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Commit f7f79b04 authored by Mark Friedrichs's avatar Mark Friedrichs
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Initial Amoeba

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plugins/amoeba/openmmapi/include/internal/AmoebaHarmonicBondForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_HARMONIC_BOND_FORCE_IMPL_H_
#define OPENMM_AMOEBA_HARMONIC_BOND_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaHarmonicBondForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaHarmonicBondForce.
*/
class AmoebaHarmonicBondForceImpl : public ForceImpl {
public:
AmoebaHarmonicBondForceImpl(AmoebaHarmonicBondForce& owner);
~AmoebaHarmonicBondForceImpl();
void initialize(ContextImpl& context);
AmoebaHarmonicBondForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaHarmonicBondForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_HARMONIC_BOND_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaHarmonicInPlaneAngleForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_IMPL_H_
#define OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaHarmonicInPlaneAngleForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaHarmonicInPlaneAngleForce.
*/
class AmoebaHarmonicInPlaneAngleForceImpl : public ForceImpl {
public:
AmoebaHarmonicInPlaneAngleForceImpl(AmoebaHarmonicInPlaneAngleForce& owner);
~AmoebaHarmonicInPlaneAngleForceImpl();
void initialize(ContextImpl& context);
AmoebaHarmonicInPlaneAngleForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaHarmonicInPlaneAngleForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaMultipoleForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_MULTIPOLE_FORCE_IMPL_H_
#define OPENMM_AMOEBA_MULTIPOLE_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaMultipoleForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaMultipoleForce.
*/
class AmoebaMultipoleForceImpl : public ForceImpl {
public:
AmoebaMultipoleForceImpl(AmoebaMultipoleForce& owner);
~AmoebaMultipoleForceImpl();
void initialize(ContextImpl& context);
AmoebaMultipoleForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaMultipoleForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_MULTIPOLE_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaOutOfPlaneBendForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_OUT_OF_PLANE_BEND_FORCE_IMPL_H_
#define OPENMM_AMOEBA_OUT_OF_PLANE_BEND_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaOutOfPlaneBendForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaOutOfPlaneBendForce.
*/
class AmoebaOutOfPlaneBendForceImpl : public ForceImpl {
public:
AmoebaOutOfPlaneBendForceImpl(AmoebaOutOfPlaneBendForce& owner);
~AmoebaOutOfPlaneBendForceImpl();
void initialize(ContextImpl& context);
AmoebaOutOfPlaneBendForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaOutOfPlaneBendForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_OUT_OF_PLANE_BEND_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaPiTorsionForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_PI_TORSION_FORCE_IMPL_H_
#define OPENMM_AMOEBA_PI_TORSION_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaPiTorsionForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaPiTorsionForce.
*/
class AmoebaPiTorsionForceImpl : public ForceImpl {
public:
AmoebaPiTorsionForceImpl(AmoebaPiTorsionForce& owner);
~AmoebaPiTorsionForceImpl();
void initialize(ContextImpl& context);
AmoebaPiTorsionForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaPiTorsionForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_PI_TORSION_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaSASAForceImpl.h 0 → 100644
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_SASA_FORCE_FIELD_IMPL_H_
#define OPENMM_AMOEBA_SASA_FORCE_FIELD_IMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaSASAForce.h"
#include "openmm/Kernel.h"
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaSASAForce.
*/
class AmoebaSASAForceImpl : public ForceImpl {
public:
AmoebaSASAForceImpl(AmoebaSASAForce& owner);
void initialize(ContextImpl& context);
AmoebaSASAForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context);
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaSASAForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_SASA_FORCE_FIELD_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaStretchBendForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_STRETCH_BEND_FORCE_IMPL_H_
#define OPENMM_AMOEBA_STRETCH_BEND_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaStretchBendForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaStretchBendForce.
*/
class AmoebaStretchBendForceImpl : public ForceImpl {
public:
AmoebaStretchBendForceImpl(AmoebaStretchBendForce& owner);
~AmoebaStretchBendForceImpl();
void initialize(ContextImpl& context);
AmoebaStretchBendForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaStretchBendForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_STRETCH_BEND_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaTorsionForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_TORSION_FORCE_IMPL_H_
#define OPENMM_AMOEBA_TORSION_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaTorsionForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <map>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaTorsionForce.
*/
class AmoebaTorsionForceImpl : public ForceImpl {
public:
AmoebaTorsionForceImpl(AmoebaTorsionForce& owner);
~AmoebaTorsionForceImpl();
void initialize(ContextImpl& context);
AmoebaTorsionForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaTorsionForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_TORSION_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaTorsionTorsionForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_TORSION_TORSION_FORCE_IMPL_H_
#define OPENMM_AMOEBA_TORSION_TORSION_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaTorsionTorsionForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaTorsionTorsionForce.
*/
class AmoebaTorsionTorsionForceImpl : public ForceImpl {
public:
AmoebaTorsionTorsionForceImpl(AmoebaTorsionTorsionForce& owner);
~AmoebaTorsionTorsionForceImpl();
void initialize(ContextImpl& context);
AmoebaTorsionTorsionForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaTorsionTorsionForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_TORSION_TORSION_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaVdwForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_VDW_FORCE_IMPL_H_
#define OPENMM_AMOEBA_VDW_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaVdwForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaVdwForce.
*/
class AmoebaVdwForceImpl : public ForceImpl {
public:
AmoebaVdwForceImpl(AmoebaVdwForce& owner);
~AmoebaVdwForceImpl();
void initialize(ContextImpl& context);
AmoebaVdwForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaVdwForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_VDW_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/internal/AmoebaWcaDispersionForceImpl.h 0 → 100755
View file @ f7f79b04
#ifndef OPENMM_AMOEBA_WCA_DISPERSION_FORCE_IMPL_H_
#define OPENMM_AMOEBA_WCA_DISPERSION_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "AmoebaWcaDispersionForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
#include <string>
namespace OpenMM {
/**
* This is the internal implementation of AmoebaWcaDispersionForce.
*/
class AmoebaWcaDispersionForceImpl : public ForceImpl {
public:
AmoebaWcaDispersionForceImpl(AmoebaWcaDispersionForce& owner);
~AmoebaWcaDispersionForceImpl();
void initialize(ContextImpl& context);
AmoebaWcaDispersionForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
// This force field doesn't update the state directly.
}
void calcForces(ContextImpl& context );
double calcEnergy(ContextImpl& context);
std::map<std::string, double> getDefaultParameters() {
return std::map<std::string, double>(); // This force field doesn't define any parameters.
}
std::vector<std::string> getKernelNames();
private:
AmoebaWcaDispersionForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_WCA_DISPERSION_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForce.cpp 0 → 100644
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "AmoebaGeneralizedKirkwoodForce.h"
#include "internal/AmoebaGeneralizedKirkwoodForceImpl.h"
using namespace OpenMM;
AmoebaGeneralizedKirkwoodForce::AmoebaGeneralizedKirkwoodForce() : nonbondedMethod(NoCutoff), cutoffDistance(1.0), solventDielectric(78.3), soluteDielectric(1.0),
dielectricOffset(0.009), includeCavityTerm(1), probeRadius(0.14) {
surfaceAreaFactor = -6.0* 3.1415926535*0.0216*1000.0*0.4184;
}
int AmoebaGeneralizedKirkwoodForce::addParticle(double charge, double radius, double scalingFactor) {
particles.push_back(ParticleInfo(charge, radius, scalingFactor));
return particles.size()-1;
}
void AmoebaGeneralizedKirkwoodForce::getParticleParameters(int index, double& charge, double& radius, double& scalingFactor) const {
charge = particles[index].charge;
radius = particles[index].radius;
scalingFactor = particles[index].scalingFactor;
}
void AmoebaGeneralizedKirkwoodForce::setParticleParameters(int index, double charge, double radius, double scalingFactor) {
particles[index].charge = charge;
particles[index].radius = radius;
particles[index].scalingFactor = scalingFactor;
}
AmoebaGeneralizedKirkwoodForce::NonbondedMethod AmoebaGeneralizedKirkwoodForce::getNonbondedMethod() const {
return nonbondedMethod;
}
void AmoebaGeneralizedKirkwoodForce::setNonbondedMethod(NonbondedMethod method) {
nonbondedMethod = method;
}
double AmoebaGeneralizedKirkwoodForce::getCutoffDistance() const {
return cutoffDistance;
}
void AmoebaGeneralizedKirkwoodForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
double AmoebaGeneralizedKirkwoodForce::getDielectricOffset() const {
return dielectricOffset;
}
void AmoebaGeneralizedKirkwoodForce::setDielectricOffset(double inputDielectricOffset ) {
dielectricOffset = inputDielectricOffset;
}
int AmoebaGeneralizedKirkwoodForce::getIncludeCavityTerm() const {
return includeCavityTerm;
}
void AmoebaGeneralizedKirkwoodForce::setIncludeCavityTerm(int inputIncludeCavityTerm ) {
includeCavityTerm = inputIncludeCavityTerm;
}
double AmoebaGeneralizedKirkwoodForce::getProbeRadius() const {
return probeRadius;
}
void AmoebaGeneralizedKirkwoodForce::setProbeRadius(double inputProbeRadius ) {
probeRadius = inputProbeRadius;
}
double AmoebaGeneralizedKirkwoodForce::getSurfaceAreaFactor() const {
return surfaceAreaFactor;
}
void AmoebaGeneralizedKirkwoodForce::setSurfaceAreaFactor(double inputSurfaceAreaFactor ) {
surfaceAreaFactor = inputSurfaceAreaFactor;
}
ForceImpl* AmoebaGeneralizedKirkwoodForce::createImpl() {
return new AmoebaGeneralizedKirkwoodForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaGeneralizedKirkwoodForceImpl.cpp 0 → 100644
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "internal/AmoebaGeneralizedKirkwoodForceImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "amoebaKernels.h"
using namespace OpenMM;
using std::vector;
AmoebaGeneralizedKirkwoodForceImpl::AmoebaGeneralizedKirkwoodForceImpl(AmoebaGeneralizedKirkwoodForce& owner) : owner(owner) {
}
void AmoebaGeneralizedKirkwoodForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaGeneralizedKirkwoodForceKernel::Name(), context);
if (owner.getNumParticles() != context.getSystem().getNumParticles())
throw OpenMMException("AmoebaGeneralizedKirkwoodForce must have exactly as many particles as the System it belongs to.");
dynamic_cast<CalcAmoebaGeneralizedKirkwoodForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void AmoebaGeneralizedKirkwoodForceImpl::calcForces(ContextImpl& context) {
dynamic_cast<CalcAmoebaGeneralizedKirkwoodForceKernel&>(kernel.getImpl()).executeForces(context);
}
double AmoebaGeneralizedKirkwoodForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcAmoebaGeneralizedKirkwoodForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
std::vector<std::string> AmoebaGeneralizedKirkwoodForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcAmoebaGeneralizedKirkwoodForceKernel::Name());
return names;
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicAngleForce.cpp 0 → 100755
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "AmoebaHarmonicAngleForce.h"
#include "internal/AmoebaHarmonicAngleForceImpl.h"
using namespace OpenMM;
AmoebaHarmonicAngleForce::AmoebaHarmonicAngleForce() {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
int AmoebaHarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double length, double quadraticK) {
angles.push_back(AngleInfo(particle1, particle2, particle3, length, quadraticK));
return angles.size()-1;
}
void AmoebaHarmonicAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3,
double& length, double& quadraticK ) const {
particle1 = angles[index].particle1;
particle2 = angles[index].particle2;
particle3 = angles[index].particle3;
length = angles[index].length;
quadraticK = angles[index].quadraticK;
}
void AmoebaHarmonicAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3,
double length, double quadraticK ) {
angles[index].particle1 = particle1;
angles[index].particle2 = particle2;
angles[index].particle3 = particle3;
angles[index].length = length;
angles[index].quadraticK = quadraticK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAngleCubic( void ) const {
return _globalCubicK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAngleCubic(double cubicK ) {
_globalCubicK = cubicK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAngleQuartic( void ) const {
return _globalQuarticK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAngleQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAnglePentic( void ) const {
return _globalPenticK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAnglePentic(double penticK ) {
_globalPenticK = penticK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAngleSextic( void ) const {
return _globalSexticK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAngleSextic(double sexticK ) {
_globalSexticK = sexticK;
}
ForceImpl* AmoebaHarmonicAngleForce::createImpl() {
return new AmoebaHarmonicAngleForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicAngleForceImpl.cpp 0 → 100755
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* Amoeba OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ContextImpl.h"
#include "internal/AmoebaHarmonicAngleForceImpl.h"
#include "amoebaKernels.h"
using namespace OpenMM;
using std::pair;
using std::vector;
using std::set;
AmoebaHarmonicAngleForceImpl::AmoebaHarmonicAngleForceImpl(AmoebaHarmonicAngleForce& owner) : owner(owner) {
}
AmoebaHarmonicAngleForceImpl::~AmoebaHarmonicAngleForceImpl() {
}
void AmoebaHarmonicAngleForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaHarmonicAngleForceKernel::Name(), context);
dynamic_cast<CalcAmoebaHarmonicAngleForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void AmoebaHarmonicAngleForceImpl::calcForces(ContextImpl& context ) {
dynamic_cast<CalcAmoebaHarmonicAngleForceKernel&>(kernel.getImpl()).executeForces(context);
}
double AmoebaHarmonicAngleForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcAmoebaHarmonicAngleForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
std::vector<std::string> AmoebaHarmonicAngleForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcAmoebaHarmonicAngleForceKernel::Name());
return names;
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicBondForce.cpp 0 → 100755
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "AmoebaHarmonicBondForce.h"
#include "internal/AmoebaHarmonicBondForceImpl.h"
using namespace OpenMM;
const double AmoebaHarmonicBondForce::DEFAULT_GLOBAL_K = -1234.567891234;
AmoebaHarmonicBondForce::AmoebaHarmonicBondForce() {
_globalCubicK = _globalQuarticK = 0.0;
}
int AmoebaHarmonicBondForce::addBond(int particle1, int particle2, double length, double quadraticK, double cubicK, double quarticK) {
bonds.push_back(BondInfo(particle1, particle2, length, quadraticK, cubicK, quarticK));
return bonds.size()-1;
}
void AmoebaHarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK, double& cubicK, double& quarticK ) const {
particle1 = bonds[index].particle1;
particle2 = bonds[index].particle2;
length = bonds[index].length;
quadraticK = bonds[index].quadraticK;
cubicK = bonds[index].cubicK == DEFAULT_GLOBAL_K ? _globalCubicK : bonds[index].cubicK;
quarticK = bonds[index].quarticK == DEFAULT_GLOBAL_K ? _globalQuarticK : bonds[index].quarticK;
}
void AmoebaHarmonicBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK, double cubicK, double quarticK ) {
bonds[index].particle1 = particle1;
bonds[index].particle2 = particle2;
bonds[index].length = length;
bonds[index].quadraticK = quadraticK;
bonds[index].cubicK = cubicK;
bonds[index].quarticK = quarticK;
}
void AmoebaHarmonicBondForce::setAmoebaGlobalHarmonicBondCubic(double cubicK ) {
_globalCubicK = cubicK;
}
void AmoebaHarmonicBondForce::setAmoebaGlobalHarmonicBondQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaHarmonicBondForce::getAmoebaGlobalHarmonicBondCubic( void ) const {
return _globalCubicK;
}
double AmoebaHarmonicBondForce::getAmoebaGlobalHarmonicBondQuartic( void ) const {
return _globalQuarticK;
}
ForceImpl* AmoebaHarmonicBondForce::createImpl() {
return new AmoebaHarmonicBondForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicBondForceImpl.cpp 0 → 100755
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/internal/ContextImpl.h"
#include "internal/AmoebaHarmonicBondForceImpl.h"
#include "amoebaKernels.h"
#include "openmm/Platform.h"
using namespace OpenMM;
using std::pair;
using std::vector;
using std::set;
AmoebaHarmonicBondForceImpl::AmoebaHarmonicBondForceImpl(AmoebaHarmonicBondForce& owner) : owner(owner) {
}
AmoebaHarmonicBondForceImpl::~AmoebaHarmonicBondForceImpl() {
}
void AmoebaHarmonicBondForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaHarmonicBondForceKernel::Name(), context);
dynamic_cast<CalcAmoebaHarmonicBondForceKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void AmoebaHarmonicBondForceImpl::calcForces(ContextImpl& context ) {
dynamic_cast<CalcAmoebaHarmonicBondForceKernel&>(kernel.getImpl()).executeForces(context);
}
double AmoebaHarmonicBondForceImpl::calcEnergy(ContextImpl& context) {
return dynamic_cast<CalcAmoebaHarmonicBondForceKernel&>(kernel.getImpl()).executeEnergy(context);
}
std::vector<std::string> AmoebaHarmonicBondForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcAmoebaHarmonicBondForceKernel::Name());
return names;
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicInPlaneAngleForce.cpp 0 → 100755
View file @ f7f79b04
/* -------------------------------------------------------------------------- *
* AmoebaOpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2009 Stanford University and the Authors. *
* Authors: *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "AmoebaHarmonicInPlaneAngleForce.h"
#include "internal/AmoebaHarmonicInPlaneAngleForceImpl.h"
using namespace OpenMM;
AmoebaHarmonicInPlaneAngleForce::AmoebaHarmonicInPlaneAngleForce() {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
int AmoebaHarmonicInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4, double length, double quadraticK ) {
angles.push_back(AngleInfo(particle1, particle2, particle3, particle4, length, quadraticK ));
return angles.size()-1;
}
void AmoebaHarmonicInPlaneAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
double& length, double& quadraticK ) const {
particle1 = angles[index].particle1;
particle2 = angles[index].particle2;
particle3 = angles[index].particle3;
particle4 = angles[index].particle4;
length = angles[index].length;
quadraticK = angles[index].quadraticK;
}
void AmoebaHarmonicInPlaneAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4,
double length, double quadraticK ) {
angles[index].particle1 = particle1;
angles[index].particle2 = particle2;
angles[index].particle3 = particle3;
angles[index].particle4 = particle4;
angles[index].length = length;
angles[index].quadraticK = quadraticK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAngleCubic(double cubicK ) {
_globalCubicK = cubicK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAngleQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAngleCubic( void ) const {
return _globalCubicK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAngleQuartic( void ) const {
return _globalQuarticK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAnglePentic(double cubicK ) {
_globalPenticK = cubicK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAngleSextic(double quarticK ) {
_globalSexticK = quarticK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAnglePentic( void ) const {
return _globalPenticK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAngleSextic( void ) const {
return _globalSexticK;
}
ForceImpl* AmoebaHarmonicInPlaneAngleForce::createImpl() {
return new AmoebaHarmonicInPlaneAngleForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaMultipoleForce.cpp 0 → 100755
View file @ f7f79b04
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