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#ifndef OPENMM_BROOKKERNELS_H_
#define OPENMM_BROOKKERNELS_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files (the "Software"), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "kernels.h"
#include "SimTKUtilities/SimTKOpenMMRealType.h"
class BrookStochasticDynamics;
class BrookShakeAlgorithm;
namespace OpenMM {
/**
* This kernel is invoked by StandardMMForceField to calculate the forces acting on the system.
*/
class BrookCalcStandardMMForceFieldKernel : public CalcStandardMMForceFieldKernel {
public:
BrookCalcStandardMMForceFieldKernel(std::string name, const Platform& platform) : CalcStandardMMForceFieldKernel(name, platform) {
}
~BrookCalcStandardMMForceFieldKernel();
/**
* Initialize the kernel, setting up the values of all the force field parameters.
*
* @param bondIndices the two atoms connected by each bond term
* @param bondParameters the force parameters (length, k) for each bond term
* @param angleIndices the three atoms connected by each angle term
* @param angleParameters the force parameters (angle, k) for each angle term
* @param periodicTorsionIndices the four atoms connected by each periodic torsion term
* @param periodicTorsionParameters the force parameters (k, phase, periodicity) for each periodic torsion term
* @param rbTorsionIndices the four atoms connected by each Ryckaert-Bellemans torsion term
* @param rbTorsionParameters the coefficients (in order of increasing powers) for each Ryckaert-Bellemans torsion term
* @param bonded14Indices each element contains the indices of two atoms whose nonbonded interactions should be reduced since
* they form a bonded 1-4 pair
* @param lj14Scale the factor by which van der Waals interactions should be reduced for bonded 1-4 pairs
* @param coulomb14Scale the factor by which Coulomb interactions should be reduced for bonded 1-4 pairs
* @param exclusions the i'th element lists the indices of all atoms with which the i'th atom should not interact through
* nonbonded forces. Bonded 1-4 pairs are also included in this list, since they should be omitted from
* the standard nonbonded calculation.
* @param nonbondedParameters the nonbonded force parameters (charge, sigma, epsilon) for each atom
*/
void initialize(const std::vector<std::vector<int> >& bondIndices, const std::vector<std::vector<double> >& bondParameters,
const std::vector<std::vector<int> >& angleIndices, const std::vector<std::vector<double> >& angleParameters,
const std::vector<std::vector<int> >& periodicTorsionIndices, const std::vector<std::vector<double> >& periodicTorsionParameters,
const std::vector<std::vector<int> >& rbTorsionIndices, const std::vector<std::vector<double> >& rbTorsionParameters,
const std::vector<std::vector<int> >& bonded14Indices, double lj14Scale, double coulomb14Scale,
const std::vector<std::set<int> >& exclusions, const std::vector<std::vector<double> >& nonbondedParameters);
/**
* Execute the kernel to calculate the forces.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param forces a Stream of type Double3 containing the force (x, y, z) on each atom. On entry, this contains the forces that
* have been calculated so far. The kernel should add its own forces to the values already in the stream.
*/
void executeForces(const Stream& positions, Stream& forces);
/**
* Execute the kernel to calculate the energy.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @return the potential energy due to the StandardMMForceField
*/
double executeEnergy(const Stream& positions);
private:
int numAtoms, numBonds, numAngles, numPeriodicTorsions, numRBTorsions, num14;
int **bondIndexArray, **angleIndexArray, **periodicTorsionIndexArray, **rbTorsionIndexArray, **exclusionArray, **bonded14IndexArray;
RealOpenMM **bondParamArray, **angleParamArray, **periodicTorsionParamArray, **rbTorsionParamArray, **atomParamArray, **bonded14ParamArray;
};
/**
* This kernel is invoked by GBSAOBCForceField to calculate the forces acting on the system.
*/
class BrookCalcGBSAOBCForceFieldKernel : public CalcGBSAOBCForceFieldKernel {
public:
BrookCalcGBSAOBCForceFieldKernel(std::string name, const Platform& platform) : CalcGBSAOBCForceFieldKernel(name, platform) {
}
/**
* Initialize the kernel, setting up the values of all the force field parameters.
*
* @param bornRadii the initial value of the Born radius for each atom
* @param atomParameters the force parameters (charge, atomic radius, scaling factor) for each atom
* @param solventDielectric the dielectric constant of the solvent
* @param soluteDielectric the dielectric constant of the solute
*/
void initialize(const std::vector<double>& bornRadii, const std::vector<std::vector<double> >& atomParameters,
double solventDielectric, double soluteDielectric);
/**
* Execute the kernel to calculate the forces.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param forces a Stream of type Double3 containing the force (x, y, z) on each atom. On entry, this contains the forces that
* have been calculated so far. The kernel should add its own forces to the values already in the stream.
*/
void executeForces(const Stream& positions, Stream& forces);
/**
* Execute the kernel to calculate the energy.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @return the potential energy due to the GBSAOBCForceField
*/
double executeEnergy(const Stream& positions);
};
/**
* This kernel is invoked by VerletIntegrator to take one time step.
*/
class BrookIntegrateVerletStepKernel : public IntegrateVerletStepKernel {
public:
BrookIntegrateVerletStepKernel(std::string name, const Platform& platform) : IntegrateVerletStepKernel(name, platform) {
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
* @param masses the mass of each atom
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained
* @param constraintLengths the required distance between each pair of constrained atoms
*/
void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths);
/**
* Execute the kernel.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param forces a Stream of type Double3 containing the force (x, y, z) on each atom
* @param stepSize the integration step size
*/
void execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize);
};
/**
* This kernel is invoked by LangevinIntegrator to take one time step.
*/
class BrookIntegrateLangevinStepKernel : public IntegrateLangevinStepKernel {
public:
BrookIntegrateLangevinStepKernel(std::string name, const Platform& platform) : IntegrateLangevinStepKernel(name, platform),
dynamics(0), shake(0), masses(0), shakeParameters(0), constraintIndices(0) {
}
~BrookIntegrateLangevinStepKernel();
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
* @param masses the mass of each atom
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained
* @param constraintLengths the required distance between each pair of constrained atoms
*/
void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths);
/**
* Execute the kernel.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param forces a Stream of type Double3 containing the force (x, y, z) on each atom
* @param temperature the temperature of the heat bath
* @param friction the friction coefficient coupling the system to the heat bath
* @param stepSize the integration step size
*/
void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
private:
BrookStochasticDynamics* dynamics;
BrookShakeAlgorithm* shake;
RealOpenMM* masses;
RealOpenMM** shakeParameters;
int** constraintIndices;
int numConstraints;
double prevTemp, prevFriction, prevStepSize;
};
/**
* This kernel is invoked by BrownianIntegrator to take one time step.
*/
class BrookIntegrateBrownianStepKernel : public IntegrateBrownianStepKernel {
public:
BrookIntegrateBrownianStepKernel(std::string name, const Platform& platform) : IntegrateBrownianStepKernel(name, platform) {
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
*
* @param masses the mass of each atom
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained
* @param constraintLengths the required distance between each pair of constrained atoms
*/
void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths);
/**
* Execute the kernel.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param forces a Stream of type Double3 containing the force (x, y, z) on each atom
* @param temperature the temperature of the heat bath
* @param friction the friction coefficient coupling the system to the heat bath
* @param stepSize the integration step size
*/
void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
};
/**
* This kernel is invoked by AndersenThermostat at the start of each time step to adjust the atom velocities.
*/
class BrookApplyAndersenThermostatKernel : public ApplyAndersenThermostatKernel {
public:
BrookApplyAndersenThermostatKernel(std::string name, const Platform& platform) : ApplyAndersenThermostatKernel(name, platform) {
}
/**
* Initialize the kernel, setting up the values of unchanging parameters.
*
* @param masses the mass of each atom
*/
void initialize(const std::vector<double>& masses);
/**
* Execute the kernel.
*
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param temperature the temperature of the heat bath
* @param collisionFrequency the frequency at which atom collide with particles in the heat bath
* @param stepSize the integration step size
*/
void execute(Stream& velocities, double temperature, double collisionFrequency, double stepSize);
};
/**
* This kernel is invoked to calculate the kinetic energy of the system.
*/
class BrookCalcKineticEnergyKernel : public CalcKineticEnergyKernel {
public:
BrookCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
}
/**
* Initialize the kernel, setting up the atomic masses.
*
* @param masses the mass of each atom
*/
void initialize(const std::vector<double>& masses);
/**
* Execute the kernel.
*
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @return the kinetic energy of the system
*/
double execute(const Stream& velocities);
private:
std::vector<double> masses;
};
} // namespace OpenMM
#endif /*OPENMM_BROOKKERNELS_H_*/
platforms/brook/src/BrookNonBonded.cpp
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platforms/brook/src/BrookNonBonded.h
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#ifndef BrookNonBonded_H_ #ifndef OPENMM_BROOK_NONBONDED_H_
#define BrookNonBonded_H_ #define OPENMM_BROOK_NONBONDED_H_
/* -------------------------------------------------------------------------- * /* -------------------------------------------------------------------------- *
* OpenMM * * OpenMM *
...@@ -35,8 +35,8 @@ ...@@ -35,8 +35,8 @@
#include <vector> #include <vector>
#include <set> #include <set>
#include "BrookFloatStreamImpl.h" #include "BrookFloatStreamInternal.h"
#include "BrookIntStreamImpl.h" #include "BrookIntStreamInternal.h"
#include "BrookPlatform.h" #include "BrookPlatform.h"
#include "BrookCommon.h" #include "BrookCommon.h"
...@@ -54,7 +54,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -54,7 +54,7 @@ class BrookNonBonded : public BrookCommon {
static const int DefaultReturnValue = 0; static const int DefaultReturnValue = 0;
static const int ErrorReturnValue = -1; static const int ErrorReturnValue = -1;
BrookNonBonded( ); BrookNonBonded( );
~BrookNonBonded(); ~BrookNonBonded();
...@@ -250,7 +250,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -250,7 +250,7 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
BrookFloatStreamImpl* getExclusionStream( void ) const; BrookFloatStreamInternal* getExclusionStream( void ) const;
/** /**
* Get vdw stream * Get vdw stream
...@@ -259,7 +259,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -259,7 +259,7 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
BrookFloatStreamImpl* getVdwStream( void ) const; BrookFloatStreamInternal* getOuterVdwStream( void ) const;
/** /**
* Get charge stream * Get charge stream
...@@ -268,7 +268,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -268,7 +268,7 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
BrookFloatStreamImpl* getChargeStream( void ) const; BrookFloatStreamInternal* getChargeStream( void ) const;
/** /**
* Get sigma-eps stream * Get sigma-eps stream
...@@ -277,7 +277,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -277,7 +277,7 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
BrookFloatStreamImpl* getSigmaStream( void ) const; BrookFloatStreamInternal* getInnerSigmaStream( void ) const;
/** /**
* Get epsilon stream * Get epsilon stream
...@@ -286,7 +286,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -286,7 +286,7 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
BrookFloatStreamImpl* getEpsilonStream( void ) const; BrookFloatStreamInternal* getInnerEpsilonStream( void ) const;
/** /**
* Get force streams * Get force streams
...@@ -295,7 +295,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -295,7 +295,7 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
BrookFloatStreamImpl** getForceStreams( void ); BrookFloatStreamInternal** getForceStreams( void );
/** /**
* Return true if force[index] stream is set * Return true if force[index] stream is set
...@@ -320,7 +320,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -320,7 +320,7 @@ class BrookNonBonded : public BrookCommon {
* */ * */
int setup( int numberOfAtoms, const std::vector<std::vector<double> >& nonbondedParameters, int setup( int numberOfAtoms, const std::vector<std::vector<double> >& nonbondedParameters,
const std::vector<std::set<int> >& exclusions, const BrookPlatform& platform ); const std::vector<std::set<int> >& exclusions, const Platform& platform );
/* /*
* Get contents of object * Get contents of object
...@@ -331,7 +331,7 @@ class BrookNonBonded : public BrookCommon { ...@@ -331,7 +331,7 @@ class BrookNonBonded : public BrookCommon {
* *
* */ * */
std::string getContents( int level ) const; std::string getContentsString( int level = 0 ) const;
private: private:
...@@ -339,6 +339,17 @@ class BrookNonBonded : public BrookCommon { ...@@ -339,6 +339,17 @@ class BrookNonBonded : public BrookCommon {
static const int NumberOfForceStreams = 4; static const int NumberOfForceStreams = 4;
// streams indices
enum {
ExclusionStream,
OuterVdwStream,
ChargeStream,
InnerSigmaStream,
InnerEpsilonStream,
LastStreamIndex
};
// atom ceiling // atom ceiling
int _atomSizeCeiling; int _atomSizeCeiling;
...@@ -370,15 +381,23 @@ class BrookNonBonded : public BrookCommon { ...@@ -370,15 +381,23 @@ class BrookNonBonded : public BrookCommon {
int _jStreamHeight; int _jStreamHeight;
int _jStreamSize; int _jStreamSize;
// streams // internal streams
BrookFloatStreamImpl* _exclusionStream; BrookFloatStreamInternal* _nonbondedStreams[LastStreamIndex];
BrookFloatStreamImpl* _vdwStream; BrookFloatStreamInternal* _nonbondedForceStreams[NumberOfForceStreams];
BrookFloatStreamImpl* _chargeStream;
BrookFloatStreamImpl* _sigmaStream;
BrookFloatStreamImpl* _epsilonStream;
BrookFloatStreamImpl* _nonbondedForceStreams[NumberOfForceStreams];
/*
* Setup of stream dimensions for exclusion stream
*
* @param atomStreamSize atom stream size
* @param atomStreamWidth atom stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
* */
int initializeExclusionStreamSize( int atomStreamSize, int atomStreamWidth );
/** /**
* Initialize exclusion stream dimensions and stream * Initialize exclusion stream dimensions and stream
* *
...@@ -416,6 +435,18 @@ class BrookNonBonded : public BrookCommon { ...@@ -416,6 +435,18 @@ class BrookNonBonded : public BrookCommon {
int initializeExclusions( const std::vector<std::set<int> >& exclusionsVector, const Platform& platform ); int initializeExclusions( const std::vector<std::set<int> >& exclusionsVector, const Platform& platform );
/**
* Initialize stream dimensions
*
* @param numberOfAtoms number of atoms
* @param platform platform
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
*/
int initializeStreamSizes( int numberOfAtoms, const Platform& platform );
/** /**
* Initialize stream dimensions and streams * Initialize stream dimensions and streams
* *
...@@ -425,8 +456,36 @@ class BrookNonBonded : public BrookCommon { ...@@ -425,8 +456,36 @@ class BrookNonBonded : public BrookCommon {
* *
*/ */
int initializeStreams( int numberOfAtoms, const Platform& platform ); int initializeStreams( const Platform& platform );
/*
* Setup of j-stream dimensions
*
* @param atomStreamSize atom stream size
* @param atomStreamWidth atom stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
* @throw OpenMMException if jStreamWidth < 1 || innerUnroll < 1
*
* */
int initializeJStreamSize( int atomStreamSize, int atomStreamWidth );
/*
* Setup of outer vdw stream size
*
* @param atomStreamSize atom stream size
* @param atomStreamWidth atom stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
* @throw OpenMMException if jStreamWidth < 1 || innerUnroll < 1
*
* */
int initializeOuterVdwStreamSize( int atomStreamSize, int atomStreamWidth );
/** /**
* Set sigma & epsilon given c6 & c12 (geometric rule) * Set sigma & epsilon given c6 & c12 (geometric rule)
* *
...@@ -453,8 +512,20 @@ class BrookNonBonded : public BrookCommon { ...@@ -453,8 +512,20 @@ class BrookNonBonded : public BrookCommon {
int initializeVdwAndCharge( const std::vector<std::vector<double> >& nonbondedParameters, const Platform& platform ); int initializeVdwAndCharge( const std::vector<std::vector<double> >& nonbondedParameters, const Platform& platform );
/*
* Setup of stream dimensions for partial force streams
*
* @param atomStreamSize atom stream size
* @param atomStreamWidth atom stream width
*
* @return ErrorReturnValue if error, else DefaultReturnValue
*
* */
int initializePartialForceStreamSize( int atomStreamSize, int atomStreamWidth );
}; };
} // namespace OpenMM } // namespace OpenMM
#endif /*OPENMM_BROOKKERNELS_H_*/ #endif /* OPENMM_BROOK_NONBONDED_H_ */
platforms/brook/src/BrookPlatform.cpp
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#ifndef OPENMM_BROOK_REMOVE_CM_MOTION_KERNEL_H_
#define OPENMM_BROOK_REMOVE_CM_MOTION_KERNEL_H_
/* -------------------------------------------------------------------------- *
* OpenMM *
* -------------------------------------------------------------------------- *
* This is part of the OpenMM molecular simulation toolkit originating from *
* Simbios, the NIH National Center for Physics-Based Simulation of *
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright ( c ) 2008 Stanford University and the Authors. *
* Authors: Peter Eastman, Mark Friedrichs *
* Contributors: *
* *
* Permission is hereby granted, free of charge, to any person obtaining a *
* copy of this software and associated documentation files ( the "Software" ), *
* to deal in the Software without restriction, including without limitation *
* the rights to use, copy, modify, merge, publish, distribute, sublicense, *
* and/or sell copies of the Software, and to permit persons to whom the *
* Software is furnished to do so, subject to the following conditions: *
* *
* The above copyright notice and this permission notice shall be included in *
* all copies or substantial portions of the Software. *
* *
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, *
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL *
* THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, *
* DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR *
* OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE *
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "kernels.h"
namespace OpenMM {
/**
* Brook class for removing center-of-mass motion
*/
class BrookRemoveCMMotionKernel : public RemoveCMMotionKernel {
public:
/**
* BrookRemoveCMMotionKernel constructor
*
* @param name name of the stream to create
* @param platform platform
*
*/
BrookRemoveCMMotionKernel( std::string name, const Platform& platform );
/**
* BrookRemoveCMMotionKernel destructor
*
*/
~BrookRemoveCMMotionKernel();
/**
* Initialize the kernel
*
* @param masses mass of each atom
*
*/
void initialize( const std::vector<double>& masses );
/**
* Execute the kernel.
*
* @param velocities stream of atom velocities
*
*/
void execute( Stream& velocities );
private:
};
} // namespace OpenMM
#endif /* OPENMM_BROOK_REMOVE_CM_MOTION_KERNEL_H_ */
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/****************************************************************
* This file is part of the gpu acceleration library for gromacs.
* Author: V. Vishal
* Copyright (C) Pande Group, Stanford, 2006
*****************************************************************/
//Harmonic bonds kernel
//Input is a stream of i, j pairs
//parms is float2( b0, kA )
//Output is two streams of forces fi, fj
//Can be optimized as necessary
kernel void kbonds_harmonic(
float xstrwidth, //atom stream width
float2 atoms<>,
float2 parms<>,
float4 posq[][],
out float3 fi<>,
out float3 fj<>
) {
float2 ai, aj;
float3 rij;
float rinv;
ai.y = floor( atoms.x / xstrwidth );
ai.x = atoms.x - ai.y * xstrwidth;
aj.y = floor( atoms.y / xstrwidth );
aj.x = atoms.y - aj.y * xstrwidth;
rij = posq[ai].xyz - posq[aj].xyz; //3
rinv = rsqrt( dot(rij, rij) ); //6
fi = -parms.y * ( 1.0f - parms.x * rinv ) * rij; //6
fj = -fi;
//Total: 15 flops
}
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