Skip to content

GitLab

Commit 8469621f authored by peastman's avatar peastman Committed by GitHub
Browse files

Merge pull request #1747 from peastman/realtype 

Eliminated RealOpenMM
parents b84e22ba 6813ca57
Expand all Show whitespace changes
Inline Side-by-side
Showing with 474 additions and 650 deletions
platforms/reference/include/ReferencePME.h
View file @ 8469621f
......@@ -32,13 +32,13 @@
#ifndef __ReferencePME_H__
#define __ReferencePME_H__
#include "RealVec.h"
#include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h"
#include <vector>
namespace OpenMM {
typedef RealOpenMM rvec[3];
typedef double rvec[3];
typedef struct pme *
......@@ -59,12 +59,12 @@ pme_t;
* epsilon_r Dielectric coefficient, typically 1.0.
*/
int OPENMM_EXPORT
pme_init(pme_t * ppme,
RealOpenMM ewaldcoeff,
pme_init(pme_t* ppme,
double ewaldcoeff,
int natoms,
const int ngrid[3],
int pme_order,
RealOpenMM epsilon_r);
double epsilon_r);
/*
* Evaluate reciprocal space PME energy and forces.
......@@ -80,14 +80,14 @@ pme_init(pme_t * ppme,
*/
int OPENMM_EXPORT
pme_exec(pme_t pme,
const std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& forces,
const std::vector<RealOpenMM>& charges,
const OpenMM::RealVec periodicBoxVectors[3],
RealOpenMM * energy);
const std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& forces,
const std::vector<double>& charges,
const OpenMM::Vec3 periodicBoxVectors[3],
double* energy);
/*
/**
* Evaluate reciprocal space PME dispersion energy and forces.
*
* Args:
......@@ -101,11 +101,11 @@ pme_exec(pme_t pme,
*/
int OPENMM_EXPORT
pme_exec_dpme(pme_t pme,
const std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& forces,
const std::vector<RealOpenMM>& c6s,
const OpenMM::RealVec periodicBoxVectors[3],
RealOpenMM * energy);
const std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& forces,
const std::vector<double>& c6s,
const OpenMM::Vec3 periodicBoxVectors[3],
double* energy);
......
platforms/reference/include/ReferencePairIxn.h
View file @ 8469621f
......@@ -25,7 +25,7 @@
#ifndef __ReferencePairIxn_H__
#define __ReferencePairIxn_H__
#include "RealVec.h"
#include "openmm/Vec3.h"
#include "openmm/internal/windowsExport.h"
#include <vector>
......@@ -68,10 +68,10 @@ class OPENMM_EXPORT ReferencePairIxn {
--------------------------------------------------------------------------------------- */
virtual void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy) const = 0;
virtual void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
double** atomParameters, int** exclusions,
double* fixedParameters, std::vector<OpenMM::Vec3>& forces,
double* energyByAtom, double* totalEnergy) const = 0;
};
......
platforms/reference/include/ReferenceProperDihedralBond.h
View file @ 8469621f
......@@ -34,7 +34,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
Vec3 boxVectors[3];
public:
......@@ -62,7 +62,7 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
void setPeriodic(OpenMM::Vec3* vectors);
/**---------------------------------------------------------------------------------------
......@@ -78,9 +78,9 @@ class OPENMM_EXPORT ReferenceProperDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs);
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
double* parameters, std::vector<OpenMM::Vec3>& forces,
double* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceRbDihedralBond.h
View file @ 8469621f
......@@ -34,7 +34,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
private:
bool usePeriodic;
RealVec boxVectors[3];
Vec3 boxVectors[3];
public:
......@@ -62,7 +62,7 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void setPeriodic(OpenMM::RealVec* vectors);
void setPeriodic(OpenMM::Vec3* vectors);
/**---------------------------------------------------------------------------------------
......@@ -76,9 +76,9 @@ class OPENMM_EXPORT ReferenceRbDihedralBond : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM* parameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs);
void calculateBondIxn(int* atomIndices, std::vector<OpenMM::Vec3>& atomCoordinates,
double* parameters, std::vector<OpenMM::Vec3>& forces,
double* totalEnergy, double* energyParamDerivs);
};
......
platforms/reference/include/ReferenceSETTLEAlgorithm.h
View file @ 8469621f
......@@ -44,7 +44,7 @@ namespace OpenMM {
class OPENMM_EXPORT ReferenceSETTLEAlgorithm : public ReferenceConstraintAlgorithm {
public:
ReferenceSETTLEAlgorithm(const std::vector<int>& atom1, const std::vector<int>& atom2, const std::vector<int>& atom3,
const std::vector<RealOpenMM>& distance1, const std::vector<RealOpenMM>& distance2, std::vector<RealOpenMM>& masses);
const std::vector<double>& distance1, const std::vector<double>& distance2, std::vector<double>& masses);
/**
* Get the number of clusters.
......@@ -60,7 +60,7 @@ public:
* @param distance1 the distance between atoms 1 and 2
* @param distance2 the distance between atoms 2 and 3
*/
void getClusterParameters(int index, int& atom1, int& atom2, int& atom3, RealOpenMM& distance1, RealOpenMM& distance2) const;
void getClusterParameters(int index, int& atom1, int& atom2, int& atom3, double& distance1, double& distance2) const;
/**
* Apply the constraint algorithm.
*
......@@ -69,7 +69,7 @@ public:
* @param inverseMasses 1/mass
* @param tolerance the constraint tolerance
*/
void apply(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& atomCoordinatesP, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance);
void apply(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& atomCoordinatesP, std::vector<double>& inverseMasses, double tolerance);
/**
* Apply the constraint algorithm to velocities.
......@@ -79,14 +79,14 @@ public:
* @param inverseMasses 1/mass
* @param tolerance the constraint tolerance
*/
void applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance);
void applyToVelocities(std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses, double tolerance);
private:
std::vector<int> atom1;
std::vector<int> atom2;
std::vector<int> atom3;
std::vector<RealOpenMM> distance1;
std::vector<RealOpenMM> distance2;
std::vector<RealOpenMM> masses;
std::vector<double> distance1;
std::vector<double> distance2;
std::vector<double> masses;
};
} // namespace OpenMM
......
platforms/reference/include/ReferenceStochasticDynamics.h
View file @ 8469621f
......@@ -34,9 +34,9 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
protected:
std::vector<OpenMM::RealVec> xPrime;
std::vector<RealOpenMM> inverseMasses;
RealOpenMM friction;
std::vector<OpenMM::Vec3> xPrime;
std::vector<double> inverseMasses;
double friction;
public:
......@@ -51,7 +51,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceStochasticDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM friction, RealOpenMM temperature);
ReferenceStochasticDynamics(int numberOfAtoms, double deltaT, double friction, double temperature);
/**---------------------------------------------------------------------------------------
......@@ -67,7 +67,7 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getFriction() const;
double getFriction() const;
/**---------------------------------------------------------------------------------------
......@@ -82,8 +82,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void update(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, RealOpenMM tolerance);
void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance);
/**---------------------------------------------------------------------------------------
......@@ -98,8 +98,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
virtual void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
virtual void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
/**---------------------------------------------------------------------------------------
......@@ -113,8 +113,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
virtual void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
virtual void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
/**---------------------------------------------------------------------------------------
......@@ -127,8 +127,8 @@ class OPENMM_EXPORT ReferenceStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
virtual void updatePart3(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<RealOpenMM>& inverseMasses, std::vector<OpenMM::RealVec>& xPrime);
virtual void updatePart3(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<double>& inverseMasses, std::vector<OpenMM::Vec3>& xPrime);
};
} // namespace OpenMM
......
platforms/reference/include/ReferenceVariableStochasticDynamics.h
View file @ 8469621f
......@@ -33,9 +33,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
private:
std::vector<OpenMM::RealVec> xPrime;
std::vector<RealOpenMM> inverseMasses;
RealOpenMM friction, _accuracy;
std::vector<OpenMM::Vec3> xPrime;
std::vector<double> inverseMasses;
double friction, _accuracy;
public:
......@@ -50,7 +50,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceVariableStochasticDynamics(int numberOfAtoms, RealOpenMM friction, RealOpenMM temperature, RealOpenMM accuracy);
ReferenceVariableStochasticDynamics(int numberOfAtoms, double friction, double temperature, double accuracy);
/**---------------------------------------------------------------------------------------
......@@ -66,7 +66,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getFriction() const;
double getFriction() const;
/**---------------------------------------------------------------------------------------
......@@ -76,7 +76,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getAccuracy() const;
double getAccuracy() const;
/**---------------------------------------------------------------------------------------
......@@ -84,7 +84,7 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void setAccuracy(RealOpenMM accuracy);
void setAccuracy(double accuracy);
/**---------------------------------------------------------------------------------------
......@@ -100,8 +100,8 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void update(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance);
void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double maxStepSize, double tolerance);
/**---------------------------------------------------------------------------------------
......@@ -118,9 +118,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void updatePart1(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, std::vector<RealOpenMM>& inverseMasses,
std::vector<OpenMM::RealVec>& xPrime, RealOpenMM maxStepSize);
void updatePart1(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, std::vector<double>& inverseMasses,
std::vector<OpenMM::Vec3>& xPrime, double maxStepSize);
/**---------------------------------------------------------------------------------------
......@@ -134,9 +134,9 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void updatePart2(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& velocities,
std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& inverseMasses,
std::vector<OpenMM::RealVec>& xPrime);
void updatePart2(int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& velocities,
std::vector<OpenMM::Vec3>& forces, std::vector<double>& inverseMasses,
std::vector<OpenMM::Vec3>& xPrime);
};
......
platforms/reference/include/ReferenceVariableVerletDynamics.h
View file @ 8469621f
......@@ -33,9 +33,9 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
private:
std::vector<OpenMM::RealVec> xPrime;
std::vector<RealOpenMM> inverseMasses;
RealOpenMM _accuracy;
std::vector<OpenMM::Vec3> xPrime;
std::vector<double> inverseMasses;
double _accuracy;
public:
......@@ -48,7 +48,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceVariableVerletDynamics(int numberOfAtoms, RealOpenMM accuracy);
ReferenceVariableVerletDynamics(int numberOfAtoms, double accuracy);
/**---------------------------------------------------------------------------------------
......@@ -66,7 +66,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
RealOpenMM getAccuracy() const;
double getAccuracy() const;
/**---------------------------------------------------------------------------------------
......@@ -74,7 +74,7 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void setAccuracy(RealOpenMM accuracy);
void setAccuracy(double accuracy);
/**---------------------------------------------------------------------------------------
......@@ -90,8 +90,8 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void update(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance);
void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double maxStepSize, double tolerance);
};
......
platforms/reference/include/ReferenceVerletDynamics.h
View file @ 8469621f
......@@ -33,8 +33,8 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
private:
std::vector<OpenMM::RealVec> xPrime;
std::vector<RealOpenMM> inverseMasses;
std::vector<OpenMM::Vec3> xPrime;
std::vector<double> inverseMasses;
public:
......@@ -49,7 +49,7 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
ReferenceVerletDynamics(int numberOfAtoms, RealOpenMM deltaT);
ReferenceVerletDynamics(int numberOfAtoms, double deltaT);
/**---------------------------------------------------------------------------------------
......@@ -72,8 +72,8 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
--------------------------------------------------------------------------------------- */
void update(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses, RealOpenMM tolerance);
void update(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses, double tolerance);
};
......
platforms/reference/include/ReferenceVirtualSites.h
View file @ 8469621f
......@@ -33,7 +33,7 @@
#define __ReferenceVirtualSites_H__
#include "openmm/System.h"
#include "RealVec.h"
#include "openmm/Vec3.h"
#include <vector>
namespace OpenMM {
......@@ -43,11 +43,11 @@ public:
/**
* Compute the positions of all virtual sites.
*/
static void computePositions(const OpenMM::System& system, std::vector<OpenMM::RealVec>& atomCoordinates);
static void computePositions(const OpenMM::System& system, std::vector<OpenMM::Vec3>& atomCoordinates);
/**
* Distribute forces from virtual sites to the atoms they are based on.
*/
static void distributeForces(const OpenMM::System& system, const std::vector<OpenMM::RealVec>& atomCoordinates, std::vector<OpenMM::RealVec>& forces);
static void distributeForces(const OpenMM::System& system, const std::vector<OpenMM::Vec3>& atomCoordinates, std::vector<OpenMM::Vec3>& forces);
};
} // namespace OpenMM
......
platforms/reference/include/SimTKOpenMMRealType.h
View file @ 8469621f
/* Portions copyright (c) 2006 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -28,46 +28,6 @@
#include <cmath>
// Set RealOpenMMType to 2 for double precision, 1 for float
#ifndef RealOpenMMType
#define RealOpenMMType 2
#endif
#if RealOpenMMType == 1
#define RealOpenMM float
#define SQRT sqrtf
#define POW powf
#define SIN sinf
#define COS cosf
#define TAN tanf
// LOG is used in Vishal's gpu code; modifying LOG -> LN
#define LN logf
#define EXP expf
#define FABS fabsf
#define ACOS acosf
#define ASIN asinf
#define ATAN atanf
#define TANH tanhf
#define FLOOR floorf
#define ATOF atoff
#define PI_M 3.141592653589f
#define TWO_SIX 1.122462048309372981f
#define RADIAN 57.29577951308f
#define RADIAN_TO_DEGREE 57.29577951308f
#define LOG_TEN 2.302585092994045684f
#define SQRT_TWO 1.41421356237309504f
#define DEGREE_TO_RADIAN 0.01745329252f
#define RADIAN_INVERSE 0.01745329252f
#else
#define RealOpenMM double
#define SQRT sqrt
#define POW pow
......@@ -98,8 +58,6 @@
#define DEGREE_TO_RADIAN 0.01745329252
#define RADIAN_INVERSE 0.01745329252
#endif
#define DOT3(u,v) ((u[0])*(v[0]) + (u[1])*(v[1]) + (u[2])*(v[2]))
#define MATRIXDOT3(u,v) u[0]*v[0] + u[1]*v[1] + u[2]*v[2] + \
......
platforms/reference/include/SimTKOpenMMUtilities.h
View file @ 8469621f
......@@ -27,7 +27,7 @@
// class of shared, static utility methods
#include "RealVec.h"
#include "SimTKOpenMMRealType.h"
#include "sfmt/SFMT.h"
#include "openmm/internal/windowsExport.h"
......@@ -49,7 +49,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
static uint32_t _randomNumberSeed;
static bool _randomInitialized;
static bool nextGaussianIsValid;
static RealOpenMM nextGaussian;
static double nextGaussian;
static OpenMM_SFMT::SFMT sfmt;
public:
......@@ -61,7 +61,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
/**---------------------------------------------------------------------------------------
Allocate 1D RealOpenMM array (Simbios)
Allocate 1D double array (Simbios)
array[i]
......@@ -75,13 +75,13 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static RealOpenMM* allocateOneDRealOpenMMArray(int iSize, RealOpenMM* array1D, int initialize,
RealOpenMM initialValue,
static double* allocateOneDRealOpenMMArray(int iSize, double* array1D, int initialize,
double initialValue,
const std::string& idString = std::string("1DArray"));
/**---------------------------------------------------------------------------------------
Allocate 2D RealOpenMM array (Simbios)
Allocate 2D double array (Simbios)
array[i][j]
......@@ -96,14 +96,14 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static RealOpenMM** allocateTwoDRealOpenMMArray(int iSize, int jSize,
RealOpenMM** array2D, int initialize,
RealOpenMM initialValue,
static double** allocateTwoDRealOpenMMArray(int iSize, int jSize,
double** array2D, int initialize,
double initialValue,
const std::string& idString = std::string("2DArray"));
/* ---------------------------------------------------------------------------------------
Free 2D RealOpenMM array (Simbios)
Free 2D double array (Simbios)
array[i][j]
......@@ -112,12 +112,12 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static void freeOneDRealOpenMMArray(RealOpenMM* array1D,
static void freeOneDRealOpenMMArray(double* array1D,
const std::string& idString = std::string("1DArray"));
/* ---------------------------------------------------------------------------------------
Free 2D RealOpenMM array (Simbios)
Free 2D double array (Simbios)
array[i][j]
......@@ -126,12 +126,12 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static void freeTwoDRealOpenMMArray(RealOpenMM** array2D,
static void freeTwoDRealOpenMMArray(double** array2D,
const std::string& idString = std::string("2DArray"));
/**---------------------------------------------------------------------------------------
Initialize 2D RealOpenMM array (Simbios)
Initialize 2D double array (Simbios)
array[i][j]
......@@ -143,7 +143,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static void initialize2DRealOpenMMArray(int iSize, int jSize,
RealOpenMM** array2D, RealOpenMM initialValue);
double** array2D, double initialValue);
/**---------------------------------------------------------------------------------------
......@@ -159,7 +159,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static void crossProductVector3(RealOpenMM* vectorX, RealOpenMM* vectorY, RealOpenMM* vectorZ);
static void crossProductVector3(double* vectorX, double* vectorY, double* vectorZ);
/**---------------------------------------------------------------------------------------
......@@ -169,7 +169,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static RealOpenMM getNormallyDistributedRandomNumber();
static double getNormallyDistributedRandomNumber();
/**---------------------------------------------------------------------------------------
......@@ -179,7 +179,7 @@ class OPENMM_EXPORT SimTKOpenMMUtilities {
--------------------------------------------------------------------------------------- */
static RealOpenMM getUniformlyDistributedRandomNumber();
static double getUniformlyDistributedRandomNumber();
/**---------------------------------------------------------------------------------------
......
platforms/reference/include/fftpack.h
View file @ 8469621f
......@@ -20,7 +20,6 @@
#include <stdio.h>
#include "RealVec.h"
#include "openmm/internal/windowsExport.h"
#ifdef __cplusplus
......@@ -33,15 +32,15 @@ extern "C" {
class t_complex {
public:
RealOpenMM re;
RealOpenMM im;
double re;
double im;
t_complex() : re(0.0), im(0.0) {
}
t_complex(RealOpenMM re, RealOpenMM im) : re(re), im(im) {
t_complex(double re, double im) : re(re), im(im) {
}
t_complex(const t_complex& c) : re(c.re), im(c.im) {
}
t_complex operator*(RealOpenMM r) {
t_complex operator*(double r) {
return t_complex(re*r, im*r);
}
t_complex operator+(const t_complex& c) const {
......
platforms/reference/src/ReferencePlatform.cpp
View file @ 8469621f
......@@ -35,7 +35,7 @@
#include "ReferenceKernels.h"
#include "openmm/internal/ContextImpl.h"
#include "SimTKOpenMMRealType.h"
#include "RealVec.h"
#include "openmm/Vec3.h"
#include <map>
#include <vector>
......@@ -82,7 +82,7 @@ double ReferencePlatform::getSpeed() const {
}
bool ReferencePlatform::supportsDoublePrecision() const {
return (sizeof(RealOpenMM) >= sizeof(double));
return true;
}
void ReferencePlatform::contextCreated(ContextImpl& context, const map<string, string>& properties) const {
......@@ -95,21 +95,21 @@ void ReferencePlatform::contextDestroyed(ContextImpl& context) const {
}
ReferencePlatform::PlatformData::PlatformData(const System& system) : time(0.0), stepCount(0), numParticles(system.getNumParticles()) {
positions = new vector<RealVec>(numParticles);
velocities = new vector<RealVec>(numParticles);
forces = new vector<RealVec>(numParticles);
periodicBoxSize = new RealVec();
periodicBoxVectors = new RealVec[3];
positions = new vector<Vec3>(numParticles);
velocities = new vector<Vec3>(numParticles);
forces = new vector<Vec3>(numParticles);
periodicBoxSize = new Vec3();
periodicBoxVectors = new Vec3[3];
constraints = new ReferenceConstraints(system);
energyParameterDerivatives = new map<string, double>();
}
ReferencePlatform::PlatformData::~PlatformData() {
delete (vector<RealVec>*) positions;
delete (vector<RealVec>*) velocities;
delete (vector<RealVec>*) forces;
delete (RealVec*) periodicBoxSize;
delete[] (RealVec*) periodicBoxVectors;
delete (vector<Vec3>*) positions;
delete (vector<Vec3>*) velocities;
delete (vector<Vec3>*) forces;
delete (Vec3*) periodicBoxSize;
delete[] (Vec3*) periodicBoxVectors;
delete (ReferenceConstraints*) constraints;
delete (map<string, double>*) energyParameterDerivatives;
}
platforms/reference/src/SimTKReference/ObcParameters.cpp
View file @ 8469621f
......@@ -28,6 +28,7 @@
#include "openmm/OpenMMException.h"
#include "ObcParameters.h"
#include "SimTKOpenMMRealType.h"
using std::vector;
using namespace OpenMM;
......@@ -121,7 +122,7 @@ void ObcParameters::setObcTypeParameters(ObcParameters::ObcType obcType) {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getDielectricOffset() const {
double ObcParameters::getDielectricOffset() const {
return _dielectricOffset;
}
......@@ -133,7 +134,7 @@ RealOpenMM ObcParameters::getDielectricOffset() const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getAlphaObc() const {
double ObcParameters::getAlphaObc() const {
return _alphaObc;
}
......@@ -145,7 +146,7 @@ RealOpenMM ObcParameters::getAlphaObc() const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getBetaObc() const {
double ObcParameters::getBetaObc() const {
return _betaObc;
}
......@@ -157,7 +158,7 @@ RealOpenMM ObcParameters::getBetaObc() const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getGammaObc() const {
double ObcParameters::getGammaObc() const {
return _gammaObc;
}
......@@ -169,7 +170,7 @@ RealOpenMM ObcParameters::getGammaObc() const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getSolventDielectric() const {
double ObcParameters::getSolventDielectric() const {
return _solventDielectric;
}
......@@ -181,7 +182,7 @@ RealOpenMM ObcParameters::getSolventDielectric() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setSolventDielectric(RealOpenMM solventDielectric) {
void ObcParameters::setSolventDielectric(double solventDielectric) {
_solventDielectric = solventDielectric;
}
/**---------------------------------------------------------------------------------------
......@@ -192,7 +193,7 @@ void ObcParameters::setSolventDielectric(RealOpenMM solventDielectric) {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getSoluteDielectric() const {
double ObcParameters::getSoluteDielectric() const {
return _soluteDielectric;
}
......@@ -204,7 +205,7 @@ RealOpenMM ObcParameters::getSoluteDielectric() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
void ObcParameters::setSoluteDielectric(double soluteDielectric) {
_soluteDielectric = soluteDielectric;
}
......@@ -216,7 +217,7 @@ void ObcParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getElectricConstant() const {
double ObcParameters::getElectricConstant() const {
return _electricConstant;
}
......@@ -228,7 +229,7 @@ RealOpenMM ObcParameters::getElectricConstant() const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getProbeRadius() const {
double ObcParameters::getProbeRadius() const {
return _probeRadius;
}
......@@ -240,25 +241,25 @@ RealOpenMM ObcParameters::getProbeRadius() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setProbeRadius(RealOpenMM probeRadius) {
void ObcParameters::setProbeRadius(double probeRadius) {
_probeRadius = probeRadius;
}
/**---------------------------------------------------------------------------------------
Get pi*4*Asolv: used in ACE approximation for nonpolar term
((RealOpenMM) M_PI)*4.0f*0.0049*1000.0; (Still)
((RealOpenMM) M_PI)*4.0f*0.0054*1000.0; (OBC)
M_PI*4.0f*0.0049*1000.0; (Still)
M_PI*4.0f*0.0054*1000.0; (OBC)
@return pi4Asolv
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getPi4Asolv() const {
double ObcParameters::getPi4Asolv() const {
return _pi4Asolv;
}
void ObcParameters::setPi4Asolv(RealOpenMM pi4Asolv) {
void ObcParameters::setPi4Asolv(double pi4Asolv) {
_pi4Asolv = pi4Asolv;
}
......@@ -270,7 +271,7 @@ void ObcParameters::setPi4Asolv(RealOpenMM pi4Asolv) {
--------------------------------------------------------------------------------------- */
const vector<RealOpenMM>& ObcParameters::getAtomicRadii() const {
const vector<double>& ObcParameters::getAtomicRadii() const {
return _atomicRadii;
}
......@@ -282,7 +283,7 @@ const vector<RealOpenMM>& ObcParameters::getAtomicRadii() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setAtomicRadii(const vector<RealOpenMM>& atomicRadii) {
void ObcParameters::setAtomicRadii(const vector<double>& atomicRadii) {
if (atomicRadii.size() == _atomicRadii.size()) {
for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
......@@ -306,7 +307,7 @@ void ObcParameters::setAtomicRadii(const vector<RealOpenMM>& atomicRadii) {
--------------------------------------------------------------------------------------- */
const vector<RealOpenMM>& ObcParameters::getScaledRadiusFactors() const {
const vector<double>& ObcParameters::getScaledRadiusFactors() const {
return _scaledRadiusFactors;
}
......@@ -318,7 +319,7 @@ const vector<RealOpenMM>& ObcParameters::getScaledRadiusFactors() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setScaledRadiusFactors(const vector<RealOpenMM>& scaledRadiusFactors) {
void ObcParameters::setScaledRadiusFactors(const vector<double>& scaledRadiusFactors) {
if (scaledRadiusFactors.size() == _scaledRadiusFactors.size()) {
for (unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++) {
......@@ -342,7 +343,7 @@ void ObcParameters::setScaledRadiusFactors(const vector<RealOpenMM>& scaledRadiu
--------------------------------------------------------------------------------------- */
void ObcParameters::setUseCutoff(RealOpenMM distance) {
void ObcParameters::setUseCutoff(double distance) {
_cutoff = true;
_cutoffDistance = distance;
......@@ -364,7 +365,7 @@ bool ObcParameters::getUseCutoff() const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getCutoffDistance() const {
double ObcParameters::getCutoffDistance() const {
return _cutoffDistance;
}
......@@ -378,7 +379,7 @@ RealOpenMM ObcParameters::getCutoffDistance() const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setPeriodic(OpenMM::RealVec* vectors) {
void ObcParameters::setPeriodic(OpenMM::Vec3* vectors) {
assert(_cutoff);
......@@ -408,6 +409,6 @@ bool ObcParameters::getPeriodic() {
--------------------------------------------------------------------------------------- */
const OpenMM::RealVec* ObcParameters::getPeriodicBox() {
const OpenMM::Vec3* ObcParameters::getPeriodicBox() {
return _periodicBoxVectors;
}
platforms/reference/src/SimTKReference/ReferenceAndersenThermostat.cpp
View file @ 8469621f
......@@ -22,6 +22,7 @@
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <cmath>
#include <string.h>
#include <sstream>
......@@ -61,10 +62,10 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
void ReferenceAndersenThermostat::applyThermostat(const vector<vector<int> >& atomGroups, vector<RealVec>& atomVelocities, vector<RealOpenMM>& atomMasses,
RealOpenMM temperature, RealOpenMM collisionFrequency, RealOpenMM stepSize) const {
void ReferenceAndersenThermostat::applyThermostat(const vector<vector<int> >& atomGroups, vector<Vec3>& atomVelocities, vector<double>& atomMasses,
double temperature, double collisionFrequency, double stepSize) const {
const RealOpenMM collisionProbability = 1.0f - EXP(-collisionFrequency*stepSize);
const double collisionProbability = 1.0f - exp(-collisionFrequency*stepSize);
for (int i = 0; i < (int) atomGroups.size(); ++i) {
if (SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() < collisionProbability) {
......@@ -73,7 +74,7 @@ using namespace OpenMM;
for (int j = 0; j < (int) atomGroups[i].size(); j++) {
int atom = atomGroups[i][j];
if (atomMasses[atom] != 0) {
const RealOpenMM velocityScale = static_cast<RealOpenMM>(sqrt(BOLTZ*temperature/atomMasses[atom]));
const double velocityScale = static_cast<double>(sqrt(BOLTZ*temperature/atomMasses[atom]));
atomVelocities[atom][0] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
atomVelocities[atom][1] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
atomVelocities[atom][2] = velocityScale*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
......
platforms/reference/src/SimTKReference/ReferenceAngleBondIxn.cpp
View file @ 8469621f
......@@ -39,13 +39,6 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn::ReferenceAngleBondIxn() : usePeriodic(false) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceAngleBondIxn::ReferenceAngleBondIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -55,16 +48,9 @@ ReferenceAngleBondIxn::ReferenceAngleBondIxn() : usePeriodic(false) {
--------------------------------------------------------------------------------------- */
ReferenceAngleBondIxn::~ReferenceAngleBondIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceAngleBondIxn::~ReferenceAngleBondIxn";
// ---------------------------------------------------------------------------------------
}
void ReferenceAngleBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceAngleBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -83,32 +69,22 @@ void ReferenceAngleBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine(RealOpenMM cosine, RealOpenMM* angleParameters,
RealOpenMM* dEdR, RealOpenMM* energyTerm) const {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceAngleBondIxn::getPrefactorsGivenAngleCosine";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM half = 0.5;
void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine(double cosine, double* angleParameters,
double* dEdR, double* energyTerm) const {
// ---------------------------------------------------------------------------------------
RealOpenMM angle;
if (cosine >= one) {
angle = zero;
} else if (cosine <= -one) {
double angle;
if (cosine >= 1.0) {
angle = 0.0;
} else if (cosine <= -1.0) {
angle = PI_M;
} else {
angle = ACOS(cosine);
angle = acos(cosine);
}
RealOpenMM deltaIdeal = angle - angleParameters[0];
RealOpenMM deltaIdeal2 = deltaIdeal*deltaIdeal;
double deltaIdeal = angle - angleParameters[0];
double deltaIdeal2 = deltaIdeal*deltaIdeal;
*dEdR = angleParameters[1]*deltaIdeal;
*energyTerm = half*angleParameters[1]*deltaIdeal2;
*energyTerm = 0.5*angleParameters[1]*deltaIdeal2;
}
......@@ -126,24 +102,14 @@ void ReferenceAngleBondIxn::getPrefactorsGivenAngleCosine(RealOpenMM cosine, Rea
--------------------------------------------------------------------------------------- */
void ReferenceAngleBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
// constants -- reduce Visual Studio warnings regarding conversions between float & double
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM three = 3.0;
static const RealOpenMM oneM = -1.0;
static const int threeI = 3;
vector<Vec3>& atomCoordinates,
double* parameters,
vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
static const int LastAtomIndex = 3;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
double deltaR[2][ReferenceForce::LastDeltaRIndex];
// ---------------------------------------------------------------------------------------
......@@ -161,37 +127,36 @@ void ReferenceAngleBondIxn::calculateBondIxn(int* atomIndices,
ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
}
RealOpenMM pVector[threeI];
double pVector[3];
SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
RealOpenMM rp = DOT3(pVector, pVector);
rp = SQRT(rp);
double rp = sqrt(DOT3(pVector, pVector));
if (rp < 1.0e-06) {
rp = (RealOpenMM) 1.0e-06;
rp = 1.0e-06;
}
RealOpenMM dot = DOT3(deltaR[0], deltaR[1]);
RealOpenMM cosine = dot/SQRT((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
double dot = DOT3(deltaR[0], deltaR[1]);
double cosine = dot/sqrt((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
RealOpenMM dEdR;
RealOpenMM energy;
double dEdR;
double energy;
getPrefactorsGivenAngleCosine(cosine, parameters, &dEdR, &energy);
RealOpenMM termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
double termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
double termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
RealOpenMM deltaCrossP[LastAtomIndex][threeI];
double deltaCrossP[LastAtomIndex][3];
SimTKOpenMMUtilities::crossProductVector3(deltaR[0], pVector, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(deltaR[1], pVector, deltaCrossP[2]);
for (int ii = 0; ii < threeI; ii++) {
for (int ii = 0; ii < 3; ii++) {
deltaCrossP[0][ii] *= termA;
deltaCrossP[2][ii] *= termC;
deltaCrossP[1][ii] = oneM*(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
deltaCrossP[1][ii] = -(deltaCrossP[0][ii] + deltaCrossP[2][ii]);
}
// accumulate forces
for (int jj = 0; jj < LastAtomIndex; jj++) {
for (int ii = 0; ii < threeI; ii++) {
for (int ii = 0; ii < 3; ii++) {
forces[atomIndices[jj]][ii] += deltaCrossP[jj][ii];
}
}
......
platforms/reference/src/SimTKReference/ReferenceBondForce.cpp
View file @ 8469621f
......@@ -38,13 +38,6 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceBondForce::ReferenceBondForce() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceBondForce::ReferenceBondForce";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -54,13 +47,6 @@ ReferenceBondForce::ReferenceBondForce() {
--------------------------------------------------------------------------------------- */
ReferenceBondForce::~ReferenceBondForce() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceBondForce::~ReferenceBondForce";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -79,19 +65,12 @@ ReferenceBondForce::~ReferenceBondForce() {
--------------------------------------------------------------------------------------- */
void ReferenceBondForce::calculateForce(int numberOfBonds, int** atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM** parameters,
vector<RealVec>& forces,
RealOpenMM *totalEnergy,
vector<Vec3>& atomCoordinates,
double** parameters,
vector<Vec3>& forces,
double *totalEnergy,
ReferenceBondIxn& referenceBondIxn) {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceBondForce::calculateForce";
// ---------------------------------------------------------------------------------------
for (int ii = 0; ii < numberOfBonds; ii++) {
// calculate bond ixn
......
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