This file is indexed.

/usr/include/palabos/multiPhysics/freeSurfaceUtil3D.h is in libplb-dev 1.5~r1+repack1-2build2.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
/* This file is part of the Palabos library.
 *
 * Copyright (C) 2011-2015 FlowKit Sarl
 * Route d'Oron 2
 * 1010 Lausanne, Switzerland
 * E-mail contact: contact@flowkit.com
 *
 * The most recent release of Palabos can be downloaded at 
 * <http://www.palabos.org/>
 *
 * The library Palabos is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Affero General Public License as
 * published by the Free Software Foundation, either version 3 of the
 * License, or (at your option) any later version.
 *
 * The library 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 Affero General Public License for more details.
 *
 * You should have received a copy of the GNU Affero General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/

#ifndef FREE_SURFACE_UTIL_3D_H
#define FREE_SURFACE_UTIL_3D_H

#include "core/globalDefs.h"
#include "core/plbDebug.h"
#include "multiBlock/multiContainerBlock3D.h"
#include "multiBlock/multiDataField3D.h"
#include "multiBlock/multiBlockLattice3D.h"

#include <vector>
#include <set>
#include <string>

namespace plb {

/// Constants used in a free surface flag matrix for cell tagging.
namespace twoPhaseFlag {
    enum Flag {empty=0, interface=1, fluid=2, wall=4, protect=5, protectEmpty=6};
    inline std::string flagToString(int flag) {
        switch(flag) {
            case empty:     return "empty";
            case interface: return "interface";
            case fluid:     return "fluid";
            case wall:      return "wall";
            case protect:   return "protect";
            case protectEmpty:   return "protectEmpty";
            default: PLB_ASSERT( false );
        }
        return std::string();
    }
    inline Flag invert(int flag) {
        switch(flag) {
            case empty:     return fluid;
            case interface: return interface;
            case fluid:     return empty;
            case wall:      return wall;
            case protect:   return protect;
            case protectEmpty: return protectEmpty;
            default: PLB_ASSERT( false );
        }
        return (Flag) (-1);
    }
    inline bool isWet(int flag) {
        return flag==interface || flag==fluid || flag==protect; 
    }
    inline bool isFullWet(int flag) {
        return flag==fluid || flag==protect; 
    }
    inline bool isEmpty(int flag) {
        return flag==empty || flag==protectEmpty; 
    }
}

/// Create a parameter-list for most free-surface data processors.
template< typename T,template<typename U> class Descriptor>
std::vector<MultiBlock3D*> aggregateFreeSurfaceParams (
        MultiBlockLattice3D<T,Descriptor>& fluid, MultiScalarField3D<T>& rhoBar,
        MultiTensorField3D<T,3>& j, MultiScalarField3D<T>& mass,
        MultiScalarField3D<T>& volumeFraction, MultiScalarField3D<int>& flag,
        MultiTensorField3D<T,3>& normal,
        MultiContainerBlock3D& interfaceLists, MultiScalarField3D<T>& curvature,
        MultiScalarField3D<T>& outsideDensity )
{
    std::vector<MultiBlock3D*> aggregation;

    aggregation.push_back(&fluid);
    aggregation.push_back(&rhoBar);
    aggregation.push_back(&j);
    aggregation.push_back(&mass);
    aggregation.push_back(&volumeFraction);
    aggregation.push_back(&flag);
    aggregation.push_back(&normal);
    aggregation.push_back(&interfaceLists);
    aggregation.push_back(&curvature);
    aggregation.push_back(&outsideDensity);

    return aggregation;
}

/// Data structure for holding lists of cells along the free surface in an AtomicContainerBlock.
template< typename T,template<typename U> class Descriptor>
struct InterfaceLists : public ContainerBlockData {
    typedef Array<plint,Descriptor<T>::d> Node;
    /// Holds all nodes which have excess mass from interface->fluid conversion.
    std::map<Node,T> filledMassExcess;
    /// Holds all nodes which have excess mass from interface->empty conversion.
    std::map<Node,T> emptiedMassExcess;
    /// Holds all nodes that need to change status from interface to fluid.
    std::set<Node>   interfaceToFluid;
    /// Holds all nodes that need to change status from interface to empty.
    std::set<Node>   interfaceToEmpty;
    /// Holds all nodes that need to change status from empty to interface.
    std::set<Node>   emptyToInterface;

    virtual InterfaceLists<T,Descriptor>* clone() const {
        return new InterfaceLists<T,Descriptor>(*this);
    }
};

/// A wrapper offering convenient access to the free-surface data provided to
/// data processors. Avoids verbous casting, asserting, etc.
template<typename T,template<typename U> class Descriptor>
class FreeSurfaceProcessorParam3D {
public:
    typedef typename InterfaceLists<T,Descriptor>::Node Node;
    FreeSurfaceProcessorParam3D(std::vector<AtomicBlock3D*>& atomicBlocks)
    {
        PLB_ASSERT(atomicBlocks.size() >= 10); 

        fluid_ = dynamic_cast<BlockLattice3D<T,Descriptor>*>(atomicBlocks[0]);
        PLB_ASSERT(fluid_);

        rhoBar_ = dynamic_cast<ScalarField3D<T>*>(atomicBlocks[1]);
        PLB_ASSERT(rhoBar_);

        j_ = dynamic_cast<TensorField3D<T,3>*>(atomicBlocks[2]);
        PLB_ASSERT(j_);

        mass_ = dynamic_cast<ScalarField3D<T>*>(atomicBlocks[3]);               
        PLB_ASSERT(mass_);

        volumeFraction_ = dynamic_cast<ScalarField3D<T>*>(atomicBlocks[4]);
        PLB_ASSERT(volumeFraction_);

        flag_ = dynamic_cast<ScalarField3D<int>*>(atomicBlocks[5]);
        PLB_ASSERT(flag_);

        normal_ = dynamic_cast<TensorField3D<T,3>*>(atomicBlocks[6]);
        PLB_ASSERT(normal_);

        containerInterfaceLists_ = dynamic_cast<AtomicContainerBlock3D*>(atomicBlocks[7]);
        PLB_ASSERT(containerInterfaceLists_);

        interfaceLists_ = dynamic_cast<InterfaceLists<T,Descriptor>*>(containerInterfaceLists_->getData());
        //PLB_ASSERT(interfaceLists_);
        //Put the assertion at the usage of interfaceLists, so we can still work with both freeSurfaceProcessorParam and twoPhaseProcessorParam.
                

        curvature_ = dynamic_cast<ScalarField3D<T>*>(atomicBlocks[8]);
        PLB_ASSERT(curvature_);

        outsideDensity_ = dynamic_cast<ScalarField3D<T>*>(atomicBlocks[9]);
        PLB_ASSERT(outsideDensity_);

        absoluteOffset       = fluid_->getLocation();
        relativeOffsetRhoBar = computeRelativeDisplacement(*fluid_,*rhoBar_);      
        relativeOffsetJ      = computeRelativeDisplacement(*fluid_,*j_);      
        relativeOffsetMass   = computeRelativeDisplacement(*fluid_,*mass_);      
        relativeOffsetVF     = computeRelativeDisplacement(*fluid_,*volumeFraction_);      
        relativeOffsetFS     = computeRelativeDisplacement(*fluid_,*flag_); 
        relativeOffsetNormal = computeRelativeDisplacement(*fluid_,*normal_); 
        relativeOffsetC      = computeRelativeDisplacement(*fluid_,*curvature_); 
        relativeOffsetOD     = computeRelativeDisplacement(*fluid_,*outsideDensity_); 
    }
    Cell<T,Descriptor>& cell(plint iX, plint iY, plint iZ) { return fluid_->get(iX,iY,iZ); }
    T& mass(plint iX, plint iY, plint iZ) {
        return mass_->get(iX+relativeOffsetMass.x,iY+relativeOffsetMass.y,iZ+relativeOffsetMass.z);
    }
    T& volumeFraction(plint iX, plint iY, plint iZ) {
        return volumeFraction_->get(iX+relativeOffsetVF.x,iY+relativeOffsetVF.y,iZ+relativeOffsetVF.z);
    }
    T& curvature(plint iX, plint iY, plint iZ) {
        return curvature_->get(iX+relativeOffsetC.x,iY+relativeOffsetC.y,iZ+relativeOffsetC.z);
    }
    T& outsideDensity(plint iX, plint iY, plint iZ) {
        return outsideDensity_->get(iX+relativeOffsetOD.x,iY+relativeOffsetOD.y,iZ+relativeOffsetOD.z);
    }
    int& flag(plint iX, plint iY, plint iZ) {
        return flag_->get(iX+relativeOffsetFS.x,iY+relativeOffsetFS.y,iZ+relativeOffsetFS.z);
    }
    void setForce(plint iX, plint iY, plint iZ, Array<T,3> const& force) {
            force.to_cArray(cell(iX,iY,iZ).getExternal(forceOffset));
    }
    Array<T,3> getForce(plint iX, plint iY, plint iZ) {
        Array<T,3> force; force.from_cArray(cell(iX,iY,iZ).getExternal(forceOffset));
        return force;
    }
    void setMomentum(plint iX, plint iY, plint iZ, Array<T,3> const& momentum) {
        j_->get(iX+relativeOffsetJ.x,iY+relativeOffsetJ.y,iZ+relativeOffsetJ.z) = momentum;
    }
    Array<T,3> getMomentum(plint iX, plint iY, plint iZ) {
        return j_->get(iX+relativeOffsetJ.x,iY+relativeOffsetJ.y,iZ+relativeOffsetJ.z);
    }
    T getDensity(plint iX, plint iY, plint iZ) {
        return Descriptor<T>::fullRho (
                    rhoBar_->get(iX+relativeOffsetRhoBar.x, iY+relativeOffsetRhoBar.y, iZ+relativeOffsetRhoBar.z) );
    }
    void setDensity(plint iX, plint iY, plint iZ, T rho) {
        rhoBar_->get(iX+relativeOffsetRhoBar.x, iY+relativeOffsetRhoBar.y, iZ+relativeOffsetRhoBar.z)
            = Descriptor<T>::rhoBar(rho);
    }
    void setNormal(plint iX, plint iY, plint iZ, Array<T,3> const& normal) {
        normal_->get(iX+relativeOffsetNormal.x,iY+relativeOffsetNormal.y,iZ+relativeOffsetNormal.z) = normal;
    }
    Array<T,3> getNormal(plint iX, plint iY, plint iZ) {
        return normal_->get(iX+relativeOffsetNormal.x,iY+relativeOffsetNormal.y,iZ+relativeOffsetNormal.z);
    }

    void attributeDynamics(plint iX, plint iY, plint iZ, Dynamics<T,Descriptor>* dynamics) {
        fluid_->attributeDynamics(iX,iY,iZ, dynamics);
    }

    bool isBoundary(plint iX, plint iY, plint iZ) {
        return cell(iX, iY, iZ).getDynamics().isBoundary();
    }

    void addToTotalMass(T addedTotalMass) {
        fluid_->getInternalStatistics().gatherSum(0, addedTotalMass);
    }
    void addToLostMass(T addedLostMass) {
        fluid_->getInternalStatistics().gatherSum(1, addedLostMass);
    }
    void addToInterfaceCells(plint addedInterfaceCells) {
        fluid_->getInternalStatistics().gatherIntSum(0, addedInterfaceCells);
    }
    T getSumMassMatrix() const {
        return fluid_->getInternalStatistics().getSum(0);
    }
    T getSumLostMass() const {
        return fluid_->getInternalStatistics().getSum(1);
    }
    T getTotalMass() const {
        return getSumMassMatrix() + getSumLostMass();
    }
    plint getNumInterfaceCells() const {
        return fluid_->getInternalStatistics().getIntSum(0);
    }

    T smoothVolumeFraction(plint iX, plint iY, plint iZ)
    {
        using namespace twoPhaseFlag;

        if (flag_->get(iX+relativeOffsetFS.x,iY+relativeOffsetFS.y,iZ+relativeOffsetFS.z) == wall) {
            return volumeFraction_->get(iX+relativeOffsetVF.x,iY+relativeOffsetVF.y,iZ+relativeOffsetVF.z);
        }

        T val = 0.0;
        int n = 0;
        for (int i = -1; i < 2; i++) {
            plint nextX = iX + i;
            for (int j = -1; j < 2; j++) {
                plint nextY = iY + j;
                for (int k = -1; k < 2; k++) {
                    plint nextZ = iZ + k;
                    if (!(i == 0 && j == 0 && k == 0) &&
                            flag_->get(nextX+relativeOffsetFS.x,nextY+relativeOffsetFS.y,nextZ+relativeOffsetFS.z) != wall) {
                        n++;
                        val += volumeFraction_->get(nextX+relativeOffsetVF.x,nextY+relativeOffsetVF.y,nextZ+relativeOffsetVF.z);
                    }
                }
            }
        }
        if (n != 0) {
            val /= (T) n;
        } else {
            val = volumeFraction_->get(iX+relativeOffsetVF.x,iY+relativeOffsetVF.y,iZ+relativeOffsetVF.z);
        }

        return val;
    }

    std::map<Node,T>& filledMassExcess() { PLB_ASSERT(interfaceLists_); return interfaceLists_ -> filledMassExcess; }
    std::map<Node,T>& emptiedMassExcess() { PLB_ASSERT(interfaceLists_); return interfaceLists_ -> emptiedMassExcess; }
    std::set<Node>& interfaceToFluid() { PLB_ASSERT(interfaceLists_); return interfaceLists_ -> interfaceToFluid; }
    std::set<Node>& interfaceToEmpty() { PLB_ASSERT(interfaceLists_); return interfaceLists_ -> interfaceToEmpty; }
    std::set<Node>& emptyToInterface() { PLB_ASSERT(interfaceLists_); return interfaceLists_ -> emptyToInterface; }

    Dot3D const& absOffset() const { return absoluteOffset; }
    Box3D getBoundingBox() const { return volumeFraction_->getBoundingBox(); }
private:
    BlockLattice3D<T,Descriptor>* fluid_;
    ScalarField3D<T>* rhoBar_;
    TensorField3D<T,3>* j_;
    ScalarField3D<T>* mass_;
    ScalarField3D<T>* volumeFraction_;
    ScalarField3D<int>* flag_;
    TensorField3D<T,3>* normal_;
    AtomicContainerBlock3D* containerInterfaceLists_;
    InterfaceLists<T,Descriptor>* interfaceLists_;
    ScalarField3D<T>* curvature_;
    ScalarField3D<T>* outsideDensity_;

    Dot3D absoluteOffset, relativeOffsetRhoBar, relativeOffsetJ, relativeOffsetMass,
          relativeOffsetVF, relativeOffsetFS, relativeOffsetNormal, relativeOffsetC,
          relativeOffsetOD;

    static const int forceOffset = Descriptor<T>::ExternalField::forceBeginsAt;
};

}  // namespace plb

#endif  // FREE_SURFACE_UTIL_3D_H