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HarmonicBondForce.h
1 #ifndef OPENMM_HARMONICBONDFORCE_H_
2 #define OPENMM_HARMONICBONDFORCE_H_
3 
4 /* -------------------------------------------------------------------------- *
5  * OpenMM *
6  * -------------------------------------------------------------------------- *
7  * This is part of the OpenMM molecular simulation toolkit originating from *
8  * Simbios, the NIH National Center for Physics-Based Simulation of *
9  * Biological Structures at Stanford, funded under the NIH Roadmap for *
10  * Medical Research, grant U54 GM072970. See https://simtk.org. *
11  * *
12  * Portions copyright (c) 2008-2012 Stanford University and the Authors. *
13  * Authors: Peter Eastman *
14  * Contributors: *
15  * *
16  * Permission is hereby granted, free of charge, to any person obtaining a *
17  * copy of this software and associated documentation files (the "Software"), *
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21  * Software is furnished to do so, subject to the following conditions: *
22  * *
23  * The above copyright notice and this permission notice shall be included in *
24  * all copies or substantial portions of the Software. *
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26  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
27  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
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29  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
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31  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
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33  * -------------------------------------------------------------------------- */
34 
35 #include "Force.h"
36 #include "Vec3.h"
37 #include <map>
38 #include <vector>
39 #include "internal/windowsExport.h"
40 
41 namespace OpenMM {
42 
50 class OPENMM_EXPORT HarmonicBondForce : public Force {
51 public:
59  int getNumBonds() const {
60  return bonds.size();
61  }
71  int addBond(int particle1, int particle2, double length, double k);
81  void getBondParameters(int index, int& particle1, int& particle2, double& length, double& k) const;
91  void setBondParameters(int index, int particle1, int particle2, double length, double k);
101  void updateParametersInContext(Context& context);
109  return false;
110  }
111 protected:
112  ForceImpl* createImpl() const;
113 private:
114  class BondInfo;
115  std::vector<BondInfo> bonds;
116 };
117 
122 class HarmonicBondForce::BondInfo {
123 public:
124  int particle1, particle2;
125  double length, k;
126  BondInfo() {
127  particle1 = particle2 = -1;
128  length = k = 0.0;
129  }
130  BondInfo(int particle1, int particle2, double length, double k) :
131  particle1(particle1), particle2(particle2), length(length), k(k) {
132  }
133 };
134 
135 } // namespace OpenMM
136 
137 #endif /*OPENMM_HARMONICBONDFORCE_H_*/
A Context stores the complete state of a simulation.
Definition: Context.h:67
bool usesPeriodicBoundaryConditions() const
Returns whether or not this force makes use of periodic boundary conditions.
Definition: HarmonicBondForce.h:108
This class implements an interaction between pairs of particles that varies harmonically with the dis...
Definition: HarmonicBondForce.h:50
Force objects apply forces to the particles in a System, or alter their behavior in other ways...
Definition: Force.h:65
int getNumBonds() const
Get the number of harmonic bond stretch terms in the potential function.
Definition: HarmonicBondForce.h:59
Definition: AndersenThermostat.h:40