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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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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 |
| 11 |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
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* 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 |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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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 |
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* documentation and/or other materials provided with the |
| 15 |
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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 |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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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 |
+ |
* |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#ifndef APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP |
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#define APPLICATION_HYDRODYNAMICS_ROUGHSHELL_HPP |
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|
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#include "applications/hydrodynamics/ApproximationModel.hpp" |
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#include "applications/hydrodynamics/CompositeShape.hpp" |
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namespace oopse { |
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/** |
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* @class Grid3d |
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* A generic 3d grid class |
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*/ |
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template<class Elem> |
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class Grid3D { |
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public: |
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Grid3D(unsigned int dim1, unsigned int dim2, unsigned int dim3) : dim1_(dim1), dim2_(dim2), dim3_(dim3) { |
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data_.resize(dim1_*dim2_*dim3_); |
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} |
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Elem& operator ()(unsigned int i, unsigned int j, unsigned int k) { |
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int index = isValidGrid(i, j , k); |
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assert(index != -1); |
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return data_[index]; |
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} |
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|
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const Elem& operator () (unsigned int i, unsigned int j, unsigned int k) const { |
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int index = isValidGrid(i, j , k); |
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assert(index != -1); |
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return data_[index]; |
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} |
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|
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std::vector<Elem> getAllNeighbors(unsigned int i, unsigned int j, unsigned int k) { |
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std::vector<Elem> result; |
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int index; |
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index = isValidGrid(i-1, j, k); |
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if (index != -1) |
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result.push_back(data_[index]); |
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< |
|
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index = isValidGrid(i+1, j, k); |
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if (index != -1) |
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result.push_back(data_[index]); |
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< |
|
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< |
index = isValidGrid(i, j-1, k); |
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< |
if (index != -1) |
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result.push_back(data_[index]); |
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< |
|
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< |
index = isValidGrid(i, j+1, k); |
| 85 |
< |
if (index != -1) |
| 86 |
< |
result.push_back(data_[index]); |
| 87 |
< |
|
| 88 |
< |
index = isValidGrid(i, j, k-1); |
| 89 |
< |
if (index != -1) |
| 90 |
< |
result.push_back(data_[index]); |
| 91 |
< |
|
| 92 |
< |
index = isValidGrid(i, j, k+1); |
| 93 |
< |
if (index != -1) |
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< |
result.push_back(data_[index]); |
| 95 |
< |
|
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< |
return result; |
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< |
} |
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private: |
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< |
|
| 100 |
< |
int isValidGrid(unsigned int i, unsigned int j, unsigned int k) const { |
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< |
int index = i * dim2_*dim3_ + j * dim3_ + k; |
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return index < data_.size() ? index : -1; |
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}; |
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< |
|
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< |
unsigned int dim1_; |
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< |
unsigned int dim2_; |
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< |
unsigned int dim3_; |
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std::vector<Elem> data_; |
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< |
|
| 110 |
< |
}; |
| 47 |
> |
#include "utils/Grid3d.hpp" |
| 48 |
> |
|
| 49 |
> |
namespace OpenMD { |
| 50 |
|
|
| 112 |
– |
|
| 51 |
|
class RoughShell : public ApproximationModel { |
| 52 |
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public: |
| 53 |
|
RoughShell(StuntDouble* sd, SimInfo* info); |
| 55 |
|
void setSigma(RealType sigma) {sigma_ = sigma;} |
| 56 |
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RealType getSigma() {return sigma_;} |
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|
private: |
| 58 |
< |
virtual bool createBeads(std::vector<BeadParam>& beads); |
| 58 |
> |
virtual bool createBeads(vector<BeadParam>& beads); |
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|
//StuntDoubleShape sdShape_; |
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|
RealType sigma_; |
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|
Shape* shape_; |
