Merge branch 'master' of ssh://noisy/home/noisy3/OpenFOAM/OpenFOAM-dev

src/OSspecific/POSIX/POSIX.C

@@ -57,6 +57,10 @@ Description
 
 #include <netinet/in.h>
 
+#ifdef USE_RANDOM
+#   include <climits>
+#endif
+
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
 defineTypeNameAndDebug(Foam::POSIX, 0);
@@ -68,16 +72,19 @@ pid_t Foam::pid()
     return ::getpid();
 }
 
+
 pid_t Foam::ppid()
 {
     return ::getppid();
 }
 
+
 pid_t Foam::pgid()
 {
     return ::getpgrp();
 }
 
+
 bool Foam::env(const word& envName)
 {
     return ::getenv(envName.c_str()) != NULL;
@@ -890,7 +897,6 @@ bool Foam::mvBak(const fileName& src, const std::string& ext)
 }
 
 
-
 // Remove a file, returning true if successful otherwise false
 bool Foam::rm(const fileName& file)
 {
@@ -1221,4 +1227,34 @@ Foam::fileNameList Foam::dlLoaded()
 }
 
 
+void Foam::osRandomSeed(const label seed)
+{
+#ifdef USE_RANDOM
+    srandom((unsigned int)seed);
+#else
+    srand48(seed);
+#endif
+}
+
+
+Foam::label Foam::osRandomInteger()
+{
+#ifdef USE_RANDOM
+    return random();
+#else
+    return lrand48();
+#endif
+}
+
+
+Foam::scalar Foam::osRandomDouble()
+{
+#ifdef USE_RANDOM
+    return (scalar)random();
+#else
+    return drand48();
+#endif
+}
+
+
 // ************************************************************************* //

src/OpenFOAM/include/OSspecific.H

@@ -200,6 +200,18 @@ bool dlSymFound(void* handle, const std::string& symbol);
 fileNameList dlLoaded();
 
 
+// Low level random numbers. Use Random class instead.
+
+//- Seed random number generator.
+void osRandomSeed(const label seed);
+
+//- Return random integer (uniform distribution between 0 and 2^31)
+label osRandomInteger();
+
+//- Return random double precision (uniform distribution between 0 and 1)
+scalar osRandomDouble();
+
+
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
 } // End namespace Foam

src/OpenFOAM/primitives/random/Random/Random.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2004-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2004-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -24,6 +24,7 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "Random.H"
+#include "OSspecific.H"
 
 // * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
 
@@ -37,11 +38,6 @@ namespace Foam
 #    error "The random number generator may not work!"
 #endif
 
-#ifdef USE_RANDOM
-#   include <climits>
-#else
-#   include <cstdlib>
-#endif
 
 
 // * * * * * * * * * * * * * * * Member Functions  * * * * * * * * * * * * * //
@@ -57,22 +53,13 @@ Random::Random(const label seed)
         Seed = 1;
     }
 
-#   ifdef USE_RANDOM
+    osRandomSeed(Seed);
-        srandom((unsigned int)Seed);
-#   else
-        srand48(Seed);
-#   endif
-
 }
 
 
 int Random::bit()
 {
-#   ifdef USE_RANDOM
+    if (osRandomInteger() > INT_MAX/2)
-    if (random() > INT_MAX/2)
-#   else
-    if (lrand48() > INT_MAX/2)
-#   endif
     {
         return 1;
     }
@@ -85,11 +72,7 @@ int Random::bit()
 
 scalar Random::scalar01()
 {
-#   ifdef USE_RANDOM
+    return osRandomDouble();
-        return (scalar)random()/INT_MAX;
-#   else
-        return drand48();
-#   endif
 }
 
 
@@ -140,11 +123,7 @@ tensor Random::tensor01()
 
 label Random::integer(const label lower, const label upper)
 {
-#   ifdef USE_RANDOM
+    return lower + (osRandomInteger() % (upper+1-lower));
-        return lower + (random() % (upper+1-lower));
-#   else
-        return lower + (lrand48() % (upper+1-lower));
-#   endif
 }
 
 

src/OpenFOAM/primitives/random/cachedRandom/cachedRandom.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2010-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2010-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -24,7 +24,7 @@ License
 \*---------------------------------------------------------------------------*/
 
 #include "cachedRandom.H"
-#include <cstdlib>
+#include "OSspecific.H"
 
 #if INT_MAX    != 2147483647
 #    error "INT_MAX    != 2147483647"
@@ -37,7 +37,7 @@ Foam::scalar Foam::cachedRandom::scalar01()
 {
     if (sampleI_ < 0)
     {
-        return drand48();
+        return osRandomDouble();
     }
 
     if (sampleI_ == samples_.size() - 1)
@@ -76,7 +76,7 @@ Foam::cachedRandom::cachedRandom(const label seed, const label count)
     }
 
     // Initialise samples
-    srand48(seed_);
+    osRandomSeed(seed_);
     forAll(samples_, i)
     {
         samples_[i] = drand48();
@@ -98,7 +98,7 @@ Foam::cachedRandom::cachedRandom(const cachedRandom& cr, const bool reset)
         )   << "Copy constructor called, but samples not being cached. "
             << "This may lead to non-repeatable behaviour" << endl;
 
-        srand48(seed_);
+        osRandomSeed(seed_);
     }
     else if (reset)
     {

src/lagrangian/intermediate/submodels/Kinematic/CollisionModel/PairCollision/PairModel/PairSpringSliderDashpot/PairSpringSliderDashpot.C

@@ -214,7 +214,8 @@ void Foam::PairSpringSliderDashpot<CloudType>::evaluatePair
             rHat_AB
            *(kN*pow(normalOverlapMag, b_) - etaN*(U_AB & rHat_AB));
 
-        // Cohesion force
+        // Cohesion force, energy density multiplied by the area of
+        // particle-particle overlap
         if (cohesion_)
         {
             fN_AB +=

src/lagrangian/intermediate/submodels/Kinematic/CollisionModel/PairCollision/WallModel/WallLocalSpringSliderDashpot/WallLocalSpringSliderDashpot.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2008-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2008-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -76,7 +76,8 @@ void Foam::WallLocalSpringSliderDashpot<CloudType>::evaluateWall
     typename CloudType::parcelType& p,
     const point& site,
     const WallSiteData<vector>& data,
-    scalar pREff
+    scalar pREff,
+    bool cohesion
 ) const
 {
     // wall patch index
@@ -88,14 +89,18 @@ void Foam::WallLocalSpringSliderDashpot<CloudType>::evaluateWall
     scalar alpha = alpha_[wPI];
     scalar b = b_[wPI];
     scalar mu = mu_[wPI];
+    scalar cohesionEnergyDensity = cohesionEnergyDensity_[wPI];
+    cohesion = cohesion && cohesion_[wPI];
 
     vector r_PW = p.position() - site;
 
     vector U_PW = p.U() - data.wallData();
 
-    scalar normalOverlapMag = max(pREff - mag(r_PW), 0.0);
+    scalar r_PW_mag = mag(r_PW);
 
-    vector rHat_PW = r_PW/(mag(r_PW) + VSMALL);
+    scalar normalOverlapMag = max(pREff - r_PW_mag, 0.0);
+
+    vector rHat_PW = r_PW/(r_PW_mag + VSMALL);
 
     scalar kN = (4.0/3.0)*sqrt(pREff)*Estar;
 
@@ -105,6 +110,16 @@ void Foam::WallLocalSpringSliderDashpot<CloudType>::evaluateWall
         rHat_PW
        *(kN*pow(normalOverlapMag, b) - etaN*(U_PW & rHat_PW));
 
+    // Cohesion force, energy density multiplied by the area of wall/particle
+    // overlap
+    if (cohesion)
+    {
+        fN_PW +=
+           -cohesionEnergyDensity
+           *mathematical::pi*(sqr(pREff) - sqr(r_PW_mag))
+           *rHat_PW;
+    }
+
     p.f() += fN_PW;
 
     vector USlip_PW =
@@ -168,6 +183,8 @@ Foam::WallLocalSpringSliderDashpot<CloudType>::WallLocalSpringSliderDashpot
     alpha_(),
     b_(),
     mu_(),
+    cohesionEnergyDensity_(),
+    cohesion_(),
     patchMap_(),
     maxEstarIndex_(-1),
     collisionResolutionSteps_
@@ -212,6 +229,8 @@ Foam::WallLocalSpringSliderDashpot<CloudType>::WallLocalSpringSliderDashpot
     alpha_.setSize(nWallPatches);
     b_.setSize(nWallPatches);
     mu_.setSize(nWallPatches);
+    cohesionEnergyDensity_.setSize(nWallPatches);
+    cohesion_.setSize(nWallPatches);
 
     scalar maxEstar = -GREAT;
 
@@ -238,6 +257,13 @@ Foam::WallLocalSpringSliderDashpot<CloudType>::WallLocalSpringSliderDashpot
 
         mu_[wPI] = readScalar(patchCoeffDict.lookup("mu"));
 
+        cohesionEnergyDensity_[wPI] = readScalar
+        (
+            patchCoeffDict.lookup("cohesionEnergyDensity")
+        );
+
+        cohesion_[wPI] = (mag(cohesionEnergyDensity_[wPI]) > VSMALL);
+
         if (Estar_[wPI] > maxEstar)
         {
             maxEstarIndex_ = wPI;
@@ -325,20 +351,22 @@ void Foam::WallLocalSpringSliderDashpot<CloudType>::evaluateWall
             p,
             flatSitePoints[siteI],
             flatSiteData[siteI],
-            pREff
+            pREff,
+            true
         );
     }
 
     forAll(sharpSitePoints, siteI)
     {
-        // Treating sharp sites like flat sites
+        // Treating sharp sites like flat sites, except suppress cohesion
 
         evaluateWall
         (
             p,
             sharpSitePoints[siteI],
             sharpSiteData[siteI],
-            pREff
+            pREff,
+            false
         );
     }
 }

src/lagrangian/intermediate/submodels/Kinematic/CollisionModel/PairCollision/WallModel/WallLocalSpringSliderDashpot/WallLocalSpringSliderDashpot.H

@@ -65,6 +65,12 @@ class WallLocalSpringSliderDashpot
         //- Coefficient of friction in for tangential sliding
         scalarList mu_;
 
+        //- Cohesion energy density [J/m^3]
+        scalarList cohesionEnergyDensity_;
+
+        // Switch cohesion on and off
+        boolList cohesion_;
+
         //- Mapping the patch index to the model data
         labelList patchMap_;
 
@@ -115,7 +121,8 @@ class WallLocalSpringSliderDashpot
             typename CloudType::parcelType& p,
             const point& site,
             const WallSiteData<vector>& data,
-            scalar pREff
+            scalar pREff,
+            bool cohesion
         ) const;
 
 

src/lagrangian/intermediate/submodels/Kinematic/CollisionModel/PairCollision/WallModel/WallSpringSliderDashpot/WallSpringSliderDashpot.C

@@ -2,7 +2,7 @@
   =========                 |
   \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox
    \\    /   O peration     |
-    \\  /    A nd           | Copyright (C) 2008-2010 OpenCFD Ltd.
+    \\  /    A nd           | Copyright (C) 2008-2011 OpenCFD Ltd.
      \\/     M anipulation  |
 -------------------------------------------------------------------------------
 License
@@ -77,16 +77,19 @@ void Foam::WallSpringSliderDashpot<CloudType>::evaluateWall
     const point& site,
     const WallSiteData<vector>& data,
     scalar pREff,
-    scalar kN
+    scalar kN,
+    bool cohesion
 ) const
 {
     vector r_PW = p.position() - site;
 
     vector U_PW = p.U() - data.wallData();
 
-    scalar normalOverlapMag = max(pREff - mag(r_PW), 0.0);
+    scalar r_PW_mag = mag(r_PW);
 
-    vector rHat_PW = r_PW/(mag(r_PW) + VSMALL);
+    scalar normalOverlapMag = max(pREff - r_PW_mag, 0.0);
+
+    vector rHat_PW = r_PW/(r_PW_mag + VSMALL);
 
     scalar etaN = alpha_*sqrt(p.mass()*kN)*pow025(normalOverlapMag);
 
@@ -94,6 +97,16 @@ void Foam::WallSpringSliderDashpot<CloudType>::evaluateWall
         rHat_PW
        *(kN*pow(normalOverlapMag, b_) - etaN*(U_PW & rHat_PW));
 
+    // Cohesion force, energy density multiplied by the area of wall/particle
+    // overlap
+    if (cohesion)
+    {
+        fN_PW +=
+           -cohesionEnergyDensity_
+           *mathematical::pi*(sqr(pREff) - sqr(r_PW_mag))
+           *rHat_PW;
+    }
+
     p.f() += fN_PW;
 
     vector USlip_PW =
@@ -157,6 +170,11 @@ Foam::WallSpringSliderDashpot<CloudType>::WallSpringSliderDashpot
     alpha_(readScalar(this->coeffDict().lookup("alpha"))),
     b_(readScalar(this->coeffDict().lookup("b"))),
     mu_(readScalar(this->coeffDict().lookup("mu"))),
+    cohesionEnergyDensity_
+    (
+        readScalar(this->coeffDict().lookup("cohesionEnergyDensity"))
+    ),
+    cohesion_(false),
     collisionResolutionSteps_
     (
         readScalar
@@ -183,6 +201,8 @@ Foam::WallSpringSliderDashpot<CloudType>::WallSpringSliderDashpot
     Estar_ = 1/((1 - sqr(pNu))/pE + (1 - sqr(nu))/E);
 
     Gstar_ = 1/(2*((2 + pNu - sqr(pNu))/pE + (2 + nu - sqr(nu))/E));
+
+    cohesion_ = (mag(cohesionEnergyDensity_) > VSMALL);
 }
 
 
@@ -266,13 +286,14 @@ void Foam::WallSpringSliderDashpot<CloudType>::evaluateWall
             flatSitePoints[siteI],
             flatSiteData[siteI],
             pREff,
-            kN
+            kN,
+            cohesion_
         );
     }
 
     forAll(sharpSitePoints, siteI)
     {
-        // Treating sharp sites like flat sites
+        // Treating sharp sites like flat sites, except suppress cohesion
 
         evaluateWall
         (
@@ -280,7 +301,8 @@ void Foam::WallSpringSliderDashpot<CloudType>::evaluateWall
             sharpSitePoints[siteI],
             sharpSiteData[siteI],
             pREff,
-            kN
+            kN,
+            false
         );
     }
 }

src/lagrangian/intermediate/submodels/Kinematic/CollisionModel/PairCollision/WallModel/WallSpringSliderDashpot/WallSpringSliderDashpot.H

@@ -65,6 +65,12 @@ class WallSpringSliderDashpot
         //- Coefficient of friction in for tangential sliding
         scalar mu_;
 
+        //- Cohesion energy density [J/m^3]
+        scalar cohesionEnergyDensity_;
+
+        // Switch cohesion on and off
+        bool cohesion_;
+
         //- The number of steps over which to resolve the minimum
         //  harmonic approximation of the collision period
         scalar collisionResolutionSteps_;
@@ -110,7 +116,8 @@ class WallSpringSliderDashpot
             const point& site,
             const WallSiteData<vector>& data,
             scalar pREff,
-            scalar kN
+            scalar kN,
+            bool cohesion
         ) const;
 
 

src/postProcessing/functionObjects/IO/partialWrite/partialWrite.C

@@ -27,6 +27,7 @@ License
 #include "dictionary.H"
 #include "Time.H"
 #include "IOobjectList.H"
+#include "polyMesh.H"
 
 // * * * * * * * * * * * * * * Static Data Members * * * * * * * * * * * * * //
 
@@ -123,14 +124,26 @@ void Foam::partialWrite::write()
         else
         {
             // Delete all but marked objects
+            fileName dbDir;
+            if (isA<polyMesh>(obr_))
+            {
+                dbDir = dynamic_cast<const polyMesh&>(obr_).dbDir();
+            }
+
             IOobjectList objects(obr_, obr_.time().timeName());
 
             forAllConstIter(HashPtrTable<IOobject>, objects, iter)
             {
                 if (!objectNames_.found(iter()->name()))
                 {
-                    const fileName f = obr_.time().timePath()/iter()->name();
+                    const fileName f =
-                    //Pout<< "   rm " << f << endl;
+                        obr_.time().timePath()
+                       /dbDir
+                       /iter()->name();
+                    if (debug)
+                    {
+                        Pout<< "   rm " << f << endl;
+                    }
                     rm(f);
                 }
             }

tutorials/combustion/fireFoam/les/oppositeBurningPanels/Allrun

@@ -32,4 +32,8 @@ decomposePar -region panelRegion > log.decomposParPanelRegion.log 2>&1
 
 runParallel `getApplication` 6
 
+paraFoam -touch
+paraFoam -touch -region panelRegion
+
+
 # ----------------------------------------------------------------- end-of-file

tutorials/lagrangian/icoUncoupledKinematicParcelFoam/hopper/hopperEmptying/constant/kinematicCloudProperties

@@ -112,6 +112,7 @@ subModels
                 alpha           0.12;
                 b               1.5;
                 mu              0.43;
+                cohesionEnergyDensity 0;
             }
             frontAndBack
             {
@@ -120,6 +121,7 @@ subModels
                 alpha           0.12;
                 b               1.5;
                 mu              0.1;
+                cohesionEnergyDensity 0;
             }
         };
     }

tutorials/lagrangian/icoUncoupledKinematicParcelFoam/hopper/hopperInitialState/constant/kinematicCloudProperties

@@ -121,6 +121,7 @@ subModels
                 alpha           0.12;
                 b               1.5;
                 mu              0.43;
+                cohesionEnergyDensity 0;
             }
             frontAndBack
             {
@@ -129,6 +130,7 @@ subModels
                 alpha           0.12;
                 b               1.5;
                 mu              0.1;
+                cohesionEnergyDensity 0;
             }
         };
     }

tutorials/lagrangian/reactingParcelFilmFoam/cylinder/Allrun.pre

@@ -8,3 +8,6 @@ runApplication setSet -batch wallFilmRegion.setSet
 mv log.setSet log.wallFilmRegion.setSet
 
 runApplication extrudeToRegionMesh -overwrite
+
+paraFoam -touch
+paraFoam -touch -region wallFilmRegion

tutorials/lagrangian/reactingParcelFilmFoam/hotBoxes/Allrun.pre

@@ -32,3 +32,6 @@ cp -r system/wallFilmRegion.org system/wallFilmRegion
 
 find ./0 -maxdepth 1 -type f -exec \
     sed -i "s/wallFilm/\"(region0_to.*)\"/g" {} \;
+
+paraFoam -touch
+paraFoam -touch -region wallFilmRegion

tutorials/lagrangian/reactingParcelFilmFoam/rivuletPanel/Allrun.pre

@@ -10,3 +10,5 @@ mv log.setSet log.wallFilmRegion.setSet
 
 runApplication extrudeToRegionMesh -overwrite
 
+paraFoam -touch
+paraFoam -touch -region wallFilmRegion

tutorials/lagrangian/reactingParcelFilmFoam/splashPanel/Allrun.pre

@@ -14,3 +14,6 @@ runApplication setSet -region wallFilmRegion -batch createWallFilmRegionPatches.
 mv log.setSet log.createWallFilmRegionPatches.setSet
 
 runApplication createPatch -region wallFilmRegion -overwrite
+
+paraFoam -touch
+paraFoam -touch -region wallFilmRegion