version 3.0

ChangeLog

@@ -8,6 +8,50 @@
 
 //************************************************************\\
 
+Version 3.0
+
+Released on 18/09/2018.
+
+o Brownian dynamics solver:
+
+	- Add: solvers, libraries, utilities and tutorials for Brownian dynamics simulations of polymer molecules.
+
+o Generic:
+
+	- Add: all solvers are now compatible with dynamic meshes. Due to this change, and for convenience, momentum equation is the first to be solved, followed by pressure equation and then the equations for the remaining variables (extra-stresses, passive scalar, etc.).
+
+	- Add: tutorial fuidDamper showing the use of rheoFoam with dynamic meshes.
+
+	- Add: added an explicit Navier slip boundary condition for velocity.
+
+	- Change: Namespace encapsulation of several derived classes.
+
+	- Change: rheoTool version compatible with OpenFOAM v2.2.2 is discontinued.
+
+	- Add: added rheoTool patch for OpenFOAM v6.0.
+
+	- Add: added note in the user-guide (Section 2.5) about parallel compilation of rheoTool.
+
+o Constitutive equations:
+
+	- Add: Papanastasiou regularization is now available for yield-stress GNF models (Hershel-Bulkley/Bingham and Casson models). 
+
+	- Add: Casson model has been added to the library of constitutive equations.
+
+	- Add: the Multi-Lambda Isotropic Kinematic Hardening (MLK-IKH) model has been added to the library of constitutive equations.
+
+	- Add: the Vasquez-Cook-Mckinley (VCM) model has been added to the library of constitutive equations.
+
+	- Add: the Reactive Rod Model (RRM) model has been added to the library of constitutive equations.
+
+	- Add: Saramito's elastoviscoplastic model has been added to the library of constitutive equations. Both stress and log-conformation versions are available.
+
+	- Add: the Bautista-Manero-Puig (BMP) model has been added to the library of constitutive equations. Both stress and log-conformation versions are available.
+
+	- Change: implemented functions tauTotal() and tauTotalMF() in base classes. Solver rheoTestFoam and the utility retrieving the wall shear-stresses were modified accordingly.
+
+//************************************************************\\
+
 Version 2.0
 
 Released on 09/02/2018.
@@ -36,7 +80,7 @@ o Post-Processing:
 
 o Multiphase flows:
 
-    - Change: (fvc::grad(U) & fvc::grad(etaS()*alpha)) has been replaced by fvc::div(etaS()*alpha*dev2(T(fvc::grad(U)))) for the use in multiphase flows (constitutiveEq.C).
+	- Change: (fvc::grad(U) & fvc::grad(etaS()*alpha)) has been replaced by fvc::div(etaS()*alpha*dev2(T(fvc::grad(U)))) for the use in multiphase flows (constitutiveEq.C).
 
 	- Fix: call to constrainPressure() in reoInterFoam, version of40, has been corrected for the SIMPLEC algorithm (pEqn.H). Added a section in the user-guide on how to use properly the fixedFluxPressure BC with reoInterFoam in versions of222 and fe40. 
 

README.md

@@ -2,22 +2,24 @@
 
 ## About
 
-[RheoTool] is an open-source toolbox based on [OpenFOAM®] to simulate Generalized Newtonian Fluids (GNF) and viscoelastic fluids under pressure-driven and/or electrically-driven flows. 
+[RheoTool] is an open-source toolbox based on [OpenFOAM®] to simulate Generalized Newtonian Fluids (GNF) and viscoelastic fluids under pressure-driven and/or electrically-driven flows. In addition to continuum mechanics solvers, [RheoTool] also has a Brownian dynamics solver to simulate polymer molecules individually.  
 
-The theory behind the single-phase flow solvers used in [RheoTool] can be found in [Pimenta F. and Alves M.A., 2017, J. Non-Newtonian Fluid Mech.](http://dx.doi.org/10.1016/j.jnnfm.2016.12.002) for pressure-driven flows, and in [Pimenta F. and Alves M.A., 2018, arXiv:1802.02843](http://arxiv.org/abs/1802.02843) for electrically-driven flows.
+The theory behind the single-phase flow solvers used in [RheoTool] can be found in [Pimenta F. and Alves M.A., 2017, J. Non-Newtonian Fluid Mech.](http://dx.doi.org/10.1016/j.jnnfm.2016.12.002) for pressure-driven flows, and in [Pimenta F. and Alves M.A., 2018, arXiv:1802.02843](http://arxiv.org/abs/1802.02843) for electrically-driven flows. The Brownian dynamics solver was presented in [Pimenta F. et al., 2018, Biomicrofluidics](https://doi.org/10.1063/1.5037472).
 
-The library containing the viscoelastic models has been developed based on the library used by _viscoelasticFluidFoam_ [(Favero et al., 2010, J. Non-Newtonian Fluid Mech.)](http://dx.doi.org/10.1016/j.jnnfm.2010.08.010), already present in [foam-extend 4.0]. 
+The library containing the viscoelastic fluid models has been developed based on the library used by _viscoelasticFluidFoam_ [(Favero et al., 2010, J. Non-Newtonian Fluid Mech.)](http://dx.doi.org/10.1016/j.jnnfm.2010.08.010), already present in [foam-extend 4.0]. 
 
 
 ## Features
 
 * all the features are available for 2D/3D problems and generic grids;
-* the code is fully-parallelized;
+* the code for continuum mechanics is fully-parallelized;
+* all solvers support either moving or static meshes;
 * wide range of electrically-driven flow models;
 * wide range of viscoelastic and GNF models;
 * the log-conformation tensor approach is available for all viscoelastic models; 
 * the transient flow solvers (_rheoFoam_ and _rheoEFoam_) are highly stable regarding pressure-stress-velocity coupling;
 * the material functions of any rheological model can be obtained numerically (_rheoTestFoam_);
+* Brownian dynamics solver implementing bead-spring models; 
 * a set of tutorials is included to illustrate the application of the solvers to different problems;
 * the theory and the tutorials are described in a user-guide;
 * a solver for two-phase flows is available (_rheoInterFoam_), where any GNF or viscoelastic model can be used for each phase (_under-development_);
@@ -27,14 +29,18 @@ The library containing the viscoelastic models has been developed based on the l
 
 [RheoTool] can be either cloned using `git` via: `git clone https://github.com/fppimenta/rheoTool` or simply downloaded from the GitHub page at https://github.com/fppimenta/rheoTool.
 
-The repository includes versions of [RheoTool] for: OpenFOAM® [v2.2.2](http://openfoam.org/version/2-2-2), OpenFOAM® [v4.1](http://openfoam.org/version/4-1)/[v4.0](http://openfoam.org/version/4-0) and foam-extend [v4.0](https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-4.0). 
+The repository includes versions of [RheoTool] for: OpenFOAM® [v4.1](http://openfoam.org/version/4-1)/[v4.0](http://openfoam.org/version/4-0)/[v6.0](http://openfoam.org/version/6-0) and foam-extend [v4.0](https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-4.0). 
 
 To install [RheoTool], please follow the instructions in Chapter 2 of the [user-guide](https://github.com/fppimenta/rheoTool/tree/master/doc).
 
 ## Docs
 
 See the [user-guide](https://github.com/fppimenta/rheoTool/tree/master/doc).
 
+## ChangeLog
+
+Follow the version updates of rheoTool in the [ChangeLog](https://github.com/fppimenta/rheoTool/tree/master/ChangeLog). They can also be found in the [user-guide](https://github.com/fppimenta/rheoTool/tree/master/doc). 
+
 ## Third-Party 
 
 [RheoTool] is using the following third-party packages:
@@ -44,10 +50,10 @@ See the [user-guide](https://github.com/fppimenta/rheoTool/tree/master/doc).
 ## Screenshots
 
 Here are some images from the tutorials included in [RheoTool]. 
-
-<img src="https://user-images.githubusercontent.com/22405564/36007099-b988edaa-0d38-11e8-8f9c-157e78f040a6.png">
+ 
+<img src="https://user-images.githubusercontent.com/22405564/45702045-ad1aae80-bb68-11e8-81e2-9afda0802faf.png">
 
 [RheoTool]:https://github.com/fppimenta/rheoTool
 [OpenFOAM®]:http://openfoam.org/
-[foam-extend]:http://www.extend-project.de/
-[foam-extend 4.0]:https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-4.0
+[foam-extend]:https://github.com/Unofficial-Extend-Project-Mirror/Unofficial-Extend-Project-Mirror.github.io/wiki
+[foam-extend 4.0]:https://github.com/Unofficial-Extend-Project-Mirror/foam-extend-foam-extend-4.0

fe40/src/libs/EDFModels/models/DebyeHuckel/DebyeHuckel.C

@@ -31,14 +31,16 @@ License
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 namespace Foam
+{
+namespace EDFEquations
 {
     defineTypeNameAndDebug(DebyeHuckel, 0);
     addToRunTimeSelectionTable(EDFEquation, DebyeHuckel, dictionary);
 }
-
+}
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::DebyeHuckel::DHSpecie::DHSpecie
+Foam::EDFEquations::DebyeHuckel::DHSpecie::DHSpecie
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -52,7 +54,7 @@ Foam::DebyeHuckel::DHSpecie::DHSpecie
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::DebyeHuckel::DebyeHuckel
+Foam::EDFEquations::DebyeHuckel::DebyeHuckel
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -141,7 +143,7 @@ Foam::DebyeHuckel::DebyeHuckel
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Foam::tmp<Foam::volVectorField> Foam::DebyeHuckel::Fe() const
+Foam::tmp<Foam::volVectorField> Foam::EDFEquations::DebyeHuckel::Fe() const
 {
 
     volScalarField rhoE( psi_ * dimensionedScalar("norm", epsilonK_.dimensions()/dimArea, 0.) );
@@ -191,7 +193,7 @@ Foam::tmp<Foam::volVectorField> Foam::DebyeHuckel::Fe() const
      }      
 }
 
-void Foam::DebyeHuckel::correct()
+void Foam::EDFEquations::DebyeHuckel::correct()
 {
 
        scalar res=GREAT; 

fe40/src/libs/EDFModels/models/DebyeHuckel/DebyeHuckel.H

@@ -37,7 +37,8 @@ SourceFiles
 
 namespace Foam
 {
-
+namespace EDFEquations
+{
 class DebyeHuckel
 :
     public EDFEquation
@@ -200,6 +201,7 @@ public:
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+} // End namespace EDFEquations
 } // End namespace Foam
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

fe40/src/libs/EDFModels/models/NernstPlanck/NernstPlanck.C

@@ -31,14 +31,17 @@ License
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 namespace Foam
+{
+namespace EDFEquations
 {
     defineTypeNameAndDebug(NernstPlanck, 0);
     addToRunTimeSelectionTable(EDFEquation, NernstPlanck, dictionary);
 }
+}
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::NernstPlanck::NPSpecie::NPSpecie
+Foam::EDFEquations::NernstPlanck::NPSpecie::NPSpecie
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -64,7 +67,7 @@ Foam::NernstPlanck::NPSpecie::NPSpecie
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::NernstPlanck::NernstPlanck
+Foam::EDFEquations::NernstPlanck::NernstPlanck
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -140,7 +143,7 @@ Foam::NernstPlanck::NernstPlanck
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Foam::tmp<Foam::volVectorField> Foam::NernstPlanck::Fe() const
+Foam::tmp<Foam::volVectorField> Foam::EDFEquations::NernstPlanck::Fe() const
 {    
     volScalarField rhoE( psi_ * dimensionedScalar("norm", epsilonK_.dimensions()/dimArea, 0.) );
 
@@ -188,7 +191,7 @@ Foam::tmp<Foam::volVectorField> Foam::NernstPlanck::Fe() const
      }      
 }
 
-void Foam::NernstPlanck::correct()
+void Foam::EDFEquations::NernstPlanck::correct()
 {
 
 // Electrokinetic coupling loop

fe40/src/libs/EDFModels/models/NernstPlanck/NernstPlanck.H

@@ -33,7 +33,8 @@ License
 
 namespace Foam
 {
-
+namespace EDFEquations
+{
 class NernstPlanck
 :
     public EDFEquation
@@ -198,6 +199,7 @@ public:
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+} // End namespace EDFEquations
 } // End namespace Foam
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

fe40/src/libs/EDFModels/models/Ohmic/Ohmic.C

@@ -31,14 +31,17 @@ License
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 namespace Foam
+{
+namespace EDFEquations
 {
     defineTypeNameAndDebug(Ohmic, 0);
     addToRunTimeSelectionTable(EDFEquation, Ohmic, dictionary);
 }
+}
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::Ohmic::OhSpecie::OhSpecie
+Foam::EDFEquations::Ohmic::OhSpecie::OhSpecie
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -52,7 +55,7 @@ Foam::Ohmic::OhSpecie::OhSpecie
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::Ohmic::Ohmic
+Foam::EDFEquations::Ohmic::Ohmic
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -118,22 +121,26 @@ Foam::Ohmic::Ohmic
     scalar z1 = mag(species_[1].zi().value());
 
     Deff_ =  2*( species_[0].Di()*species_[1].Di() )
-           / ( species_[0].Di() + species_[1].Di() );  
+           / ( species_[0].Di() + species_[1].Di() ); 
 
-
+    // This is a fix to avoid FP error when the electric module
+    // is computed after hydrodynamics. This call ensures that on
+    // first time-step the electric component is the 1st computed.
+    // Issue appeared after reordering solving sequence (v3.0).     
+    correct();        
 }
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Foam::tmp<Foam::volVectorField> Foam::Ohmic::Fe() const
+Foam::tmp<Foam::volVectorField> Foam::EDFEquations::Ohmic::Fe() const
 {
     return
     (
          fvc::laplacian(epsilonK_*relPerm_, phiE_, "rhoE") * ( fvc::grad(phiE_) + extraE_) 
     );     
 }
 
-void Foam::Ohmic::correct()
+void Foam::EDFEquations::Ohmic::correct()
 {
 
        scalar res=GREAT; 

fe40/src/libs/EDFModels/models/Ohmic/Ohmic.H

@@ -33,7 +33,8 @@ License
 
 namespace Foam
 {
-
+namespace EDFEquations
+{
 class Ohmic
 :
     public EDFEquation
@@ -172,6 +173,7 @@ public:
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+} // End namespace EDFEquations
 } // End namespace Foam
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //

fe40/src/libs/EDFModels/models/PoissonBoltzmann/PoissonBoltzmann.C

@@ -31,14 +31,17 @@ License
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 namespace Foam
+{
+namespace EDFEquations
 {
     defineTypeNameAndDebug(PoissonBoltzmann, 0);
     addToRunTimeSelectionTable(EDFEquation, PoissonBoltzmann, dictionary);
 }
+}
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::PoissonBoltzmann::PBSpecie::PBSpecie
+Foam::EDFEquations::PoissonBoltzmann::PBSpecie::PBSpecie
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -52,7 +55,7 @@ Foam::PoissonBoltzmann::PBSpecie::PBSpecie
 
 // * * * * * * * * * * * * * * * * Constructors  * * * * * * * * * * * * * * //
 
-Foam::PoissonBoltzmann::PoissonBoltzmann
+Foam::EDFEquations::PoissonBoltzmann::PoissonBoltzmann
 (
     const word& name,
     const surfaceScalarField& phi,
@@ -140,7 +143,7 @@ Foam::PoissonBoltzmann::PoissonBoltzmann
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
 
-Foam::tmp<Foam::volVectorField> Foam::PoissonBoltzmann::Fe() const
+Foam::tmp<Foam::volVectorField> Foam::EDFEquations::PoissonBoltzmann::Fe() const
 {
     volScalarField rhoE( psi_ * dimensionedScalar("norm", epsilonK_.dimensions()/dimArea, 0.) );
 
@@ -189,7 +192,7 @@ Foam::tmp<Foam::volVectorField> Foam::PoissonBoltzmann::Fe() const
      }         
 }
 
-void Foam::PoissonBoltzmann::correct()
+void Foam::EDFEquations::PoissonBoltzmann::correct()
 {
 
        scalar res=GREAT; 

fe40/src/libs/EDFModels/models/PoissonBoltzmann/PoissonBoltzmann.H

@@ -33,7 +33,8 @@ License
 
 namespace Foam
 {
-
+namespace EDFEquations
+{
 class PoissonBoltzmann
 :
     public EDFEquation
@@ -196,6 +197,7 @@ public:
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
+} // End namespace EDFEquations
 } // End namespace Foam
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //