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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 |
| 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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* |
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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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|
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/** |
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#define BRAINS_FORCEMANAGER_HPP |
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|
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#include "brains/SimInfo.hpp" |
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+ |
#include "primitives/Molecule.hpp" |
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+ |
#include "nonbonded/LJ.hpp" |
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+ |
#include "nonbonded/GB.hpp" |
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+ |
#include "nonbonded/Sticky.hpp" |
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+ |
#include "nonbonded/EAM.hpp" |
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+ |
#include "nonbonded/SC.hpp" |
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#include "nonbonded/Morse.hpp" |
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+ |
#include "nonbonded/Electrostatic.hpp" |
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|
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< |
namespace oopse { |
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< |
|
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> |
namespace OpenMD { |
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/** |
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* @class ForceManager ForceManager.hpp "brains/ForceManager.hpp" |
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* ForceManager is responsible for calculating the short range interactions (c++) and |
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* long range interactions(fortran). If fortran side is not setup before the force calculation, |
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* call SimInfo's update function to settle it down. |
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< |
* @note the reason we delay fortran side's setup is that some applications (Dump2XYZ etc.) |
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< |
* may not need force calculation, why bother? |
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> |
* ForceManager is responsible for calculating the short range |
| 67 |
> |
* interactions (C++) and long range interactions (Fortran). If the |
| 68 |
> |
* Fortran side is not set up before the force calculation, call |
| 69 |
> |
* SimInfo's update function to settle it down. |
| 70 |
> |
* |
| 71 |
> |
* @note the reason we delay fortran side's setup is that some |
| 72 |
> |
* applications (Dump2XYZ etc.) may not need force calculation, so why |
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* bother? |
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*/ |
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class ForceManager { |
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|
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public: |
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< |
ForceManager(SimInfo * info) : info_(info) {} |
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|
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> |
|
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> |
ForceManager(SimInfo * info); |
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virtual ~ForceManager() {} |
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|
|
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//public virtual function should be avoided |
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/**@todo need refactory */ |
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virtual void calcForces(bool needPotential, bool needStress); |
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> |
// public virtual functions should be avoided |
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> |
/**@todo needs refactoring */ |
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> |
virtual void calcForces(); |
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> |
virtual void init() {}; |
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|
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– |
virtual void init() {} |
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protected: |
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|
|
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virtual void preCalculation(); |
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|
| 89 |
> |
virtual void preCalculation(); |
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virtual void calcShortRangeInteraction(); |
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|
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virtual void calcLongRangeInteraction(bool needPotential, bool needStress); |
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< |
|
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> |
virtual void calcLongRangeInteraction(); |
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virtual void postCalculation(); |
| 93 |
|
|
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SimInfo * info_; |
| 95 |
+ |
std::map<Bend*, BendDataSet> bendDataSets; |
| 96 |
+ |
std::map<Torsion*, TorsionDataSet> torsionDataSets; |
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+ |
std::map<Inversion*, InversionDataSet> inversionDataSets; |
| 98 |
+ |
Mat3x3d tau; |
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|
|
| 100 |
+ |
bool NBforcesInitialized_; |
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+ |
LJ* lj_; |
| 102 |
+ |
GB* gb_; |
| 103 |
+ |
Sticky* sticky_; |
| 104 |
+ |
EAM* eam_; |
| 105 |
+ |
SC* sc_; |
| 106 |
+ |
Morse* morse_; |
| 107 |
+ |
Electrostatic* electrostatic_; |
| 108 |
+ |
|
| 109 |
|
}; |
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|
|
| 111 |
< |
} //end namespace oopse |
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> |
} //end namespace OpenMD |
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#endif //BRAINS_FORCEMANAGER_HPP |
