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Commit 74e2ca75 authored by Mark Friedrichs's avatar Mark Friedrichs
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Cleanup

parent fff7aa03
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Showing with 113 additions and 26 deletions
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -43,12 +43,13 @@ namespace OpenMM {
* <p>
* To use this class, create a AmoebaGeneralizedKirkwoodForce object, then call addParticle() once for each particle in the
* System to define its parameters. The number of particles for which you define GBSA parameters must
* be exactly equal to the number of particles in the System, or else an exception will be thrown when you
* be equal to the number of particles in the System, or else an exception will be thrown when you
* try to create a Context. After a particle has been added, you can modify its force field parameters
* by calling setParticleParameters().
*/
class OPENMM_EXPORT AmoebaGeneralizedKirkwoodForce : public Force {
public:
/*
......
plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicAngleForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -44,8 +44,10 @@ namespace OpenMM {
* a angle has been added, you can modify its force field parameters by calling setAngleParameters().
*/
class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
public:
/**
* Create a Amoeba HarmonicAngleForce.
*/
......@@ -124,8 +126,7 @@ public:
* @param quadratic k the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
* @return the index of the angle that was added
*/
int addAngle(int particle1, int particle2, int particle3, double length,
double quadraticK );
int addAngle(int particle1, int particle2, int particle3, double length, double quadraticK );
/**
* Get the force field parameters for a angle term.
......@@ -137,8 +138,7 @@ public:
* @param length the equilibrium angle, measured in radians
* @param quadratic k the quadratic harmonic force constant for the angle, measured in kJ/mol/radian^2
*/
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length,
double& quadraticK ) const;
void getAngleParameters(int index, int& particle1, int& particle2, int& particle3, double& length, double& quadraticK ) const;
/**
* Set the force field parameters for a angle term.
......
plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicBondForce.h
View file @ 74e2ca75
......@@ -34,9 +34,9 @@
#include "openmm/Force.h"
#include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h"
#include <map>
#include <vector>
#include "openmm/internal/windowsExport.h"
namespace OpenMM {
......@@ -46,8 +46,10 @@ namespace OpenMM {
* a bond has been added, you can modify its force field parameters by calling setBondParameters().
*/
class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force {
class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force {
public:
/**
* Create a Amoeba HarmonicBondForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicInPlaneAngleForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -45,8 +45,10 @@ namespace OpenMM {
* a angle has been added, you can modify its force field parameters by calling setAngleParameters().
*/
class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
public:
/**
* Create a Amoeba HarmonicAngleForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 74e2ca75
......@@ -48,14 +48,17 @@ namespace OpenMM {
*/
class OPENMM_EXPORT AmoebaMultipoleForce : public Force {
public:
enum AmoebaNonbondedMethod {
/**
* No cutoff is applied to nonbonded interactions. The full set of N^2 interactions is computed exactly.
* This necessarily means that periodic boundary conditions cannot be used. This is the default.
*/
NoCutoff = 0,
/**
* Periodic boundary conditions are used, and Particle-Mesh Ewald (PME) summation is used to compute the interaction of each particle
* with all periodic copies of every other particle.
......@@ -88,12 +91,12 @@ public:
}
/**
* Get the method used for handling long range nonbonded interactions.
* Get the method used for handling long-range nonbonded interactions.
*/
AmoebaNonbondedMethod getNonbondedMethod( void ) const;
/**
* Set the method used for handling long range nonbonded interactions.
* Set the method used for handling long-range nonbonded interactions.
*/
void setNonbondedMethod(AmoebaNonbondedMethod method);
......
plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -45,7 +45,9 @@ namespace OpenMM {
*/
class OPENMM_EXPORT AmoebaOutOfPlaneBendForce : public Force {
public:
/**
* Create a Amoeba OutOfPlaneBendForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -44,8 +44,10 @@ namespace OpenMM {
* a torsion has been added, you can modify its force field parameters by calling setPiTorsionParameters().
*/
class OPENMM_EXPORT AmoebaPiTorsionForce : public Force {
class OPENMM_EXPORT AmoebaPiTorsionForce : public Force {
public:
/**
* Create a Amoeba PiTorsionForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -44,8 +44,10 @@ namespace OpenMM {
* a stretchBend has been added, you can modify its force field parameters by calling setStretchBendParameters().
*/
class OPENMM_EXPORT AmoebaStretchBendForce : public Force {
class OPENMM_EXPORT AmoebaStretchBendForce : public Force {
public:
/**
* Create a Amoeba StretchBendForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionForce.h
View file @ 74e2ca75
......@@ -47,6 +47,7 @@ namespace OpenMM {
*/
class OPENMM_EXPORT AmoebaTorsionForce : public Force {
public:
static const unsigned int ParametersPerTorsion = 2;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaTorsionTorsionForce.h
View file @ 74e2ca75
......@@ -33,9 +33,10 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include "openmm/internal/windowsExport.h"
#include <vector>
#include <cmath>
#include "openmm/internal/windowsExport.h"
namespace OpenMM {
......@@ -158,7 +159,9 @@ private:
};
class AmoebaTorsionTorsionForce::TorsionTorsionInfo {
public:
int particle1, particle2, particle3, particle4, particle5;
int chiralCheckAtomIndex;
int gridIndex;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaUreyBradleyForce.h
View file @ 74e2ca75
......@@ -34,9 +34,10 @@
#include "openmm/Force.h"
#include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h"
#include <map>
#include <vector>
#include "openmm/internal/windowsExport.h"
namespace OpenMM {
......@@ -46,8 +47,10 @@ namespace OpenMM {
* a bond has been added, you can modify its force field parameters by calling setUreyBradleyParameters().
*/
class OPENMM_EXPORT AmoebaUreyBradleyForce : public Force {
class OPENMM_EXPORT AmoebaUreyBradleyForce : public Force {
public:
/**
* Create a Amoeba UreyBradleyForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -44,8 +44,10 @@ namespace OpenMM {
* a angle has been added, you can modify its force field parameters by calling setAngleParameters().
*/
class OPENMM_EXPORT AmoebaVdwForce : public Force {
class OPENMM_EXPORT AmoebaVdwForce : public Force {
public:
/**
* Create a Amoeba VdwForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h
View file @ 74e2ca75
......@@ -33,8 +33,8 @@
* -------------------------------------------------------------------------- */
#include "openmm/Force.h"
#include <vector>
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
......@@ -44,8 +44,10 @@ namespace OpenMM {
* a angle has been added, you can modify its force field parameters by calling setAngleParameters().
*/
class OPENMM_EXPORT AmoebaWcaDispersionForce : public Force {
class OPENMM_EXPORT AmoebaWcaDispersionForce : public Force {
public:
/**
* Create a Amoeba WcaDispersionForce.
*/
......
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ 74e2ca75
......@@ -47,12 +47,16 @@ namespace OpenMM {
* This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaHarmonicBondForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaHarmonicBondForce";
}
CalcAmoebaHarmonicBondForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -60,6 +64,7 @@ public:
* @param force the AmoebaHarmonicBondForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaHarmonicBondForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -69,16 +74,20 @@ public:
* @return the potential energy due to the force
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
class CalcAmoebaUreyBradleyForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaUreyBradleyForce";
}
CalcAmoebaUreyBradleyForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -86,6 +95,7 @@ public:
* @param force the AmoebaUreyBradleyForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaUreyBradleyForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -95,18 +105,23 @@ public:
* @return the potential energy due to the force
*/
virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
};
/**
* This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaHarmonicAngleForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaHarmonicAngleForce";
}
CalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -114,6 +129,7 @@ public:
* @param force the HarmonicAngleForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaHarmonicAngleForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -129,12 +145,16 @@ public:
* This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaHarmonicInPlaneAngleForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaHarmonicInPlaneAngleForce";
}
CalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -142,6 +162,7 @@ public:
* @param force the HarmonicInPlaneAngleForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -157,12 +178,16 @@ public:
* This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaTorsionForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaTorsionForce";
}
CalcAmoebaTorsionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -170,6 +195,7 @@ public:
* @param force the TorsionForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaTorsionForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -185,12 +211,16 @@ public:
* This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaPiTorsionForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaPiTorsionForce";
}
CalcAmoebaPiTorsionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -198,6 +228,7 @@ public:
* @param force the PiTorsionForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaPiTorsionForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -213,12 +244,16 @@ public:
* This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaStretchBendForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaStretchBendForce";
}
CalcAmoebaStretchBendForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -226,6 +261,7 @@ public:
* @param force the StretchBendForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaStretchBendForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -241,12 +277,16 @@ public:
* This kernel is invoked by AmoebaTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaOutOfPlaneBendForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaOutOfPlaneBendForce";
}
CalcAmoebaOutOfPlaneBendForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -254,6 +294,7 @@ public:
* @param force the OutOfPlaneBendForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaOutOfPlaneBendForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -269,12 +310,16 @@ public:
* This kernel is invoked by AmoebaTorsionTorsionForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaTorsionTorsionForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaTorsionTorsionForce";
}
CalcAmoebaTorsionTorsionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -282,6 +327,7 @@ public:
* @param force the TorsionTorsionForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaTorsionTorsionForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -297,12 +343,16 @@ public:
* This kernel is invoked by AmoebaMultipoleForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaMultipoleForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaMultipoleForce";
}
CalcAmoebaMultipoleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
......@@ -310,6 +360,7 @@ public:
* @param force the MultipoleForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaMultipoleForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -325,10 +376,13 @@ public:
* This kernel is invoked by AmoebaGeneralizedKirkwoodForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaGeneralizedKirkwoodForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaGeneralizedKirkwoodForce";
}
CalcAmoebaGeneralizedKirkwoodForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
......@@ -339,6 +393,7 @@ public:
* @param force the GBSAOBCForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaGeneralizedKirkwoodForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -356,9 +411,11 @@ public:
*/
class CalcAmoebaVdwForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaVdwForce";
}
CalcAmoebaVdwForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
......@@ -369,6 +426,7 @@ public:
* @param force the GBSAOBCForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaVdwForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -384,10 +442,13 @@ public:
* This kernel is invoked by AmoebaWcaDispersionForce to calculate the WCA dispersion forces acting on the system and the WCA dispersion energy of the system.
*/
class CalcAmoebaWcaDispersionForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaWcaDispersionForce";
}
CalcAmoebaWcaDispersionForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
......@@ -398,6 +459,7 @@ public:
* @param force the GBSAOBCForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaWcaDispersionForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
*
......
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