| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 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 |
< |
* |
| 18 |
< |
* 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 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* 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, 24107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 53 |
|
|
| 54 |
|
#include "brains/SimInfo.hpp" |
| 55 |
|
#include "primitives/Molecule.hpp" |
| 56 |
< |
namespace oopse { |
| 56 |
> |
#include "nonbonded/Cutoffs.hpp" |
| 57 |
> |
#include "nonbonded/SwitchingFunction.hpp" |
| 58 |
> |
#include "nonbonded/InteractionManager.hpp" |
| 59 |
> |
#include "perturbations/Perturbation.hpp" |
| 60 |
> |
#include "parallel/ForceDecomposition.hpp" |
| 61 |
> |
|
| 62 |
> |
#define PREPAIR_LOOP 0 |
| 63 |
> |
#define PAIR_LOOP 1 |
| 64 |
> |
|
| 65 |
> |
using namespace std; |
| 66 |
> |
namespace OpenMD { |
| 67 |
|
/** |
| 68 |
|
* @class ForceManager ForceManager.hpp "brains/ForceManager.hpp" |
| 69 |
< |
* ForceManager is responsible for calculating the short range interactions (c++) and |
| 70 |
< |
* long range interactions(fortran). If fortran side is not setup before the force calculation, |
| 71 |
< |
* call SimInfo's update function to settle it down. |
| 72 |
< |
* @note the reason we delay fortran side's setup is that some applications (Dump2XYZ etc.) |
| 73 |
< |
* may not need force calculation, why bother? |
| 69 |
> |
* ForceManager is responsible for calculating both the short range |
| 70 |
> |
* (bonded) interactions and long range (non-bonded) interactions. |
| 71 |
> |
* |
| 72 |
> |
* @note the reason we delay some of the setup is that |
| 73 |
> |
* initialization must wait until after the force field has been |
| 74 |
> |
* parsed so that the atom types are known. |
| 75 |
|
*/ |
| 76 |
|
class ForceManager { |
| 77 |
|
|
| 78 |
|
public: |
| 79 |
< |
ForceManager(SimInfo * info) : info_(info) {} |
| 68 |
< |
|
| 79 |
> |
ForceManager(SimInfo * info); |
| 80 |
|
virtual ~ForceManager() {} |
| 81 |
+ |
virtual void calcForces(); |
| 82 |
+ |
void initialize(); |
| 83 |
|
|
| 84 |
< |
//public virtual function should be avoided |
| 85 |
< |
/**@todo need refactory */ |
| 86 |
< |
virtual void calcForces(bool needPotential, bool needStress); |
| 84 |
> |
protected: |
| 85 |
> |
bool initialized_; |
| 86 |
> |
bool doParticlePot_; |
| 87 |
> |
bool doHeatFlux_; |
| 88 |
|
|
| 89 |
< |
virtual void init() {} |
| 90 |
< |
protected: |
| 89 |
> |
virtual void setupCutoffs(); |
| 90 |
> |
virtual void preCalculation(); |
| 91 |
> |
virtual void shortRangeInteractions(); |
| 92 |
> |
virtual void longRangeInteractions(); |
| 93 |
> |
virtual void postCalculation(); |
| 94 |
|
|
| 95 |
< |
virtual void preCalculation(); |
| 96 |
< |
|
| 97 |
< |
virtual void calcShortRangeInteraction(); |
| 95 |
> |
SimInfo* info_; |
| 96 |
> |
ForceField* forceField_; |
| 97 |
> |
InteractionManager* interactionMan_; |
| 98 |
> |
ForceDecomposition* fDecomp_; |
| 99 |
> |
SwitchingFunction* switcher_; |
| 100 |
|
|
| 101 |
< |
virtual void calcLongRangeInteraction(bool needPotential, bool needStress); |
| 101 |
> |
SwitchingFunctionType sft_;/**< Type of switching function in use */ |
| 102 |
> |
RealType rCut_; /**< cutoff radius for non-bonded interactions */ |
| 103 |
> |
RealType rSwitch_; /**< inner radius of switching function */ |
| 104 |
> |
CutoffMethod cutoffMethod_;/**< Cutoff Method for most non-bonded interactions */ |
| 105 |
> |
CutoffPolicy cutoffPolicy_;/**< Cutoff Policy for non-bonded interactions */ |
| 106 |
|
|
| 107 |
< |
virtual void postCalculation(); |
| 108 |
< |
|
| 109 |
< |
SimInfo * info_; |
| 107 |
> |
map<Bend*, BendDataSet> bendDataSets; |
| 108 |
> |
map<Torsion*, TorsionDataSet> torsionDataSets; |
| 109 |
> |
map<Inversion*, InversionDataSet> inversionDataSets; |
| 110 |
> |
vector<pair<int, int> > neighborList; |
| 111 |
|
|
| 112 |
< |
std::map<Bend*, BendDataSet> bendDataSets; |
| 113 |
< |
std::map<Torsion*, TorsionDataSet> torsionDataSets; |
| 90 |
< |
|
| 91 |
< |
}; |
| 112 |
> |
vector<RealType> vdwScale_; |
| 113 |
> |
vector<RealType> electrostaticScale_; |
| 114 |
|
|
| 115 |
< |
} //end namespace oopse |
| 115 |
> |
Mat3x3d stressTensor; |
| 116 |
> |
|
| 117 |
> |
vector<Perturbation*> perturbations_; |
| 118 |
> |
}; |
| 119 |
> |
} |
| 120 |
|
#endif //BRAINS_FORCEMANAGER_HPP |
