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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 |
| 10 |
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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 |
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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 |
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> |
* 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 |
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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 |
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* 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 |
| 30 |
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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 |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* 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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#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 "applications/hydrodynamics/MoleculeShape.hpp" |
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#include "utils/any.hpp" |
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namespace oopse { |
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struct HydrodynamicProps { |
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Vector3d diffCenter; |
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Mat3x3d transDiff; |
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Mat3x3d rotDiff; |
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Mat3x3d transRotDiff; |
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}; |
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> |
#include "hydrodynamics/HydroProp.hpp" |
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> |
#include "utils/PhysicalConstants.hpp" |
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|
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struct BeadParam { |
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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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Vector3d pos; |
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< |
double radius; |
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}; |
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> |
RealType radius; |
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> |
}; |
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> |
|
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> |
class Shape; |
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> |
class Sphere; |
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> |
class Ellipsoid; |
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> |
class CompositeShape; |
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> |
|
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> |
class HydrodynamicsModel { |
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> |
public: |
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> |
HydrodynamicsModel(StuntDouble* sd, SimInfo* info) : sd_(sd), info_(info) {} |
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virtual ~HydrodynamicsModel() {} |
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|
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typedef std::map<std::string, boost::any> DynamicProperty; |
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|
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class HydrodynamicsModel { |
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public: |
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< |
HydrodynamicsModel(Molecule* mol, const DynamicProperty& extraParams) : mol_(mol) {} |
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bool calcHydrodyanmicsProps(double eta); |
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|
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Vector3d getDiffCenter(); |
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Mat3x3d getTransDiff(); |
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Mat3x3d getRotDiff(); |
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Mat3x3d getTransRotDiff(); |
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< |
void writeBeads(std::ostream& os); |
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< |
void writeDiffCenterAndDiffTensor(std::ostream& os); |
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protected: |
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< |
Molecule* mol_; |
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< |
private: |
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< |
virtual bool createBeads(std::vector<BeadParam>& beads) = 0; |
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< |
|
| 88 |
< |
|
| 89 |
< |
HydrodynamicProps props_; |
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< |
std::vector<BeadParam> beads_; |
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< |
|
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< |
}; |
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|
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< |
|
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> |
virtual bool calcHydroProps(Shape* shape, RealType viscosity, RealType temperature); |
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> |
|
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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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> |
HydroProp* getHydroPropsAtCR() {return cr_;} |
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> |
HydroProp* getHydroPropsAtCD() {return cd_;} |
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> |
|
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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: |
| 82 |
> |
StuntDouble* sd_; |
| 83 |
> |
SimInfo* info_; |
| 84 |
> |
private: |
| 85 |
> |
HydroProp* cr_; |
| 86 |
> |
HydroProp* cd_; |
| 87 |
> |
std::vector<BeadParam> beads_; |
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> |
}; |
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> |
|
| 90 |
|
} |
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|
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#endif |
