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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 |
| 15 |
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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 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
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* 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] 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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|
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/** |
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|
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#include "brains/SimInfo.hpp" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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> |
#include "nonbonded/Cutoffs.hpp" |
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> |
#include "nonbonded/SwitchingFunction.hpp" |
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> |
#include "nonbonded/InteractionManager.hpp" |
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> |
#include "parallel/ForceDecomposition.hpp" |
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> |
|
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> |
#define PREPAIR_LOOP 0 |
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> |
#define PAIR_LOOP 1 |
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> |
|
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> |
using namespace std; |
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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 |
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* interactions (C++) and long range interactions (Fortran). If the |
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* Fortran side is not set up before the force calculation, call |
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* SimInfo's update function to settle it down. |
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> |
* ForceManager is responsible for calculating both the short range |
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* (bonded) interactions and long range (non-bonded) interactions. |
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* |
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* @note the reason we delay fortran side's setup is that some |
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* applications (Dump2XYZ etc.) may not need force calculation, so why |
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* bother? |
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> |
* @note the reason we delay some of the setup is that |
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* initialization must wait until after the force field has been |
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> |
* parsed so that the atom types are known. |
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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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> |
ForceManager(SimInfo * info); |
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virtual ~ForceManager() {} |
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virtual void calcForces(); |
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void initialize(); |
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|
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// public virtual functions should be avoided |
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/**@todo needs refactoring */ |
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virtual void calcForces(bool needPotential, bool needStress); |
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protected: |
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> |
bool initialized_; |
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|
|
| 86 |
< |
virtual void init() {} |
| 87 |
< |
protected: |
| 86 |
> |
virtual void setupCutoffs(); |
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> |
virtual void preCalculation(); |
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> |
virtual void shortRangeInteractions(); |
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> |
virtual void longRangeInteractions(); |
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> |
virtual void postCalculation(); |
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|
|
| 92 |
< |
virtual void preCalculation(); |
| 93 |
< |
|
| 94 |
< |
virtual void calcShortRangeInteraction(); |
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> |
SimInfo* info_; |
| 93 |
> |
ForceField* forceField_; |
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> |
InteractionManager* interactionMan_; |
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> |
ForceDecomposition* fDecomp_; |
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> |
SwitchingFunction* switcher_; |
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|
|
| 98 |
< |
virtual void calcLongRangeInteraction(bool needPotential, bool needStress); |
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> |
SwitchingFunctionType sft_;/**< Type of switching function in use */ |
| 99 |
|
|
| 87 |
– |
virtual void postCalculation(bool needStress); |
| 88 |
– |
|
| 89 |
– |
SimInfo * info_; |
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|
|
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< |
std::map<Bend*, BendDataSet> bendDataSets; |
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< |
std::map<Torsion*, TorsionDataSet> torsionDataSets; |
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> |
RealType rCut_; /**< cutoff radius for non-bonded interactions */ |
| 102 |
> |
RealType rSwitch_; /**< inner radius of switching function */ |
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> |
CutoffMethod cutoffMethod_;/**< Cutoff Method for most non-bonded interactions */ |
| 104 |
> |
CutoffPolicy cutoffPolicy_;/**< Cutoff Policy for non-bonded interactions */ |
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> |
|
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> |
map<Bend*, BendDataSet> bendDataSets; |
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> |
map<Torsion*, TorsionDataSet> torsionDataSets; |
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> |
map<Inversion*, InversionDataSet> inversionDataSets; |
| 109 |
> |
vector<pair<int, int> > neighborList; |
| 110 |
> |
|
| 111 |
> |
vector<RealType> vdwScale_; |
| 112 |
> |
vector<RealType> electrostaticScale_; |
| 113 |
> |
|
| 114 |
|
Mat3x3d tau; |
| 94 |
– |
|
| 95 |
– |
}; |
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|
|
| 116 |
< |
} //end namespace oopse |
| 116 |
> |
}; |
| 117 |
> |
} |
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|
#endif //BRAINS_FORCEMANAGER_HPP |
