| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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 |
/** |
| 44 |
* @file Integrator.hpp |
| 45 |
* @author tlin |
| 46 |
* @date 11/08/2004 |
| 47 |
* @time 13:25am |
| 48 |
* @version 1.0 |
| 49 |
*/ |
| 50 |
|
| 51 |
#ifndef INTEGRATORS_INTEGRATOR_HPP |
| 52 |
#define INTEGRATORS_INTEGRATOR_HPP |
| 53 |
|
| 54 |
#include "brains/ForceManager.hpp" |
| 55 |
#include "restraints/ThermoIntegrationForceManager.hpp" |
| 56 |
#include "io/DumpWriter.hpp" |
| 57 |
#include "io/StatWriter.hpp" |
| 58 |
#include "integrators/Velocitizer.hpp" |
| 59 |
#include "integrators/RNEMD.hpp" |
| 60 |
|
| 61 |
namespace OpenMD { |
| 62 |
|
| 63 |
|
| 64 |
/** |
| 65 |
* @class Integrator Integrator.hpp "integrators/Integrator.hpp" |
| 66 |
* @brief Base class of Integrator |
| 67 |
* @todo document |
| 68 |
*/ |
| 69 |
class Integrator { |
| 70 |
public: |
| 71 |
|
| 72 |
virtual ~Integrator(); |
| 73 |
|
| 74 |
//avoid public virtual function |
| 75 |
void integrate() { |
| 76 |
doIntegrate(); |
| 77 |
} |
| 78 |
|
| 79 |
void update() { |
| 80 |
doUpdate(); |
| 81 |
} |
| 82 |
|
| 83 |
void setForceManager(ForceManager* forceMan) { |
| 84 |
|
| 85 |
if (forceMan_ != forceMan && forceMan_ != NULL) { |
| 86 |
delete forceMan_; |
| 87 |
} |
| 88 |
forceMan_ = forceMan; |
| 89 |
} |
| 90 |
|
| 91 |
void setVelocitizer(Velocitizer* velocitizer) { |
| 92 |
if (velocitizer_ != velocitizer && velocitizer_ != NULL) { |
| 93 |
delete velocitizer_; |
| 94 |
} |
| 95 |
velocitizer_ = velocitizer; |
| 96 |
} |
| 97 |
|
| 98 |
void setRNEMD(RNEMD* rnemd) { |
| 99 |
if (rnemd_ != rnemd && rnemd_ != NULL) { |
| 100 |
delete rnemd_; |
| 101 |
} |
| 102 |
rnemd_ = rnemd; |
| 103 |
} |
| 104 |
|
| 105 |
protected: |
| 106 |
|
| 107 |
Integrator(SimInfo* info); |
| 108 |
|
| 109 |
virtual void doIntegrate() = 0; |
| 110 |
|
| 111 |
virtual void doUpdate() {} |
| 112 |
|
| 113 |
void saveConservedQuantity() { |
| 114 |
currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity(); |
| 115 |
} |
| 116 |
|
| 117 |
SimInfo* info_; |
| 118 |
Globals* simParams; |
| 119 |
ForceManager* forceMan_; |
| 120 |
bool needPotential; |
| 121 |
bool needStress; |
| 122 |
bool needReset; |
| 123 |
Velocitizer* velocitizer_; |
| 124 |
RNEMD* rnemd_; |
| 125 |
bool needVelocityScaling; |
| 126 |
RealType targetScalingTemp; |
| 127 |
|
| 128 |
bool useRNEMD; |
| 129 |
|
| 130 |
DumpWriter* dumpWriter; |
| 131 |
StatWriter* statWriter; |
| 132 |
Thermo thermo; |
| 133 |
|
| 134 |
RealType runTime; |
| 135 |
RealType sampleTime; |
| 136 |
RealType statusTime; |
| 137 |
RealType thermalTime; |
| 138 |
RealType resetTime; |
| 139 |
RealType RNEMD_exchangeTime; |
| 140 |
RealType dt; |
| 141 |
|
| 142 |
Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change |
| 143 |
|
| 144 |
|
| 145 |
private: |
| 146 |
|
| 147 |
virtual RealType calcConservedQuantity() = 0; |
| 148 |
|
| 149 |
virtual DumpWriter* createDumpWriter() = 0; |
| 150 |
|
| 151 |
virtual StatWriter* createStatWriter() = 0; |
| 152 |
}; |
| 153 |
|
| 154 |
|
| 155 |
} |
| 156 |
#endif //INTEGRATORS_INTEGRATOR_HPP |
