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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 |
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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 |
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* work. Good starting points are: |
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* |
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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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< |
#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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/** @todo need refactorying */ |
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const int MIN_LSERROR = -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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double dotProduct(const std::vector<double>& v1, const std::vector<double>& v2); |
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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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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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virtual int doLineSearch(std::vector<double>& direction, double stepSize); |
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> |
virtual int doLineSearch(std::vector<RealType>& direction, RealType stepSize); |
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|
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virtual int checkConvg() = 0; |
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|
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void setVerbose(bool verbose) { bVerbose = verbose;} |
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|
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//get and set the coordinate |
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std::vector<double> getX() { return curX; } |
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void setX(std::vector<double>& x); |
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std::vector<RealType> getX() { return curX; } |
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void setX(std::vector<RealType>& x); |
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|
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//get and set the value of object function |
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double getF() { return curF; } |
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void setF(double f) { curF = f; } |
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> |
RealType getF() { return curF; } |
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> |
void setF(RealType f) { curF = f; } |
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|
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std::vector<double> getG() { return curG; } |
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void setG(std::vector<double>& g); |
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> |
std::vector<RealType> getG() { return curG; } |
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> |
void setG(std::vector<RealType>& g); |
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|
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//get and set the gradient |
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std::vector<double> getGrad() { return curG; } |
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void setGrad(std::vector<double>& g) { curG = g; } |
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> |
std::vector<RealType> getGrad() { return curG; } |
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> |
void setGrad(std::vector<RealType>& g) { curG = g; } |
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|
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//interal function to evaluate the energy and gradient in OOPSE |
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void calcEnergyGradient(std::vector<double>& x, std::vector<double>& grad, double& |
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> |
//interal function to evaluate the energy and gradient in OpenMD |
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> |
void calcEnergyGradient(std::vector<RealType>& x, std::vector<RealType>& grad, RealType& |
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energy, int& status); |
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|
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//calculate the value of object function |
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virtual void calcF(); |
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< |
virtual void calcF(std::vector<double>& x, double&f, int& status); |
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> |
virtual void calcF(std::vector<RealType>& x, RealType&f, int& status); |
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|
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//calculate the gradient |
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virtual void calcG(); |
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< |
virtual void calcG(std::vector<double>& x, std::vector<double>& g, double& f, int& status); |
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> |
virtual void calcG(std::vector<RealType>& x, std::vector<RealType>& g, RealType& f, int& status); |
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|
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|
//calculate the hessian |
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//virtual void calcH(int& status); |
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< |
//virtual void calcH(vector<double>& x, std::vector<dobule>& g, SymMatrix& h, int& status); |
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> |
//virtual void calcH(vector<RealType>& x, std::vector<dobule>& g, SymMatrix& h, int& status); |
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|
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friend std::ostream& operator<<(std::ostream& os, const Minimizer& minimizer); |
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|
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protected: |
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|
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// transfrom cartesian and rotational coordinates into minimization coordinates |
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std::vector<double> getCoor(); |
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> |
std::vector<RealType> getCoor(); |
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|
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// transfrom minimization coordinates into cartesian and rotational coordinates |
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< |
void setCoor(std::vector<double>& x); |
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> |
void setCoor(std::vector<RealType>& x); |
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|
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|
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|
|
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//remove the force component along the bond direction |
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int shakeF() { return 0;} |
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|
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< |
double calcPotential(); |
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> |
RealType calcPotential(); |
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|
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SimInfo* info; |
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|
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int egEvalStatus; |
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|
|
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//initial coordinates |
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//vector<double> initX; |
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> |
//vector<RealType> initX; |
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|
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//current value of the function |
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double curF; |
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> |
RealType curF; |
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|
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// current coordinates |
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std::vector<double> curX; |
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> |
std::vector<RealType> curX; |
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|
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//gradient at curent coordinates |
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std::vector<double> curG; |
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std::vector<RealType> curG; |
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|
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//hessian at current coordinates |
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//SymMatrix curH; |
