| 77 |
|
}; |
| 78 |
|
bool RoughShell::createBeads(std::vector<BeadParam>& beads) { |
| 79 |
|
std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBox(); |
| 80 |
< |
double len = boxBoundary.second[0] - boxBoundary.first[0]; |
| 81 |
< |
int numLattices = static_cast<int>(len/sigma_) + 1; |
| 80 |
> |
double firstMin = std::min(std::min(boxBoundary.first[0], boxBoundary.first[1]), boxBoundary.first[2]); |
| 81 |
> |
double secondMax = std::max(std::max(boxBoundary.second[0], boxBoundary.second[1]), boxBoundary.second[2]); |
| 82 |
> |
double len = secondMax - firstMin; |
| 83 |
> |
int numLattices = static_cast<int>(len/sigma_) + 2; |
| 84 |
|
Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices); |
| 85 |
|
|
| 86 |
|
//fill beads |
| 88 |
|
for (int j = 0; j < numLattices; ++j) { |
| 89 |
|
for (int k = 0; k < numLattices; ++k) { |
| 90 |
|
BeadLattice& currentBead = grid(i, j, k); |
| 91 |
< |
currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]); |
| 91 |
> |
currentBead.origin = Vector3d((i-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]); |
| 92 |
|
currentBead.radius = sigma_; |
| 93 |
|
currentBead.interior = shape_->isInterior(grid(i, j, k).origin); |
| 94 |
|
} |
| 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 |
|
|
| 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()) { |
| 105 |
> |
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 = "Bead"; |
| 119 |
> |
surfaceBead.atomName = "H"; |
| 120 |
|
surfaceBead.pos = grid(i, j, k).origin; |
| 121 |
|
surfaceBead.radius = grid(i, j, k).radius; |
| 122 |
< |
beads.push_back(surfaceBead); |
| 112 |
< |
} |
| 122 |
> |
beads.push_back(surfaceBead); |
| 123 |
|
|
| 124 |
+ |
} |
| 125 |
|
} |
| 126 |
|
} |
| 127 |
|
} |
