OpenMD 3.1
Molecular Dynamics in the Open
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PotentialEnergyObjectiveFunction.hpp
1/*
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32 * research, please cite the appropriate papers when you publish your
33 * work. Good starting points are:
34 *
35 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#ifndef OPTIMIZATION_POTENTIALENERGYOBJECTIVEFUNCTION_HPP
46#define OPTIMIZATION_POTENTIALENERGYOBJECTIVEFUNCTION_HPP
47
49#include "brains/Thermo.hpp"
50#include "constraints/Shake.hpp"
51#include "flucq/FluctuatingChargeConstraints.hpp"
53
54using namespace QuantLib;
55namespace OpenMD {
57 public:
59
60 RealType value(const DynamicVector<RealType>& x);
65
66 DynamicVector<RealType> setInitialCoords();
67
68 private:
69 // transform minimization coordinates into cartesian and
70 // rotational coordinates
71 void setCoor(const DynamicVector<RealType>& x) const;
72 // transform cartesian and rotational coordinates into minimization
73 // coordinates
74 void getGrad(DynamicVector<RealType>& grad);
75
76 SimInfo* info_ {nullptr};
77 ForceManager* forceMan_;
78 Shake* shake_;
79 FluctuatingChargeConstraints* fqConstraints_;
80 Thermo thermo;
81 bool hasFlucQ_;
82 int ndf_;
83
84#ifdef IS_MPI
85 int nproc_;
86 int myrank_;
87 std::vector<int> displacements_;
88#endif
89 };
90} // namespace OpenMD
91
92#endif
Optimization objective function class.
Dynamically-sized vector class.
ForceManager is responsible for calculating both the short range (bonded) interactions and long range...
RealType value(const DynamicVector< RealType > &x)
method to overload to compute the objective function value in x
void gradient(DynamicVector< RealType > &grad, const DynamicVector< RealType > &x)
method to overload to compute grad_f, the first derivative of
RealType valueAndGradient(DynamicVector< RealType > &grad, const DynamicVector< RealType > &x)
method to overload to compute grad_f, the first derivative
One of the heavy-weight classes of OpenMD, SimInfo maintains objects and variables relating to the cu...
Definition SimInfo.hpp:93
Objective function abstract class for optimization problem.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.