Skip to content

GitLab

Commit 162d69a2 authored by peastman's avatar peastman
Browse files

Merge pull request #827 from peastman/reference 

Lots of cleanup to reference platform
parents 2379b982 c44c956d
Hide whitespace changes
Inline Side-by-side
Showing with 119 additions and 148 deletions
openmmapi/include/openmm/GBVIForce.h
View file @ 162d69a2
......@@ -157,7 +157,7 @@ public:
*
* @return number of bonds
*/
int getNumBonds( void ) const;
int getNumBonds() const;
/**
* Get the dielectric constant for the solvent.
......@@ -208,7 +208,7 @@ public:
/**
* Get Born radius scaling method
*/
BornRadiusScalingMethod getBornRadiusScalingMethod( void ) const;
BornRadiusScalingMethod getBornRadiusScalingMethod() const;
/**
* Set Born radius scaling method
*/
......@@ -216,7 +216,7 @@ public:
/**
* Get the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
double getQuinticLowerLimitFactor( void ) const;
double getQuinticLowerLimitFactor() const;
/**
* Set the lower limit factor used in the quintic spline scaling method (typically 0.5-0.8)
*/
......@@ -224,7 +224,7 @@ public:
/**
* Get the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
double getQuinticUpperBornRadiusLimit( void ) const;
double getQuinticUpperBornRadiusLimit() const;
/**
* Set the upper limit used in the quintic spline scaling method, measured in nm (~5.0)
*/
......
openmmapi/src/GBVIForce.cpp
View file @ 162d69a2
......@@ -77,7 +77,7 @@ void GBVIForce::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod( void ) const {
GBVIForce::BornRadiusScalingMethod GBVIForce::getBornRadiusScalingMethod() const {
return scalingMethod;
}
......@@ -85,7 +85,7 @@ void GBVIForce::setBornRadiusScalingMethod(BornRadiusScalingMethod method) {
scalingMethod = method;
}
double GBVIForce::getQuinticLowerLimitFactor( void ) const {
double GBVIForce::getQuinticLowerLimitFactor() const {
return quinticLowerLimitFactor;
}
......@@ -93,7 +93,7 @@ void GBVIForce::setQuinticLowerLimitFactor(double inputQuinticLowerLimitFactor )
quinticLowerLimitFactor = inputQuinticLowerLimitFactor;
}
double GBVIForce::getQuinticUpperBornRadiusLimit( void ) const {
double GBVIForce::getQuinticUpperBornRadiusLimit() const {
return quinticUpperBornRadiusLimit;
}
......@@ -113,7 +113,7 @@ void GBVIForce::setBondParameters( int index, int particle1, int particle2, doub
bonds[index].bondLength = bondLength;
}
int GBVIForce::getNumBonds( void ) const {
int GBVIForce::getNumBonds() const {
return (int) bonds.size();
}
......
openmmapi/src/GBVIForceImpl.cpp
View file @ 162d69a2
......@@ -145,8 +145,6 @@ int GBVIForceImpl::getBondsFromForces(ContextImpl& context) {
}
*/
#define GBVIDebug 0
void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<std::vector<int> >& bondIndices,
const std::vector<double> & bondLengths, std::vector<double> & scaledRadii) const {
......@@ -219,26 +217,6 @@ void GBVIForceImpl::findScaledRadii( int numberOfParticles, const std::vector<st
if( errors ){
throw OpenMMException("GBVIForceImpl::findScaledRadii errors -- aborting");
}
#if GBVIDebug
(void) fprintf( stderr, " R q gamma scaled radii no. bnds\n" );
double totalQ = 0.0;
for( int i = 0; i < (int) scaledRadii.size(); i++ ){
double charge;
double gamma;
double radiusI;
owner.getParticleParameters(i, charge, radiusI, gamma);
totalQ += charge;
(void) fprintf( stderr, "%4d %14.5e %14.5e %14.5e %14.5e %d\n", i, radiusI, charge, gamma, scaledRadii[i], (int) bonded12[i].size() );
}
(void) fprintf( stderr, "Total charge=%e\n", totalQ );
(void) fflush( stderr );
#endif
#undef GBVIDebug
}
double GBVIForceImpl::calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups) {
......
platforms/cpu/include/CpuLangevinDynamics.h
View file @ 162d69a2
......@@ -31,7 +31,7 @@
#include "openmm/internal/ThreadPool.h"
#include "sfmt/SFMT.h"
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class CpuLangevinDynamics : public ReferenceStochasticDynamics {
public:
......@@ -95,6 +95,6 @@ private:
OpenMM::RealVec* xPrime;
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __CPU_LANGEVIN_DYNAMICS_H__
platforms/cpu/src/CpuCustomGBForce.cpp
View file @ 162d69a2
......@@ -25,8 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomGBForce.h"
......
platforms/cpu/src/CpuCustomManyParticleForce.cpp
View file @ 162d69a2
......@@ -26,8 +26,6 @@
#include <sstream>
#include <utility>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomManyParticleForce.h"
......
platforms/cpu/src/CpuCustomNonbondedForce.cpp
View file @ 162d69a2
......@@ -25,8 +25,6 @@
#include <string.h>
#include <sstream>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceForce.h"
#include "CpuCustomNonbondedForce.h"
......
platforms/cpu/src/CpuLangevinDynamics.cpp
View file @ 162d69a2
......@@ -23,8 +23,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMLog.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuLangevinDynamics.h"
......
platforms/cpu/src/CpuNonbondedForce.cpp
View file @ 162d69a2
......@@ -24,7 +24,6 @@
#include <complex>
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForce.h"
#include "ReferenceForce.h"
......
platforms/cpu/src/CpuNonbondedForceVec4.cpp
View file @ 162d69a2
......@@ -22,7 +22,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec4.h"
......
platforms/cpu/src/CpuNonbondedForceVec8.cpp
View file @ 162d69a2
......@@ -22,7 +22,6 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "CpuNonbondedForceVec8.h"
#include "openmm/OpenMMException.h"
......
platforms/reference/include/GBVIParameters.h
View file @ 162d69a2
......@@ -25,9 +25,10 @@
#ifndef __GBVIParameters_H__
#define __GBVIParameters_H__
#include "SimTKOpenMMCommon.h"
#include "RealVec.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class GBVIParameters {
......@@ -57,9 +58,9 @@ class GBVIParameters {
// parameter vectors
RealOpenMMVector _atomicRadii;
RealOpenMMVector _scaledRadii;
RealOpenMMVector _gammaParameters;
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _scaledRadii;
std::vector<RealOpenMM> _gammaParameters;
// cutoff and periodic boundary conditions
......@@ -82,7 +83,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
GBVIParameters( int numberOfAtoms );
GBVIParameters(int numberOfAtoms);
/**---------------------------------------------------------------------------------------
......@@ -90,7 +91,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
~GBVIParameters( );
~GBVIParameters();
/**---------------------------------------------------------------------------------------
......@@ -100,7 +101,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
int getNumberOfAtoms( void ) const;
int getNumberOfAtoms() const;
/**---------------------------------------------------------------------------------------
......@@ -110,7 +111,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getElectricConstant( void ) const;
RealOpenMM getElectricConstant() const;
/**---------------------------------------------------------------------------------------
......@@ -120,7 +121,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSolventDielectric( void ) const;
RealOpenMM getSolventDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -130,7 +131,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setSolventDielectric( RealOpenMM solventDielectric );
void setSolventDielectric(RealOpenMM solventDielectric);
/**---------------------------------------------------------------------------------------
......@@ -140,7 +141,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSoluteDielectric( void ) const;
RealOpenMM getSoluteDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -150,7 +151,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setSoluteDielectric( RealOpenMM soluteDielectric );
void setSoluteDielectric(RealOpenMM soluteDielectric);
/**---------------------------------------------------------------------------------------
......@@ -160,7 +161,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadii( void ) const;
const std::vector<RealOpenMM>& getScaledRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -170,7 +171,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadii( const RealOpenMMVector& scaledRadii );
void setScaledRadii(const std::vector<RealOpenMM>& scaledRadii);
/**---------------------------------------------------------------------------------------
......@@ -180,7 +181,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii( void ) const;
const std::vector<RealOpenMM>& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -190,7 +191,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
/**---------------------------------------------------------------------------------------
......@@ -200,7 +201,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getGammaParameters( void ) const;
const std::vector<RealOpenMM>& getGammaParameters() const;
/**---------------------------------------------------------------------------------------
......@@ -210,7 +211,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setGammaParameters( const RealOpenMMVector& gammaParameters );
void setGammaParameters(const std::vector<RealOpenMM>& gammaParameters);
/**---------------------------------------------------------------------------------------
......@@ -220,7 +221,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance );
void setUseCutoff(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
......@@ -274,7 +275,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getTau( void ) const;
RealOpenMM getTau() const;
/**---------------------------------------------------------------------------------------
......@@ -284,7 +285,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
int getBornRadiusScalingMethod( void ) const;
int getBornRadiusScalingMethod() const;
/**---------------------------------------------------------------------------------------
......@@ -294,7 +295,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setBornRadiusScalingMethod( int bornRadiusScalingMethod );
void setBornRadiusScalingMethod(int bornRadiusScalingMethod);
/**---------------------------------------------------------------------------------------
......@@ -304,7 +305,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getQuinticLowerLimitFactor( void ) const;
RealOpenMM getQuinticLowerLimitFactor() const;
/**---------------------------------------------------------------------------------------
......@@ -314,7 +315,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFactor );
void setQuinticLowerLimitFactor(RealOpenMM quinticLowerLimitFactor);
/**---------------------------------------------------------------------------------------
......@@ -324,7 +325,7 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getQuinticUpperBornRadiusLimit( void ) const;
RealOpenMM getQuinticUpperBornRadiusLimit() const;
/**---------------------------------------------------------------------------------------
......@@ -334,8 +335,10 @@ class GBVIParameters {
--------------------------------------------------------------------------------------- */
void setQuinticUpperBornRadiusLimit( RealOpenMM quinticUpperSplineLimit );
void setQuinticUpperBornRadiusLimit(RealOpenMM quinticUpperSplineLimit);
};
} // namespace OpenMM
#endif // __GBVIParameters_H__
platforms/reference/include/ObcParameters.h
View file @ 162d69a2
......@@ -25,9 +25,10 @@
#ifndef __ObcParameters_H__
#define __ObcParameters_H__
#include "SimTKOpenMMCommon.h"
#include "RealVec.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class ObcParameters {
......@@ -57,8 +58,8 @@ class ObcParameters {
// scaled radius factors (S_kk in HCT paper)
RealOpenMMVector _atomicRadii;
RealOpenMMVector _scaledRadiusFactors;
std::vector<RealOpenMM> _atomicRadii;
std::vector<RealOpenMM> _scaledRadiusFactors;
// cutoff and periodic boundary conditions
......@@ -75,7 +76,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setDielectricOffset( RealOpenMM dielectricOffset );
void setDielectricOffset(RealOpenMM dielectricOffset);
public:
......@@ -87,7 +88,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType = ObcTypeII );
ObcParameters(int numberOfAtoms, ObcParameters::ObcType obcType = ObcTypeII);
/**---------------------------------------------------------------------------------------
......@@ -95,7 +96,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
~ObcParameters( );
~ObcParameters();
/**---------------------------------------------------------------------------------------
......@@ -105,7 +106,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
int getNumberOfAtoms( void ) const;
int getNumberOfAtoms() const;
/**---------------------------------------------------------------------------------------
......@@ -115,7 +116,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getElectricConstant( void ) const;
RealOpenMM getElectricConstant() const;
/**---------------------------------------------------------------------------------------
......@@ -125,7 +126,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getProbeRadius( void ) const;
RealOpenMM getProbeRadius() const;
/**---------------------------------------------------------------------------------------
......@@ -135,7 +136,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setProbeRadius( RealOpenMM probeRadius );
void setProbeRadius(RealOpenMM probeRadius);
/**---------------------------------------------------------------------------------------
......@@ -146,7 +147,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getPi4Asolv( void ) const;
RealOpenMM getPi4Asolv() const;
/**---------------------------------------------------------------------------------------
......@@ -154,7 +155,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setPi4Asolv( RealOpenMM pi4Asolv );
void setPi4Asolv(RealOpenMM pi4Asolv);
/**---------------------------------------------------------------------------------------
......@@ -164,7 +165,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSolventDielectric( void ) const;
RealOpenMM getSolventDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -174,7 +175,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setSolventDielectric( RealOpenMM solventDielectric );
void setSolventDielectric(RealOpenMM solventDielectric);
/**---------------------------------------------------------------------------------------
......@@ -184,7 +185,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getSoluteDielectric( void ) const;
RealOpenMM getSoluteDielectric() const;
/**---------------------------------------------------------------------------------------
......@@ -194,7 +195,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setSoluteDielectric( RealOpenMM soluteDielectric );
void setSoluteDielectric(RealOpenMM soluteDielectric);
/**---------------------------------------------------------------------------------------
......@@ -204,7 +205,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
ObcParameters::ObcType getObcType( void ) const;
ObcParameters::ObcType getObcType() const;
/**---------------------------------------------------------------------------------------
......@@ -214,7 +215,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setObcTypeParameters( ObcParameters::ObcType obcType );
void setObcTypeParameters(ObcParameters::ObcType obcType);
/**---------------------------------------------------------------------------------------
......@@ -224,7 +225,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getAlphaObc( void ) const;
RealOpenMM getAlphaObc() const;
/**---------------------------------------------------------------------------------------
......@@ -234,7 +235,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getBetaObc( void ) const;
RealOpenMM getBetaObc() const;
/**---------------------------------------------------------------------------------------
......@@ -244,7 +245,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getGammaObc( void ) const;
RealOpenMM getGammaObc() const;
/**---------------------------------------------------------------------------------------
......@@ -254,7 +255,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
RealOpenMM getDielectricOffset( void ) const;
RealOpenMM getDielectricOffset() const;
/**---------------------------------------------------------------------------------------
......@@ -264,7 +265,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getScaledRadiusFactors( void ) const;
const std::vector<RealOpenMM>& getScaledRadiusFactors() const;
/**---------------------------------------------------------------------------------------
......@@ -274,7 +275,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors );
void setScaledRadiusFactors(const std::vector<RealOpenMM>& scaledRadiusFactors);
/**---------------------------------------------------------------------------------------
......@@ -284,7 +285,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& getAtomicRadii( void ) const;
const std::vector<RealOpenMM>& getAtomicRadii() const;
/**---------------------------------------------------------------------------------------
......@@ -294,7 +295,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setAtomicRadii( const RealOpenMMVector& atomicRadii );
void setAtomicRadii(const std::vector<RealOpenMM>& atomicRadii);
/**---------------------------------------------------------------------------------------
......@@ -305,7 +306,7 @@ class ObcParameters {
--------------------------------------------------------------------------------------- */
void setUseCutoff( RealOpenMM distance );
void setUseCutoff(RealOpenMM distance);
/**---------------------------------------------------------------------------------------
......@@ -352,7 +353,7 @@ class ObcParameters {
const OpenMM::RealVec* getPeriodicBox();
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ObcParameters_H__
platforms/reference/include/ReferenceAndersenThermostat.h
View file @ 162d69a2
......@@ -25,10 +25,9 @@
#ifndef __ReferenceAndersenThermostat_H__
#define __ReferenceAndersenThermostat_H__
#include "SimTKOpenMMCommon.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class ReferenceAndersenThermostat {
......@@ -42,7 +41,7 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */
ReferenceAndersenThermostat( );
ReferenceAndersenThermostat();
/**---------------------------------------------------------------------------------------
......@@ -50,7 +49,7 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */
~ReferenceAndersenThermostat( );
~ReferenceAndersenThermostat();
/**---------------------------------------------------------------------------------------
......@@ -65,11 +64,11 @@ class ReferenceAndersenThermostat {
--------------------------------------------------------------------------------------- */
void applyThermostat( const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize ) const;
void applyThermostat(const std::vector<std::vector<int> >& atomGroups, std::vector<OpenMM::RealVec>& atomVelocities, std::vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const;
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ReferenceAndersenThermostat_H__
platforms/reference/include/ReferenceAngleBondIxn.h
View file @ 162d69a2
......@@ -27,7 +27,7 @@
#include "ReferenceBondIxn.h"
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class ReferenceAngleBondIxn : public ReferenceBondIxn {
......@@ -41,7 +41,7 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn( );
ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -49,7 +49,7 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceAngleBondIxn( );
~ReferenceAngleBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -63,8 +63,8 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void getPrefactorsGivenAngleCosine( RealOpenMM cosine, RealOpenMM* angleParameters,
RealOpenMM* dEdR, RealOpenMM* energyTerm ) const;
void getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM* angleParameters,
RealOpenMM* dEdR, RealOpenMM* energyTerm) const;
/**---------------------------------------------------------------------------------------
......@@ -79,13 +79,13 @@ class ReferenceAngleBondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ReferenceAngleBondIxn_H__
platforms/reference/include/ReferenceBondForce.h
View file @ 162d69a2
......@@ -28,7 +28,7 @@
#include "ReferenceForce.h"
#include "ReferenceBondIxn.h"
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
......@@ -42,7 +42,7 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */
ReferenceBondForce( );
ReferenceBondForce();
/**---------------------------------------------------------------------------------------
......@@ -50,7 +50,7 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */
~ReferenceBondForce( );
~ReferenceBondForce();
/**---------------------------------------------------------------------------------------
......@@ -67,13 +67,13 @@ class OPENMM_EXPORT ReferenceBondForce : public ReferenceForce {
--------------------------------------------------------------------------------------- */
void calculateForce( int numberOfBonds, int** atomIndices,
void calculateForce(int numberOfBonds, int** atomIndices,
std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn );
RealOpenMM* totalEnergy, ReferenceBondIxn& referenceBondIxn);
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ReferenceBondForce_H__
platforms/reference/include/ReferenceBondIxn.h
View file @ 162d69a2
......@@ -29,7 +29,7 @@
#include "openmm/internal/windowsExport.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class OPENMM_EXPORT ReferenceBondIxn {
......@@ -43,7 +43,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
ReferenceBondIxn( );
ReferenceBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
~ReferenceBondIxn( );
~ReferenceBondIxn();
/**---------------------------------------------------------------------------------------
......@@ -65,9 +65,9 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
virtual void calculateBondIxn( int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
virtual void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy ) const;
RealOpenMM* totalEnergy) const;
/**---------------------------------------------------------------------------------------
......@@ -82,7 +82,7 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
static RealOpenMM getNormedDotProduct( RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry );
static RealOpenMM getNormedDotProduct(RealOpenMM* vector1, RealOpenMM* vector2, int hasREntry);
/**---------------------------------------------------------------------------------------
......@@ -98,8 +98,8 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
static RealOpenMM getAngleBetweenTwoVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct, int hasREntry );
static RealOpenMM getAngleBetweenTwoVectors(RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct, int hasREntry);
/**---------------------------------------------------------------------------------------
......@@ -119,13 +119,13 @@ class OPENMM_EXPORT ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
static RealOpenMM getDihedralAngleBetweenThreeVectors( RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM** outputCrossProduct,
RealOpenMM* cosineOfAngle, RealOpenMM* signVector,
RealOpenMM* signOfAngle, int hasREntry );
static RealOpenMM getDihedralAngleBetweenThreeVectors(RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* vector3, RealOpenMM** outputCrossProduct,
RealOpenMM* cosineOfAngle, RealOpenMM* signVector,
RealOpenMM* signOfAngle, int hasREntry);
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ReferenceBondIxn_H__
platforms/reference/include/ReferenceBrownianDynamics.h
View file @ 162d69a2
......@@ -27,7 +27,7 @@
#include "ReferenceDynamics.h"
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class ReferenceBrownianDynamics : public ReferenceDynamics {
......@@ -50,7 +50,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceBrownianDynamics( int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature );
ReferenceBrownianDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature);
/**---------------------------------------------------------------------------------------
......@@ -58,7 +58,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
~ReferenceBrownianDynamics( );
~ReferenceBrownianDynamics();
/**---------------------------------------------------------------------------------------
......@@ -68,7 +68,7 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getFriction( void ) const;
RealOpenMM getFriction() const;
/**---------------------------------------------------------------------------------------
......@@ -88,6 +88,6 @@ class ReferenceBrownianDynamics : public ReferenceDynamics {
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ReferenceBrownianDynamics_H__
platforms/reference/include/ReferenceCCMAAlgorithm.h
View file @ 162d69a2
......@@ -30,7 +30,7 @@
#include <vector>
#include <set>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class OPENMM_EXPORT ReferenceCCMAAlgorithm : public ReferenceConstraintAlgorithm {
......@@ -69,22 +69,22 @@ public:
*/
ReferenceCCMAAlgorithm(int numberOfAtoms, int numberOfConstraints, const std::vector<std::pair<int, int> >& atomIndices, const std::vector<RealOpenMM>& distance, std::vector<RealOpenMM>& masses, std::vector<AngleInfo>& angles);
~ReferenceCCMAAlgorithm( );
~ReferenceCCMAAlgorithm();
/**
* Get the number of constraints.
*/
int getNumberOfConstraints( void ) const;
int getNumberOfConstraints() const;
/**
* Get the maximum number of iterations to perform.
*/
int getMaximumNumberOfIterations( void ) const;
int getMaximumNumberOfIterations() const;
/**
* Set the maximum number of iterations to perform.
*/
void setMaximumNumberOfIterations( int maximumNumberOfIterations );
void setMaximumNumberOfIterations(int maximumNumberOfIterations);
/**
* Apply the constraint algorithm.
......@@ -120,6 +120,6 @@ public:
}
};
// ---------------------------------------------------------------------------------------
} // namespace OpenMM
#endif // __ReferenceCCMAAlgorithm_H__
platforms/reference/include/ReferenceCMAPTorsionIxn.h
View file @ 162d69a2
......@@ -25,12 +25,11 @@
#ifndef __ReferenceCMAPTorsionIxn_H__
#define __ReferenceCMAPTorsionIxn_H__
#include "SimTKOpenMMCommon.h"
#include "SimTKOpenMMUtilities.h"
#include "ReferenceBondIxn.h"
#include <vector>
// ---------------------------------------------------------------------------------------
namespace OpenMM {
class ReferenceCMAPTorsionIxn : public ReferenceBondIxn {
......@@ -92,4 +91,6 @@ public:
};
} // namespace OpenMM
#endif // __ReferenceCMAPTorsionIxn_H__
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment