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Commit c6ebf6e2 authored by Peter Eastman's avatar Peter Eastman
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Removed the word "harmonic" from lots of places it didn't belong, including class and method names

parent 58b094ce
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Showing with 279 additions and 279 deletions
plugins/amoeba/openmmapi/include/OpenMMAmoeba.h
View file @ c6ebf6e2
......@@ -32,9 +32,9 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "openmm/AmoebaHarmonicBondForce.h"
#include "openmm/AmoebaHarmonicAngleForce.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
#include "openmm/AmoebaBondForce.h"
#include "openmm/AmoebaAngleForce.h"
#include "openmm/AmoebaInPlaneAngleForce.h"
#include "openmm/AmoebaPiTorsionForce.h"
#include "openmm/AmoebaStretchBendForce.h"
#include "openmm/AmoebaOutOfPlaneBendForce.h"
......
plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicAngleForce.h → plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_H_
#define OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_H_
#ifndef OPENMM_AMOEBA_ANGLE_FORCE_H_
#define OPENMM_AMOEBA_ANGLE_FORCE_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
......@@ -44,21 +44,21 @@ namespace OpenMM {
* is set per-angle. The coefficients of the higher order terms each have a single value that
* is set globally.
*
* To use it, create an AmoebaHarmonicAngleForce object then call addAngle() once for each angle. After
* To use it, create an AmoebaAngleForce object then call addAngle() once for each angle. After
* an angle has been added, you can modify its force field parameters by calling setAngleParameters().
*/
class OPENMM_EXPORT AmoebaHarmonicAngleForce : public Force {
class OPENMM_EXPORT AmoebaAngleForce : public Force {
public:
/**
* Create an AmoebaHarmonicAngleForce.
* Create an AmoebaAngleForce.
*/
AmoebaHarmonicAngleForce();
AmoebaAngleForce();
/**
* Get the number of harmonic angle stretch terms in the potential function
* Get the number of angle stretch terms in the potential function
*/
int getNumAngles() const {
return angles.size();
......@@ -69,56 +69,56 @@ public:
*
* @param cubicK the cubic force constant for the angle
*/
void setAmoebaGlobalHarmonicAngleCubic( double cubicK );
void setAmoebaGlobalAngleCubic( double cubicK );
/**
* Get the global cubic term
*
* @return global cubicK term
*/
double getAmoebaGlobalHarmonicAngleCubic( void ) const;
double getAmoebaGlobalAngleCubic( void ) const;
/**
* Set the global quartic term
*
* @param quarticK the quartic force constant for the angle
*/
void setAmoebaGlobalHarmonicAngleQuartic( double quarticK );
void setAmoebaGlobalAngleQuartic( double quarticK );
/**
* Get the global quartic term
*
* @return global quartic term
*/
double getAmoebaGlobalHarmonicAngleQuartic( void ) const;
double getAmoebaGlobalAngleQuartic( void ) const;
/**
* Set the global pentic term
*
* @param penticK the pentic force constant for the angle
*/
void setAmoebaGlobalHarmonicAnglePentic( double penticK );
void setAmoebaGlobalAnglePentic( double penticK );
/**
* Get the global pentic term
*
* @return global penticK term
*/
double getAmoebaGlobalHarmonicAnglePentic( void ) const;
double getAmoebaGlobalAnglePentic( void ) const;
/**
* Set the global sextic term
*
* @param sexticK the sextic force constant for the angle
*/
void setAmoebaGlobalHarmonicAngleSextic( double sexticK );
void setAmoebaGlobalAngleSextic( double sexticK );
/**
* Get the global sextic term
*
* @return global sextic term
*/
double getAmoebaGlobalHarmonicAngleSextic( void ) const;
double getAmoebaGlobalAngleSextic( void ) const;
/**
* Add an angle term to the force field.
......@@ -164,7 +164,7 @@ private:
std::vector<AngleInfo> angles;
};
class AmoebaHarmonicAngleForce::AngleInfo {
class AmoebaAngleForce::AngleInfo {
public:
int particle1, particle2, particle3;
double length, quadraticK;
......@@ -179,4 +179,4 @@ public:
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_H_*/
#endif /*OPENMM_AMOEBA_ANGLE_FORCE_H_*/
plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicBondForce.h → plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_BOND_FORCE_H_
#define OPENMM_AMOEBA_HARMONIC_BOND_FORCE_H_
#ifndef OPENMM_AMOEBA_BOND_FORCE_H_
#define OPENMM_AMOEBA_BOND_FORCE_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
......@@ -46,18 +46,18 @@ namespace OpenMM {
* is set per-bond. The coefficients of the higher order terms each have a single value that
* is set globally.
*
* To use it, create an AmoebaHarmonicBondForce object then call addBond() once for each bond. After
* To use it, create an AmoebaBondForce object then call addBond() once for each bond. After
* a bond has been added, you can modify its force field parameters by calling setBondParameters().
*/
class OPENMM_EXPORT AmoebaHarmonicBondForce : public Force {
class OPENMM_EXPORT AmoebaBondForce : public Force {
public:
/**
* Create an AmoebaHarmonicBondForce.
* Create an AmoebaBondForce.
*/
AmoebaHarmonicBondForce();
AmoebaBondForce();
/**
* Get the number of bond stretch terms in the potential function
*/
......@@ -70,28 +70,28 @@ public:
*
* @param cubicK the cubic force constant for the bond
*/
void setAmoebaGlobalHarmonicBondCubic( double cubicK );
void setAmoebaGlobalBondCubic( double cubicK );
/**
* Get the global cubic term
*
* @return global cubicK term
*/
double getAmoebaGlobalHarmonicBondCubic( void ) const;
double getAmoebaGlobalBondCubic( void ) const;
/**
* Set the global quartic term
*
* @param quarticK the quartic force constant for the bond
*/
void setAmoebaGlobalHarmonicBondQuartic( double quarticK );
void setAmoebaGlobalBondQuartic( double quarticK );
/**
* Get the global quartic term
*
* @return global quartic term
*/
double getAmoebaGlobalHarmonicBondQuartic( void ) const;
double getAmoebaGlobalBondQuartic( void ) const;
/**
* Add a bond term to the force field.
......@@ -136,7 +136,7 @@ private:
std::vector<BondInfo> bonds;
};
class AmoebaHarmonicBondForce::BondInfo {
class AmoebaBondForce::BondInfo {
public:
int particle1, particle2;
double length, quadraticK;
......@@ -151,4 +151,4 @@ public:
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_BOND_FORCE_H_*/
#endif /*OPENMM_AMOEBA_BOND_FORCE_H_*/
plugins/amoeba/openmmapi/include/openmm/AmoebaHarmonicInPlaneAngleForce.h → plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_H_
#define OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_H_
#ifndef OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_H_
#define OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
......@@ -44,18 +44,18 @@ namespace OpenMM {
* quadratic term is set per-angle. The coefficients of the higher order terms each have a single value that
* is set globally.
*
* To use it, create an AmoebaHarmonicInPlaneAngle object then call addAngle() once for each angle. After
* To use it, create an AmoebaInPlaneAngleForce object then call addAngle() once for each angle. After
* an angle has been added, you can modify its force field parameters by calling setAngleParameters().
*/
class OPENMM_EXPORT AmoebaHarmonicInPlaneAngleForce : public Force {
class OPENMM_EXPORT AmoebaInPlaneAngleForce : public Force {
public:
/**
* Create an AmoebaHarmonicAngleForce.
* Create an AmoebaAngleForce.
*/
AmoebaHarmonicInPlaneAngleForce();
AmoebaInPlaneAngleForce();
/**
* Get the number of in-plane angle terms in the potential function
......@@ -69,56 +69,56 @@ public:
*
* @param cubicK the cubic force constant for the angle
*/
void setAmoebaGlobalHarmonicInPlaneAngleCubic( double cubicK );
void setAmoebaGlobalInPlaneAngleCubic( double cubicK );
/**
* Get the global cubic term
*
* @return global cubicK term
*/
double getAmoebaGlobalHarmonicInPlaneAngleCubic( void ) const;
double getAmoebaGlobalInPlaneAngleCubic( void ) const;
/**
* Set the global quartic term
*
* @param quarticK the quartic force constant for the angle
*/
void setAmoebaGlobalHarmonicInPlaneAngleQuartic( double quarticK );
void setAmoebaGlobalInPlaneAngleQuartic( double quarticK );
/**
* Get the global quartic term
*
* @return global quartic term
*/
double getAmoebaGlobalHarmonicInPlaneAngleQuartic( void ) const;
double getAmoebaGlobalInPlaneAngleQuartic( void ) const;
/**
* Set the global pentic term
*
* @param penticK the pentic force constant for the angle
*/
void setAmoebaGlobalHarmonicInPlaneAnglePentic( double penticK );
void setAmoebaGlobalInPlaneAnglePentic( double penticK );
/**
* Get the global pentic term
*
* @return global penticK term
*/
double getAmoebaGlobalHarmonicInPlaneAnglePentic( void ) const;
double getAmoebaGlobalInPlaneAnglePentic( void ) const;
/**
* Set the global sextic term
*
* @param sexticK the sextic force constant for the angle
*/
void setAmoebaGlobalHarmonicInPlaneAngleSextic( double sexticK );
void setAmoebaGlobalInPlaneAngleSextic( double sexticK );
/**
* Get the global sextic term
*
* @return global sextic term
*/
double getAmoebaGlobalHarmonicInPlaneAngleSextic( void ) const;
double getAmoebaGlobalInPlaneAngleSextic( void ) const;
/**
* Add an angle term to the force field.
......@@ -169,7 +169,7 @@ private:
std::vector<AngleInfo> angles;
};
class AmoebaHarmonicInPlaneAngleForce::AngleInfo {
class AmoebaInPlaneAngleForce::AngleInfo {
public:
int particle1, particle2, particle3, particle4;
double length, quadraticK;
......@@ -185,4 +185,4 @@ public:
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_H_*/
#endif /*OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_H_*/
plugins/amoeba/openmmapi/include/openmm/amoebaKernels.h
View file @ c6ebf6e2
......@@ -44,26 +44,26 @@
namespace OpenMM {
/**
* This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaBondForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaHarmonicBondForceKernel : public KernelImpl {
class CalcAmoebaBondForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaHarmonicBondForce";
return "CalcAmoebaBondForce";
}
CalcAmoebaHarmonicBondForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
CalcAmoebaBondForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicBondForce this kernel will be used for
* @param force the AmoebaBondForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaHarmonicBondForce& force) = 0;
virtual void initialize(const System& system, const AmoebaBondForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
......@@ -78,26 +78,26 @@ public:
};
/**
* This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaHarmonicAngleForceKernel : public KernelImpl {
class CalcAmoebaAngleForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaHarmonicAngleForce";
return "CalcAmoebaAngleForce";
}
CalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
CalcAmoebaAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the HarmonicAngleForce this kernel will be used for
* @param force the AmoebaAngleForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaHarmonicAngleForce& force) = 0;
virtual void initialize(const System& system, const AmoebaAngleForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
......@@ -111,26 +111,26 @@ public:
};
/**
* This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CalcAmoebaHarmonicInPlaneAngleForceKernel : public KernelImpl {
class CalcAmoebaInPlaneAngleForceKernel : public KernelImpl {
public:
static std::string Name() {
return "CalcAmoebaHarmonicInPlaneAngleForce";
return "CalcAmoebaInPlaneAngleForce";
}
CalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
CalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the HarmonicInPlaneAngleForce this kernel will be used for
* @param force the AmoebaInPlaneAngleForce this kernel will be used for
*/
virtual void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) = 0;
virtual void initialize(const System& system, const AmoebaInPlaneAngleForce& force) = 0;
/**
* Execute the kernel to calculate the forces and/or energy.
......
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaHarmonicAngleForceImpl.h → plugins/amoeba/openmmapi/include/openmm/internal/AmoebaAngleForceImpl.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_IMPL_H_
#define OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_IMPL_H_
#ifndef OPENMM_AMOEBA_ANGLE_FORCE_IMPL_H_
#define OPENMM_AMOEBA_ANGLE_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
......@@ -33,7 +33,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "openmm/AmoebaHarmonicAngleForce.h"
#include "openmm/AmoebaAngleForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
......@@ -42,15 +42,15 @@
namespace OpenMM {
/**
* This is the internal implementation of AmoebaHarmonicAngleForce.
* This is the internal implementation of AmoebaAngleForce.
*/
class AmoebaHarmonicAngleForceImpl : public ForceImpl {
class AmoebaAngleForceImpl : public ForceImpl {
public:
AmoebaHarmonicAngleForceImpl(AmoebaHarmonicAngleForce& owner);
~AmoebaHarmonicAngleForceImpl();
AmoebaAngleForceImpl(AmoebaAngleForce& owner);
~AmoebaAngleForceImpl();
void initialize(ContextImpl& context);
AmoebaHarmonicAngleForce& getOwner() {
AmoebaAngleForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
......@@ -62,10 +62,10 @@ public:
}
std::vector<std::string> getKernelNames();
private:
AmoebaHarmonicAngleForce& owner;
AmoebaAngleForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_IMPL_H_*/
#endif /*OPENMM_AMOEBA_ANGLE_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaHarmonicBondForceImpl.h → plugins/amoeba/openmmapi/include/openmm/internal/AmoebaBondForceImpl.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_BOND_FORCE_IMPL_H_
#define OPENMM_AMOEBA_HARMONIC_BOND_FORCE_IMPL_H_
#ifndef OPENMM_AMOEBA_BOND_FORCE_IMPL_H_
#define OPENMM_AMOEBA_BOND_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
......@@ -33,7 +33,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "openmm/AmoebaHarmonicBondForce.h"
#include "openmm/AmoebaBondForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
......@@ -43,15 +43,15 @@
namespace OpenMM {
/**
* This is the internal implementation of AmoebaHarmonicBondForce.
* This is the internal implementation of AmoebaBondForce.
*/
class AmoebaHarmonicBondForceImpl : public ForceImpl {
class AmoebaBondForceImpl : public ForceImpl {
public:
AmoebaHarmonicBondForceImpl(AmoebaHarmonicBondForce& owner);
~AmoebaHarmonicBondForceImpl();
AmoebaBondForceImpl(AmoebaBondForce& owner);
~AmoebaBondForceImpl();
void initialize(ContextImpl& context);
AmoebaHarmonicBondForce& getOwner() {
AmoebaBondForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
......@@ -65,10 +65,10 @@ public:
std::vector< std::pair<int, int> > getBondedParticles() const;
private:
AmoebaHarmonicBondForce& owner;
AmoebaBondForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_HARMONIC_BOND_FORCE_IMPL_H_*/
#endif /*OPENMM_BOND_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/include/openmm/internal/AmoebaHarmonicInPlaneAngleForceImpl.h → plugins/amoeba/openmmapi/include/openmm/internal/AmoebaInPlaneAngleForceImpl.h
View file @ c6ebf6e2
#ifndef OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_IMPL_H_
#define OPENMM_AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE_IMPL_H_
#ifndef OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_IMPL_H_
#define OPENMM_AMOEBA_IN_PLANE_ANGLE_FORCE_IMPL_H_
/* -------------------------------------------------------------------------- *
* OpenMMAmoeba *
......@@ -33,7 +33,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/ForceImpl.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
#include "openmm/AmoebaInPlaneAngleForce.h"
#include "openmm/Kernel.h"
#include <utility>
#include <set>
......@@ -42,15 +42,15 @@
namespace OpenMM {
/**
* This is the internal implementation of AmoebaHarmonicInPlaneAngleForce.
* This is the internal implementation of AmoebaInPlaneAngleForce.
*/
class AmoebaHarmonicInPlaneAngleForceImpl : public ForceImpl {
class AmoebaInPlaneAngleForceImpl : public ForceImpl {
public:
AmoebaHarmonicInPlaneAngleForceImpl(AmoebaHarmonicInPlaneAngleForce& owner);
~AmoebaHarmonicInPlaneAngleForceImpl();
AmoebaInPlaneAngleForceImpl(AmoebaInPlaneAngleForce& owner);
~AmoebaInPlaneAngleForceImpl();
void initialize(ContextImpl& context);
AmoebaHarmonicInPlaneAngleForce& getOwner() {
AmoebaInPlaneAngleForce& getOwner() {
return owner;
}
void updateContextState(ContextImpl& context) {
......@@ -62,10 +62,10 @@ public:
}
std::vector<std::string> getKernelNames();
private:
AmoebaHarmonicInPlaneAngleForce& owner;
AmoebaInPlaneAngleForce& owner;
Kernel kernel;
};
} // namespace OpenMM
#endif /*OPENMM_AMOEBA_HARMONIC_ANGLE_FORCE_IMPL_H_*/
#endif /*OPENMM_AMOEBA_ANGLE_FORCE_IMPL_H_*/
plugins/amoeba/openmmapi/src/AmoebaHarmonicAngleForce.cpp → plugins/amoeba/openmmapi/src/AmoebaAngleForce.cpp
View file @ c6ebf6e2
......@@ -31,21 +31,21 @@
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/AmoebaHarmonicAngleForce.h"
#include "openmm/internal/AmoebaHarmonicAngleForceImpl.h"
#include "openmm/AmoebaAngleForce.h"
#include "openmm/internal/AmoebaAngleForceImpl.h"
using namespace OpenMM;
AmoebaHarmonicAngleForce::AmoebaHarmonicAngleForce() {
AmoebaAngleForce::AmoebaAngleForce() {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
int AmoebaHarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double length, double quadraticK) {
int AmoebaAngleForce::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,
void AmoebaAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3,
double& length, double& quadraticK ) const {
particle1 = angles[index].particle1;
particle2 = angles[index].particle2;
......@@ -54,7 +54,7 @@ void AmoebaHarmonicAngleForce::getAngleParameters(int index, int& particle1, int
quadraticK = angles[index].quadraticK;
}
void AmoebaHarmonicAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3,
void AmoebaAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3,
double length, double quadraticK ) {
angles[index].particle1 = particle1;
angles[index].particle2 = particle2;
......@@ -63,38 +63,38 @@ void AmoebaHarmonicAngleForce::setAngleParameters(int index, int particle1, int
angles[index].quadraticK = quadraticK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAngleCubic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleCubic( void ) const {
return _globalCubicK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAngleCubic(double cubicK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleCubic(double cubicK ) {
_globalCubicK = cubicK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAngleQuartic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleQuartic( void ) const {
return _globalQuarticK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAngleQuartic(double quarticK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAnglePentic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAnglePentic( void ) const {
return _globalPenticK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAnglePentic(double penticK ) {
void AmoebaAngleForce::setAmoebaGlobalAnglePentic(double penticK ) {
_globalPenticK = penticK;
}
double AmoebaHarmonicAngleForce::getAmoebaGlobalHarmonicAngleSextic( void ) const {
double AmoebaAngleForce::getAmoebaGlobalAngleSextic( void ) const {
return _globalSexticK;
}
void AmoebaHarmonicAngleForce::setAmoebaGlobalHarmonicAngleSextic(double sexticK ) {
void AmoebaAngleForce::setAmoebaGlobalAngleSextic(double sexticK ) {
_globalSexticK = sexticK;
}
ForceImpl* AmoebaHarmonicAngleForce::createImpl() {
return new AmoebaHarmonicAngleForceImpl(*this);
ForceImpl* AmoebaAngleForce::createImpl() {
return new AmoebaAngleForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicAngleForceImpl.cpp → plugins/amoeba/openmmapi/src/AmoebaAngleForceImpl.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/AmoebaHarmonicAngleForceImpl.h"
#include "openmm/internal/AmoebaAngleForceImpl.h"
#include "openmm/amoebaKernels.h"
using namespace OpenMM;
......@@ -39,26 +39,26 @@ using std::pair;
using std::vector;
using std::set;
AmoebaHarmonicAngleForceImpl::AmoebaHarmonicAngleForceImpl(AmoebaHarmonicAngleForce& owner) : owner(owner) {
AmoebaAngleForceImpl::AmoebaAngleForceImpl(AmoebaAngleForce& owner) : owner(owner) {
}
AmoebaHarmonicAngleForceImpl::~AmoebaHarmonicAngleForceImpl() {
AmoebaAngleForceImpl::~AmoebaAngleForceImpl() {
}
void AmoebaHarmonicAngleForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaHarmonicAngleForceKernel::Name(), context);
kernel.getAs<CalcAmoebaHarmonicAngleForceKernel>().initialize(context.getSystem(), owner);
void AmoebaAngleForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaAngleForceKernel::Name(), context);
kernel.getAs<CalcAmoebaAngleForceKernel>().initialize(context.getSystem(), owner);
}
double AmoebaHarmonicAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
double AmoebaAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
if ((groups&(1<<owner.getForceGroup())) != 0)
return kernel.getAs<CalcAmoebaHarmonicAngleForceKernel>().execute(context, includeForces, includeEnergy);
return kernel.getAs<CalcAmoebaAngleForceKernel>().execute(context, includeForces, includeEnergy);
return 0.0;
}
std::vector<std::string> AmoebaHarmonicAngleForceImpl::getKernelNames() {
std::vector<std::string> AmoebaAngleForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcAmoebaHarmonicAngleForceKernel::Name());
names.push_back(CalcAmoebaAngleForceKernel::Name());
return names;
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicBondForce.cpp → plugins/amoeba/openmmapi/src/AmoebaBondForce.cpp
View file @ c6ebf6e2
......@@ -31,50 +31,50 @@
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/AmoebaHarmonicBondForce.h"
#include "openmm/internal/AmoebaHarmonicBondForceImpl.h"
#include "openmm/AmoebaBondForce.h"
#include "openmm/internal/AmoebaBondForceImpl.h"
using namespace OpenMM;
AmoebaHarmonicBondForce::AmoebaHarmonicBondForce() {
AmoebaBondForce::AmoebaBondForce() {
_globalCubicK = _globalQuarticK = 0.0;
}
int AmoebaHarmonicBondForce::addBond(int particle1, int particle2, double length, double quadraticK) {
int AmoebaBondForce::addBond(int particle1, int particle2, double length, double quadraticK) {
bonds.push_back(BondInfo(particle1, particle2, length, quadraticK ));
return bonds.size()-1;
}
void AmoebaHarmonicBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const {
void AmoebaBondForce::getBondParameters(int index, int& particle1, int& particle2, double& length, double& quadraticK ) const {
particle1 = bonds[index].particle1;
particle2 = bonds[index].particle2;
length = bonds[index].length;
quadraticK = bonds[index].quadraticK;
}
void AmoebaHarmonicBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK ) {
void AmoebaBondForce::setBondParameters(int index, int particle1, int particle2, double length, double quadraticK ) {
bonds[index].particle1 = particle1;
bonds[index].particle2 = particle2;
bonds[index].length = length;
bonds[index].quadraticK = quadraticK;
}
void AmoebaHarmonicBondForce::setAmoebaGlobalHarmonicBondCubic(double cubicK ) {
void AmoebaBondForce::setAmoebaGlobalBondCubic(double cubicK ) {
_globalCubicK = cubicK;
}
void AmoebaHarmonicBondForce::setAmoebaGlobalHarmonicBondQuartic(double quarticK ) {
void AmoebaBondForce::setAmoebaGlobalBondQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaHarmonicBondForce::getAmoebaGlobalHarmonicBondCubic( void ) const {
double AmoebaBondForce::getAmoebaGlobalBondCubic( void ) const {
return _globalCubicK;
}
double AmoebaHarmonicBondForce::getAmoebaGlobalHarmonicBondQuartic( void ) const {
double AmoebaBondForce::getAmoebaGlobalBondQuartic( void ) const {
return _globalQuarticK;
}
ForceImpl* AmoebaHarmonicBondForce::createImpl() {
return new AmoebaHarmonicBondForceImpl(*this);
ForceImpl* AmoebaBondForce::createImpl() {
return new AmoebaBondForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicBondForceImpl.cpp → plugins/amoeba/openmmapi/src/AmoebaBondForceImpl.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/AmoebaHarmonicBondForceImpl.h"
#include "openmm/internal/AmoebaBondForceImpl.h"
#include "openmm/amoebaKernels.h"
#include "openmm/Platform.h"
......@@ -40,30 +40,30 @@ using std::pair;
using std::vector;
using std::set;
AmoebaHarmonicBondForceImpl::AmoebaHarmonicBondForceImpl(AmoebaHarmonicBondForce& owner) : owner(owner) {
AmoebaBondForceImpl::AmoebaBondForceImpl(AmoebaBondForce& owner) : owner(owner) {
}
AmoebaHarmonicBondForceImpl::~AmoebaHarmonicBondForceImpl() {
AmoebaBondForceImpl::~AmoebaBondForceImpl() {
}
void AmoebaHarmonicBondForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaHarmonicBondForceKernel::Name(), context);
kernel.getAs<CalcAmoebaHarmonicBondForceKernel>().initialize(context.getSystem(), owner);
void AmoebaBondForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaBondForceKernel::Name(), context);
kernel.getAs<CalcAmoebaBondForceKernel>().initialize(context.getSystem(), owner);
}
double AmoebaHarmonicBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
double AmoebaBondForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
if ((groups&(1<<owner.getForceGroup())) != 0)
return kernel.getAs<CalcAmoebaHarmonicBondForceKernel>().execute(context, includeForces, includeEnergy);
return kernel.getAs<CalcAmoebaBondForceKernel>().execute(context, includeForces, includeEnergy);
return 0.0;
}
std::vector<std::string> AmoebaHarmonicBondForceImpl::getKernelNames() {
std::vector<std::string> AmoebaBondForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcAmoebaHarmonicBondForceKernel::Name());
names.push_back(CalcAmoebaBondForceKernel::Name());
return names;
}
vector<pair<int, int> > AmoebaHarmonicBondForceImpl::getBondedParticles() const {
vector<pair<int, int> > AmoebaBondForceImpl::getBondedParticles() const {
int numBonds = owner.getNumBonds();
vector<pair<int, int> > bonds(numBonds);
for (int i = 0; i < numBonds; i++) {
......
plugins/amoeba/openmmapi/src/AmoebaHarmonicInPlaneAngleForce.cpp → plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForce.cpp
View file @ c6ebf6e2
......@@ -31,21 +31,21 @@
#include "openmm/Force.h"
#include "openmm/OpenMMException.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
#include "openmm/internal/AmoebaHarmonicInPlaneAngleForceImpl.h"
#include "openmm/AmoebaInPlaneAngleForce.h"
#include "openmm/internal/AmoebaInPlaneAngleForceImpl.h"
using namespace OpenMM;
AmoebaHarmonicInPlaneAngleForce::AmoebaHarmonicInPlaneAngleForce() {
AmoebaInPlaneAngleForce::AmoebaInPlaneAngleForce() {
_globalCubicK = _globalQuarticK = _globalPenticK = _globalSexticK = 0.0;
}
int AmoebaHarmonicInPlaneAngleForce::addAngle(int particle1, int particle2, int particle3, int particle4, double length, double quadraticK ) {
int AmoebaInPlaneAngleForce::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,
void AmoebaInPlaneAngleForce::getAngleParameters(int index, int& particle1, int& particle2, int& particle3, int& particle4,
double& length, double& quadraticK ) const {
particle1 = angles[index].particle1;
particle2 = angles[index].particle2;
......@@ -55,7 +55,7 @@ void AmoebaHarmonicInPlaneAngleForce::getAngleParameters(int index, int& particl
quadraticK = angles[index].quadraticK;
}
void AmoebaHarmonicInPlaneAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4,
void AmoebaInPlaneAngleForce::setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4,
double length, double quadraticK ) {
angles[index].particle1 = particle1;
angles[index].particle2 = particle2;
......@@ -65,38 +65,38 @@ void AmoebaHarmonicInPlaneAngleForce::setAngleParameters(int index, int particle
angles[index].quadraticK = quadraticK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAngleCubic(double cubicK ) {
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleCubic(double cubicK ) {
_globalCubicK = cubicK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAngleQuartic(double quarticK ) {
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleQuartic(double quarticK ) {
_globalQuarticK = quarticK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAngleCubic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleCubic( void ) const {
return _globalCubicK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAngleQuartic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleQuartic( void ) const {
return _globalQuarticK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAnglePentic(double cubicK ) {
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAnglePentic(double cubicK ) {
_globalPenticK = cubicK;
}
void AmoebaHarmonicInPlaneAngleForce::setAmoebaGlobalHarmonicInPlaneAngleSextic(double quarticK ) {
void AmoebaInPlaneAngleForce::setAmoebaGlobalInPlaneAngleSextic(double quarticK ) {
_globalSexticK = quarticK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAnglePentic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAnglePentic( void ) const {
return _globalPenticK;
}
double AmoebaHarmonicInPlaneAngleForce::getAmoebaGlobalHarmonicInPlaneAngleSextic( void ) const {
double AmoebaInPlaneAngleForce::getAmoebaGlobalInPlaneAngleSextic( void ) const {
return _globalSexticK;
}
ForceImpl* AmoebaHarmonicInPlaneAngleForce::createImpl() {
return new AmoebaHarmonicInPlaneAngleForceImpl(*this);
ForceImpl* AmoebaInPlaneAngleForce::createImpl() {
return new AmoebaInPlaneAngleForceImpl(*this);
}
plugins/amoeba/openmmapi/src/AmoebaHarmonicInPlaneAngleForceImpl.cpp → plugins/amoeba/openmmapi/src/AmoebaInPlaneAngleForceImpl.cpp
View file @ c6ebf6e2
......@@ -30,7 +30,7 @@
* -------------------------------------------------------------------------- */
#include "openmm/internal/ContextImpl.h"
#include "openmm/internal/AmoebaHarmonicInPlaneAngleForceImpl.h"
#include "openmm/internal/AmoebaInPlaneAngleForceImpl.h"
#include "openmm/amoebaKernels.h"
using namespace OpenMM;
......@@ -39,26 +39,26 @@ using std::pair;
using std::vector;
using std::set;
AmoebaHarmonicInPlaneAngleForceImpl::AmoebaHarmonicInPlaneAngleForceImpl(AmoebaHarmonicInPlaneAngleForce& owner) : owner(owner) {
AmoebaInPlaneAngleForceImpl::AmoebaInPlaneAngleForceImpl(AmoebaInPlaneAngleForce& owner) : owner(owner) {
}
AmoebaHarmonicInPlaneAngleForceImpl::~AmoebaHarmonicInPlaneAngleForceImpl() {
AmoebaInPlaneAngleForceImpl::~AmoebaInPlaneAngleForceImpl() {
}
void AmoebaHarmonicInPlaneAngleForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), context);
kernel.getAs<CalcAmoebaHarmonicInPlaneAngleForceKernel>().initialize(context.getSystem(), owner);
void AmoebaInPlaneAngleForceImpl::initialize(ContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcAmoebaInPlaneAngleForceKernel::Name(), context);
kernel.getAs<CalcAmoebaInPlaneAngleForceKernel>().initialize(context.getSystem(), owner);
}
double AmoebaHarmonicInPlaneAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
double AmoebaInPlaneAngleForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
if ((groups&(1<<owner.getForceGroup())) != 0)
return kernel.getAs<CalcAmoebaHarmonicInPlaneAngleForceKernel>().execute(context, includeForces, includeEnergy);
return kernel.getAs<CalcAmoebaInPlaneAngleForceKernel>().execute(context, includeForces, includeEnergy);
return 0.0;
}
std::vector<std::string> AmoebaHarmonicInPlaneAngleForceImpl::getKernelNames() {
std::vector<std::string> AmoebaInPlaneAngleForceImpl::getKernelNames() {
std::vector<std::string> names;
names.push_back(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name());
names.push_back(CalcAmoebaInPlaneAngleForceKernel::Name());
return names;
}
plugins/amoeba/platforms/cuda-old/src/AmoebaCudaData.h
View file @ c6ebf6e2
......@@ -35,7 +35,7 @@
namespace OpenMM {
/**
* This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaBondForce to calculate the forces acting on the system and the energy of the system.
*/
class AmoebaCudaData {
public:
......
plugins/amoeba/platforms/cuda-old/src/AmoebaCudaKernelFactory.cpp
View file @ c6ebf6e2
......@@ -43,9 +43,9 @@ extern "C" OPENMMCUDA_EXPORT void registerKernelFactories() {
AmoebaCudaKernelFactory* factory = new AmoebaCudaKernelFactory();
platform.registerKernelFactory(CalcAmoebaHarmonicBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaHarmonicInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaBondForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaInPlaneAngleForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaPiTorsionForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaStretchBendForceKernel::Name(), factory);
platform.registerKernelFactory(CalcAmoebaOutOfPlaneBendForceKernel::Name(), factory);
......@@ -113,14 +113,14 @@ KernelImpl* AmoebaCudaKernelFactory::createKernelImpl(std::string name, const Pl
amoebaCudaData = mapIterator->second;
}
if (name == CalcAmoebaHarmonicBondForceKernel::Name())
return new CudaCalcAmoebaHarmonicBondForceKernel(name, platform, *amoebaCudaData, context.getSystem());
if (name == CalcAmoebaBondForceKernel::Name())
return new CudaCalcAmoebaBondForceKernel(name, platform, *amoebaCudaData, context.getSystem());
if (name == CalcAmoebaHarmonicAngleForceKernel::Name())
return new CudaCalcAmoebaHarmonicAngleForceKernel(name, platform, *amoebaCudaData, context.getSystem());
if (name == CalcAmoebaAngleForceKernel::Name())
return new CudaCalcAmoebaAngleForceKernel(name, platform, *amoebaCudaData, context.getSystem());
if (name == CalcAmoebaHarmonicInPlaneAngleForceKernel::Name())
return new CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform, *amoebaCudaData, context.getSystem());
if (name == CalcAmoebaInPlaneAngleForceKernel::Name())
return new CudaCalcAmoebaInPlaneAngleForceKernel(name, platform, *amoebaCudaData, context.getSystem());
if (name == CalcAmoebaPiTorsionForceKernel::Name())
return new CudaCalcAmoebaPiTorsionForceKernel(name, platform, *amoebaCudaData, context.getSystem());
......
plugins/amoeba/platforms/cuda-old/src/AmoebaCudaKernels.cpp
View file @ c6ebf6e2
......@@ -64,12 +64,12 @@ static void computeAmoebaLocalForces( AmoebaCudaData& data ) {
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicBond *
* AmoebaBondForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicBondForceKernel::ForceInfo : public CudaForceInfo {
class CudaCalcAmoebaBondForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const AmoebaHarmonicBondForce& force) : force(force) {
ForceInfo(const AmoebaBondForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumBonds();
......@@ -90,19 +90,19 @@ public:
return (length1 == length2 && k1 == k2);
}
private:
const AmoebaHarmonicBondForce& force;
const AmoebaBondForce& force;
};
CudaCalcAmoebaHarmonicBondForceKernel::CudaCalcAmoebaHarmonicBondForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system) :
CalcAmoebaHarmonicBondForceKernel(name, platform), data(data), system(system) {
CudaCalcAmoebaBondForceKernel::CudaCalcAmoebaBondForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system) :
CalcAmoebaBondForceKernel(name, platform), data(data), system(system) {
data.incrementKernelCount();
}
CudaCalcAmoebaHarmonicBondForceKernel::~CudaCalcAmoebaHarmonicBondForceKernel() {
CudaCalcAmoebaBondForceKernel::~CudaCalcAmoebaBondForceKernel() {
data.decrementKernelCount();
}
void CudaCalcAmoebaHarmonicBondForceKernel::initialize(const System& system, const AmoebaHarmonicBondForce& force) {
void CudaCalcAmoebaBondForceKernel::initialize(const System& system, const AmoebaBondForce& force) {
data.setAmoebaLocalForcesKernel( this );
......@@ -124,12 +124,12 @@ void CudaCalcAmoebaHarmonicBondForceKernel::initialize(const System& system, con
quadratic[i] = static_cast<float>( kValue );
}
gpuSetAmoebaBondParameters( data.getAmoebaGpu(), particle1, particle2, length, quadratic,
static_cast<float>(force.getAmoebaGlobalHarmonicBondCubic()),
static_cast<float>(force.getAmoebaGlobalHarmonicBondQuartic()) );
static_cast<float>(force.getAmoebaGlobalBondCubic()),
static_cast<float>(force.getAmoebaGlobalBondQuartic()) );
data.getAmoebaGpu()->gpuContext->forces.push_back(new ForceInfo(force));
}
double CudaCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double CudaCalcAmoebaBondForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if( data.getAmoebaLocalForcesKernel() == this ){
computeAmoebaLocalForces( data );
}
......@@ -137,12 +137,12 @@ double CudaCalcAmoebaHarmonicBondForceKernel::execute(ContextImpl& context, bool
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicAngle *
* AmoebaInPlaneAngleForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicAngleForceKernel::ForceInfo : public CudaForceInfo {
class CudaCalcAmoebaAngleForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const AmoebaHarmonicAngleForce& force) : force(force) {
ForceInfo(const AmoebaAngleForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -164,19 +164,19 @@ public:
return (angle1 == angle2 && k1 == k2);
}
private:
const AmoebaHarmonicAngleForce& force;
const AmoebaAngleForce& force;
};
CudaCalcAmoebaHarmonicAngleForceKernel::CudaCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system) :
CalcAmoebaHarmonicAngleForceKernel(name, platform), data(data), system(system) {
CudaCalcAmoebaAngleForceKernel::CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system) :
CalcAmoebaAngleForceKernel(name, platform), data(data), system(system) {
data.incrementKernelCount();
}
CudaCalcAmoebaHarmonicAngleForceKernel::~CudaCalcAmoebaHarmonicAngleForceKernel() {
CudaCalcAmoebaAngleForceKernel::~CudaCalcAmoebaAngleForceKernel() {
data.decrementKernelCount();
}
void CudaCalcAmoebaHarmonicAngleForceKernel::initialize(const System& system, const AmoebaHarmonicAngleForce& force) {
void CudaCalcAmoebaAngleForceKernel::initialize(const System& system, const AmoebaAngleForce& force) {
data.setAmoebaLocalForcesKernel( this );
......@@ -194,14 +194,14 @@ void CudaCalcAmoebaHarmonicAngleForceKernel::initialize(const System& system, co
k[i] = static_cast<float>( kQuadratic );
}
gpuSetAmoebaAngleParameters(data.getAmoebaGpu(), particle1, particle2, particle3, angle, k,
static_cast<float>(force.getAmoebaGlobalHarmonicAngleCubic()),
static_cast<float>(force.getAmoebaGlobalHarmonicAngleQuartic()),
static_cast<float>(force.getAmoebaGlobalHarmonicAnglePentic()),
static_cast<float>(force.getAmoebaGlobalHarmonicAngleSextic()) );
static_cast<float>(force.getAmoebaGlobalAngleCubic()),
static_cast<float>(force.getAmoebaGlobalAngleQuartic()),
static_cast<float>(force.getAmoebaGlobalAnglePentic()),
static_cast<float>(force.getAmoebaGlobalAngleSextic()) );
data.getAmoebaGpu()->gpuContext->forces.push_back(new ForceInfo(force));
}
double CudaCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double CudaCalcAmoebaAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if( data.getAmoebaLocalForcesKernel() == this ){
computeAmoebaLocalForces( data );
}
......@@ -209,12 +209,12 @@ double CudaCalcAmoebaHarmonicAngleForceKernel::execute(ContextImpl& context, boo
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicInPlaneAngle *
* AmoebaInPlaneAngleForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::ForceInfo : public CudaForceInfo {
class CudaCalcAmoebaInPlaneAngleForceKernel::ForceInfo : public CudaForceInfo {
public:
ForceInfo(const AmoebaHarmonicInPlaneAngleForce& force) : force(force) {
ForceInfo(const AmoebaInPlaneAngleForce& force) : force(force) {
}
int getNumParticleGroups() {
return force.getNumAngles();
......@@ -237,19 +237,19 @@ public:
return (angle1 == angle2 && k1 == k2);
}
private:
const AmoebaHarmonicInPlaneAngleForce& force;
const AmoebaInPlaneAngleForce& force;
};
CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system) :
CalcAmoebaHarmonicInPlaneAngleForceKernel(name, platform), data(data), system(system) {
CudaCalcAmoebaInPlaneAngleForceKernel::CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system) :
CalcAmoebaInPlaneAngleForceKernel(name, platform), data(data), system(system) {
data.incrementKernelCount();
}
CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::~CudaCalcAmoebaHarmonicInPlaneAngleForceKernel() {
CudaCalcAmoebaInPlaneAngleForceKernel::~CudaCalcAmoebaInPlaneAngleForceKernel() {
data.decrementKernelCount();
}
void CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force) {
void CudaCalcAmoebaInPlaneAngleForceKernel::initialize(const System& system, const AmoebaInPlaneAngleForce& force) {
data.setAmoebaLocalForcesKernel( this );
......@@ -270,14 +270,14 @@ void CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::initialize(const System& sys
k[i] = static_cast<float>( kQuadratic );
}
gpuSetAmoebaInPlaneAngleParameters(data.getAmoebaGpu(), particle1, particle2, particle3, particle4, angle, k,
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAngleCubic()),
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAngleQuartic()),
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAnglePentic()),
static_cast<float>( force.getAmoebaGlobalHarmonicInPlaneAngleSextic() ) );
static_cast<float>( force.getAmoebaGlobalInPlaneAngleCubic()),
static_cast<float>( force.getAmoebaGlobalInPlaneAngleQuartic()),
static_cast<float>( force.getAmoebaGlobalInPlaneAnglePentic()),
static_cast<float>( force.getAmoebaGlobalInPlaneAngleSextic() ) );
data.getAmoebaGpu()->gpuContext->forces.push_back(new ForceInfo(force));
}
double CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
double CudaCalcAmoebaInPlaneAngleForceKernel::execute(ContextImpl& context, bool includeForces, bool includeEnergy) {
if( data.getAmoebaLocalForcesKernel() == this ){
computeAmoebaLocalForces( data );
}
......@@ -285,7 +285,7 @@ double CudaCalcAmoebaHarmonicInPlaneAngleForceKernel::execute(ContextImpl& conte
}
/* -------------------------------------------------------------------------- *
* AmoebaHarmonicPiTorsion *
* AmoebaPiTorsionForce *
* -------------------------------------------------------------------------- */
class CudaCalcAmoebaPiTorsionForceKernel::ForceInfo : public CudaForceInfo {
......
plugins/amoeba/platforms/cuda-old/src/AmoebaCudaKernels.h
View file @ c6ebf6e2
......@@ -36,22 +36,22 @@
namespace OpenMM {
/**
* This kernel is invoked by AmoebaHarmonicBondForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaBondForce to calculate the forces acting on the system and the energy of the system.
*/
class CudaCalcAmoebaHarmonicBondForceKernel : public CalcAmoebaHarmonicBondForceKernel {
class CudaCalcAmoebaBondForceKernel : public CalcAmoebaBondForceKernel {
public:
CudaCalcAmoebaHarmonicBondForceKernel(std::string name,
CudaCalcAmoebaBondForceKernel(std::string name,
const Platform& platform,
AmoebaCudaData& data,
System& system);
~CudaCalcAmoebaHarmonicBondForceKernel();
~CudaCalcAmoebaBondForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicBondForce this kernel will be used for
* @param force the AmoebaBondForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicBondForce& force);
void initialize(const System& system, const AmoebaBondForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -69,19 +69,19 @@ private:
};
/**
* This kernel is invoked by AmoebaHarmonicAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CudaCalcAmoebaHarmonicAngleForceKernel : public CalcAmoebaHarmonicAngleForceKernel {
class CudaCalcAmoebaAngleForceKernel : public CalcAmoebaAngleForceKernel {
public:
CudaCalcAmoebaHarmonicAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system);
~CudaCalcAmoebaHarmonicAngleForceKernel();
CudaCalcAmoebaAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system);
~CudaCalcAmoebaAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicAngleForce this kernel will be used for
* @param force the AmoebaAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicAngleForce& force);
void initialize(const System& system, const AmoebaAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......@@ -99,19 +99,19 @@ private:
};
/**
* This kernel is invoked by AmoebaHarmonicInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
* This kernel is invoked by AmoebaInPlaneAngleForce to calculate the forces acting on the system and the energy of the system.
*/
class CudaCalcAmoebaHarmonicInPlaneAngleForceKernel : public CalcAmoebaHarmonicInPlaneAngleForceKernel {
class CudaCalcAmoebaInPlaneAngleForceKernel : public CalcAmoebaInPlaneAngleForceKernel {
public:
CudaCalcAmoebaHarmonicInPlaneAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system);
~CudaCalcAmoebaHarmonicInPlaneAngleForceKernel();
CudaCalcAmoebaInPlaneAngleForceKernel(std::string name, const Platform& platform, AmoebaCudaData& data, System& system);
~CudaCalcAmoebaInPlaneAngleForceKernel();
/**
* Initialize the kernel.
*
* @param system the System this kernel will be applied to
* @param force the AmoebaHarmonicInPlaneAngleForce this kernel will be used for
* @param force the AmoebaInPlaneAngleForce this kernel will be used for
*/
void initialize(const System& system, const AmoebaHarmonicInPlaneAngleForce& force);
void initialize(const System& system, const AmoebaInPlaneAngleForce& force);
/**
* Execute the kernel to calculate the forces and/or energy.
*
......
plugins/amoeba/platforms/cuda-old/tests/AmoebaTinkerParameterFile.cpp
View file @ c6ebf6e2
......@@ -735,7 +735,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
throwException(__FILE__, __LINE__, buffer );
}
AmoebaHarmonicBondForce* bondForce = new AmoebaHarmonicBondForce();
AmoebaBondForce* bondForce = new AmoebaBondForce();
MapStringIntI forceActive = forceMap.find( AMOEBA_HARMONIC_BOND_FORCE );
if( forceActive != forceMap.end() && (*forceActive).second ){
system.addForce( bondForce );
......@@ -763,7 +763,7 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
bondForce->addBond( particle1, particle2, length, k );
} else {
char buffer[1024];
(void) sprintf( buffer, "%s AmoebaHarmonicBondForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) sprintf( buffer, "%s AmoebaBondForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) fprintf( log, "%s", buffer );
throwException(__FILE__, __LINE__, buffer );
}
......@@ -788,11 +788,11 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
} else if( field == "AmoebaHarmonicBondCubic" ){
double cubicParameter = atof( tokens[1].c_str() );
bondForce->setAmoebaGlobalHarmonicBondCubic( cubicParameter );
bondForce->setAmoebaGlobalBondCubic( cubicParameter );
hits++;
} else if( field == "AmoebaHarmonicBondQuartic" ){
double quarticParameter = atof( tokens[1].c_str() );
bondForce->setAmoebaGlobalHarmonicBondQuartic( quarticParameter );
bondForce->setAmoebaGlobalBondQuartic( quarticParameter );
hits++;
}
}
......@@ -817,8 +817,8 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
double cubic = 0.0;
double quartic = 0.0;
bondForce->setAmoebaGlobalHarmonicBondCubic( cubic );
bondForce->setAmoebaGlobalHarmonicBondQuartic( quartic );
bondForce->setAmoebaGlobalBondCubic( cubic );
bondForce->setAmoebaGlobalBondQuartic( quartic );
for( int ii = 0; ii < bondForce->getNumBonds(); ii++ ){
int particle1, particle2;
......@@ -831,11 +831,11 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
if( useOpenMMUnits ){
double cubic = bondForce->getAmoebaGlobalHarmonicBondCubic()/AngstromToNm;
double quartic = bondForce->getAmoebaGlobalHarmonicBondQuartic()/(AngstromToNm*AngstromToNm);
double cubic = bondForce->getAmoebaGlobalBondCubic()/AngstromToNm;
double quartic = bondForce->getAmoebaGlobalBondQuartic()/(AngstromToNm*AngstromToNm);
bondForce->setAmoebaGlobalHarmonicBondCubic( cubic );
bondForce->setAmoebaGlobalHarmonicBondQuartic( quartic );
bondForce->setAmoebaGlobalBondCubic( cubic );
bondForce->setAmoebaGlobalBondQuartic( quartic );
// scale equilibrium bond lengths/force prefactor k
......@@ -854,9 +854,9 @@ static int readAmoebaHarmonicBondParameters( FILE* filePtr, MapStringInt& forceM
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(bondForce->getNumBonds());
(void) fprintf( log, "%s: %u sample of AmoebaHarmonicBondForce parameters in %s units; cubic=%15.7e quartic=%15.7e\n",
(void) fprintf( log, "%s: %u sample of AmoebaBondForce parameters in %s units; cubic=%15.7e quartic=%15.7e\n",
methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
bondForce->getAmoebaGlobalHarmonicBondCubic(), bondForce->getAmoebaGlobalHarmonicBondQuartic() );
bondForce->getAmoebaGlobalBondCubic(), bondForce->getAmoebaGlobalBondQuartic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2;
double length, k;
......@@ -906,7 +906,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
throwException(__FILE__, __LINE__, buffer );
}
AmoebaHarmonicAngleForce* angleForce = new AmoebaHarmonicAngleForce();
AmoebaAngleForce* angleForce = new AmoebaAngleForce();
MapStringIntI forceActive = forceMap.find( AMOEBA_HARMONIC_ANGLE_FORCE );
if( forceActive != forceMap.end() && (*forceActive).second ){
system.addForce( angleForce );
......@@ -936,7 +936,7 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
angleForce->addAngle( particle1, particle2, particle3, angle, k );
} else {
char buffer[1024];
(void) sprintf( buffer, "%s AmoebaHarmonicAngleForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) sprintf( buffer, "%s AmoebaAngleForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) fprintf( log, "%s", buffer );
throwException(__FILE__, __LINE__, buffer );
}
......@@ -960,16 +960,16 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
}
} else if( field == "AmoebaHarmonicAngleCubic" ){
angleForce->setAmoebaGlobalHarmonicAngleCubic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalAngleCubic( atof( tokens[1].c_str() ) );
hits++;
} else if( field == "AmoebaHarmonicAngleQuartic" ){
angleForce->setAmoebaGlobalHarmonicAngleQuartic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalAngleQuartic( atof( tokens[1].c_str() ) );
hits++;
} else if( field == "AmoebaHarmonicAnglePentic" ){
angleForce->setAmoebaGlobalHarmonicAnglePentic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalAnglePentic( atof( tokens[1].c_str() ) );
hits++;
} else if( field == "AmoebaHarmonicAngleSextic" ){
angleForce->setAmoebaGlobalHarmonicAngleSextic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalAngleSextic( atof( tokens[1].c_str() ) );
hits++;
}
}
......@@ -992,11 +992,11 @@ static int readAmoebaHarmonicAngleParameters( FILE* filePtr, MapStringInt& force
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles());
(void) fprintf( log, "%s: %u sample of AmoebaHarmonicAngleForce parameters in %s units; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
(void) fprintf( log, "%s: %u sample of AmoebaAngleForce parameters in %s units; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
angleForce->getAmoebaGlobalHarmonicAngleCubic(),
angleForce->getAmoebaGlobalHarmonicAngleQuartic(), angleForce->getAmoebaGlobalHarmonicAnglePentic(),
angleForce->getAmoebaGlobalHarmonicAngleSextic() );
angleForce->getAmoebaGlobalAngleCubic(),
angleForce->getAmoebaGlobalAngleQuartic(), angleForce->getAmoebaGlobalAnglePentic(),
angleForce->getAmoebaGlobalAngleSextic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3;
......@@ -1048,7 +1048,7 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
throwException(__FILE__, __LINE__, buffer );
}
AmoebaHarmonicInPlaneAngleForce* angleForce = new AmoebaHarmonicInPlaneAngleForce();
AmoebaInPlaneAngleForce* angleForce = new AmoebaInPlaneAngleForce();
MapStringIntI forceActive = forceMap.find( AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE );
if( forceActive != forceMap.end() && (*forceActive).second ){
system.addForce( angleForce );
......@@ -1078,7 +1078,7 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
angleForce->addAngle( particle1, particle2, particle3, particle4, angle, k );
} else {
char buffer[1024];
(void) sprintf( buffer, "%s AmoebaHarmonicInPlaneAngleForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) sprintf( buffer, "%s AmoebaInPlaneAngleForce tokens incomplete at line=%d\n", methodName.c_str(), *lineCount );
(void) fprintf( log, "%s", buffer );
throwException(__FILE__, __LINE__, buffer );
}
......@@ -1101,16 +1101,16 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
}
} else if( field == "AmoebaHarmonicInPlaneAngleCubic" ){
angleForce->setAmoebaGlobalHarmonicInPlaneAngleCubic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalInPlaneAngleCubic( atof( tokens[1].c_str() ) );
hits++;
} else if( field == "AmoebaHarmonicInPlaneAngleQuartic" ){
angleForce->setAmoebaGlobalHarmonicInPlaneAngleQuartic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalInPlaneAngleQuartic( atof( tokens[1].c_str() ) );
hits++;
} else if( field == "AmoebaHarmonicInPlaneAnglePentic" ){
angleForce->setAmoebaGlobalHarmonicInPlaneAnglePentic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalInPlaneAnglePentic( atof( tokens[1].c_str() ) );
hits++;
} else if( field == "AmoebaHarmonicInPlaneAngleSextic" ){
angleForce->setAmoebaGlobalHarmonicInPlaneAngleSextic( atof( tokens[1].c_str() ) );
angleForce->setAmoebaGlobalInPlaneAngleSextic( atof( tokens[1].c_str() ) );
hits++;
}
}
......@@ -1133,12 +1133,12 @@ static int readAmoebaHarmonicInPlaneAngleParameters( FILE* filePtr, MapStringInt
if( log ){
static const unsigned int maxPrint = MAX_PRINT;
unsigned int arraySize = static_cast<unsigned int>(angleForce->getNumAngles());
(void) fprintf( log, "%s: %u sample of AmoebaHarmonicInPlaneAngleForce parameters in %s units; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
(void) fprintf( log, "%s: %u sample of AmoebaInPlaneAngleForce parameters in %s units; cubic=%15.7e quartic=%15.7e pentic=%15.7e sextic=%15.7e\n",
methodName.c_str(), arraySize, (useOpenMMUnits ? "OpenMM" : "Amoeba"),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleCubic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleQuartic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAnglePentic(),
angleForce->getAmoebaGlobalHarmonicInPlaneAngleSextic() );
angleForce->getAmoebaGlobalInPlaneAngleCubic(),
angleForce->getAmoebaGlobalInPlaneAngleQuartic(),
angleForce->getAmoebaGlobalInPlaneAnglePentic(),
angleForce->getAmoebaGlobalInPlaneAngleSextic() );
for( unsigned int ii = 0; ii < arraySize; ii++ ){
int particle1, particle2, particle3, particle4;
......@@ -3452,7 +3452,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l
if( !hit ){
try {
AmoebaHarmonicBondForce& harmonicBondForce = dynamic_cast<AmoebaHarmonicBondForce&>(force);
AmoebaBondForce& harmonicBondForce = dynamic_cast<AmoebaBondForce&>(force);
forceMap[AMOEBA_HARMONIC_BOND_FORCE] = &force;
hit++;
} catch( std::bad_cast ){
......@@ -3570,7 +3570,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l
if( !hit ){
try {
AmoebaHarmonicAngleForce & harmonicAngleForce = dynamic_cast<AmoebaHarmonicAngleForce&>(force);
AmoebaAngleForce & harmonicAngleForce = dynamic_cast<AmoebaAngleForce&>(force);
forceMap[AMOEBA_HARMONIC_ANGLE_FORCE] = &force;
hit++;
} catch( std::bad_cast ){
......@@ -3582,7 +3582,7 @@ static void getStringForceMap( System& system, MapStringForce& forceMap, FILE* l
if( !hit ){
try {
AmoebaHarmonicInPlaneAngleForce & harmonicAngleForce = dynamic_cast<AmoebaHarmonicInPlaneAngleForce&>(force);
AmoebaInPlaneAngleForce & harmonicAngleForce = dynamic_cast<AmoebaInPlaneAngleForce&>(force);
forceMap[AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE] = &force;
hit++;
} catch( std::bad_cast ){
......@@ -3737,7 +3737,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
} else if( field == "AmoebaHarmonicBondParameters" ){
readAmoebaHarmonicBondParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, inputArgumentMap,&lineCount, log );
} else if( field == "AmoebaHarmonicBondForce" ){
} else if( field == "AmoebaBondForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_HARMONIC_BOND_FORCE], &lineCount, field, log );
} else if( field == "AmoebaHarmonicBondEnergy" ){
if( tokens.size() > 1 ){
......@@ -3759,7 +3759,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
} else if( field == "AmoebaHarmonicAngleParameters" ){
readAmoebaHarmonicAngleParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, inputArgumentMap, &lineCount, log );
} else if( field == "AmoebaHarmonicAngleForce" ){
} else if( field == "AmoebaAngleForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_HARMONIC_ANGLE_FORCE], &lineCount, field, log );
} else if( field == "AmoebaHarmonicAngleEnergy" ){
if( tokens.size() > 1 ){
......@@ -3770,7 +3770,7 @@ Integrator* readAmoebaParameterFile( const std::string& inputParameterFile, MapS
} else if( field == "AmoebaHarmonicInPlaneAngleParameters" ){
readAmoebaHarmonicInPlaneAngleParameters( filePtr, forceMap, tokens, system, useOpenMMUnits, inputArgumentMap, &lineCount, log );
} else if( field == "AmoebaHarmonicInPlaneAngleForce" ){
} else if( field == "AmoebaInPlaneAngleForce" ){
readVec3( filePtr, tokens, forces[AMOEBA_HARMONIC_IN_PLANE_ANGLE_FORCE], &lineCount, field, log );
} else if( field == "AmoebaHarmonicInPlaneAngleEnergy" ){
if( tokens.size() > 1 ){
......
plugins/amoeba/platforms/cuda-old/tests/AmoebaTinkerParameterFile.h
View file @ c6ebf6e2
......@@ -35,9 +35,9 @@
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/BrownianIntegrator.h"
#include "openmm/AmoebaHarmonicBondForce.h"
#include "openmm/AmoebaHarmonicAngleForce.h"
#include "openmm/AmoebaHarmonicInPlaneAngleForce.h"
#include "openmm/AmoebaBondForce.h"
#include "openmm/AmoebaAngleForce.h"
#include "openmm/AmoebaInPlaneAngleForce.h"
#include "openmm/AmoebaTorsionForce.h"
#include "openmm/AmoebaPiTorsionForce.h"
#include "openmm/AmoebaStretchBendForce.h"
......
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