| 6 |
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* redistribute this software in source and binary code form, provided |
| 7 |
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* 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 |
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* distribution. |
| 28 |
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* 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). |
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*/ |
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|
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< |
#ifndef MINIMIZERS_OOPSEMINIMIZER_HPP |
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< |
#define MINIMIZERS_OOPSEMINIMIZER_HPP |
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> |
#ifndef MINIMIZERS_MINIMIZER_HPP |
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> |
#define MINIMIZERS_MINIMIZER_HPP |
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|
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#include <iostream> |
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|
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|
|
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// base class of minimizer |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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> |
|
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> |
/** minimizer stop codes */ |
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> |
enum{MIN_MAXITER, |
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> |
MIN_MAXEVAL, |
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> |
MIN_ETOL, |
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> |
MIN_FTOL, |
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> |
MIN_DOWNHILL, |
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> |
MIN_ZEROALPHA, |
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> |
MIN_ZEROFORCE, |
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> |
MIN_ZEROQUAD}; |
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> |
|
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> |
typedef int (*FnPtr)(std::vector<RealType> &, std::vector<RealType> &, RealType &); |
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|
|
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– |
/** @todo need refactorying */ |
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– |
const int MIN_LSERROR = -1; |
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– |
const int MIN_MAXITER = 0; |
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– |
const int MIN_CONVERGE = 1; |
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– |
|
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– |
const int CONVG_UNCONVG = 0; |
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– |
const int CONVG_FTOL = 1; |
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– |
const int CONVG_GTOL = 2; |
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– |
const int CONVG_ABSGTOL = 3; |
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– |
const int CONVG_STEPTOL = 4; |
| 66 |
– |
|
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– |
const int LS_SUCCEED =1; |
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– |
const int LS_ERROR = -1; |
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– |
|
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– |
/** @todo move to math module */ |
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– |
RealType dotProduct(const std::vector<RealType>& v1, const std::vector<RealType>& v2); |
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– |
|
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|
/** |
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* @class Minimizer |
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* base minimizer class |
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*/ |
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class Minimizer { |
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public: |
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– |
|
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|
Minimizer(SimInfo *rhs); |
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– |
|
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virtual ~Minimizer(); |
| 83 |
– |
|
| 84 |
– |
// |
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virtual void init() {} |
| 86 |
– |
|
| 78 |
|
//driver function of minimization method |
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virtual void minimize(); |
| 89 |
– |
|
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– |
// |
| 80 |
|
virtual int step() = 0; |
| 92 |
– |
|
| 93 |
– |
// |
| 81 |
|
virtual void prepareStep() {}; |
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|
|
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< |
//line search algorithm, for the time being, we use back track algorithm |
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> |
//line search algorithm, for the time being, we use a back track |
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> |
//algorithm |
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virtual int doLineSearch(std::vector<RealType>& direction, RealType stepSize); |
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+ |
virtual int checkConvergence() = 0; |
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|
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– |
virtual int checkConvg() = 0; |
| 100 |
– |
|
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|
//save the result when minimization method is done |
| 89 |
|
virtual void saveResult(){} |
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< |
|
| 90 |
> |
|
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|
//get the status of minimization |
| 92 |
< |
int getMinStatus() {return minStatus;} |
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> |
int getMinimizerStatus() {return minStatus;} |
| 93 |
|
|
| 94 |
|
// get the dimension of the model |
| 95 |
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int getDim() { return ndim; } |
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|
//get the name of minimizer method |
| 98 |
|
std::string getMinimizerName() { return minimizerName; } |
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|
|
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< |
//return number of current Iteration |
| 101 |
< |
int getCurIter() { return curIter; } |
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> |
//return number of the current Iteration |
| 101 |
> |
int getCurrentIteration() { return curIter; } |
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|
|
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|
// set the verbose mode of minimizer |
| 104 |
|
void setVerbose(bool verbose) { bVerbose = verbose;} |
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|
|
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< |
//get and set the coordinate |
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> |
//get and set the coordinates |
| 107 |
|
std::vector<RealType> getX() { return curX; } |
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|
void setX(std::vector<RealType>& x); |
| 109 |
|
|
| 118 |
|
std::vector<RealType> getGrad() { return curG; } |
| 119 |
|
void setGrad(std::vector<RealType>& g) { curG = g; } |
| 120 |
|
|
| 121 |
< |
//interal function to evaluate the energy and gradient in OOPSE |
| 135 |
< |
void calcEnergyGradient(std::vector<RealType>& x, std::vector<RealType>& grad, RealType& |
| 136 |
< |
energy, int& status); |
| 121 |
> |
void setGradientFunction(FnPtr efunc) { calcEnergyGradient = efunc; } |
| 122 |
|
|
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|
//calculate the value of object function |
| 124 |
|
virtual void calcF(); |
| 136 |
|
|
| 137 |
|
protected: |
| 138 |
|
|
| 139 |
+ |
typedef int (*FnPtr)(std::vector<RealType> &, std::vector<RealType> &, RealType &); |
| 140 |
+ |
FnPtr calcEnergyGradient; |
| 141 |
+ |
|
| 142 |
|
// transfrom cartesian and rotational coordinates into minimization coordinates |
| 143 |
|
std::vector<RealType> getCoor(); |
| 144 |
|
|
| 145 |
|
// transfrom minimization coordinates into cartesian and rotational coordinates |
| 146 |
|
void setCoor(std::vector<RealType>& x); |
| 147 |
|
|
| 160 |
– |
|
| 161 |
– |
|
| 148 |
|
//constraint the bonds; |
| 149 |
|
int shakeR() { return 0;} |
| 150 |
|
|
| 151 |
|
//remove the force component along the bond direction |
| 152 |
|
int shakeF() { return 0;} |
| 167 |
– |
|
| 153 |
|
RealType calcPotential(); |
| 154 |
|
|
| 155 |
|
SimInfo* info; |
| 156 |
< |
|
| 172 |
< |
ForceManager* forceMan; |
| 173 |
< |
|
| 156 |
> |
ForceManager* forceMan; |
| 157 |
|
//parameter set of minimization method |
| 158 |
|
MinimizerParameterSet* paramSet; |
| 159 |
|
|
| 193 |
|
//SymMatrix curH; |
| 194 |
|
|
| 195 |
|
private: |
| 196 |
< |
|
| 214 |
< |
//calculate the dimension od the model for minimization |
| 196 |
> |
//calculate the dimension of the model for minimization |
| 197 |
|
void calcDim(); |
| 216 |
– |
|
| 198 |
|
}; |
| 199 |
|
|
| 200 |
|
} |
