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 |
|
} |