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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: |
| 8 |
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* |
| 9 |
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* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
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* |
| 18 |
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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 |
|
* |
| 12 |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
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* |
| 32 |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
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* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "applications/hydrodynamics/CompositeShape.hpp" |
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#include "utils/MemoryUtils.hpp" |
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#include "applications/hydrodynamics/HydrodynamicsModel.hpp" |
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namespace oopse { |
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< |
|
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< |
CompositeShape::~CompositeShape() { |
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> |
namespace OpenMD { |
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> |
|
| 48 |
> |
CompositeShape::~CompositeShape() { |
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|
MemoryUtils::deletePointers(shapes_); |
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< |
} |
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bool CompositeShape::isInterior(Vector3d pos) { |
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> |
} |
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> |
bool CompositeShape::isInterior(Vector3d pos) { |
| 52 |
|
bool result = false; |
| 53 |
|
std::vector<Shape*>::iterator iter; |
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for (iter = shapes_.begin(); iter != shapes_.end(); ++ iter) { |
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< |
if ((*iter)->isInterior(pos)) { |
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< |
result = true; |
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< |
break; |
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< |
} |
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> |
if ((*iter)->isInterior(pos)) { |
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> |
result = true; |
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> |
break; |
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> |
} |
| 59 |
|
} |
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< |
|
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> |
|
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|
return result; |
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< |
} |
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< |
|
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< |
template<class Cont, class Predict> |
| 65 |
< |
void swap_if(Cont& b1, Cont& b2, Predict predict) { |
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> |
} |
| 63 |
> |
|
| 64 |
> |
template<class Cont, class Predict> |
| 65 |
> |
void swap_if(Cont& b1, Cont& b2, Predict predict) { |
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unsigned int size = b1.size(); |
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|
assert(size == b2.size()); |
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for (unsigned int i = 0 ; i < size; ++i) { |
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if (predict(b1[i], b2[i])) |
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std::swap(b1[i], b2[i]); |
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> |
if (predict(b1[i], b2[i])) |
| 70 |
> |
std::swap(b1[i], b2[i]); |
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} |
| 72 |
< |
|
| 73 |
< |
} |
| 74 |
< |
|
| 75 |
< |
std::pair<Vector3d, Vector3d> CompositeShape::getBox() { |
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> |
|
| 73 |
> |
} |
| 74 |
> |
|
| 75 |
> |
std::pair<Vector3d, Vector3d> CompositeShape::getBoundingBox() { |
| 76 |
|
std::vector<Shape*>::iterator iter = shapes_.begin(); |
| 77 |
< |
std::pair<Vector3d, Vector3d> boundary = (*iter)->getBox(); |
| 77 |
> |
std::pair<Vector3d, Vector3d> boundary = (*iter)->getBoundingBox(); |
| 78 |
|
for (++iter; iter != shapes_.end(); ++iter) { |
| 79 |
< |
std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBox(); |
| 80 |
< |
swap_if(boundary.first, currBoundary.first, std::less<double>()); |
| 81 |
< |
swap_if(boundary.second, currBoundary.second, std::greater<double>()); |
| 79 |
> |
std::pair<Vector3d, Vector3d> currBoundary = (*iter)->getBoundingBox(); |
| 80 |
> |
swap_if(boundary.first, currBoundary.first, std::greater<RealType>()); |
| 81 |
> |
swap_if(boundary.second, currBoundary.second, std::less<RealType>()); |
| 82 |
|
} |
| 83 |
< |
|
| 83 |
> |
|
| 84 |
|
return boundary; |
| 85 |
+ |
} |
| 86 |
+ |
|
| 87 |
+ |
HydroProp* CompositeShape::getHydroProp(RealType viscosity, RealType temperature) { |
| 88 |
+ |
HydroProp* props = new HydroProp(); |
| 89 |
+ |
props->setCOR(V3Zero); |
| 90 |
+ |
sprintf( painCave.errMsg, |
| 91 |
+ |
"CompositeShape was asked to return an analytic HydroProps.\n"); |
| 92 |
+ |
painCave.severity = OPENMD_ERROR; |
| 93 |
+ |
painCave.isFatal = 1; |
| 94 |
+ |
simError(); |
| 95 |
+ |
return props; |
| 96 |
+ |
} |
| 97 |
|
} |
| 85 |
– |
|
| 86 |
– |
bool CompositeShape::calcHydroProps(HydrodynamicsModel* model, double viscosity, double temperature) { |
| 87 |
– |
return model->calcHydroProps(this, viscosity, temperature); |
| 88 |
– |
} |
| 89 |
– |
|
| 90 |
– |
} |
