| 6 |
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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 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* 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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< |
* 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 |
< |
* 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 |
|
* such damages. |
| 31 |
+ |
* |
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+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* 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). |
| 40 |
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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_HYDRODYNAMICSMODEL_HPP |
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#define APPLICATION_HYDRODYNAMICS_HYDRODYNAMICSMODEL_HPP |
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#include "math/SquareMatrix3.hpp" |
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#include "math/DynamicRectMatrix.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/HydroProps.hpp" |
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#include "utils/OOPSEConstant.hpp" |
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#include "utils/HydroProps.hpp" |
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> |
#include "hydrodynamics/HydroProp.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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|
|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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struct BeadParam { |
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std::string atomName; |
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virtual void init() {}; |
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virtual void writeBeads(std::ostream& os) = 0; |
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void writeHydroProps(std::ostream& os); |
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< |
HydroProps getHydroPropsAtCR() {return cr_;} |
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< |
HydroProps getHydroPropsAtCD() {return cd_;} |
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> |
HydroProp* getHydroPropsAtCR() {return cr_;} |
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> |
HydroProp* getHydroPropsAtCD() {return cd_;} |
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|
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< |
void setCR(const HydroProps cr) {cr_ = cr;} |
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< |
void setCD(const HydroProps cd) { cd_ = cd;} |
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> |
void setCR(HydroProp* cr) {cr_ = cr;} |
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> |
void setCD(HydroProp* cd) {cd_ = cd;} |
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std::string getStuntDoubleName() { return sd_->getType();} |
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protected: |
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|
StuntDouble* sd_; |
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|
SimInfo* info_; |
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private: |
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< |
HydroProps cr_; |
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< |
HydroProps cd_; |
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> |
HydroProp* cr_; |
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> |
HydroProp* cd_; |
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std::vector<BeadParam> beads_; |
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}; |
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|
