions.so" and "libporousModels.so"
-  are compiled in the standard OpenFOAM user directory : $FOAM_USER_LIBBIN;
-
-- The executable solver "impesFoam" is placed in the standard OpenFOAM user
-  directory $FOAM_USER_APPBIN.
-
-- Each tutorial directory contains "run" and "clean" files to test installation
-  and validate the solver.
-
-- A python script runTutorials.py can be used to test all components.
-
-- To remove compilation and temporary files, run :
-
-	./Allwclean
-
-- see the ReleaseNotes.txt file for detailed information about the toolbox.
-
-**************************************************************************
+**************************************************************************
+************* PorousMultiphaseFoam (PMF) for OpenFOAM ********************
+**************************************************************************
+
+* General Informations
+
+- The current branches (last version of the toolbox)
+
+  - branch "openfoam-v1906" > PMFv1912
+  - branch "openfoam-v7"    > PMFv1912
+
+- Old branches not updated
+
+  - branch "openfoam-v1812"  > PMFv1906
+  - branch "openfoam-v6"     > PMFv1906
+  - branch "openfoam-v5"     > PMFv1809
+  - branch "foam-extend-4.0" > PMFv1809
+  - branch "openfoam-v1806"  > PMFv1809
+  - branch "openfoam-v1712"  > PMFv1805
+
+- Older version (no branches)
+
+  - OpenFOAM 4.0	PMFv1.4.1
+  - OpenFOAM 3.0	PMFv1.2
+
+- version not supported:
+
+  - OpenFOAM 2.4 and older
+  - foam-extend 3.2 and older
+  - OpenFOAM v1706 and older
+
+- This toolbox needs only a standard OpenFOAM installation
+  (see www.openfoam.org or openfoam.com)
+
+- Please cite the related paper in the "doc" folder if you are using this
+  toolbox.
+
+- Read the COPYING_OPENFOAM file for information about OpenFOAM and this
+  toolbox Copyrights.
+
+* Installation instructions :
+
+- First, source the OpenFOAM configuration file, i.e. (example for ubuntu
+  version) :
+
+  	  source /opt/openfoamv6/etc/bashrc
+
+- then in the "porousMultiphaseFoam" directory, run :
+
+       	  ./Allwmake
+
+  to install the package.
+
+- Dynamic libraries are compiled in the standard OpenFOAM user directory :
+
+  $FOAM_USER_LIBBIN
+
+- The executable solver "impesFoam" is placed in the standard OpenFOAM user
+  directory $FOAM_USER_APPBIN.
+
+- Each tutorial directory contains "run" and "clean" files to test installation
+  and validate the solver.
+
+- A python script runTutorials.py can be used to test all components.
+
+- To remove compilation and temporary files, run :
+
+	./Allwclean
+
+- see the ReleaseNotes.txt file for detailed information about the toolbox.
+
+********************************************************************************

ReleaseNotes.txt

@@ -1,3 +1,145 @@
+************************
+*** 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
@@ -57,7 +199,7 @@
   - 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).
+    dictionary using the keyword "eventFile" (as for fixedFlux)
 
   - eventFlux
     replace old fixedFlux BC for porousScalarTransportFoam