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# AmoebaBondForce.h

    00001 #ifndef OPENMM_AMOEBA_BOND_FORCE_H_
    00002 #define OPENMM_AMOEBA_BOND_FORCE_H_
    00003
    00004 /* -------------------------------------------------------------------------- *
    00005  *                              OpenMMAmoeba                                  *
    00006  * -------------------------------------------------------------------------- *
    00007  * This is part of the OpenMM molecular simulation toolkit originating from   *
    00008  * Simbios, the NIH National Center for Physics-Based Simulation of           *
    00009  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
    00010  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
    00011  *                                                                            *
    00012  * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
    00013  * Authors: Mark Friedrichs, Peter Eastman                                    *
    00014  * Contributors:                                                              *
    00015  *                                                                            *
    00016  * Permission is hereby granted, free of charge, to any person obtaining a    *
    00017  * copy of this software and associated documentation files (the "Software"), *
    00018  * to deal in the Software without restriction, including without limitation  *
    00019  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
    00020  * and/or sell copies of the Software, and to permit persons to whom the      *
    00021  * Software is furnished to do so, subject to the following conditions:       *
    00022  *                                                                            *
    00023  * The above copyright notice and this permission notice shall be included in *
    00024  * all copies or substantial portions of the Software.                        *
    00025  *                                                                            *
    00026  * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
    00027  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
    00028  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
    00029  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
    00030  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
    00031  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
    00032  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
    00033  * -------------------------------------------------------------------------- */
    00034
    00035 #include "openmm/Force.h"
    00036 #include "openmm/Vec3.h"
    00037 #include "internal/windowsExportAmoeba.h"
    00038 #include <map>
    00039 #include <vector>
    00040
    00041 namespace OpenMM {
    00042
    00054 class OPENMM_EXPORT_AMOEBA AmoebaBondForce : public Force {
    00055
    00056 public:
    00057
    00061     AmoebaBondForce();
    00065     int getNumBonds() const {
    00066         return bonds.size();
    00067     }
    00068
    00074     void setAmoebaGlobalBondCubic( double cubicK );
    00075
    00081     double getAmoebaGlobalBondCubic( void ) const;
    00082
    00088     void setAmoebaGlobalBondQuartic( double quarticK );
    00089
    00095     double getAmoebaGlobalBondQuartic( void ) const;
    00096
    00107     int addBond(int particle1, int particle2, double length, double quadraticK );
    00108
    00119     void getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const;
    00120
    00130     void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK );
    00140     void updateParametersInContext(Context& context);
    00141
    00142 protected:
    00143     double _globalQuarticK, _globalCubicK;
    00144     ForceImpl* createImpl() const;
    00145 private:
    00146     class BondInfo;
    00147     std::vector<BondInfo> bonds;
    00148 };
    00149
    00154 class AmoebaBondForce::BondInfo {
    00155 public:
    00156     int particle1, particle2;
    00157     double length, quadraticK;
    00158     BondInfo() {
    00159         particle1 = particle2    = -1;
    00160         length    = quadraticK   = 0.0;
    00161     }
    00162     BondInfo(int particle1, int particle2, double length, double  quadraticK ) :
    00163         particle1(particle1), particle2(particle2), length(length), quadraticK(quadraticK) {
    00164     }
    00165 };
    00166
    00167 } // namespace OpenMM
    00168
    00169 #endif /*OPENMM_AMOEBA_BOND_FORCE_H_*/