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#include "applications/hydrodynamics/ShapeBuilder.hpp" |
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#include "brains/SimInfo.hpp" |
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namespace oopse { |
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|
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RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){ |
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|
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RoughShell::RoughShell(StuntDouble* sd, SimInfo* info) : ApproximationModel(sd, info){ |
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shape_=ShapeBuilder::createShape(sd); |
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Globals* simParams = info->getSimParams(); |
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if (simParams->haveBeadSize()) { |
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sigma_ = simParams->getBeadSize(); |
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sigma_ = simParams->getBeadSize(); |
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}else { |
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|
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|
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} |
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} |
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|
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struct BeadLattice { |
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} |
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> |
|
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struct BeadLattice { |
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Vector3d origin; |
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double radius; |
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RealType radius; |
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bool interior; |
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}; |
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|
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struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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|
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}; |
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> |
|
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> |
struct ExteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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> |
|
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bool operator() (const BeadLattice& bead) { |
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return !bead.interior; |
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> |
return !bead.interior; |
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} |
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|
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}; |
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|
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struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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|
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> |
|
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}; |
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> |
|
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> |
struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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> |
|
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bool operator() (const BeadLattice& bead) { |
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< |
return bead.interior; |
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> |
return bead.interior; |
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} |
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< |
|
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< |
}; |
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< |
bool RoughShell::createBeads(std::vector<BeadParam>& beads) { |
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std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBox(); |
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double len = boxBoundary.second[0] - boxBoundary.first[0]; |
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int numLattices = static_cast<int>(len/sigma_) + 1; |
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> |
|
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> |
}; |
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> |
bool RoughShell::createBeads(std::vector<BeadParam>& beads) { |
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> |
std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBoundingBox(); |
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> |
RealType firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]); |
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RealType secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]); |
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RealType len = secondMax - firstMin; |
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int numLattices = static_cast<int>(len/sigma_) + 2; |
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Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices); |
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|
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> |
|
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//fill beads |
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for (int i = 0; i < numLattices; ++i) { |
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< |
for (int j = 0; j < numLattices; ++j) { |
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< |
for (int k = 0; k < numLattices; ++k) { |
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< |
BeadLattice& currentBead = grid(i, j, k); |
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< |
currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]); |
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< |
currentBead.radius = sigma_; |
| 93 |
< |
currentBead.interior = shape_->isInterior(grid(i, j, k).origin); |
| 92 |
< |
} |
| 88 |
> |
for (int j = 0; j < numLattices; ++j) { |
| 89 |
> |
for (int k = 0; k < numLattices; ++k) { |
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> |
BeadLattice& currentBead = grid(i, j, k); |
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> |
currentBead.origin = Vector3d((i-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]); |
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currentBead.radius = sigma_ / 2.0; |
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> |
currentBead.interior = shape_->isInterior(grid(i, j, k).origin); |
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} |
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+ |
} |
| 96 |
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} |
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< |
|
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> |
|
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//remove embedded beads |
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|
for (int i = 0; i < numLattices; ++i) { |
| 100 |
< |
for (int j = 0; j < numLattices; ++j) { |
| 101 |
< |
for (int k = 0; k < numLattices; ++k) { |
| 102 |
< |
std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k); |
| 103 |
< |
//if one of its neighbor cells is exterior, current cell is on the surface |
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< |
|
| 105 |
< |
std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor()); |
| 106 |
< |
std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor()); |
| 107 |
< |
|
| 108 |
< |
if (ei != neighborCells.end() && ii != neighborCells.end()) { |
| 109 |
< |
BeadParam surfaceBead; |
| 110 |
< |
surfaceBead.atomName = "Bead"; |
| 111 |
< |
surfaceBead.pos = grid(i, j, k).origin; |
| 112 |
< |
surfaceBead.radius = grid(i, j, k).radius; |
| 111 |
< |
beads.push_back(surfaceBead); |
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< |
} |
| 113 |
< |
|
| 100 |
> |
for (int j = 0; j < numLattices; ++j) { |
| 101 |
> |
for (int k = 0; k < numLattices; ++k) { |
| 102 |
> |
std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k); |
| 103 |
> |
//if one of its neighbor cells is exterior, current cell is on the surface |
| 104 |
> |
|
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> |
if (grid(i, j, k).interior){ |
| 106 |
> |
|
| 107 |
> |
bool allNeighBorIsInterior = true; |
| 108 |
> |
for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) { |
| 109 |
> |
if (!l->interior) { |
| 110 |
> |
allNeighBorIsInterior = false; |
| 111 |
> |
break; |
| 112 |
> |
} |
| 113 |
|
} |
| 114 |
+ |
|
| 115 |
+ |
if (allNeighBorIsInterior) |
| 116 |
+ |
continue; |
| 117 |
+ |
|
| 118 |
+ |
BeadParam surfaceBead; |
| 119 |
+ |
surfaceBead.atomName = "H"; |
| 120 |
+ |
surfaceBead.pos = grid(i, j, k).origin; |
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+ |
surfaceBead.radius = grid(i, j, k).radius; |
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+ |
beads.push_back(surfaceBead); |
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+ |
|
| 124 |
+ |
} |
| 125 |
|
} |
| 126 |
+ |
} |
| 127 |
|
} |
| 128 |
< |
|
| 128 |
> |
|
| 129 |
|
return true; |
| 130 |
+ |
} |
| 131 |
+ |
|
| 132 |
|
} |
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– |
|
| 121 |
– |
} |
