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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
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* |
| 9 |
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* 1. Acknowledgement of the program authors must be made in any |
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< |
* publication of scientific results based in part on use of the |
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< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
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< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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> |
* 2. Redistributions in binary form must reproduce the above copyright |
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|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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+ |
* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
| 35 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "applications/hydrodynamics/RoughShell.hpp" |
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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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> |
namespace OpenMD { |
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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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< |
|
| 70 |
< |
}; |
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< |
|
| 72 |
< |
struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
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< |
|
| 69 |
> |
|
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> |
}; |
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> |
|
| 72 |
> |
struct InteriorFunctor : public std::unary_function<BeadLattice, bool>{ |
| 73 |
> |
|
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|
bool operator() (const BeadLattice& bead) { |
| 75 |
< |
return bead.interior; |
| 75 |
> |
return bead.interior; |
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} |
| 77 |
< |
|
| 78 |
< |
}; |
| 79 |
< |
bool RoughShell::createBeads(std::vector<BeadParam>& beads) { |
| 80 |
< |
std::pair<Vector3d, Vector3d> boxBoundary = shape_->getBox(); |
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< |
double len = boxBoundary.second[0] - boxBoundary.first[0]; |
| 82 |
< |
int numLattices = static_cast<int>(len/sigma_) + 1; |
| 77 |
> |
|
| 78 |
> |
}; |
| 79 |
> |
bool RoughShell::createBeads(std::vector<BeadParam>& beads) { |
| 80 |
> |
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]); |
| 83 |
> |
RealType len = secondMax - firstMin; |
| 84 |
> |
int numLattices = static_cast<int>(len/sigma_) + 2; |
| 85 |
|
Grid3D<BeadLattice> grid(numLattices, numLattices, numLattices); |
| 86 |
< |
|
| 86 |
> |
|
| 87 |
|
//fill beads |
| 88 |
|
for (int i = 0; i < numLattices; ++i) { |
| 89 |
< |
for (int j = 0; j < numLattices; ++j) { |
| 90 |
< |
for (int k = 0; k < numLattices; ++k) { |
| 91 |
< |
BeadLattice& currentBead = grid(i, j, k); |
| 92 |
< |
currentBead.origin = Vector3d(i*sigma_ + boxBoundary.first[0], j *sigma_ + boxBoundary.first[1], k*sigma_+ boxBoundary.first[2]); |
| 93 |
< |
currentBead.radius = sigma_; |
| 94 |
< |
currentBead.interior = shape_->isInterior(grid(i, j, k).origin); |
| 92 |
< |
} |
| 89 |
> |
for (int j = 0; j < numLattices; ++j) { |
| 90 |
> |
for (int k = 0; k < numLattices; ++k) { |
| 91 |
> |
BeadLattice& currentBead = grid(i, j, k); |
| 92 |
> |
currentBead.origin = Vector3d((i-1)*sigma_ + boxBoundary.first[0], (j-1) *sigma_ + boxBoundary.first[1], (k-1)*sigma_+ boxBoundary.first[2]); |
| 93 |
> |
currentBead.radius = sigma_ / 2.0; |
| 94 |
> |
currentBead.interior = shape_->isInterior(grid(i, j, k).origin); |
| 95 |
|
} |
| 96 |
+ |
} |
| 97 |
|
} |
| 98 |
< |
|
| 98 |
> |
|
| 99 |
|
//remove embedded beads |
| 100 |
|
for (int i = 0; i < numLattices; ++i) { |
| 101 |
< |
for (int j = 0; j < numLattices; ++j) { |
| 102 |
< |
for (int k = 0; k < numLattices; ++k) { |
| 103 |
< |
std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k); |
| 104 |
< |
//if one of its neighbor cells is exterior, current cell is on the surface |
| 105 |
< |
|
| 106 |
< |
std::vector<BeadLattice>::iterator ei = std::find_if(neighborCells.begin(), neighborCells.end(), ExteriorFunctor()); |
| 107 |
< |
std::vector<BeadLattice>::iterator ii = std::find_if(neighborCells.begin(), neighborCells.end(), InteriorFunctor()); |
| 108 |
< |
|
| 109 |
< |
if (ei != neighborCells.end() && ii != neighborCells.end()) { |
| 110 |
< |
BeadParam surfaceBead; |
| 111 |
< |
surfaceBead.atomName = "Bead"; |
| 112 |
< |
surfaceBead.pos = grid(i, j, k).origin; |
| 113 |
< |
surfaceBead.radius = grid(i, j, k).radius; |
| 111 |
< |
beads.push_back(surfaceBead); |
| 112 |
< |
} |
| 113 |
< |
|
| 101 |
> |
for (int j = 0; j < numLattices; ++j) { |
| 102 |
> |
for (int k = 0; k < numLattices; ++k) { |
| 103 |
> |
std::vector<BeadLattice> neighborCells = grid.getAllNeighbors(i, j, k); |
| 104 |
> |
//if one of its neighbor cells is exterior, current cell is on the surface |
| 105 |
> |
|
| 106 |
> |
if (grid(i, j, k).interior){ |
| 107 |
> |
|
| 108 |
> |
bool allNeighBorIsInterior = true; |
| 109 |
> |
for (std::vector<BeadLattice>::iterator l = neighborCells.begin(); l != neighborCells.end(); ++l) { |
| 110 |
> |
if (!l->interior) { |
| 111 |
> |
allNeighBorIsInterior = false; |
| 112 |
> |
break; |
| 113 |
> |
} |
| 114 |
|
} |
| 115 |
+ |
|
| 116 |
+ |
if (allNeighBorIsInterior) |
| 117 |
+ |
continue; |
| 118 |
+ |
|
| 119 |
+ |
BeadParam surfaceBead; |
| 120 |
+ |
surfaceBead.atomName = "H"; |
| 121 |
+ |
surfaceBead.pos = grid(i, j, k).origin; |
| 122 |
+ |
surfaceBead.radius = grid(i, j, k).radius; |
| 123 |
+ |
beads.push_back(surfaceBead); |
| 124 |
+ |
|
| 125 |
+ |
} |
| 126 |
|
} |
| 127 |
+ |
} |
| 128 |
|
} |
| 129 |
< |
|
| 129 |
> |
|
| 130 |
|
return true; |
| 131 |
+ |
} |
| 132 |
+ |
|
| 133 |
|
} |
| 120 |
– |
|
| 121 |
– |
} |
