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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 |
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* program. An acceptable form of acknowledgement is citation of |
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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. |
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|
* |
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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 |
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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: |
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* |
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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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#ifndef INTEGRATOR_LDFORCEMANAGER_HPP |
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#include "brains/ForceManager.hpp" |
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#include "primitives/Molecule.hpp" |
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|
#include "math/SeqRandNumGen.hpp" |
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#include "hydrodynamics/Shape.hpp" |
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#include "integrators/Velocitizer.hpp" |
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|
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namespace oopse { |
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|
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struct HydroProp{ |
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Vector3d cod; |
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Mat3x3d Ddtt; |
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Mat3x3d Ddtr; |
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Mat3x3d Ddrr; |
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Mat3x3d Xidtt; |
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Mat3x3d Xidrt; |
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Mat3x3d Xidtr; |
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< |
Mat3x3d Xidrr; |
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< |
|
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< |
}; |
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< |
|
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> |
namespace OpenMD { |
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> |
|
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> |
struct SDShape{ |
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> |
StuntDouble* sd; |
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> |
Shape* shape; |
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> |
}; |
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> |
|
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/** |
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* @class LDForceManager |
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* Force manager for Lagevin Dynamics applying friction and random forces as well as torques. |
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> |
* Force manager for Lagevin Dynamics applying friction and random |
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* forces as well as torques. |
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*/ |
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class LDForceManager : public ForceManager{ |
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|
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> |
class LDForceManager : public ForceManager{ |
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> |
|
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public: |
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LDForceManager(SimInfo * info); |
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+ |
|
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+ |
int getMaxIterationNumber() { |
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return maxIterNum_; |
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} |
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|
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+ |
void setMaxIterationNumber(int maxIter) { |
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maxIterNum_ = maxIter; |
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} |
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|
|
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protected: |
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virtual void postCalculation(); |
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> |
RealType getForceTolerance() { |
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> |
return forceTolerance_; |
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> |
} |
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|
|
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+ |
void setForceTolerance(RealType tol) { |
| 81 |
+ |
forceTolerance_ = tol; |
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+ |
} |
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+ |
|
| 84 |
+ |
RealType getDt2() { |
| 85 |
+ |
return dt2_; |
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+ |
} |
| 87 |
+ |
|
| 88 |
+ |
void setDt2(RealType dt2) { |
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+ |
dt2_ = dt2; |
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} |
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+ |
|
| 92 |
+ |
|
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protected: |
| 94 |
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virtual void postCalculation(bool needStress); |
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|
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private: |
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std::map<std::string, HydroProp> parseFrictionFile(const std::string& filename); |
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void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, double variance); |
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std::vector<HydroProp> hydroProps_; |
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> |
std::map<std::string, HydroProp*> parseFrictionFile(const std::string& filename); |
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> |
void genRandomForceAndTorque(Vector3d& force, Vector3d& torque, unsigned int index, RealType variance); |
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> |
std::vector<HydroProp*> hydroProps_; |
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|
SeqRandNumGen randNumGen_; |
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< |
double variance_; |
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< |
}; |
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< |
|
| 104 |
< |
} //end namespace oopse |
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> |
RealType variance_; |
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> |
RealType langevinBufferRadius_; |
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> |
RealType frozenBufferRadius_; |
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> |
bool sphericalBoundaryConditions_; |
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> |
Globals* simParams; |
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> |
Velocitizer* veloMunge; |
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> |
// convergence parameters: |
| 108 |
> |
int maxIterNum_; |
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> |
RealType forceTolerance_; |
| 110 |
> |
RealType dt2_; |
| 111 |
> |
}; |
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> |
|
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> |
} //end namespace OpenMD |
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|
#endif //BRAINS_FORCEMANAGER_HPP |
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|
