diff --git a/applications/solvers/compressible/sonicDyMFoam/createFields.H b/applications/solvers/compressible/sonicDyMFoam/createFields.H
index 93dac20e076c44a31a4848b83987429bafa87b1d..4344a4f5e49451f647a322eb45b08bd07bf062b5 100644
--- a/applications/solvers/compressible/sonicDyMFoam/createFields.H
+++ b/applications/solvers/compressible/sonicDyMFoam/createFields.H
@@ -7,7 +7,7 @@
basicPsiThermo& thermo = pThermo();
volScalarField& p = thermo.p();
- volScalarField& e = thermo.h();
+ volScalarField& e = thermo.e();
const volScalarField& psi = thermo.psi();
volScalarField rho
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C b/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
index a124288dc5b64961f7dd48742525216ac3a2e39c..ea10d9129fae5ad178d0f0bb2ade20bf95cfa7fe 100644
--- a/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
+++ b/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/mdEquilibrationFoam.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H b/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
index 8289d014b03da3f2519d34be134ab4bcaa6ab2b9..b94745d9df20114094e7b75fdff62d15042164eb 100644
--- a/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
+++ b/applications/solvers/discreteMethods/molecularDynamics/mdEquilibrationFoam/readmdEquilibrationDict.H
@@ -14,5 +14,5 @@ IOdictionary mdEquilibrationDict
scalar targetTemperature = readScalar
(
- mdEquilibrationDict.lookup("equilibrationTargetTemperature")
+ mdEquilibrationDict.lookup("targetTemperature")
);
diff --git a/applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C b/applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C
index 287065754e39c115a4c9b3a5a04e61faf631c332..9fafafe1c9e7f4a58a8d7e4c181505e688b96948 100644
--- a/applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C
+++ b/applications/solvers/discreteMethods/molecularDynamics/mdFoam/mdFoam.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/Make/options b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/Make/options
index a53061a93cc503d9368d9d3a900ac6ef801015ba..041d2e0605468bb86b7eee749a4be8de8076f910 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/Make/options
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/Make/options
@@ -1,4 +1,5 @@
EXE_INC = \
+ -I../buoyantBoussinesqSimpleFoam \
-I$(LIB_SRC)/finiteVolume/lnInclude \
-I$(LIB_SRC)/turbulenceModels \
-I$(LIB_SRC)/turbulenceModels/incompressible/RAS/lnInclude \
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/TEqn.H b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/TEqn.H
index e2a89d1441582292fcb5a33ec7e092eac455a5a5..ece4b8ffe5c70d80f68e7093baffe960d5e76433 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/TEqn.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/TEqn.H
@@ -2,7 +2,7 @@
volScalarField kappaEff
(
"kappaEff",
- turbulence->nu() + turbulence->nut()/Prt
+ turbulence->nu()/Pr + turbulence->nut()/Prt
);
fvScalarMatrix TEqn
@@ -15,4 +15,6 @@
TEqn.relax();
TEqn.solve();
+
+ rhok = 1.0 - beta*(T - TRef);
}
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/UEqn.H b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/UEqn.H
index 3b5b5be24923c1b410d47c34fd14da319e117026..35387f4ff40468426b6ebc31a6fb517553759fe4 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/UEqn.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/UEqn.H
@@ -1,23 +1,26 @@
// Solve the momentum equation
- tmp<fvVectorMatrix> UEqn
+ fvVectorMatrix UEqn
(
fvm::ddt(U)
+ fvm::div(phi, U)
+ turbulence->divDevReff(U)
);
- UEqn().relax();
+ UEqn.relax();
- solve
- (
- UEqn()
- ==
- -fvc::reconstruct
+ if (momentumPredictor)
+ {
+ solve
(
+ UEqn
+ ==
+ fvc::reconstruct
(
- fvc::snGrad(pd)
- - betaghf*fvc::snGrad(T)
- ) * mesh.magSf()
- )
- );
+ (
+ fvc::interpolate(rhok)*(g & mesh.Sf())
+ - fvc::snGrad(p)*mesh.magSf()
+ )
+ )
+ );
+ }
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/buoyantBoussinesqPisoFoam.C b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/buoyantBoussinesqPisoFoam.C
index 067ae6a992487e9e1c2d113e1e330b4aa306db30..a8ff18374220e04a17c01dcd59325f030ea38361 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/buoyantBoussinesqPisoFoam.C
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/buoyantBoussinesqPisoFoam.C
@@ -30,18 +30,18 @@ Description
Uses the Boussinesq approximation:
\f[
- rho_{eff} = 1 - beta(T - T_{ref})
+ rho_{k} = 1 - beta(T - T_{ref})
\f]
where:
- \f$ rho_{eff} \f$ = the effective (driving) density
+ \f$ rho_{k} \f$ = the effective (driving) kinematic density
beta = thermal expansion coefficient [1/K]
T = temperature [K]
\f$ T_{ref} \f$ = reference temperature [K]
Valid when:
\f[
- rho_{eff} << 1
+ rho_{k} << 1
\f]
\*---------------------------------------------------------------------------*/
@@ -78,20 +78,17 @@ int main(int argc, char *argv[])
#include "setDeltaT.H"
#include "UEqn.H"
+ #include "TEqn.H"
// --- PISO loop
for (int corr=0; corr<nCorr; corr++)
{
- #include "TEqn.H"
- #include "pdEqn.H"
+ #include "pEqn.H"
}
turbulence->correct();
- if (runTime.write())
- {
- #include "writeAdditionalFields.H"
- }
+ runTime.write();
Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/createFields.H b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/createFields.H
index 5f3f13626db0a860d7058e76ce5a90f397558c95..dde0e38b339348ac1693d4bfdf3da9889610a354 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/createFields.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/createFields.H
@@ -14,13 +14,12 @@
mesh
);
- // kinematic pd
- Info<< "Reading field pd\n" << endl;
- volScalarField pd
+ Info<< "Reading field p\n" << endl;
+ volScalarField p
(
IOobject
(
- "pd",
+ "p",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
@@ -53,15 +52,25 @@
incompressible::RASModel::New(U, phi, laminarTransport)
);
- Info<< "Calculating field beta*(g.h)\n" << endl;
- surfaceScalarField betaghf("betagh", beta*(g & mesh.Cf()));
-
- label pdRefCell = 0;
- scalar pdRefValue = 0.0;
+ label pRefCell = 0;
+ scalar pRefValue = 0.0;
setRefCell
(
- pd,
- mesh.solutionDict().subDict("SIMPLE"),
- pdRefCell,
- pdRefValue
+ p,
+ mesh.solutionDict().subDict("PISO"),
+ pRefCell,
+ pRefValue
+ );
+
+
+ // Kinematic density for buoyancy force
+ volScalarField rhok
+ (
+ IOobject
+ (
+ "rhok",
+ runTime.timeName(),
+ mesh
+ ),
+ 1.0 - beta*(T - TRef)
);
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/pdEqn.H b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/pEqn.H
similarity index 55%
rename from applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/pdEqn.H
rename to applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/pEqn.H
index 25e2a9817fbe680f3b52b91b5a7fc187d52a3643..ff0c26f05893f6e625e7a8a5193c2f6a08882bc5 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/pdEqn.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/pEqn.H
@@ -1,9 +1,8 @@
{
- volScalarField rUA("rUA", 1.0/UEqn().A());
+ volScalarField rUA("rUA", 1.0/UEqn.A());
surfaceScalarField rUAf("(1|A(U))", fvc::interpolate(rUA));
- U = rUA*UEqn().H();
- UEqn.clear();
+ U = rUA*UEqn.H();
surfaceScalarField phiU
(
@@ -11,31 +10,31 @@
+ fvc::ddtPhiCorr(rUA, U, phi)
);
- phi = phiU + betaghf*fvc::snGrad(T)*rUAf*mesh.magSf();
+ phi = phiU + rUAf*fvc::interpolate(rhok)*(g & mesh.Sf());
for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
{
- fvScalarMatrix pdEqn
+ fvScalarMatrix pEqn
(
- fvm::laplacian(rUAf, pd) == fvc::div(phi)
+ fvm::laplacian(rUAf, p) == fvc::div(phi)
);
if (corr == nCorr-1 && nonOrth == nNonOrthCorr)
{
- pdEqn.solve(mesh.solver(pd.name() + "Final"));
+ pEqn.solve(mesh.solver(p.name() + "Final"));
}
else
{
- pdEqn.solve(mesh.solver(pd.name()));
+ pEqn.solve(mesh.solver(p.name()));
}
if (nonOrth == nNonOrthCorr)
{
- phi += pdEqn.flux();
+ phi -= pEqn.flux();
}
}
- U -= rUA*fvc::reconstruct((phi - phiU)/rUAf);
+ U += rUA*fvc::reconstruct((phi - phiU)/rUAf);
U.correctBoundaryConditions();
#include "continuityErrs.H"
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/readTransportProperties.H b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/readTransportProperties.H
deleted file mode 100644
index 585128dfdeb7d5e5212f9412d9b415c05c15b752..0000000000000000000000000000000000000000
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/readTransportProperties.H
+++ /dev/null
@@ -1,13 +0,0 @@
- singlePhaseTransportModel laminarTransport(U, phi);
-
- // thermal expansion coefficient [1/K]
- dimensionedScalar beta(laminarTransport.lookup("beta"));
-
- // reference temperature [K]
- dimensionedScalar TRef(laminarTransport.lookup("TRef"));
-
- // reference kinematic pressure [m2/s2]
- dimensionedScalar pRef(laminarTransport.lookup("pRef"));
-
- // turbulent Prandtl number
- dimensionedScalar Prt(laminarTransport.lookup("Prt"));
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/writeAdditionalFields.H b/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/writeAdditionalFields.H
deleted file mode 100644
index 20f7c6ae1dcff80630dc2ca21253b1e824ea5d77..0000000000000000000000000000000000000000
--- a/applications/solvers/heatTransfer/buoyantBoussinesqPisoFoam/writeAdditionalFields.H
+++ /dev/null
@@ -1,29 +0,0 @@
-{
- volScalarField rhoEff
- (
- IOobject
- (
- "rhoEff",
- runTime.timeName(),
- mesh,
- IOobject::NO_READ,
- IOobject::AUTO_WRITE
- ),
- 1.0 - beta*(T - TRef)
- );
- rhoEff.write();
-
- volScalarField p
- (
- IOobject
- (
- "p",
- runTime.timeName(),
- mesh,
- IOobject::NO_READ,
- IOobject::AUTO_WRITE
- ),
- pd + rhoEff*(g & mesh.C()) + pRef
- );
- p.write();
-}
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/TEqn.H b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/TEqn.H
index d00f0877eaf592058b956d3c9f78979d91d6dbc1..7452a0495adf2207ffb0f66e9e4484e1e7c9bad2 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/TEqn.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/TEqn.H
@@ -2,7 +2,7 @@
volScalarField kappaEff
(
"kappaEff",
- turbulence->nu() + turbulence->nut()/Prt
+ turbulence->nu()/Pr + turbulence->nut()/Prt
);
fvScalarMatrix TEqn
@@ -16,4 +16,6 @@
eqnResidual = TEqn.solve().initialResidual();
maxResidual = max(eqnResidual, maxResidual);
+
+ rhok = 1.0 - beta*(T - TRef);
}
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/UEqn.H b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/UEqn.H
index cf5c4a197893afff99ffec01847b2ce9bbd57b3e..a813a2d8b7aab17f8a45dfc9295e9ee6f161a683 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/UEqn.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/UEqn.H
@@ -13,12 +13,12 @@
(
UEqn()
==
- -fvc::reconstruct
+ fvc::reconstruct
(
(
- fvc::snGrad(pd)
- - betaghf*fvc::snGrad(T)
- ) * mesh.magSf()
+ fvc::interpolate(rhok)*(g & mesh.Sf())
+ - fvc::snGrad(p)*mesh.magSf()
+ )
)
).initialResidual();
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/buoyantBoussinesqSimpleFoam.C b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/buoyantBoussinesqSimpleFoam.C
index 58947fe295498057e57fb51c557a5782b8f2ef9e..63b938fa3625c2a15475b5ab5eb2157ce4cd9416 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/buoyantBoussinesqSimpleFoam.C
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/buoyantBoussinesqSimpleFoam.C
@@ -72,21 +72,18 @@ int main(int argc, char *argv[])
#include "readSIMPLEControls.H"
#include "initConvergenceCheck.H"
- pd.storePrevIter();
+ p.storePrevIter();
// Pressure-velocity SIMPLE corrector
{
#include "UEqn.H"
#include "TEqn.H"
- #include "pdEqn.H"
+ #include "pEqn.H"
}
turbulence->correct();
- if (runTime.write())
- {
- #include "writeAdditionalFields.H"
- }
+ runTime.write();
Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/createFields.H b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/createFields.H
index 5f3f13626db0a860d7058e76ce5a90f397558c95..0e668e9d987c132605e1aa28daee9e9aa0bf9a94 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/createFields.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/createFields.H
@@ -14,13 +14,12 @@
mesh
);
- // kinematic pd
- Info<< "Reading field pd\n" << endl;
- volScalarField pd
+ Info<< "Reading field p\n" << endl;
+ volScalarField p
(
IOobject
(
- "pd",
+ "p",
runTime.timeName(),
mesh,
IOobject::MUST_READ,
@@ -56,12 +55,25 @@
Info<< "Calculating field beta*(g.h)\n" << endl;
surfaceScalarField betaghf("betagh", beta*(g & mesh.Cf()));
- label pdRefCell = 0;
- scalar pdRefValue = 0.0;
+ label pRefCell = 0;
+ scalar pRefValue = 0.0;
setRefCell
(
- pd,
+ p,
mesh.solutionDict().subDict("SIMPLE"),
- pdRefCell,
- pdRefValue
+ pRefCell,
+ pRefValue
+ );
+
+
+ // Kinematic density for buoyancy force
+ volScalarField rhok
+ (
+ IOobject
+ (
+ "rhok",
+ runTime.timeName(),
+ mesh
+ ),
+ 1.0 - beta*(T - TRef)
);
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/pdEqn.H b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/pEqn.H
similarity index 64%
rename from applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/pdEqn.H
rename to applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/pEqn.H
index e782d26c8dc5ad4374d1b5a76ab7dfd72f6b9601..e1d42d738e8deff2eda578436baca131809f352f 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/pdEqn.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/pEqn.H
@@ -6,41 +6,42 @@
UEqn.clear();
phi = fvc::interpolate(U) & mesh.Sf();
- adjustPhi(phi, U, pd);
- surfaceScalarField buoyancyPhi = -betaghf*fvc::snGrad(T)*rUAf*mesh.magSf();
- phi -= buoyancyPhi;
+ adjustPhi(phi, U, p);
+ surfaceScalarField buoyancyPhi =
+ rUAf*fvc::interpolate(rhok)*(g & mesh.Sf());
+ phi += buoyancyPhi;
for (int nonOrth=0; nonOrth<=nNonOrthCorr; nonOrth++)
{
- fvScalarMatrix pdEqn
+ fvScalarMatrix pEqn
(
- fvm::laplacian(rUAf, pd) == fvc::div(phi)
+ fvm::laplacian(rUAf, p) == fvc::div(phi)
);
- pdEqn.setReference(pdRefCell, pdRefValue);
+ pEqn.setReference(pRefCell, pRefValue);
// retain the residual from the first iteration
if (nonOrth == 0)
{
- eqnResidual = pdEqn.solve().initialResidual();
+ eqnResidual = pEqn.solve().initialResidual();
maxResidual = max(eqnResidual, maxResidual);
}
else
{
- pdEqn.solve();
+ pEqn.solve();
}
if (nonOrth == nNonOrthCorr)
{
// Calculate the conservative fluxes
- phi -= pdEqn.flux();
+ phi -= pEqn.flux();
// Explicitly relax pressure for momentum corrector
- pd.relax();
+ p.relax();
// Correct the momentum source with the pressure gradient flux
// calculated from the relaxed pressure
- U -= rUA*fvc::reconstruct((buoyancyPhi + pdEqn.flux())/rUAf);
+ U += rUA*fvc::reconstruct((buoyancyPhi - pEqn.flux())/rUAf);
U.correctBoundaryConditions();
}
}
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/readTransportProperties.H b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/readTransportProperties.H
index 585128dfdeb7d5e5212f9412d9b415c05c15b752..82d101d8c1b18d88c41af9ffd0f7e4d10fa89cd2 100644
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/readTransportProperties.H
+++ b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/readTransportProperties.H
@@ -1,13 +1,13 @@
singlePhaseTransportModel laminarTransport(U, phi);
- // thermal expansion coefficient [1/K]
+ // Thermal expansion coefficient [1/K]
dimensionedScalar beta(laminarTransport.lookup("beta"));
- // reference temperature [K]
+ // Reference temperature [K]
dimensionedScalar TRef(laminarTransport.lookup("TRef"));
- // reference kinematic pressure [m2/s2]
- dimensionedScalar pRef(laminarTransport.lookup("pRef"));
+ // Laminar Prandtl number
+ dimensionedScalar Pr(laminarTransport.lookup("Pr"));
- // turbulent Prandtl number
+ // Turbulent Prandtl number
dimensionedScalar Prt(laminarTransport.lookup("Prt"));
diff --git a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/writeAdditionalFields.H b/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/writeAdditionalFields.H
deleted file mode 100644
index 20f7c6ae1dcff80630dc2ca21253b1e824ea5d77..0000000000000000000000000000000000000000
--- a/applications/solvers/heatTransfer/buoyantBoussinesqSimpleFoam/writeAdditionalFields.H
+++ /dev/null
@@ -1,29 +0,0 @@
-{
- volScalarField rhoEff
- (
- IOobject
- (
- "rhoEff",
- runTime.timeName(),
- mesh,
- IOobject::NO_READ,
- IOobject::AUTO_WRITE
- ),
- 1.0 - beta*(T - TRef)
- );
- rhoEff.write();
-
- volScalarField p
- (
- IOobject
- (
- "p",
- runTime.timeName(),
- mesh,
- IOobject::NO_READ,
- IOobject::AUTO_WRITE
- ),
- pd + rhoEff*(g & mesh.C()) + pRef
- );
- p.write();
-}
diff --git a/applications/solvers/heatTransfer/buoyantPisoFoam/createFields.H b/applications/solvers/heatTransfer/buoyantPisoFoam/createFields.H
index b5c84e435e3b2a95ad2cb8b67e215559d49758a0..b8ac5595e47cec77aa257c54a1710f91b08f20f7 100644
--- a/applications/solvers/heatTransfer/buoyantPisoFoam/createFields.H
+++ b/applications/solvers/heatTransfer/buoyantPisoFoam/createFields.H
@@ -65,4 +65,3 @@
dimensionedScalar initialMass = fvc::domainIntegrate(rho);
dimensionedScalar totalVolume = sum(mesh.V());
-
diff --git a/applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/buoyantSimpleRadiationFoam.C b/applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/buoyantSimpleRadiationFoam.C
index 0862d20bb2ce9fe649be9b286df8b149ae3e024f..c869eff89956a1b4e581fcdf6e1adf4643ecbfe4 100644
--- a/applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/buoyantSimpleRadiationFoam.C
+++ b/applications/solvers/heatTransfer/buoyantSimpleRadiationFoam/buoyantSimpleRadiationFoam.C
@@ -41,16 +41,15 @@ Description
int main(int argc, char *argv[])
{
+ #include "setRootCase.H"
+ #include "createTime.H"
+ #include "createMesh.H"
+ #include "readEnvironmentalProperties.H"
+ #include "createFields.H"
+ #include "createRadiationModel.H"
+ #include "initContinuityErrs.H"
-# include "setRootCase.H"
-# include "createTime.H"
-# include "createMesh.H"
-# include "readEnvironmentalProperties.H"
-# include "createFields.H"
-# include "createRadiationModel.H"
-# include "initContinuityErrs.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+ // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Info<< "\nStarting time loop\n" << endl;
@@ -58,17 +57,17 @@ int main(int argc, char *argv[])
{
Info<< "Time = " << runTime.timeName() << nl << endl;
-# include "readSIMPLEControls.H"
-# include "initConvergenceCheck.H"
+ #include "readSIMPLEControls.H"
+ #include "initConvergenceCheck.H"
p.storePrevIter();
rho.storePrevIter();
// Pressure-velocity SIMPLE corrector
{
-# include "UEqn.H"
-# include "hEqn.H"
-# include "pEqn.H"
+ #include "UEqn.H"
+ #include "hEqn.H"
+ #include "pEqn.H"
}
turbulence->correct();
@@ -79,7 +78,7 @@ int main(int argc, char *argv[])
<< " ClockTime = " << runTime.elapsedClockTime() << " s"
<< nl << endl;
-# include "convergenceCheck.H"
+ #include "convergenceCheck.H"
}
Info<< "End\n" << endl;
diff --git a/applications/solvers/incompressible/channelFoam/readTransportProperties.H b/applications/solvers/incompressible/channelFoam/readTransportProperties.H
index c99d0ae4b5b97f4ed18765efe9a69103ba08e2c3..87c93c9195880f243c7ac035020345c283fd2450 100644
--- a/applications/solvers/incompressible/channelFoam/readTransportProperties.H
+++ b/applications/solvers/incompressible/channelFoam/readTransportProperties.H
@@ -7,7 +7,8 @@
runTime.constant(),
mesh,
IOobject::MUST_READ,
- IOobject::NO_WRITE
+ IOobject::NO_WRITE,
+ false
)
);
diff --git a/applications/utilities/mesh/generation/blockMesh/mergePatchPairs.H b/applications/utilities/mesh/generation/blockMesh/mergePatchPairs.H
index 3347db180bbe769eefeb5a41762550409e5b16e2..aeb3137adfe091daaabbda9490016527a066afe9 100644
--- a/applications/utilities/mesh/generation/blockMesh/mergePatchPairs.H
+++ b/applications/utilities/mesh/generation/blockMesh/mergePatchPairs.H
@@ -1,7 +1,7 @@
- Info<< "Creating merge patch pairs" << nl << endl;
-
if (mergePatchPairs.size())
{
+ Info<< "Creating merge patch pairs" << nl << endl;
+
// Create and add point and face zones and mesh modifiers
List<pointZone*> pz(mergePatchPairs.size());
List<faceZone*> fz(3*mergePatchPairs.size());
diff --git a/applications/utilities/mesh/manipulation/cellSet/cellSetDict b/applications/utilities/mesh/manipulation/cellSet/cellSetDict
index 95465d8f5421d2316b2a74f0404ea79e10700010..fd11ab871d9b66a0bb4b3c89feb0d7d8015b40c4 100644
--- a/applications/utilities/mesh/manipulation/cellSet/cellSetDict
+++ b/applications/utilities/mesh/manipulation/cellSet/cellSetDict
@@ -26,12 +26,31 @@ action new;
topoSetSources
(
+ // Select by explicitly providing cell labels
+ labelToCell
+ {
+ value (12 13 56); // labels of cells
+ }
+
// Copy elements from cellSet
cellToCell
{
set c1;
}
+ // Cells in cell zone
+ zoneToCell
+ {
+ name ".*Zone"; // Name of cellZone, regular expressions allowed
+ }
+
+ // Cells on master or slave side of faceZone
+ faceZoneToCell
+ {
+ name ".*Zone"; // Name of faceZone, regular expressions allowed
+ option master; // master/slave
+ }
+
// Select based on faceSet
faceToCell
{
@@ -51,12 +70,6 @@ topoSetSources
//option all; // cell with all points in pointSet
}
- // Select by explicitly providing cell labels
- labelToCell
- {
- value (12 13 56); // labels of cells
- }
-
// Select based on cellShape
shapeToCell
{
@@ -87,7 +100,6 @@ topoSetSources
radius 5.0;
}
-
// Cells with centre within sphere
sphereToCell
{
@@ -95,20 +107,6 @@ topoSetSources
radius 5.0;
}
- // Cells in cell zone
- zoneToCell
- {
- name ".*Zone"; // Name of cellZone, regular expressions allowed
- }
-
- // values of field within certain range
- fieldToCell
- {
- fieldName U; // Note: uses mag(U) since volVectorField
- min 0.1;
- max 0.5;
- }
-
// Cells with cellCentre nearest to coordinates
nearestToCell
{
@@ -129,6 +127,22 @@ topoSetSources
// and near surf curvature
// (set to -100 if not used)
}
+
+ // values of field within certain range
+ fieldToCell
+ {
+ fieldName U; // Note: uses mag(U) since volVectorField
+ min 0.1;
+ max 0.5;
+ }
+
+ // Mesh region (non-face connected part of (subset of)mesh)
+ regionToCell
+ {
+ set c0; // name of cellSet giving mesh subset
+ insidePoint (1 2 3); // point inside region to select
+ }
+
);
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
index 14f57048365684cd02cdb66cb879dcd868c37cb2..9ce34cda1c73f4638439af2c837f24b1a89eb23e 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.C
@@ -7,6 +7,31 @@
#include "pointSet.H"
#include "IOmanip.H"
+bool Foam::checkSync(const wordList& names)
+{
+ List<wordList> allNames(Pstream::nProcs());
+ allNames[Pstream::myProcNo()] = names;
+ Pstream::gatherList(allNames);
+
+ bool hasError = false;
+
+ for (label procI = 1; procI < allNames.size(); procI++)
+ {
+ if (allNames[procI] != allNames[0])
+ {
+ hasError = true;
+
+ Info<< " ***Inconsistent zones across processors, "
+ "processor 0 has zones:" << allNames[0]
+ << ", processor " << procI << " has zones:"
+ << allNames[procI]
+ << endl;
+ }
+ }
+ return hasError;
+}
+
+
Foam::label Foam::checkTopology
(
const polyMesh& mesh,
@@ -24,6 +49,31 @@ Foam::label Foam::checkTopology
// Check if the boundary processor patches are correct
mesh.boundaryMesh().checkParallelSync(true);
+ // Check names of zones are equal
+ if (checkSync(mesh.cellZones().names()))
+ {
+ noFailedChecks++;
+ }
+ if (checkSync(mesh.faceZones().names()))
+ {
+ noFailedChecks++;
+ }
+ if (checkSync(mesh.pointZones().names()))
+ {
+ noFailedChecks++;
+ }
+
+ // Check contents of faceZones consistent
+ {
+ forAll(mesh.faceZones(), zoneI)
+ {
+ if (mesh.faceZones()[zoneI].checkParallelSync(true))
+ {
+ noFailedChecks++;
+ }
+ }
+ }
+
{
pointSet points(mesh, "unusedPoints", mesh.nPoints()/100);
if (mesh.checkPoints(true, &points))
diff --git a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H
index 787aa4318d21cbe49eb162932f74f94ff5444757..4790765d16e408c18d9ada199da97235e4c82975 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H
+++ b/applications/utilities/mesh/manipulation/checkMesh/checkTopology.H
@@ -1,8 +1,11 @@
#include "label.H"
+#include "wordList.H"
namespace Foam
{
class polyMesh;
+ bool checkSync(const wordList& names);
+
label checkTopology(const polyMesh&, const bool, const bool);
}
diff --git a/applications/utilities/mesh/manipulation/checkMesh/printMeshStats.C b/applications/utilities/mesh/manipulation/checkMesh/printMeshStats.C
index 9a2c9396afba0a645483f86eec3d65239372cb43..269656594c5c6524c6508c7c602967ac419173df 100644
--- a/applications/utilities/mesh/manipulation/checkMesh/printMeshStats.C
+++ b/applications/utilities/mesh/manipulation/checkMesh/printMeshStats.C
@@ -69,13 +69,13 @@ void Foam::printMeshStats(const polyMesh& mesh, const bool allTopology)
<< " cells: "
<< returnReduce(mesh.cells().size(), sumOp<label>()) << nl
<< " boundary patches: "
- << returnReduce(mesh.boundaryMesh().size(), sumOp<label>()) << nl
+ << mesh.boundaryMesh().size() << nl
<< " point zones: "
- << returnReduce(mesh.pointZones().size(), sumOp<label>()) << nl
+ << mesh.pointZones().size() << nl
<< " face zones: "
- << returnReduce(mesh.faceZones().size(), sumOp<label>()) << nl
+ << mesh.faceZones().size() << nl
<< " cell zones: "
- << returnReduce(mesh.cellZones().size(), sumOp<label>()) << nl
+ << mesh.cellZones().size() << nl
<< endl;
diff --git a/applications/utilities/mesh/manipulation/createBaffles/createBaffles.C b/applications/utilities/mesh/manipulation/createBaffles/createBaffles.C
index 1fb8cc64efe26da5a52ac4f31de7a293d6d7274f..88af3a1f2915628a05fe5b70306c4b3daa770fae 100644
--- a/applications/utilities/mesh/manipulation/createBaffles/createBaffles.C
+++ b/applications/utilities/mesh/manipulation/createBaffles/createBaffles.C
@@ -43,16 +43,89 @@ Description
#include "ReadFields.H"
#include "volFields.H"
#include "surfaceFields.H"
+#include "ZoneIDs.H"
using namespace Foam;
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+void modifyOrAddFace
+(
+ polyTopoChange& meshMod,
+ const face& f,
+ const label faceI,
+ const label own,
+ const bool flipFaceFlux,
+ const label newPatchI,
+ const label zoneID,
+ const bool zoneFlip,
+
+ PackedBoolList& modifiedFace
+)
+{
+ if (!modifiedFace[faceI])
+ {
+ // First usage of face. Modify.
+ meshMod.setAction
+ (
+ polyModifyFace
+ (
+ f, // modified face
+ faceI, // label of face
+ own, // owner
+ -1, // neighbour
+ flipFaceFlux, // face flip
+ newPatchI, // patch for face
+ false, // remove from zone
+ zoneID, // zone for face
+ zoneFlip // face flip in zone
+ )
+ );
+ modifiedFace[faceI] = 1;
+ }
+ else
+ {
+ // Second or more usage of face. Add.
+ meshMod.setAction
+ (
+ polyAddFace
+ (
+ f, // modified face
+ own, // owner
+ -1, // neighbour
+ -1, // master point
+ -1, // master edge
+ faceI, // master face
+ flipFaceFlux, // face flip
+ newPatchI, // patch for face
+ zoneID, // zone for face
+ zoneFlip // face flip in zone
+ )
+ );
+ }
+}
+
+
+label findPatchID(const polyMesh& mesh, const word& name)
+{
+ label patchI = mesh.boundaryMesh().findPatchID(name);
+
+ if (patchI == -1)
+ {
+ FatalErrorIn("findPatchID(const polyMesh&, const word&)")
+ << "Cannot find patch " << name << endl
+ << "Valid patches are " << mesh.boundaryMesh().names()
+ << exit(FatalError);
+ }
+ return patchI;
+}
+
+
// Main program:
int main(int argc, char *argv[])
{
- argList::validArgs.append("set");
+ argList::validArgs.append("faceZone");
argList::validArgs.append("patch");
argList::validOptions.insert("additionalPatches", "(patch2 .. patchN)");
argList::validOptions.insert("overwrite", "");
@@ -67,30 +140,28 @@ int main(int argc, char *argv[])
const faceZoneMesh& faceZones = mesh.faceZones();
// Faces to baffle
- word setName(args.additionalArgs()[0]);
- Info<< "Reading faceSet from " << setName << nl << endl;
- faceSet facesToSplit(mesh, setName);
- // Make sure set is synchronised across couples
- facesToSplit.sync(mesh);
- Info<< "Read " << returnReduce(facesToSplit.size(), sumOp<label>())
- << " faces from " << setName << nl << endl;
+ faceZoneID zoneID(args.additionalArgs()[0], faceZones);
+
+ Info<< "Converting faces on zone " << zoneID.name()
+ << " into baffles." << nl << endl;
+
+ const faceZone& fZone = faceZones[zoneID.index()];
+
+ Info<< "Found " << returnReduce(fZone.size(), sumOp<label>())
+ << " faces on zone " << zoneID.name() << nl << endl;
+ // Make sure patches and zoneFaces are synchronised across couples
+ patches.checkParallelSync(true);
+ fZone.checkParallelSync(true);
// Patches to put baffles into
DynamicList<label> newPatches(1);
word patchName(args.additionalArgs()[1]);
- newPatches.append(patches.findPatchID(patchName));
- Pout<< "Using patch " << patchName
+ newPatches.append(findPatchID(mesh, patchName));
+ Info<< "Using patch " << patchName
<< " at index " << newPatches[0] << endl;
- if (newPatches[0] == -1)
- {
- FatalErrorIn(args.executable())
- << "Cannot find patch " << patchName << endl
- << "Valid patches are " << patches.names() << exit(FatalError);
- }
-
// Additional patches
if (args.optionFound("additionalPatches"))
@@ -103,19 +174,9 @@ int main(int argc, char *argv[])
newPatches.reserve(patchNames.size() + 1);
forAll(patchNames, i)
{
- label patchI = patches.findPatchID(patchNames[i]);
+ newPatches.append(findPatchID(mesh, patchNames[i]));
Info<< "Using additional patch " << patchNames[i]
- << " at index " << patchI << endl;
-
- if (patchI == -1)
- {
- FatalErrorIn(args.executable())
- << "Cannot find patch " << patchNames[i] << endl
- << "Valid patches are " << patches.names()
- << exit(FatalError);
- }
-
- newPatches.append(patchI);
+ << " at index " << newPatches[newPatches.size()-1] << endl;
}
}
@@ -166,111 +227,112 @@ int main(int argc, char *argv[])
polyTopoChange meshMod(mesh);
- // Do the actual changes
- // Note order in which faces are modified/added is so they end up correctly
- // for cyclic patches (original faces first and then reversed faces)
- // since otherwise it will have trouble matching baffles.
+ // Do the actual changes. Note:
+ // - loop in incrementing face order (not necessary if faceZone ordered).
+ // Preserves any existing ordering on patch faces.
+ // - two passes, do non-flip faces first and flip faces second. This
+ // guarantees that when e.g. creating a cyclic all faces from one
+ // side come first and faces from the other side next.
- label nBaffled = 0;
+ PackedBoolList modifiedFace(mesh.nFaces());
forAll(newPatches, i)
{
label newPatchI = newPatches[i];
+ // Pass 1. Do selected side of zone
+ // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
{
- if (facesToSplit.found(faceI))
- {
- const face& f = mesh.faces()[faceI];
- label zoneID = faceZones.whichZone(faceI);
- bool zoneFlip = false;
- if (zoneID >= 0)
- {
- const faceZone& fZone = faceZones[zoneID];
- zoneFlip = fZone.flipMap()[fZone.whichFace(faceI)];
- }
+ label zoneFaceI = fZone.whichFace(faceI);
- if (i == 0)
+ if (zoneFaceI != -1)
+ {
+ if (!fZone.flipMap()[zoneFaceI])
{
- // First usage of face. Modify.
- meshMod.setAction
+ // Use owner side of face
+ modifyOrAddFace
(
- polyModifyFace
- (
- f, // modified face
- faceI, // label of face
- mesh.faceOwner()[faceI], // owner
- -1, // neighbour
- false, // face flip
- newPatchI, // patch for face
- false, // remove from zone
- zoneID, // zone for face
- zoneFlip // face flip in zone
- )
+ meshMod,
+ mesh.faces()[faceI], // modified face
+ faceI, // label of face
+ mesh.faceOwner()[faceI],// owner
+ false, // face flip
+ newPatchI, // patch for face
+ zoneID.index(), // zone for face
+ false, // face flip in zone
+ modifiedFace // modify or add status
);
}
else
{
- // Second or more usage of face. Add.
- meshMod.setAction
+ // Use neighbour side of face
+ modifyOrAddFace
(
- polyAddFace
- (
- f, // modified face
- mesh.faceOwner()[faceI], // owner
- -1, // neighbour
- -1, // master point
- -1, // master edge
- faceI, // master face
- false, // face flip
- newPatchI, // patch for face
- zoneID, // zone for face
- zoneFlip // face flip in zone
- )
+ meshMod,
+ mesh.faces()[faceI].reverseFace(), // modified face
+ faceI, // label of face
+ mesh.faceNeighbour()[faceI],// owner
+ true, // face flip
+ newPatchI, // patch for face
+ zoneID.index(), // zone for face
+ true, // face flip in zone
+ modifiedFace // modify or add status
);
}
-
- nBaffled++;
}
}
- // Add the reversed face.
+
+ // Pass 2. Do other side of zone
+ // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
for (label faceI = 0; faceI < mesh.nInternalFaces(); faceI++)
{
- if (facesToSplit.found(faceI))
+ label zoneFaceI = fZone.whichFace(faceI);
+
+ if (zoneFaceI != -1)
{
- const face& f = mesh.faces()[faceI];
- label zoneID = faceZones.whichZone(faceI);
- bool zoneFlip = false;
- if (zoneID >= 0)
+ if (!fZone.flipMap()[zoneFaceI])
{
- const faceZone& fZone = faceZones[zoneID];
- zoneFlip = fZone.flipMap()[fZone.whichFace(faceI)];
+ // Use neighbour side of face
+ modifyOrAddFace
+ (
+ meshMod,
+ mesh.faces()[faceI].reverseFace(), // modified face
+ faceI, // label of face
+ mesh.faceNeighbour()[faceI], // owner
+ true, // face flip
+ newPatchI, // patch for face
+ zoneID.index(), // zone for face
+ true, // face flip in zone
+ modifiedFace // modify or add
+ );
}
- label nei = mesh.faceNeighbour()[faceI];
-
- meshMod.setAction
- (
- polyAddFace
+ else
+ {
+ // Use owner side of face
+ modifyOrAddFace
(
- f.reverseFace(), // modified face
- nei, // owner
- -1, // neighbour
- -1, // masterPointID
- -1, // masterEdgeID
- faceI, // masterFaceID,
- true, // face flip
- newPatchI, // patch for face
- zoneID, // zone for face
- zoneFlip // face flip in zone
- )
- );
-
- nBaffled++;
+ meshMod,
+ mesh.faces()[faceI], // modified face
+ faceI, // label of face
+ mesh.faceOwner()[faceI],// owner
+ false, // face flip
+ newPatchI, // patch for face
+ zoneID.index(), // zone for face
+ false, // face flip in zone
+ modifiedFace // modify or add status
+ );
+ }
}
}
+
// Modify any boundary faces
+ // ~~~~~~~~~~~~~~~~~~~~~~~~~
+
forAll(patches, patchI)
{
const polyPatch& pp = patches[patchI];
@@ -286,58 +348,22 @@ int main(int argc, char *argv[])
{
label faceI = pp.start()+i;
- if (facesToSplit.found(faceI))
+ label zoneFaceI = fZone.whichFace(faceI);
+
+ if (zoneFaceI != -1)
{
- const face& f = mesh.faces()[faceI];
- label zoneID = faceZones.whichZone(faceI);
- bool zoneFlip = false;
- if (zoneID >= 0)
- {
- const faceZone& fZone = faceZones[zoneID];
- zoneFlip = fZone.flipMap()[fZone.whichFace(faceI)];
- }
-
- if (i == 0)
- {
- // First usage of face. Modify.
- meshMod.setAction
- (
- polyModifyFace
- (
- f, // modified face
- faceI, // label of face
- mesh.faceOwner()[faceI],// owner
- -1, // neighbour
- false, // face flip
- newPatchI, // patch for face
- false, // remove from zone
- zoneID, // zone for face
- zoneFlip // face flip in zone
- )
- );
- }
- else
- {
- // Second or more usage of face. Add.
- meshMod.setAction
- (
- polyAddFace
- (
- f, // modified face
- mesh.faceOwner()[faceI],// owner
- -1, // neighbour
- -1, // master point
- -1, // master edge
- faceI, // master face
- false, // face flip
- newPatchI, // patch for face
- zoneID, // zone for face
- zoneFlip // face flip in zone
- )
- );
- }
-
- nBaffled++;
+ modifyOrAddFace
+ (
+ meshMod,
+ mesh.faces()[faceI], // modified face
+ faceI, // label of face
+ mesh.faceOwner()[faceI], // owner
+ false, // face flip
+ newPatchI, // patch for face
+ zoneID.index(), // zone for face
+ fZone.flipMap()[zoneFaceI], // face flip in zone
+ modifiedFace // modify or add status
+ );
}
}
}
@@ -345,7 +371,7 @@ int main(int argc, char *argv[])
}
- Info<< "Converted " << returnReduce(nBaffled, sumOp<label>())
+ Info<< "Converted " << returnReduce(modifiedFace.count(), sumOp<label>())
<< " faces into boundary faces on patch " << patchName << nl << endl;
if (!overwrite)
diff --git a/applications/utilities/mesh/manipulation/pointSet/pointSetDict b/applications/utilities/mesh/manipulation/pointSet/pointSetDict
index 1c704a1868fe88c46be3e5d7f53a7eb184eae708..895dcd7f0aec3d01e875c335962a85ae0c6211f7 100644
--- a/applications/utilities/mesh/manipulation/pointSet/pointSetDict
+++ b/applications/utilities/mesh/manipulation/pointSet/pointSetDict
@@ -51,18 +51,24 @@ topoSetSources
value (12 13 56); // labels of points
}
- // Points with coordinate within box
- boxToPoint
- {
- box (0 0 0) (1 1 1);
- }
-
// All points in pointzone
zoneToPoint
{
name ".*Zone"; // name of pointZone, regular expressions allowed
}
+ // Points nearest to coordinates
+ nearestToPoint
+ {
+ points ((0 0 0) (1 1 1));
+ }
+
+ // Points with coordinate within box
+ boxToPoint
+ {
+ box (0 0 0) (1 1 1);
+ }
+
// Select based on surface
surfaceToPoint
{
diff --git a/applications/utilities/mesh/manipulation/setSet/setSet.C b/applications/utilities/mesh/manipulation/setSet/setSet.C
index d79d516806e040de45f70483eec4cdd195bacd04..42ad6110ea9bf258e29b23c075755bfa66e321a9 100644
--- a/applications/utilities/mesh/manipulation/setSet/setSet.C
+++ b/applications/utilities/mesh/manipulation/setSet/setSet.C
@@ -367,7 +367,7 @@ bool doCommand
{
r = IOobject::NO_READ;
- backup(mesh, setName, setName + "_old");
+ //backup(mesh, setName, setName + "_old");
currentSetPtr = topoSet::New(setType, mesh, setName, typSize);
}
@@ -399,11 +399,11 @@ bool doCommand
<< " Action:" << actionName
<< endl;
- if ((r == IOobject::MUST_READ) && (action != topoSetSource::LIST))
- {
- // currentSet has been read so can make copy.
- backup(mesh, setName, currentSet, setName + "_old");
- }
+ //if ((r == IOobject::MUST_READ) && (action != topoSetSource::LIST))
+ //{
+ // // currentSet has been read so can make copy.
+ // backup(mesh, setName, currentSet, setName + "_old");
+ //}
switch (action)
{
@@ -558,7 +558,8 @@ void printMesh(const Time& runTime, const polyMesh& mesh)
<< " cells:" << mesh.nCells()
<< " faces:" << mesh.nFaces()
<< " points:" << mesh.nPoints()
- << " patches:" << mesh.boundaryMesh().size() << nl;
+ << " patches:" << mesh.boundaryMesh().size()
+ << " bb:" << mesh.bounds() << nl;
}
diff --git a/applications/utilities/mesh/manipulation/setsToZones/setsToZones.C b/applications/utilities/mesh/manipulation/setsToZones/setsToZones.C
index dfd7262fd17ba65a287bd041289dbcc95475c7df..a369a195b8c8dcf1d22b6bb60656993fe04c5417 100644
--- a/applications/utilities/mesh/manipulation/setsToZones/setsToZones.C
+++ b/applications/utilities/mesh/manipulation/setsToZones/setsToZones.C
@@ -28,8 +28,8 @@ Description
There is one catch: for faceZones you also need to specify a flip
condition which basically denotes the side of the face. In this app
- it reads a cellSet (xxxCells if 'xxx' is the name of the faceSet) and
- any face whose neighbour is in the cellSet gets a flip=true.
+ it reads a cellSet (xxxCells if 'xxx' is the name of the faceSet) which
+ is the masterCells of the zone.
There are lots of situations in which this will go wrong but it is the
best I can think of for now.
@@ -87,7 +87,7 @@ int main(int argc, char *argv[])
polyMesh::meshSubDir/"sets"
);
- Pout<< "Searched : " << mesh.pointsInstance()/polyMesh::meshSubDir/"sets"
+ Info<< "Searched : " << mesh.pointsInstance()/polyMesh::meshSubDir/"sets"
<< nl
<< "Found : " << objects.names() << nl
<< endl;
@@ -95,7 +95,7 @@ int main(int argc, char *argv[])
IOobjectList pointObjects(objects.lookupClass(pointSet::typeName));
- Pout<< "pointSets:" << pointObjects.names() << endl;
+ //Pout<< "pointSets:" << pointObjects.names() << endl;
for
(
@@ -126,6 +126,7 @@ int main(int argc, char *argv[])
)
);
mesh.pointZones().writeOpt() = IOobject::AUTO_WRITE;
+ mesh.pointZones().instance() = mesh.facesInstance();
}
else
{
@@ -133,57 +134,17 @@ int main(int argc, char *argv[])
<< " with that of set " << set.name() << "." << endl;
mesh.pointZones()[zoneID] = pointLabels;
mesh.pointZones().writeOpt() = IOobject::AUTO_WRITE;
+ mesh.pointZones().instance() = mesh.facesInstance();
}
}
- IOobjectList cellObjects(objects.lookupClass(cellSet::typeName));
-
- Pout<< "cellSets:" << cellObjects.names() << endl;
-
- for
- (
- IOobjectList::const_iterator iter = cellObjects.begin();
- iter != cellObjects.end();
- ++iter
- )
- {
- // Not in memory. Load it.
- cellSet set(*iter());
- SortableList<label> cellLabels(set.toc());
-
- label zoneID = mesh.cellZones().findZoneID(set.name());
- if (zoneID == -1)
- {
- Info<< "Adding set " << set.name() << " as a cellZone." << endl;
- label sz = mesh.cellZones().size();
- mesh.cellZones().setSize(sz+1);
- mesh.cellZones().set
- (
- sz,
- new cellZone
- (
- set.name(), //name
- cellLabels, //addressing
- sz, //index
- mesh.cellZones() //pointZoneMesh
- )
- );
- mesh.cellZones().writeOpt() = IOobject::AUTO_WRITE;
- }
- else
- {
- Info<< "Overwriting contents of existing cellZone " << zoneID
- << " with that of set " << set.name() << "." << endl;
- mesh.cellZones()[zoneID] = cellLabels;
- mesh.cellZones().writeOpt() = IOobject::AUTO_WRITE;
- }
- }
-
IOobjectList faceObjects(objects.lookupClass(faceSet::typeName));
- Pout<< "faceSets:" << faceObjects.names() << endl;
+ HashSet<word> slaveCellSets;
+
+ //Pout<< "faceSets:" << faceObjects.names() << endl;
for
(
@@ -201,14 +162,11 @@ int main(int argc, char *argv[])
if (!noFlipMap)
{
- word setName(set.name() + "Cells");
-
- Pout<< "Trying to load cellSet " << setName
- << " to find out the flipMap." << nl
- << "If the neighbour side of the face is in the cellSet"
- << " the flipMap becomes true," << nl
- << "in all other cases it stays false."
- << " If you do not care about the flipMap"
+ word setName(set.name() + "SlaveCells");
+
+ Info<< "Trying to load cellSet " << setName
+ << " to find out the slave side of the zone." << nl
+ << "If you do not care about the flipMap"
<< " (i.e. do not use the sideness)" << nl
<< "use the -noFlipMap command line option."
<< endl;
@@ -216,6 +174,9 @@ int main(int argc, char *argv[])
// Load corresponding cells
cellSet cells(mesh, setName);
+ // Store setName to exclude from cellZones further on
+ slaveCellSets.insert(setName);
+
forAll(faceLabels, i)
{
label faceI = faceLabels[i];
@@ -302,6 +263,7 @@ int main(int argc, char *argv[])
)
);
mesh.faceZones().writeOpt() = IOobject::AUTO_WRITE;
+ mesh.faceZones().instance() = mesh.facesInstance();
}
else
{
@@ -313,10 +275,63 @@ int main(int argc, char *argv[])
flipMap.shrink()
);
mesh.faceZones().writeOpt() = IOobject::AUTO_WRITE;
+ mesh.faceZones().instance() = mesh.facesInstance();
+ }
+ }
+
+
+
+ IOobjectList cellObjects(objects.lookupClass(cellSet::typeName));
+
+ //Pout<< "cellSets:" << cellObjects.names() << endl;
+
+ for
+ (
+ IOobjectList::const_iterator iter = cellObjects.begin();
+ iter != cellObjects.end();
+ ++iter
+ )
+ {
+ if (!slaveCellSets.found(iter.key()))
+ {
+ // Not in memory. Load it.
+ cellSet set(*iter());
+ SortableList<label> cellLabels(set.toc());
+
+ label zoneID = mesh.cellZones().findZoneID(set.name());
+ if (zoneID == -1)
+ {
+ Info<< "Adding set " << set.name() << " as a cellZone." << endl;
+ label sz = mesh.cellZones().size();
+ mesh.cellZones().setSize(sz+1);
+ mesh.cellZones().set
+ (
+ sz,
+ new cellZone
+ (
+ set.name(), //name
+ cellLabels, //addressing
+ sz, //index
+ mesh.cellZones() //pointZoneMesh
+ )
+ );
+ mesh.cellZones().writeOpt() = IOobject::AUTO_WRITE;
+ mesh.cellZones().instance() = mesh.facesInstance();
+ }
+ else
+ {
+ Info<< "Overwriting contents of existing cellZone " << zoneID
+ << " with that of set " << set.name() << "." << endl;
+ mesh.cellZones()[zoneID] = cellLabels;
+ mesh.cellZones().writeOpt() = IOobject::AUTO_WRITE;
+ mesh.cellZones().instance() = mesh.facesInstance();
+ }
}
}
- Pout<< "Writing mesh." << endl;
+
+
+ Info<< "Writing mesh." << endl;
if (!mesh.write())
{
@@ -325,7 +340,7 @@ int main(int argc, char *argv[])
<< exit(FatalError);
}
- Pout << nl << "End" << endl;
+ Info<< nl << "End" << endl;
return 0;
}
diff --git a/applications/utilities/preProcessing/mdInitialise/mdInitialise.C b/applications/utilities/preProcessing/mdInitialise/mdInitialise.C
index 2f06531e335727955a2c8ac97d908da5d71c1937..ecd0221957f1a6836a9b98f838917a907e3d7149 100644
--- a/applications/utilities/preProcessing/mdInitialise/mdInitialise.C
+++ b/applications/utilities/preProcessing/mdInitialise/mdInitialise.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/Make/files b/applications/utilities/preProcessing/mdInitialise/molConfig_old/Make/files
deleted file mode 100755
index 6501e68426960c755a310e7a12b7b53548ddeb98..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/Make/files
+++ /dev/null
@@ -1,8 +0,0 @@
-latticeStructures = latticeStructures
-velocityDistributions = velocityDistributions
-
-createMolecules.C
-molConfig.C
-genMolConfig.C
-
-EXE = $(FOAM_APPBIN)/molConfig
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/Make/options b/applications/utilities/preProcessing/mdInitialise/molConfig_old/Make/options
deleted file mode 100755
index aab9a2ca4f7e9119ebfa389b5b14b74911317f1a..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/Make/options
+++ /dev/null
@@ -1,17 +0,0 @@
-EXE_INC = \
- -I$(latticeStructures) \
- -I$(velocityDistributions) \
- -I$(LIB_SRC)/meshTools/lnInclude \
- -I$(LIB_SRC)/dynamicMesh/lnInclude \
- -I$(LIB_SRC)/lagrangian/molecularDynamics/molecule/lnInclude \
- -I$(LIB_SRC)/lagrangian/molecularDynamics/potential/lnInclude \
- -I$(LIB_SRC)/lagrangian/basic/lnInclude \
- -I$(LIB_SRC)/finiteVolume/lnInclude
-
-EXE_LIBS = \
- -lmeshTools \
- -ldynamicMesh \
- -lfiniteVolume \
- -llagrangian \
- -lmolecule \
- -lpotential
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/correctVelocities.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/correctVelocities.H
deleted file mode 100644
index 0c69f15c7cda7cff0fa4387196c1dbea09c096e1..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/correctVelocities.H
+++ /dev/null
@@ -1,21 +0,0 @@
-for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-{
-
- // Remove bulk momentum introduced by random numbers and add
- // desired bulk velocity
-
- // For systems with molecules of significantly differing masses, this may
- // need to be an iterative process or employ a better algorithm for
- // removing an appropriate share of the excess momentum from each molecule.
-
- initialVelocities(molN) += bulkVelocity - momentumSum/totalZoneMols/mass;
-}
-
-// momentumSum = vector::zero;
-//
-// for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-// {
-// momentumSum += mass*initialVelocities(molN);
-// }
-//
-// Info << "Check momentum adjustment: " << momentumSum << endl;
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/createMolecules.C b/applications/utilities/preProcessing/mdInitialise/molConfig_old/createMolecules.C
deleted file mode 100644
index dbb0f680ce2ee87e3e0846f9a4c8b50b3ca4c876..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/createMolecules.C
+++ /dev/null
@@ -1,253 +0,0 @@
-/*---------------------------------------------------------------------------*\
- ========= |
- \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
- \\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
- \\/ M anipulation |
--------------------------------------------------------------------------------
-License
- This file is part of OpenFOAM.
-
- OpenFOAM is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2 of the License, or (at your
- option) any later version.
-
- OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- for more details.
-
- You should have received a copy of the GNU General Public License
- along with OpenFOAM; if not, write to the Free Software Foundation,
- Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-\*----------------------------------------------------------------------------*/
-
-#include "molConfig.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-void Foam::molConfig::createMolecules()
-{
- Info<< nl << "Creating molecules from zone specifications\n" << endl;
-
- DynamicList<vector> initialPositions(0);
-
- DynamicList<label> initialIds(0);
-
- DynamicList<scalar> initialMasses(0);
-
- DynamicList<label> initialCelli(0);
-
- DynamicList<vector> initialVelocities(0);
-
- DynamicList<vector> initialAccelerations(0);
-
- DynamicList<label> initialTethered(0);
-
- DynamicList<vector> initialTetherPositions(0);
-
- label totalMols = 0;
-
- label idAssign;
-
- Random rand(clock::getTime());
-
-// * * * * * * * * Building the IdList * * * * * * * * * //
-
-//Notes: - each processor will have an identical idList_.
-// - The order of id's inside the idList_ depends on the order
-// of subDicts inside the molConigDict.
-
- Info<< "Building the idList: " ;
-
- forAll(molConfigDescription_.toc(), cZs)
- {
- word subDictName (molConfigDescription_.toc()[cZs]);
-
- word iD (molConfigDescription_.subDict(subDictName).lookup("id"));
-
- if (findIndex(idList_,iD) == -1)
- {
- idList_.append(iD);
- }
- }
-
- forAll(idList_, i)
- {
- Info << " " << idList_[i];
- }
-
- Info << nl << endl;
-
-// * * * * * * * * Filling the Mesh * * * * * * * * * //
-
- const cellZoneMesh& cellZoneI = mesh_.cellZones();
-
- if (cellZoneI.size())
- {
- Info<< "Filling the zones with molecules." << nl << endl;
- }
- else
- {
- FatalErrorIn("void createMolecules()\n")
- << "No cellZones found in mesh description."
- << abort(FatalError);
- }
-
- forAll (cellZoneI, cZ)
- {
- if (cellZoneI[cZ].size())
- {
- if (!molConfigDescription_.found(cellZoneI[cZ].name()))
- {
- Info << "Zone specification subDictionary: "
- << cellZoneI[cZ].name() << " not found." << endl;
- }
- else
- {
- label n = 0;
-
- label totalZoneMols = 0;
-
- label molsPlacedThisIteration;
-
-# include "readZoneSubDict.H"
-
- idAssign = findIndex(idList_,id);
-
-# include "startingPoint.H"
-
- // Continue trying to place molecules as long as at
- // least one molecule is placed in each iteration.
- // The "|| totalZoneMols == 0" condition means that the
- // algorithm will continue if the origin is outside the
- // zone - it will cause an infinite loop if no molecules
- // are ever placed by the algorithm.
-
- if (latticeStructure != "empty")
- {
-
- while
- (
- molsPlacedThisIteration != 0
- || totalZoneMols == 0
- )
- {
- molsPlacedThisIteration = 0;
-
- bool partOfLayerInBounds = false;
-
-# include "createPositions.H"
-
- if
- (
- totalZoneMols == 0
- && !partOfLayerInBounds
- )
- {
- WarningIn("molConfig::createMolecules()")
- << "A whole layer of unit cells was placed "
- << "outside the bounds of the mesh, but no "
- << "molecules have been placed in zone '"
- << cellZoneI[cZ].name()
- << "'. This is likely to be because the zone "
- << "has few cells ("
- << cellZoneI[cZ].size()
- << " in this case) and no lattice position "
- << "fell inside them. "
- << "Aborting filling this zone."
- << endl;
-
- break;
- }
-
- totalZoneMols += molsPlacedThisIteration;
-
- n++;
- }
-
- label molN;
-
- for
- (
- molN = totalMols;
- molN < totalMols + totalZoneMols;
- molN++
- )
- {
- initialIds.append(idAssign);
-
- initialMasses.append(mass);
-
- initialAccelerations.append(vector::zero);
-
- if (tethered)
- {
- initialTethered.append(1);
-
- initialTetherPositions.append
- (
- initialPositions[molN]
- );
- }
-
- else
- {
- initialTethered.append(0);
-
- initialTetherPositions.append(vector::zero);
- }
- }
-
-# include "createVelocities.H"
-
-# include "correctVelocities.H"
-
- }
-
- totalMols += totalZoneMols;
- }
- }
- }
-
- idList_.shrink();
-
- positions_ = initialPositions;
-
- positions_.setSize(initialPositions.size());
-
- id_ = initialIds;
-
- id_.setSize(initialIds.size());
-
- mass_ = initialMasses;
-
- mass_.setSize(initialMasses.size());
-
- cells_ = initialCelli;
-
- cells_.setSize(initialCelli.size());
-
- U_ = initialVelocities;
-
- U_.setSize(initialVelocities.size());
-
- A_ = initialAccelerations;
-
- A_.setSize(initialAccelerations.size());
-
- tethered_ = initialTethered;
-
- tethered_.setSize(initialTethered.size());
-
- tetherPositions_ = initialTetherPositions;
-
- tetherPositions_.setSize(initialTetherPositions.size());
-
- nMol_ = totalMols;
-}
-
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/createPositions.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/createPositions.H
deleted file mode 100644
index b26486338caf7228188244aac4e989fb9380cb0d..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/createPositions.H
+++ /dev/null
@@ -1,26 +0,0 @@
-vector latticePosition;
-
-vector globalPosition;
-
-if (latticeStructure == "SC")
-{
-# include "SC.H"
-}
-
-else if (latticeStructure == "FCC")
-{
-# include "FCC.H"
-}
-
-else if (latticeStructure == "BCC")
-{
-# include "BCC.H"
-}
-
-else
-{
- FatalErrorIn("createPositions.H\n")
- << "latticeStructure " << latticeStructure
- << " not supported."
- << abort(FatalError);
-}
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/createVelocities.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/createVelocities.H
deleted file mode 100644
index d014ffd146044db0be9307b511e793ee490f0464..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/createVelocities.H
+++ /dev/null
@@ -1,13 +0,0 @@
-vector velocity;
-
-vector momentumSum = vector::zero;
-
-if (velocityDistribution == "uniform")
-{
-# include "uniform.H"
-}
-
-if (velocityDistribution == "maxwellian")
-{
-# include "maxwellian.H"
-}
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/genMolConfig.C b/applications/utilities/preProcessing/mdInitialise/molConfig_old/genMolConfig.C
deleted file mode 100644
index 7df9ce562228a12973103ba1ea7ce7d95b7d47e3..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/genMolConfig.C
+++ /dev/null
@@ -1,129 +0,0 @@
-/*---------------------------------------------------------------------------*\
- ========= |
- \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
- \\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
- \\/ M anipulation |
--------------------------------------------------------------------------------
-License
- This file is part of OpenFOAM.
-
- OpenFOAM is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2 of the License, or (at your
- option) any later version.
-
- OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- for more details.
-
- You should have received a copy of the GNU General Public License
- along with OpenFOAM; if not, write to the Free Software Foundation,
- Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-\*---------------------------------------------------------------------------*/
-
-#include "molConfig.H"
-#include "fvCFD.H"
-
-using namespace Foam;
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// Main program:
-
-int main(int argc, char *argv[])
-{
-# include "setRootCase.H"
-# include "createTime.H"
-# include "createMesh.H"
-
- Info<< nl << "Reading molecular configuration description dictionary"
- << endl;
-
- IOobject molConfigDescriptionIOobject
- (
- "molConfigDict",
- runTime.system(),
- runTime,
- IOobject::MUST_READ,
- IOobject::NO_WRITE,
- false
- );
-
- if (!molConfigDescriptionIOobject.headerOk())
- {
- FatalErrorIn(args.executable())
- << "Cannot find molConfig description file " << nl
- << args.caseName()/runTime.system()/"molConfig"/"molConfigDict"
- << nl << exit(FatalError);
- }
-
- IOdictionary molConfigDescription(molConfigDescriptionIOobject);
-
-
- // Create molCloud, registering object with mesh
-
- Info<< nl << "Creating molecular configuration" << endl;
-
- molConfig molecules(molConfigDescription, mesh);
-
- label totalMolecules = molecules.nMol();
-
- if (Pstream::parRun())
- {
- reduce(totalMolecules, sumOp<label>());
- }
-
- Info<< nl << "Total number of molecules added: " << totalMolecules
- << nl << endl;
-
- moleculeCloud molCloud
- (
- mesh,
- molecules.nMol(),
- molecules.id(),
- molecules.mass(),
- molecules.positions(),
- molecules.cells(),
- molecules.U(),
- molecules.A(),
- molecules.tethered(),
- molecules.tetherPositions()
- );
-
- IOdictionary idListDict
- (
- IOobject
- (
- "idList",
- mesh.time().constant(),
- mesh,
- IOobject::NO_READ,
- IOobject::AUTO_WRITE
- )
- );
-
- idListDict.add("idList", molecules.molIdList());
-
- IOstream::defaultPrecision(12);
-
- Info << nl << "Writing molecular configuration" << endl;
-
- if (!mesh.write())
- {
- FatalErrorIn(args.executable())
- << "Failed writing moleculeCloud."
- << nl << exit(FatalError);
- }
-
- Info<< nl << "ClockTime = " << runTime.elapsedClockTime() << " s"
- << nl << endl;
-
- Info << nl << "End\n" << endl;
-
- return 0;
-}
-
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/BCC.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/BCC.H
deleted file mode 100644
index cd3cbdf100ba1c7fcafecca68e2c730ebfc2b97c..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/BCC.H
+++ /dev/null
@@ -1,179 +0,0 @@
-labelVector iN(0,0,0);
-
-vector gap = (vector::one)*pow((numberDensity/2.0),-(1.0/3.0));
-
-#include "origin.H"
-
-// Info<< "gap = " << gap << endl;
-
-// Special treatment is required for the first position, i.e. iteration zero.
-
-if (n == 0)
-{
- latticePosition.x() = (iN.x()*gap.x());
-
- latticePosition.y() = (iN.y()*gap.y());
-
- latticePosition.z() = (iN.z()*gap.z());
-
- // Placing 2 molecules in each unit cell, using the algorithm from
- // D. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Ed, p68
-
- for (label iU = 0; iU < 2; iU++)
- {
- vector unitCellLatticePosition = latticePosition;
-
- if (iU == 1)
- {
- unitCellLatticePosition += 0.5 * gap;
- }
-
- if (originSpecifies == "corner")
- {
- unitCellLatticePosition -= 0.25*gap;
- }
-
-// Info << nl << n << ", " << unitCellLatticePosition;
-
- globalPosition =
- origin + transform(latticeToGlobal,unitCellLatticePosition);
-
- partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition))
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
-}
-else
-{
- // Place top and bottom caps.
-
- for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
- {
- for (iN.y() = -n; iN.y() <= n; iN.y()++)
- {
- for (iN.x() = -n; iN.x() <= n; iN.x()++)
- {
- latticePosition.x() = (iN.x() * gap.x());
-
- latticePosition.y() = (iN.y() * gap.y());
-
- latticePosition.z() = (iN.z() * gap.z());
-
- for (label iU = 0; iU < 2; iU++)
- {
- vector unitCellLatticePosition = latticePosition;
-
- if (iU == 1)
- {
- unitCellLatticePosition += 0.5*gap;
- }
-
- if(originSpecifies == "corner")
- {
- unitCellLatticePosition -= 0.25*gap;
- }
-
-// Info << nl << iN << ", " << unitCellLatticePosition;
-
- globalPosition =
- origin
- + transform(latticeToGlobal,unitCellLatticePosition);
-
- partOfLayerInBounds =
- mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex
- (
- mesh_.cellZones()[cZ],
- mesh_.findCell(globalPosition)
- )
- != -1)
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
- }
- }
- }
-
-// Placing sides
-
- for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
- {
- for (label iR = 0; iR <= 2*n -1; iR++)
- {
- latticePosition.x() = (n*gap.x());
-
- latticePosition.y() = ((-n + (iR + 1))*gap.y());
-
- latticePosition.z() = (iN.z() * gap.z());
-
- for (label iK = 0; iK < 4; iK++)
- {
- for (label iU = 0; iU < 2; iU++)
- {
- vector unitCellLatticePosition = latticePosition;
-
- if (iU == 1)
- {
- unitCellLatticePosition += 0.5 * gap;
- }
-
- if (originSpecifies == "corner")
- {
- unitCellLatticePosition -= 0.25*gap;
- }
-
- globalPosition =
- origin
- + transform(latticeToGlobal,unitCellLatticePosition);
-
- partOfLayerInBounds =
- mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex
- (
- mesh_.cellZones()[cZ],
- mesh_.findCell(globalPosition)
- )
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
-
- latticePosition =
- vector
- (
- - latticePosition.y(),
- latticePosition.x(),
- latticePosition.z()
- );
- }
- }
- }
-}
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/FCC.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/FCC.H
deleted file mode 100644
index 313ebf96cb89bf2b1111b45fe1de462133fb5197..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/FCC.H
+++ /dev/null
@@ -1,217 +0,0 @@
-labelVector iN(0,0,0);
-
-vector gap = (vector::one)*pow((numberDensity/4.0),-(1.0/3.0));
-
-#include "origin.H"
-
-// Info<< "gap = " << gap << endl;
-
-// Special treatment is required for the first position, i.e. iteration zero.
-
-if (n == 0)
-{
- latticePosition.x() = (iN.x() * gap.x());
-
- latticePosition.y() = (iN.y() * gap.y());
-
- latticePosition.z() = (iN.z() * gap.z());
-
- // Placing 4 molecules in each unit cell, using the algorithm from
- // D. Rapaport, The Art of Molecular Dynamics Simulation, 2nd Ed, p68
-
- for (label iU = 0; iU < 4; iU++)
- {
- vector unitCellLatticePosition = latticePosition;
-
- if (iU != 3)
- {
- if (iU != 0)
- {
- unitCellLatticePosition.x() += 0.5 * gap.x();
- }
-
- if (iU != 1)
- {
- unitCellLatticePosition.y() += 0.5 * gap.y();
- }
-
- if (iU != 2)
- {
- unitCellLatticePosition.z() += 0.5 * gap.z();
- }
- }
-
- if (originSpecifies == "corner")
- {
- unitCellLatticePosition -= 0.25*gap;
- }
-
-// Info << nl << n << ", " << unitCellLatticePosition;
-
- globalPosition =
- origin + transform(latticeToGlobal,unitCellLatticePosition);
-
- partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition))
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
-}
-else
-{
- // Place top and bottom caps.
-
- for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
- {
- for (iN.y() = -n; iN.y() <= n; iN.y()++)
- {
- for (iN.x() = -n; iN.x() <= n; iN.x()++)
- {
- latticePosition.x() = (iN.x() * gap.x());
-
- latticePosition.y() = (iN.y() * gap.y());
-
- latticePosition.z() = (iN.z() * gap.z());
-
- for (label iU = 0; iU < 4; iU++)
- {
- vector unitCellLatticePosition = latticePosition;
-
- if (iU != 3)
- {
- if (iU != 0)
- {
- unitCellLatticePosition.x() += 0.5 * gap.x();
- }
-
- if (iU != 1)
- {
- unitCellLatticePosition.y() += 0.5 * gap.y();
- }
-
- if (iU != 2)
- {
- unitCellLatticePosition.z() += 0.5 * gap.z();
- }
- }
-
- if (originSpecifies == "corner")
- {
- unitCellLatticePosition -= 0.25*gap;
- }
-
- globalPosition =
- origin
- + transform(latticeToGlobal,unitCellLatticePosition);
-
- partOfLayerInBounds =
- mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex
- (
- mesh_.cellZones()[cZ],
- mesh_.findCell(globalPosition)
- )
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
- }
- }
- }
-
-// Placing sides
-
- for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
- {
- for (label iR = 0; iR <= 2*n -1; iR++)
- {
- latticePosition.x() = (n * gap.x());
-
- latticePosition.y() = ((-n + (iR + 1)) * gap.y());
-
- latticePosition.z() = (iN.z() * gap.z());
-
- for (label iK = 0; iK < 4; iK++)
- {
- for (label iU = 0; iU < 4; iU++)
- {
- vector unitCellLatticePosition = latticePosition;
-
- if (iU != 3)
- {
- if (iU != 0)
- {
- unitCellLatticePosition.x() += 0.5 * gap.x();
- }
-
- if (iU != 1)
- {
- unitCellLatticePosition.y() += 0.5 * gap.y();
- }
-
- if (iU != 2)
- {
- unitCellLatticePosition.z() += 0.5 * gap.z();
- }
- }
-
- if (originSpecifies == "corner")
- {
- unitCellLatticePosition -= 0.25*gap;
- }
-
- globalPosition =
- origin
- + transform(latticeToGlobal,unitCellLatticePosition);
-
- partOfLayerInBounds =
- mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex
- (
- mesh_.cellZones()[cZ],
- mesh_.findCell(globalPosition)
- )
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
-
- latticePosition =
- vector
- (
- - latticePosition.y(),
- latticePosition.x(),
- latticePosition.z()
- );
- }
- }
- }
-}
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/SC.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/SC.H
deleted file mode 100644
index dd0ff7c00f67453884b5693ed32003566f90b1b0..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/latticeStructures/SC.H
+++ /dev/null
@@ -1,127 +0,0 @@
-labelVector iN(0,0,0);
-
-vector gap = (vector::one)*pow(numberDensity, -(1.0/3.0));
-
-#include "origin.H"
-
-// Info<< "gap = " << gap << endl;
-
-// Special treatment is required for the first position, i.e. iteration zero.
-
-if (n == 0)
-{
- latticePosition = vector::zero;
-
- if (originSpecifies == "corner")
- {
- latticePosition += 0.5*gap;
- }
-
- globalPosition = origin + transform(latticeToGlobal,latticePosition);
-
- partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
- if (findIndex(mesh_.cellZones()[cZ], mesh_.findCell(globalPosition)) != -1)
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
-}
-else
-{
- for (iN.z() = -n; iN.z() <= n; iN.z() += 2*n)
- {
- for (iN.y() = -n; iN.y() <= n; iN.y()++)
- {
- for (iN.x() = -n; iN.x() <= n; iN.x()++)
- {
- latticePosition.x() = (iN.x() * gap.x());
-
- latticePosition.y() = (iN.y() * gap.y());
-
- latticePosition.z() = (iN.z() * gap.z());
-
- if (originSpecifies == "corner")
- {
- latticePosition += 0.5*gap;
- }
-
- globalPosition =
- origin + transform(latticeToGlobal,latticePosition);
-
- partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex
- (
- mesh_.cellZones()[cZ],
- mesh_.findCell(globalPosition)
- )
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
- }
- }
- }
-
- tensor quarterRotate(EulerCoordinateRotation(-90, 0, 0, true).R());
-
- iN.x() = n;
- for (iN.z() = -(n-1); iN.z() <= (n-1); iN.z()++)
- {
- for (iN.y() = -(n-1); iN.y() <= n; iN.y()++)
- {
- latticePosition.x() = (iN.x()*gap.x());
-
- latticePosition.y() = (iN.y()*gap.y());
-
- latticePosition.z() = (iN.z()*gap.z());
-
- for (label iR = 0; iR < 4; iR++)
- {
- vector offsetCorrectedLatticePosition = latticePosition;
-
- if (originSpecifies == "corner")
- {
- offsetCorrectedLatticePosition += 0.5*gap;
- }
-
- globalPosition =
- origin
- + transform(latticeToGlobal,offsetCorrectedLatticePosition);
-
- partOfLayerInBounds = mesh_.bounds().contains(globalPosition);
-
- if
- (
- findIndex
- (
- mesh_.cellZones()[cZ],
- mesh_.findCell(globalPosition)
- )
- != -1
- )
- {
- molsPlacedThisIteration++;
-
- initialPositions.append(globalPosition);
-
- initialCelli.append(mesh_.findCell(globalPosition));
- }
-
- latticePosition = transform(quarterRotate,latticePosition);
- }
- }
- }
-}
-
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfig.C b/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfig.C
deleted file mode 100644
index e81c24ca6a3cda74c841511a8519496ddcdf1638..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfig.C
+++ /dev/null
@@ -1,50 +0,0 @@
-/*---------------------------------------------------------------------------*\
- ========= |
- \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
- \\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
- \\/ M anipulation |
--------------------------------------------------------------------------------
-License
- This file is part of OpenFOAM.
-
- OpenFOAM is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2 of the License, or (at your
- option) any later version.
-
- OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- for more details.
-
- You should have received a copy of the GNU General Public License
- along with OpenFOAM; if not, write to the Free Software Foundation,
- Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-\*---------------------------------------------------------------------------*/
-
-#include "molConfig.H"
-
-// * * * * * * * * * * * * * * * * Constructor * * * * * * * * * * * * * * * //
-
-Foam::molConfig::molConfig
-(
- IOdictionary& molConfigDescription,
- const polyMesh& mesh
-)
-:
- molConfigDescription_(molConfigDescription),
- mesh_(mesh)
-{
- createMolecules();
-}
-
-
-// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
-
-Foam::molConfig::~molConfig()
-{}
-
-
-// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/origin.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/origin.H
deleted file mode 100644
index 24bc994d34fe8eaee58b7c77a71613d1bf8bc004..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/origin.H
+++ /dev/null
@@ -1,49 +0,0 @@
-// Please refer to notes
-
-// 1. Determine the unit cell dimensions: xU, yU and zU
-
-const scalar xU = gap.x();
-const scalar yU = gap.y();
-const scalar zU = gap.z();
-
-// 2. Determine the anchorPoint co-ordinates: xA, yA and zA
-
-const scalar xA = anchorPoint.x();
-const scalar yA = anchorPoint.y();
-const scalar zA = anchorPoint.z();
-
-// 3. Determine the vector rAB from global co-ordinate system:
-
-const vector rAB((xMid - xA), (yMid - yA), (zMid - zA));
-
-// 4. Transform vector rAS into lattice co-ordinate system:
-
-const vector rASTransf = transform(latticeToGlobal.T(), rAB);
-
-// Info << "The vector rAS = " << rAS << endl;
-// Info << "The vector rAStransf = " << rAStransf << endl;
-
-// 5. Calculate the integer values: ni, nj and nk
-scalar nIscalar = rASTransf.x()/xU;
-scalar nJscalar = rASTransf.y()/yU;
-scalar nKscalar = rASTransf.z()/zU;
-
-// Info << "The nI, nJ, nK values before are: " << nIscalar <<" "<< nJscalar <<" "<< nKscalar << endl;
-
-label nI = label(nIscalar + 0.5*sign(nIscalar));
-label nJ = label(nJscalar + 0.5*sign(nJscalar));
-label nK = label(nKscalar + 0.5*sign(nKscalar));
-
-// Info << "The nI, nJ, nK values after are: " << nI <<" "<< nJ <<" "<< nK << endl;
-
-// 6. Calculate the corrected starting point, rAC (in the lattice co-ordinate system):
-const vector rAC((nI*xU), (nJ*yU), (nK*zU));
-
-// 7. Transform the corrected starting point in the global co-ordinate system, rC:
-const vector rC = anchorPoint + transform(latticeToGlobal, rAC);
-
-
-const vector& origin = rC;
-
-// Pout << "The Corrected Starting Point: " << origin << endl;
-
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/readZoneSubDict.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/readZoneSubDict.H
deleted file mode 100644
index 72705c761e2650f4ec4f7faa72078235e1f288df..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/readZoneSubDict.H
+++ /dev/null
@@ -1,93 +0,0 @@
-
-// Info << "Zone description subDict " << cZ <<": " << cellZoneI[cZ].name() << endl;
-
-const dictionary& subDictI =
- molConfigDescription_.subDict(cellZoneI[cZ].name());
-
-const scalar temperature(readScalar(subDictI.lookup("temperature")));
-
-const word velocityDistribution(subDictI.lookup("velocityDistribution"));
-
-const vector bulkVelocity(subDictI.lookup("bulkVelocity"));
-
-const word id(subDictI.lookup("id"));
-
-const scalar mass(readScalar(subDictI.lookup("mass")));
-
-scalar numberDensity_read(0.0);
-
-if (subDictI.found("numberDensity"))
-{
- numberDensity_read = readScalar(subDictI.lookup("numberDensity"));
-}
-else if (subDictI.found("massDensity"))
-{
- numberDensity_read = readScalar(subDictI.lookup("massDensity"))/mass;
-}
-else
-{
- FatalErrorIn("readZoneSubDict.H\n")
- << "massDensity or numberDensity not specified " << nl
- << abort(FatalError);
-}
-
-const scalar numberDensity(numberDensity_read);
-
-const word latticeStructure(subDictI.lookup("latticeStructure"));
-
-const vector anchorPoint(subDictI.lookup("anchor"));
-
-const word originSpecifies(subDictI.lookup("anchorSpecifies"));
-
-if
-(
- originSpecifies != "corner"
- && originSpecifies != "molecule"
-)
-{
- FatalErrorIn("readZoneSubDict.H\n")
- << "anchorSpecifies must be either 'corner' or 'molecule', found "
- << originSpecifies << nl
- << abort(FatalError);
-}
-
-bool tethered = false;
-
-if (subDictI.found("tethered"))
-{
- tethered = Switch(subDictI.lookup("tethered"));
-}
-
-const vector orientationAngles(subDictI.lookup("orientationAngles"));
-
-scalar phi(orientationAngles.x()*mathematicalConstant::pi/180.0);
-scalar theta(orientationAngles.y()*mathematicalConstant::pi/180.0);
-scalar psi(orientationAngles.z()*mathematicalConstant::pi/180.0);
-
-const tensor latticeToGlobal
-(
- cos(psi)*cos(phi) - cos(theta)*sin(phi)*sin(psi),
- cos(psi)*sin(phi) + cos(theta)*cos(phi)*sin(psi),
- sin(psi)*sin(theta),
- - sin(psi)*cos(phi) - cos(theta)*sin(phi)*cos(psi),
- - sin(psi)*sin(phi) + cos(theta)*cos(phi)*cos(psi),
- cos(psi)*sin(theta),
- sin(theta)*sin(phi),
- - sin(theta)*cos(phi),
- cos(theta)
-);
-
-// Info << "\tcells: " << cellZoneI[cZ].size() << endl;
-// Info << "\tnumberDensity: " << numberDensity << endl;
-// Info << "\ttemperature: " << temperature << endl;
-// Info << "\tvelocityDistribution: " << velocityDistribution << endl;
-// Info << "\tbulkVelocity: " << bulkVelocity << endl;
-// Info << "\tid: " << id << endl;
-// Info << "\tmass: " << mass << endl;
-// Info << "\tlatticeStructure: " << latticeStructure << endl;
-// Info << "\tanchor: " << anchorPoint << endl;
-// Info << "\toriginSpecifies: " << originSpecifies << endl;
-// Info << "\ttethered: " << tethered << endl;
-// Info << "\torientationAngles: " << orientationAngles << endl;
-// Info << "\tlatticeToGlobal: " << latticeToGlobal << endl;
-
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/startingPoint.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/startingPoint.H
deleted file mode 100644
index 6ae01c83f11039a01d4307816c08951f1ad33d1c..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/startingPoint.H
+++ /dev/null
@@ -1,97 +0,0 @@
-scalar xMax = 0;
-
-scalar yMax = 0;
-
-scalar zMax = 0;
-
-scalar xMin = 0;
-
-scalar yMin = 0;
-
-scalar zMin = 0;
-
-label xMaxPtLabel = 0;
-
-label yMaxPtLabel = 0;
-
-label zMaxPtLabel = 0;
-
-label xMinPtLabel = 0;
-
-label yMinPtLabel = 0;
-
-label zMinPtLabel = 0;
-
-forAll (cellZoneI[cZ], nC)
-{
- const labelList& cellPointsJ = mesh_.cellPoints()[cellZoneI[cZ][nC]];
-
- forAll(cellPointsJ, nP)
- {
- const point& ptI = mesh_.points()[cellPointsJ[nP]];
-
- const label& ptILabel = cellPointsJ[nP];
-
- if (ptI.x() > xMax || nC == 0)
- {
- xMax = ptI.x();
- xMaxPtLabel = ptILabel;
- }
- if (ptI.y() > yMax || nC == 0)
- {
- yMax = ptI.y();
- yMaxPtLabel = ptILabel;
- }
- if (ptI.z() > zMax || nC == 0)
- {
- zMax = ptI.z();
- zMaxPtLabel = ptILabel;
- }
- if (ptI.x() < xMin || nC == 0)
- {
- xMin = ptI.x();
- xMinPtLabel = ptILabel;
- }
- if (ptI.y() < yMin || nC == 0)
- {
- yMin = ptI.y();
- yMinPtLabel = ptILabel;
- }
- if (ptI.z() < zMin || nC == 0)
- {
- zMin = ptI.z();
- zMinPtLabel = ptILabel;
- }
- }
-}
-
-// Info << "Xmax: label = " << xMaxPtLabel2 << "; vector = " <<mesh_.points()[xMaxPtLabel2]
-// <<"; x-component = " << mesh_.points()[xMaxPtLabel2].x() << endl;
-// Info << "Ymax: label = " << yMaxPtLabel2 << "; vector = " <<mesh_.points()[yMaxPtLabel2]
-// <<"; y-component = " << mesh_.points()[yMaxPtLabel2].y() << endl;
-// Info << "Zmax: label = " << zMaxPtLabel2 << "; vector = " <<mesh_.points()[zMaxPtLabel2]
-// <<"; z-component = " << mesh_.points()[zMaxPtLabel2].z() << endl;
-//
-// Info << "Xmin: label = " << xMinPtLabel << "; vector = " <<mesh_.points()[xMinPtLabel]
-// <<"; x-component = " << mesh_.points()[xMinPtLabel].x() << endl;
-// Info << "Ymin: label = " << yMinPtLabel << "; vector = " <<mesh_.points()[yMinPtLabel]
-// <<"; y-component = " << mesh_.points()[yMinPtLabel].y() << endl;
-// Info << "Zmin: label = " << zMinPtLabel << "; vector = " <<mesh_.points()[zMinPtLabel]
-// <<"; z-component = " << mesh_.points()[zMinPtLabel].z() << endl;
-
-scalar xMid =
- (mesh_.points()[xMaxPtLabel].x()
- + mesh_.points()[xMinPtLabel].x()) / 2;
-
-scalar yMid =
- (mesh_.points()[yMaxPtLabel].y()
- + mesh_.points()[yMinPtLabel].y()) / 2;
-
-scalar zMid =
- (mesh_.points()[zMaxPtLabel].z()
- + mesh_.points()[zMinPtLabel].z()) / 2;
-
-vector rS(xMid, yMid, zMid);
-
-// Info << "\t The Estimated Starting Point: " << rS << endl;
-
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/velocityDistributions/maxwellian.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/velocityDistributions/maxwellian.H
deleted file mode 100644
index 01c3ff87168fc1a4057b4512472f58afec0bb5e0..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/velocityDistributions/maxwellian.H
+++ /dev/null
@@ -1,26 +0,0 @@
-scalar velCmptMag = sqrt(moleculeCloud::kb*temperature/mass);
-
-for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-{
- // Assign velocity: random direction, magnitude determined by desired
- // maxwellian distribution at temperature
-
- // Temperature gradients could be created by specifying a gradient in the
- // zone subDict, or by reading a field from a mesh.
-
- // The velocities are treated on a zone-by-zone basis for the purposes of
- // removal of bulk momentum - hence nMols becomes totalZoneMols
-
- velocity = vector
- (
- velCmptMag*rand.GaussNormal(),
- velCmptMag*rand.GaussNormal(),
- velCmptMag*rand.GaussNormal()
- );
-
- momentumSum += mass*velocity;
-
- initialVelocities.append(velocity);
-}
-
-
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/velocityDistributions/uniform.H b/applications/utilities/preProcessing/mdInitialise/molConfig_old/velocityDistributions/uniform.H
deleted file mode 100644
index 9c178af262aabb88a239f9711b1c334cdd39e4e1..0000000000000000000000000000000000000000
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/velocityDistributions/uniform.H
+++ /dev/null
@@ -1,27 +0,0 @@
-scalar initVelMag =
- sqrt
- (
- 3.0*(1.0 - 1.0 / totalZoneMols)
- *moleculeCloud::kb*temperature
- /mass
- );
-
-for (molN = totalMols; molN < totalMols + totalZoneMols; molN++)
-{
- // Assign velocity: random direction, magnitude determined by desired
- // temperature
-
- // Temperature gradients could be created by specifying a gradient in the
- // zone subDict, or by reading a field from a mesh.
-
- // The velocities are treated on a zone-by-zone basis for the purposes of
- // removal of bulk momentum - hence nMols becomes totalZoneMols
-
- velocity = (2.0*rand.vector01() - vector::one);
-
- velocity *= initVelMag/mag(velocity);
-
- momentumSum += mass*velocity;
-
- initialVelocities.append(velocity);
-}
diff --git a/src/OpenFOAM/containers/Lists/List/List.C b/src/OpenFOAM/containers/Lists/List/List.C
index 3fa3dcc8748bb8a3fbb8e775a4510baa705ab189..08422fd9ba23333451a1123d5ebf7217b4f9bfd6 100644
--- a/src/OpenFOAM/containers/Lists/List/List.C
+++ b/src/OpenFOAM/containers/Lists/List/List.C
@@ -35,8 +35,6 @@ License
#include "BiIndirectList.H"
#include "contiguous.H"
-#include <algorithm>
-
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * * //
@@ -442,34 +440,6 @@ void Foam::List<T>::transfer(SortableList<T>& a)
}
-template<class T>
-void Foam::sort(List<T>& a)
-{
- std::sort(a.begin(), a.end());
-}
-
-
-template<class T, class Cmp>
-void Foam::sort(List<T>& a, const Cmp& cmp)
-{
- std::sort(a.begin(), a.end(), cmp);
-}
-
-
-template<class T>
-void Foam::stableSort(List<T>& a)
-{
- std::stable_sort(a.begin(), a.end());
-}
-
-
-template<class T, class Cmp>
-void Foam::stableSort(List<T>& a, const Cmp& cmp)
-{
- std::stable_sort(a.begin(), a.end(), cmp);
-}
-
-
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
// Assignment to UList operator. Takes linear time.
diff --git a/src/OpenFOAM/containers/Lists/List/List.H b/src/OpenFOAM/containers/Lists/List/List.H
index a6bf29686a56ff15d07e61a26c8ee2145d351efb..b89f6c95a9f15c2bfe07eddfb3aa537a30c1d9b1 100644
--- a/src/OpenFOAM/containers/Lists/List/List.H
+++ b/src/OpenFOAM/containers/Lists/List/List.H
@@ -248,18 +248,6 @@ public:
template<class T>
List<T> readList(Istream&);
-template<class T>
-void sort(List<T>&);
-
-template<class T, class Cmp>
-void sort(List<T>&, const Cmp&);
-
-template<class T>
-void stableSort(List<T>&);
-
-template<class T, class Cmp>
-void stableSort(List<T>&, const Cmp&);
-
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
diff --git a/src/OpenFOAM/containers/Lists/UList/UList.C b/src/OpenFOAM/containers/Lists/UList/UList.C
index 255a91ecfecc83484da0f0f6873795e82dbf586d..42d00bc41e7ede72f47b9e4dcf9490e0891c2f33 100644
--- a/src/OpenFOAM/containers/Lists/UList/UList.C
+++ b/src/OpenFOAM/containers/Lists/UList/UList.C
@@ -30,6 +30,8 @@ License
#include "ListLoopM.H"
#include "contiguous.H"
+#include <algorithm>
+
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
template<class T>
@@ -116,6 +118,34 @@ Foam::label Foam::UList<T>::byteSize() const
}
+template<class T>
+void Foam::sort(UList<T>& a)
+{
+ std::sort(a.begin(), a.end());
+}
+
+
+template<class T, class Cmp>
+void Foam::sort(UList<T>& a, const Cmp& cmp)
+{
+ std::sort(a.begin(), a.end(), cmp);
+}
+
+
+template<class T>
+void Foam::stableSort(UList<T>& a)
+{
+ std::stable_sort(a.begin(), a.end());
+}
+
+
+template<class T, class Cmp>
+void Foam::stableSort(UList<T>& a, const Cmp& cmp)
+{
+ std::stable_sort(a.begin(), a.end(), cmp);
+}
+
+
// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
template<class T>
diff --git a/src/OpenFOAM/containers/Lists/UList/UList.H b/src/OpenFOAM/containers/Lists/UList/UList.H
index f7db8226ff74d5dc0efa82edc11533b372481c79..087f685ff6cf182cee3be9fe3a4c24370d3f25fa 100644
--- a/src/OpenFOAM/containers/Lists/UList/UList.H
+++ b/src/OpenFOAM/containers/Lists/UList/UList.H
@@ -320,6 +320,18 @@ public:
);
};
+template<class T>
+void sort(UList<T>&);
+
+template<class T, class Cmp>
+void sort(UList<T>&, const Cmp&);
+
+template<class T>
+void stableSort(UList<T>&);
+
+template<class T, class Cmp>
+void stableSort(UList<T>&, const Cmp&);
+
// Reverse the first n elements of the list
template<class T>
inline void reverse(UList<T>&, const label n);
diff --git a/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndex.H b/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndex.H
index 0ed207057a347a07612bb089c2575777aeaf88f8..e394f679d042dd0c425f6fa7a869ebafeb5f2a4a 100644
--- a/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndex.H
+++ b/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndex.H
@@ -106,6 +106,15 @@ public:
//- Global sum of localSizes
inline label size() const;
+ //- Size of procI data
+ inline label localSize(const label procI) const;
+
+ //- From local to global on procI
+ inline label toGlobal(const label procI, const label i) const;
+
+ //- Is on processor procI
+ inline bool isLocal(const label procI, const label i) const;
+
//- From global to local on procI
inline label toLocal(const label procI, const label i) const;
@@ -115,9 +124,6 @@ public:
//- Start of procI data
inline label offset(const label procI) const;
- //- Size of procI data
- inline label localSize(const label procI) const;
-
// IOstream Operators
diff --git a/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndexI.H b/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndexI.H
index f9444fe54b0291f32f3d19b9476bf21dfbcf8618..d7c44107c665e29d0fd38900b2767e116b5e1b57 100644
--- a/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndexI.H
+++ b/src/OpenFOAM/meshes/polyMesh/globalMeshData/globalIndexI.H
@@ -63,27 +63,39 @@ inline Foam::label Foam::globalIndex::size() const
}
+inline Foam::label Foam::globalIndex::toGlobal
+(
+ const label procI,
+ const label i
+) const
+{
+ return(procI == 0 ? i : i + offsets_[procI-1]);
+}
+
+
inline Foam::label Foam::globalIndex::toGlobal(const label i) const
{
- return
- (
- Pstream::myProcNo() == 0
- ? i
- : i + offsets_[Pstream::myProcNo()-1]
- );
+ return toGlobal(Pstream::myProcNo(), i);
}
+
//- Is on local processor
-inline bool Foam::globalIndex::isLocal(const label i) const
+inline bool Foam::globalIndex::isLocal(const label procI, const label i) const
{
return
- (i < offsets_[Pstream::myProcNo()])
- && (i >= (Pstream::myProcNo() == 0 ? 0 : offsets_[Pstream::myProcNo()-1]));
+ (i < offsets_[procI])
+ && (i >= (procI == 0 ? 0 : offsets_[procI-1]));
+}
+
+
+inline bool Foam::globalIndex::isLocal(const label i) const
+{
+ return isLocal(Pstream::myProcNo(), i);
}
inline Foam::label Foam::globalIndex::toLocal(const label procI, const label i)
- const
+const
{
label localI = (procI == 0 ? i : i - offsets_[procI-1]);
diff --git a/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/coupled/coupledPolyPatch.H b/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/coupled/coupledPolyPatch.H
index 690fb1083b4a4fce2f27c84df711fe8e5d33ea10..de1d9cc9f98c4fe60502606c3842c1057e7c8c9c 100644
--- a/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/coupled/coupledPolyPatch.H
+++ b/src/OpenFOAM/meshes/polyMesh/polyPatches/basic/coupled/coupledPolyPatch.H
@@ -32,7 +32,6 @@ Description
SourceFiles
coupledPolyPatch.C
- coupledPolyPatchMorph.C
\*---------------------------------------------------------------------------*/
diff --git a/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.C b/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.C
index 5b688c64000f37ec36d79c6016e5d0abc0ae9a4d..d4cc0a284360f45bab1dd8ff9f995dfce256e606 100644
--- a/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.C
+++ b/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.C
@@ -34,6 +34,7 @@ Description
#include "primitiveMesh.H"
#include "demandDrivenData.H"
#include "mapPolyMesh.H"
+#include "syncTools.H"
// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
@@ -530,6 +531,87 @@ bool Foam::faceZone::checkDefinition(const bool report) const
}
+bool Foam::faceZone::checkParallelSync(const bool report) const
+{
+ const polyMesh& mesh = zoneMesh().mesh();
+ const polyBoundaryMesh& bm = mesh.boundaryMesh();
+
+ bool boundaryError = false;
+
+
+ // Check that zone faces are synced
+ // ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ {
+ boolList neiZoneFace(mesh.nFaces()-mesh.nInternalFaces(), false);
+ boolList neiZoneFlip(mesh.nFaces()-mesh.nInternalFaces(), false);
+ forAll(*this, i)
+ {
+ label faceI = operator[](i);
+
+ if (!mesh.isInternalFace(faceI))
+ {
+ neiZoneFace[faceI-mesh.nInternalFaces()] = true;
+ neiZoneFlip[faceI-mesh.nInternalFaces()] = flipMap()[i];
+ }
+ }
+ boolList myZoneFace(neiZoneFace);
+ syncTools::swapBoundaryFaceList(mesh, neiZoneFace, false);
+ boolList myZoneFlip(neiZoneFlip);
+ syncTools::swapBoundaryFaceList(mesh, neiZoneFlip, false);
+
+ forAll(*this, i)
+ {
+ label faceI = operator[](i);
+
+ label patchI = bm.whichPatch(faceI);
+
+ if (patchI != -1 && bm[patchI].coupled())
+ {
+ label bFaceI = faceI-mesh.nInternalFaces();
+
+ // Check face in zone on both sides
+ if (myZoneFace[bFaceI] != neiZoneFace[bFaceI])
+ {
+ boundaryError = true;
+
+ if (report)
+ {
+ Pout<< " ***Problem with faceZone " << index()
+ << " named " << name()
+ << ". Face " << faceI
+ << " on coupled patch "
+ << bm[patchI].name()
+ << " is not consistent with its coupled neighbour."
+ << endl;
+ }
+ }
+
+ // Flip state should be opposite.
+ if (myZoneFlip[bFaceI] == neiZoneFlip[bFaceI])
+ {
+ boundaryError = true;
+
+ if (report)
+ {
+ Pout<< " ***Problem with faceZone " << index()
+ << " named " << name()
+ << ". Face " << faceI
+ << " on coupled patch "
+ << bm[patchI].name()
+ << " does not have consistent flipMap"
+ << " across coupled faces."
+ << endl;
+ }
+ }
+ }
+ }
+ }
+
+ return returnReduce(boundaryError, orOp<bool>());
+}
+
+
void Foam::faceZone::movePoints(const pointField& p)
{
if (patchPtr_)
diff --git a/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.H b/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.H
index f96c1dc189fb884bbe8e1d9ba34136dbb8e30003..16c7e82b09c0ad272d99d1f9d60ecd552afcf3f9 100644
--- a/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.H
+++ b/src/OpenFOAM/meshes/polyMesh/zones/faceZone/faceZone.H
@@ -302,6 +302,10 @@ public:
//- Check zone definition. Return true if in error.
bool checkDefinition(const bool report = false) const;
+ //- Check whether all procs have faces synchronised. Return
+ // true if in error.
+ bool checkParallelSync(const bool report = false) const;
+
//- Correct patch after moving points
virtual void movePoints(const pointField&);
diff --git a/src/OpenFOAM/meshes/primitiveShapes/triangle/triangleI.H b/src/OpenFOAM/meshes/primitiveShapes/triangle/triangleI.H
index 33b3cab15e67775129d8997818a299add2d687f9..e43d4b9d2948219c3c4f11d2b1eb653200609992 100644
--- a/src/OpenFOAM/meshes/primitiveShapes/triangle/triangleI.H
+++ b/src/OpenFOAM/meshes/primitiveShapes/triangle/triangleI.H
@@ -607,6 +607,18 @@ inline bool triangle<Point, PointRef>::classify
// system E0, E1
//
+ //Pout<< "alpha:" << alpha << endl;
+ //Pout<< "beta:" << beta << endl;
+ //Pout<< "hit:" << hit << endl;
+ //Pout<< "tol:" << tol << endl;
+
+ if (hit)
+ {
+ // alpha,beta might get negative due to precision errors
+ alpha = max(0.0, min(1.0, alpha));
+ beta = max(0.0, min(1.0, beta));
+ }
+
nearType = NONE;
nearLabel = -1;
diff --git a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
index baa2e5d463b10845b076713ce6112b99634dd4e1..0839e621cb1d273cb254280b2db067fe8e0459d2 100644
--- a/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
+++ b/src/autoMesh/autoHexMesh/meshRefinement/meshRefinementBaffles.C
@@ -110,7 +110,7 @@ Foam::label Foam::meshRefinement::createBaffle
-1, // masterPointID
-1, // masterEdgeID
faceI, // masterFaceID,
- false, // face flip
+ true, // face flip
neiPatch, // patch for face
zoneID, // zone for face
zoneFlip // face flip in zone
@@ -1017,7 +1017,7 @@ void Foam::meshRefinement::findCellZoneGeometric
if (namedSurfaceIndex[faceI] == -1 && (ownZone != neiZone))
{
- // Give face the zone of the owner
+ // Give face the zone of max cell zone
namedSurfaceIndex[faceI] = findIndex
(
surfaceToCellZone,
@@ -1059,7 +1059,7 @@ void Foam::meshRefinement::findCellZoneGeometric
if (namedSurfaceIndex[faceI] == -1 && (ownZone != neiZone))
{
- // Give face the zone of the owner
+ // Give face the max cell zone
namedSurfaceIndex[faceI] = findIndex
(
surfaceToCellZone,
@@ -2211,16 +2211,14 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
{
label faceI = testFaces[i];
- label own = mesh_.faceOwner()[faceI];
-
if (mesh_.isInternalFace(faceI))
{
- start[i] = cellCentres[own];
- end[i] = cellCentres[mesh_.faceNeighbour()[faceI]];
+ start[i] = cellCentres[faceOwner[faceI]];
+ end[i] = cellCentres[faceNeighbour[faceI]];
}
else
{
- start[i] = cellCentres[own];
+ start[i] = cellCentres[faceOwner[faceI]];
end[i] = neiCc[faceI-mesh_.nInternalFaces()];
}
}
@@ -2357,6 +2355,20 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
if (surfI != -1)
{
+ // Orient face zone to have slave cells in max cell zone.
+ label ownZone = cellToZone[faceOwner[faceI]];
+ label neiZone = cellToZone[faceNeighbour[faceI]];
+
+ bool flip;
+ if (ownZone == max(ownZone, neiZone))
+ {
+ flip = false;
+ }
+ else
+ {
+ flip = true;
+ }
+
meshMod.setAction
(
polyModifyFace
@@ -2369,12 +2381,31 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
-1, // patch for face
false, // remove from zone
surfaceToFaceZone[surfI], // zone for face
- false // face flip in zone
+ flip // face flip in zone
)
);
}
}
+ // Get coupled neighbour cellZone. Set to -1 on non-coupled patches.
+ labelList neiCellZone(mesh_.nFaces()-mesh_.nInternalFaces(), -1);
+ forAll(patches, patchI)
+ {
+ const polyPatch& pp = patches[patchI];
+
+ if (pp.coupled())
+ {
+ forAll(pp, i)
+ {
+ label faceI = pp.start()+i;
+ neiCellZone[faceI-mesh_.nInternalFaces()] =
+ cellToZone[mesh_.faceOwner()[faceI]];
+ }
+ }
+ }
+ syncTools::swapBoundaryFaceList(mesh_, neiCellZone, false);
+
+ // Set owner as no-flip
forAll(patches, patchI)
{
const polyPatch& pp = patches[patchI];
@@ -2387,6 +2418,19 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
if (surfI != -1)
{
+ label ownZone = cellToZone[faceOwner[faceI]];
+ label neiZone = neiCellZone[faceI-mesh_.nInternalFaces()];
+
+ bool flip;
+ if (ownZone == max(ownZone, neiZone))
+ {
+ flip = false;
+ }
+ else
+ {
+ flip = true;
+ }
+
meshMod.setAction
(
polyModifyFace
@@ -2399,7 +2443,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::meshRefinement::zonify
patchI, // patch for face
false, // remove from zone
surfaceToFaceZone[surfI], // zone for face
- false // face flip in zone
+ flip // face flip in zone
)
);
}
diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/localPointRegion.H b/src/dynamicMesh/polyTopoChange/polyTopoChange/localPointRegion.H
index cecd70d390de58cb2199b1291f170470b675f6cc..8a2eff1eb91fa3597e4e332fd7926ae520153acb 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/localPointRegion.H
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/localPointRegion.H
@@ -159,7 +159,7 @@ public:
// return nRegions_;
//}
- //- Per point that is to duplicated to the local index
+ //- Per point that is to be duplicated the local index
const Map<label>& meshPointMap() const
{
return meshPointMap_;
diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
index 5e7a0b010bec6621e7340df8853e3f516f9add28..27f81f3081f193ac4816f19b848de54c2fc69cc2 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.C
@@ -58,23 +58,6 @@ const Foam::point Foam::polyTopoChange::greatPoint
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
-// Renumber
-void Foam::polyTopoChange::renumber
-(
- const labelList& map,
- DynamicList<label>& elems
-)
-{
- forAll(elems, elemI)
- {
- if (elems[elemI] >= 0)
- {
- elems[elemI] = map[elems[elemI]];
- }
- }
-}
-
-
// Renumber with special handling for merged items (marked with <-1)
void Foam::polyTopoChange::renumberReverseMap
(
@@ -208,6 +191,20 @@ void Foam::polyTopoChange::countMap
}
+Foam::labelHashSet Foam::polyTopoChange::getSetIndices(const PackedBoolList& lst)
+{
+ labelHashSet values(lst.count());
+ forAll(lst, i)
+ {
+ if (lst[i])
+ {
+ values.insert(i);
+ }
+ }
+ return values;
+}
+
+
void Foam::polyTopoChange::writeMeshStats(const polyMesh& mesh, Ostream& os)
{
const polyBoundaryMesh& patches = mesh.boundaryMesh();
@@ -782,9 +779,11 @@ void Foam::polyTopoChange::reorderCompactFaces
renumberKey(oldToNew, faceFromPoint_);
renumberKey(oldToNew, faceFromEdge_);
- renumber(oldToNew, flipFaceFlux_);
+ inplaceReorder(oldToNew, flipFaceFlux_);
+ flipFaceFlux_.setCapacity(newSize);
renumberKey(oldToNew, faceZone_);
- renumberKey(oldToNew, faceZoneFlip_);
+ inplaceReorder(oldToNew, faceZoneFlip_);
+ faceZoneFlip_.setCapacity(newSize);
}
@@ -1097,6 +1096,18 @@ void Foam::polyTopoChange::compact
{
faces_[faceI] = faces_[faceI].reverseFace();
Swap(faceOwner_[faceI], faceNeighbour_[faceI]);
+ flipFaceFlux_[faceI] =
+ (
+ flipFaceFlux_[faceI]
+ ? 0
+ : 1
+ );
+ faceZoneFlip_[faceI] =
+ (
+ faceZoneFlip_[faceI]
+ ? 0
+ : 1
+ );
}
}
}
@@ -2302,9 +2313,9 @@ void Foam::polyTopoChange::addMesh
faceMap_.setCapacity(faceMap_.size() + nAllFaces);
faceFromPoint_.resize(faceFromPoint_.size() + nAllFaces/100);
faceFromEdge_.resize(faceFromEdge_.size() + nAllFaces/100);
- flipFaceFlux_.resize(flipFaceFlux_.size() + nAllFaces/100);
+ flipFaceFlux_.setCapacity(faces_.size() + nAllFaces);
faceZone_.resize(faceZone_.size() + nAllFaces/100);
- faceZoneFlip_.resize(faceZoneFlip_.size() + nAllFaces/100);
+ faceZoneFlip_.setCapacity(faces_.size() + nAllFaces);
// Precalc offset zones
@@ -2716,16 +2727,13 @@ Foam::label Foam::polyTopoChange::addFace
}
reverseFaceMap_.append(faceI);
- if (flipFaceFlux)
- {
- flipFaceFlux_.insert(faceI);
- }
+ flipFaceFlux_[faceI] = (flipFaceFlux ? 1 : 0);
if (zoneID >= 0)
{
faceZone_.insert(faceI, zoneID);
- faceZoneFlip_.insert(faceI, zoneFlip);
}
+ faceZoneFlip_[faceI] = (zoneFlip ? 1 : 0);
return faceI;
}
@@ -2754,14 +2762,7 @@ void Foam::polyTopoChange::modifyFace
faceNeighbour_[faceI] = nei;
region_[faceI] = patchID;
- if (flipFaceFlux)
- {
- flipFaceFlux_.insert(faceI);
- }
- else
- {
- flipFaceFlux_.erase(faceI);
- }
+ flipFaceFlux_[faceI] = (flipFaceFlux ? 1 : 0);
Map<label>::iterator faceFnd = faceZone_.find(faceI);
@@ -2770,19 +2771,17 @@ void Foam::polyTopoChange::modifyFace
if (zoneID >= 0)
{
faceFnd() = zoneID;
- faceZoneFlip_.find(faceI)() = zoneFlip;
}
else
{
faceZone_.erase(faceFnd);
- faceZoneFlip_.erase(faceI);
}
}
else if (zoneID >= 0)
{
faceZone_.insert(faceI, zoneID);
- faceZoneFlip_.insert(faceI, zoneFlip);
}
+ faceZoneFlip_[faceI] = (zoneFlip ? 1 : 0);
}
@@ -2823,9 +2822,9 @@ void Foam::polyTopoChange::removeFace(const label faceI, const label mergeFaceI)
}
faceFromEdge_.erase(faceI);
faceFromPoint_.erase(faceI);
- flipFaceFlux_.erase(faceI);
+ flipFaceFlux_[faceI] = 0;
faceZone_.erase(faceI);
- faceZoneFlip_.erase(faceI);
+ faceZoneFlip_[faceI] = 0;
}
@@ -3119,6 +3118,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::changeMesh
labelListList faceZonePointMap(mesh.faceZones().size());
calcFaceZonePointMap(mesh, oldFaceZoneMeshPointMaps, faceZonePointMap);
+ labelHashSet flipFaceFluxSet(getSetIndices(flipFaceFlux_));
return autoPtr<mapPolyMesh>
(
@@ -3147,7 +3147,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::changeMesh
reverseFaceMap_,
reverseCellMap_,
- flipFaceFlux_,
+ flipFaceFluxSet,
patchPointMap,
@@ -3410,6 +3410,8 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::makeMesh
writeMeshStats(mesh, Pout);
}
+ labelHashSet flipFaceFluxSet(getSetIndices(flipFaceFlux_));
+
return autoPtr<mapPolyMesh>
(
new mapPolyMesh
@@ -3437,7 +3439,7 @@ Foam::autoPtr<Foam::mapPolyMesh> Foam::polyTopoChange::makeMesh
reverseFaceMap_,
reverseCellMap_,
- flipFaceFlux_,
+ flipFaceFluxSet,
patchPointMap,
diff --git a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.H b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.H
index 9d0dce468c6cb288b2659587a5a5100931195fb8..77801e21f0dc33b703585f15ef3ffbd65a5c70ad 100644
--- a/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.H
+++ b/src/dynamicMesh/polyTopoChange/polyTopoChange/polyTopoChange.H
@@ -171,13 +171,13 @@ class polyTopoChange
Map<label> faceFromEdge_;
//- In mapping whether to reverse the flux.
- labelHashSet flipFaceFlux_;
+ PackedBoolList flipFaceFlux_;
//- Zone of face
Map<label> faceZone_;
//- Orientation of face in zone
- Map<bool> faceZoneFlip_;
+ PackedBoolList faceZoneFlip_;
//- Active faces
label nActiveFaces_;
@@ -216,8 +216,7 @@ class polyTopoChange
template<class T>
static void renumberKey(const labelList& map, Map<T>&);
- //- Renumber elements of list according to map
- static void renumber(const labelList&, DynamicList<label>&);
+ //- Renumber elements of container according to map
static void renumber(const labelList&, labelHashSet&);
//- Special handling of reverse maps which have <-1 in them
static void renumberReverseMap(const labelList&, DynamicList<label>&);
@@ -225,6 +224,9 @@ class polyTopoChange
//- Renumber & compact elements of list according to map
static void renumberCompact(const labelList&, labelList&);
+ //- Get all set elements as a labelHashSet
+ static labelHashSet getSetIndices(const PackedBoolList&);
+
//- Count number of added and removed quantities from maps.
static void countMap
(
diff --git a/src/finiteVolume/Make/files b/src/finiteVolume/Make/files
index 313110bd43ad9541a65a0d4199803aa3420141c3..37b59c523a3e541665964c469a5fbe75bee38012 100644
--- a/src/finiteVolume/Make/files
+++ b/src/finiteVolume/Make/files
@@ -109,7 +109,6 @@ $(derivedFvPatchFields)/directMappedFixedValue/directMappedFixedValueFvPatchFiel
$(derivedFvPatchFields)/directMappedVelocityFluxFixedValue/directMappedVelocityFluxFixedValueFvPatchField.C
$(derivedFvPatchFields)/fan/fanFvPatchFields.C
$(derivedFvPatchFields)/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C
-$(derivedFvPatchFields)/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
$(derivedFvPatchFields)/fixedFluxPressure/fixedFluxPressureFvPatchScalarField.C
$(derivedFvPatchFields)/fixedInternalValueFvPatchField/fixedInternalValueFvPatchFields.C
$(derivedFvPatchFields)/fixedNormalSlip/fixedNormalSlipFvPatchFields.C
@@ -148,6 +147,7 @@ $(derivedFvPatchFields)/turbulentInlet/turbulentInletFvPatchFields.C
$(derivedFvPatchFields)/turbulentIntensityKineticEnergyInlet/turbulentIntensityKineticEnergyInletFvPatchScalarField.C
$(derivedFvPatchFields)/uniformFixedValue/uniformFixedValueFvPatchFields.C
$(derivedFvPatchFields)/waveTransmissive/waveTransmissiveFvPatchFields.C
+$(derivedFvPatchFields)/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.C
fvsPatchFields = fields/fvsPatchFields
$(fvsPatchFields)/fvsPatchField/fvsPatchFields.C
diff --git a/src/finiteVolume/cfdTools/general/findRefCell/findRefCell.C b/src/finiteVolume/cfdTools/general/findRefCell/findRefCell.C
index 370b13747d204dad917ba3da9b4bdc6af2176252..3d92d45ce7de3210f3c4d79b0f391cbefaced773 100644
--- a/src/finiteVolume/cfdTools/general/findRefCell/findRefCell.C
+++ b/src/finiteVolume/cfdTools/general/findRefCell/findRefCell.C
@@ -92,6 +92,7 @@ void Foam::setRefCell
dict
) << "Unable to set reference cell for field " << field.name()
<< nl << " Reference point " << refPointName
+ << " " << refPointi
<< " found on " << sumHasRef << " domains (should be one)"
<< nl << exit(FatalIOError);
}
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C b/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
deleted file mode 100644
index 9a75eed1688a05b8c3f308220f2033a7bb6f05d8..0000000000000000000000000000000000000000
--- a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
+++ /dev/null
@@ -1,149 +0,0 @@
-/*---------------------------------------------------------------------------*\
- ========= |
- \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
- \\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
- \\/ M anipulation |
--------------------------------------------------------------------------------
-License
- This file is part of OpenFOAM.
-
- OpenFOAM is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2 of the License, or (at your
- option) any later version.
-
- OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- for more details.
-
- You should have received a copy of the GNU General Public License
- along with OpenFOAM; if not, write to the Free Software Foundation,
- Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-\*---------------------------------------------------------------------------*/
-
-#include "fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.H"
-#include "addToRunTimeSelectionTable.H"
-#include "fvPatchFieldMapper.H"
-#include "volFields.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-namespace Foam
-{
-
-// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
-
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
-(
- const fvPatch& p,
- const DimensionedField<scalar, volMesh>& iF
-)
-:
- fixedGradientFvPatchScalarField(p, iF)
-{}
-
-
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
-(
- const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField& ptf,
- const fvPatch& p,
- const DimensionedField<scalar, volMesh>& iF,
- const fvPatchFieldMapper& mapper
-)
-:
- fixedGradientFvPatchScalarField(ptf, p, iF, mapper)
-{}
-
-
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
-(
- const fvPatch& p,
- const DimensionedField<scalar, volMesh>& iF,
- const dictionary&
-)
-:
- fixedGradientFvPatchScalarField(p, iF)
-{
- fvPatchField<scalar>::operator=(patchInternalField());
- gradient() = 0.0;
-}
-
-
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
-(
- const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField& wbppsf
-)
-:
- fixedGradientFvPatchScalarField(wbppsf)
-{}
-
-
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::
-fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
-(
- const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField& wbppsf,
- const DimensionedField<scalar, volMesh>& iF
-)
-:
- fixedGradientFvPatchScalarField(wbppsf, iF)
-{}
-
-
-// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
-
-void fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::updateCoeffs()
-{
- if (updated())
- {
- return;
- }
-
- const dictionary& environmentalProperties
- = db().lookupObject<IOdictionary>("environmentalProperties");
-
- dimensionedVector g(environmentalProperties.lookup("g"));
-
- const dictionary& transportProperties
- = db().lookupObject<IOdictionary>("transportProperties");
-
- dimensionedScalar beta(transportProperties.lookup("beta"));
-
- const fvPatchField<scalar>& T =
- patch().lookupPatchField<volScalarField, scalar>("T");
-
- gradient() = beta.value()*T.snGrad()*(g.value() & patch().Cf());
-
- fixedGradientFvPatchScalarField::updateCoeffs();
-}
-
-
-void fixedFluxBoussinesqBuoyantPressureFvPatchScalarField::write
-(
- Ostream& os
-) const
-{
- fixedGradientFvPatchScalarField::write(os);
- writeEntry("value", os);
-}
-
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-makePatchTypeField
-(
- fvPatchScalarField,
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
-);
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-} // End namespace Foam
-
-// ************************************************************************* //
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C b/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C
index b6f48ff6ada8e214e41f83c848bafabdb32de46e..279918b47af95cdb9d91b7344ff5844af91888bd 100644
--- a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C
+++ b/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.C
@@ -43,56 +43,61 @@ fixedFluxBuoyantPressureFvPatchScalarField
const DimensionedField<scalar, volMesh>& iF
)
:
- fixedGradientFvPatchScalarField(p, iF)
+ fixedGradientFvPatchScalarField(p, iF),
+ rhoName_("rho")
{}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
- const fixedFluxBuoyantPressureFvPatchScalarField& ptf,
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
- const fvPatchFieldMapper& mapper
+ const dictionary& dict
)
:
- fixedGradientFvPatchScalarField(ptf, p, iF, mapper)
-{}
+ fixedGradientFvPatchScalarField(p, iF),
+ rhoName_(dict.lookupOrDefault<word>("rho", "rho"))
+{
+ fvPatchField<scalar>::operator=(patchInternalField());
+ gradient() = 0.0;
+}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
+ const fixedFluxBuoyantPressureFvPatchScalarField& ptf,
const fvPatch& p,
const DimensionedField<scalar, volMesh>& iF,
- const dictionary&
+ const fvPatchFieldMapper& mapper
)
:
- fixedGradientFvPatchScalarField(p, iF)
-{
- fvPatchField<scalar>::operator=(patchInternalField());
- gradient() = 0.0;
-}
+ fixedGradientFvPatchScalarField(ptf, p, iF, mapper),
+ rhoName_(ptf.rhoName_)
+{}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
- const fixedFluxBuoyantPressureFvPatchScalarField& wbppsf
+ const fixedFluxBuoyantPressureFvPatchScalarField& ptf
)
:
- fixedGradientFvPatchScalarField(wbppsf)
+ fixedGradientFvPatchScalarField(ptf),
+ rhoName_(ptf.rhoName_)
{}
fixedFluxBuoyantPressureFvPatchScalarField::
fixedFluxBuoyantPressureFvPatchScalarField
(
- const fixedFluxBuoyantPressureFvPatchScalarField& wbppsf,
+ const fixedFluxBuoyantPressureFvPatchScalarField& ptf,
const DimensionedField<scalar, volMesh>& iF
)
:
- fixedGradientFvPatchScalarField(wbppsf, iF)
+ fixedGradientFvPatchScalarField(ptf, iF),
+ rhoName_(ptf.rhoName_)
{}
@@ -111,7 +116,7 @@ void fixedFluxBuoyantPressureFvPatchScalarField::updateCoeffs()
dimensionedVector g(environmentalProperties.lookup("g"));
const fvPatchField<scalar>& rho =
- patch().lookupPatchField<volScalarField, scalar>("rho");
+ patch().lookupPatchField<volScalarField, scalar>(rhoName_);
// If the variable name is "pd" assume it is p - rho*g.h
// and set the gradient appropriately.
@@ -132,6 +137,7 @@ void fixedFluxBuoyantPressureFvPatchScalarField::updateCoeffs()
void fixedFluxBuoyantPressureFvPatchScalarField::write(Ostream& os) const
{
fixedGradientFvPatchScalarField::write(os);
+ os.writeKeyword("rho") << rhoName_ << token::END_STATEMENT << nl;
writeEntry("value", os);
}
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.H b/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.H
index 8e433cb8f167f0304ec840bb270c4521c9230e5b..ec5dc7dd990d69170621c253ca5b73b5d9e91b74 100644
--- a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.H
+++ b/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBuoyantPressure/fixedFluxBuoyantPressureFvPatchScalarField.H
@@ -55,6 +55,11 @@ class fixedFluxBuoyantPressureFvPatchScalarField
:
public fixedGradientFvPatchScalarField
{
+ // Private data
+
+ //- Name of the density field used to calculate the buoyancy force
+ word rhoName_;
+
public:
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/totalPressure/totalPressureFvPatchScalarField.C b/src/finiteVolume/fields/fvPatchFields/derived/totalPressure/totalPressureFvPatchScalarField.C
index 76267d4fa6a86f2083f6720b2eb58fe255610d4d..56ee8a0753d38e9eef05c766677ca1d4eccfa64d 100644
--- a/src/finiteVolume/fields/fvPatchFields/derived/totalPressure/totalPressureFvPatchScalarField.C
+++ b/src/finiteVolume/fields/fvPatchFields/derived/totalPressure/totalPressureFvPatchScalarField.C
@@ -30,7 +30,6 @@ License
#include "volFields.H"
#include "surfaceFields.H"
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.C b/src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.C
new file mode 100644
index 0000000000000000000000000000000000000000..dfda8caf521d7e6f3733d3e4bf640fbfd58ee22f
--- /dev/null
+++ b/src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.C
@@ -0,0 +1,168 @@
+/*---------------------------------------------------------------------------*\
+ ========= |
+ \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
+ \\ / O peration |
+ \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\/ M anipulation |
+-------------------------------------------------------------------------------
+License
+ This file is part of OpenFOAM.
+
+ OpenFOAM is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2 of the License, or (at your
+ option) any later version.
+
+ OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with OpenFOAM; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+#include "uniformDensityHydrostaticPressureFvPatchScalarField.H"
+#include "addToRunTimeSelectionTable.H"
+#include "fvPatchFieldMapper.H"
+#include "volFields.H"
+#include "surfaceFields.H"
+
+
+// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
+
+Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
+uniformDensityHydrostaticPressureFvPatchScalarField
+(
+ const fvPatch& p,
+ const DimensionedField<scalar, volMesh>& iF
+)
+:
+ fixedValueFvPatchScalarField(p, iF),
+ rho_(0.0),
+ pRefValue_(0.0),
+ pRefPoint_(vector::zero)
+{}
+
+
+Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
+uniformDensityHydrostaticPressureFvPatchScalarField
+(
+ const fvPatch& p,
+ const DimensionedField<scalar, volMesh>& iF,
+ const dictionary& dict
+)
+:
+ fixedValueFvPatchScalarField(p, iF),
+ rho_(readScalar(dict.lookup("rho"))),
+ pRefValue_(readScalar(dict.lookup("pRefValue"))),
+ pRefPoint_(dict.lookup("pRefPoint"))
+{
+ if (dict.found("value"))
+ {
+ fvPatchField<scalar>::operator=
+ (
+ scalarField("value", dict, p.size())
+ );
+ }
+ else
+ {
+ evaluate();
+ }
+}
+
+
+Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
+uniformDensityHydrostaticPressureFvPatchScalarField
+(
+ const uniformDensityHydrostaticPressureFvPatchScalarField& ptf,
+ const fvPatch& p,
+ const DimensionedField<scalar, volMesh>& iF,
+ const fvPatchFieldMapper& mapper
+)
+:
+ fixedValueFvPatchScalarField(ptf, p, iF, mapper),
+ rho_(ptf.rho_),
+ pRefValue_(ptf.pRefValue_),
+ pRefPoint_(ptf.pRefPoint_)
+{}
+
+
+Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
+uniformDensityHydrostaticPressureFvPatchScalarField
+(
+ const uniformDensityHydrostaticPressureFvPatchScalarField& ptf
+)
+:
+ fixedValueFvPatchScalarField(ptf),
+ rho_(ptf.rho_),
+ pRefValue_(ptf.pRefValue_),
+ pRefPoint_(ptf.pRefPoint_)
+{}
+
+
+Foam::uniformDensityHydrostaticPressureFvPatchScalarField::
+uniformDensityHydrostaticPressureFvPatchScalarField
+(
+ const uniformDensityHydrostaticPressureFvPatchScalarField& ptf,
+ const DimensionedField<scalar, volMesh>& iF
+)
+:
+ fixedValueFvPatchScalarField(ptf, iF),
+ rho_(ptf.rho_),
+ pRefValue_(ptf.pRefValue_),
+ pRefPoint_(ptf.pRefPoint_)
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
+
+void Foam::uniformDensityHydrostaticPressureFvPatchScalarField::updateCoeffs()
+{
+ if (updated())
+ {
+ return;
+ }
+
+ const dictionary& environmentalProperties
+ = db().lookupObject<IOdictionary>("environmentalProperties");
+
+ dimensionedVector g(environmentalProperties.lookup("g"));
+
+ operator==
+ (
+ pRefValue_
+ + rho_*((g.value() & patch().Cf()) - (g.value() & pRefPoint_))
+ );
+
+ fixedValueFvPatchScalarField::updateCoeffs();
+}
+
+
+void Foam::uniformDensityHydrostaticPressureFvPatchScalarField::write
+(
+ Ostream& os
+) const
+{
+ fvPatchScalarField::write(os);
+ os.writeKeyword("rho") << rho_ << token::END_STATEMENT << nl;
+ os.writeKeyword("pRefValue") << pRefValue_ << token::END_STATEMENT << nl;
+ os.writeKeyword("pRefPoint") << pRefPoint_ << token::END_STATEMENT << nl;
+ writeEntry("value", os);
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+ makePatchTypeField
+ (
+ fvPatchScalarField,
+ uniformDensityHydrostaticPressureFvPatchScalarField
+ );
+}
+
+// ************************************************************************* //
diff --git a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.H b/src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.H
similarity index 53%
rename from src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.H
rename to src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.H
index 094f8805606650a1f2b087d1404dcad78fd1c680..8b129fe3ab3ac5e9bc834f38f9124ffd53742454 100644
--- a/src/finiteVolume/fields/fvPatchFields/derived/fixedFluxBoussinesqBuoyantPressure/fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.H
+++ b/src/finiteVolume/fields/fvPatchFields/derived/uniformDensityHydrostaticPressure/uniformDensityHydrostaticPressureFvPatchScalarField.H
@@ -23,23 +23,24 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
- Foam::fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ Foam::uniformDensityHydrostaticPressureFvPatchScalarField
Description
- Boundary condition on pressure for use with buoyant solvers employing the
- Boussinesq approximation to balance the flux generated by the temperature
- gradient.
+ Hydrostatic pressure boundary condition calculated as
+
+ pRefValue + rho*g.(x - pRefPoint)
+
+ where rho is provided and assumed uniform.
SourceFiles
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField.C
+ uniformDensityHydrostaticPressureFvPatchScalarField.C
\*---------------------------------------------------------------------------*/
-#ifndef fixedFluxBoussinesqBuoyantPressureFvPatchScalarFields_H
-#define fixedFluxBoussinesqBuoyantPressureFvPatchScalarFields_H
+#ifndef uniformDensityHydrostaticPressureFvPatchScalarField_H
+#define uniformDensityHydrostaticPressureFvPatchScalarField_H
-#include "fvPatchFields.H"
-#include "fixedGradientFvPatchFields.H"
+#include "fixedValueFvPatchFields.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -47,30 +48,42 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class fixedFluxBoussinesqBuoyantPressureFvPatchScalarField Declaration
+ Class uniformDensityHydrostaticPressureFvPatch Declaration
\*---------------------------------------------------------------------------*/
-class fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+class uniformDensityHydrostaticPressureFvPatchScalarField
:
- public fixedGradientFvPatchScalarField
+ public fixedValueFvPatchScalarField
{
+ // Private data
+
+ //- Constant density in the far-field
+ scalar rho_;
+
+ //- Reference pressure
+ scalar pRefValue_;
+
+ //- Reference pressure location
+ vector pRefPoint_;
+
+
public:
//- Runtime type information
- TypeName("fixedFluxBoussinesqBuoyantPressure");
+ TypeName("uniformDensityHydrostaticPressure");
// Constructors
//- Construct from patch and internal field
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ uniformDensityHydrostaticPressureFvPatchScalarField
(
const fvPatch&,
const DimensionedField<scalar, volMesh>&
);
//- Construct from patch, internal field and dictionary
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ uniformDensityHydrostaticPressureFvPatchScalarField
(
const fvPatch&,
const DimensionedField<scalar, volMesh>&,
@@ -78,20 +91,19 @@ public:
);
//- Construct by mapping given
- // fixedFluxBoussinesqBuoyantPressureFvPatchScalarField onto a new
- // patch
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ // uniformDensityHydrostaticPressureFvPatchScalarField onto a new patch
+ uniformDensityHydrostaticPressureFvPatchScalarField
(
- const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField&,
+ const uniformDensityHydrostaticPressureFvPatchScalarField&,
const fvPatch&,
const DimensionedField<scalar, volMesh>&,
const fvPatchFieldMapper&
);
//- Construct as copy
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ uniformDensityHydrostaticPressureFvPatchScalarField
(
- const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField&
+ const uniformDensityHydrostaticPressureFvPatchScalarField&
);
//- Construct and return a clone
@@ -99,14 +111,14 @@ public:
{
return tmp<fvPatchScalarField>
(
- new fixedFluxBoussinesqBuoyantPressureFvPatchScalarField(*this)
+ new uniformDensityHydrostaticPressureFvPatchScalarField(*this)
);
}
//- Construct as copy setting internal field reference
- fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ uniformDensityHydrostaticPressureFvPatchScalarField
(
- const fixedFluxBoussinesqBuoyantPressureFvPatchScalarField&,
+ const uniformDensityHydrostaticPressureFvPatchScalarField&,
const DimensionedField<scalar, volMesh>&
);
@@ -118,7 +130,7 @@ public:
{
return tmp<fvPatchScalarField>
(
- new fixedFluxBoussinesqBuoyantPressureFvPatchScalarField
+ new uniformDensityHydrostaticPressureFvPatchScalarField
(
*this,
iF
@@ -129,8 +141,52 @@ public:
// Member functions
- //- Update the coefficients associated with the patch field
- virtual void updateCoeffs();
+ // Access
+
+ //- Return the constant density in the far-field
+ scalar rho() const
+ {
+ return rho_;
+ }
+
+ //- Return reference to the constant density in the far-field
+ // to allow adjustment
+ scalar& rho()
+ {
+ return rho_;
+ }
+
+ //- Return the reference pressure
+ scalar pRefValue() const
+ {
+ return pRefValue_;
+ }
+
+ //- Return reference to the reference pressure to allow adjustment
+ scalar& pRefValue()
+ {
+ return pRefValue_;
+ }
+
+ //- Return the pressure reference location
+ const vector& pRefPoint() const
+ {
+ return pRefPoint_;
+ }
+
+ //- Return reference to the pressure reference location
+ // to allow adjustment
+ vector& pRefPoint()
+ {
+ return pRefPoint_;
+ }
+
+
+ // Evaluation functions
+
+ //- Update the coefficients associated with the patch field
+ virtual void updateCoeffs();
+
//- Write
virtual void write(Ostream&) const;
diff --git a/src/fvMotionSolver/Make/files b/src/fvMotionSolver/Make/files
index 41f31c0ecc79dd3972e667e08041002a0e9099ae..f229ae322ef04b4bf61dd4bb0eb336fed3764e48 100644
--- a/src/fvMotionSolver/Make/files
+++ b/src/fvMotionSolver/Make/files
@@ -30,5 +30,6 @@ pointPatchFields/derived/angularOscillatingVelocity/angularOscillatingVelocityPo
pointPatchFields/derived/oscillatingDisplacement/oscillatingDisplacementPointPatchVectorField.C
pointPatchFields/derived/angularOscillatingDisplacement/angularOscillatingDisplacementPointPatchVectorField.C
pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.C
+pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.C
LIB = $(FOAM_LIBBIN)/libfvMotionSolvers
diff --git a/src/fvMotionSolver/pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.C b/src/fvMotionSolver/pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.C
new file mode 100644
index 0000000000000000000000000000000000000000..bbafb189faa97eba4faea0aa5e69ad1d163e70fd
--- /dev/null
+++ b/src/fvMotionSolver/pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.C
@@ -0,0 +1,514 @@
+/*---------------------------------------------------------------------------*\
+ ========= |
+ \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
+ \\ / O peration |
+ \\ / A nd | Copyright (C) 1991-2007 OpenCFD Ltd.
+ \\/ M anipulation |
+-------------------------------------------------------------------------------
+License
+ This file is part of OpenFOAM.
+
+ OpenFOAM is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2 of the License, or (at your
+ option) any later version.
+
+ OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with OpenFOAM; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+#include "surfaceDisplacementPointPatchVectorField.H"
+#include "addToRunTimeSelectionTable.H"
+#include "Time.H"
+#include "transformField.H"
+#include "fvMesh.H"
+#include "displacementLaplacianFvMotionSolver.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+template<>
+const char*
+NamedEnum<surfaceDisplacementPointPatchVectorField::projectMode, 3>::
+names[] =
+{
+ "nearest",
+ "pointNormal",
+ "fixedNormal"
+};
+
+const NamedEnum<surfaceDisplacementPointPatchVectorField::projectMode, 3>
+ surfaceDisplacementPointPatchVectorField::projectModeNames_;
+
+
+// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
+
+void surfaceDisplacementPointPatchVectorField::calcProjection
+(
+ vectorField& displacement
+) const
+{
+ const polyMesh& mesh = patch().boundaryMesh().mesh()();
+ const pointField& localPoints = patch().localPoints();
+ const labelList& meshPoints = patch().meshPoints();
+
+ //const scalar deltaT = mesh.time().deltaT().value();
+
+ // Construct large enough vector in direction of projectDir so
+ // we're guaranteed to hit something.
+
+ //- Per point projection vector:
+ const scalar projectLen = mag(mesh.bounds().max()-mesh.bounds().min());
+
+ // For case of fixed projection vector:
+ vector projectVec;
+ if (projectMode_ == FIXEDNORMAL)
+ {
+ vector n = projectDir_/mag(projectDir_);
+ projectVec = projectLen*n;
+ }
+
+
+ // Get fixed points (bit of a hack)
+ const pointZone* zonePtr = NULL;
+
+ if (frozenPointsZone_.size() > 0)
+ {
+ const pointZoneMesh& pZones = mesh.pointZones();
+
+ zonePtr = &pZones[pZones.findZoneID(frozenPointsZone_)];
+
+ Pout<< "surfaceDisplacementPointPatchVectorField : Fixing all "
+ << zonePtr->size() << " points in pointZone " << zonePtr->name()
+ << endl;
+ }
+
+ // Get the starting locations from the motionSolver
+ const pointField& points0 = mesh.lookupObject<displacementFvMotionSolver>
+ (
+ "dynamicMeshDict"
+ ).points0();
+
+
+ pointField start(meshPoints.size());
+ forAll(start, i)
+ {
+ start[i] = points0[meshPoints[i]] + displacement[i];
+ }
+
+ label nNotProjected = 0;
+
+ if (projectMode_ == NEAREST)
+ {
+ List<pointIndexHit> nearest;
+ labelList hitSurfaces;
+ surfaces().findNearest
+ (
+ start,
+ scalarField(start.size(), sqr(projectLen)),
+ hitSurfaces,
+ nearest
+ );
+
+ forAll(nearest, i)
+ {
+ if (zonePtr && (zonePtr->whichPoint(meshPoints[i]) >= 0))
+ {
+ // Fixed point. Reset to point0 location.
+ displacement[i] = points0[meshPoints[i]] - localPoints[i];
+ }
+ else if (nearest[i].hit())
+ {
+ displacement[i] =
+ nearest[i].hitPoint()
+ - points0[meshPoints[i]];
+ }
+ else
+ {
+ nNotProjected++;
+
+ if (debug)
+ {
+ Pout<< " point:" << meshPoints[i]
+ << " coord:" << localPoints[i]
+ << " did not find any surface within " << projectLen
+ << endl;
+ }
+ }
+ }
+ }
+ else
+ {
+ // Do tests on all points. Combine later on.
+
+ // 1. Check if already on surface
+ List<pointIndexHit> nearest;
+ {
+ labelList nearestSurface;
+ surfaces().findNearest
+ (
+ start,
+ scalarField(start.size(), sqr(SMALL)),
+ nearestSurface,
+ nearest
+ );
+ }
+
+ // 2. intersection. (combined later on with information from nearest
+ // above)
+ vectorField projectVecs(start.size(), projectVec);
+
+ if (projectMode_ == POINTNORMAL)
+ {
+ projectVecs = projectLen*patch().pointNormals();
+ }
+
+ // Knock out any wedge component
+ scalarField offset(start.size(), 0.0);
+ if (wedgePlane_ >= 0 && wedgePlane_ <= vector::nComponents)
+ {
+ forAll(offset, i)
+ {
+ offset[i] = start[i][wedgePlane_];
+ start[i][wedgePlane_] = 0;
+ projectVecs[i][wedgePlane_] = 0;
+ }
+ }
+
+ List<pointIndexHit> rightHit;
+ {
+ labelList rightSurf;
+ surfaces().findAnyIntersection
+ (
+ start,
+ start+projectVecs,
+ rightSurf,
+ rightHit
+ );
+ }
+
+ List<pointIndexHit> leftHit;
+ {
+ labelList leftSurf;
+ surfaces().findAnyIntersection
+ (
+ start,
+ start-projectVecs,
+ leftSurf,
+ leftHit
+ );
+ }
+
+ // 3. Choose either -fixed, nearest, right, left.
+ forAll(displacement, i)
+ {
+ if (zonePtr && (zonePtr->whichPoint(meshPoints[i]) >= 0))
+ {
+ // Fixed point. Reset to point0 location.
+ displacement[i] = points0[meshPoints[i]] - localPoints[i];
+ }
+ else if (nearest[i].hit())
+ {
+ // Found nearest.
+ displacement[i] =
+ nearest[i].hitPoint()
+ - points0[meshPoints[i]];
+ }
+ else
+ {
+ pointIndexHit interPt;
+
+ if (rightHit[i].hit())
+ {
+ if (leftHit[i].hit())
+ {
+ if
+ (
+ magSqr(rightHit[i].hitPoint()-start[i])
+ < magSqr(leftHit[i].hitPoint()-start[i])
+ )
+ {
+ interPt = rightHit[i];
+ }
+ else
+ {
+ interPt = leftHit[i];
+ }
+ }
+ else
+ {
+ interPt = rightHit[i];
+ }
+ }
+ else
+ {
+ if (leftHit[i].hit())
+ {
+ interPt = leftHit[i];
+ }
+ }
+
+
+ if (interPt.hit())
+ {
+ if (wedgePlane_ >= 0 && wedgePlane_ <= vector::nComponents)
+ {
+ interPt.rawPoint()[wedgePlane_] += offset[i];
+ }
+ displacement[i] = interPt.rawPoint()-points0[meshPoints[i]];
+ }
+ else
+ {
+ nNotProjected++;
+
+ if (debug)
+ {
+ Pout<< " point:" << meshPoints[i]
+ << " coord:" << localPoints[i]
+ << " did not find any intersection between"
+ << " ray from " << start[i]-projectVecs[i]
+ << " to " << start[i]+projectVecs[i] << endl;
+ }
+ }
+ }
+ }
+ }
+
+ reduce(nNotProjected, sumOp<label>());
+
+ if (nNotProjected > 0)
+ {
+ Info<< "surfaceDisplacement :"
+ << " on patch " << patch().name()
+ << " did not project " << nNotProjected
+ << " out of " << returnReduce(localPoints.size(), sumOp<label>())
+ << " points." << endl;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
+
+surfaceDisplacementPointPatchVectorField::
+surfaceDisplacementPointPatchVectorField
+(
+ const pointPatch& p,
+ const DimensionedField<vector, pointMesh>& iF
+)
+:
+ fixedValuePointPatchVectorField(p, iF),
+ velocity_(vector::zero),
+ projectMode_(NEAREST),
+ projectDir_(vector::zero),
+ wedgePlane_(-1)
+{}
+
+
+surfaceDisplacementPointPatchVectorField::
+surfaceDisplacementPointPatchVectorField
+(
+ const pointPatch& p,
+ const DimensionedField<vector, pointMesh>& iF,
+ const dictionary& dict
+)
+:
+ fixedValuePointPatchVectorField(p, iF, dict),
+ velocity_(dict.lookup("velocity")),
+ surfacesDict_(dict.subDict("geometry")),
+ projectMode_(projectModeNames_.read(dict.lookup("projectMode"))),
+ projectDir_(dict.lookup("projectDirection")),
+ wedgePlane_(readLabel(dict.lookup("wedgePlane"))),
+ frozenPointsZone_(dict.lookupOrDefault("frozenPointsZone", word::null))
+{
+ if (velocity_.x() < 0 || velocity_.y() < 0 || velocity_.z() < 0)
+ {
+ FatalErrorIn
+ (
+ "surfaceDisplacementPointPatchVectorField::\n"
+ "surfaceDisplacementPointPatchVectorField\n"
+ "(\n"
+ " const pointPatch& p,\n"
+ " const DimensionedField<vector, pointMesh>& iF,\n"
+ " const dictionary& dict\n"
+ ")\n"
+ ) << "All components of velocity have to be positive : "
+ << velocity_ << nl
+ << "Set velocity components to a great value if no clipping"
+ << " necessary." << exit(FatalError);
+ }
+}
+
+
+surfaceDisplacementPointPatchVectorField::
+surfaceDisplacementPointPatchVectorField
+(
+ const surfaceDisplacementPointPatchVectorField& ppf,
+ const pointPatch& p,
+ const DimensionedField<vector, pointMesh>& iF,
+ const pointPatchFieldMapper& mapper
+)
+:
+ fixedValuePointPatchVectorField(ppf, p, iF, mapper),
+ velocity_(ppf.velocity_),
+ surfacesDict_(ppf.surfacesDict_),
+ projectMode_(ppf.projectMode_),
+ projectDir_(ppf.projectDir_),
+ wedgePlane_(ppf.wedgePlane_),
+ frozenPointsZone_(ppf.frozenPointsZone_)
+{}
+
+
+surfaceDisplacementPointPatchVectorField::
+surfaceDisplacementPointPatchVectorField
+(
+ const surfaceDisplacementPointPatchVectorField& ppf
+)
+:
+ fixedValuePointPatchVectorField(ppf),
+ velocity_(ppf.velocity_),
+ surfacesDict_(ppf.surfacesDict_),
+ projectMode_(ppf.projectMode_),
+ projectDir_(ppf.projectDir_),
+ wedgePlane_(ppf.wedgePlane_),
+ frozenPointsZone_(ppf.frozenPointsZone_)
+{}
+
+
+surfaceDisplacementPointPatchVectorField::
+surfaceDisplacementPointPatchVectorField
+(
+ const surfaceDisplacementPointPatchVectorField& ppf,
+ const DimensionedField<vector, pointMesh>& iF
+)
+:
+ fixedValuePointPatchVectorField(ppf, iF),
+ velocity_(ppf.velocity_),
+ surfacesDict_(ppf.surfacesDict_),
+ projectMode_(ppf.projectMode_),
+ projectDir_(ppf.projectDir_),
+ wedgePlane_(ppf.wedgePlane_),
+ frozenPointsZone_(ppf.frozenPointsZone_)
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
+
+const searchableSurfaces&
+surfaceDisplacementPointPatchVectorField::surfaces() const
+{
+ if (surfacesPtr_.empty())
+ {
+ surfacesPtr_.reset
+ (
+ new searchableSurfaces
+ (
+ IOobject
+ (
+ "abc", // dummy name
+ db().time().constant(), // directory
+ "triSurface", // instance
+ db().time(), // registry
+ IOobject::MUST_READ,
+ IOobject::NO_WRITE
+ ),
+ surfacesDict_
+ )
+ );
+ }
+ return surfacesPtr_();
+}
+
+
+void surfaceDisplacementPointPatchVectorField::updateCoeffs()
+{
+ if (this->updated())
+ {
+ return;
+ }
+
+ const polyMesh& mesh = patch().boundaryMesh().mesh()();
+
+ vectorField currentDisplacement = this->patchInternalField();
+
+ // Calculate intersections with surface w.r.t points0.
+ vectorField displacement(currentDisplacement);
+ calcProjection(displacement);
+
+ // offset wrt current displacement
+ vectorField offset = displacement-currentDisplacement;
+
+ // Clip offset to maximum displacement possible: velocity*timestep
+
+ const scalar deltaT = mesh.time().deltaT().value();
+ const vector clipVelocity = velocity_*deltaT;
+
+ forAll(displacement, i)
+ {
+ vector& d = offset[i];
+
+ for (direction cmpt = 0; cmpt < vector::nComponents; cmpt++)
+ {
+ if (d[cmpt] < 0)
+ {
+ d[cmpt] = max(d[cmpt], -clipVelocity[cmpt]);
+ }
+ else
+ {
+ d[cmpt] = min(d[cmpt], clipVelocity[cmpt]);
+ }
+ }
+ }
+
+ this->operator==(currentDisplacement+offset);
+
+ fixedValuePointPatchVectorField::updateCoeffs();
+}
+
+
+void surfaceDisplacementPointPatchVectorField::write(Ostream& os) const
+{
+ fixedValuePointPatchVectorField::write(os);
+ os.writeKeyword("velocity") << velocity_
+ << token::END_STATEMENT << nl;
+ os.writeKeyword("geometry") << surfacesDict_
+ << token::END_STATEMENT << nl;
+ os.writeKeyword("projectMode") << projectModeNames_[projectMode_]
+ << token::END_STATEMENT << nl;
+ os.writeKeyword("projectDirection") << projectDir_
+ << token::END_STATEMENT << nl;
+ os.writeKeyword("wedgePlane") << wedgePlane_
+ << token::END_STATEMENT << nl;
+ if (frozenPointsZone_ != word::null)
+ {
+ os.writeKeyword("frozenPointsZone") << frozenPointsZone_
+ << token::END_STATEMENT << nl;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+makePointPatchTypeField
+(
+ fixedValuePointPatchVectorField,
+ surfaceDisplacementPointPatchVectorField
+);
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/src/fvMotionSolver/pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.H b/src/fvMotionSolver/pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.H
new file mode 100644
index 0000000000000000000000000000000000000000..7b3ecd7c2ff4437b825b1b17238ce0ba2cc6c10f
--- /dev/null
+++ b/src/fvMotionSolver/pointPatchFields/derived/surfaceDisplacement/surfaceDisplacementPointPatchVectorField.H
@@ -0,0 +1,223 @@
+/*---------------------------------------------------------------------------*\
+ ========= |
+ \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
+ \\ / O peration |
+ \\ / A nd | Copyright (C) 1991-2007 OpenCFD Ltd.
+ \\/ M anipulation |
+-------------------------------------------------------------------------------
+License
+ This file is part of OpenFOAM.
+
+ OpenFOAM is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2 of the License, or (at your
+ option) any later version.
+
+ OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with OpenFOAM; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+Class
+ surfaceDisplacementPointPatchVectorField
+
+Description
+ Displacement fixed by projection onto triSurface.
+ Use in a displacement fvMotionSolver
+ as a bc on the pointDisplacement field.
+
+ Calculates the projection onto the surface according
+ to the projectMode
+ - NEAREST : nearest
+ - POINTNORMAL : intersection with point normal
+ - FIXEDNORMAL : intersection with fixed vector
+
+ This displacement is then clipped with the specified velocity * deltaT.
+
+ Optionally (intersection only) removes a component ("wedgePlane") to
+ stay in 2D.
+
+ Needs:
+ - geometry : dictionary with searchableSurfaces. (usually
+ triSurfaceMeshes in constant/triSurface)
+ - projectMode : see above
+ - projectDirection : if projectMode = fixedNormal
+ - wedgePlane : -1 or component to knock out of intersection normal
+ - frozenPointsZone : empty or name of pointZone containing points
+ that do not move
+
+SourceFiles
+ surfaceDisplacementPointPatchVectorField.C
+
+\*---------------------------------------------------------------------------*/
+
+#ifndef surfaceDisplacementPointPatchVectorField_H
+#define surfaceDisplacementPointPatchVectorField_H
+
+#include "pointPatchFields.H"
+#include "fixedValuePointPatchFields.H"
+#include "searchableSurfaces.H"
+#include "Switch.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+/*---------------------------------------------------------------------------*\
+ Class surfaceDisplacementPointPatchVectorField Declaration
+\*---------------------------------------------------------------------------*/
+
+class surfaceDisplacementPointPatchVectorField
+:
+ public fixedValuePointPatchVectorField
+{
+
+public:
+
+ // Public data types
+
+ enum projectMode
+ {
+ NEAREST,
+ POINTNORMAL,
+ FIXEDNORMAL
+ };
+
+private:
+
+ // Private data
+
+ //- project mode names
+ static const NamedEnum<projectMode, 3> projectModeNames_;
+
+ //- Maximum velocity
+ const vector velocity_;
+
+ //- names of surfaces
+ const dictionary surfacesDict_;
+
+ //- How to project/project onto surface
+ const projectMode projectMode_;
+
+ //- direction to project
+ const vector projectDir_;
+
+ //- plane for 2D wedge case or -1.
+ const label wedgePlane_;
+
+ //- pointZone with frozen points
+ const word frozenPointsZone_;
+
+ //- Demand driven: surface to project
+ mutable autoPtr<searchableSurfaces> surfacesPtr_;
+
+
+ // Private Member Functions
+
+ //- Calculate displacement (w.r.t. points0()) to project onto surface
+ void calcProjection(vectorField& displacement) const;
+
+
+ //- Disallow default bitwise assignment
+ void operator=(const surfaceDisplacementPointPatchVectorField&);
+
+public:
+
+ //- Runtime type information
+ TypeName("surfaceDisplacement");
+
+
+ // Constructors
+
+ //- Construct from patch and internal field
+ surfaceDisplacementPointPatchVectorField
+ (
+ const pointPatch&,
+ const DimensionedField<vector, pointMesh>&
+ );
+
+ //- Construct from patch, internal field and dictionary
+ surfaceDisplacementPointPatchVectorField
+ (
+ const pointPatch&,
+ const DimensionedField<vector, pointMesh>&,
+ const dictionary&
+ );
+
+ //- Construct by mapping given patchField<vector> onto a new patch
+ surfaceDisplacementPointPatchVectorField
+ (
+ const surfaceDisplacementPointPatchVectorField&,
+ const pointPatch&,
+ const DimensionedField<vector, pointMesh>&,
+ const pointPatchFieldMapper&
+ );
+
+ //- Construct as copy
+ surfaceDisplacementPointPatchVectorField
+ (
+ const surfaceDisplacementPointPatchVectorField&
+ );
+
+ //- Construct and return a clone
+ virtual autoPtr<pointPatchVectorField> clone() const
+ {
+ return autoPtr<pointPatchVectorField>
+ (
+ new surfaceDisplacementPointPatchVectorField
+ (
+ *this
+ )
+ );
+ }
+
+ //- Construct as copy setting internal field reference
+ surfaceDisplacementPointPatchVectorField
+ (
+ const surfaceDisplacementPointPatchVectorField&,
+ const DimensionedField<vector, pointMesh>&
+ );
+
+ //- Construct and return a clone setting internal field reference
+ virtual autoPtr<pointPatchVectorField> clone
+ (
+ const DimensionedField<vector, pointMesh>& iF
+ ) const
+ {
+ return autoPtr<pointPatchVectorField>
+ (
+ new surfaceDisplacementPointPatchVectorField
+ (
+ *this,
+ iF
+ )
+ );
+ }
+
+ // Member Functions
+
+ //- Surface to follow. Demand loads surfaceNames.
+ const searchableSurfaces& surfaces() const;
+
+ //- Update the coefficients associated with the patch field
+ virtual void updateCoeffs();
+
+ //- Write
+ virtual void write(Ostream&) const;
+};
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace Foam
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
+// ************************************************************************* //
diff --git a/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.C b/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.C
index 8c310481d7c5ae20dfda44ff7e402437cf2f4b7a..8f37cd91abadbe0bc26a3f7a49985a961902721c 100644
--- a/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.C
+++ b/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.C
@@ -40,7 +40,7 @@ namespace Foam
template<>
const char*
-NamedEnum<surfaceSlipDisplacementPointPatchVectorField::followMode, 3>::
+NamedEnum<surfaceSlipDisplacementPointPatchVectorField::projectMode, 3>::
names[] =
{
"nearest",
@@ -48,8 +48,8 @@ names[] =
"fixedNormal"
};
-const NamedEnum<surfaceSlipDisplacementPointPatchVectorField::followMode, 3>
- surfaceSlipDisplacementPointPatchVectorField::followModeNames_;
+const NamedEnum<surfaceSlipDisplacementPointPatchVectorField::projectMode, 3>
+ surfaceSlipDisplacementPointPatchVectorField::projectModeNames_;
// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
@@ -95,12 +95,10 @@ void surfaceSlipDisplacementPointPatchVectorField::calcProjection
}
// Get the starting locations from the motionSolver
- const displacementFvMotionSolver& motionSolver =
- mesh.lookupObject<displacementFvMotionSolver>
- (
- "dynamicMeshDict"
- );
- const pointField& points0 = motionSolver.points0();
+ const pointField& points0 = mesh.lookupObject<displacementFvMotionSolver>
+ (
+ "dynamicMeshDict"
+ ).points0();
pointField start(meshPoints.size());
@@ -326,7 +324,7 @@ surfaceSlipDisplacementPointPatchVectorField
:
pointPatchVectorField(p, iF, dict),
surfacesDict_(dict.subDict("geometry")),
- projectMode_(followModeNames_.read(dict.lookup("followMode"))),
+ projectMode_(projectModeNames_.read(dict.lookup("projectMode"))),
projectDir_(dict.lookup("projectDirection")),
wedgePlane_(readLabel(dict.lookup("wedgePlane"))),
frozenPointsZone_(dict.lookupOrDefault("frozenPointsZone", word::null))
@@ -343,11 +341,11 @@ surfaceSlipDisplacementPointPatchVectorField
)
:
pointPatchVectorField(p, iF),
- surfacesDict_(ppf.surfacesDict()),
- projectMode_(ppf.projectMode()),
- projectDir_(ppf.projectDir()),
- wedgePlane_(ppf.wedgePlane()),
- frozenPointsZone_(ppf.frozenPointsZone())
+ surfacesDict_(ppf.surfacesDict_),
+ projectMode_(ppf.projectMode_),
+ projectDir_(ppf.projectDir_),
+ wedgePlane_(ppf.wedgePlane_),
+ frozenPointsZone_(ppf.frozenPointsZone_)
{}
@@ -358,11 +356,11 @@ surfaceSlipDisplacementPointPatchVectorField
)
:
pointPatchVectorField(ppf),
- surfacesDict_(ppf.surfacesDict()),
- projectMode_(ppf.projectMode()),
- projectDir_(ppf.projectDir()),
- wedgePlane_(ppf.wedgePlane()),
- frozenPointsZone_(ppf.frozenPointsZone())
+ surfacesDict_(ppf.surfacesDict_),
+ projectMode_(ppf.projectMode_),
+ projectDir_(ppf.projectDir_),
+ wedgePlane_(ppf.wedgePlane_),
+ frozenPointsZone_(ppf.frozenPointsZone_)
{}
@@ -374,11 +372,11 @@ surfaceSlipDisplacementPointPatchVectorField
)
:
pointPatchVectorField(ppf, iF),
- surfacesDict_(ppf.surfacesDict()),
- projectMode_(ppf.projectMode()),
- projectDir_(ppf.projectDir()),
- wedgePlane_(ppf.wedgePlane()),
- frozenPointsZone_(ppf.frozenPointsZone())
+ surfacesDict_(ppf.surfacesDict_),
+ projectMode_(ppf.projectMode_),
+ projectDir_(ppf.projectDir_),
+ wedgePlane_(ppf.wedgePlane_),
+ frozenPointsZone_(ppf.frozenPointsZone_)
{}
@@ -435,7 +433,7 @@ void surfaceSlipDisplacementPointPatchVectorField::write(Ostream& os) const
pointPatchVectorField::write(os);
os.writeKeyword("geometry") << surfacesDict_
<< token::END_STATEMENT << nl;
- os.writeKeyword("followMode") << followModeNames_[projectMode_]
+ os.writeKeyword("projectMode") << projectModeNames_[projectMode_]
<< token::END_STATEMENT << nl;
os.writeKeyword("projectDirection") << projectDir_
<< token::END_STATEMENT << nl;
diff --git a/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.H b/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.H
index 9edb42ac0d8764334c014267bbdbb327bb808596..2b2b89819fd98faeefb5ad658c75813273fa59e2 100644
--- a/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.H
+++ b/src/fvMotionSolver/pointPatchFields/derived/surfaceSlipDisplacement/surfaceSlipDisplacementPointPatchVectorField.H
@@ -26,8 +26,10 @@ Class
Foam::surfaceSlipDisplacementPointPatchVectorField
Description
- Displacement follows a triSurface. Use in a displacement fvMotionSolver.
- Following is either
+ Displacement follows a triSurface. Use in a displacement fvMotionSolver
+ as a bc on the pointDisplacement field.
+ Following is done by calculating the projection onto the surface according
+ to the projectMode
- NEAREST : nearest
- POINTNORMAL : intersection with point normal
- FIXEDNORMAL : intersection with fixed vector
@@ -36,9 +38,10 @@ Description
stay in 2D.
Needs:
- - projectSurfaces : names of triSurfaceMeshes (in constant/triSurface)
- - followMode : see above
- - projectDirection : if followMode = fixedNormal
+ - geometry : dictionary with searchableSurfaces. (usually
+ triSurfaceMeshes in constant/triSurface)
+ - projectMode : see above
+ - projectDirection : if projectMode = fixedNormal
- wedgePlane : -1 or component to knock out of intersection normal
- frozenPointsZone : empty or name of pointZone containing points
that do not move
@@ -72,7 +75,7 @@ public:
// Public data types
- enum followMode
+ enum projectMode
{
NEAREST,
POINTNORMAL,
@@ -83,14 +86,14 @@ private:
// Private data
- //- follow mode names
- static const NamedEnum<followMode, 3> followModeNames_;
+ //- project mode names
+ static const NamedEnum<projectMode, 3> projectModeNames_;
//- names of surfaces
const dictionary surfacesDict_;
- //- How to follow/project onto surface
- const followMode projectMode_;
+ //- How to project/project onto surface
+ const projectMode projectMode_;
//- direction to project
const vector projectDir_;
@@ -101,13 +104,13 @@ private:
//- pointZone with frozen points
const word frozenPointsZone_;
- //- Demand driven: surface to follow
+ //- Demand driven: surface to project
mutable autoPtr<searchableSurfaces> surfacesPtr_;
// Private Member Functions
- //- Calculate displacement to project onto surface
+ //- Calculate displacement (w.r.t. points0()) to project onto surface
void calcProjection(vectorField& displacement) const;
//- Disallow default bitwise assignment
@@ -189,40 +192,9 @@ public:
// Member Functions
- //- Surfaces to follow
- const dictionary& surfacesDict() const
- {
- return surfacesDict_;
- }
-
//- Surface to follow. Demand loads surfaceNames.
const searchableSurfaces& surfaces() const;
- //- Mode of projection/following
- followMode projectMode() const
- {
- return projectMode_;
- }
-
- //- Direction to project back onto surface
- const vector& projectDir() const
- {
- return projectDir_;
- }
-
- //- Normal of wedgeplane (0, 1, 2) or -1. Note: should be obtained
- // from twoDPointCorrector.
- label wedgePlane() const
- {
- return wedgePlane_;
- }
-
- //- Zone containing frozen points
- const word& frozenPointsZone() const
- {
- return frozenPointsZone_;
- }
-
//- Update the patch field
virtual void evaluate
(
diff --git a/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H b/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
index 4b422bdd3176e4ac3320ec6e32a8f9956e3fe699..0dc8f02ea7d73f24da679049d2a3172e442e2c0d 100644
--- a/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
+++ b/src/lagrangian/dsmc/submodels/BinaryCollisionModel/BinaryCollisionModel/BinaryCollisionModel.H
@@ -152,26 +152,26 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-#define makeBinaryCollisionModel(CloudType) \
+#define makeBinaryCollisionModel(CloudType) \
\
defineNamedTemplateTypeNameAndDebug \
( \
- BinaryCollisionModel<CloudType>, \
+ BinaryCollisionModel<CloudType>, \
0 \
); \
\
defineTemplateRunTimeSelectionTable \
( \
- BinaryCollisionModel<CloudType>, \
+ BinaryCollisionModel<CloudType>, \
dictionary \
);
-#define makeBinaryCollisionModelType(SS, CloudType, ParcelType) \
+#define makeBinaryCollisionModelType(SS, CloudType, ParcelType) \
\
defineNamedTemplateTypeNameAndDebug(SS<CloudType<ParcelType> >, 0); \
\
- BinaryCollisionModel<CloudType<ParcelType> >:: \
+ BinaryCollisionModel<CloudType<ParcelType> >:: \
adddictionaryConstructorToTable<SS<CloudType<ParcelType> > > \
add##SS##CloudType##ParcelType##ConstructorToTable_;
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
index 18d46cb90a7fc2b5ee9a1f67422df61d9e7e1c41..de7d31fcb5291c99895422b2b75fe76be6439db7 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -126,6 +126,7 @@ void Foam::bufferedAccumulator<Type>::setSizes
}
}
+
template<class Type>
Foam::label Foam::bufferedAccumulator<Type>::addToBuffers
(
@@ -184,11 +185,10 @@ Foam::Field<Type> Foam::bufferedAccumulator<Type>::averaged() const
WarningIn
(
"bufferedAccumulator<Type>::averagedbufferedAccumulator() const"
- )
- << "Averaged correlation function requested but averagesTaken = "
- << averagesTaken_
- << ". Returning empty field."
- << endl;
+ ) << "Averaged correlation function requested but averagesTaken = "
+ << averagesTaken_
+ << ". Returning empty field."
+ << endl;
return Field<Type>(bufferLength(), pTraits<Type>::zero);
}
@@ -218,8 +218,7 @@ void Foam::bufferedAccumulator<Type>::operator=
FatalErrorIn
(
"bufferedAccumulator<Type>::operator=(const bufferedAccumulator&)"
- )
- << "Attempted assignment to self"
+ ) << "Attempted assignment to self"
<< abort(FatalError);
}
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.H b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.H
index 53b8f9371dd64468a985ff1d25f0fa3bb8d93159..ed8afa2115883a602a094c2fe13aa07345a7ea72 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulator.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorI.H b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorI.H
index 96531509c8e0d2ea371b09409cdbe4866890a0ca..28bcde97a990a81bddd15374513182f1773eea60 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorI.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
index 8e5d7c9d729d0f2d6c1a273143c80cceb3083333..ec1956a345dba0d1454ebec2a1e73da58e92a2db 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/bufferedAccumulator/bufferedAccumulatorIO.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -34,9 +34,9 @@ Foam::Ostream&
Foam::operator<<(Ostream& os, const bufferedAccumulator<Type>& bA)
{
- os<< bA.averagesTaken_
- << static_cast<const List< Field<Type> >&>(bA)
- << bA.bufferOffsets();
+ os << bA.averagesTaken_
+ << static_cast<const List< Field<Type> >&>(bA)
+ << bA.bufferOffsets();
// Check state of Ostream
os.check
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
index eca654aa2dd4302c0e25ffdae2ffd40e3416f7df..cce0d86a22c0d6f9000d2f3b6f2d9a35e48b10bc 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -138,7 +138,7 @@ void Foam::correlationFunction<Type>::calculateCorrelationFunction
FatalErrorIn("correlationFunction<Type>::calculateCorrelationFunction")
<< "Trying to supply a Field of length"
<< currentValues.size()
- <<" to calculate the correlation function. "
+ << " to calculate the correlation function. "
<< "Expecting a Field of length "
<< measurandFieldSize() << nl
<< abort(FatalError);
@@ -205,7 +205,7 @@ Foam::scalar Foam::correlationFunction<Type>::integral() const
scalar cFIntegral = 0.0;
- for(label v = 0; v < averageCF.size() - 1; v++)
+ for (label v = 0; v < averageCF.size() - 1; v++)
{
cFIntegral +=
0.5
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
index 2b8753676c5a67253808bdcad17c2d291e5ffe0a..fe2071aff372af8f680c640fd4559afb74dcba3b 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunction.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -155,7 +155,10 @@ public:
// IOstream Operators
friend Ostream& operator<< <Type>
- (Ostream&, const correlationFunction<Type>&);
+ (
+ Ostream&,
+ const correlationFunction<Type>&
+ );
};
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionI.H b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionI.H
index d07d54eca0ac442309a989a15941c76bb48a836b..adbf70505994612da152d42fd4b95ae273507c2b 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionI.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
index 7dcbcc1eda11ad23905087e6f196b29fd45d016a..aa62cdcaf6e0797077492306873cf8db4aea0679 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/correlationFunction/correlationFunctionIO.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -34,10 +34,10 @@ bool Foam::correlationFunction<Type>::writeAveraged(Ostream& os) const
forAll(averageCF, v)
{
- os<< v*sampleInterval()
- << token::SPACE
- << averageCF[v]
- << nl;
+ os << v*sampleInterval()
+ << token::SPACE
+ << averageCF[v]
+ << nl;
}
return os.good();
@@ -51,12 +51,12 @@ Foam::Ostream& Foam::operator<<
const correlationFunction<Type>& cF
)
{
- os<< cF.duration()
- << nl << cF.sampleInterval()
- << nl << cF.averagingInterval()
- << nl << cF.sampleSteps()
- << nl << cF.tZeroBuffers()
- << nl << static_cast<const bufferedAccumulator<scalar>&>(cF);
+ os << cF.duration()
+ << nl << cF.sampleInterval()
+ << nl << cF.averagingInterval()
+ << nl << cF.sampleSteps()
+ << nl << cF.tZeroBuffers()
+ << nl << static_cast<const bufferedAccumulator<scalar>&>(cF);
// Check state of Ostream
os.check
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
index a4a08b08fa6efd78597d0be45985c227f4d094ad..439ed64bdf06229f8b13fd6424a9336f14f43187 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -75,7 +75,7 @@ label distribution::totalEntries() const
<< "sumOfEntries = " << sumOfEntries
<< ". This is most likely to be because too many samples "
<< "have been added to the bins and the label has 'rolled "
- << "round'. Try distribution::approxTotalEntries which "
+ << "round'. Try distribution::approxTotalEntries which "
<< "returns a scalar." << endl;
sumOfEntries = -1;
@@ -336,8 +336,8 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
*(oldDist[u].second() - oldDist[u-1].second())
+
(
- oldDist[u-1].second() * oldDist[u].first()
- - oldDist[u].second() * oldDist[u-1].first()
+ oldDist[u-1].second()*oldDist[u].first()
+ - oldDist[u].second()*oldDist[u-1].first()
)
/binWidth_;
}
@@ -348,7 +348,7 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
{
newDist[u].second() =
(0.5 + scalar(newKey))*-oldDist[u].second()
- + oldDist[u].second() * (oldDist[u].first() + binWidth_)
+ + oldDist[u].second()*(oldDist[u].first() + binWidth_)
/binWidth_;
}
else
@@ -358,8 +358,8 @@ List< Pair<scalar> > distribution::normalisedShifted(const scalar shiftValue)
*(oldDist[u+1].second() - oldDist[u].second())
+
(
- oldDist[u].second() * oldDist[u+1].first()
- - oldDist[u+1].second() * oldDist[u].first()
+ oldDist[u].second()*oldDist[u+1].first()
+ - oldDist[u+1].second()*oldDist[u].first()
)
/binWidth_;
}
@@ -395,7 +395,7 @@ List<Pair<scalar> > distribution::raw()
{
label key = keys[k];
- rawDist[k].first() = (0.5 + scalar(key)) * binWidth_;
+ rawDist[k].first() = (0.5 + scalar(key))*binWidth_;
rawDist[k].second() = scalar((*this)[key]);
}
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
index 597d2eedb087aa8af9427a1cfa659e1f8820bf6e..da1ce973bc7d3fa9dceabbcf4dd2e5f2b39a1b87 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distribution.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -30,7 +30,6 @@ Description
SourceFiles
distributionI.H
distribution.C
- distributionIO.C
\*---------------------------------------------------------------------------*/
@@ -46,7 +45,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class distribution Declaration
+ Class distribution Declaration
\*---------------------------------------------------------------------------*/
class distribution
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H
index 988d76de31c8e38ca0a41f91d94c331d052f0111..4bc3596a50957e656072444188f5c02267d37c12 100644
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H
+++ b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C b/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C
deleted file mode 100644
index 65743800e84b540ee59895c3c4458f8783fff082..0000000000000000000000000000000000000000
--- a/src/lagrangian/molecularDynamics/molecularMeasurements/distribution/distributionIO.C
+++ /dev/null
@@ -1,35 +0,0 @@
-/*---------------------------------------------------------------------------*\
- ========= |
- \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
- \\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
- \\/ M anipulation |
--------------------------------------------------------------------------------
-License
- This file is part of OpenFOAM.
-
- OpenFOAM is free software; you can redistribute it and/or modify it
- under the terms of the GNU General Public License as published by the
- Free Software Foundation; either version 2 of the License, or (at your
- option) any later version.
-
- OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
- ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
- FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
- for more details.
-
- You should have received a copy of the GNU General Public License
- along with OpenFOAM; if not, write to the Free Software Foundation,
- Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-\*---------------------------------------------------------------------------*/
-
-#include "distribution.H"
-#include "IOstreams.H"
-
-// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
-
-// construct from Istream
-
-
-// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
index ba3a3d90669ec95b43e98e780b7f7bb0c1324f79..1556db83178b50ca625860d22292e4de7612069a 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -79,8 +79,12 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellI],
- cellJ) == -1
+ findIndex
+ (
+ directInteractionList[cellI],
+ cellJ
+ )
+ == -1
)
{
directInteractionList[cellI].append(cellJ);
@@ -91,8 +95,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellJ],
- cellI) == -1
+ findIndex
+ (
+ directInteractionList[cellJ],
+ cellI
+ )
+ ==
+ -1
)
{
directInteractionList[cellJ].append(cellI);
@@ -109,18 +118,16 @@ void Foam::directInteractionList::buildDirectInteractionList
Info<< tab << "Point-Face, Edge-Edge direct interaction list build."
<< endl;
- forAll (mesh.points(), p)
+ forAll(mesh.points(), p)
{
forAll(mesh.faces(), f)
{
- if(il_.testPointFaceDistance(p, f))
+ if (il_.testPointFaceDistance(p, f))
{
const labelList& pCells(mesh.pointCells()[p]);
const label cellO(mesh.faceOwner()[f]);
- const label cellN(mesh.faceNeighbour()[f]);
-
forAll(pCells, pC)
{
const label cellI(pCells[pC]);
@@ -131,8 +138,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellI],
- cellO) == -1
+ findIndex
+ (
+ directInteractionList[cellI],
+ cellO
+ )
+ ==
+ -1
)
{
directInteractionList[cellI].append(cellO);
@@ -143,8 +155,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellO],
- cellI) == -1
+ findIndex
+ (
+ directInteractionList[cellO],
+ cellI
+ )
+ ==
+ -1
)
{
directInteractionList[cellO].append(cellI);
@@ -156,12 +173,19 @@ void Foam::directInteractionList::buildDirectInteractionList
// boundary faces will not have neighbour
// information
+ const label cellN(mesh.faceNeighbour()[f]);
+
if (cellN > cellI)
{
if
(
- findIndex(directInteractionList[cellI],
- cellN) == -1
+ findIndex
+ (
+ directInteractionList[cellI],
+ cellN
+ )
+ ==
+ -1
)
{
directInteractionList[cellI].append(cellN);
@@ -172,8 +196,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellN],
- cellI) == -1
+ findIndex
+ (
+ directInteractionList[cellN],
+ cellI
+ )
+ ==
+ -1
)
{
directInteractionList[cellN].append(cellI);
@@ -187,7 +216,7 @@ void Foam::directInteractionList::buildDirectInteractionList
label edgeJIndex;
- forAll (mesh.edges(), edgeIIndex)
+ forAll(mesh.edges(), edgeIIndex)
{
const edge& eI(mesh.edges()[edgeIIndex]);
@@ -218,8 +247,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellI],
- cellJ) == -1
+ findIndex
+ (
+ directInteractionList[cellI],
+ cellJ
+ )
+ ==
+ -1
)
{
directInteractionList[cellI].append(cellJ);
@@ -230,8 +264,13 @@ void Foam::directInteractionList::buildDirectInteractionList
{
if
(
- findIndex(directInteractionList[cellJ],
- cellI) == -1
+ findIndex
+ (
+ directInteractionList[cellJ],
+ cellI
+ )
+ ==
+ -1
)
{
directInteractionList[cellJ].append(cellI);
@@ -272,11 +311,11 @@ Foam::directInteractionList::directInteractionList
labelListList(il.mesh().nCells()),
il_(il)
{
- if((*this).size() > 1)
+ if ((*this).size() > 1)
{
buildDirectInteractionList(pointPointListBuild);
}
- else if((*this).size() == 1)
+ else if ((*this).size() == 1)
{
Info<< nl
<< "Single cell mesh, no direct interaction lists required."
@@ -305,16 +344,4 @@ Foam::directInteractionList::~directInteractionList()
{}
-// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
-
-
-// * * * * * * * * * * * * * * * Member Operators * * * * * * * * * * * * * //
-
-
-// * * * * * * * * * * * * * * * Friend Functions * * * * * * * * * * * * * //
-
-
-// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
index 3777b0b098e7552bf8d78724a4e205e0c098d4cd..8a85404ca04d3c962da39ff74237be3742090092 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionList.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -59,6 +59,7 @@ class directInteractionList
const interactionLists& il_;
+
// Private Member Functions
void buildDirectInteractionList
@@ -72,6 +73,7 @@ class directInteractionList
//- Disallow default bitwise assignment
void operator=(const directInteractionList&);
+
public:
// Constructors
@@ -89,6 +91,7 @@ public:
const interactionLists& il
);
+
// Destructor
~directInteractionList();
@@ -100,12 +103,6 @@ public:
inline const interactionLists& il() const;
- // Check
-
- // Edit
-
- // Write
-
// IOstream Operators
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
index 7c1ded995b372b0fb911ee6d75c22666c43bc657..34c1d65080664619ce92f4df416337ffee87c774 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/directInteractionList/directInteractionListI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::interactionLists& Foam::directInteractionList::il() const
@@ -34,7 +32,4 @@ inline const Foam::interactionLists& Foam::directInteractionList::il() const
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
index 411d6dbfba2c3f8a0cbb30a6bbdbd72825a6ea3d..f1036eaa0e937bd2121f80187ef61199cd3d75e4 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -342,6 +342,7 @@ bool Foam::interactionLists::testPointFaceDistance
);
}
+
bool Foam::interactionLists::testPointFaceDistance
(
const vector& p,
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
index a8d28133eb7fd3d516878407a28843b79558db20..744b59b067a17867b1cd4906281183f9c30d6f6a 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionLists.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -52,7 +52,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class interactionLists Declaration
+ Class interactionLists Declaration
\*---------------------------------------------------------------------------*/
class interactionLists
@@ -71,6 +71,7 @@ class interactionLists
List<receivingReferralList> cellReceivingReferralLists_;
+
// Private Member Functions
//- Build referralLists which define how to send information
@@ -83,6 +84,7 @@ class interactionLists
//- Disallow default bitwise assignment
void operator=(const interactionLists&);
+
public:
// Static data members
@@ -90,6 +92,7 @@ public:
//- Tolerance for checking that faces on a patch segment
static scalar transTol;
+
// Constructors
//- Construct and create all information from the mesh
@@ -103,6 +106,7 @@ public:
//- Construct from file
interactionLists(const polyMesh& mesh);
+
// Destructor
~interactionLists();
@@ -177,6 +181,7 @@ public:
const labelList& segmentPoints
) const;
+
// Access
inline const polyMesh& mesh() const;
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionListsI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionListsI.H
index 6749e05be018287c98f4385ab4bd05a5bf195f00..7c5c4ec1227cb102a33473e80dacca1c265c76dd 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionListsI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/interactionListsI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
index db0831eaee88874b252d43d33b984394d284d712..2f646fcba5f50ccc11ada22d43874e35f69674e4 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -143,7 +143,7 @@ bool operator==
Foam::Istream& Foam::operator>>(Istream& is, receivingReferralList& rRL)
{
- is >> rRL.sourceProc_ >> static_cast<labelListList&>(rRL);
+ is >> rRL.sourceProc_ >> static_cast<labelListList&>(rRL);
is.check
(
@@ -160,7 +160,7 @@ Foam::Ostream& Foam::operator<<
const receivingReferralList& rRL
)
{
- os << rRL.sourceProc() << token::SPACE
+ os << rRL.sourceProc() << token::SPACE
<< static_cast< const labelListList& >(rRL);
os.check
@@ -171,7 +171,5 @@ Foam::Ostream& Foam::operator<<
return os;
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.H
index b7ec5a26fac197a1a140a13feea420ad2c0e0065..91ebe8eb32c9ff2fa0781c6e29739d95bf0ffe54 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralList.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
index 48b11405b4d5013ffd9e8cdf9617dfe45aa5e405..084863b01a0ee09739adcff006d103eedae04306 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/receivingReferralListI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::receivingReferralList::sourceProc() const
@@ -46,7 +44,4 @@ inline bool operator!=
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
index bb0b3b1e529dba4a01554d02009c0673bd738cb4..6235ddabfad51cd0d2c79c59e691926ef1cdd6c0 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -145,7 +145,7 @@ Foam::Istream& Foam::operator>>
sendingReferralList& sRL
)
{
- is >> sRL.destinationProc_ >> static_cast<labelList&>(sRL);
+ is >> sRL.destinationProc_ >> static_cast<labelList&>(sRL);
is.check("Istream& operator<<(Istream& f, const sendingReferralList& sRL");
@@ -159,7 +159,7 @@ Foam::Ostream& Foam::operator<<
const sendingReferralList& rL
)
{
- os << rL.destinationProc() << token::SPACE
+ os << rL.destinationProc() << token::SPACE
<< static_cast< const labelList& >(rL);
os.check("Ostream& operator<<(Ostream& f, const sendingReferralList& rL");
@@ -168,6 +168,4 @@ Foam::Ostream& Foam::operator<<
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.H
index 30afadebee5fb469aa4c62100a2bb04b7930450e..b7b9bf082cc971abc4c66e82687633a1684f22ad 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralList.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
index 51c569cfd20ca906ce2ecb12a4369eaf3c6bfac5..d34ffd3595413511dfaabdb643ae0991db287a64 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referralLists/sendingReferralListI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::sendingReferralList::destinationProc() const
@@ -46,6 +44,4 @@ inline bool operator!=
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
index 194caa11e2c5066838cf1fb3ba1033c493a3baec..225ad5902a01ca024526ef4e8b43326f90e4f677 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -38,7 +38,7 @@ void referredCell::setConstructionData
const label sourceCell
)
{
- // * * * * * * * * * * * Points * * * * * * * * * * *
+ // Points
const labelList& points = mesh.cellPoints()[sourceCell];
@@ -51,7 +51,8 @@ void referredCell::setConstructionData
vertexPositions_ = referPositions(sourceCellVertices);
- // * * * * * * * * * * * Edges * * * * * * * * * * *
+
+ // Edges
const labelList& edges = mesh.cellEdges()[sourceCell];
@@ -64,7 +65,8 @@ void referredCell::setConstructionData
locallyMapEdgeList(points, sourceCellEdges);
- // * * * * * * * * * * * Faces * * * * * * * * * * *
+
+ // Faces
labelList faces(mesh.cells()[sourceCell]);
@@ -383,8 +385,8 @@ bool referredCell::duplicate(const referredCell& refCellDupl) const
return
(
sourceProc_ == refCellDupl.sourceProc()
- && sourceCell_ == refCellDupl.sourceCell()
- && mag(offset_ - refCellDupl.offset()) < interactionLists::transTol
+ && sourceCell_ == refCellDupl.sourceCell()
+ && mag(offset_ - refCellDupl.offset()) < interactionLists::transTol
);
}
@@ -394,8 +396,8 @@ bool referredCell::duplicate(const label procNo,const label nCells) const
return
(
sourceProc_ == procNo
- && sourceCell_ < nCells
- && mag(offset_) < interactionLists::transTol
+ && sourceCell_ < nCells
+ && mag(offset_) < interactionLists::transTol
);
}
@@ -405,7 +407,7 @@ bool referredCell::duplicate(const label procNo,const label nCells) const
Istream& operator>>(Istream& is, referredCell& rC)
{
- is >> rC.sourceProc_
+ is >> rC.sourceProc_
>> rC.sourceCell_
>> rC.vertexPositions_
>> rC.edges_
@@ -424,7 +426,7 @@ Istream& operator>>(Istream& is, referredCell& rC)
Ostream& operator<<(Ostream& os, const referredCell& rC)
{
- os << rC.sourceProc()
+ os << rC.sourceProc()
<< token::SPACE << rC.sourceCell()
<< token::SPACE << rC.vertexPositions()
<< token::SPACE << rC.edges()
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
index 789c9e4d4143ceca47ccd82cf31c51ff33433623..666b4f9268297675083c85fb810e85723951d14f 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCell.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -53,7 +53,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class referredCell Declaration
+ Class referredCell Declaration
\*---------------------------------------------------------------------------*/
class referredCell
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCellI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCellI.H
index a7427c141da9f57cd6febff42d33b6acc4bce4ba..bd3954e83cd678b91428e7dabd33ecfa100f4b7d 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCellI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCell/referredCellI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
index fbc5c1740be6b14d7b1d8fd475f2c3a53d2011d6..2ba95daa18e09e821868d574cebe524b087c94cc 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -357,7 +357,7 @@ void Foam::referredCellList::buildReferredCellList
label iterationNo = 0;
- while(cellsReferredThisIteration)
+ while (cellsReferredThisIteration)
{
label refIntListStartSize = referredInteractionList.size();
@@ -499,7 +499,10 @@ void Foam::referredCellList::buildReferredCellList
(
meshPointsOnThisSegment,
facePoint
- ) == -1)
+ )
+ ==
+ -1
+ )
{
meshPointsOnThisSegment.append(facePoint);
}
@@ -610,18 +613,20 @@ void Foam::referredCellList::buildReferredCellList
forAll(referredCellsFoundInRange,cFIR)
{
- referredCell& existingRefCell = referredInteractionList
- [
- referredCellsFoundInRange[cFIR]
- ];
+ referredCell& existingRefCell =
+ referredInteractionList
+ [
+ referredCellsFoundInRange[cFIR]
+ ];
- referredCell cellToReRefer = existingRefCell.reRefer
- (
- patch.faceCentres()[0],
- patch.faceCentres()[patch.size()/2],
- patch.faceNormals()[0],
- patch.faceNormals()[patch.size()/2]
- );
+ referredCell cellToReRefer =
+ existingRefCell.reRefer
+ (
+ patch.faceCentres()[0],
+ patch.faceCentres()[patch.size()/2],
+ patch.faceNormals()[0],
+ patch.faceNormals()[patch.size()/2]
+ );
// Test all existing referred and real cells to check
// duplicates are not being made or cells aren't being
@@ -705,7 +710,9 @@ void Foam::referredCellList::buildReferredCellList
(
meshEdgesOnThisSegment,
faceEdge
- ) == -1
+ )
+ ==
+ -1
)
{
meshEdgesOnThisSegment.append(faceEdge);
@@ -724,7 +731,10 @@ void Foam::referredCellList::buildReferredCellList
(
meshPointsOnThisSegment,
facePoint
- ) == -1)
+ )
+ ==
+ -1
+ )
{
meshPointsOnThisSegment.append(facePoint);
}
@@ -823,28 +833,30 @@ void Foam::referredCellList::buildReferredCellList
referredInteractionList.shrink();
referredCellsFoundInRange =
- il_.referredCellsInRangeOfSegment
- (
- referredInteractionList,
- meshFacesOnThisSegment,
- meshEdgesOnThisSegment,
- meshPointsOnThisSegment
- );
+ il_.referredCellsInRangeOfSegment
+ (
+ referredInteractionList,
+ meshFacesOnThisSegment,
+ meshEdgesOnThisSegment,
+ meshPointsOnThisSegment
+ );
forAll(referredCellsFoundInRange,cFIR)
{
- referredCell& existingRefCell = referredInteractionList
- [
- referredCellsFoundInRange[cFIR]
- ];
+ referredCell& existingRefCell =
+ referredInteractionList
+ [
+ referredCellsFoundInRange[cFIR]
+ ];
- referredCell cellToReRefer = existingRefCell.reRefer
- (
- patch.faceCentres()[patch.size()/2],
- patch.faceCentres()[0],
- patch.faceNormals()[patch.size()/2],
- patch.faceNormals()[0]
- );
+ referredCell cellToReRefer =
+ existingRefCell.reRefer
+ (
+ patch.faceCentres()[patch.size()/2],
+ patch.faceCentres()[0],
+ patch.faceNormals()[patch.size()/2],
+ patch.faceNormals()[0]
+ );
// Test all existing referred and real cells to check
// duplicates are not being made or cells aren't being
@@ -901,15 +913,15 @@ void Foam::referredCellList::buildReferredCellList
forAll(procPatches,pP)
{
const processorPolyPatch& patch =
- refCast<const processorPolyPatch>
- (
- mesh.boundaryMesh()[procPatches[pP]]
- );
+ refCast<const processorPolyPatch>
+ (
+ mesh.boundaryMesh()[procPatches[pP]]
+ );
DynamicList<referredCell> referredCellsToTransfer;
const vectorList& neighbFaceCentres =
- allNeighbourFaceCentres[pP];
+ allNeighbourFaceCentres[pP];
const vectorList& neighbFaceAreas = allNeighbourFaceAreas[pP];
@@ -971,7 +983,9 @@ void Foam::referredCellList::buildReferredCellList
(
meshEdgesOnThisSegment,
faceEdge
- ) == -1
+ )
+ ==
+ -1
)
{
meshEdgesOnThisSegment.append(faceEdge);
@@ -990,7 +1004,9 @@ void Foam::referredCellList::buildReferredCellList
(
meshPointsOnThisSegment,
facePoint
- ) == -1
+ )
+ ==
+ -1
)
{
meshPointsOnThisSegment.append(facePoint);
@@ -1032,7 +1048,7 @@ void Foam::referredCellList::buildReferredCellList
forAll(realCellsFoundInRange,cFIR)
{
const label realCell =
- realCellsFoundInRange[cFIR];
+ realCellsFoundInRange[cFIR];
referredCell cellToRefer
(
@@ -1074,19 +1090,20 @@ void Foam::referredCellList::buildReferredCellList
forAll(referredCellsFoundInRange,cFIR)
{
referredCell& existingRefCell =
- referredInteractionList
- [
- referredCellsFoundInRange[cFIR]
- ];
+ referredInteractionList
+ [
+ referredCellsFoundInRange[cFIR]
+ ];
- referredCell cellToReRefer = existingRefCell.reRefer
- (
- patch.faceCentres()[faceT],
- neighbFaceCentres[faceT],
- patch.faceNormals()[faceT],
- neighbFaceAreas[faceT]
- /(mag(neighbFaceAreas[faceT]) + VSMALL)
- );
+ referredCell cellToReRefer =
+ existingRefCell.reRefer
+ (
+ patch.faceCentres()[faceT],
+ neighbFaceCentres[faceT],
+ patch.faceNormals()[faceT],
+ neighbFaceAreas[faceT]
+ /(mag(neighbFaceAreas[faceT]) + VSMALL)
+ );
referredCellsToTransfer.append(cellToReRefer);
}
@@ -1409,6 +1426,7 @@ void Foam::referredCellList::buildReferredCellList
}
}
+
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::referredCellList::referredCellList
@@ -1557,7 +1575,4 @@ void Foam::referredCellList::referMolecules
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
index e323a9dcb661ae3af8add5b25d9ee764936e804d..c8a77cb27f320ad9a4c8f46921725363b4e1c569 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellList.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -48,7 +48,7 @@ namespace Foam
class interactionLists;
/*---------------------------------------------------------------------------*\
- Class referredCellList Declaration
+ Class referredCellList Declaration
\*---------------------------------------------------------------------------*/
class referredCellList
@@ -59,7 +59,8 @@ class referredCellList
const interactionLists& il_;
- // Private Member Functions
+
+ // Private Member Functions
void buildReferredCellList
(
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellListI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellListI.H
index a81d6cf8e834faf72acb2f36d5859fec030d2b0f..588bf94eabb916d7a36caddc02f72cc99c1f6a21 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellListI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredCellList/referredCellListI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
index 3db08989c320039f1df76b76456b4cd82898db03..c1e2e487695d4f1305809dde4c3a8412ed6ecac5 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -83,6 +83,4 @@ Foam::Ostream& Foam::operator<<
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
index 13fd0983d74d342b793c7b328b39cb27e8aaaf97..27c3c98ee39f45991318c192ba51c0ff34b01b7b 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMolecule.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,7 +45,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class referredMolecule Declaration
+ Class referredMolecule Declaration
\*---------------------------------------------------------------------------*/
class referredMolecule
diff --git a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
index 102bd5e30fb0db48a965283f9bb49cc41f636173..1db2f9a923f957a4c4e4a64b22c29bba34f22e69 100644
--- a/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
+++ b/src/lagrangian/molecularDynamics/molecule/interactionLists/referredMolecule/referredMoleculeI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,6 +45,7 @@ Foam::referredMolecule::sitePositions() const
return sitePositions_;
}
+
// * * * * * * * * * * * * * * * Friend Operators * * * * * * * * * * * * * //
inline bool Foam::operator==
@@ -71,6 +72,4 @@ inline bool Foam::operator!=
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
index db0c24bc95e00bc77c0de6f358e5434ecffbf0fa..9781c9d70f415b8c92d90d29d3b05ec015bcebcc 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/averageMDFields.H
@@ -5,68 +5,68 @@ if (runTime.outputTime())
\*-----------------------------------------------------------------------*/
scalarField totalRhoN_sum(mesh.nCells(), 0.0);
-
+
forAll (allSpeciesRhoN, rN)
{
allSpeciesRhoN[rN].internalField() =
allSpeciesN_RU[rN]
/mesh.cellVolumes()
/nAveragingSteps;
-
+
totalRhoN_sum += allSpeciesRhoN[rN].internalField();
}
-
+
totalRhoN.internalField() = totalRhoN_sum;
-
-
+
+
/*-----------------------------------------------------------------------*\
Mass density
\*-----------------------------------------------------------------------*/
-
+
scalarField totalRhoM_sum(mesh.nCells(), 0.0);
-
+
forAll (allSpeciesRhoM, rM)
{
allSpeciesRhoM[rM].internalField() =
allSpeciesM_RU[rM]
/mesh.cellVolumes()
/nAveragingSteps;
-
+
totalRhoM_sum += allSpeciesRhoM[rM].internalField();
}
-
+
totalRhoM.internalField() = totalRhoM_sum;
-
+
/*-----------------------------------------------------------------------*\
Bulk velocity
\*-----------------------------------------------------------------------*/
-
+
vectorField totalMomentum_sum(mesh.nCells(), vector::zero);
-
+
scalarField totalMass_sum(mesh.nCells(), 0.0);
-
+
forAll (allSpeciesVelocity, v)
{
// A check for 1/0 molecules is required.
-
+
vectorField& singleSpeciesVelocity
(
allSpeciesVelocity[v].internalField()
);
-
+
forAll(singleSpeciesVelocity, sSV)
{
- if(allSpeciesN_RU[v][sSV])
+ if (allSpeciesN_RU[v][sSV])
{
- singleSpeciesVelocity[sSV] =
+ singleSpeciesVelocity[sSV] =
allSpeciesVelocitySum_RU[v][sSV]
/allSpeciesN_RU[v][sSV];
-
+
totalMomentum_sum[sSV] +=
allSpeciesM_RU[v][sSV]
/allSpeciesN_RU[v][sSV]
*allSpeciesVelocitySum_RU[v][sSV];
-
+
totalMass_sum[sSV] += allSpeciesM_RU[v][sSV];
}
else
@@ -75,10 +75,10 @@ if (runTime.outputTime())
}
}
}
-
+
forAll(totalVelocity.internalField(), tV)
{
- if(totalMass_sum[tV] > VSMALL)
+ if (totalMass_sum[tV] > VSMALL)
{
totalVelocity.internalField()[tV] =
totalMomentum_sum[tV]
@@ -90,34 +90,33 @@ if (runTime.outputTime())
vector::zero;
}
}
-
+
/*-----------------------------------------------------------------------*\
Kinetic temperature
\*-----------------------------------------------------------------------*/
-
+
scalarField totalTemperatureVTerms_sum(mesh.nCells(), 0.0);
-
+
scalarField totalN_sum(mesh.nCells(), 0.0);
-
+
forAll (allSpeciesTemperature, t)
{
// A check for 1/0 molecules is required.
-
+
scalarField& singleSpeciesTemp
(
allSpeciesTemperature[t].internalField()
);
-
+
forAll(singleSpeciesTemp, sST)
{
- if(allSpeciesN_RU[t][sST])
+ if (allSpeciesN_RU[t][sST])
{
- singleSpeciesTemp[sST] =
+ singleSpeciesTemp[sST] =
allSpeciesM_RU[t][sST]
/allSpeciesN_RU[t][sST]
/(3.0 * moleculeCloud::kb * allSpeciesN_RU[t][sST])
- *
- (
+ *(
allSpeciesVelocityMagSquaredSum_RU[t][sST]
-
(
@@ -127,14 +126,13 @@ if (runTime.outputTime())
)
/allSpeciesN_RU[t][sST]
);
-
+
totalTemperatureVTerms_sum[sST] +=
allSpeciesM_RU[t][sST]
- /allSpeciesN_RU[t][sST]
- *
- (
+ /allSpeciesN_RU[t][sST]
+ *(
allSpeciesVelocityMagSquaredSum_RU[t][sST]
- -
+ -
(
allSpeciesVelocitySum_RU[t][sST]
&
@@ -142,7 +140,7 @@ if (runTime.outputTime())
)
/allSpeciesN_RU[t][sST]
);
-
+
totalN_sum[sST] += allSpeciesN_RU[t][sST];
}
else
@@ -151,7 +149,7 @@ if (runTime.outputTime())
}
}
}
-
+
forAll(totalTemperature.internalField(), tT)
{
if(totalN_sum[tT] > 0)
@@ -165,41 +163,39 @@ if (runTime.outputTime())
totalTemperature.internalField()[tT] = 0.0;
}
}
-
+
/*-----------------------------------------------------------------------*\
Mean kinetic energy
\*-----------------------------------------------------------------------*/
-
+
scalarField totalKE_sum(mesh.nCells(), 0.0);
-
+
forAll (allSpeciesMeanKE, mKE)
{
// A check for 1/0 molecules is required.
-
+
scalarField& singleSpeciesMeanKE
(
allSpeciesMeanKE[mKE].internalField()
);
-
+
forAll(singleSpeciesMeanKE, sSMKE)
{
if(allSpeciesN_RU[mKE][sSMKE])
{
- singleSpeciesMeanKE[sSMKE] =
+ singleSpeciesMeanKE[sSMKE] =
allSpeciesM_RU[mKE][sSMKE]
- /allSpeciesN_RU[mKE][sSMKE]
- /(2.0 * allSpeciesN_RU[mKE][sSMKE])
- *
- (
+ /allSpeciesN_RU[mKE][sSMKE]
+ /(2.0*allSpeciesN_RU[mKE][sSMKE])
+ *(
allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
);
-
+
totalKE_sum[sSMKE] +=
allSpeciesM_RU[mKE][sSMKE]
/allSpeciesN_RU[mKE][sSMKE]
/2.0
- *
- (
+ *(
allSpeciesVelocityMagSquaredSum_RU[mKE][sSMKE]
);
}
@@ -209,7 +205,7 @@ if (runTime.outputTime())
}
}
}
-
+
forAll(totalMeanKE.internalField(), tMKE)
{
if(totalN_sum[tMKE] > 0)
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
index ce0113352e38b7ce230510a5786346efa706bb47..968cfa93cb80339db241aaf317418d678dbbcaa5 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateAutoCorrelationFunctions.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -60,18 +60,15 @@ if (mesh.time().timeIndex() % pacf.sampleSteps() == 0)
{
p.x() +=
mol().mass() * mol().U().y() * mol().U().z()
- +
- 0.5 * mol().rf().yz();
+ + 0.5*mol().rf().yz();
p.y() +=
mol().mass() * mol().U().z() * mol().U().x()
- +
- 0.5 * mol().rf().zx();
+ + 0.5*mol().rf().zx();
p.z() +=
mol().mass() * mol().U().x() * mol().U().y()
- +
- 0.5 * mol().rf().xy();
+ + 0.5*mol().rf().xy();
}
pacf.calculateCorrelationFunction(p);
@@ -93,12 +90,10 @@ if (mesh.time().timeIndex() % hfacf.sampleSteps() == 0)
{
s +=
(
- 0.5 * mol().mass() * magSqr(mol().U())
- +
- mol().potentialEnergy()
- ) * mol().U()
- +
- 0.5 * ( mol().rf() & mol().U() );
+ 0.5*mol().mass()*magSqr(mol().U())
+ + mol().potentialEnergy()
+ )*mol().U()
+ + 0.5*(mol().rf() & mol().U());
}
hfacf.calculateCorrelationFunction(s);
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
index 1ffbcc15b79d4b45fd462d6c799747370b7d137b..0ee094ff149a2d25a9b9ff89d8f31420557039b0 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/calculateTransportProperties.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -37,7 +37,7 @@ if (writeVacf)
}
}
-Info << "Diffusion coefficient = "
+Info<< "Diffusion coefficient = "
<< vacf.integral() << endl;
if (writePacf)
@@ -57,13 +57,13 @@ Info<< "Viscosity = "
<< pacf.integral()/averageTemperature/moleculeCloud::kb/meshVolume
<< endl;
-if(writeHFacf)
+if (writeHFacf)
{
OFstream hfacfFile
(
runTime.path()/ + "hfacf"
);
-
+
if (!hfacf.writeAveraged(hfacfFile))
{
FatalErrorIn(args.executable())
@@ -73,7 +73,7 @@ if(writeHFacf)
}
}
-Info << "Thermal conductivity = "
+Info<< "Thermal conductivity = "
<< hfacf.integral()
/averageTemperature
/averageTemperature
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H b/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
index 6821055ae0036f84b57eaabda6ee2eff4d2842ca..ab2d593cc682aec604752381264053cc4edc3840 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/createAutoCorrelationFunctions.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/md.H b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
index ae4ab08124268c2dbeb756c5c8fc932abc84b07e..9a079764ae823abdac17a56236003610c44863df 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/md.H
@@ -1,11 +1,9 @@
#ifndef md_H
#define md_H
-
-# include "potential.H"
-# include "moleculeCloud.H"
-# include "correlationFunction.H"
-# include "distribution.H"
-# include "reducedUnits.H"
-
+ #include "potential.H"
+ #include "moleculeCloud.H"
+ #include "correlationFunction.H"
+ #include "distribution.H"
+ #include "reducedUnits.H"
#endif
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
index 8688d63669bbda4a361b5d4b91d348b2bb2cdc21..fb5118bb5a484f0ce77bb3dd7a88b0e88aa2fd14 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/meanMomentumEnergyAndNMols.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -52,6 +52,8 @@ scalar singleStepTotalrDotf = 0.0;
label singleStepNMols = molecules.size();
+label singleStepDOFs = 0;
+
{
IDLList<molecule>::iterator mol(molecules.begin());
@@ -85,9 +87,11 @@ label singleStepNMols = molecules.size();
{
label molId = mol().id();
- scalar molMass(molecules.constProps(molId).mass());
+ const molecule::constantProperties cP(molecules.constProps(molId));
+
+ scalar molMass(cP.mass());
- const diagTensor& molMoI(molecules.constProps(molId).momentOfInertia());
+ const diagTensor& molMoI(cP.momentOfInertia());
const vector& molV(mol().v());
@@ -112,6 +116,8 @@ label singleStepNMols = molecules.size();
singleStepTotalPE += mol().potentialEnergy();
singleStepTotalrDotf += tr(mol().rf());
+
+ singleStepDOFs += cP.degreesOfFreedom();
}
}
@@ -134,50 +140,53 @@ if (Pstream::parRun())
reduce(singleStepTotalrDotf, sumOp<scalar>());
reduce(singleStepNMols, sumOp<label>());
+
+ reduce(singleStepDOFs, sumOp<label>());
}
if (singleStepNMols)
{
- Info<< "Number of mols in system = "
+ Info<< "Number of molecules in system = "
<< singleStepNMols << nl
<< "Overall number density = "
<< singleStepNMols/meshVolume << nl
<< "Overall mass density = "
<< singleStepTotalMass/meshVolume << nl
- << "Average linear momentum per mol = "
+ << "Average linear momentum per molecule = "
<< singleStepTotalLinearMomentum/singleStepNMols << ' '
<< mag(singleStepTotalLinearMomentum)/singleStepNMols << nl
- << "Average angular momentum per mol = "
+ << "Average angular momentum per molecule = "
<< singleStepTotalAngularMomentum << ' '
<< mag(singleStepTotalAngularMomentum)/singleStepNMols << nl
<< "Maximum |velocity| = "
<< singleStepMaxVelocityMag << nl
- << "Average linear KE per mol = "
+ << "Average linear KE per molecule = "
<< singleStepTotalLinearKE/singleStepNMols << nl
- << "Average angular KE per mol = "
+ << "Average angular KE per molecule = "
<< singleStepTotalAngularKE/singleStepNMols << nl
- << "Average PE per mol = "
+ << "Average PE per molecule = "
<< singleStepTotalPE/singleStepNMols << nl
- << "Average TE per mol = "
+ << "Average TE per molecule = "
<<
(
singleStepTotalLinearKE
- + singleStepTotalAngularKE
- + singleStepTotalPE
+ + singleStepTotalAngularKE
+ + singleStepTotalPE
)
/singleStepNMols
<< endl;
-// Info << singleStepNMols << " "
-// // << singleStepTotalMomentum/singleStepTotalMass << " "
-// << singleStepMaxVelocityMag << " "
-// << singleStepTotalKE/singleStepNMols << " "
-// << singleStepTotalPE/singleStepNMols << " "
-// << (singleStepTotalKE + singleStepTotalPE)/singleStepNMols << endl;
+ // Info << singleStepNMols << " "
+ // << singleStepTotalMomentum/singleStepTotalMass << " "
+ // << singleStepMaxVelocityMag << " "
+ // << singleStepTotalKE/singleStepNMols << " "
+ // << singleStepTotalPE/singleStepNMols << " "
+ // << (singleStepTotalKE + singleStepTotalPE)
+ // /singleStepNMols << endl;
}
else
{
- Info << "No molecules in system" << endl;
+ Info<< "No molecules in system" << endl;
}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
index ff274a33366d579e1a12ae49cf425bd7f9b34cc9..af0197b5fe4dc0fc2e75858e9f49ba86f3b0a273 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/resetMDFields.H
@@ -3,24 +3,24 @@ if (runTime.outputTime())
allSpeciesN_RU = List< scalarField >
(
molecules.potential().nIds(),
- scalarField (mesh.nCells(), 0.0)
+ scalarField(mesh.nCells(), 0.0)
);
allSpeciesM_RU = List< scalarField >
(
molecules.potential().nIds(),
- scalarField (mesh.nCells(), 0.0)
+ scalarField(mesh.nCells(), 0.0)
);
allSpeciesVelocitySum_RU = List< vectorField >
(
molecules.potential().nIds(),
- vectorField (mesh.nCells(), vector::zero)
+ vectorField(mesh.nCells(), vector::zero)
);
allSpeciesVelocityMagSquaredSum_RU = List< scalarField >
(
molecules.potential().nIds(),
- scalarField (mesh.nCells(), 0.0)
+ scalarField(mesh.nCells(), 0.0)
);
}
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
index 4ba2bc1bc4d3188c4137b20d50626f963f0550bc..788763b163df63c6e173b91ce6905bd81384f758 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressure.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -47,17 +47,17 @@ accumulatedTotalrDotfSum += singleStepTotalrDotf;
accumulatedNMols += singleStepNMols;
+accumulatedDOFs += singleStepDOFs;
+
if (runTime.outputTime())
{
- // calculate averages
-
if (accumulatedNMols)
{
Info << "calculating averages" << endl;
averageTemperature =
(
- 2.0/(6.0 * moleculeCloud::kb * accumulatedNMols)
+ 2.0/(moleculeCloud::kb * accumulatedDOFs)
*
(
accumulatedTotalLinearKE + accumulatedTotalAngularKE
@@ -79,27 +79,20 @@ if (runTime.outputTime())
meshVolume
);
- // output values
-
Info << "----------------------------------------" << nl
<< "Averaged properties" << nl
<< "Average |velocity| = "
- << mag(accumulatedTotalLinearMomentum)/accumulatedTotalMass
- << " m/s" << nl
- << "Average temperature = "
- << averageTemperature << " K" << nl
- << "Average pressure = "
- << averagePressure << " N/m^2" << nl
+ << mag(accumulatedTotalLinearMomentum)/accumulatedTotalMass << nl
+ << "Average temperature = " << averageTemperature << nl
+ << "Average pressure = " << averagePressure << nl
<< "----------------------------------------" << endl;
}
else
{
- Info << "Not averaging temperature and pressure: "
+ Info<< "Not averaging temperature and pressure: "
<< "no molecules in system" << endl;
}
- // reset counters
-
accumulatedTotalLinearMomentum = vector::zero;
accumulatedTotalMass = 0.0;
@@ -113,6 +106,9 @@ if (runTime.outputTime())
accumulatedTotalrDotfSum = 0.0;
accumulatedNMols = 0;
+
+ accumulatedDOFs = 0;
}
+
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
index e5e236271f834659d2c1662427e95e66164408a3..9856c9d4da82a62412ce5a96c73bd8c7656456fc 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureAndPressureVariables.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -44,6 +44,8 @@ scalar accumulatedTotalrDotfSum = 0.0;
label accumulatedNMols = 0;
+label accumulatedDOFs = 0;
+
scalar averageTemperature = 0.0;
scalar averagePressure = 0.0;
diff --git a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
index 1d924db4b49ad84b14895c13d45152e0ee4c0134..b1ac5d4230e4de124495c8f45e53542380a961db 100644
--- a/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
+++ b/src/lagrangian/molecularDynamics/molecule/mdTools/temperatureEquilibration.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
index bc9c502ffb57f90181a70127c23c67563e4eb8f1..64c5c45ccf9bc54036aca97284dbe6d218a314f2 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
index 0ee16f461f00cc2b61c28b694aa290a877448175..ef2de145c464a7e5cefe15e652bcf34cd440c908 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/molecule.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -82,6 +82,8 @@ public:
Field<vector> siteReferencePositions_;
+ List<scalar> siteMasses_;
+
List<scalar> siteCharges_;
List<label> siteIds_;
@@ -106,6 +108,7 @@ public:
bool linearMoleculeTest() const;
+
public:
inline constantProperties();
@@ -117,6 +120,8 @@ public:
inline const Field<vector>& siteReferencePositions() const;
+ inline const List<scalar>& siteMasses() const;
+
inline const List<scalar>& siteCharges() const;
inline const List<label>& siteIds() const;
@@ -137,6 +142,8 @@ public:
inline bool pointMolecule() const;
+ inline label degreesOfFreedom() const;
+
inline scalar mass() const;
inline label nSites() const;
@@ -208,6 +215,7 @@ private:
List<vector> sitePositions_;
+
// Private Member Functions
tensor rotationTensorX(scalar deltaT) const;
@@ -216,6 +224,7 @@ private:
tensor rotationTensorZ(scalar deltaT) const;
+
public:
friend class Cloud<molecule>;
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
index eb80dd930fb7fa22ad6ed70d27cbd78930433340..447a04e4ea3e047f045ac56cf55af05aa2849cac 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -29,6 +29,7 @@ License
inline Foam::molecule::constantProperties::constantProperties()
:
siteReferencePositions_(Field<vector>(0)),
+ siteMasses_(List<scalar>(0)),
siteCharges_(List<scalar>(0)),
siteIds_(List<label>(0)),
pairPotentialSites_(List<bool>(false)),
@@ -44,6 +45,7 @@ inline Foam::molecule::constantProperties::constantProperties
)
:
siteReferencePositions_(dict.lookup("siteReferencePositions")),
+ siteMasses_(dict.lookup("siteMasses")),
siteCharges_(dict.lookup("siteCharges")),
siteIds_(List<word>(dict.lookup("siteIds")).size(), -1),
pairPotentialSites_(),
@@ -59,9 +61,7 @@ inline Foam::molecule::constantProperties::constantProperties
List<word>(dict.lookup("pairPotentialSiteIds"))
);
- scalarList siteMasses(dict.lookup("siteMasses"));
-
- mass_ = sum(siteMasses);
+ mass_ = sum(siteMasses_);
vector centreOfMass(vector::zero);
@@ -70,7 +70,7 @@ inline Foam::molecule::constantProperties::constantProperties
forAll(siteReferencePositions_, i)
{
- centreOfMass += siteReferencePositions_[i]*siteMasses[i];
+ centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
}
centreOfMass /= mass_;
@@ -106,7 +106,7 @@ inline Foam::molecule::constantProperties::constantProperties
forAll(siteReferencePositions_, i)
{
- centreOfMass += siteReferencePositions_[i]*siteMasses[i];
+ centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
}
centreOfMass /= mass_;
@@ -119,10 +119,8 @@ inline Foam::molecule::constantProperties::constantProperties
{
const vector& p(siteReferencePositions_[i]);
- momOfInertia += siteMasses[i]*diagTensor
- (
- 0, p.x()*p.x(), p.x()*p.x()
- );
+ momOfInertia +=
+ siteMasses_[i]*diagTensor(0, p.x()*p.x(), p.x()*p.x());
}
momentOfInertia_ = diagTensor
@@ -144,7 +142,7 @@ inline Foam::molecule::constantProperties::constantProperties
{
const vector& p(siteReferencePositions_[i]);
- momOfInertia += siteMasses[i]*tensor
+ momOfInertia += siteMasses_[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
@@ -156,8 +154,7 @@ inline Foam::molecule::constantProperties::constantProperties
{
FatalErrorIn("molecule::constantProperties::constantProperties")
<< "An eigenvalue of the inertia tensor is zero, the molecule "
- << dict.name()
- << " is not a valid 6DOF shape."
+ << dict.name() << " is not a valid 6DOF shape."
<< nl << abort(FatalError);
}
@@ -172,7 +169,7 @@ inline Foam::molecule::constantProperties::constantProperties
// global axes
tensor Q =
- vector(1,0,0)*e.x() + vector(0,1,0)*e.y() + vector(0,0,1)*e.z();
+ vector(1,0,0)*e.x() + vector(0,1,0)*e.y() + vector(0,0,1)*e.z();
// Transform the site positions
@@ -187,7 +184,7 @@ inline Foam::molecule::constantProperties::constantProperties
forAll(siteReferencePositions_, i)
{
- centreOfMass += siteReferencePositions_[i]*siteMasses[i];
+ centreOfMass += siteReferencePositions_[i]*siteMasses_[i];
}
centreOfMass /= mass_;
@@ -203,7 +200,7 @@ inline Foam::molecule::constantProperties::constantProperties
{
const vector& p(siteReferencePositions_[i]);
- momOfInertia += siteMasses[i]*tensor
+ momOfInertia += siteMasses_[i]*tensor
(
p.y()*p.y() + p.z()*p.z(), -p.x()*p.y(), -p.x()*p.z(),
-p.y()*p.x(), p.x()*p.x() + p.z()*p.z(), -p.y()*p.z(),
@@ -337,6 +334,13 @@ Foam::molecule::constantProperties::siteReferencePositions() const
}
+inline const Foam::List<Foam::scalar>&
+Foam::molecule::constantProperties::siteMasses() const
+{
+ return siteMasses_;
+}
+
+
inline const Foam::List<Foam::scalar>&
Foam::molecule::constantProperties::siteCharges() const
{
@@ -372,7 +376,7 @@ inline bool Foam::molecule::constantProperties::pairPotentialSite
{
label s = findIndex(siteIds_, sId);
- if(s == -1)
+ if (s == -1)
{
FatalErrorIn("moleculeI.H") << nl
<< sId << " site not found."
@@ -396,10 +400,12 @@ inline bool Foam::molecule::constantProperties::electrostaticSite
{
label s = findIndex(siteIds_, sId);
- if(s == -1)
+ if (s == -1)
{
- FatalErrorIn("moleculeI.H") << nl
- << sId << " site not found."
+ FatalErrorIn
+ (
+ "molecule::constantProperties::electrostaticSite(label)"
+ ) << sId << " site not found."
<< nl << abort(FatalError);
}
@@ -416,7 +422,7 @@ Foam::molecule::constantProperties::momentOfInertia() const
inline bool Foam::molecule::constantProperties::linearMolecule() const
{
- return (momentOfInertia_.xx() < 0);
+ return ((momentOfInertia_.xx() < 0) && (momentOfInertia_.yy() > 0));
}
@@ -426,6 +432,23 @@ inline bool Foam::molecule::constantProperties::pointMolecule() const
}
+inline Foam::label Foam::molecule::constantProperties::degreesOfFreedom() const
+{
+ if (linearMolecule())
+ {
+ return 5;
+ }
+ else if (pointMolecule())
+ {
+ return 3;
+ }
+ else
+ {
+ return 6;
+ }
+}
+
+
inline Foam::scalar Foam::molecule::constantProperties::mass() const
{
return mass_;
@@ -592,6 +615,4 @@ inline Foam::label Foam::molecule::id() const
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
index c1e99d8a0bd06b79cf0dbdf36b4b1dde46485ea2..04ae825df59f5914dfc968ee84c58c13b387de62 100644
--- a/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
+++ b/src/lagrangian/molecularDynamics/molecule/molecule/moleculeIO.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -55,16 +55,16 @@ Foam::molecule::molecule
{
if (is.format() == IOstream::ASCII)
{
- is >> Q_;
- is >> v_;
- is >> a_;
- is >> pi_;
- is >> tau_;
- is >> siteForces_;
- is >> sitePositions_;
- is >> specialPosition_;
+ is >> Q_;
+ is >> v_;
+ is >> a_;
+ is >> pi_;
+ is >> tau_;
+ is >> siteForces_;
+ is >> sitePositions_;
+ is >> specialPosition_;
potentialEnergy_ = readScalar(is);
- is >> rf_;
+ is >> rf_;
special_ = readLabel(is);
id_ = readLabel(is);
}
@@ -74,18 +74,18 @@ Foam::molecule::molecule
(
reinterpret_cast<char*>(&Q_),
sizeof(Q_)
- + sizeof(v_)
- + sizeof(a_)
- + sizeof(pi_)
- + sizeof(tau_)
- + sizeof(specialPosition_)
- + sizeof(potentialEnergy_)
- + sizeof(rf_)
- + sizeof(special_)
- + sizeof(id_)
+ + sizeof(v_)
+ + sizeof(a_)
+ + sizeof(pi_)
+ + sizeof(tau_)
+ + sizeof(specialPosition_)
+ + sizeof(potentialEnergy_)
+ + sizeof(rf_)
+ + sizeof(special_)
+ + sizeof(id_)
);
- is >> siteForces_ >> sitePositions_;
+ is >> siteForces_ >> sitePositions_;
}
}
@@ -169,6 +169,38 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
IOField<label> special(mC.fieldIOobject("special", IOobject::NO_READ), np);
IOField<label> id(mC.fieldIOobject("id", IOobject::NO_READ), np);
+ // Post processing fields
+
+ IOField<vector> piGlobal
+ (
+ mC.fieldIOobject("piGlobal", IOobject::NO_READ),
+ np
+ );
+
+ IOField<vector> tauGlobal
+ (
+ mC.fieldIOobject("tauGlobal", IOobject::NO_READ),
+ np
+ );
+
+ IOField<vector> orientation1
+ (
+ mC.fieldIOobject("orientation1", IOobject::NO_READ),
+ np
+ );
+
+ IOField<vector> orientation2
+ (
+ mC.fieldIOobject("orientation2", IOobject::NO_READ),
+ np
+ );
+
+ IOField<vector> orientation3
+ (
+ mC.fieldIOobject("orientation3", IOobject::NO_READ),
+ np
+ );
+
label i = 0;
forAllConstIter(moleculeCloud, mC, iter)
{
@@ -182,6 +214,14 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
specialPosition[i] = mol.specialPosition_;
special[i] = mol.special_;
id[i] = mol.id_;
+
+ piGlobal[i] = mol.Q_ & mol.pi_;
+ tauGlobal[i] = mol.Q_ & mol.tau_;
+
+ orientation1[i] = mol.Q_ & vector(1,0,0);
+ orientation2[i] = mol.Q_ & vector(0,1,0);
+ orientation3[i] = mol.Q_ & vector(0,0,1);
+
i++;
}
@@ -193,6 +233,18 @@ void Foam::molecule::writeFields(const moleculeCloud& mC)
specialPosition.write();
special.write();
id.write();
+
+ piGlobal.write();
+ tauGlobal.write();
+
+ orientation1.write();
+ orientation2.write();
+ orientation3.write();
+
+ mC.writeXYZ
+ (
+ mC.mesh().time().timePath() + "/lagrangian" + "/moleculeCloud.xmol"
+ );
}
@@ -225,17 +277,17 @@ Foam::Ostream& Foam::operator<<(Ostream& os, const molecule& mol)
(
reinterpret_cast<const char*>(&mol.Q_),
sizeof(mol.Q_)
- + sizeof(mol.v_)
- + sizeof(mol.a_)
- + sizeof(mol.pi_)
- + sizeof(mol.tau_)
- + sizeof(mol.specialPosition_)
- + sizeof(mol.potentialEnergy_)
- + sizeof(mol.rf_)
- + sizeof(mol.special_)
- + sizeof(mol.id_)
+ + sizeof(mol.v_)
+ + sizeof(mol.a_)
+ + sizeof(mol.pi_)
+ + sizeof(mol.tau_)
+ + sizeof(mol.specialPosition_)
+ + sizeof(mol.potentialEnergy_)
+ + sizeof(mol.rf_)
+ + sizeof(mol.special_)
+ + sizeof(mol.id_)
);
- os << mol.siteForces_ << mol.sitePositions_;
+ os << mol.siteForces_ << mol.sitePositions_;
}
// Check state of Ostream
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
index a0c45a73655871aaf5b819f6e0f854bb40310790..b747373e3a71e2682a01f0cb335262bc916ce8dc 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -928,7 +928,6 @@ void Foam::moleculeCloud::initialiseMolecules
n++;
}
-
}
}
}
@@ -1025,6 +1024,21 @@ void Foam::moleculeCloud::createMolecule
}
+Foam::label Foam::moleculeCloud::nSites() const
+{
+ label n = 0;
+
+ const_iterator mol(this->begin());
+
+ for (mol = this->begin(); mol != this->end(); ++mol)
+ {
+ n += constProps(mol().id()).nSites();
+ }
+
+ return n;
+}
+
+
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::moleculeCloud::moleculeCloud
@@ -1158,4 +1172,30 @@ void Foam::moleculeCloud::writeFields() const
}
+void Foam::moleculeCloud::writeXYZ(const fileName& fName) const
+{
+ OFstream str(fName);
+
+ str << nSites() << nl << "moleculeCloud site positions in angstroms" << nl;
+
+ const_iterator mol(this->begin());
+
+ for (mol = this->begin(); mol != this->end(); ++mol)
+ {
+ const molecule::constantProperties& cP = constProps(mol().id());
+
+ forAll(mol().sitePositions(), i)
+ {
+ const point& sP = mol().sitePositions()[i];
+
+ str << pot_.siteIdList()[cP.siteIds()[i]]
+ << ' ' << sP.x()*1e10
+ << ' ' << sP.y()*1e10
+ << ' ' << sP.z()*1e10
+ << nl;
+ }
+ }
+}
+
+
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
index d6f961ca0ce573329508db010a106d1cd901f9af..6863227c12ceb43c81f07e51e7dea4b1bc2ee5e5 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloud.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -44,6 +44,7 @@ SourceFiles
#include "interactionLists.H"
#include "labelVector.H"
#include "Random.H"
+#include "fileName.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -51,7 +52,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class moleculeCloud Declaration
+ Class moleculeCloud Declaration
\*---------------------------------------------------------------------------*/
class moleculeCloud
@@ -75,6 +76,7 @@ private:
Random rndGen_;
+
// Private Member Functions
void buildConstProps();
@@ -131,6 +133,8 @@ private:
const vector& bulkVelocity
);
+ label nSites() const;
+
inline vector equipartitionLinearVelocity
(
scalar temperature,
@@ -160,6 +164,7 @@ public:
static scalar vacuumPermittivity;
+
// Constructors
//- Construct given mesh and potential references
@@ -177,8 +182,8 @@ public:
const IOdictionary& mdInitialiseDict
);
- // Member Functions
+ // Member Functions
//- Evolve the molecules (move, calculate forces, control state etc)
void evolve();
@@ -191,6 +196,7 @@ public:
const scalar measuredTemperature
);
+
// Access
inline const polyMesh& mesh() const;
@@ -204,15 +210,18 @@ public:
inline const List<molecule::constantProperties> constProps() const;
inline const molecule::constantProperties&
- constProps(label id) const;
+ constProps(label id) const;
inline Random& rndGen();
+
// Member Operators
//- Write fields
+ void writeFields() const;
- void writeFields() const;
+ //- Write molecule sites in XYZ format
+ void writeXYZ(const fileName& fName) const;
};
diff --git a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
index 55813e665812c14d992c6883802ccdd35df27e74..94c9f49286bda8afbdbd62eef7ca2dd8cb19327e 100644
--- a/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
+++ b/src/lagrangian/molecularDynamics/molecule/moleculeCloud/moleculeCloudI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -32,9 +32,9 @@ inline void Foam::moleculeCloud::evaluatePair
molecule* molJ
)
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const electrostaticPotential& electrostatic(pot_.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idI = molI->id();
@@ -67,7 +67,7 @@ inline void Foam::moleculeCloud::evaluatePair
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
{
vector rsIsJ =
- molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
+ molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
scalar rsIsJMagSq = magSqr(rsIsJ);
@@ -75,8 +75,9 @@ inline void Foam::moleculeCloud::evaluatePair
{
scalar rsIsJMag = mag(rsIsJ);
- vector fsIsJ = (rsIsJ/rsIsJMag)
- *pairPot.force(idsI, idsJ, rsIsJMag);
+ vector fsIsJ =
+ (rsIsJ/rsIsJMag)
+ *pairPot.force(idsI, idsJ, rsIsJMag);
molI->siteForces()[sI] += fsIsJ;
@@ -91,9 +92,18 @@ inline void Foam::moleculeCloud::evaluatePair
molJ->potentialEnergy() += 0.5*potentialEnergy;
- molI->rf() += rsIsJ * fsIsJ;
+ vector rIJ = molI->position() - molJ->position();
+
+ tensor virialContribution =
+ (rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
+
+ molI->rf() += virialContribution;
+
+ molJ->rf() += virialContribution;
- molJ->rf() += rsIsJ * fsIsJ;
+ // molI->rf() += rsIsJ * fsIsJ;
+
+ // molJ->rf() += rsIsJ * fsIsJ;
}
}
@@ -104,7 +114,7 @@ inline void Foam::moleculeCloud::evaluatePair
scalar rsIsJMagSq = magSqr(rsIsJ);
- if(pairPot.rCutMaxSqr(rsIsJMagSq))
+ if(rsIsJMagSq <= electrostatic.rCutSqr())
{
scalar rsIsJMag = mag(rsIsJ);
@@ -112,38 +122,50 @@ inline void Foam::moleculeCloud::evaluatePair
scalar chargeJ = constPropJ.siteCharges()[sJ];
- vector fsIsJ = (rsIsJ/rsIsJMag)
- *chargeI*chargeJ*electrostatic.force(rsIsJMag);
+ vector fsIsJ =
+ (rsIsJ/rsIsJMag)
+ *chargeI*chargeJ*electrostatic.force(rsIsJMag);
molI->siteForces()[sI] += fsIsJ;
molJ->siteForces()[sJ] += -fsIsJ;
- scalar potentialEnergy = chargeI*chargeJ
- *electrostatic.energy(rsIsJMag);
+ scalar potentialEnergy =
+ chargeI*chargeJ
+ *electrostatic.energy(rsIsJMag);
molI->potentialEnergy() += 0.5*potentialEnergy;
molJ->potentialEnergy() += 0.5*potentialEnergy;
- molI->rf() += rsIsJ * fsIsJ;
+ vector rIJ = molI->position() - molJ->position();
+
+ tensor virialContribution =
+ (rsIsJ*fsIsJ)*(rsIsJ & rIJ)/rsIsJMagSq;
+
+ molI->rf() += virialContribution;
+
+ molJ->rf() += virialContribution;
- molJ->rf() += rsIsJ * fsIsJ;
+ // molI->rf() += rsIsJ * fsIsJ;
+
+ // molJ->rf() += rsIsJ * fsIsJ;
}
}
}
}
}
+
inline void Foam::moleculeCloud::evaluatePair
(
molecule* molReal,
referredMolecule* molRef
)
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const electrostaticPotential& electrostatic(pot_.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idReal = molReal->id();
@@ -176,16 +198,18 @@ inline void Foam::moleculeCloud::evaluatePair
if (pairPotentialSitesReal[sReal] && pairPotentialSitesRef[sRef])
{
vector rsRealsRef =
- molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
+ molReal->sitePositions()[sReal]
+ - molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
- if(pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
+ if (pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
{
scalar rsRealsRefMag = mag(rsRealsRef);
- vector fsRealsRef = (rsRealsRef/rsRealsRefMag)
- *pairPot.force(idsReal, idsRef, rsRealsRefMag);
+ vector fsRealsRef =
+ (rsRealsRef/rsRealsRefMag)
+ *pairPot.force(idsReal, idsRef, rsRealsRefMag);
molReal->siteForces()[sReal] += fsRealsRef;
@@ -196,7 +220,14 @@ inline void Foam::moleculeCloud::evaluatePair
molReal->potentialEnergy() += 0.5*potentialEnergy;
- molReal->rf() += rsRealsRef * fsRealsRef;
+ vector rRealRef = molReal->position() - molRef->position();
+
+ molReal->rf() +=
+ (rsRealsRef*fsRealsRef)
+ *(rsRealsRef & rRealRef)
+ /rsRealsRefMagSq;
+
+ // molReal->rf() += rsRealsRef * fsRealsRef;
}
}
@@ -204,11 +235,12 @@ inline void Foam::moleculeCloud::evaluatePair
if (electrostaticSitesReal[sReal] && electrostaticSitesRef[sRef])
{
vector rsRealsRef =
- molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
+ molReal->sitePositions()[sReal]
+ - molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
- if(pairPot.rCutMaxSqr(rsRealsRefMagSq))
+ if (rsRealsRefMagSq <= electrostatic.rCutSqr())
{
scalar rsRealsRefMag = mag(rsRealsRef);
@@ -216,18 +248,27 @@ inline void Foam::moleculeCloud::evaluatePair
scalar chargeRef = constPropRef.siteCharges()[sRef];
- vector fsRealsRef = (rsRealsRef/rsRealsRefMag)
- *chargeReal*chargeRef
- *electrostatic.force(rsRealsRefMag);
+ vector fsRealsRef =
+ (rsRealsRef/rsRealsRefMag)
+ *chargeReal*chargeRef
+ *electrostatic.force(rsRealsRefMag);
molReal->siteForces()[sReal] += fsRealsRef;
- scalar potentialEnergy = chargeReal*chargeRef
- *electrostatic.energy(rsRealsRefMag);
+ scalar potentialEnergy =
+ chargeReal*chargeRef
+ *electrostatic.energy(rsRealsRefMag);
molReal->potentialEnergy() += 0.5*potentialEnergy;
- molReal->rf() += rsRealsRef * fsRealsRef;
+ vector rRealRef = molReal->position() - molRef->position();
+
+ molReal->rf() +=
+ (rsRealsRef*fsRealsRef)
+ *(rsRealsRef & rRealRef)
+ /rsRealsRefMagSq;
+
+ // molReal->rf() += rsRealsRef * fsRealsRef;
}
}
}
@@ -241,9 +282,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
molecule* molJ
) const
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const electrostaticPotential& electrostatic(pot_.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idI = molI->id();
@@ -276,11 +317,11 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (pairPotentialSitesI[sI] && pairPotentialSitesJ[sJ])
{
vector rsIsJ =
- molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
+ molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
scalar rsIsJMagSq = magSqr(rsIsJ);
- if(pairPot.rCutSqr(idsI, idsJ, rsIsJMagSq))
+ if (pairPot.rCutSqr(idsI, idsJ, rsIsJMagSq))
{
scalar rsIsJMag = mag(rsIsJ);
@@ -291,7 +332,7 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsIsJMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
- << "Molecule site pair closer than "
+ << "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsIsJMag
<< ". These may have been placed on top of each"
@@ -325,11 +366,11 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (electrostaticSitesI[sI] && electrostaticSitesJ[sJ])
{
vector rsIsJ =
- molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
+ molI->sitePositions()[sI] - molJ->sitePositions()[sJ];
scalar rsIsJMagSq = magSqr(rsIsJ);
- if(pairPot.rCutMaxSqr(rsIsJMagSq))
+ if (pairPot.rCutMaxSqr(rsIsJMagSq))
{
scalar rsIsJMag = mag(rsIsJ);
@@ -340,18 +381,23 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsIsJMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
- << "Molecule site pair closer than "
+ << "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsIsJMag
<< ". These may have been placed on top of each"
- << " other by a rounding error in molConfig in"
- << " parallel or a block filled with molecules "
+ << " other by a rounding error in mdInitialise in"
+ << " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
return true;
}
+ if (rsIsJMag < electrostatic.rMin())
+ {
+ return true;
+ }
+
scalar chargeI = constPropI.siteCharges()[sI];
scalar chargeJ = constPropJ.siteCharges()[sJ];
@@ -379,9 +425,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
referredMolecule* molRef
) const
{
- const pairPotentialList& pairPot(pot_.pairPotentials());
+ const pairPotentialList& pairPot = pot_.pairPotentials();
- const electrostaticPotential& electrostatic(pot_.electrostatic());
+ const pairPotential& electrostatic = pairPot.electrostatic();
label idReal = molReal->id();
@@ -414,11 +460,12 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (pairPotentialSitesReal[sReal] && pairPotentialSitesRef[sRef])
{
vector rsRealsRef =
- molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
+ molReal->sitePositions()[sReal]
+ - molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
- if(pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
+ if (pairPot.rCutSqr(idsReal, idsRef, rsRealsRefMagSq))
{
scalar rsRealsRefMag = mag(rsRealsRef);
@@ -429,12 +476,12 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsRealsRefMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
- << "Molecule site pair closer than "
+ << "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsRealsRefMag
<< ". These may have been placed on top of each"
- << " other by a rounding error in molConfig in"
- << " parallel or a block filled with molecules "
+ << " other by a rounding error in mdInitialise in"
+ << " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
@@ -464,11 +511,12 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (electrostaticSitesReal[sReal] && electrostaticSitesRef[sRef])
{
vector rsRealsRef =
- molReal->sitePositions()[sReal] - molRef->sitePositions()[sRef];
+ molReal->sitePositions()[sReal]
+ - molRef->sitePositions()[sRef];
scalar rsRealsRefMagSq = magSqr(rsRealsRef);
- if(pairPot.rCutMaxSqr(rsRealsRefMagSq))
+ if (pairPot.rCutMaxSqr(rsRealsRefMagSq))
{
scalar rsRealsRefMag = mag(rsRealsRef);
@@ -479,18 +527,23 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
if (rsRealsRefMag < SMALL)
{
WarningIn("moleculeCloud::removeHighEnergyOverlaps()")
- << "Molecule site pair closer than "
+ << "Molecule site pair closer than "
<< SMALL
<< ": mag separation = " << rsRealsRefMag
<< ". These may have been placed on top of each"
- << " other by a rounding error in molConfig in"
- << " parallel or a block filled with molecules "
+ << " other by a rounding error in mdInitialise in"
+ << " parallel or a block filled with molecules"
<< " twice. Removing one of the molecules."
<< endl;
return true;
}
+ if (rsRealsRefMag < electrostatic.rMin())
+ {
+ return true;
+ }
+
scalar chargeReal = constPropReal.siteCharges()[sReal];
scalar chargeRef = constPropRef.siteCharges()[sRef];
@@ -499,8 +552,9 @@ inline bool Foam::moleculeCloud::evaluatePotentialLimit
(
mag
(
- chargeReal*chargeRef
- *electrostatic.energy(rsRealsRefMag)
+ chargeReal
+ *chargeRef
+ *electrostatic.energy(rsRealsRefMag)
)
> pot_.potentialEnergyLimit()
)
@@ -559,6 +613,7 @@ inline Foam::vector Foam::moleculeCloud::equipartitionAngularMomentum
}
}
+
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline const Foam::polyMesh& Foam::moleculeCloud::mesh() const
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
index e9b048507bd61d9e01d0ed0c7e3957fd5a5a0e49..6836c2bc277e3f13ee476df76d7aca0b250a5102 100644
--- a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
index 294aa7770e6de424c553ce159de0f514186835d2..acefe4b8151c571323d955d8d69b8485eebd9df3 100644
--- a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnits.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class reducedUnits Declaration
+ Class reducedUnits Declaration
\*---------------------------------------------------------------------------*/
class reducedUnits
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
index 8f3ae51b16ac067f64e75f59906e982e29fe6d5f..72ff243776432aaa5b77cee3581b7553b602a972 100644
--- a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
index 175a2aa4899b2c04029a26e65ca2717830f634e7..03b4489ec5a34ac510a6170de116bc6a97e3202b 100644
--- a/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
+++ b/src/lagrangian/molecularDynamics/molecule/reducedUnits/reducedUnitsIO.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/potential/Make/files b/src/lagrangian/molecularDynamics/potential/Make/files
index 7b16b6e2b61938fcc029900b8db8322f0b933055..4afe4de3d950a1a9cc18af997d5324566b275fb2 100644
--- a/src/lagrangian/molecularDynamics/potential/Make/files
+++ b/src/lagrangian/molecularDynamics/potential/Make/files
@@ -15,6 +15,7 @@ $(pairPotential)/derived/maitlandSmith/maitlandSmith.C
$(pairPotential)/derived/azizChen/azizChen.C
$(pairPotential)/derived/exponentialRepulsion/exponentialRepulsion.C
$(pairPotential)/derived/coulomb/coulomb.C
+$(pairPotential)/derived/dampedCoulomb/dampedCoulomb.C
$(pairPotential)/derived/noInteraction/noInteraction.C
energyScalingFunction = energyScalingFunction
@@ -43,4 +44,4 @@ electrostaticPotential = electrostaticPotential
$(electrostaticPotential)/electrostaticPotential.C
-LIB = $(FOAM_LIBBIN)/libpotential
+LIB = $(FOAM_LIBBIN)/libpotential
\ No newline at end of file
diff --git a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
index 17fe776235acbd98aa65e2e11eed5c15e3e53156..1dff432741c4766ee3c86003af8a62f97fde9a4a 100644
--- a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -27,8 +27,6 @@ License
#include "electrostaticPotential.H"
#include "mathematicalConstants.H"
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::electrostaticPotential::electrostaticPotential()
diff --git a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
index 0bc0e0d4d04416b75f3d0f732db5b44684556c71..d2c4bb88b917388875cccdc52b0f3d5c06128f2e 100644
--- a/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
+++ b/src/lagrangian/molecularDynamics/potential/electrostaticPotential/electrostaticPotential.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -44,7 +44,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class electrostaticPotential Declaration
+ Class electrostaticPotential Declaration
\*---------------------------------------------------------------------------*/
class electrostaticPotential
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
index c06f90ea27ea0ba7f4235a224680bdc982888986..df247d84dea90ba5f5d0b698436b7da1bfd55b44 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -36,8 +36,6 @@ namespace Foam
defineTypeNameAndDebug(energyScalingFunction, 0);
defineRunTimeSelectionTable(energyScalingFunction, dictionary);
-// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::energyScalingFunction::energyScalingFunction
@@ -66,6 +64,7 @@ bool Foam::energyScalingFunction::read
return true;
}
+
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
} // End namespace Foam
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
index 4473fe2bb043b280524a92221d267de2b83bd358..8815151bcf0392705dc4e5309521460abfe44d54 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/energyScalingFunction.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -48,7 +48,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class energyScalingFunction Declaration
+ Class energyScalingFunction Declaration
\*---------------------------------------------------------------------------*/
class energyScalingFunction
@@ -144,8 +144,6 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
#endif
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
index 92166f863215f4d9daaf373700d0aad2d2088607..ccbdb8c92e7d2fa386df5ca3578e46f8c9b0d6b6 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/basic/newEnergyScalingFunction.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -58,8 +58,8 @@ autoPtr<energyScalingFunction> energyScalingFunction::New
(
"energyScalingFunction::New()"
) << "Unknown energyScalingFunction type "
- << energyScalingFunctionTypeName << endl << endl
- << "Valid energyScalingFunctions are : " << endl
+ << energyScalingFunctionTypeName << nl << nl
+ << "Valid energyScalingFunctions are: " << nl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
index 6ca0fff321cd6fce75773f319be56a91775191fe..defeb779a0620c7d75eb381111bf016c99cc96a5 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -57,6 +57,7 @@ scalar doubleSigmoid::sigmoidScale
return 1.0 / (1.0 + exp( scale * (r - shift)));
}
+
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
doubleSigmoid::doubleSigmoid
@@ -67,13 +68,17 @@ doubleSigmoid::doubleSigmoid
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
- doubleSigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
+ doubleSigmoidCoeffs_
+ (
+ energyScalingFunctionProperties.subDict(typeName + "Coeffs")
+ ),
shift1_(readScalar(doubleSigmoidCoeffs_.lookup("shift1"))),
scale1_(readScalar(doubleSigmoidCoeffs_.lookup("scale1"))),
shift2_(readScalar(doubleSigmoidCoeffs_.lookup("shift2"))),
scale2_(readScalar(doubleSigmoidCoeffs_.lookup("scale2")))
{}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void doubleSigmoid::scaleEnergy(scalar& e, const scalar r) const
@@ -81,17 +86,19 @@ void doubleSigmoid::scaleEnergy(scalar& e, const scalar r) const
e *= sigmoidScale(r, shift1_, scale1_) * sigmoidScale(r, shift2_, scale2_);
}
+
bool doubleSigmoid::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
- doubleSigmoidCoeffs_ = energyScalingFunctionProperties.subDict(typeName + "Coeffs");
+ doubleSigmoidCoeffs_ =
+ energyScalingFunctionProperties.subDict(typeName + "Coeffs");
doubleSigmoidCoeffs_.lookup("shift1") >> shift1_;
doubleSigmoidCoeffs_.lookup("scale1") >> scale1_;
doubleSigmoidCoeffs_.lookup("shift2") >> shift2_;
doubleSigmoidCoeffs_.lookup("scale2") >> scale2_;
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
index 07c4dfbd49003d6306e850b11f8d027c490462f7..27e75fb1901a72c6450b7448f5eaac75910f5819 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/doubleSigmoid/doubleSigmoid.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
- Class doubleSigmoid Declaration
+ Class doubleSigmoid Declaration
\*---------------------------------------------------------------------------*/
class doubleSigmoid
@@ -62,6 +62,7 @@ class doubleSigmoid
scalar shift2_;
scalar scale2_;
+
// Private Member Functions
scalar sigmoidScale
@@ -98,7 +99,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
index ea4ec88ed43c657840b7d8ae7b80ae7f23d91202..412f7538876e19b72daa78e4e36176595d013802 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -60,15 +58,17 @@ noScaling::noScaling
energyScalingFunction(name, energyScalingFunctionProperties, pairPot)
{}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void noScaling::scaleEnergy(scalar& e, const scalar r) const
{}
+
bool noScaling::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
index 192c862fb4330fff66ca6d78346dc6a5b9e115af..ea2ad62aef18327594f59483d3b95f39493d1ec1 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/noScaling/noScaling.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -80,7 +80,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
index 90eccc9b8021ff9b4b5399c28821d03a171abae5..d6866cfc8f9878cde632284ebe34349ac18a1c27 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -61,6 +59,7 @@ shifted::shifted
e_at_rCut_(pairPot.unscaledEnergy(pairPot.rCut()))
{}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void shifted::scaleEnergy(scalar& e, const scalar r) const
@@ -68,10 +67,11 @@ void shifted::scaleEnergy(scalar& e, const scalar r) const
e -= e_at_rCut_;
}
+
bool shifted::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
index 6f95adbdb90f89b0d3a4c375ff1acca31e25543e..01b0b413f34e9abc72ed5d054492a79751513041 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shifted/shifted.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -57,6 +57,7 @@ class shifted
scalar e_at_rCut_;
+
public:
//- Runtime type information
@@ -79,11 +80,12 @@ public:
~shifted()
{}
+
// Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
index dec8729fae9841bb18906bea8cf863669fbb2181..72041de3e05c77b8c4781e7675d06b2f5e8d6846 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -63,6 +61,7 @@ shiftedForce::shiftedForce
de_dr_at_rCut_(pairPot.energyDerivative(rCut_, false))
{}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void shiftedForce::scaleEnergy(scalar& e, const scalar r) const
@@ -70,10 +69,11 @@ void shiftedForce::scaleEnergy(scalar& e, const scalar r) const
e -= ( e_at_rCut_ + de_dr_at_rCut_ * (r - rCut_) );
}
+
bool shiftedForce::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
index d67164c64e544a9930bbbbc1e6a149f89697a8b1..f6d97d002b633f28908820d6973697da22a85f30 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/shiftedForce/shiftedForce.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace energyScalingFunctions
{
/*---------------------------------------------------------------------------*\
- Class shiftedForce Declaration
+ Class shiftedForce Declaration
\*---------------------------------------------------------------------------*/
class shiftedForce
@@ -89,7 +89,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
index 43483221ae562c28d4e29ec69bc2cc2b6f18b389..c689608172acc735d5d4fbb408de72985ba9c07c 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,6 +45,7 @@ addToRunTimeSelectionTable
dictionary
);
+
// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
scalar sigmoid::sigmoidScale
@@ -57,6 +58,7 @@ scalar sigmoid::sigmoidScale
return 1.0 / (1.0 + exp( scale * (r - shift)));
}
+
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
sigmoid::sigmoid
@@ -67,11 +69,15 @@ sigmoid::sigmoid
)
:
energyScalingFunction(name, energyScalingFunctionProperties, pairPot),
- sigmoidCoeffs_(energyScalingFunctionProperties.subDict(typeName + "Coeffs")),
+ sigmoidCoeffs_
+ (
+ energyScalingFunctionProperties.subDict(typeName + "Coeffs")
+ ),
shift_(readScalar(sigmoidCoeffs_.lookup("shift"))),
scale_(readScalar(sigmoidCoeffs_.lookup("scale")))
{}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
void sigmoid::scaleEnergy(scalar& e, const scalar r) const
@@ -79,15 +85,17 @@ void sigmoid::scaleEnergy(scalar& e, const scalar r) const
e *= sigmoidScale(r, shift_, scale_);
}
+
bool sigmoid::read(const dictionary& energyScalingFunctionProperties)
{
energyScalingFunction::read(energyScalingFunctionProperties);
- sigmoidCoeffs_ = energyScalingFunctionProperties.subDict(typeName + "Coeffs");
+ sigmoidCoeffs_ =
+ energyScalingFunctionProperties.subDict(typeName + "Coeffs");
sigmoidCoeffs_.lookup("shift") >> shift_;
sigmoidCoeffs_.lookup("scale") >> shift_;
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
index 42d0ac85b83b7bc3a4b99c6bb9be42ffb716e525..8a37ad86003f460c036fb51df247c61642a85617 100644
--- a/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
+++ b/src/lagrangian/molecularDynamics/potential/energyScalingFunction/derived/sigmoid/sigmoid.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -98,7 +98,7 @@ public:
void scaleEnergy(scalar& e, const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& energyScalingFunctionProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
index b5251d733c89d6919807429be5c1d3b07e130541..2986a0e5394f73a6e2a6f63996668057536bb215 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/newPairPotential.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -54,8 +54,8 @@ autoPtr<pairPotential> pairPotential::New
(
"pairPotential::New()"
) << "Unknown pairPotential type "
- << pairPotentialTypeName << endl << endl
- << "Valid pairPotentials are : " << endl
+ << pairPotentialTypeName << nl << nl
+ << "Valid pairPotentials are: " << nl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
index d4a807f352f91577f281dfa344ab8ba82cf3ccee..b3e609f4e77140c17b98e4ec7f2ae47dc129d555 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -93,7 +93,7 @@ void Foam::pairPotential::setLookupTables()
}
-Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
+Foam::scalar Foam::pairPotential::force(const scalar r) const
{
scalar k_rIJ = (r - rMin_)/dr_;
@@ -102,7 +102,7 @@ Foam::scalar Foam::pairPotential::forceLookup(const scalar r) const
if (k < 0)
{
FatalErrorIn("pairPotential.C") << nl
- << "r less than rMin" << nl
+ << "r less than rMin in pair potential " << name_ << nl
<< abort(FatalError);
}
@@ -130,7 +130,7 @@ Foam::pairPotential::forceTable() const
}
-Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
+Foam::scalar Foam::pairPotential::energy(const scalar r) const
{
scalar k_rIJ = (r - rMin_)/dr_;
@@ -139,7 +139,7 @@ Foam::scalar Foam::pairPotential::energyLookup(const scalar r) const
if (k < 0)
{
FatalErrorIn("pairPotential.C") << nl
- << "r less than rMin" << nl
+ << "r less than rMin in pair potential " << name_ << nl
<< abort(FatalError);
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
index 6d6701a106c013bea2241d08b6cc2174db8e64af..9be12ebd0c840a0ec84e5c75f25d036586eaa338 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotential.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -54,7 +54,7 @@ namespace Foam
class energyScalingFunction;
/*---------------------------------------------------------------------------*\
- Class pairPotential Declaration
+ Class pairPotential Declaration
\*---------------------------------------------------------------------------*/
class pairPotential
@@ -80,6 +80,7 @@ protected:
bool writeTables_;
+
// Private Member Functions
void scaleEnergy(scalar& e, const scalar r) const;
@@ -94,7 +95,7 @@ protected:
public:
//- Runtime type information
- TypeName("pairPotential");
+ TypeName("pairPotential");
// Declare run-time constructor selection table
@@ -150,9 +151,9 @@ public:
inline scalar rCutSqr() const;
- scalar energyLookup (const scalar r) const;
+ scalar energy (const scalar r) const;
- scalar forceLookup (const scalar r) const;
+ scalar force (const scalar r) const;
List<Pair<scalar> > energyTable() const;
@@ -160,7 +161,7 @@ public:
inline bool writeTables() const;
- virtual scalar unscaledEnergy (const scalar r) const = 0;
+ virtual scalar unscaledEnergy(const scalar r) const = 0;
scalar scaledEnergy(const scalar r) const;
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
index f39140c38bb0c346e78a3c1cc0c352aa26c5a770..4c2ef76b8e5248cd886c95f32a7615d42e941c43 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
index 5c0893045a417fa84e61fb01ff18339d4f713406..a07f21beceb54a1924936adab91f8ffa99286a88 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/basic/pairPotentialIO.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -38,12 +38,12 @@ bool Foam::pairPotential::writeEnergyAndForceTables(Ostream& os) const
forAll(eTab, e)
{
- os<< eTab[e].first()
- << token::SPACE
- << eTab[e].second()
- << token::SPACE
- << fTab[e].second()
- << nl;
+ os << eTab[e].first()
+ << token::SPACE
+ << eTab[e].second()
+ << token::SPACE
+ << fTab[e].second()
+ << nl;
}
return os.good();
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
index 0327f163d56a6fb38d681b627a73b52ad14e979a..2e44f617da378c4911fb5987bc458ae9e718fe31 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -71,6 +69,7 @@ azizChen::azizChen
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar azizChen::unscaledEnergy(const scalar r) const
@@ -84,15 +83,16 @@ scalar azizChen::unscaledEnergy(const scalar r) const
F = exp(-pow(((D_ / x) - 1.0),2));
}
- return epsilon_ *
- (
- A_ * Foam::pow(x, gamma_) * exp(-alpha_ * x)
- - (
- (C6_/ Foam::pow(x, 6))
- + (C8_/ Foam::pow(x, 8))
- + (C10_/ Foam::pow(x, 10))
- )
- * F
+ return
+ epsilon_
+ *(
+ A_ * Foam::pow(x, gamma_)*exp(-alpha_*x)
+ - (
+ (C6_/ Foam::pow(x, 6))
+ + (C8_/ Foam::pow(x, 8))
+ + (C10_/ Foam::pow(x, 10))
+ )
+ *F
);
}
@@ -112,7 +112,7 @@ bool azizChen::read(const dictionary& azizChen)
azizChenCoeffs_.lookup("C10") >> C10_;
azizChenCoeffs_.lookup("D") >> D_;
azizChenCoeffs_.lookup("gamma") >> gamma_;
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
index 43a1ee9dca61e3c2d3926982a78153790fb3195a..53f93481281922d2094172101628956067d0137d 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/azizChen/azizChen.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -85,6 +85,7 @@ class azizChen
scalar D_;
scalar gamma_;
+
public:
//- Runtime type information
@@ -111,7 +112,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
index 0476e378da3fcde4a8417d81baa367da813652cc..7dd02320322136e8f29a46ed1e0a7010c46615db 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -25,6 +25,7 @@ License
\*---------------------------------------------------------------------------*/
#include "coulomb.H"
+#include "mathematicalConstants.H"
#include "addToRunTimeSelectionTable.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -45,7 +46,8 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
+scalar coulomb::oneOverFourPiEps0 =
+ 1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -61,11 +63,12 @@ coulomb::coulomb
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar coulomb::unscaledEnergy(const scalar r) const
{
- return 1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12 * r);
+ return oneOverFourPiEps0/r;
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
index 44e5e2cc5cfdeb1fe1290f9a8ccc57ac4d07fc85..f1e06712bb7b8ff3984a2ff62c41cacda0ce5c1e 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/coulomb/coulomb.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -23,7 +23,7 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
- Foam::pairPotentials::coulomb
+ Foam::pairPotentials::electrostatic
Description
@@ -53,13 +53,16 @@ class coulomb
:
public pairPotential
{
-
public:
//- Runtime type information
TypeName("coulomb");
+ // Static data members
+
+ static scalar oneOverFourPiEps0;
+
// Constructors
//- Construct from components
@@ -80,7 +83,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C
new file mode 100644
index 0000000000000000000000000000000000000000..fd771e1854e3d44980b6dd86cfa1e746a4d40b78
--- /dev/null
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.C
@@ -0,0 +1,98 @@
+/*---------------------------------------------------------------------------*\
+ ========= |
+ \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
+ \\ / O peration |
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
+ \\/ M anipulation |
+-------------------------------------------------------------------------------
+License
+ This file is part of OpenFOAM.
+
+ OpenFOAM is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2 of the License, or (at your
+ option) any later version.
+
+ OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with OpenFOAM; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+#include "dampedCoulomb.H"
+#include "mathematicalConstants.H"
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+namespace Foam
+{
+namespace pairPotentials
+{
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+defineTypeNameAndDebug(dampedCoulomb, 0);
+
+addToRunTimeSelectionTable
+(
+ pairPotential,
+ dampedCoulomb,
+ dictionary
+);
+
+scalar dampedCoulomb::oneOverFourPiEps0 =
+ 1.0/(4.0 * mathematicalConstant::pi * 8.854187817e-12);
+
+
+// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
+
+dampedCoulomb::dampedCoulomb
+(
+ const word& name,
+ const dictionary& pairPotentialProperties
+)
+:
+ pairPotential(name, pairPotentialProperties),
+ dampedCoulombCoeffs_
+ (
+ pairPotentialProperties.subDict(typeName + "Coeffs")
+ ),
+ alpha_(readScalar(dampedCoulombCoeffs_.lookup("alpha")))
+{
+ setLookupTables();
+}
+
+
+// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
+
+scalar dampedCoulomb::unscaledEnergy(const scalar r) const
+{
+ return oneOverFourPiEps0*erfc(alpha_*r)/r;
+}
+
+
+bool dampedCoulomb::read(const dictionary& pairPotentialProperties)
+{
+ pairPotential::read(pairPotentialProperties);
+
+ dampedCoulombCoeffs_ =
+ pairPotentialProperties.subDict(typeName + "Coeffs");
+
+ dampedCoulombCoeffs_.lookup("alpha") >> alpha_;
+
+ return true;
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+} // End namespace pairPotentials
+} // End namespace Foam
+
+// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfigI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H
similarity index 53%
rename from applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfigI.H
rename to src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H
index 2cfd5bf57bcf750224f9d2c42f55633d36f4e4e9..377b531824e4d520ccf3621672e1ae537e9e7585 100644
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfigI.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/dampedCoulomb/dampedCoulomb.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -22,77 +22,87 @@ License
along with OpenFOAM; if not, write to the Free Software Foundation,
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+Class
+ Foam::pairPotentials::electrostatic
+
+Description
+
+
+SourceFiles
+ dampedCoulomb.C
+
\*---------------------------------------------------------------------------*/
+#ifndef dampedCoulomb_H
+#define dampedCoulomb_H
+
+#include "pairPotential.H"
+
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
namespace Foam
{
+namespace pairPotentials
+{
-// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
+/*---------------------------------------------------------------------------*\
+ Class dampedCoulomb Declaration
+\*---------------------------------------------------------------------------*/
-inline const List<word>& molConfig::molIdList() const
+class dampedCoulomb
+:
+ public pairPotential
{
- return idList_;
-}
+ // Private data
+ dictionary dampedCoulombCoeffs_;
-inline const labelField& molConfig::id() const
-{
- return id_;
-}
+ scalar alpha_;
-inline const scalarField& molConfig::mass() const
-{
- return mass_;
-}
+public:
+ //- Runtime type information
+ TypeName("dampedCoulomb");
-inline const vectorField& molConfig::positions() const
-{
- return positions_;
-}
+ // Static data members
-inline const labelField& molConfig::cells() const
-{
- return cells_;
-}
+ static scalar oneOverFourPiEps0;
-inline const vectorField& molConfig::U() const
-{
- return U_;
-}
+ // Constructors
+ //- Construct from components
+ dampedCoulomb
+ (
+ const word& name,
+ const dictionary& pairPotentialProperties
+ );
-inline const vectorField& molConfig::A() const
-{
- return A_;
-}
+ // Destructor
-inline const labelField& molConfig::tethered() const
-{
- return tethered_;
-}
+ ~dampedCoulomb()
+ {}
-inline const vectorField& molConfig::tetherPositions() const
-{
- return tetherPositions_;
-}
+ // Member Functions
+ scalar unscaledEnergy(const scalar r) const;
-inline label molConfig::nMol() const
-{
- return nMol_;
-}
+ //- Read dictionary
+ bool read(const dictionary& pairPotentialProperties);
+};
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+} // End namespace pairPotentials
} // End namespace Foam
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+#endif
+
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
index ccd54ec787dd8a14a6ca466ed38f95a077beaf45..ae34ef4cdbc30f5dc58c3927f7a2f2c1eeb583a1 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -57,13 +55,17 @@ exponentialRepulsion::exponentialRepulsion
)
:
pairPotential(name, exponentialRepulsion),
- exponentialRepulsionCoeffs_(exponentialRepulsion.subDict(typeName + "Coeffs")),
+ exponentialRepulsionCoeffs_
+ (
+ exponentialRepulsion.subDict(typeName + "Coeffs")
+ ),
rm_(readScalar(exponentialRepulsionCoeffs_.lookup("rm"))),
epsilon_(readScalar(exponentialRepulsionCoeffs_.lookup("epsilon")))
{
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar exponentialRepulsion::unscaledEnergy(const scalar r) const
@@ -76,7 +78,8 @@ bool exponentialRepulsion::read(const dictionary& exponentialRepulsion)
{
pairPotential::read(exponentialRepulsion);
- exponentialRepulsionCoeffs_ = exponentialRepulsion.subDict(typeName + "Coeffs");
+ exponentialRepulsionCoeffs_ =
+ exponentialRepulsion.subDict(typeName + "Coeffs");
exponentialRepulsionCoeffs_.lookup("rm") >> rm_;
exponentialRepulsionCoeffs_.lookup("epsilon") >> epsilon_;
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
index cef45b7a3ae9c512305da12fa2c2c2291bedc38b..8ce1ee4a0f914faae42488a1712b370c29a4c978 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/exponentialRepulsion/exponentialRepulsion.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
- Class exponentialRepulsion Declaration
+ Class exponentialRepulsion Declaration
\*---------------------------------------------------------------------------*/
class exponentialRepulsion
@@ -60,6 +60,7 @@ class exponentialRepulsion
scalar rm_;
scalar epsilon_;
+
public:
//- Runtime type information
@@ -86,7 +87,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
index 9c93f3a70e017ca9a285b9992370dd9052ef36c4..d5a1deb88e6e8c0426a8ffad5c6a2ebead09c4ac 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -64,6 +62,7 @@ lennardJones::lennardJones
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar lennardJones::unscaledEnergy(const scalar r) const
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
index f12027d1151eafa256ea8ced6130c17432cfa319..2ae3c036ae4bc893689d10de81741bfa6a22a22d 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/lennardJones/lennardJones.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
- Class lennardJones Declaration
+ Class lennardJones Declaration
\*---------------------------------------------------------------------------*/
class lennardJones
@@ -60,6 +60,7 @@ class lennardJones
scalar sigma_;
scalar epsilon_;
+
public:
//- Runtime type information
@@ -86,7 +87,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
index a813495f2678ce51f2b2091a8d1858139827da90..7545573591bf22809f92db844cd65234b28a9809 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -66,6 +64,7 @@ maitlandSmith::maitlandSmith
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar maitlandSmith::unscaledEnergy(const scalar r) const
@@ -90,7 +89,7 @@ bool maitlandSmith::read(const dictionary& maitlandSmith)
maitlandSmithCoeffs_.lookup("gamma") >> gamma_;
maitlandSmithCoeffs_.lookup("rm") >> rm_;
maitlandSmithCoeffs_.lookup("epsilon") >> epsilon_;
-
+
return true;
}
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
index af4612644b5cd14bc3695a8b399da5d135bda24b..cdeb01211b58630e31f5d1044a94363a54ee28a8 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/maitlandSmith/maitlandSmith.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -72,7 +72,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
- Class maitlandSmith Declaration
+ Class maitlandSmith Declaration
\*---------------------------------------------------------------------------*/
class maitlandSmith
@@ -88,6 +88,7 @@ class maitlandSmith
scalar rm_;
scalar epsilon_;
+
public:
//- Runtime type information
@@ -114,7 +115,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
index ca43080d7485662917c3fd3158d510bf12794a21..3326fd7fe1f41e5a723e0df06f75d91350cdf834 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -61,6 +59,7 @@ noInteraction::noInteraction
setLookupTables();
}
+
// * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * * //
scalar noInteraction::unscaledEnergy(const scalar r) const
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
index d09564ef882ab3d5b4f849c13e770c6b425590c4..5d3fd5742dbf0fe3290b28968a923659c6e7839f 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/derived/noInteraction/noInteraction.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace pairPotentials
{
/*---------------------------------------------------------------------------*\
- Class noInteraction Declaration
+ Class noInteraction Declaration
\*---------------------------------------------------------------------------*/
class noInteraction
@@ -80,7 +80,7 @@ public:
scalar unscaledEnergy(const scalar r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& pairPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
index ef856bc50527ad70f8a554a9ce3ded45a89fd322..2d77c4ce59505c320590182f5eae168637f48cc4 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -60,9 +60,9 @@ void Foam::pairPotentialList::readPairPotentialDict
else
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
- << "Pair pairPotential specification subDict "
- << idA << "-" << idB << " not found"
- << nl << abort(FatalError);
+ << "Pair pairPotential specification subDict "
+ << idA << "-" << idB << " not found"
+ << nl << abort(FatalError);
}
}
else
@@ -80,10 +80,10 @@ void Foam::pairPotentialList::readPairPotentialDict
else
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
- << "Pair pairPotential specification subDict "
- << idA << "-" << idB << " or "
- << idB << "-" << idA << " not found"
- << nl << abort(FatalError);
+ << "Pair pairPotential specification subDict "
+ << idA << "-" << idB << " or "
+ << idB << "-" << idA << " not found"
+ << nl << abort(FatalError);
}
if
@@ -93,10 +93,10 @@ void Foam::pairPotentialList::readPairPotentialDict
)
{
FatalErrorIn("pairPotentialList::buildPotentials") << nl
- << "Pair pairPotential specification subDict "
- << idA << "-" << idB << " and "
- << idB << "-" << idA << " found multiple definition"
- << nl << abort(FatalError);
+ << "Pair pairPotential specification subDict "
+ << idA << "-" << idB << " and "
+ << idB << "-" << idA << " found multiple definition"
+ << nl << abort(FatalError);
}
}
@@ -136,9 +136,41 @@ void Foam::pairPotentialList::readPairPotentialDict
}
}
+ if (!pairPotentialDict.found("electrostatic"))
+ {
+ FatalErrorIn("pairPotentialList::buildPotentials") << nl
+ << "Pair pairPotential specification subDict electrostatic"
+ << nl << abort(FatalError);
+ }
+
+ electrostaticPotential_ = pairPotential::New
+ (
+ "electrostatic",
+ pairPotentialDict.subDict("electrostatic")
+ );
+
+ if (electrostaticPotential_->rCut() > rCutMax_)
+ {
+ rCutMax_ = electrostaticPotential_->rCut();
+ }
+
+ if (electrostaticPotential_->writeTables())
+ {
+ OFstream ppTabFile(mesh.time().path()/"electrostatic");
+
+ if(!electrostaticPotential_->writeEnergyAndForceTables(ppTabFile))
+ {
+ FatalErrorIn("pairPotentialList::readPairPotentialDict")
+ << "Failed writing to "
+ << ppTabFile.name() << nl
+ << abort(FatalError);
+ }
+ }
+
rCutMaxSqr_ = rCutMax_*rCutMax_;
}
+
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
Foam::pairPotentialList::pairPotentialList()
@@ -146,6 +178,7 @@ Foam::pairPotentialList::pairPotentialList()
PtrList<pairPotential>()
{}
+
Foam::pairPotentialList::pairPotentialList
(
const List<word>& idList,
@@ -188,13 +221,13 @@ const Foam::pairPotential& Foam::pairPotentialList::pairPotentialFunction
const label b
) const
{
- return (*this)[pairPotentialIndex (a, b)];
+ return (*this)[pairPotentialIndex(a, b)];
}
bool Foam::pairPotentialList::rCutMaxSqr(const scalar rIJMagSqr) const
{
- if (rIJMagSqr <= rCutMaxSqr_)
+ if (rIJMagSqr < rCutMaxSqr_)
{
return true;
}
@@ -212,7 +245,7 @@ bool Foam::pairPotentialList::rCutSqr
const scalar rIJMagSqr
) const
{
- if (rIJMagSqr <= rCutSqr (a, b))
+ if (rIJMagSqr < rCutSqr(a, b))
{
return true;
}
@@ -229,7 +262,7 @@ Foam::scalar Foam::pairPotentialList::rMin
const label b
) const
{
- return (*this)[pairPotentialIndex (a, b)].rMin();
+ return (*this)[pairPotentialIndex(a, b)].rMin();
}
@@ -239,7 +272,7 @@ Foam::scalar Foam::pairPotentialList::dr
const label b
) const
{
- return (*this)[pairPotentialIndex (a, b)].dr();
+ return (*this)[pairPotentialIndex(a, b)].dr();
}
@@ -249,7 +282,7 @@ Foam::scalar Foam::pairPotentialList::rCutSqr
const label b
) const
{
- return (*this)[pairPotentialIndex (a, b)].rCutSqr();
+ return (*this)[pairPotentialIndex(a, b)].rCutSqr();
}
@@ -259,7 +292,7 @@ Foam::scalar Foam::pairPotentialList::rCut
const label b
) const
{
- return (*this)[pairPotentialIndex (a, b)].rCut();
+ return (*this)[pairPotentialIndex(a, b)].rCut();
}
@@ -270,7 +303,7 @@ Foam::scalar Foam::pairPotentialList::force
const scalar rIJMag
) const
{
- scalar f = (*this)[pairPotentialIndex (a, b)].forceLookup(rIJMag);
+ scalar f = (*this)[pairPotentialIndex(a, b)].force(rIJMag);
return f;
}
@@ -283,11 +316,10 @@ Foam::scalar Foam::pairPotentialList::energy
const scalar rIJMag
) const
{
- scalar e = (*this)[pairPotentialIndex (a, b)].energyLookup(rIJMag);
+ scalar e = (*this)[pairPotentialIndex(a, b)].energy(rIJMag);
return e;
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
index a7e8190a01bfccd986ffa79817fd492f500e78c2..b4193a46ae49df57ed5cbcda74f8657e4cdcece4 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialList.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -47,7 +47,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class pairPotentialList Declaration
+ Class pairPotentialList Declaration
\*---------------------------------------------------------------------------*/
class pairPotentialList
@@ -62,6 +62,9 @@ class pairPotentialList
scalar rCutMaxSqr_;
+ autoPtr<pairPotential> electrostaticPotential_;
+
+
// Private Member Functions
inline label pairPotentialIndex
@@ -83,6 +86,7 @@ class pairPotentialList
//- Disallow default bitwise copy construct
pairPotentialList(const pairPotentialList&);
+
public:
// Constructors
@@ -97,10 +101,12 @@ public:
const polyMesh& mesh
);
+
// Destructor
~pairPotentialList();
+
// Member Functions
void buildPotentials
@@ -110,6 +116,7 @@ public:
const polyMesh& mesh
);
+
// Access
inline scalar rCutMax() const;
@@ -132,13 +139,13 @@ public:
const scalar rIJMagSqr
) const;
- scalar rMin (const label a, const label b) const;
+ scalar rMin(const label a, const label b) const;
- scalar dr (const label a, const label b) const;
+ scalar dr(const label a, const label b) const;
- scalar rCutSqr (const label a, const label b) const;
+ scalar rCutSqr(const label a, const label b) const;
- scalar rCut (const label a, const label b) const;
+ scalar rCut(const label a, const label b) const;
scalar force
(
@@ -153,6 +160,8 @@ public:
const label b,
const scalar rIJMag
) const;
+
+ inline const pairPotential& electrostatic() const;
};
diff --git a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
index 413ffea05eb663c8bc7184801475fefee38d6dda..c14aa3695e189388a7be344c3ace053909b75249 100644
--- a/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
+++ b/src/lagrangian/molecularDynamics/potential/pairPotential/pairPotentialList/pairPotentialListI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -56,6 +56,7 @@ inline Foam::label Foam::pairPotentialList::pairPotentialIndex
return index;
}
+
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::scalar Foam::pairPotentialList::rCutMax() const
@@ -70,4 +71,10 @@ inline Foam::scalar Foam::pairPotentialList::rCutMaxSqr() const
}
+inline const Foam::pairPotential& Foam::pairPotentialList::electrostatic() const
+{
+ return electrostaticPotential_;
+}
+
+
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/potential/potential.C b/src/lagrangian/molecularDynamics/potential/potential/potential.C
index 16a7fca6cd8b56a16894df3363e8964d92e28f12..5532c2f105c0751eeb4bf966918e91fb12c09c10 100644
--- a/src/lagrangian/molecularDynamics/potential/potential/potential.C
+++ b/src/lagrangian/molecularDynamics/potential/potential/potential.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -365,8 +365,7 @@ void Foam::potential::potential::readMdInitialiseDict
Foam::potential::potential(const polyMesh& mesh)
:
- mesh_(mesh),
- electrostaticPotential_()
+ mesh_(mesh)
{
readPotentialDict();
}
@@ -379,8 +378,7 @@ Foam::potential::potential
IOdictionary& idListDict
)
:
- mesh_(mesh),
- electrostaticPotential_()
+ mesh_(mesh)
{
readMdInitialiseDict(mdInitialiseDict, idListDict);
}
diff --git a/src/lagrangian/molecularDynamics/potential/potential/potential.H b/src/lagrangian/molecularDynamics/potential/potential/potential.H
index 7accf239cd0f6fde38fca7dac2645b1f8206cfb5..32f9b2a1d29d98b82af3b4e760910f0548a057b2 100644
--- a/src/lagrangian/molecularDynamics/potential/potential/potential.H
+++ b/src/lagrangian/molecularDynamics/potential/potential/potential.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -49,7 +49,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class potential Declaration
+ Class potential Declaration
\*---------------------------------------------------------------------------*/
class potential
@@ -70,12 +70,11 @@ class potential
pairPotentialList pairPotentials_;
- electrostaticPotential electrostaticPotential_;
-
tetherPotentialList tetherPotentials_;
vector gravity_;
+
// Private Member Functions
void setSiteIdList(const IOdictionary& moleculePropertiesDict);
@@ -110,6 +109,7 @@ public:
IOdictionary& idListDict
);
+
// Destructor
~potential();
@@ -133,8 +133,6 @@ public:
inline const pairPotentialList& pairPotentials() const;
- inline const electrostaticPotential& electrostatic() const;
-
inline const tetherPotentialList& tetherPotentials() const;
inline const vector& gravity() const;
diff --git a/src/lagrangian/molecularDynamics/potential/potential/potentialI.H b/src/lagrangian/molecularDynamics/potential/potential/potentialI.H
index eddd2b047ccdbb3d04e3997e20c47f304ccc8812..38ba634455761cc7416fe2123b48edc088304200 100644
--- a/src/lagrangian/molecularDynamics/potential/potential/potentialI.H
+++ b/src/lagrangian/molecularDynamics/potential/potential/potentialI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -24,8 +24,6 @@ License
\*---------------------------------------------------------------------------*/
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
inline Foam::label Foam::potential::nIds() const
@@ -70,13 +68,6 @@ inline const Foam::pairPotentialList& Foam::potential::pairPotentials() const
}
-inline const Foam::electrostaticPotential&
-Foam::potential::electrostatic() const
-{
- return electrostaticPotential_;
-}
-
-
inline const Foam::tetherPotentialList&
Foam::potential::tetherPotentials() const
{
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
index 4caba50778c52157ff789479ec2e6f4c61acf14b..85c8a703596579aca1b3af84b2dcb84a24ef0773 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/newTetherPotential.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -39,7 +39,11 @@ autoPtr<tetherPotential> tetherPotential::New
const dictionary& tetherPotentialProperties
)
{
- word tetherPotentialTypeName(tetherPotentialProperties.lookup("tetherPotential"));
+ word
+ tetherPotentialTypeName
+ (
+ tetherPotentialProperties.lookup("tetherPotential")
+ );
Info<< nl << "Selecting tether potential "
<< tetherPotentialTypeName << " for "
@@ -54,8 +58,8 @@ autoPtr<tetherPotential> tetherPotential::New
(
"tetherPotential::New()"
) << "Unknown tetherPotential type "
- << tetherPotentialTypeName << endl << endl
- << "Valid tetherPotentials are : " << endl
+ << tetherPotentialTypeName << nl << nl
+ << "Valid tetherPotentials are: " << nl
<< dictionaryConstructorTablePtr_->toc()
<< exit(FatalError);
}
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C
index 462be334561a6c1b3af9fd186d7f6b0c5c4e39b5..4c4708ba96a320c07cd81c7738ad0fa67477e9b7 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
index 19a9cddb77743a3d038ac9a51a457b21a9e12067..f65e5bb6b8593e9bfa28caec2dabd15c5ded5659 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/basic/tetherPotential.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -48,7 +48,7 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class tetherPotential Declaration
+ Class tetherPotential Declaration
\*---------------------------------------------------------------------------*/
class tetherPotential
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
index 453d5898ab85917cd511b02032dbd18f3f8f14bc..1edcc70a155fa5f1242623f97f6d4011226a7458 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
index 6508adaec902e78461435887b6f13081a6046210..4af51cfdff80706857f0a50322c78b5f73bf4b46 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/harmonicSpring/harmonicSpring.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace tetherPotentials
{
/*---------------------------------------------------------------------------*\
- Class harmonicSpring Declaration
+ Class harmonicSpring Declaration
\*---------------------------------------------------------------------------*/
class harmonicSpring
@@ -88,7 +88,7 @@ public:
vector force(const vector r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& tetherPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.C
index 7e12f9ab74e93b82c2b5c9b25e28529c1c032fd9..8a3a081f6fc6bbdcf1e8cdb39df46f233dc97b2c 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H
index 82b93b087b7fc542067afdb2d90aa4063f80bf5c..2bb98e39bd2063ccff4809f187f970de80baef46 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/pitchForkRing/pitchForkRing.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace tetherPotentials
{
/*---------------------------------------------------------------------------*\
- Class pitchForkRing Declaration
+ Class pitchForkRing Declaration
\*---------------------------------------------------------------------------*/
class pitchForkRing
@@ -90,7 +90,7 @@ public:
vector force(const vector r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& tetherPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
index 45a48a4c623fbfa663b889ad142463c3d22d8c3f..5396013a173a973aa7302f5cc07e69889ff61b54 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -45,8 +45,6 @@ addToRunTimeSelectionTable
dictionary
);
-// * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * * //
-
// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
@@ -88,6 +86,7 @@ scalar restrainedHarmonicSpring::energy(const vector r) const
}
}
+
vector restrainedHarmonicSpring::force(const vector r) const
{
scalar magR = mag(r);
@@ -102,7 +101,11 @@ vector restrainedHarmonicSpring::force(const vector r) const
}
}
-bool restrainedHarmonicSpring::read(const dictionary& tetherPotentialProperties)
+
+bool restrainedHarmonicSpring::read
+(
+ const dictionary& tetherPotentialProperties
+)
{
tetherPotential::read(tetherPotentialProperties);
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
index 62b92618591cde2ab81918375ee98cf5d0638bd4..1711c4f5f3e5db5b35723de84bdc8aa082026f21 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/derived/restrainedHarmonicSpring/restrainedHarmonicSpring.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -46,7 +46,7 @@ namespace tetherPotentials
{
/*---------------------------------------------------------------------------*\
- Class restrainedHarmonicSpring Declaration
+ Class restrainedHarmonicSpring Declaration
\*---------------------------------------------------------------------------*/
class restrainedHarmonicSpring
@@ -90,7 +90,7 @@ public:
vector force(const vector r) const;
- //- Read transportProperties dictionary
+ //- Read dictionary
bool read(const dictionary& tetherPotentialProperties);
};
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
index 79a1ce83d7a0922f4c4b5d7472d6ffa1fe555286..93498b8f711a2a8dc050e950e27eb51cc2ea1407 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.C
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -131,7 +131,7 @@ const Foam::tetherPotential& Foam::tetherPotentialList::tetherPotentialFunction
const label a
) const
{
- return (*this)[tetherPotentialIndex (a)];
+ return (*this)[tetherPotentialIndex(a)];
}
@@ -141,7 +141,7 @@ Foam::vector Foam::tetherPotentialList::force
const vector rIT
) const
{
- return (*this)[tetherPotentialIndex (a)].force(rIT);
+ return (*this)[tetherPotentialIndex(a)].force(rIT);
}
@@ -151,9 +151,8 @@ Foam::scalar Foam::tetherPotentialList::energy
const vector rIT
) const
{
- return (*this)[tetherPotentialIndex (a)].energy(rIT);
+ return (*this)[tetherPotentialIndex(a)].energy(rIT);
}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
// ************************************************************************* //
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
index a48cc21edec46f805845e4fa84b7504660a39c37..8ca770f52351cd1de3f749428afb9be8474e8e6a 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialList.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
@@ -57,6 +57,7 @@ class tetherPotentialList
List<label> idMap_;
+
// Private Member Functions
inline label tetherPotentialIndex
@@ -92,10 +93,12 @@ public:
const List<word>& tetherSiteIdList
);
+
// Destructor
~tetherPotentialList();
+
// Member Functions
void buildPotentials
diff --git a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
index 67b1e4dbe62a97c3b38a41863bcd5e9c77b1d4b8..73834281efd0b4f92749800b1526b35841f0d440 100644
--- a/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
+++ b/src/lagrangian/molecularDynamics/potential/tetherPotential/tetherPotentialList/tetherPotentialListI.H
@@ -2,7 +2,7 @@
========= |
\\ / F ield | OpenFOAM: The Open Source CFD Toolbox
\\ / O peration |
- \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\ / A nd | Copyright (C) 2008-2009 OpenCFD Ltd.
\\/ M anipulation |
-------------------------------------------------------------------------------
License
diff --git a/src/meshTools/Make/files b/src/meshTools/Make/files
index d5133cb33dad9e45beb50fa4785fdaee749b2d39..a61d00246e04323e182603105061d72d9150acd6 100644
--- a/src/meshTools/Make/files
+++ b/src/meshTools/Make/files
@@ -90,6 +90,7 @@ $(cellSources)/nbrToCell/nbrToCell.C
$(cellSources)/zoneToCell/zoneToCell.C
$(cellSources)/sphereToCell/sphereToCell.C
$(cellSources)/cylinderToCell/cylinderToCell.C
+$(cellSources)/faceZoneToCell/faceZoneToCell.C
faceSources = sets/faceSources
$(faceSources)/faceToFace/faceToFace.C
diff --git a/src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.C b/src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.C
new file mode 100644
index 0000000000000000000000000000000000000000..526620fe14746be56d0e433274be25edb0b5d8cd
--- /dev/null
+++ b/src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.C
@@ -0,0 +1,185 @@
+/*---------------------------------------------------------------------------*\
+ ========= |
+ \\ / F ield | OpenFOAM: The Open Source CFD Toolbox
+ \\ / O peration |
+ \\ / A nd | Copyright (C) 1991-2009 OpenCFD Ltd.
+ \\/ M anipulation |
+-------------------------------------------------------------------------------
+License
+ This file is part of OpenFOAM.
+
+ OpenFOAM is free software; you can redistribute it and/or modify it
+ under the terms of the GNU General Public License as published by the
+ Free Software Foundation; either version 2 of the License, or (at your
+ option) any later version.
+
+ OpenFOAM is distributed in the hope that it will be useful, but WITHOUT
+ ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with OpenFOAM; if not, write to the Free Software Foundation,
+ Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+\*---------------------------------------------------------------------------*/
+
+#include "faceZoneToCell.H"
+#include "polyMesh.H"
+
+#include "addToRunTimeSelectionTable.H"
+
+// * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
+
+namespace Foam
+{
+
+defineTypeNameAndDebug(faceZoneToCell, 0);
+
+addToRunTimeSelectionTable(topoSetSource, faceZoneToCell, word);
+
+addToRunTimeSelectionTable(topoSetSource, faceZoneToCell, istream);
+
+}
+
+
+Foam::topoSetSource::addToUsageTable Foam::faceZoneToCell::usage_
+(
+ faceZoneToCell::typeName,
+ "\n Usage: faceZoneToCell zone master|slave\n\n"
+ " Select master or slave side of the faceZone."
+ " Note:accepts wildcards for zone.\n\n"
+);
+
+
+template<>
+const char* Foam::NamedEnum<Foam::faceZoneToCell::faceAction, 2>::names[] =
+{
+ "master",
+ "slave"
+};
+
+
+const Foam::NamedEnum<Foam::faceZoneToCell::faceAction, 2>
+ Foam::faceZoneToCell::faceActionNames_;
+
+
+// * * * * * * * * * * * * * Private Member Functions * * * * * * * * * * * //
+
+void Foam::faceZoneToCell::combine(topoSet& set, const bool add) const
+{
+ bool hasMatched = false;
+
+ forAll(mesh_.faceZones(), i)
+ {
+ const faceZone& zone = mesh_.faceZones()[i];
+
+ if (zoneName_.match(zone.name()))
+ {
+ const labelList& cellLabels =
+ (
+ option_ == MASTER
+ ? zone.masterCells()
+ : zone.slaveCells()
+ );
+
+ Info<< " Found matching zone " << zone.name()
+ << " with " << cellLabels.size() << " cells on selected side."
+ << endl;
+
+ hasMatched = true;
+
+ forAll(cellLabels, i)
+ {
+ // Only do active cells
+ if (cellLabels[i] < mesh_.nCells())
+ {
+ addOrDelete(set, cellLabels[i], add);
+ }
+ }
+ }
+ }
+
+ if (!hasMatched)
+ {
+ WarningIn("faceZoneToCell::combine(topoSet&, const bool)")
+ << "Cannot find any faceZone named " << zoneName_ << endl
+ << "Valid names are " << mesh_.faceZones().names() << endl;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * Constructors * * * * * * * * * * * * * * //
+
+// Construct from components
+Foam::faceZoneToCell::faceZoneToCell
+(
+ const polyMesh& mesh,
+ const word& zoneName,
+ const faceAction option
+)
+:
+ topoSetSource(mesh),
+ zoneName_(zoneName),
+ option_(option)
+{}
+
+
+// Construct from dictionary
+Foam::faceZoneToCell::faceZoneToCell
+(
+ const polyMesh& mesh,
+ const dictionary& dict
+)
+:
+ topoSetSource(mesh),
+ zoneName_(dict.lookup("name")),
+ option_(faceActionNames_.read(dict.lookup("option")))
+{}
+
+
+// Construct from Istream
+Foam::faceZoneToCell::faceZoneToCell
+(
+ const polyMesh& mesh,
+ Istream& is
+)
+:
+ topoSetSource(mesh),
+ zoneName_(checkIs(is)),
+ option_(faceActionNames_.read(checkIs(is)))
+{}
+
+
+// * * * * * * * * * * * * * * * * Destructor * * * * * * * * * * * * * * * //
+
+Foam::faceZoneToCell::~faceZoneToCell()
+{}
+
+
+// * * * * * * * * * * * * * * * Member Functions * * * * * * * * * * * * * //
+
+void Foam::faceZoneToCell::applyToSet
+(
+ const topoSetSource::setAction action,
+ topoSet& set
+) const
+{
+ if ((action == topoSetSource::NEW) || (action == topoSetSource::ADD))
+ {
+ Info<< " Adding all " << faceActionNames_[option_]
+ << " cells of faceZone " << zoneName_ << " ..." << endl;
+
+ combine(set, true);
+ }
+ else if (action == topoSetSource::DELETE)
+ {
+ Info<< " Removing all " << faceActionNames_[option_]
+ << " cells of faceZone " << zoneName_ << " ..." << endl;
+
+ combine(set, false);
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfig.H b/src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.H
similarity index 53%
rename from applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfig.H
rename to src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.H
index 3b0ba8fd504846ecb073c7083593eff38dec23c0..b09c58399fcca136725ec959690542ff25221318 100644
--- a/applications/utilities/preProcessing/mdInitialise/molConfig_old/molConfig.H
+++ b/src/meshTools/sets/cellSources/faceZoneToCell/faceZoneToCell.H
@@ -23,34 +23,21 @@ License
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
Class
- Foam::molConfig
+ Foam::faceZoneToCell
Description
+ A topoSetSource to select cells based on side of faceZone.
SourceFiles
- molConfigI.H
- molConfig.C
- molConfigIO.C
+ faceZoneToCell.C
\*---------------------------------------------------------------------------*/
-#ifndef molConfig_H
-#define molConfig_H
+#ifndef faceZoneToCell_H
+#define faceZoneToCell_H
-#include "labelVector.H"
-#include "scalar.H"
-#include "vector.H"
-#include "labelField.H"
-#include "scalarField.H"
-#include "vectorField.H"
-#include "IOField.H"
-#include "EulerCoordinateRotation.H"
-#include "Random.H"
-
-#include "Time.H"
-#include "IOdictionary.H"
-#include "IOstreams.H"
-#include "moleculeCloud.H"
+#include "topoSetSource.H"
+#include "wordRe.H"
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -58,77 +45,85 @@ namespace Foam
{
/*---------------------------------------------------------------------------*\
- Class molConfig Declaration
+ Class faceZoneToCell Declaration
\*---------------------------------------------------------------------------*/
-class molConfig
+class faceZoneToCell
+:
+ public topoSetSource
{
- // Private data
-
- const IOdictionary& molConfigDescription_;
-
- const polyMesh& mesh_;
-
- DynamicList<word> idList_;
+public:
+ //- Enumeration defining the valid options
+ enum faceAction
+ {
+ MASTER,
+ SLAVE
+ };
- labelField id_;
+private:
- scalarField mass_;
+ // Private data
- vectorField positions_;
+ static const NamedEnum<faceAction, 2> faceActionNames_;
- labelField cells_;
+ //- Add usage string
+ static addToUsageTable usage_;
- vectorField U_;
+ //- Name/regular expression of faceZone
+ wordRe zoneName_;
- vectorField A_;
+ //- Option
+ faceAction option_;
- labelField tethered_;
- vectorField tetherPositions_;
+ // Private Member Functions
- label nMol_;
+ void combine(topoSet& set, const bool add) const;
public:
+ //- Runtime type information
+ TypeName("faceZoneToCell");
+
// Constructors
- //- Construct from IOdictionary and mesh
- molConfig(IOdictionary&, const polyMesh&);
+ //- Construct from components
+ faceZoneToCell
+ (
+ const polyMesh& mesh,
+ const word& zoneName,
+ const faceAction option
+ );
+
+ //- Construct from dictionary
+ faceZoneToCell
+ (
+ const polyMesh& mesh,
+ const dictionary& dict
+ );
+
+ //- Construct from Istream
+ faceZoneToCell
+ (
+ const polyMesh& mesh,
+ Istream&
+ );
// Destructor
- ~molConfig();
+ virtual ~faceZoneToCell();
// Member Functions
- void createMolecules();
-
-
- // Access
-
- inline const List<word>& molIdList() const;
+ virtual void applyToSet
+ (
+ const topoSetSource::setAction action,
+ topoSet&
+ ) const;
- inline const labelField& id() const;
-
- inline const scalarField& mass() const;
-
- inline const vectorField& positions() const;
-
- inline const labelField& cells() const;
-
- inline const vectorField& U() const;
-
- inline const vectorField& A() const;
-
- inline const labelField& tethered() const;
-
- inline const vectorField& tetherPositions() const;
-
- inline label nMol() const;
};
@@ -138,10 +133,6 @@ public:
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-#include "molConfigI.H"
-
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
#endif
// ************************************************************************* //
diff --git a/src/meshTools/sets/cellSources/zoneToCell/zoneToCell.C b/src/meshTools/sets/cellSources/zoneToCell/zoneToCell.C
index 0dcd1e0ffb8b733911aebf50cdaab88e67a0c0f9..14b6deb7f37771b062c29e8d635f7feae33448aa 100644
--- a/src/meshTools/sets/cellSources/zoneToCell/zoneToCell.C
+++ b/src/meshTools/sets/cellSources/zoneToCell/zoneToCell.C
@@ -47,7 +47,8 @@ Foam::topoSetSource::addToUsageTable Foam::zoneToCell::usage_
(
zoneToCell::typeName,
"\n Usage: zoneToCell zone\n\n"
- " Select all cells in the cellZone\n\n"
+ " Select all cells in the cellZone."
+ " Note:accepts wildcards for zone.\n\n"
);
diff --git a/src/meshTools/sets/faceSources/patchToFace/patchToFace.C b/src/meshTools/sets/faceSources/patchToFace/patchToFace.C
index 9bcf49690ffc285ae3db1568476ba31edc0e9353..000db639a96180f2e24ada7aa4f08b4a621685e4 100644
--- a/src/meshTools/sets/faceSources/patchToFace/patchToFace.C
+++ b/src/meshTools/sets/faceSources/patchToFace/patchToFace.C
@@ -49,7 +49,7 @@ Foam::topoSetSource::addToUsageTable Foam::patchToFace::usage_
(
patchToFace::typeName,
"\n Usage: patchToFace patch\n\n"
- " Select all faces in the patch\n\n"
+ " Select all faces in the patch. Note:accepts wildcards for patch.\n\n"
);
diff --git a/src/meshTools/sets/faceSources/zoneToFace/zoneToFace.C b/src/meshTools/sets/faceSources/zoneToFace/zoneToFace.C
index 12cbab560d68ff36281aa34ca6bead1a4b8926f9..465632f2b1091fcdf774b99a0eb076ab16600d15 100644
--- a/src/meshTools/sets/faceSources/zoneToFace/zoneToFace.C
+++ b/src/meshTools/sets/faceSources/zoneToFace/zoneToFace.C
@@ -47,7 +47,8 @@ Foam::topoSetSource::addToUsageTable Foam::zoneToFace::usage_
(
zoneToFace::typeName,
"\n Usage: zoneToFace zone\n\n"
- " Select all faces in the faceZone\n\n"
+ " Select all faces in the faceZone."
+ " Note:accepts wildcards for zone.\n\n"
);
diff --git a/src/meshTools/sets/pointSources/zoneToPoint/zoneToPoint.C b/src/meshTools/sets/pointSources/zoneToPoint/zoneToPoint.C
index 4b5148c558c8d0915109d9e87591076d705db5fc..0558093afa54d58b53c6c6eed6435a7dba6f6798 100644
--- a/src/meshTools/sets/pointSources/zoneToPoint/zoneToPoint.C
+++ b/src/meshTools/sets/pointSources/zoneToPoint/zoneToPoint.C
@@ -47,7 +47,8 @@ Foam::topoSetSource::addToUsageTable Foam::zoneToPoint::usage_
(
zoneToPoint::typeName,
"\n Usage: zoneToPoint zone\n\n"
- " Select all points in the pointZone\n\n"
+ " Select all points in the pointZone."
+ " Note:accepts wildcards for zone.\n\n"
);
diff --git a/tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines b/tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines
deleted file mode 100644
index c1ebafec0159993aab2b1525f952e5b28e714776..0000000000000000000000000000000000000000
--- a/tutorials/compressible/rhoCentralFoam/LadenburgJet60psi/system/machines
+++ /dev/null
@@ -1,8 +0,0 @@
-borg1
-borg2
-borg3
-borg4
-borg5
-borg6
-borg7
-borg8
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
deleted file mode 100644
index ee03c904028a9b25f447b0cd74457e8a2439d6fb..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/blockMeshDict
+++ /dev/null
@@ -1,163 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- object blockMeshDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-convertToMeters 0.25e-9;
-
-vertices
-(
- (0 0 0) //0
- (15 0 0)
- (15 3 0)
- (0 3 0)
- (0 0 12)
- (15 0 12)
- (15 3 12)
- (0 3 12) //7
- (22 0 0)
- (22 3 0)
- (22 0 12)
- (22 3 12) //11
- (31 0 0)
- (31 3 0)
- (31 0 12)
- (31 3 12) //15
- (20 9 0)
- (17 9 0)
- (20 9 12)
- (17 9 12) //19
- (0 9 0)
- (0 9 12) //21
- (31 9 0)
- (31 9 12) //23
- (17 18 0)
- (0 18 0)
- (17 18 12)
- (0 18 12) //27
- (31 18 0)
- (20 18 0)
- (31 18 12)
- (20 18 12) //31
- (17 21 0)
- (0 21 0)
- (17 21 12)
- (0 21 12) //35
- (31 21 0)
- (20 21 0)
- (31 21 12)
- (20 21 12) //39
- (17 25 0)
- (0 25 0)
- (17 25 12)
- (0 25 12) // 43
- (31 25 0)
- (20 25 0)
- (31 25 12)
- (20 25 12) // 47
-);
-
-blocks
-(
- hex (0 1 2 3 4 5 6 7) bottomWall (15 3 6) simpleGrading (1 1 1) //1
- hex (1 8 9 2 5 10 11 6) bottomWall (3 3 6) simpleGrading (1 1 1) //2
- hex (2 9 16 17 6 11 18 19) bottomWall (3 6 6) simpleGrading (1 1 1) //3
- hex (8 12 13 9 10 14 15 11) bottomWall (9 3 6) simpleGrading (1 1 1) //4
- hex (3 2 17 20 7 6 19 21) liquid (15 6 6) simpleGrading (1 1 1) //5
- hex (20 17 24 25 21 19 26 27) liquid (15 9 6) simpleGrading (1 1 1) //6
- hex (25 24 32 33 27 26 34 35) liquid (15 3 6) simpleGrading (1 1 1) //6A
- hex (17 16 29 24 19 18 31 26) liquid (3 9 6) simpleGrading (1 1 1) //7
- hex (16 22 28 29 18 23 30 31) liquid (9 9 6) simpleGrading (1 1 1) //8
- hex (29 28 36 37 31 30 38 39) liquid (9 3 6) simpleGrading (1 1 1) //8A
- hex (9 13 22 16 11 15 23 18) liquid (9 6 6) simpleGrading (1 1 1) //9
- hex (33 32 40 41 35 34 42 43) topWall (15 3 6) simpleGrading (1 1 1) //10
- hex (32 37 45 40 34 39 47 42) topWall (3 3 6) simpleGrading (1 1 1) //11
- hex (24 29 37 32 26 31 39 34) topWall (3 3 6) simpleGrading (1 1 1) //12
- hex (37 36 44 45 39 38 46 47) topWall (9 3 6) simpleGrading (1 1 1) //13
-);
-
-patches
-(
- cyclic
- periodicX
- (
- (0 4 7 3)
- (3 7 21 20)
- (20 21 27 25)
- (25 27 35 33)
- (33 35 43 41)
- (12 13 15 14)
- (13 22 23 15)
- (22 28 30 23)
- (28 36 38 30)
- (36 44 46 38)
- )
-
- cyclic
- periodicZ
- (
- (0 3 2 1)
- (1 2 9 8)
- (8 9 13 12)
- (2 17 16 9)
- (2 3 20 17)
- (9 16 22 13)
- (17 20 25 24)
- (16 29 28 22)
- (16 17 24 29)
- (24 25 33 32)
- (28 29 37 36)
- (32 33 41 40)
- (36 37 45 44)
- (32 40 45 37)
- (24 32 37 29)
- (4 5 6 7)
- (5 10 11 6)
- (10 14 15 11)
- (6 11 18 19)
- (7 6 19 21)
- (11 15 23 18)
- (19 26 27 21)
- (18 23 30 31)
- (18 31 26 19)
- (26 34 35 27)
- (30 38 39 31)
- (34 42 43 35)
- (38 46 47 39)
- (34 39 47 42)
- (26 31 39 34)
- )
-
- wall
- outerBoundaryBottom
- (
- (0 1 5 4)
- (1 8 10 5)
- (8 12 14 10)
- )
-
- wall
- outerBoundaryTop
- (
- (40 41 43 42)
- (44 45 47 46)
- (40 42 47 45)
- )
-);
-
-mergePatchPairs
-(
-);
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict
deleted file mode 100644
index 6bd9f1538e2c0723d9505442bdf2453015012738..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/molConfigDict
+++ /dev/null
@@ -1,64 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object molConfigDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-bottomWall
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( 0 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure FCC;
- anchor ( 1.05e-09 3.18e-09 2.87e-09 );
- anchorSpecifies molecule;
- tethered yes;
- orientationAngles ( 30 0 0 );
-}
-
-liquid
-{
- massDensity 1100;
- temperature 250;
- velocityDistribution maxwellian;
- bulkVelocity ( 245 0 0 );
- id Ne;
- mass 3.350996347e-26;
- latticeStructure SC;
- anchor ( 1.05e-09 3.18e-09 2.87e-09 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 45 0 0 );
-}
-
-topWall
-{
- massDensity 1220;
- temperature 200;
- velocityDistribution maxwellian;
- bulkVelocity ( 0 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure BCC;
- anchor ( 1.05e-09 3.18e-09 2.87e-09 );
- anchorSpecifies corner;
- tethered yes;
- orientationAngles ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict
deleted file mode 100644
index 56a7bbee713bf0a24860dad6ad2e592c9e17f464..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/potentialDict
+++ /dev/null
@@ -1,104 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object potentialDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-removalOrder 2 ( Ne Ar );
-
-pair
-{
- Ar-Ar
- {
- pairPotential maitlandSmith;
- rCut 1e-09;
- rMin 1.5e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 7.5;
- rm 3.756e-10;
- epsilon 1.990108438e-21;
- }
-
- energyScalingFunction doubleSigmoid;
- doubleSigmoidCoeffs
- {
- shift1 9e-10;
- scale1 -64771072;
- shift2 9.7e-10;
- scale2 -259084288;
- }
-
- writeTables yes;
- }
-
- Ar-Ne
- {
- pairPotential maitlandSmith;
- rCut 9e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 4;
- rm 3.48e-10;
- epsilon 8.765026657e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables yes;
- }
-
- Ne-Ne
- {
- pairPotential maitlandSmith;
- rCut 8e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 5;
- rm 3.0739e-10;
- epsilon 5.813260729e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables yes;
- }
-}
-
-tether
-{
- Ar
- {
- tetherPotential restrainedHarmonicSpring;
- restrainedHarmonicSpringCoeffs
- {
- springConstant 0.1;
- rR 1.2e-09;
- }
- }
-}
-
-external
-{
- gravity ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict
deleted file mode 100644
index 937130f4ac3ba22f29b727686566f27b6adfa45a..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/molConfigDict
+++ /dev/null
@@ -1,64 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object molConfigDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-sectionA
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( -250 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-sectionB
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( -250 0 0 );
- id Ne;
- mass 3.350917e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-sectionC
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( -250 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict
deleted file mode 100644
index 0386a6994e0d9708901895788978e11f2d5bf453..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/potentialDict
+++ /dev/null
@@ -1,86 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object potentialDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-removalOrder 1 ( Ar );
-
-pair
-{
- Ar-Ar
- {
- pairPotential maitlandSmith;
- rCut 1e-09;
- rMin 1.5e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 7.5;
- rm 3.756e-10;
- epsilon 1.990108438e-21;
- }
-
- energyScalingFunction doubleSigmoid;
- doubleSigmoidCoeffs
- {
- shift1 9e-10;
- scale1 -64771072;
- shift2 9.7e-10;
- scale2 -259084288;
- }
-
- writeTables no;
- }
-
- Ar-Ne
- {
- pairPotential maitlandSmith;
- rCut 9e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 4;
- rm 3.48e-10;
- epsilon 8.765026657e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables no;
- }
-
- Ne-Ne
- {
- pairPotential maitlandSmith;
- rCut 8e-10;
- rMin 1e-10;
- dr 5e-14;
- maitlandSmithCoeffs
- {
- m 13;
- gamma 5;
- rm 3.0739e-10;
- epsilon 5.813260729e-22;
- }
-
- energyScalingFunction shiftedForce;
- writeTables no;
- }
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
index 00dd874d7638805cf31b2c56b01b659e0792e1c4..d8245cb12bceacb3316f8f922262a9e911b9b155 100755
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allclean
@@ -3,9 +3,20 @@
# Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions
-cd periodicCube
- rm -rf 0
- rm -rf Ar-Ar
- rm -rf constant/idList
+cd periodicCubeArgon
+ rm -rf 0/*
+ rm -f Ar-Ar
+ rm -f electrostatic
+ rm -f constant/idList
+ rm -rf constant/polyMesh/sets
+ cleanCase
+cd ..
+
+cd periodicCubeWater
+ rm -rf 0/*
+ rm -f O-O
+ rm -f electrostatic
+ rm -f constant/idList
+ rm -rf constant/polyMesh/sets
cleanCase
cd ..
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
index 0c590da09a8c91a0815034deba71b3d4d681e762..0d8c6de9d1b4ecf76f0d6b46642adac9dd514c8c 100755
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/Allrun
@@ -5,9 +5,14 @@
application="mdEquilibrationFoam"
-cd periodicCube
+# cd periodicCubeArgon
+# runApplication blockMesh
+# runApplication mdInitialise
+# runApplication $application
+# cd ..
+
+cd periodicCubeWater
runApplication blockMesh
- runApplication molConfig
+ runApplication mdInitialise
runApplication $application
-cd ..
-
+cd ..
\ No newline at end of file
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict
deleted file mode 100644
index 6f48e375e8c3ba101230631096b6ecd6df24a156..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/molConfigDict
+++ /dev/null
@@ -1,34 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object molConfigDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-liquid
-{
- massDensity 1220;
- temperature 300;
- velocityDistribution maxwellian;
- bulkVelocity ( 0 0 0 );
- id Ar;
- mass 6.63352033e-26;
- latticeStructure SC;
- anchor ( 0 0 0 );
- anchorSpecifies molecule;
- tethered no;
- orientationAngles ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict
deleted file mode 100644
index 1abf7b0e569b0a3b4dd0530d9c9f3ec332d43f6c..0000000000000000000000000000000000000000
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/potentialDict
+++ /dev/null
@@ -1,65 +0,0 @@
-/*--------------------------------*- C++ -*----------------------------------*\
-| ========= | |
-| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
-| \\/ M anipulation | |
-\*---------------------------------------------------------------------------*/
-FoamFile
-{
- version 2.0;
- format ascii;
- class dictionary;
- location "system";
- object potentialDict;
-}
-// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-
-removalOrder 1 ( Ar );
-
-pair
-{
- Ar-Ar
- {
- pairPotential azizChen;
- rCut 1.2e-09;
- rMin 1.5e-10;
- dr 2e-14;
- azizChenCoeffs
- {
- epsilon 1.97742255e-21;
- rm 3.759e-10;
- A 9502720;
- alpha 16.345655;
- C6 1.0914254;
- C8 0.6002595;
- C10 0.3700113;
- D 1.4;
- gamma 2;
- }
-
- energyScalingFunction noScaling;
- writeTables yes;
- }
-}
-
-tether
-{
- Ar
- {
- tetherPotential restrainedHarmonicSpring;
- restrainedHarmonicSpringCoeffs
- {
- springConstant 0.0277;
- rR 1.2e-09;
- }
- }
-}
-
-external
-{
- gravity ( 0 0 0 );
-}
-
-
-// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties
new file mode 100644
index 0000000000000000000000000000000000000000..567fce489ce0f0bd6805f2a72cb5001db238cbcd
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/moleculeProperties
@@ -0,0 +1,36 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+Ar
+{
+ siteIds (Ar);
+ pairPotentialSiteIds (Ar);
+ siteReferencePositions
+ (
+ (0 0 0)
+ );
+ siteMasses
+ (
+ 6.63352033e-26
+ );
+ siteCharges
+ (
+ 0
+ );
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..23a2ee9874ef09ad03276bbe470cc179802a227c
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/blockMeshDict
@@ -0,0 +1,73 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object blockMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 2.462491658e-9;
+
+vertices
+(
+ (-1 -1 -1)
+ (1 -1 -1)
+ (1 1 -1)
+ (-1 1 -1)
+ (-1 -1 1)
+ (1 -1 1)
+ (1 1 1)
+ (-1 1 1)
+);
+
+blocks
+(
+ hex (0 1 2 3 4 5 6 7) liquid (12 12 12) simpleGrading (1 1 1)
+);
+
+patches
+(
+ cyclic
+ periodicX
+ (
+ (1 2 6 5)
+ (0 4 7 3)
+ )
+
+ cyclic
+ periodicY
+ (
+ (2 3 7 6)
+ (0 1 5 4)
+ )
+
+ cyclic
+ periodicZ
+ (
+ (0 3 2 1)
+ (4 5 6 7)
+ )
+)
+
+mergePatchPairs
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
similarity index 90%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
index b3548de91cf4646aa6692d8e02914c5ed4755ff7..850c9baa1ec078697b17ec724c99578c6047e10d 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/boundary
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/constant/polyMesh/boundary
@@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
similarity index 92%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
index f1052a4864fad271f58b2d6f62e0f3898d42c81d..76f7ed8a7ee4afac7f47fb4c97b4a42a01147053 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/controlDict
@@ -2,7 +2,7 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -10,7 +10,6 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no;
-
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict
new file mode 100644
index 0000000000000000000000000000000000000000..958e14c73370e57528f6fd38a15607b7ba3c2bcd
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/decomposeParDict
@@ -0,0 +1,64 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 2;
+
+method simple;
+
+simpleCoeffs
+{
+ n (2 1 1);
+ delta 0.001;
+}
+
+hierarchicalCoeffs
+{
+ n (1 1 1);
+ delta 0.001;
+ order xyz;
+}
+
+metisCoeffs
+{
+ processorWeights
+ (
+ 1
+ 3
+ );
+}
+
+manualCoeffs
+{
+ dataFile "";
+}
+
+distributed no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
similarity index 76%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
index f923afcfacf038c5cd521b7e67b1c11b4d535866..42fda7921ca0a70a5b1f415666f49d4d07befb7b 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSchemes
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSchemes
@@ -17,43 +17,37 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default none;
}
gradSchemes
{
- default Gauss linear;
- grad(p) Gauss linear;
+ default none;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
- default linear;
- interpolate(HbyA) linear;
+ default none;
}
snGradSchemes
{
- default corrected;
+ default none;
}
fluxRequired
{
default no;
- p ;
}
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
similarity index 91%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
index 2dd296045bbd9676b0bf078bc53d2dc5e4958365..1e39435250fcc6c21b5ca292d31d085533ce9716 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdEquilibrationDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/fvSolution
@@ -11,11 +11,12 @@ FoamFile
format ascii;
class dictionary;
location "system";
- object mdEquilibrationDict;
+ object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-equilibrationTargetTemperature 300;
-
+solvers
+{
+}
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict
new file mode 100644
index 0000000000000000000000000000000000000000..e044b8378542974b38127b812d5a4e04aa9e2ac3
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdEquilibrationDict
@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+equilibrationTargetTemperature 300.0;
+
+// ************************************************************************* //
\ No newline at end of file
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..cb562f34a6c148531c9a243458edb24af24b5de7
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/mdInitialiseDict
@@ -0,0 +1,44 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+liquid
+{
+ massDensity 1220;
+ temperature 300;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds (Ar);
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..190428f399ffe941ecd05be8492411c4497c5b6c
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeArgon/system/potentialDict
@@ -0,0 +1,121 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+n| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( Ar );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither is an error)
+
+pair
+{
+ Ar-Ar
+ {
+ pairPotential maitlandSmith;
+ rCut 1.0e-9;
+ rMin 0.15e-9;
+ dr 5e-14;
+ maitlandSmithCoeffs
+ {
+ m 13.0;
+ gamma 7.5;
+ rm 0.3756e-9;
+ epsilon 1.990108438e-21;
+ }
+ energyScalingFunction doubleSigmoid;
+ doubleSigmoidCoeffs
+ {
+ shift1 0.9e-9;
+ scale1 0.3e11;
+ shift2 0.97e-9;
+ scale2 1.2e11;
+ }
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties
new file mode 100644
index 0000000000000000000000000000000000000000..2486f3c146ba4495cb003f1912db45ff57b5aa55
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/moleculeProperties
@@ -0,0 +1,72 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+water
+{
+ siteIds (H H O M);
+ pairPotentialSiteIds (O);
+ siteReferencePositions
+ (
+ (7.56950327263661e-11 5.85882276618295e-11 0)
+ (-7.56950327263661e-11 5.85882276618295e-11 0)
+ (0 0 0)
+ (0 1.5e-11 0)
+ );
+ siteMasses
+ (
+ 1.67353255e-27
+ 1.67353255e-27
+ 2.6560176e-26
+ 0
+ );
+ siteCharges
+ (
+ 8.3313177324e-20
+ 8.3313177324e-20
+ 0
+ -1.66626354648e-19
+ );
+}
+
+water2
+{
+ siteIds (H2 H2 O M2);
+ pairPotentialSiteIds (O);
+ siteReferencePositions
+ (
+ (7.56950327263661e-11 5.85882276618295e-11 0)
+ (-7.56950327263661e-11 5.85882276618295e-11 0)
+ (0 0 0)
+ (0 1.5e-11 0)
+ );
+ siteMasses
+ (
+ 1.67353255e-27
+ 1.67353255e-27
+ 2.6560176e-26
+ 0
+ );
+ siteCharges
+ (
+ 8.3313177324e-20
+ 8.3313177324e-20
+ 0
+ -1.66626354648e-19
+ );
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..b78ecf45c974246d6545e6265c8e459946d467bf
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/blockMeshDict
@@ -0,0 +1,73 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object blockMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 2.10840e-9;
+
+vertices
+(
+ (-1 -1 -1)
+ (1 -1 -1)
+ (1 1 -1)
+ (-1 1 -1)
+ (-1 -1 1)
+ (1 -1 1)
+ (1 1 1)
+ (-1 1 1)
+);
+
+blocks
+(
+ hex (0 1 2 3 4 5 6 7) liquid (12 12 11) simpleGrading (1 1 1)
+);
+
+patches
+(
+ cyclic
+ periodicX
+ (
+ (1 2 6 5)
+ (0 4 7 3)
+ )
+
+ cyclic
+ periodicY
+ (
+ (2 3 7 6)
+ (0 1 5 4)
+ )
+
+ cyclic
+ periodicZ
+ (
+ (0 3 2 1)
+ (4 5 6 7)
+ )
+)
+
+mergePatchPairs
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
similarity index 67%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
index e9d933420b7298f5aa2fef9909433f031b113f5a..27cc5e87df98bf4826a1a86391e91fbf982a59f1 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/constant/polyMesh/boundary
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/constant/polyMesh/boundary
@@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -15,33 +15,28 @@ FoamFile
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-4
+3
(
periodicX
{
type cyclic;
- nFaces 288;
- startFace 10710;
+ nFaces 264;
+ startFace 4344;
featureCos 0.9;
}
- periodicZ
+ periodicY
{
type cyclic;
- nFaces 1296;
- startFace 10998;
+ nFaces 264;
+ startFace 4608;
featureCos 0.9;
}
- outerBoundaryBottom
- {
- type wall;
- nFaces 162;
- startFace 12294;
- }
- outerBoundaryTop
+ periodicZ
{
- type wall;
- nFaces 162;
- startFace 12456;
+ type cyclic;
+ nFaces 288;
+ startFace 4872;
+ featureCos 0.9;
}
)
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
similarity index 86%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
index 46436871638186b4ead04e658ceeadd2579b9a5f..51a42ecc0e828d90fd725f5c361eae36c95f5f15 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/controlDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/controlDict
@@ -2,7 +2,7 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -10,7 +10,6 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
object controlDict;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
@@ -21,13 +20,13 @@ startTime 0;
stopAt endTime;
-endTime 3e-11;
+endTime 5e-12;
-deltaT 1e-14;
+deltaT 1e-15;
writeControl runTime;
-writeInterval 1e-12;
+writeInterval 2e-13;
purgeWrite 0;
@@ -45,5 +44,4 @@ runTimeModifiable yes;
adjustTimeStep no;
-
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict
new file mode 100644
index 0000000000000000000000000000000000000000..e0302aafcc9b69d045a7b00b3a4a108a44973291
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/decomposeParDict
@@ -0,0 +1,64 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 4;
+
+method simple;
+
+simpleCoeffs
+{
+ n (2 2 1);
+ delta 0.001;
+}
+
+hierarchicalCoeffs
+{
+ n (1 1 1);
+ delta 0.001;
+ order xyz;
+}
+
+metisCoeffs
+{
+ processorWeights
+ (
+ 1
+ 3
+ );
+}
+
+manualCoeffs
+{
+ dataFile "";
+}
+
+distributed no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
similarity index 76%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
index f923afcfacf038c5cd521b7e67b1c11b4d535866..42fda7921ca0a70a5b1f415666f49d4d07befb7b 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSchemes
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSchemes
@@ -17,43 +17,37 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default none;
}
gradSchemes
{
- default Gauss linear;
- grad(p) Gauss linear;
+ default none;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
- default linear;
- interpolate(HbyA) linear;
+ default none;
}
snGradSchemes
{
- default corrected;
+ default none;
}
fluxRequired
{
default no;
- p ;
}
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
similarity index 89%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution
rename to tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
index dfef948901fc9407d740d27c3f58e12fc09f78c8..1e39435250fcc6c21b5ca292d31d085533ce9716 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/mdSolution
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/fvSolution
@@ -11,13 +11,12 @@ FoamFile
format ascii;
class dictionary;
location "system";
- object mdSolution;
+ object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
-
+solvers
+{
+}
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict
new file mode 100644
index 0000000000000000000000000000000000000000..de8cb745e1f62f9f76556059a8d34a750d5b808f
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdEquilibrationDict
@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature 298;
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..ff1444ead5acf93663635513847686618cb704e5
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/mdInitialiseDict
@@ -0,0 +1,53 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+liquid
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ water2
+ water
+ water2
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ (0 0.5 0.5)
+ (0.5 0 0.5)
+ (0.5 0.5 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..25b268e74c7e3e102b49eeaa23186dc47031e338
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater/system/potentialDict
@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( water );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If a pair are not present here it is assumed that they do not interact.
+
+// Electrostatic pair interactions are not listed here - they are handled
+// separately.
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither will throw an error)
+
+pair
+{
+ O-O
+ {
+ pairPotential lennardJones;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 1e-13;
+ lennardJonesCoeffs
+ {
+ sigma 3.154e-10;
+ epsilon 1.07690722e-21;
+ }
+ energyScalingFunction noScaling;
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1e-9;
+ rMin 2e-11;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
similarity index 57%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
index 11f901ce8e07f87b4c4e41b1be30311c5ecd5589..7ff7776cb12c793a7bed32339e31b6ded3897549 100755
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allclean
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allclean
@@ -3,14 +3,8 @@
# Source tutorial clean functions
. $WM_PROJECT_DIR/bin/tools/CleanFunctions
-cd constrictedChannel
- rm -rf 0
- rm -rf Ar-Ar Ar-Ne Ne-Ne
- rm -rf constant/idList
- cleanCase
-cd ..
-
cd nanoNozzle
+ rm -rf constant/polyMesh/sets
rm -rf processor[0-9]
cleanCase
cd ..
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
similarity index 60%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
index 640ecd9bdc14899a37fe41bf908956b6623fa5f3..c756b2ca7e7a3d0ac97842edb011c9f6891abc98 100755
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/Allrun
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/Allrun
@@ -3,13 +3,7 @@
# Source tutorial run functions
. $WM_PROJECT_DIR/bin/tools/RunFunctions
-application="gnemdFoam"
-
-cd constrictedChannel
- runApplication blockMesh
- runApplication molConfig
- runApplication $application
-cd ..
+application="mdFoam"
cd nanoNozzle
runApplication blockMesh
@@ -17,7 +11,7 @@ cd nanoNozzle
runApplication decomposePar
hostname > system/machines
- runParallel molConfig 4 system/machines
+ runParallel mdInitialise 4 system/machines
runParallel $application 4 system/machines
runApplication reconstructPar
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties
new file mode 100644
index 0000000000000000000000000000000000000000..faf53865886ddd2133a0f6ad01f43d111d94c951
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/moleculeProperties
@@ -0,0 +1,45 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object moleculeProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+water
+{
+ siteIds (H H O M);
+ pairPotentialSiteIds (O);
+ siteReferencePositions
+ (
+ (7.56950327263661e-11 5.85882276618295e-11 0)
+ (-7.56950327263661e-11 5.85882276618295e-11 0)
+ (0 0 0)
+ (0 1.5e-11 0)
+ );
+ siteMasses
+ (
+ 1.67353255e-27
+ 1.67353255e-27
+ 2.6560176e-26
+ 0
+ );
+ siteCharges
+ (
+ 8.3313177324e-20
+ 8.3313177324e-20
+ 0
+ -1.66626354648e-19
+ );
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
similarity index 65%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
index 024f66a3838c1a7bd2348707c3fca7e080686015..bfd56736e27cc02fb354b8ce9de41ef67748dd03 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/blockMeshDict
@@ -14,9 +14,9 @@ FoamFile
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-convertToMeters 3e-9;
+convertToMeters 3.2e-9;
-vertices
+vertices
(
(0 0 0)
(3.5 0 0)
@@ -44,47 +44,19 @@ vertices
(16 2.5 3.5)
);
-blocks
+blocks
(
- hex (0 1 2 3 4 5 6 7) sectionA (16 15 15) simpleGrading (1 1 1)
- hex (1 8 9 2 5 10 11 6) sectionA (16 15 15) simpleGrading (0.4 1 1)
- hex (8 12 13 9 10 14 15 11) sectionB (16 15 15) simpleGrading (1 1 1)
- hex (12 16 17 13 14 18 19 15) sectionC (11 15 15) simpleGrading (2.8 1 1)
- hex (16 20 21 17 18 22 23 19) sectionC (16 15 15) simpleGrading (1 1 1)
+ hex (0 1 2 3 4 5 6 7) sectionA (20 16 16) simpleGrading (1 1 1)
+ hex (1 8 9 2 5 10 11 6) sectionA (20 16 16) simpleGrading (1 1 1)
+ hex (8 12 13 9 10 14 15 11) sectionB (29 16 16) simpleGrading (1 1 1)
+ hex (12 16 17 13 14 18 19 15) sectionC (17 16 16) simpleGrading (1 1 1)
+ hex (16 20 21 17 18 22 23 19) sectionC (20 16 16) simpleGrading (1 1 1)
);
-edges
-(
- simpleSpline 12 16
- (
- (10.375 0.875 0.4)
- (10.75 0.75 0)
- (11.125 0.625 -0.4)
- )
-
- simpleSpline 14 18
- (
- (10.375 0.875 2.6)
- (10.75 0.75 3)
- (11.125 0.625 3.4)
- )
-
- simpleSpline 15 19
- (
- (10.375 2.125 2.6)
- (10.75 2.25 3)
- (11.125 2.375 3.4)
- )
-
- simpleSpline 13 17
- (
- (10.375 2.125 0.4)
- (10.75 2.25 0)
- (11.125 2.375 -0.4)
- )
-);
+edges
+();
-patches
+patches
(
patch
sectionAEnd
@@ -92,12 +64,12 @@ patches
(0 4 7 3)
)
- patch
+ wall
sectionCEnd
(
(20 21 23 22)
)
-
+
wall
front
(
@@ -107,7 +79,7 @@ patches
(12 16 18 14)
(16 20 22 18)
)
-
+
wall
back
(
@@ -117,7 +89,7 @@ patches
(13 15 19 17)
(17 19 23 21)
)
-
+
wall
top
(
@@ -127,7 +99,7 @@ patches
(14 18 19 15)
(18 22 23 19)
)
-
+
wall
bottom
(
@@ -139,7 +111,7 @@ patches
)
);
-mergePatchPairs
+mergePatchPairs
(
);
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
similarity index 66%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
index a58d17ed7f51a0b1d98167dadad04ec7b6a21c8b..8f1b5f6505e47c52d85bd170a7fae0d85f55ec1c 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/constant/polyMesh/boundary
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/constant/polyMesh/boundary
@@ -1,8 +1,8 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
@@ -20,38 +20,38 @@ FoamFile
sectionAEnd
{
type patch;
- nFaces 225;
- startFace 48150;
+ nFaces 256;
+ startFace 77760;
}
sectionCEnd
{
- type patch;
- nFaces 225;
- startFace 48375;
+ type wall;
+ nFaces 256;
+ startFace 78016;
}
front
{
type wall;
- nFaces 1125;
- startFace 48600;
+ nFaces 1696;
+ startFace 78272;
}
back
{
type wall;
- nFaces 1125;
- startFace 49725;
+ nFaces 1696;
+ startFace 79968;
}
top
{
type wall;
- nFaces 1125;
- startFace 50850;
+ nFaces 1696;
+ startFace 81664;
}
bottom
{
type wall;
- nFaces 1125;
- startFace 51975;
+ nFaces 1696;
+ startFace 83360;
}
)
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
new file mode 100644
index 0000000000000000000000000000000000000000..8a3ba006163857eb4fafe09388c1ae873b0f23bf
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/controlDict
@@ -0,0 +1,47 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+startFrom startTime;
+
+startTime 0;
+
+stopAt endTime;
+
+endTime 1e-10;
+
+deltaT 1e-15;
+
+writeControl runTime;
+
+writeInterval 2e-13;
+
+purgeWrite 0;
+
+writeFormat ascii;
+
+writePrecision 12;
+
+writeCompression uncompressed;
+
+timeFormat general;
+
+timePrecision 6;
+
+runTimeModifiable yes;
+
+adjustTimeStep no;
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict
new file mode 100644
index 0000000000000000000000000000000000000000..a3946a745f2169cea62449bd32b9365bd539cd69
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/decomposeParDict
@@ -0,0 +1,66 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+numberOfSubdomains 4;
+
+method metis;
+
+simpleCoeffs
+{
+ n (2 2 1);
+ delta 0.001;
+}
+
+hierarchicalCoeffs
+{
+ n (1 1 1);
+ delta 0.001;
+ order xyz;
+}
+
+metisCoeffs
+{
+ processorWeights
+ (
+ 1
+ 1
+ 1
+ 1
+ );
+}
+
+manualCoeffs
+{
+ dataFile "";
+}
+
+distributed no;
+
+roots
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
similarity index 76%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
index f923afcfacf038c5cd521b7e67b1c11b4d535866..42fda7921ca0a70a5b1f415666f49d4d07befb7b 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSchemes
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSchemes
@@ -17,43 +17,37 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default none;
}
gradSchemes
{
- default Gauss linear;
- grad(p) Gauss linear;
+ default none;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
}
interpolationSchemes
{
- default linear;
- interpolate(HbyA) linear;
+ default none;
}
snGradSchemes
{
- default corrected;
+ default none;
}
fluxRequired
{
default no;
- p ;
}
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
similarity index 89%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution
rename to tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
index dfef948901fc9407d740d27c3f58e12fc09f78c8..1e39435250fcc6c21b5ca292d31d085533ce9716 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/mdSolution
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/fvSolution
@@ -11,13 +11,12 @@ FoamFile
format ascii;
class dictionary;
location "system";
- object mdSolution;
+ object fvSolution;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
-
+solvers
+{
+}
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict
new file mode 100644
index 0000000000000000000000000000000000000000..de8cb745e1f62f9f76556059a8d34a750d5b808f
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdEquilibrationDict
@@ -0,0 +1,19 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object mdEquilibrationDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+targetTemperature 298;
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict
new file mode 100644
index 0000000000000000000000000000000000000000..ac85160f5cb2e1cbc774f42df6b87eb70ccd320d
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/mdInitialiseDict
@@ -0,0 +1,85 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.3 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object molConfigDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Euler angles, expressed in degrees as phi, theta, psi, see
+// http://mathworld.wolfram.com/EulerAngles.html
+
+sectionA
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+sectionB
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+sectionC
+{
+ massDensity 980;
+ temperature 298;
+ bulkVelocity (0.0 0.0 0.0);
+ latticeIds
+ (
+ water
+ );
+ tetherSiteIds ();
+ latticePositions
+ (
+ (0 0 0)
+ );
+ anchor (0 0 0);
+ orientationAngles (0 0 0);
+ latticeCellShape (1 1 1);
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict
new file mode 100644
index 0000000000000000000000000000000000000000..25b268e74c7e3e102b49eeaa23186dc47031e338
--- /dev/null
+++ b/tutorials/discreteMethods/molecularDynamics/mdFoam/nanoNozzle/system/potentialDict
@@ -0,0 +1,118 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object potentials;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+// Subdictionaries specifying types of intermolecular potential.
+// Sub-sub dictionaries specify the potentials themselves.
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Removal order
+
+// This is the order in which to remove overlapping pairs if more than one
+// type of molecule is present. The most valuable molecule type is at the
+// right hand end, the molecule that will be removed 1st is 1st on the list.
+// Not all types need to be present, a molecule that is not present is
+// automatically less valuable than any on the list. For molecules of the
+// same type there is no control over which is removed.
+
+removalOrder ( water );
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Potential Energy Limit
+
+// Maximum permissible pair energy allowed at startup. Used to remove
+// overlapping molecules created during preprocessing.
+
+potentialEnergyLimit 1e-18;
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Pair potentials
+
+// If a pair are not present here it is assumed that they do not interact.
+
+// Electrostatic pair interactions are not listed here - they are handled
+// separately.
+
+// If there are r different type of molecules, and a pair force is required
+// between all combinations, then there are C = r(r+1)/2 combinations,
+// i.e. for r = {1,2,3,4}, C = {1,3,6,10} (sum of triangular numbers).
+
+// Pair potentials are specified by the combinaition of their ids,
+// for MOLA and MOLB, "MOLA-MOLB" OR "MOLB-MOLA" is acceptable
+// (strictly OR, both or neither will throw an error)
+
+pair
+{
+ O-O
+ {
+ pairPotential lennardJones;
+ rCut 1.0e-9;
+ rMin 0.1e-9;
+ dr 1e-13;
+ lennardJonesCoeffs
+ {
+ sigma 3.154e-10;
+ epsilon 1.07690722e-21;
+ }
+ energyScalingFunction noScaling;
+ writeTables yes;
+ }
+
+ electrostatic
+ {
+ pairPotential dampedCoulomb;
+ rCut 1e-9;
+ rMin 2e-11;
+ dr 2e-12;
+ dampedCoulombCoeffs
+ {
+ alpha 2e9;
+ }
+ energyScalingFunction shiftedForce;
+ writeTables yes;
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// Tethering Potentials
+
+tether
+{
+ O
+ {
+ tetherPotential restrainedHarmonicSpring;
+ restrainedHarmonicSpringCoeffs
+ {
+ springConstant 0.277;
+ rR 1.2e-9;
+ }
+ }
+}
+
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+// External Forces
+
+// Bulk external forces (namely gravity) will be specified as forces rather
+// than potentials to allow their direction to be controlled.
+
+external
+{
+ gravity (0 0 0);
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/T b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/T
new file mode 100644
index 0000000000000000000000000000000000000000..a5a03f6a2e3944867bd11d1adb15e3f468569dc6
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/T
@@ -0,0 +1,443 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object T;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 0 0 1 0 0 0];
+
+internalField uniform 300;
+
+boundaryField
+{
+ floor
+ {
+ type fixedValue;
+ value nonuniform List<scalar>
+400
+(
+300
+300
+300
+300
+300
+300
+300
+300
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+300
+300
+300
+300
+300
+300
+300
+300
+300
+300
+)
+;
+ }
+ ceiling
+ {
+ type fixedValue;
+ value uniform 300;
+ }
+ fixedWalls
+ {
+ type zeroGradient;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/T.org b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/T.org
new file mode 100644
index 0000000000000000000000000000000000000000..a5a03f6a2e3944867bd11d1adb15e3f468569dc6
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/T.org
@@ -0,0 +1,443 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object T;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 0 0 1 0 0 0];
+
+internalField uniform 300;
+
+boundaryField
+{
+ floor
+ {
+ type fixedValue;
+ value nonuniform List<scalar>
+400
+(
+300
+300
+300
+300
+300
+300
+300
+300
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+300
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+300
+300
+300
+300
+300
+300
+300
+300
+300
+300
+300
+)
+;
+ }
+ ceiling
+ {
+ type fixedValue;
+ value uniform 300;
+ }
+ fixedWalls
+ {
+ type zeroGradient;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/U
similarity index 59%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/U
index 46670343363af32a79fcf7bd788316556b9de7d7..0b6b191dab023e6aa4c9701188dd93252aeb7aa9 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/fvSolution
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/U
@@ -2,45 +2,41 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
- class dictionary;
- location "system";
- object fvSolution;
+ class volVectorField;
+ object U;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-solvers
+dimensions [0 1 -1 0 0 0 0];
+
+internalField uniform (0 0 0);
+
+boundaryField
{
- p
+ floor
{
- solver PCG;
- preconditioner DIC;
- tolerance 1e-06;
- relTol 0;
+ type fixedValue;
+ value uniform (0 0 0);
}
- U
+ ceiling
{
- solver PBiCG;
- preconditioner DILU;
- tolerance 1e-05;
- relTol 0;
+ type fixedValue;
+ value uniform (0 0 0);
}
-}
-PISO
-{
- nCorrectors 2;
- nNonOrthogonalCorrectors 0;
- pRefCell 0;
- pRefValue 0;
+ fixedWalls
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
}
-
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/alphat
similarity index 59%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/alphat
index 46670343363af32a79fcf7bd788316556b9de7d7..3bcb9c03b13cf7d96e3456eabea33e5f6d0ee8e1 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/system/fvSolution
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/alphat
@@ -2,44 +2,40 @@
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
| \\ / O peration | Version: 1.5 |
-| \\ / A nd | Web: www.OpenFOAM.org |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
FoamFile
{
version 2.0;
format ascii;
- class dictionary;
- location "system";
- object fvSolution;
+ class volScalarField;
+ location "0";
+ object alphat;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-solvers
+dimensions [1 -1 -1 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
{
- p
+ floor
{
- solver PCG;
- preconditioner DIC;
- tolerance 1e-06;
- relTol 0;
+ type alphatWallFunction;
+ value uniform 0;
}
-
- U
+ ceiling
{
- solver PBiCG;
- preconditioner DILU;
- tolerance 1e-05;
- relTol 0;
+ type alphatWallFunction;
+ value uniform 0;
+ }
+ fixedWalls
+ {
+ type alphatWallFunction;
+ value uniform 0;
}
-}
-
-PISO
-{
- nCorrectors 2;
- nNonOrthogonalCorrectors 0;
- pRefCell 0;
- pRefValue 0;
}
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/epsilon b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/epsilon
new file mode 100644
index 0000000000000000000000000000000000000000..892d69375d9d5eab2aa804a87ee6661bbc1a9f06
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/epsilon
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object epsilon;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -3 0 0 0 0];
+
+internalField uniform 0.01;
+
+boundaryField
+{
+ floor
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+ ceiling
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+ fixedWalls
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/epsilon.old b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/epsilon.old
new file mode 100644
index 0000000000000000000000000000000000000000..23851291dc60d3b0df3be887acfbeb0bb5067ef8
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/epsilon.old
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object epsilon;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -3 0 0 0 0];
+
+internalField uniform 0.01;
+
+boundaryField
+{
+ floor
+ {
+ type compressible::epsilonWallFunction;
+ value uniform 0.01;
+ }
+ ceiling
+ {
+ type compressible::epsilonWallFunction;
+ value uniform 0.01;
+ }
+ fixedWalls
+ {
+ type compressible::epsilonWallFunction;
+ value uniform 0.01;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/k b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/k
new file mode 100644
index 0000000000000000000000000000000000000000..38c2a542ef4c0c57799adb46dbd114f24947f474
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/k
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0.1;
+
+boundaryField
+{
+ floor
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+ ceiling
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+ fixedWalls
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/k.old b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/k.old
new file mode 100644
index 0000000000000000000000000000000000000000..4ec7f08960c175a6d955e2c1d3cfb98453524647
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/k.old
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0.1;
+
+boundaryField
+{
+ floor
+ {
+ type compressible::kQRWallFunction;
+ value uniform 0.1;
+ }
+ ceiling
+ {
+ type compressible::kQRWallFunction;
+ value uniform 0.1;
+ }
+ fixedWalls
+ {
+ type compressible::kQRWallFunction;
+ value uniform 0.1;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/nut
similarity index 58%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/nut
index 2b1855ea4634bda4d66c8129ce2d08d57a2fb0c9..a81ad6b59fd8d4b8617763e08058fbb36b3b8aef 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/decomposeParDict
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/nut
@@ -1,7 +1,7 @@
/*--------------------------------*- C++ -*----------------------------------*\
| ========= | |
| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
-| \\ / O peration | Version: 1.5 |
+| \\ / O peration | Version: dev |
| \\ / A nd | Web: www.OpenFOAM.org |
| \\/ M anipulation | |
\*---------------------------------------------------------------------------*/
@@ -9,42 +9,34 @@ FoamFile
{
version 2.0;
format ascii;
- class dictionary;
- location "system";
- object decomposeParDict;
+ class volScalarField;
+ location "0";
+ object nut;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-numberOfSubdomains 4;
+dimensions [0 2 -1 0 0 0 0];
-method metis;
+internalField uniform 0;
-simpleCoeffs
+boundaryField
{
- n ( 4 1 1 );
- delta 0.001;
+ floor
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+ ceiling
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+ fixedWalls
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
}
-hierarchicalCoeffs
-{
- n ( 1 1 1 );
- delta 0.001;
- order xyz;
-}
-
-metisCoeffs
-{
- processorWeights ( 1 1 1 1 );
-}
-
-manualCoeffs
-{
- dataFile "";
-}
-
-distributed no;
-
-roots ( );
-
// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/p b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/p
new file mode 100644
index 0000000000000000000000000000000000000000..2014ca6e8c05c4140f60fa97f5d77545a31b68c8
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/0/p
@@ -0,0 +1,45 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ floor
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ ceiling
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ fixedWalls
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/Allclean b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/Allclean
new file mode 100755
index 0000000000000000000000000000000000000000..83fcec83ecad6243fdfd74b8afb16acd55518f36
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/Allclean
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+cleanCase
+cp 0/T.org 0/T
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/Allrun b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/Allrun
new file mode 100755
index 0000000000000000000000000000000000000000..92490b5b5ea392da192d42ec102f629c87c73e60
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/Allrun
@@ -0,0 +1,10 @@
+#!/bin/sh
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+application="buoyantBoussinesqPisoFoam"
+
+compileApplication ../../buoyantPisoFoam/hotRoom/setHotRoom
+runApplication blockMesh
+runApplication setHotRoom
+runApplication $application
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/RASProperties b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/RASProperties
new file mode 100644
index 0000000000000000000000000000000000000000..35b5a409f230c180f07469bfe0679cdf00cb419d
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/RASProperties
@@ -0,0 +1,100 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object RASProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+RASModel kEpsilon;
+
+turbulence on;
+
+printCoeffs on;
+
+laminarCoeffs
+{
+}
+
+kEpsilonCoeffs
+{
+ Cmu 0.09;
+ C1 1.44;
+ C2 1.92;
+ C3 0.85;
+ alphah 1;
+ alphak 1;
+ alphaEps 0.76923;
+}
+
+RNGkEpsilonCoeffs
+{
+ Cmu 0.0845;
+ C1 1.42;
+ C2 1.68;
+ C3 -0.33;
+ alphah 1;
+ alphak 1.39;
+ alphaEps 1.39;
+ eta0 4.38;
+ beta 0.012;
+}
+
+LaunderSharmaKECoeffs
+{
+ Cmu 0.09;
+ C1 1.44;
+ C2 1.92;
+ C3 -0.33;
+ alphah 1;
+ alphak 1;
+ alphaEps 0.76923;
+}
+
+LRRCoeffs
+{
+ Cmu 0.09;
+ Clrr1 1.8;
+ Clrr2 0.6;
+ C1 1.44;
+ C2 1.92;
+ alphah 1;
+ Cs 0.25;
+ Ceps 0.15;
+ alphaR 1;
+ alphaEps 0.76923;
+}
+
+LaunderGibsonRSTMCoeffs
+{
+ Cmu 0.09;
+ Clg1 1.8;
+ Clg2 0.6;
+ C1 1.44;
+ C2 1.92;
+ alphah 1;
+ C1Ref 0.5;
+ C2Ref 0.3;
+ Cs 0.25;
+ Ceps 0.15;
+ alphaR 1;
+ alphaEps 0.76923;
+}
+
+wallFunctionCoeffs
+{
+ kappa 0.4187;
+ E 9;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/environmentalProperties
similarity index 86%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/environmentalProperties
index dfef948901fc9407d740d27c3f58e12fc09f78c8..a866ff549fd799e63d2d6946a66cf3da14d092bd 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/nanoNozzle/system/mdSolution
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/environmentalProperties
@@ -10,14 +10,12 @@ FoamFile
version 2.0;
format ascii;
class dictionary;
- location "system";
- object mdSolution;
+ location "constant";
+ object environmentalProperties;
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-integrationMethod verletLeapfrog;
-
-potentialEnergyLimit 5.256e-20;
+g g [ 0 1 -2 0 0 0 0 ] ( 0 -9.81 0 );
// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/polyMesh/blockMeshDict
similarity index 72%
rename from tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/polyMesh/blockMeshDict
index 187c2c7784d60dda7a64455a321799191e21c95e..fa2bb5c4c6e834caba8be30e1825ea1a45c22c92 100644
--- a/tutorials/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCube/constant/polyMesh/blockMeshDict
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/polyMesh/blockMeshDict
@@ -14,48 +14,47 @@ FoamFile
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-convertToMeters 2.462491658e-9;
+convertToMeters 1;
-vertices
+vertices
(
- (-1 -1 -1)
- (1 -1 -1)
- (1 1 -1)
- (-1 1 -1)
- (-1 -1 1)
- (1 -1 1)
- (1 1 1)
- (-1 1 1)
+ (0 0 0)
+ (10 0 0)
+ (10 5 0)
+ (0 5 0)
+ (0 0 10)
+ (10 0 10)
+ (10 5 10)
+ (0 5 10)
);
-blocks
+blocks
(
- hex (0 1 2 3 4 5 6 7) liquid (12 12 12) simpleGrading (1 1 1)
+ hex (0 1 2 3 4 5 6 7) (20 10 20) simpleGrading (1 1 1)
);
-patches
+edges
(
- cyclic
- periodicX
+);
+
+patches
+(
+ wall floor
(
- (1 2 6 5)
- (0 4 7 3)
+ (1 5 4 0)
)
-
- cyclic
- periodicY
+ wall ceiling
(
- (2 3 7 6)
- (0 1 5 4)
+ (3 7 6 2)
)
-
- cyclic
- periodicZ
+ wall fixedWalls
(
+ (0 4 7 3)
+ (2 6 5 1)
(0 3 2 1)
(4 5 6 7)
)
-)
+);
mergePatchPairs
(
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/polyMesh/boundary b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/polyMesh/boundary
new file mode 100644
index 0000000000000000000000000000000000000000..0d4d0e498dae524c835cc1addc9707eb5af47fb3
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/polyMesh/boundary
@@ -0,0 +1,40 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class polyBoundaryMesh;
+ location "constant/polyMesh";
+ object boundary;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+3
+(
+ floor
+ {
+ type wall;
+ nFaces 400;
+ startFace 11200;
+ }
+ ceiling
+ {
+ type wall;
+ nFaces 400;
+ startFace 11600;
+ }
+ fixedWalls
+ {
+ type wall;
+ nFaces 800;
+ startFace 12000;
+ }
+)
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/transportProperties b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/transportProperties
new file mode 100644
index 0000000000000000000000000000000000000000..f48fda19ccac705f76f1573b7ba40cce45abfd5b
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/constant/transportProperties
@@ -0,0 +1,42 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5.x |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object transportProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+transportModel Newtonian;
+
+// Laminar viscosity
+nu nu [0 2 -1 0 0 0 0] 1e-05;
+
+// Thermal expansion coefficient
+beta beta [0 0 0 -1 0 0 0] 3e-03;
+
+// Reference temperature
+TRef TRef [0 0 0 1 0 0 0] 300;
+
+// Laminar Prandtl number
+Pr Pr [0 0 0 0 0 0 0] 0.9;
+
+// Turbulent Prandtl number
+Prt Prt [0 0 0 0 0 0 0] 0.7;
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/controlDict
similarity index 89%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/controlDict
index c43b52a4489940816c201cd8c03c5ca1f7694a2e..26a1219ee04433266c5a0540f5ecf239fc0d0f93 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/controlDict
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/controlDict
@@ -21,19 +21,19 @@ startTime 0;
stopAt endTime;
-endTime 8e-11;
+endTime 1000;
-deltaT 1e-14;
+deltaT 1;
-writeControl runTime;
+writeControl timeStep;
-writeInterval 2e-12;
+writeInterval 100;
purgeWrite 0;
writeFormat ascii;
-writePrecision 12;
+writePrecision 6;
writeCompression uncompressed;
@@ -45,5 +45,6 @@ runTimeModifiable yes;
adjustTimeStep no;
+maxCo 0.5;
// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/fvSchemes b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/fvSchemes
new file mode 100644
index 0000000000000000000000000000000000000000..6be8f0129f6c5ae27dae2d20c5e0cd28fcf26f12
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/fvSchemes
@@ -0,0 +1,68 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "system";
+ object fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+ default Euler;
+}
+
+gradSchemes
+{
+ default Gauss linear;
+}
+
+divSchemes
+{
+ default none;
+ div(phi,U) Gauss upwind;
+ div(phi,T) Gauss upwind;
+ div(phi,k) Gauss upwind;
+ div(phi,epsilon) Gauss upwind;
+ div(phi,R) Gauss upwind;
+ div(R) Gauss linear;
+ div((nuEff*dev(grad(U).T()))) Gauss linear;
+}
+
+laplacianSchemes
+{
+ default none;
+ laplacian(nuEff,U) Gauss linear corrected;
+ laplacian((1|A(U)),p) Gauss linear corrected;
+ laplacian(kappaEff,T) Gauss linear corrected;
+ laplacian(DkEff,k) Gauss linear corrected;
+ laplacian(DepsilonEff,epsilon) Gauss linear corrected;
+ laplacian(DREff,R) Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+ default linear;
+}
+
+snGradSchemes
+{
+ default corrected;
+}
+
+fluxRequired
+{
+ default no;
+ p ;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/fvSolution
similarity index 61%
rename from tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution
rename to tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/fvSolution
index 46670343363af32a79fcf7bd788316556b9de7d7..7afa2f50aa9b1dc663a24bada8c0971be911c656 100644
--- a/tutorials/discreteMethods/molecularDynamics/gnemdFoam/constrictedChannel/system/fvSolution
+++ b/tutorials/heatTransfer/buoyantBoussinesqPisoFoam/hotRoom/system/fvSolution
@@ -21,7 +21,15 @@ solvers
{
solver PCG;
preconditioner DIC;
- tolerance 1e-06;
+ tolerance 1e-07;
+ relTol 0.1;
+ }
+
+ pFinal
+ {
+ solver PCG;
+ preconditioner DIC;
+ tolerance 1e-07;
relTol 0;
}
@@ -32,10 +40,43 @@ solvers
tolerance 1e-05;
relTol 0;
}
+
+ T
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0;
+ }
+
+ k
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0;
+ }
+
+ epsilon
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0;
+ }
+
+ R
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0;
+ }
}
PISO
{
+ momentumPredictor yes;
nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/T b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/T
new file mode 100644
index 0000000000000000000000000000000000000000..a5a03f6a2e3944867bd11d1adb15e3f468569dc6
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/T
@@ -0,0 +1,443 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object T;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 0 0 1 0 0 0];
+
+internalField uniform 300;
+
+boundaryField
+{
+ floor
+ {
+ type fixedValue;
+ value nonuniform List<scalar>
+400
+(
+300
+300
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+300
+300
+300
+300
+300
+300
+300
+300
+300
+300
+)
+;
+ }
+ ceiling
+ {
+ type fixedValue;
+ value uniform 300;
+ }
+ fixedWalls
+ {
+ type zeroGradient;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/T.org b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/T.org
new file mode 100644
index 0000000000000000000000000000000000000000..a5a03f6a2e3944867bd11d1adb15e3f468569dc6
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/T.org
@@ -0,0 +1,443 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object T;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 0 0 1 0 0 0];
+
+internalField uniform 300;
+
+boundaryField
+{
+ floor
+ {
+ type fixedValue;
+ value nonuniform List<scalar>
+400
+(
+300
+300
+300
+300
+300
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+300
+300
+300
+300
+300
+)
+;
+ }
+ ceiling
+ {
+ type fixedValue;
+ value uniform 300;
+ }
+ fixedWalls
+ {
+ type zeroGradient;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/U b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/U
new file mode 100644
index 0000000000000000000000000000000000000000..0b6b191dab023e6aa4c9701188dd93252aeb7aa9
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/U
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volVectorField;
+ object U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 1 -1 0 0 0 0];
+
+internalField uniform (0 0 0);
+
+boundaryField
+{
+ floor
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+
+ ceiling
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+
+ fixedWalls
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/alphat b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/alphat
new file mode 100644
index 0000000000000000000000000000000000000000..3bcb9c03b13cf7d96e3456eabea33e5f6d0ee8e1
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/alphat
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object alphat;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [1 -1 -1 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ floor
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+ ceiling
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+ fixedWalls
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/epsilon b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/epsilon
new file mode 100644
index 0000000000000000000000000000000000000000..892d69375d9d5eab2aa804a87ee6661bbc1a9f06
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/epsilon
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object epsilon;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -3 0 0 0 0];
+
+internalField uniform 0.01;
+
+boundaryField
+{
+ floor
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+ ceiling
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+ fixedWalls
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/epsilon.old b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/epsilon.old
new file mode 100644
index 0000000000000000000000000000000000000000..23851291dc60d3b0df3be887acfbeb0bb5067ef8
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/epsilon.old
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object epsilon;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -3 0 0 0 0];
+
+internalField uniform 0.01;
+
+boundaryField
+{
+ floor
+ {
+ type compressible::epsilonWallFunction;
+ value uniform 0.01;
+ }
+ ceiling
+ {
+ type compressible::epsilonWallFunction;
+ value uniform 0.01;
+ }
+ fixedWalls
+ {
+ type compressible::epsilonWallFunction;
+ value uniform 0.01;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/k b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/k
new file mode 100644
index 0000000000000000000000000000000000000000..38c2a542ef4c0c57799adb46dbd114f24947f474
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/k
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0.1;
+
+boundaryField
+{
+ floor
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+ ceiling
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+ fixedWalls
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/k.old b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/k.old
new file mode 100644
index 0000000000000000000000000000000000000000..4ec7f08960c175a6d955e2c1d3cfb98453524647
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/k.old
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0.1;
+
+boundaryField
+{
+ floor
+ {
+ type compressible::kQRWallFunction;
+ value uniform 0.1;
+ }
+ ceiling
+ {
+ type compressible::kQRWallFunction;
+ value uniform 0.1;
+ }
+ fixedWalls
+ {
+ type compressible::kQRWallFunction;
+ value uniform 0.1;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/nut b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/nut
new file mode 100644
index 0000000000000000000000000000000000000000..a81ad6b59fd8d4b8617763e08058fbb36b3b8aef
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/nut
@@ -0,0 +1,42 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object nut;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -1 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ floor
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+ ceiling
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+ fixedWalls
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/p b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/p
new file mode 100644
index 0000000000000000000000000000000000000000..2014ca6e8c05c4140f60fa97f5d77545a31b68c8
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/0/p
@@ -0,0 +1,45 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ floor
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ ceiling
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ fixedWalls
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/Allclean b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/Allclean
new file mode 100755
index 0000000000000000000000000000000000000000..83fcec83ecad6243fdfd74b8afb16acd55518f36
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/Allclean
@@ -0,0 +1,7 @@
+#!/bin/sh
+
+# Source tutorial clean functions
+. $WM_PROJECT_DIR/bin/tools/CleanFunctions
+
+cleanCase
+cp 0/T.org 0/T
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/Allrun b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/Allrun
new file mode 100755
index 0000000000000000000000000000000000000000..628624c70292d70d593effaa1a4e9fc9e2281550
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/Allrun
@@ -0,0 +1,10 @@
+#!/bin/sh
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+application="buoyantBoussinesqSimpleFoam"
+
+compileApplication ../../buoyantPisoFoam/hotRoom/setHotRoom
+runApplication blockMesh
+runApplication setHotRoom
+runApplication $application
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/RASProperties b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/RASProperties
new file mode 100644
index 0000000000000000000000000000000000000000..35b5a409f230c180f07469bfe0679cdf00cb419d
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/RASProperties
@@ -0,0 +1,100 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object RASProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+RASModel kEpsilon;
+
+turbulence on;
+
+printCoeffs on;
+
+laminarCoeffs
+{
+}
+
+kEpsilonCoeffs
+{
+ Cmu 0.09;
+ C1 1.44;
+ C2 1.92;
+ C3 0.85;
+ alphah 1;
+ alphak 1;
+ alphaEps 0.76923;
+}
+
+RNGkEpsilonCoeffs
+{
+ Cmu 0.0845;
+ C1 1.42;
+ C2 1.68;
+ C3 -0.33;
+ alphah 1;
+ alphak 1.39;
+ alphaEps 1.39;
+ eta0 4.38;
+ beta 0.012;
+}
+
+LaunderSharmaKECoeffs
+{
+ Cmu 0.09;
+ C1 1.44;
+ C2 1.92;
+ C3 -0.33;
+ alphah 1;
+ alphak 1;
+ alphaEps 0.76923;
+}
+
+LRRCoeffs
+{
+ Cmu 0.09;
+ Clrr1 1.8;
+ Clrr2 0.6;
+ C1 1.44;
+ C2 1.92;
+ alphah 1;
+ Cs 0.25;
+ Ceps 0.15;
+ alphaR 1;
+ alphaEps 0.76923;
+}
+
+LaunderGibsonRSTMCoeffs
+{
+ Cmu 0.09;
+ Clg1 1.8;
+ Clg2 0.6;
+ C1 1.44;
+ C2 1.92;
+ alphah 1;
+ C1Ref 0.5;
+ C2Ref 0.3;
+ Cs 0.25;
+ Ceps 0.15;
+ alphaR 1;
+ alphaEps 0.76923;
+}
+
+wallFunctionCoeffs
+{
+ kappa 0.4187;
+ E 9;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/environmentalProperties b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/environmentalProperties
new file mode 100644
index 0000000000000000000000000000000000000000..a866ff549fd799e63d2d6946a66cf3da14d092bd
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/environmentalProperties
@@ -0,0 +1,21 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object environmentalProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+g g [ 0 1 -2 0 0 0 0 ] ( 0 -9.81 0 );
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/polyMesh/blockMeshDict b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/polyMesh/blockMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..fa2bb5c4c6e834caba8be30e1825ea1a45c22c92
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/polyMesh/blockMeshDict
@@ -0,0 +1,63 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ object blockMeshDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+convertToMeters 1;
+
+vertices
+(
+ (0 0 0)
+ (10 0 0)
+ (10 5 0)
+ (0 5 0)
+ (0 0 10)
+ (10 0 10)
+ (10 5 10)
+ (0 5 10)
+);
+
+blocks
+(
+ hex (0 1 2 3 4 5 6 7) (20 10 20) simpleGrading (1 1 1)
+);
+
+edges
+(
+);
+
+patches
+(
+ wall floor
+ (
+ (1 5 4 0)
+ )
+ wall ceiling
+ (
+ (3 7 6 2)
+ )
+ wall fixedWalls
+ (
+ (0 4 7 3)
+ (2 6 5 1)
+ (0 3 2 1)
+ (4 5 6 7)
+ )
+);
+
+mergePatchPairs
+(
+);
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/polyMesh/boundary b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/polyMesh/boundary
new file mode 100644
index 0000000000000000000000000000000000000000..0d4d0e498dae524c835cc1addc9707eb5af47fb3
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/polyMesh/boundary
@@ -0,0 +1,40 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class polyBoundaryMesh;
+ location "constant/polyMesh";
+ object boundary;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+3
+(
+ floor
+ {
+ type wall;
+ nFaces 400;
+ startFace 11200;
+ }
+ ceiling
+ {
+ type wall;
+ nFaces 400;
+ startFace 11600;
+ }
+ fixedWalls
+ {
+ type wall;
+ nFaces 800;
+ startFace 12000;
+ }
+)
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/transportProperties b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/transportProperties
new file mode 100644
index 0000000000000000000000000000000000000000..f48fda19ccac705f76f1573b7ba40cce45abfd5b
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/constant/transportProperties
@@ -0,0 +1,42 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5.x |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object transportProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+transportModel Newtonian;
+
+// Laminar viscosity
+nu nu [0 2 -1 0 0 0 0] 1e-05;
+
+// Thermal expansion coefficient
+beta beta [0 0 0 -1 0 0 0] 3e-03;
+
+// Reference temperature
+TRef TRef [0 0 0 1 0 0 0] 300;
+
+// Laminar Prandtl number
+Pr Pr [0 0 0 0 0 0 0] 0.9;
+
+// Turbulent Prandtl number
+Prt Prt [0 0 0 0 0 0 0] 0.7;
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/controlDict b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/controlDict
new file mode 100644
index 0000000000000000000000000000000000000000..bfc52cf914e6d70563729bb9790dda8a20daaa70
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/controlDict
@@ -0,0 +1,47 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "system";
+ object controlDict;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+startFrom latestTime;
+
+startTime 0;
+
+stopAt endTime;
+
+endTime 1000;
+
+deltaT 1;
+
+writeControl timeStep;
+
+writeInterval 100;
+
+purgeWrite 0;
+
+writeFormat ascii;
+
+writePrecision 6;
+
+writeCompression uncompressed;
+
+timeFormat general;
+
+timePrecision 6;
+
+runTimeModifiable yes;
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/fvSchemes b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/fvSchemes
new file mode 100644
index 0000000000000000000000000000000000000000..b54bb8631600a594830b214816d8a858bcf83a02
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/fvSchemes
@@ -0,0 +1,68 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "system";
+ object fvSchemes;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+ default steadyState;
+}
+
+gradSchemes
+{
+ default Gauss linear;
+}
+
+divSchemes
+{
+ default none;
+ div(phi,U) Gauss upwind;
+ div(phi,T) Gauss upwind;
+ div(phi,k) Gauss upwind;
+ div(phi,epsilon) Gauss upwind;
+ div(phi,R) Gauss upwind;
+ div(R) Gauss linear;
+ div((nuEff*dev(grad(U).T()))) Gauss linear;
+}
+
+laplacianSchemes
+{
+ default none;
+ laplacian(nuEff,U) Gauss linear corrected;
+ laplacian((1|A(U)),p) Gauss linear corrected;
+ laplacian(kappaEff,T) Gauss linear corrected;
+ laplacian(DkEff,k) Gauss linear corrected;
+ laplacian(DepsilonEff,epsilon) Gauss linear corrected;
+ laplacian(DREff,R) Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+ default linear;
+}
+
+snGradSchemes
+{
+ default corrected;
+}
+
+fluxRequired
+{
+ default no;
+ p ;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/fvSolution b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/fvSolution
new file mode 100644
index 0000000000000000000000000000000000000000..429a10a7fdef11317fd88716d83302a85e16d099
--- /dev/null
+++ b/tutorials/heatTransfer/buoyantBoussinesqSimpleFoam/hotRoom/system/fvSolution
@@ -0,0 +1,88 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "system";
+ object fvSolution;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+ p
+ {
+ solver PCG;
+ preconditioner DIC;
+ tolerance 1e-08;
+ relTol 0.01;
+ }
+
+ U
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ T
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ k
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ epsilon
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ R
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+}
+
+SIMPLE
+{
+ nNonOrthogonalCorrectors 0;
+ pRefCell 0;
+ pRefValue 0;
+}
+
+relaxationFactors
+{
+ rho 1;
+ p 0.7;
+ U 0.2;
+ T 0.7;
+ k 0.7;
+ epsilon 0.7;
+ R 0.7;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/heatTransfer/buoyantPisoFoam/hotRoom/system/controlDict b/tutorials/heatTransfer/buoyantPisoFoam/hotRoom/system/controlDict
index cb2e7470f67597540554a58b19942872bab68d34..26a1219ee04433266c5a0540f5ecf239fc0d0f93 100644
--- a/tutorials/heatTransfer/buoyantPisoFoam/hotRoom/system/controlDict
+++ b/tutorials/heatTransfer/buoyantPisoFoam/hotRoom/system/controlDict
@@ -21,9 +21,9 @@ startTime 0;
stopAt endTime;
-endTime 400;
+endTime 1000;
-deltaT 0.25;
+deltaT 1;
writeControl timeStep;
diff --git a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun
index 68d74e3f344237944e77206bc85e3c7df36d36e6..8378f1f44bd4f26fb3c1d54117242f35a5b0cf5b 100755
--- a/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun
+++ b/tutorials/lagrangian/porousExplicitSourceReactingParcelFoam/filter/Allrun
@@ -1,24 +1,23 @@
#!/bin/sh
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+application="porousExplicitSourceReactingParcelFoam"
+
# create mesh
-blockMesh >& log.blockMesh
+runApplication blockMesh
-# create sets - 1
+# create sets
setSet -batch system/sets.setSet >& log.setSet1
+# convert sets to zones
+setsToZones -noFlipMap >& log.setsToZones
+
# create the first cyclic - lhs of porous zone
createBaffles cycLeft cycLeft -overwrite >& log.createBaffles1
-# create sets - 2 (ordering changed after createBaffles)
-setSet -batch system/sets.setSet >& log.setSet2
-
# create the second cyclic - rhs of porous zone
createBaffles cycRight cycRight -overwrite >& log.createBaffles2
-# create sets - 3 (ordering changed after createBaffles)
-setSet -batch system/sets.setSet >& log.setSet3
-
-# convert sets to zones
-setsToZones -noFlipMap >& log.setsToZones
-
-
+runApplication $application
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/0/pointDisplacement b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/0/pointDisplacement
new file mode 100644
index 0000000000000000000000000000000000000000..5ffe633e920154cef1f96201e351f496c7a5d85b
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/0/pointDisplacement
@@ -0,0 +1,114 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.4 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "/home/hunt2/mattijs/OpenFOAM/mattijs-1.4/run/testLoop1.4/moveMesh";
+ case "cone";
+ instance "0";
+ local "";
+
+ class pointVectorField;
+ object pointMotionU;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 1 0 0 0 0 0];
+
+internalField uniform (0 0 0);
+
+boundaryField
+{
+ maxZ
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+
+ minZ
+ {
+ type surfaceDisplacement;
+ value uniform (0 0 0);
+
+ // Clip displacement to surface by max deltaT*velocity.
+ velocity (10 10 10);
+
+ geometry
+ {
+ AcrossRiver.stl
+ {
+ type triSurfaceMesh;
+ }
+ };
+
+ // Find projection with surface:
+ // fixedNormal : intersections along prespecified direction
+ // pointNormal : intersections along current pointNormal of patch
+ // nearest : nearest point on surface
+ // Other
+ projectMode fixedNormal;
+
+ // if fixedNormal : normal
+ projectDirection (0 0 1);
+
+ //- -1 or component to knock out before doing projection
+ wedgePlane -1;
+
+ //- Points that should remain fixed
+ //frozenPointsZone fixedPointsZone;
+ }
+
+// minZ
+// {
+// type surfaceSlipDisplacement;
+// geometry
+// {
+// hellskull.stl
+// {
+// type triSurfaceMesh;
+// }
+// };
+//
+// followMode fixedNormal;
+//
+// projectDirection (0 0 1);
+//
+// //- -1 or component to knock out before doing projection
+// wedgePlane -1;
+//
+// //- Points that should remain fixed
+// //frozenPointsZone fixedPointsZone;
+// }
+
+ maxX
+ {
+ type slip;
+ }
+
+ minX
+ {
+ type slip;
+ }
+
+ minY
+ {
+ type slip;
+ }
+
+ maxY
+ {
+ type slip;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/dynamicMeshDict b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/dynamicMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..65894a796caaf1962610c6b42de10f9558625237
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/dynamicMeshDict
@@ -0,0 +1,40 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.4 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object motionProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dynamicFvMesh dynamicMotionSolverFvMesh;
+
+motionSolverLibs ("libfvMotionSolvers.so");
+
+solver displacementSBRStress; //displacementLaplacian; //displacementSBRStress;
+diffusivity quadratic quadratic inverseDistance 1(minZ);
+
+//solver velocityComponentLaplacian z;
+//diffusivity uniform;
+//diffusivity directional (1 200 0);
+// diffusivity motionDirectional (1 1000 0);
+// diffusivity file motionDiffusivity;
+diffusivity quadratic inverseDistance 1(minZ);
+// diffusivity exponential 2000 inverseDistance 1(movingWall);
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict
new file mode 100644
index 0000000000000000000000000000000000000000..9f348cb6e7ca3be15559a5b0b8fc75040342c787
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/blockMeshDict
@@ -0,0 +1,82 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.0 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object blockMeshDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+
+convertToMeters 1;
+
+vertices
+(
+ ( 659531 4.7513e+06 1028)
+ ( 659531 4.7513e+06 2100)
+ ( 662381 4.7513e+06 2100)
+ ( 662381 4.7513e+06 1028)
+ ( 659531 4.75454e+06 1028)
+ ( 659531 4.75454e+06 2100)
+ ( 662381 4.75454e+06 2100)
+ ( 662381 4.75454e+06 1028)
+);
+blocks
+(
+ hex (0 1 2 3 4 5 6 7) (20 60 60) simpleGrading (10.0 1 1)
+);
+
+
+edges
+(
+);
+
+patches
+(
+ wall maxX
+ (
+ (3 7 6 2)
+ )
+ wall minZ
+ (
+ (0 4 7 3)
+ )
+ wall maxZ
+ (
+ (2 6 5 1)
+ )
+ wall minX
+ (
+ (1 5 4 0)
+ )
+ wall minY
+ (
+ (0 3 2 1)
+ )
+ wall maxY
+ (
+ (4 5 6 7)
+ )
+);
+
+mergePatchPairs
+(
+);
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary
new file mode 100644
index 0000000000000000000000000000000000000000..9afeb87c10f1682e87741c684a769070dc28dddb
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/polyMesh/boundary
@@ -0,0 +1,58 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class polyBoundaryMesh;
+ location "constant/polyMesh";
+ object boundary;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+6
+(
+ maxX
+ {
+ type wall;
+ nFaces 1200;
+ startFace 210000;
+ }
+ minZ
+ {
+ type wall;
+ nFaces 3600;
+ startFace 211200;
+ }
+ maxZ
+ {
+ type wall;
+ nFaces 3600;
+ startFace 214800;
+ }
+ minX
+ {
+ type wall;
+ nFaces 1200;
+ startFace 218400;
+ }
+ minY
+ {
+ type wall;
+ nFaces 1200;
+ startFace 219600;
+ }
+ maxY
+ {
+ type wall;
+ nFaces 1200;
+ startFace 220800;
+ }
+)
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/transportProperties b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/transportProperties
new file mode 100644
index 0000000000000000000000000000000000000000..7aed29e935555a12f3b45025d985ca1888dea38a
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/transportProperties
@@ -0,0 +1,28 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.4 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object transportProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+nu nu [0 2 -1 0 0 0 0] 0.01;
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/ACROSSCYN.JPG b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/ACROSSCYN.JPG
new file mode 100644
index 0000000000000000000000000000000000000000..259c021d0b422dd5846c9d8c365afe4ca74682b9
Binary files /dev/null and b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/ACROSSCYN.JPG differ
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/AcrossCyn.XYZ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/AcrossCyn.XYZ
new file mode 100644
index 0000000000000000000000000000000000000000..9a23da569b73ee8ecccc63d23ff7ace9a1939c84
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/AcrossCyn.XYZ
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+ 662381 4754121 969
+ 662381 4754151 970
+ 662381 4754181 970
+ 662381 4754211 971
+ 662381 4754241 970
+ 662381 4754271 970
+ 662381 4754301 971
+ 662381 4754331 972
+ 662381 4754361 973
+ 662381 4754391 973
+ 662381 4754421 973
+ 662381 4754451 973
+ 662381 4754481 972
+ 662381 4754511 973
+ 662381 4754541 973
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/AcrossRiver.stl.gz b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/AcrossRiver.stl.gz
new file mode 100644
index 0000000000000000000000000000000000000000..5262e4745c4c016ff8a807160f7a11ac10487e0c
Binary files /dev/null and b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/constant/triSurface/AcrossRiver.stl.gz differ
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/controlDict b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/controlDict
new file mode 100644
index 0000000000000000000000000000000000000000..195bead7baea5d18eb7d18ceae29684416c71a65
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/controlDict
@@ -0,0 +1,56 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.4 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object controlDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+application icoFoam;
+
+startFrom startTime;
+
+startTime 0;
+
+stopAt endTime;
+
+endTime 25;
+
+deltaT 1;
+
+writeControl timeStep;
+
+writeInterval 5;
+
+purgeWrite 0;
+
+writeFormat ascii;
+
+writePrecision 6;
+
+writeCompression uncompressed;
+
+timeFormat general;
+
+timePrecision 6;
+
+runTimeModifiable yes;
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/decomposeParDict b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/decomposeParDict
new file mode 100644
index 0000000000000000000000000000000000000000..441595307a666b321687565d5b91940861cc1178
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/decomposeParDict
@@ -0,0 +1,72 @@
+/*-------------------------------*- C++ -*---------------------------------*\
+| ========= |
+| \\ / OpenFOAM |
+| \\ / |
+| \\ / The Open Source CFD Toolbox |
+| \\/ http://www.OpenFOAM.org |
+\*-------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ note "mesh decomposition control dictionary";
+ location "system";
+ object decomposeParDict;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+numberOfSubdomains 2;
+
+// preservePatches (inlet);
+// preserveFaceZones (heater solid1 solid3);
+
+// method simple;
+method hierarchical;
+// method metis;
+// method manual;
+
+simpleCoeffs
+{
+ n (2 2 1);
+ delta 0.001;
+}
+
+hierarchicalCoeffs
+{
+ n (2 1 1);
+ delta 0.001;
+ order xyz;
+}
+
+metisCoeffs
+{
+ /*
+ processorWeights
+ (
+ 1
+ 1
+ 1
+ 1
+ );
+ */
+}
+
+manualCoeffs
+{
+ dataFile "decompositionData";
+}
+
+
+//// Is the case distributed
+//distributed yes;
+//// Per slave (so nProcs-1 entries) the directory above the case.
+//roots
+//(
+// "/tmp"
+// "/tmp"
+//);
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/fvSchemes b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/fvSchemes
new file mode 100644
index 0000000000000000000000000000000000000000..ebcd68557528c297120d8e5e1e9ee43f0b933650
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/fvSchemes
@@ -0,0 +1,69 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.4 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object fvSchemes;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+ddtSchemes
+{
+ default Euler;
+}
+
+gradSchemes
+{
+ default Gauss linear;
+ grad(p) Gauss linear;
+}
+
+divSchemes
+{
+ default none;
+ div(phi,U) Gauss linear;
+}
+
+laplacianSchemes
+{
+ default none;
+ laplacian(nu,U) Gauss linear corrected;
+ laplacian((1|A(U)),p) Gauss linear corrected;
+ laplacian(diffusivity,cellDisplacement) Gauss linear corrected;
+ laplacian(diffusivity,cellMotionU) Gauss linear corrected;
+}
+
+interpolationSchemes
+{
+ default linear;
+ interpolate(HbyA) linear;
+}
+
+snGradSchemes
+{
+ default corrected;
+}
+
+fluxRequired
+{
+ default no;
+ p;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/fvSolution b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/fvSolution
new file mode 100644
index 0000000000000000000000000000000000000000..9fff602af62a0a26a5ab6375eda77db671abcf3f
--- /dev/null
+++ b/tutorials/mesh/moveDynamicMesh/SnakeRiverCanyon/system/fvSolution
@@ -0,0 +1,82 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.4 |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object fvSolution;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+solvers
+{
+ p
+ {
+ solver PCG;
+ preconditioner DIC;
+ tolerance 1e-06;
+ relTol 0;
+ };
+
+ U
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0;
+ };
+ cellDisplacement
+ {
+ solver GAMG;
+ tolerance 1e-8;
+ relTol 0;
+ smoother GaussSeidel;
+ cacheAgglomeration true;
+ nCellsInCoarsestLevel 10;
+ agglomerator faceAreaPair;
+ mergeLevels 1;
+ };
+ cellMotionU
+ {
+ solver PCG;
+ preconditioner DIC;
+ tolerance 1e-08;
+ relTol 0;
+ };
+ cellMotionUz
+ {
+ solver PCG;
+ preconditioner DIC;
+ tolerance 1e-08;
+ relTol 0;
+ };
+}
+
+//PISO
+//{
+// nCorrectors 2;
+// nNonOrthogonalCorrectors 2;
+// pRefCell 0;
+// pRefValue 0;
+//}
+//
+//relaxationFactors
+//{
+//}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/T b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/T
new file mode 100644
index 0000000000000000000000000000000000000000..2f930360fd37896b527889abe6270f3643cca6e6
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/T
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object T;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 0 0 1 0 0 0];
+
+internalField uniform 265;
+
+boundaryField
+{
+ ground
+ {
+ type fixedValue;
+ value uniform 265;
+ }
+
+ igloo_region0
+ {
+ type fixedValue;
+ value uniform 265;
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type fixedValue;
+ value uniform 303;
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type fixedValue;
+ value uniform 303;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/U b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/U
new file mode 100644
index 0000000000000000000000000000000000000000..5d70f2a9c021a7c55ded01f6296f0113bb31029b
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/U
@@ -0,0 +1,48 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volVectorField;
+ object U;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 1 -1 0 0 0 0];
+
+internalField uniform (0 0 0);
+
+boundaryField
+{
+ ground
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+
+ igloo_region0
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type fixedValue;
+ value uniform (0 0 0);
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/alphat b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/alphat
new file mode 100644
index 0000000000000000000000000000000000000000..acdcda178a7d947cf732c6668ddf055b5bc51d05
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/alphat
@@ -0,0 +1,50 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object alphat;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [1 -1 -1 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ ground
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+
+ igloo_region0
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type alphatWallFunction;
+ value uniform 0;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/epsilon b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/epsilon
new file mode 100644
index 0000000000000000000000000000000000000000..0fa9bf60f265f63d0b0c957fc39f70ec920c8323
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/epsilon
@@ -0,0 +1,50 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object epsilon;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -3 0 0 0 0];
+
+internalField uniform 0.01;
+
+boundaryField
+{
+ ground
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+
+ igloo_region0
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type epsilonWallFunction;
+ value uniform 0.01;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/k b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/k
new file mode 100644
index 0000000000000000000000000000000000000000..bd0cf46f0db295c3f0170202b33472417c20bca3
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/k
@@ -0,0 +1,50 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object k;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0.1;
+
+boundaryField
+{
+ ground
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+
+ igloo_region0
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type kQRWallFunction;
+ value uniform 0.1;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/nut b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/nut
new file mode 100644
index 0000000000000000000000000000000000000000..e9e5f16e555dccc27b4fd7c11b0b4877afc1bb4f
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/nut
@@ -0,0 +1,50 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: dev |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ location "0";
+ object nut;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -1 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ ground
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+
+ igloo_region0
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type nutWallFunction;
+ value uniform 0;
+ }
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/p b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/p
new file mode 100644
index 0000000000000000000000000000000000000000..2b90b18e74e8b30535be502ed783da524727c7df
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/0/p
@@ -0,0 +1,52 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: http://www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class volScalarField;
+ object p;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+dimensions [0 2 -2 0 0 0 0];
+
+internalField uniform 0;
+
+boundaryField
+{
+ ground
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ igloo_region0
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ twoFridgeFreezers_seal_0
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+
+ twoFridgeFreezers_herring_1
+ {
+ type fixedFluxBuoyantPressure;
+ rho rhok;
+ value uniform 0;
+ }
+}
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/Allrun b/tutorials/mesh/snappyHexMesh/iglooWithFridges/Allrun
new file mode 100755
index 0000000000000000000000000000000000000000..79dc3f4b95e1f1dff9646fd6dd1ba9fa3bbae4ac
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/Allrun
@@ -0,0 +1,9 @@
+#!/bin/sh
+# Source tutorial run functions
+. $WM_PROJECT_DIR/bin/tools/RunFunctions
+
+runApplication blockMesh
+runApplication snappyHexMesh -overwrite
+runApplication setFields
+runApplication buoyantBoussinesqSimpleFoam
+
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/RASProperties b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/RASProperties
new file mode 100644
index 0000000000000000000000000000000000000000..35b5a409f230c180f07469bfe0679cdf00cb419d
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/RASProperties
@@ -0,0 +1,100 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object RASProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+RASModel kEpsilon;
+
+turbulence on;
+
+printCoeffs on;
+
+laminarCoeffs
+{
+}
+
+kEpsilonCoeffs
+{
+ Cmu 0.09;
+ C1 1.44;
+ C2 1.92;
+ C3 0.85;
+ alphah 1;
+ alphak 1;
+ alphaEps 0.76923;
+}
+
+RNGkEpsilonCoeffs
+{
+ Cmu 0.0845;
+ C1 1.42;
+ C2 1.68;
+ C3 -0.33;
+ alphah 1;
+ alphak 1.39;
+ alphaEps 1.39;
+ eta0 4.38;
+ beta 0.012;
+}
+
+LaunderSharmaKECoeffs
+{
+ Cmu 0.09;
+ C1 1.44;
+ C2 1.92;
+ C3 -0.33;
+ alphah 1;
+ alphak 1;
+ alphaEps 0.76923;
+}
+
+LRRCoeffs
+{
+ Cmu 0.09;
+ Clrr1 1.8;
+ Clrr2 0.6;
+ C1 1.44;
+ C2 1.92;
+ alphah 1;
+ Cs 0.25;
+ Ceps 0.15;
+ alphaR 1;
+ alphaEps 0.76923;
+}
+
+LaunderGibsonRSTMCoeffs
+{
+ Cmu 0.09;
+ Clg1 1.8;
+ Clg2 0.6;
+ C1 1.44;
+ C2 1.92;
+ alphah 1;
+ C1Ref 0.5;
+ C2Ref 0.3;
+ Cs 0.25;
+ Ceps 0.15;
+ alphaR 1;
+ alphaEps 0.76923;
+}
+
+wallFunctionCoeffs
+{
+ kappa 0.4187;
+ E 9;
+}
+
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/environmentalProperties b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/environmentalProperties
new file mode 100644
index 0000000000000000000000000000000000000000..8ecb2a440203a35f242328826e7484e672012712
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/environmentalProperties
@@ -0,0 +1,20 @@
+/*--------------------------------*- C++ -*----------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5 |
+| \\ / A nd | Web: www.OpenFOAM.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+FoamFile
+{
+ version 2.0;
+ format ascii;
+ class dictionary;
+ location "constant";
+ object environmentalProperties;
+}
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+g g [0 1 -2 0 0 0 0] (0 0 -9.81);
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/polyMesh/blockMeshDict b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/polyMesh/blockMeshDict
index d97dbb8e268c425f32326827a59e880e05e07eda..39d94d804fadab1df4f1ac72260fbd477d5f9204 100644
--- a/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/polyMesh/blockMeshDict
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/polyMesh/blockMeshDict
@@ -40,27 +40,32 @@ edges
patches
(
- patch maxY
+ empty maxY
(
(3 7 6 2)
)
- patch minX
+
+ empty minX
(
(0 4 7 3)
)
- patch maxX
+
+ empty maxX
(
(2 6 5 1)
)
- patch minY
+
+ empty minY
(
(1 5 4 0)
)
- patch minZ
+
+ wall ground
(
(0 3 2 1)
)
- patch maxZ
+
+ empty maxZ
(
(4 5 6 7)
)
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/transportProperties b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/transportProperties
new file mode 100644
index 0000000000000000000000000000000000000000..f48fda19ccac705f76f1573b7ba40cce45abfd5b
--- /dev/null
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/constant/transportProperties
@@ -0,0 +1,42 @@
+/*---------------------------------------------------------------------------*\
+| ========= | |
+| \\ / F ield | OpenFOAM: The Open Source CFD Toolbox |
+| \\ / O peration | Version: 1.5.x |
+| \\ / A nd | Web: http://www.openfoam.org |
+| \\/ M anipulation | |
+\*---------------------------------------------------------------------------*/
+
+FoamFile
+{
+ version 2.0;
+ format ascii;
+
+ root "";
+ case "";
+ instance "";
+ local "";
+
+ class dictionary;
+ object transportProperties;
+}
+
+// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
+
+transportModel Newtonian;
+
+// Laminar viscosity
+nu nu [0 2 -1 0 0 0 0] 1e-05;
+
+// Thermal expansion coefficient
+beta beta [0 0 0 -1 0 0 0] 3e-03;
+
+// Reference temperature
+TRef TRef [0 0 0 1 0 0 0] 300;
+
+// Laminar Prandtl number
+Pr Pr [0 0 0 0 0 0 0] 0.9;
+
+// Turbulent Prandtl number
+Prt Prt [0 0 0 0 0 0 0] 0.7;
+
+// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/controlDict b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/controlDict
index ef80311ee11931792c1d637b6d45c5a9b75c24de..46e7cd00c334efd3d10a44f4e932cef57ccff22d 100644
--- a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/controlDict
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/controlDict
@@ -15,25 +15,25 @@ FoamFile
}
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
-startFrom latestTime;
+startFrom startTime;
startTime 0;
stopAt endTime;
-endTime 100;
+endTime 1000;
deltaT 1;
writeControl timeStep;
-writeInterval 1;
+writeInterval 100;
purgeWrite 0;
writeFormat ascii;
-writePrecision 7;
+writePrecision 6;
writeCompression uncompressed;
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSchemes b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSchemes
index 2fa85964b7e2113902ff5be6f03334f6777d84b6..b54bb8631600a594830b214816d8a858bcf83a02 100644
--- a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSchemes
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSchemes
@@ -17,33 +17,40 @@ FoamFile
ddtSchemes
{
- default Euler;
+ default steadyState;
}
gradSchemes
{
default Gauss linear;
- grad(p) Gauss linear;
}
divSchemes
{
default none;
- div(phi,U) Gauss linear;
+ div(phi,U) Gauss upwind;
+ div(phi,T) Gauss upwind;
+ div(phi,k) Gauss upwind;
+ div(phi,epsilon) Gauss upwind;
+ div(phi,R) Gauss upwind;
+ div(R) Gauss linear;
+ div((nuEff*dev(grad(U).T()))) Gauss linear;
}
laplacianSchemes
{
default none;
- laplacian(nu,U) Gauss linear corrected;
- laplacian(1|A(U),p) Gauss linear corrected;
- laplacian(diffusivity,cellMotionU) Gauss linear uncorrected;
+ laplacian(nuEff,U) Gauss linear corrected;
+ laplacian((1|A(U)),p) Gauss linear corrected;
+ laplacian(kappaEff,T) Gauss linear corrected;
+ laplacian(DkEff,k) Gauss linear corrected;
+ laplacian(DepsilonEff,epsilon) Gauss linear corrected;
+ laplacian(DREff,R) Gauss linear corrected;
}
interpolationSchemes
{
default linear;
- interpolate(HbyA) linear;
}
snGradSchemes
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSolution b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSolution
index 876c8c233f9dece81ca38c9186f66b783bae4ec9..c2053ee47d6e6890ba5dc9b2e9041cdd7eb269d5 100644
--- a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSolution
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/fvSolution
@@ -16,15 +16,73 @@ FoamFile
// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
solvers
-{}
+{
+ p
+ {
+ solver PCG;
+ preconditioner DIC;
+ tolerance 1e-08;
+ relTol 0.01;
+ }
+
+ U
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ T
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ k
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+
+ epsilon
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
-PISO
+ R
+ {
+ solver PBiCG;
+ preconditioner DILU;
+ tolerance 1e-05;
+ relTol 0.1;
+ }
+}
+
+SIMPLE
{
- nCorrectors 2;
nNonOrthogonalCorrectors 0;
pRefCell 0;
pRefValue 0;
}
+relaxationFactors
+{
+ rho 1;
+ p 0.3;
+ U 0.7;
+ T 0.7;
+ k 0.7;
+ epsilon 0.7;
+ R 0.7;
+}
+
// ************************************************************************* //
diff --git a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/snappyHexMeshDict b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/snappyHexMeshDict
index 30da45333116a695a3d463d85d30aa98babc1b38..d31010ace7ef8ced9166f5e0bd4e2ec0ad4c347c 100644
--- a/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/snappyHexMeshDict
+++ b/tutorials/mesh/snappyHexMesh/iglooWithFridges/system/snappyHexMeshDict
@@ -42,12 +42,13 @@ geometry
min (0 0 0);
max (1 1 1);
}
+
fridgeFreezer
{
type searchableSurfaceCollection;
mergeSubRegions true;
-
+
freezer
{
surface box1;
@@ -73,16 +74,17 @@ geometry
}
}
}
+
twoFridgeFreezers
{
type searchableSurfaceCollection;
-
+
mergeSubRegions true;
-
+
seal
{
- surface fridgeFreezer;
- scale (1.0 1.0 1.0);
+ surface box1;
+ scale (1.0 1.0 2.1);
transform
{
type cartesian;
@@ -93,8 +95,8 @@ geometry
}
herring
{
- surface fridgeFreezer;
- scale (1.0 1.0 1.0);
+ surface box1;
+ scale (1.0 1.0 2.1);
transform
{
type cartesian;
diff --git a/tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines b/tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines
deleted file mode 100644
index 4b24efafd5ca1ad451a6018d16f638079b1a4f8b..0000000000000000000000000000000000000000
--- a/tutorials/multiphase/compressibleInterFoam/les/depthCharge3D/system/machines
+++ /dev/null
@@ -1 +0,0 @@
-noisy
diff --git a/tutorials/multiphase/interFoam/ras/Allclean b/tutorials/multiphase/interFoam/ras/Allclean
index 62275784712aebe76b90f3356879dce098912e1e..6ad97e1a0bd7ffd8f0073bb9a1f9f9d3391d7c6b 100755
--- a/tutorials/multiphase/interFoam/ras/Allclean
+++ b/tutorials/multiphase/interFoam/ras/Allclean
@@ -12,7 +12,7 @@ do
if [ "$case" = "damBreak" ]
then
- cp $case/0/gamma.org $case/0/gamma
+ cp $case/0/alpha1.org $case/0/alpha1
fi
done