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Commit a138663d authored by Peter Eastman's avatar Peter Eastman
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Changed how kernels get initialized. StandardMMForceField now has you set the... 

Changed how kernels get initialized.  StandardMMForceField now has you set the 1-4 interactions explicitly.  CMMotionRemover allows the removal frequency to be set.
parent bf93e42f
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olla/include/kernels.h
View file @ a138663d
......@@ -32,8 +32,16 @@
* USE OR OTHER DEALINGS IN THE SOFTWARE. *
* -------------------------------------------------------------------------- */
#include "AndersenThermostat.h"
#include "BrownianIntegrator.h"
#include "CMMotionRemover.h"
#include "GBSAOBCForceField.h"
#include "KernelImpl.h"
#include "LangevinIntegrator.h"
#include "StandardMMForceField.h"
#include "Stream.h"
#include "System.h"
#include "VerletIntegrator.h"
#include <set>
#include <string>
#include <vector>
......@@ -56,50 +64,28 @@ public:
CalcStandardMMForceFieldKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up the values of all the force field parameters.
* Initialize the kernel.
*
* @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
* @param nonbondedMethod the method to use for handling long range nonbonded interactions
* @param nonbondedCutoff the cutoff distance for nonbonded interactions (if nonbondedMethod involves a cutoff)
* @param periodicBoxSize the size of the periodic box (if nonbondedMethod involves a periodic boundary conditions)
* @param system the System this kernel will be applied to
* @param force the StandardMMForceField this kernel will be used for
* @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.
*/
virtual 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,
NonbondedMethod nonbondedMethod, double nonbondedCutoff, double periodicBoxSize[3]) = 0;
virtual void initialize(const System& system, const StandardMMForceField& force, const std::vector<std::set<int> >& exclusions) = 0;
/**
* 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.
* @param context the context in which to execute this kernel
*/
virtual void executeForces(const Stream& positions, Stream& forces) = 0;
virtual void executeForces(OpenMMContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param context the context in which to execute this kernel
* @return the potential energy due to the StandardMMForceField
*/
virtual double executeEnergy(const Stream& positions) = 0;
virtual double executeEnergy(OpenMMContextImpl& context) = 0;
};
/**
......@@ -113,28 +99,25 @@ public:
CalcGBSAOBCForceFieldKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up the values of all the force field parameters.
* Initialize the kernel.
*
* @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
* @param system the System this kernel will be applied to
* @param force the GBSAOBCForceField this kernel will be used for
*/
virtual void initialize(const std::vector<std::vector<double> >& atomParameters, double solventDielectric, double soluteDielectric) = 0;
virtual void initialize(const System& system, const GBSAOBCForceField& force) = 0;
/**
* 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.
* @param context the context in which to execute this kernel
*/
virtual void executeForces(const Stream& positions, Stream& forces) = 0;
virtual void executeForces(OpenMMContextImpl& context) = 0;
/**
* Execute the kernel to calculate the energy.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForceField
*/
virtual double executeEnergy(const Stream& positions) = 0;
virtual double executeEnergy(OpenMMContextImpl& context) = 0;
};
/**
......@@ -148,23 +131,19 @@ public:
IntegrateVerletStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
* Initialize the kernel.
*
* @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
* @param system the System this kernel will be applied to
* @param integrator the VerletIntegrator this kernel will be used for
*/
virtual void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths) = 0;
virtual void initialize(const System& system, const VerletIntegrator& integrator) = 0;
/**
* 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
* @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for
*/
virtual void execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize) = 0;
virtual void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator) = 0;
};
/**
......@@ -178,25 +157,19 @@ public:
IntegrateLangevinStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
* Initialize the kernel.
*
* @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
* @param system the System this kernel will be applied to
* @param integrator the LangevinIntegrator this kernel will be used for
*/
virtual void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths) = 0;
virtual void initialize(const System& system, const LangevinIntegrator& integrator) = 0;
/**
* 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
* @param context the context in which to execute this kernel
* @param integrator the LangevinIntegrator this kernel is being used for
*/
virtual void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) = 0;
virtual void execute(OpenMMContextImpl& context, const LangevinIntegrator& integrator) = 0;
};
/**
......@@ -210,25 +183,19 @@ public:
IntegrateBrownianStepKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up all parameters related to integrator.
* Initialize the kernel.
*
* @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
* @param system the System this kernel will be applied to
* @param integrator the BrownianIntegrator this kernel will be used for
*/
virtual void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths) = 0;
virtual void initialize(const System& system, const BrownianIntegrator& integrator) = 0;
/**
* 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
* @param context the context in which to execute this kernel
* @param integrator the BrownianIntegrator this kernel is being used for
*/
virtual void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) = 0;
virtual void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator) = 0;
};
/**
......@@ -242,20 +209,18 @@ public:
ApplyAndersenThermostatKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up the values of unchanging parameters.
* Initialize the kernel.
*
* @param masses the mass of each atom
* @param system the System this kernel will be applied to
* @param thermostat the AndersenThermostat this kernel will be used for
*/
virtual void initialize(const std::vector<double>& masses) = 0;
virtual void initialize(const System& system, const AndersenThermostat& thermostat) = 0;
/**
* 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
* @param context the context in which to execute this kernel
*/
virtual void execute(Stream& velocities, double temperature, double collisionFrequency, double stepSize) = 0;
virtual void execute(OpenMMContextImpl& context) = 0;
};
/**
......@@ -269,18 +234,17 @@ public:
CalcKineticEnergyKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up the atomic masses.
* Initialize the kernel.
*
* @param masses the mass of each atom
* @param system the System this kernel will be applied to
*/
virtual void initialize(const std::vector<double>& masses) = 0;
virtual void initialize(const System& system) = 0;
/**
* 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
* @param context the context in which to execute this kernel
*/
virtual double execute(const Stream& velocities) = 0;
virtual double execute(OpenMMContextImpl& context) = 0;
};
/**
......@@ -294,17 +258,18 @@ public:
RemoveCMMotionKernel(std::string name, const Platform& platform) : KernelImpl(name, platform) {
}
/**
* Initialize the kernel, setting up the atomic masses.
* Initialize the kernel.
*
* @param masses the mass of each atom
* @param system the System this kernel will be applied to
* @param force the CMMotionRemover this kernel will be used for
*/
virtual void initialize(const std::vector<double>& masses) = 0;
virtual void initialize(const System& system, const CMMotionRemover& force) = 0;
/**
* Execute the kernel.
*
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param context the context in which to execute this kernel
*/
virtual void execute(Stream& velocities) = 0;
virtual void execute(OpenMMContextImpl& context) = 0;
};
} // namespace OpenMM
......
openmmapi/include/CMMotionRemover.h
View file @ a138663d
......@@ -48,9 +48,23 @@ public:
/**
* Create a CMMotionRemover.
*/
CMMotionRemover();
CMMotionRemover(int frequency = 1);
/**
* Get the frequency (in time steps) at which center of mass motion should be removed
*/
int getFrequency() const {
return frequency;
}
/**
* Set the frequency (in time steps) at which center of mass motion should be removed
*/
void setFrequency(int freq) {
frequency = freq;
}
protected:
ForceImpl* createImpl();
private:
int frequency;
};
} // namespace OpenMM
......
openmmapi/include/StandardMMForceField.h
View file @ a138663d
......@@ -80,8 +80,9 @@ public:
* @param numAngles the number of harmonic bond angle terms in the potential function
* @param numPeriodicTorsions the number of periodic torsion terms in the potential function
* @param numRBTorsions the number of Ryckaert-Bellemans torsion terms in the potential function
* @param numNonbonded14 the number of nonbonded 1-4 terms in the potential function
*/
StandardMMForceField(int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions);
StandardMMForceField(int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions, int numNonbonded14);
/**
* Get the number of atoms in the system.
*/
......@@ -112,10 +113,16 @@ public:
int getNumRBTorsions() const {
return rbTorsions.size();
}
/**
* Get the number of nonbonded 1-4 terms in the potential function
*/
int getNumNonbonded14() const {
return nb14s.size();
}
/**
* Get the method used for handling long range nonbonded interactions.
*/
NonbondedMethod getNonbondedMethod();
NonbondedMethod getNonbondedMethod() const;
/**
* Set the method used for handling long range nonbonded interactions.
*/
......@@ -124,7 +131,7 @@ public:
* Get the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* does not use cutoffs, this value will have no effect.
*/
double getCutoffDistance();
double getCutoffDistance() const;
/**
* Set the cutoff distance (in nm) being used for nonbonded interactions. If the NonbondedMethod in use
* does not use cutoffs, this value will have no effect.
......@@ -138,7 +145,7 @@ public:
* @param y on exit, this contains the width of the periodic box along the y axis
* @param z on exit, this contains the width of the periodic box along the z axis
*/
void getPeriodicBoxSize(double& x, double& y, double& z);
void getPeriodicBoxSize(double& x, double& y, double& z) const;
/**
* Set the dimensions of the periodic box (in nm). If the NonbondedMethod in use does not use periodic
* boundary conditions, these values will have no effect.
......@@ -266,6 +273,28 @@ public:
* @param c5 the coefficient of the 5th order term
*/
void setRBTorsionParameters(int index, int atom1, int atom2, int atom3, int atom4, double c0, double c1, double c2, double c3, double c4, double c5);
/**
* Get the force field parameters for a nonbonded 1-4 term.
*
* @param index the index of the interaction for which to get parameters
* @param atom1 the index of the first atom involved in the interaction
* @param atom2 the index of the second atom involved in the interaction
* @param charge the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge
* @param radius the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in nm
* @param depth the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
*/
void getNonbonded14Parameters(int index, int& atom1, int& atom2, double& charge, double& radius, double& depth) const;
/**
* Set the force field parameters for a nonbonded 1-4 term.
*
* @param index the index of the interaction for which to get parameters
* @param atom1 the index of the first atom involved in the interaction
* @param atom2 the index of the second atom involved in the interaction
* @param charge the scaled product of the atomic charges (i.e. the strength of the Coulomb interaction), measured in units of the proton charge
* @param radius the van der Waals radius of the atom (sigma in the Lennard Jones potential), measured in nm
* @param depth the well depth of the van der Waals interaction (epsilon in the Lennard Jones potential), measured in kJ/mol
*/
void setNonbonded14Parameters(int index, int atom1, int atom2, double charge, double radius, double depth);
protected:
ForceImpl* createImpl();
private:
......@@ -274,6 +303,7 @@ private:
class AngleInfo;
class PeriodicTorsionInfo;
class RBTorsionInfo;
class NB14Info;
NonbondedMethod nonbondedMethod;
double cutoffDistance;
double periodicBoxSize[3];
......@@ -291,6 +321,7 @@ private:
std::vector<AngleInfo> angles;
std::vector<PeriodicTorsionInfo> periodicTorsions;
std::vector<RBTorsionInfo> rbTorsions;
std::vector<NB14Info> nb14s;
#if defined(_MSC_VER)
#pragma warning(pop)
......@@ -347,6 +378,16 @@ public:
}
};
class StandardMMForceField::NB14Info {
public:
int atom1, atom2;
double charge, radius, depth;
NB14Info() {
atom1 = atom2 = -1;
charge = radius = depth = 0.0;
}
};
} // namespace OpenMM
#endif /*OPENMM_STANDARDMMFORCEFIELD_H_*/
openmmapi/src/AndersenThermostatImpl.cpp
View file @ a138663d
......@@ -44,16 +44,11 @@ AndersenThermostatImpl::AndersenThermostatImpl(AndersenThermostat& owner) : owne
void AndersenThermostatImpl::initialize(OpenMMContextImpl& context) {
kernel = context.getPlatform().createKernel(ApplyAndersenThermostatKernel::Name(), context);
const System& system = context.getSystem();
vector<double> masses(system.getNumAtoms());
for (int i = 0; i < system.getNumAtoms(); ++i)
masses[i] = system.getAtomMass(i);
dynamic_cast<ApplyAndersenThermostatKernel&>(kernel.getImpl()).initialize(masses);
dynamic_cast<ApplyAndersenThermostatKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void AndersenThermostatImpl::updateContextState(OpenMMContextImpl& context) {
dynamic_cast<ApplyAndersenThermostatKernel&>(kernel.getImpl()).execute(context.getVelocities(), context.getParameter(AndersenThermostat::Temperature),
context.getParameter(AndersenThermostat::CollisionFrequency), context.getIntegrator().getStepSize());
dynamic_cast<ApplyAndersenThermostatKernel&>(kernel.getImpl()).execute(context);
}
std::map<std::string, double> AndersenThermostatImpl::getDefaultParameters() {
......
openmmapi/src/BrownianIntegrator.cpp
View file @ a138663d
......@@ -62,7 +62,7 @@ void BrownianIntegrator::initialize(OpenMMContextImpl& contextRef) {
constraintIndices[i].push_back(atom2);
constraintLengths[i] = distance;
}
dynamic_cast<IntegrateBrownianStepKernel&>(kernel.getImpl()).initialize(masses, constraintIndices, constraintLengths);
dynamic_cast<IntegrateBrownianStepKernel&>(kernel.getImpl()).initialize(system, *this);
}
vector<string> BrownianIntegrator::getKernelNames() {
......@@ -75,8 +75,7 @@ void BrownianIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForces();
dynamic_cast<IntegrateBrownianStepKernel&>(kernel.getImpl()).execute(context->getPositions(), context->getVelocities(), context->getForces(), temperature,
friction, getStepSize());
dynamic_cast<IntegrateBrownianStepKernel&>(kernel.getImpl()).execute(*context, *this);
context->setTime(context->getTime()+getStepSize());
}
}
openmmapi/src/CMMotionRemover.cpp
View file @ a138663d
......@@ -34,7 +34,7 @@
using namespace OpenMM;
CMMotionRemover::CMMotionRemover() {
CMMotionRemover::CMMotionRemover(int frequency) : frequency(frequency) {
}
ForceImpl* CMMotionRemover::createImpl() {
......
openmmapi/src/CMMotionRemoverImpl.cpp
View file @ a138663d
......@@ -45,14 +45,11 @@ CMMotionRemoverImpl::CMMotionRemoverImpl(CMMotionRemover& owner) : owner(owner)
void CMMotionRemoverImpl::initialize(OpenMMContextImpl& context) {
kernel = context.getPlatform().createKernel(RemoveCMMotionKernel::Name(), context);
const System& system = context.getSystem();
vector<double> masses(system.getNumAtoms());
for (int i = 0; i < system.getNumAtoms(); ++i)
masses[i] = system.getAtomMass(i);
dynamic_cast<RemoveCMMotionKernel&>(kernel.getImpl()).initialize(masses);
dynamic_cast<RemoveCMMotionKernel&>(kernel.getImpl()).initialize(system, owner);
}
void CMMotionRemoverImpl::updateContextState(OpenMMContextImpl& context) {
dynamic_cast<RemoveCMMotionKernel&>(kernel.getImpl()).execute(context.getVelocities());
dynamic_cast<RemoveCMMotionKernel&>(kernel.getImpl()).execute(context);
}
std::vector<std::string> CMMotionRemoverImpl::getKernelNames() {
......
openmmapi/src/GBSAOBCForceFieldImpl.cpp
View file @ a138663d
......@@ -42,23 +42,15 @@ GBSAOBCForceFieldImpl::GBSAOBCForceFieldImpl(GBSAOBCForceField& owner) : owner(o
void GBSAOBCForceFieldImpl::initialize(OpenMMContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcGBSAOBCForceFieldKernel::Name(), context);
vector<vector<double> > atomParameters(owner.getNumAtoms());
for (int i = 0; i < owner.getNumAtoms(); ++i) {
double charge, radius, scalingFactor;
owner.getAtomParameters(i, charge, radius, scalingFactor);
atomParameters[i].push_back(charge);
atomParameters[i].push_back(radius);
atomParameters[i].push_back(scalingFactor);
}
dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).initialize(atomParameters, owner.getSolventDielectric(), owner.getSoluteDielectric());
dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner);
}
void GBSAOBCForceFieldImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).executeForces(context.getPositions(), forces);
dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).executeForces(context);
}
double GBSAOBCForceFieldImpl::calcEnergy(OpenMMContextImpl& context) {
return dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).executeEnergy(context.getPositions());
return dynamic_cast<CalcGBSAOBCForceFieldKernel&>(kernel.getImpl()).executeEnergy(context);
}
std::vector<std::string> GBSAOBCForceFieldImpl::getKernelNames() {
......
openmmapi/src/LangevinIntegrator.cpp
View file @ a138663d
......@@ -48,21 +48,7 @@ LangevinIntegrator::LangevinIntegrator(double temperature, double frictionCoeff,
void LangevinIntegrator::initialize(OpenMMContextImpl& contextRef) {
context = &contextRef;
kernel = context->getPlatform().createKernel(IntegrateLangevinStepKernel::Name(), contextRef);
const System& system = context->getSystem();
vector<double> masses(system.getNumAtoms());
vector<std::vector<int> > constraintIndices(system.getNumConstraints());
vector<double> constraintLengths(system.getNumConstraints());
for (int i = 0; i < system.getNumAtoms(); ++i)
masses[i] = system.getAtomMass(i);
for (int i = 0; i < system.getNumConstraints(); ++i) {
int atom1, atom2;
double distance;
system.getConstraintParameters(i, atom1, atom2, distance);
constraintIndices[i].push_back(atom1);
constraintIndices[i].push_back(atom2);
constraintLengths[i] = distance;
}
dynamic_cast<IntegrateLangevinStepKernel&>(kernel.getImpl()).initialize(masses, constraintIndices, constraintLengths);
dynamic_cast<IntegrateLangevinStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
}
vector<string> LangevinIntegrator::getKernelNames() {
......@@ -75,8 +61,7 @@ void LangevinIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForces();
dynamic_cast<IntegrateLangevinStepKernel&>(kernel.getImpl()).execute(context->getPositions(), context->getVelocities(), context->getForces(), temperature,
friction, getStepSize());
dynamic_cast<IntegrateLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this);
context->setTime(context->getTime()+getStepSize());
}
}
openmmapi/src/OpenMMContextImpl.cpp
View file @ a138663d
......@@ -70,7 +70,7 @@ OpenMMContextImpl::OpenMMContextImpl(OpenMMContext& owner, System& system, Integ
vector<double> masses(system.getNumAtoms());
for (size_t i = 0; i < masses.size(); ++i)
masses[i] = system.getAtomMass(i);
dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).initialize(masses);
dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).initialize(system);
for (size_t i = 0; i < forceImpls.size(); ++i)
forceImpls[i]->initialize(*this);
integrator.initialize(*this);
......@@ -107,7 +107,7 @@ void OpenMMContextImpl::calcForces() {
}
double OpenMMContextImpl::calcKineticEnergy() {
return dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).execute(velocities);
return dynamic_cast<CalcKineticEnergyKernel&>(kineticEnergyKernel.getImpl()).execute(*this);
}
double OpenMMContextImpl::calcPotentialEnergy() {
......
openmmapi/src/StandardMMForceField.cpp
View file @ a138663d
......@@ -36,13 +36,13 @@
using namespace OpenMM;
StandardMMForceField::StandardMMForceField(int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions) :
atoms(numAtoms), bonds(numBonds), angles(numAngles), periodicTorsions(numPeriodicTorsions), rbTorsions(numRBTorsions),
StandardMMForceField::StandardMMForceField(int numAtoms, int numBonds, int numAngles, int numPeriodicTorsions, int numRBTorsions, int numNonbonded14) :
atoms(numAtoms), bonds(numBonds), angles(numAngles), periodicTorsions(numPeriodicTorsions), rbTorsions(numRBTorsions), nb14s(numNonbonded14),
nonbondedMethod(NoCutoff), cutoffDistance(1.0) {
periodicBoxSize[0] = periodicBoxSize[1] = periodicBoxSize[2] = 2.0;
}
StandardMMForceField::NonbondedMethod StandardMMForceField::getNonbondedMethod() {
StandardMMForceField::NonbondedMethod StandardMMForceField::getNonbondedMethod() const {
return nonbondedMethod;
}
......@@ -50,7 +50,7 @@ void StandardMMForceField::setNonbondedMethod(NonbondedMethod method) {
nonbondedMethod = method;
}
double StandardMMForceField::getCutoffDistance() {
double StandardMMForceField::getCutoffDistance() const {
return cutoffDistance;
}
......@@ -58,7 +58,7 @@ void StandardMMForceField::setCutoffDistance(double distance) {
cutoffDistance = distance;
}
void StandardMMForceField::getPeriodicBoxSize(double& x, double& y, double& z) {
void StandardMMForceField::getPeriodicBoxSize(double& x, double& y, double& z) const {
x = periodicBoxSize[0];
y = periodicBoxSize[1];
z = periodicBoxSize[2];
......@@ -158,6 +158,22 @@ void StandardMMForceField::setRBTorsionParameters(int index, int atom1, int atom
rbTorsions[index].c[5] = c5;
}
void StandardMMForceField::getNonbonded14Parameters(int index, int& atom1, int& atom2, double& charge, double& radius, double& depth) const {
atom1 = nb14s[index].atom1;
atom2 = nb14s[index].atom2;
charge = nb14s[index].charge;
radius = nb14s[index].radius;
depth = nb14s[index].depth;
}
void StandardMMForceField::setNonbonded14Parameters(int index, int atom1, int atom2, double charge, double radius, double depth) {
nb14s[index].atom1 = atom1;
nb14s[index].atom2 = atom2;
nb14s[index].charge = charge;
nb14s[index].radius = radius;
nb14s[index].depth = depth;
}
ForceImpl* StandardMMForceField::createImpl() {
return new StandardMMForceFieldImpl(*this);
}
openmmapi/src/StandardMMForceFieldImpl.cpp
View file @ a138663d
......@@ -46,91 +46,26 @@ StandardMMForceFieldImpl::~StandardMMForceFieldImpl() {
void StandardMMForceFieldImpl::initialize(OpenMMContextImpl& context) {
kernel = context.getPlatform().createKernel(CalcStandardMMForceFieldKernel::Name(), context);
vector<vector<int> > bondIndices(owner.getNumBonds());
vector<vector<double> > bondParameters(owner.getNumBonds());
vector<vector<int> > angleIndices(owner.getNumAngles());
vector<vector<double> > angleParameters(owner.getNumAngles());
vector<vector<int> > periodicTorsionIndices(owner.getNumPeriodicTorsions());
vector<vector<double> > periodicTorsionParameters(owner.getNumPeriodicTorsions());
vector<vector<int> > rbTorsionIndices(owner.getNumRBTorsions());
vector<vector<double> > rbTorsionParameters(owner.getNumRBTorsions());
vector<vector<int> > bonded14Indices;
vector<set<int> > exclusions(owner.getNumAtoms());
vector<vector<double> > nonbondedParameters(owner.getNumAtoms());
vector<vector<int> > bondIndices(owner.getNumBonds());
set<pair<int, int> > bonded14set;
for (int i = 0; i < owner.getNumBonds(); ++i) {
int atom1, atom2;
double length, k;
owner.getBondParameters(i, atom1, atom2, length, k);
bondIndices[i].push_back(atom1);
bondIndices[i].push_back(atom2);
bondParameters[i].push_back(length);
bondParameters[i].push_back(k);
}
for (int i = 0; i < owner.getNumAngles(); ++i) {
int atom1, atom2, atom3;
double angle, k;
owner.getAngleParameters(i, atom1, atom2, atom3, angle, k);
angleIndices[i].push_back(atom1);
angleIndices[i].push_back(atom2);
angleIndices[i].push_back(atom3);
angleParameters[i].push_back(angle);
angleParameters[i].push_back(k);
}
for (int i = 0; i < owner.getNumPeriodicTorsions(); ++i) {
int atom1, atom2, atom3, atom4, periodicity;
double phase, k;
owner.getPeriodicTorsionParameters(i, atom1, atom2, atom3, atom4, periodicity, phase, k);
periodicTorsionIndices[i].push_back(atom1);
periodicTorsionIndices[i].push_back(atom2);
periodicTorsionIndices[i].push_back(atom3);
periodicTorsionIndices[i].push_back(atom4);
periodicTorsionParameters[i].push_back(k);
periodicTorsionParameters[i].push_back(phase);
periodicTorsionParameters[i].push_back(periodicity);
}
for (int i = 0; i < owner.getNumRBTorsions(); ++i) {
int atom1, atom2, atom3, atom4;
double c0, c1, c2, c3, c4, c5;
owner.getRBTorsionParameters(i, atom1, atom2, atom3, atom4, c0, c1, c2, c3, c4, c5);
rbTorsionIndices[i].push_back(atom1);
rbTorsionIndices[i].push_back(atom2);
rbTorsionIndices[i].push_back(atom3);
rbTorsionIndices[i].push_back(atom4);
rbTorsionParameters[i].push_back(c0);
rbTorsionParameters[i].push_back(c1);
rbTorsionParameters[i].push_back(c2);
rbTorsionParameters[i].push_back(c3);
rbTorsionParameters[i].push_back(c4);
rbTorsionParameters[i].push_back(c5);
}
for (int i = 0; i < owner.getNumAtoms(); ++i) {
double charge, radius, depth;
owner.getAtomParameters(i, charge, radius, depth);
nonbondedParameters[i].push_back(charge);
nonbondedParameters[i].push_back(radius);
nonbondedParameters[i].push_back(depth);
}
set<pair<int, int> > bonded14set;
findExclusions(bondIndices, exclusions, bonded14set);
bonded14Indices.resize(bonded14set.size());
int index = 0;
for (set<pair<int, int> >::const_iterator iter = bonded14set.begin(); iter != bonded14set.end(); ++iter) {
bonded14Indices[index].push_back(iter->first);
bonded14Indices[index++].push_back(iter->second);
}
double boxSize[3];
owner.getPeriodicBoxSize(boxSize[0], boxSize[1], boxSize[2]);
dynamic_cast<CalcStandardMMForceFieldKernel&>(kernel.getImpl()).initialize(bondIndices, bondParameters, angleIndices, angleParameters,
periodicTorsionIndices, periodicTorsionParameters, rbTorsionIndices, rbTorsionParameters, bonded14Indices, 0.5, 1.0/1.2, exclusions,
nonbondedParameters, CalcStandardMMForceFieldKernel::NonbondedMethod(owner.getNonbondedMethod()), owner.getCutoffDistance(), boxSize);
dynamic_cast<CalcStandardMMForceFieldKernel&>(kernel.getImpl()).initialize(context.getSystem(), owner, exclusions);
}
void StandardMMForceFieldImpl::calcForces(OpenMMContextImpl& context, Stream& forces) {
dynamic_cast<CalcStandardMMForceFieldKernel&>(kernel.getImpl()).executeForces(context.getPositions(), forces);
dynamic_cast<CalcStandardMMForceFieldKernel&>(kernel.getImpl()).executeForces(context);
}
double StandardMMForceFieldImpl::calcEnergy(OpenMMContextImpl& context) {
return dynamic_cast<CalcStandardMMForceFieldKernel&>(kernel.getImpl()).executeEnergy(context.getPositions());
return dynamic_cast<CalcStandardMMForceFieldKernel&>(kernel.getImpl()).executeEnergy(context);
}
std::vector<std::string> StandardMMForceFieldImpl::getKernelNames() {
......
openmmapi/src/VerletIntegrator.cpp
View file @ a138663d
......@@ -46,21 +46,7 @@ VerletIntegrator::VerletIntegrator(double stepSize) {
void VerletIntegrator::initialize(OpenMMContextImpl& contextRef) {
context = &contextRef;
kernel = context->getPlatform().createKernel(IntegrateVerletStepKernel::Name(), contextRef);
const System& system = context->getSystem();
vector<double> masses(system.getNumAtoms());
vector<std::vector<int> > constraintIndices(system.getNumConstraints());
vector<double> constraintLengths(system.getNumConstraints());
for (int i = 0; i < system.getNumAtoms(); ++i)
masses[i] = system.getAtomMass(i);
for (int i = 0; i < system.getNumConstraints(); ++i) {
int atom1, atom2;
double distance;
system.getConstraintParameters(i, atom1, atom2, distance);
constraintIndices[i].push_back(atom1);
constraintIndices[i].push_back(atom2);
constraintLengths[i] = distance;
}
dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).initialize(masses, constraintIndices, constraintLengths);
dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).initialize(contextRef.getSystem(), *this);
}
vector<string> VerletIntegrator::getKernelNames() {
......@@ -73,7 +59,7 @@ void VerletIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) {
context->updateContextState();
context->calcForces();
dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).execute(context->getPositions(), context->getVelocities(), context->getForces(), getStepSize());
dynamic_cast<IntegrateVerletStepKernel&>(kernel.getImpl()).execute(*context, *this);
context->setTime(context->getTime()+getStepSize());
}
}
platforms/cuda/include/CudaPlatform.h
View file @ a138663d
......@@ -68,6 +68,7 @@ public:
_gpuContext* gpu;
bool removeCM;
bool useOBC;
int cmMotionFrequency;
};
} // namespace OpenMM
......
platforms/cuda/src/CudaKernels.cpp
View file @ a138663d
......@@ -35,6 +35,7 @@
#include "CudaStreamImpl.h"
#include "LangevinIntegrator.h"
#include "ReferencePlatform.h"
#include "internal/OpenMMContextImpl.h"
#include "kernels/gputypes.h"
#include "kernels/cudaKernels.h"
#include <cmath>
......@@ -47,19 +48,13 @@ using namespace std;
CudaCalcStandardMMForceFieldKernel::~CudaCalcStandardMMForceFieldKernel() {
}
void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >& bondIndices, const vector<vector<double> >& bondParameters,
const vector<vector<int> >& angleIndices, const vector<vector<double> >& angleParameters,
const vector<vector<int> >& periodicTorsionIndices, const vector<vector<double> >& periodicTorsionParameters,
const vector<vector<int> >& rbTorsionIndices, const vector<vector<double> >& rbTorsionParameters,
const vector<vector<int> >& bonded14Indices, double lj14Scale, double coulomb14Scale,
const vector<set<int> >& exclusions, const vector<vector<double> >& nonbondedParameters,
NonbondedMethod nonbondedMethod, double nonbondedCutoff, double periodicBoxSize[3]) {
numAtoms = nonbondedParameters.size();
numBonds = bondIndices.size();
numAngles = angleIndices.size();
numPeriodicTorsions = periodicTorsionIndices.size();
numRBTorsions = rbTorsionIndices.size();
num14 = bonded14Indices.size();
void CudaCalcStandardMMForceFieldKernel::initialize(const System& system, const StandardMMForceField& force, const std::vector<std::set<int> >& exclusions) {
numAtoms = force.getNumAtoms();
numBonds = force.getNumBonds();
numAngles = force.getNumAngles();
numPeriodicTorsions = force.getNumPeriodicTorsions();
numRBTorsions = force.getNumRBTorsions();
num14 = force.getNumNonbonded14();
const float RadiansToDegrees = 180.0/3.14159265;
_gpuContext* gpu = data.gpu;
......@@ -71,10 +66,10 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
vector<float> length(numBonds);
vector<float> k(numBonds);
for (int i = 0; i < numBonds; i++) {
atom1[i] = bondIndices[i][0];
atom2[i] = bondIndices[i][1];
length[i] = (float) bondParameters[i][0];
k[i] = (float) bondParameters[i][1];
double lengthValue, kValue;
force.getBondParameters(i, atom1[i], atom2[i], lengthValue, kValue);
length[i] = (float) lengthValue;
k[i] = (float) kValue;
}
gpuSetBondParameters(gpu, atom1, atom2, length, k);
}
......@@ -88,11 +83,10 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
vector<float> angle(numAngles);
vector<float> k(numAngles);
for (int i = 0; i < numAngles; i++) {
atom1[i] = angleIndices[i][0];
atom2[i] = angleIndices[i][1];
atom3[i] = angleIndices[i][2];
angle[i] = (float) (angleParameters[i][0]*RadiansToDegrees);
k[i] = (float) angleParameters[i][1];
double angleValue, kValue;
force.getAngleParameters(i, atom1[i], atom2[i], atom3[i], angleValue, kValue);
angle[i] = (float) (angleValue*RadiansToDegrees);
k[i] = (float) kValue;
}
gpuSetBondAngleParameters(gpu, atom1, atom2, atom3, angle, k);
}
......@@ -108,13 +102,10 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
vector<float> phase(numPeriodicTorsions);
vector<int> periodicity(numPeriodicTorsions);
for (int i = 0; i < numPeriodicTorsions; i++) {
atom1[i] = periodicTorsionIndices[i][0];
atom2[i] = periodicTorsionIndices[i][1];
atom3[i] = periodicTorsionIndices[i][2];
atom4[i] = periodicTorsionIndices[i][3];
k[i] = (float) periodicTorsionParameters[i][0];
phase[i] = (float) (periodicTorsionParameters[i][1]*RadiansToDegrees);
periodicity[i] = (int) periodicTorsionParameters[i][2];
double kValue, phaseValue;
force.getPeriodicTorsionParameters(i, atom1[i], atom2[i], atom3[i], atom4[i], periodicity[i], phaseValue, kValue);
k[i] = (float) kValue;
phase[i] = (float) (phaseValue*RadiansToDegrees);
}
gpuSetDihedralParameters(gpu, atom1, atom2, atom3, atom4, k, phase, periodicity);
}
......@@ -133,16 +124,14 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
vector<float> c4(numRBTorsions);
vector<float> c5(numRBTorsions);
for (int i = 0; i < numRBTorsions; i++) {
atom1[i] = rbTorsionIndices[i][0];
atom2[i] = rbTorsionIndices[i][1];
atom3[i] = rbTorsionIndices[i][2];
atom4[i] = rbTorsionIndices[i][3];
c0[i] = (float) rbTorsionParameters[i][0];
c1[i] = (float) rbTorsionParameters[i][1];
c2[i] = (float) rbTorsionParameters[i][2];
c3[i] = (float) rbTorsionParameters[i][3];
c4[i] = (float) rbTorsionParameters[i][4];
c5[i] = (float) rbTorsionParameters[i][5];
double c[6];
force.getRBTorsionParameters(i, atom1[i], atom2[i], atom3[i], atom4[i], c[0], c[1], c[2], c[3], c[4], c[5]);
c0[i] = (float) c[0];
c1[i] = (float) c[1];
c2[i] = (float) c[2];
c3[i] = (float) c[3];
c4[i] = (float) c[4];
c5[i] = (float) c[5];
}
gpuSetRbDihedralParameters(gpu, atom1, atom2, atom3, atom4, c0, c1, c2, c3, c4, c5);
}
......@@ -157,10 +146,12 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
vector<char> symbol;
vector<vector<int> > exclusionList(numAtoms);
for (int i = 0; i < numAtoms; i++) {
double charge, radius, depth;
force.getAtomParameters(i, charge, radius, depth);
atom[i] = i;
q[i] = (float) nonbondedParameters[i][0];
c6[i] = (float) (4*nonbondedParameters[i][2]*pow(nonbondedParameters[i][1], 6.0));
c12[i] = (float) (4*nonbondedParameters[i][2]*pow(nonbondedParameters[i][1], 12.0));
q[i] = (float) charge;
c6[i] = (float) (4*depth*pow(radius, 6.0));
c12[i] = (float) (4*depth*pow(radius, 12.0));
exclusionList[i] = vector<int>(exclusions[i].begin(), exclusions[i].end());
exclusionList[i].push_back(i);
}
......@@ -177,20 +168,19 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
vector<float> q1(num14);
vector<float> q2(num14);
for (int i = 0; i < num14; i++) {
atom1[i] = bonded14Indices[i][0];
atom2[i] = bonded14Indices[i][1];
double sig = 0.5*(nonbondedParameters[atom1[i]][1]+nonbondedParameters[atom2[i]][1]);
double eps = sqrt(nonbondedParameters[atom1[i]][2]*nonbondedParameters[atom2[i]][2]);
c6[i] = (float) (4*eps*pow(sig, 6.0)*lj14Scale);
c12[i] = (float) (4*eps*pow(sig, 12.0)*lj14Scale);
q1[i] = (float) nonbondedParameters[atom1[i]][0];
q2[i] = (float) nonbondedParameters[atom2[i]][0];
double charge, sig, eps;
force.getNonbonded14Parameters(i, atom1[i], atom2[i], charge, sig, eps);
c6[i] = (float) (4*eps*pow(sig, 6.0));
c12[i] = (float) (4*eps*pow(sig, 12.0));
float q = (float) std::sqrt(charge);
q1[i] = q;
q2[i] = q;
}
gpuSetLJ14Parameters(gpu, 138.935485f, (float) coulomb14Scale, atom1, atom2, c6, c12, q1, q2);
gpuSetLJ14Parameters(gpu, 138.935485f, 1.0f, atom1, atom2, c6, c12, q1, q2);
}
}
void CudaCalcStandardMMForceFieldKernel::executeForces(const Stream& positions, Stream& forces) {
void CudaCalcStandardMMForceFieldKernel::executeForces(OpenMMContextImpl& context) {
_gpuContext* gpu = data.gpu;
if (data.useOBC) {
kCalculateCDLJObcGbsaForces1(gpu);
......@@ -205,84 +195,90 @@ void CudaCalcStandardMMForceFieldKernel::executeForces(const Stream& positions,
kReduceBornSumAndForces(gpu);
}
double CudaCalcStandardMMForceFieldKernel::executeEnergy(const Stream& positions) {
double CudaCalcStandardMMForceFieldKernel::executeEnergy(OpenMMContextImpl& context) {
// We don't currently have GPU kernels to calculate energy, so instead we have the reference
// platform do it. This is VERY slow.
LangevinIntegrator integrator(0.0, 1.0, 0.0);
ReferencePlatform platform;
OpenMMContext context(system, integrator, platform);
OpenMMContext refContext(system, integrator, platform);
const Stream& positions = context.getPositions();
double* posData = new double[positions.getSize()*3];
positions.saveToArray(posData);
vector<Vec3> pos(positions.getSize());
for (int i = 0; i < pos.size(); i++)
pos[i] = Vec3(posData[3*i], posData[3*i+1], posData[3*i+2]);
delete[] posData;
context.setPositions(pos);
return context.getState(State::Energy).getPotentialEnergy();
refContext.setPositions(pos);
return refContext.getState(State::Energy).getPotentialEnergy();
}
CudaCalcGBSAOBCForceFieldKernel::~CudaCalcGBSAOBCForceFieldKernel() {
}
void CudaCalcGBSAOBCForceFieldKernel::initialize(const vector<vector<double> >& atomParameters, double solventDielectric, double soluteDielectric) {
int numAtoms = atomParameters.size();
void CudaCalcGBSAOBCForceFieldKernel::initialize(const System& system, const GBSAOBCForceField& force) {
int numAtoms = system.getNumAtoms();
_gpuContext* gpu = data.gpu;
vector<int> atom(numAtoms);
vector<float> radius(numAtoms);
vector<float> scale(numAtoms);
for (int i = 0; i < numAtoms; i++) {
double charge, atomRadius, scalingFactor;
force.getAtomParameters(i, charge, atomRadius, scalingFactor);
atom[i] = i;
radius[i] = (float) atomParameters[i][1];
scale[i] = (float) atomParameters[i][2];
radius[i] = (float) atomRadius;
scale[i] = (float) scalingFactor;
}
gpuSetObcParameters(gpu, soluteDielectric, solventDielectric, atom, radius, scale);
gpuSetObcParameters(gpu, force.getSoluteDielectric(), force.getSolventDielectric(), atom, radius, scale);
data.useOBC = true;
}
void CudaCalcGBSAOBCForceFieldKernel::executeForces(const Stream& positions, Stream& forces) {
void CudaCalcGBSAOBCForceFieldKernel::executeForces(OpenMMContextImpl& context) {
}
double CudaCalcGBSAOBCForceFieldKernel::executeEnergy(const Stream& positions) {
double CudaCalcGBSAOBCForceFieldKernel::executeEnergy(OpenMMContextImpl& context) {
}
//CudaIntegrateVerletStepKernel::~CudaIntegrateVerletStepKernel() {
//}
//
//void CudaIntegrateVerletStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
//void CudaIntegrateVerletStepKernel::initialize(const System& system, const VerletIntegrator& integrator) {
//}
//
//void CudaIntegrateVerletStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize) {
//void CudaIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const VerletIntegrator& integrator) {
//}
CudaIntegrateLangevinStepKernel::~CudaIntegrateLangevinStepKernel() {
}
void CudaIntegrateLangevinStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
const vector<double>& constraintLengths) {
void CudaIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
// Set masses.
_gpuContext* gpu = data.gpu;
vector<float> mass(masses.size());
for (int i = 0; i < (int) mass.size(); i++)
mass[i] = (float) masses[i];
int numAtoms = system.getNumAtoms();
vector<float> mass(numAtoms);
for (int i = 0; i < numAtoms; i++)
mass[i] = (float) system.getAtomMass(i);
gpuSetMass(gpu, mass);
// Set constraints.
int numConstraints = constraintLengths.size();
int numConstraints = system.getNumConstraints();
vector<int> atom1(numConstraints);
vector<int> atom2(numConstraints);
vector<float> distance(numConstraints);
vector<float> invMass1(numConstraints);
vector<float> invMass2(numConstraints);
for (int i = 0; i < numConstraints; i++) {
atom1[i] = constraintIndices[i][0];
atom2[i] = constraintIndices[i][1];
distance[i] = (float) constraintLengths[i];
invMass1[i] = 1.0f/mass[atom1[i]];
invMass2[i] = 1.0f/mass[atom2[i]];
int atom1Index, atom2Index;
double constraintDistance;
system.getConstraintParameters(i, atom1Index, atom2Index, constraintDistance);
atom1[i] = atom1Index;
atom2[i] = atom2Index;
distance[i] = (float) constraintDistance;
invMass1[i] = 1.0f/mass[atom1Index];
invMass2[i] = 1.0f/mass[atom2Index];
}
gpuSetShakeParameters(gpu, atom1, atom2, distance, invMass1, invMass2);
gpuBuildThreadBlockWorkList(gpu);
......@@ -297,8 +293,11 @@ void CudaIntegrateLangevinStepKernel::initialize(const vector<double>& masses, c
prevStepSize = -1.0;
}
void CudaIntegrateLangevinStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) {
void CudaIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const LangevinIntegrator& integrator) {
_gpuContext* gpu = data.gpu;
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
if (temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Initialize the GPU parameters.
......@@ -312,8 +311,11 @@ void CudaIntegrateLangevinStepKernel::execute(Stream& positions, Stream& velocit
}
kUpdatePart1(gpu);
kApplyFirstShake(gpu);
if (data.removeCM)
gpu->bCalculateCM = true;
if (data.removeCM) {
int step = context.getTime()/stepSize;
if (step%data.cmMotionFrequency == 0)
gpu->bCalculateCM = true;
}
kUpdatePart2(gpu);
kApplySecondShake(gpu);
}
......@@ -321,30 +323,33 @@ void CudaIntegrateLangevinStepKernel::execute(Stream& positions, Stream& velocit
//CudaIntegrateBrownianStepKernel::~CudaIntegrateBrownianStepKernel() {
//}
//
//void CudaIntegrateBrownianStepKernel::initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices,
// const vector<double>& constraintLengths) {
//void CudaIntegrateBrownianStepKernel::initialize(const System& system, const BrownianIntegrator& integrator) {
//}
//
//void CudaIntegrateBrownianStepKernel::execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize) {
//void CudaIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator) {
//}
//
//CudaApplyAndersenThermostatKernel::~CudaApplyAndersenThermostatKernel() {
//}
//
//void CudaApplyAndersenThermostatKernel::initialize(const vector<double>& masses) {
//void CudaApplyAndersenThermostatKernel::initialize(const System& system, const AndersenThermostat& thermostat) {
//}
//
//void CudaApplyAndersenThermostatKernel::execute(Stream& velocities, double temperature, double collisionFrequency, double stepSize) {
//void CudaApplyAndersenThermostatKernel::execute(OpenMMContextImpl& context) {
//}
void CudaCalcKineticEnergyKernel::initialize(const vector<double>& masses) {
this->masses = masses;
void CudaCalcKineticEnergyKernel::initialize(const System& system) {
int numAtoms = system.getNumAtoms();
masses.resize(numAtoms);
for (size_t i = 0; i < numAtoms; ++i)
masses[i] = system.getAtomMass(i);
}
double CudaCalcKineticEnergyKernel::execute(const Stream& velocities) {
double CudaCalcKineticEnergyKernel::execute(OpenMMContextImpl& context) {
// We don't currently have a GPU kernel to do this, so we retrieve the velocities and calculate the energy
// on the CPU.
const Stream& velocities = context.getVelocities();
double* v = new double[velocities.getSize()*3];
velocities.saveToArray(v);
double energy = 0.0;
......@@ -354,9 +359,10 @@ double CudaCalcKineticEnergyKernel::execute(const Stream& velocities) {
return 0.5*energy;
}
void CudaRemoveCMMotionKernel::initialize(const vector<double>& masses) {
void CudaRemoveCMMotionKernel::initialize(const System& system, const CMMotionRemover& force) {
data.removeCM = true;
data.cmMotionFrequency = force.getFrequency();
}
void CudaRemoveCMMotionKernel::execute(Stream& velocities) {
void CudaRemoveCMMotionKernel::execute(OpenMMContextImpl& context) {
}
platforms/cuda/src/CudaKernels.h
View file @ a138663d
......@@ -54,47 +54,28 @@ public:
}
~CudaCalcStandardMMForceFieldKernel();
/**
* Initialize the kernel, setting up the values of all the force field parameters.
* Initialize the kernel.
*
* @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
* @param system the System this kernel will be applied to
* @param force the StandardMMForceField this kernel will be used for
* @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.
*/
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,
NonbondedMethod nonbondedMethod, double nonbondedCutoff, double periodicBoxSize[3]);
void initialize(const System& system, const StandardMMForceField& force, const std::vector<std::set<int> >& exclusions);
/**
* 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.
* @param context the context in which to execute this kernel
*/
void executeForces(const Stream& positions, Stream& forces);
void executeForces(OpenMMContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param context the context in which to execute this kernel
* @return the potential energy due to the StandardMMForceField
*/
double executeEnergy(const Stream& positions);
double executeEnergy(OpenMMContextImpl& context);
private:
CudaPlatform::PlatformData& data;
int numAtoms, numBonds, numAngles, numPeriodicTorsions, numRBTorsions, num14;
......@@ -110,28 +91,25 @@ public:
}
~CudaCalcGBSAOBCForceFieldKernel();
/**
* Initialize the kernel, setting up the values of all the force field parameters.
* Initialize the kernel.
*
* @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
* @param system the System this kernel will be applied to
* @param force the GBSAOBCForceField this kernel will be used for
*/
void initialize(const std::vector<std::vector<double> >& atomParameters, double solventDielectric, double soluteDielectric);
void initialize(const System& system, const GBSAOBCForceField& force);
/**
* 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.
* @param context the context in which to execute this kernel
*/
void executeForces(const Stream& positions, Stream& forces);
void executeForces(OpenMMContextImpl& context);
/**
* Execute the kernel to calculate the energy.
*
* @param positions a Stream of type Double3 containing the position (x, y, z) of each atom
* @param context the context in which to execute this kernel
* @return the potential energy due to the GBSAOBCForceField
*/
double executeEnergy(const Stream& positions);
double executeEnergy(OpenMMContextImpl& context);
private:
CudaPlatform::PlatformData& data;
};
......@@ -146,23 +124,19 @@ private:
// }
// ~CudaIntegrateVerletStepKernel();
// /**
// * Initialize the kernel, setting up all parameters related to integrator.
// * Initialize the kernel.
// *
// * @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
// * @param system the System this kernel will be applied to
// * @param integrator the VerletIntegrator this kernel will be used for
// */
// void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
// const std::vector<double>& constraintLengths);
// void initialize(const System& system, const VerletIntegrator& integrator);
// /**
// * 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
// * @param context the context in which to execute this kernel
// * @param integrator the VerletIntegrator this kernel is being used for
// */
// void execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize);
// void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator);
//private:
// CudaVerletDynamics* dynamics;
// CudaShakeAlgorithm* shake;
......@@ -182,25 +156,19 @@ public:
}
~CudaIntegrateLangevinStepKernel();
/**
* Initialize the kernel, setting up all parameters related to integrator.
* Initialize the kernel, setting up the atomic masses.
*
* @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
* @param system the System this kernel will be applied to
* @param integrator the LangevinIntegrator this kernel will be used for
*/
void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
const std::vector<double>& constraintLengths);
void initialize(const System& system, const LangevinIntegrator& integrator);
/**
* 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
* @param context the context in which to execute this kernel
* @param integrator the LangevinIntegrator this kernel is being used for
*/
void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
void execute(OpenMMContextImpl& context, const LangevinIntegrator& integrator);
private:
CudaPlatform::PlatformData& data;
double prevTemp, prevFriction, prevStepSize;
......@@ -216,25 +184,19 @@ private:
// }
// ~CudaIntegrateBrownianStepKernel();
// /**
// * Initialize the kernel, setting up all parameters related to integrator.
// * Initialize the kernel.
// *
// * @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
// * @param system the System this kernel will be applied to
// * @param integrator the BrownianIntegrator this kernel will be used for
// */
// void initialize(const std::vector<double>& masses, const std::vector<std::vector<int> >& constraintIndices,
// const std::vector<double>& constraintLengths);
// void initialize(const System& system, const BrownianIntegrator& integrator);
// /**
// * 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
// * @param context the context in which to execute this kernel
// * @param integrator the BrownianIntegrator this kernel is being used for
// */
// void execute(Stream& positions, Stream& velocities, const Stream& forces, double temperature, double friction, double stepSize);
// void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator);
//private:
// CudaBrownianDynamics* dynamics;
// CudaShakeAlgorithm* shake;
......@@ -254,20 +216,18 @@ private:
// }
// ~CudaApplyAndersenThermostatKernel();
// /**
// * Initialize the kernel, setting up the values of unchanging parameters.
// * Initialize the kernel.
// *
// * @param masses the mass of each atom
// * @param system the System this kernel will be applied to
// * @param thermostat the AndersenThermostat this kernel will be used for
// */
// void initialize(const std::vector<double>& masses);
// void initialize(const System& system, const AndersenThermostat& thermostat);
// /**
// * 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
// * @param context the context in which to execute this kernel
// */
// void execute(Stream& velocities, double temperature, double collisionFrequency, double stepSize);
// void execute(OpenMMContextImpl& context);
//private:
// CudaAndersenThermostat* thermostat;
// RealOpenMM* masses;
......@@ -281,18 +241,17 @@ public:
CudaCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
}
/**
* Initialize the kernel, setting up the atomic masses.
* Initialize the kernel.
*
* @param masses the mass of each atom
* @param system the System this kernel will be applied to
*/
void initialize(const std::vector<double>& masses);
void initialize(const System& system);
/**
* 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
* @param context the context in which to execute this kernel
*/
double execute(const Stream& velocities);
double execute(OpenMMContextImpl& context);
private:
std::vector<double> masses;
};
......@@ -307,15 +266,16 @@ public:
/**
* Initialize the kernel, setting up the atomic masses.
*
* @param masses the mass of each atom
* @param system the System this kernel will be applied to
* @param force the CMMotionRemover this kernel will be used for
*/
void initialize(const std::vector<double>& masses);
void initialize(const System& system, const CMMotionRemover& force);
/**
* Execute the kernel.
*
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom
* @param context the context in which to execute this kernel
*/
void execute(Stream& velocities);
void execute(OpenMMContextImpl& context);
private:
CudaPlatform::PlatformData& data;
};
......
platforms/cuda/tests/TestCudaCMMotionRemover.cpp
View file @ a138663d
......@@ -63,7 +63,7 @@ void testMotionRemoval() {
CudaPlatform platform;
System system(numAtoms, 0);
LangevinIntegrator integrator(0.0, 1e-5, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 1, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 1, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, i+1);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
......
platforms/cuda/tests/TestCudaGBSAOBCForceField.cpp
View file @ a138663d
......@@ -58,7 +58,7 @@ void testSingleAtom() {
GBSAOBCForceField* forceField = new GBSAOBCForceField(1);
forceField->setAtomParameters(0, 0.5, 0.15, 1);
system.addForce(forceField);
system.addForce(new StandardMMForceField(1, 0, 0, 0, 0));
system.addForce(new StandardMMForceField(1, 0, 0, 0, 0, 0));
OpenMMContext context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
......@@ -81,7 +81,7 @@ void testForce() {
for (int i = 0; i < numAtoms; ++i)
forceField->setAtomParameters(i, i%2 == 0 ? -1 : 1, 0.15, 1);
system.addForce(forceField);
system.addForce(new StandardMMForceField(numAtoms, 0, 0, 0, 0));
system.addForce(new StandardMMForceField(numAtoms, 0, 0, 0, 0, 0));
OpenMMContext context(system, integrator, platform);
// Set random positions for all the atoms.
......
platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
View file @ a138663d
......@@ -55,7 +55,7 @@ void testSingleBond() {
system.setAtomMass(0, 2.0);
system.setAtomMass(1, 2.0);
LangevinIntegrator integrator(0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(2, 1, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(2, 1, 0, 0, 0, 0);
forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
......@@ -99,7 +99,7 @@ void testTemperature() {
CudaPlatform platform;
System system(numAtoms, 0);
LangevinIntegrator integrator(temp, 2.0, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 2.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
......@@ -135,7 +135,7 @@ void testConstraints() {
CudaPlatform platform;
System system(numAtoms, numConstraints);
LangevinIntegrator integrator(temp, 2.0, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, 0, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 10.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
......
platforms/cuda/tests/TestCudaStandardMMForceField.cpp
View file @ a138663d
......@@ -52,7 +52,7 @@ void testBonds() {
CudaPlatform platform;
System system(3, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(3, 2, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(3, 2, 0, 0, 0, 0);
forceField->setBondParameters(0, 0, 1, 1.5, 0.8);
forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
system.addForce(forceField);
......@@ -74,7 +74,7 @@ void testAngles() {
CudaPlatform platform;
System system(4, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 2, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 2, 0, 0, 0);
forceField->setAngleParameters(0, 0, 1, 2, PI_M/3, 1.1);
forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField);
......@@ -99,7 +99,7 @@ void testPeriodicTorsions() {
CudaPlatform platform;
System system(4, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 0, 1, 0);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 0, 1, 0, 0);
forceField->setPeriodicTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
......@@ -122,7 +122,7 @@ void testRBTorsions() {
CudaPlatform platform;
System system(4, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 0, 0, 1);
StandardMMForceField* forceField = new StandardMMForceField(4, 0, 0, 0, 1, 0);
forceField->setRBTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
......@@ -155,7 +155,7 @@ void testCoulomb() {
CudaPlatform platform;
System system(2, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(2, 0, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(2, 0, 0, 0, 0, 0);
forceField->setAtomParameters(0, 0.5, 1, 0);
forceField->setAtomParameters(1, -1.5, 1, 0);
system.addForce(forceField);
......@@ -176,7 +176,7 @@ void testLJ() {
CudaPlatform platform;
System system(2, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(2, 0, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(2, 0, 0, 0, 0, 0);
forceField->setAtomParameters(0, 0, 1.2, 1);
forceField->setAtomParameters(1, 0, 1.4, 2);
system.addForce(forceField);
......@@ -199,7 +199,7 @@ void testExclusionsAnd14() {
CudaPlatform platform;
System system(5, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(5, 4, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(5, 4, 0, 0, 0, 2);
forceField->setBondParameters(0, 0, 1, 1, 0);
forceField->setBondParameters(1, 1, 2, 1, 0);
forceField->setBondParameters(2, 2, 3, 1, 0);
......@@ -217,6 +217,8 @@ void testExclusionsAnd14() {
}
forceField->setAtomParameters(0, 0, 1.5, 1);
forceField->setAtomParameters(i, 0, 1.5, 1);
forceField->setNonbonded14Parameters(0, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
forceField->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
positions[i] = Vec3(r, 0, 0);
OpenMMContext context(system, integrator, platform);
context.setPositions(positions);
......@@ -242,6 +244,8 @@ void testExclusionsAnd14() {
forceField->setAtomParameters(0, 2, 1.5, 0);
forceField->setAtomParameters(i, 2, 1.5, 0);
forceField->setNonbonded14Parameters(0, 0, 3, i == 3 ? 4/1.2 : 0, 1.5, 0);
forceField->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0);
OpenMMContext context2(system, integrator, platform);
context2.setPositions(positions);
state = context2.getState(State::Forces | State::Energy);
......@@ -266,7 +270,7 @@ void testCutoff() {
CudaPlatform platform;
System system(3, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(3, 0, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(3, 0, 0, 0, 0, 0);
forceField->setAtomParameters(0, 1.0, 1, 0);
forceField->setAtomParameters(1, 1.0, 1, 0);
forceField->setAtomParameters(2, 1.0, 1, 0);
......@@ -299,7 +303,7 @@ void testCutoff14() {
CudaPlatform platform;
System system(5, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(5, 4, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(5, 4, 0, 0, 0, 2);
forceField->setBondParameters(0, 0, 1, 1, 0);
forceField->setBondParameters(1, 1, 2, 1, 0);
forceField->setBondParameters(2, 2, 3, 1, 0);
......@@ -323,6 +327,8 @@ void testCutoff14() {
for (int j = 1; j < 5; ++j)
forceField->setAtomParameters(j, 0, 1.5, 0);
forceField->setAtomParameters(i, 0, 1.5, 1);
forceField->setNonbonded14Parameters(0, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
forceField->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0.0);
context.reinitialize();
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
......@@ -349,6 +355,8 @@ void testCutoff14() {
const double q = 0.7;
forceField->setAtomParameters(0, q, 1.5, 0);
forceField->setAtomParameters(i, q, 1.5, 0);
forceField->setNonbonded14Parameters(0, 0, 3, i == 3 ? q*q/1.2 : 0, 1.5, 0);
forceField->setNonbonded14Parameters(1, 1, 4, 0, 1.5, 0);
context.reinitialize();
context.setPositions(positions);
state = context.getState(State::Forces | State::Energy);
......@@ -376,7 +384,7 @@ void testPeriodic() {
CudaPlatform platform;
System system(3, 0);
LangevinIntegrator integrator(0.0, 0.1, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(3, 1, 0, 0, 0);
StandardMMForceField* forceField = new StandardMMForceField(3, 1, 0, 0, 0, 0);
forceField->setAtomParameters(0, 1.0, 1, 0);
forceField->setAtomParameters(1, 1.0, 1, 0);
forceField->setAtomParameters(2, 1.0, 1, 0);
......
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