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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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platforms/reference/src/ReferenceKernels.h
View file @ a138663d
...@@ -54,50 +54,28 @@ public: ...@@ -54,50 +54,28 @@ public:
} }
~ReferenceCalcStandardMMForceFieldKernel(); ~ReferenceCalcStandardMMForceFieldKernel();
/** /**
* 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 system the System this kernel will be applied to
* @param bondParameters the force parameters (length, k) for each bond term * @param force the StandardMMForceField this kernel will be used for
* @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 * @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 * nonbonded forces. Bonded 1-4 pairs are also included in this list, since they should be omitted from
* the standard nonbonded calculation. * 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)
*/ */
void initialize(const std::vector<std::vector<int> >& bondIndices, const std::vector<std::vector<double> >& bondParameters, void initialize(const System& system, const StandardMMForceField& force, const std::vector<std::set<int> >& exclusions);
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]);
/** /**
* Execute the kernel to calculate the forces. * Execute the kernel to calculate the forces.
* *
* @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
* @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); void executeForces(OpenMMContextImpl& context);
/** /**
* Execute the kernel to calculate the energy. * 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 * @return the potential energy due to the StandardMMForceField
*/ */
double executeEnergy(const Stream& positions); double executeEnergy(OpenMMContextImpl& context);
private: private:
int numAtoms, numBonds, numAngles, numPeriodicTorsions, numRBTorsions, num14; int numAtoms, numBonds, numAngles, numPeriodicTorsions, numRBTorsions, num14;
int **bondIndexArray, **angleIndexArray, **periodicTorsionIndexArray, **rbTorsionIndexArray, **exclusionArray, **bonded14IndexArray; int **bondIndexArray, **angleIndexArray, **periodicTorsionIndexArray, **rbTorsionIndexArray, **exclusionArray, **bonded14IndexArray;
...@@ -117,28 +95,25 @@ public: ...@@ -117,28 +95,25 @@ public:
} }
~ReferenceCalcGBSAOBCForceFieldKernel(); ~ReferenceCalcGBSAOBCForceFieldKernel();
/** /**
* 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 system the System this kernel will be applied to
* @param solventDielectric the dielectric constant of the solvent * @param force the GBSAOBCForceField this kernel will be used for
* @param soluteDielectric the dielectric constant of the solute
*/ */
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. * Execute the kernel to calculate the forces.
* *
* @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
* @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); void executeForces(OpenMMContextImpl& context);
/** /**
* Execute the kernel to calculate the energy. * 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 * @return the potential energy due to the GBSAOBCForceField
*/ */
double executeEnergy(const Stream& positions); double executeEnergy(OpenMMContextImpl& context);
private: private:
CpuObc* obc; CpuObc* obc;
std::vector<RealOpenMM> charges; std::vector<RealOpenMM> charges;
...@@ -154,23 +129,19 @@ public: ...@@ -154,23 +129,19 @@ public:
} }
~ReferenceIntegrateVerletStepKernel(); ~ReferenceIntegrateVerletStepKernel();
/** /**
* Initialize the kernel, setting up all parameters related to integrator. * Initialize the kernel.
* *
* @param masses the mass of each atom * @param system the System this kernel will be applied to
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained * @param integrator the VerletIntegrator this kernel will be used for
* @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, void initialize(const System& system, const VerletIntegrator& integrator);
const std::vector<double>& constraintLengths);
/** /**
* Execute the kernel. * Execute the kernel.
* *
* @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
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom * @param integrator the VerletIntegrator this kernel is being used for
* @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); void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator);
private: private:
ReferenceVerletDynamics* dynamics; ReferenceVerletDynamics* dynamics;
ReferenceShakeAlgorithm* shake; ReferenceShakeAlgorithm* shake;
...@@ -191,25 +162,19 @@ public: ...@@ -191,25 +162,19 @@ public:
} }
~ReferenceIntegrateLangevinStepKernel(); ~ReferenceIntegrateLangevinStepKernel();
/** /**
* 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 system the System this kernel will be applied to
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained * @param integrator the LangevinIntegrator this kernel will be used for
* @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, void initialize(const System& system, const LangevinIntegrator& integrator);
const std::vector<double>& constraintLengths);
/** /**
* Execute the kernel. * Execute the kernel.
* *
* @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
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom * @param integrator the LangevinIntegrator this kernel is being used for
* @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); void execute(OpenMMContextImpl& context, const LangevinIntegrator& integrator);
private: private:
ReferenceStochasticDynamics* dynamics; ReferenceStochasticDynamics* dynamics;
ReferenceShakeAlgorithm* shake; ReferenceShakeAlgorithm* shake;
...@@ -230,25 +195,19 @@ public: ...@@ -230,25 +195,19 @@ public:
} }
~ReferenceIntegrateBrownianStepKernel(); ~ReferenceIntegrateBrownianStepKernel();
/** /**
* Initialize the kernel, setting up all parameters related to integrator. * Initialize the kernel.
* *
* @param masses the mass of each atom * @param system the System this kernel will be applied to
* @param constraintIndices each element contains the indices of two atoms whose distance should be constrained * @param integrator the BrownianIntegrator this kernel will be used for
* @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, void initialize(const System& system, const BrownianIntegrator& integrator);
const std::vector<double>& constraintLengths);
/** /**
* Execute the kernel. * Execute the kernel.
* *
* @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
* @param velocities a Stream of type Double3 containing the velocity (x, y, z) of each atom * @param integrator the BrownianIntegrator this kernel is being used for
* @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); void execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator);
private: private:
ReferenceBrownianDynamics* dynamics; ReferenceBrownianDynamics* dynamics;
ReferenceShakeAlgorithm* shake; ReferenceShakeAlgorithm* shake;
...@@ -268,20 +227,18 @@ public: ...@@ -268,20 +227,18 @@ public:
} }
~ReferenceApplyAndersenThermostatKernel(); ~ReferenceApplyAndersenThermostatKernel();
/** /**
* 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. * 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
* @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); void execute(OpenMMContextImpl& context);
private: private:
ReferenceAndersenThermostat* thermostat; ReferenceAndersenThermostat* thermostat;
RealOpenMM* masses; RealOpenMM* masses;
...@@ -295,18 +252,17 @@ public: ...@@ -295,18 +252,17 @@ public:
ReferenceCalcKineticEnergyKernel(std::string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) { ReferenceCalcKineticEnergyKernel(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. * 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
* @return the kinetic energy of the system
*/ */
double execute(const Stream& velocities); double execute(OpenMMContextImpl& context);
private: private:
std::vector<double> masses; std::vector<double> masses;
}; };
...@@ -321,17 +277,19 @@ public: ...@@ -321,17 +277,19 @@ public:
/** /**
* Initialize the kernel, setting up the atomic masses. * 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. * 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: private:
std::vector<double> masses; std::vector<double> masses;
int frequency;
}; };
} // namespace OpenMM } // namespace OpenMM
......
platforms/reference/tests/TestReferenceAndersenThermostat.cpp
View file @ a138663d
...@@ -55,7 +55,7 @@ void testTemperature() { ...@@ -55,7 +55,7 @@ void testTemperature() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, 0); System system(numAtoms, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 2.0); system.setAtomMass(i, 2.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0); forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
......
platforms/reference/tests/TestReferenceBrownianIntegrator.cpp
View file @ a138663d
...@@ -56,7 +56,7 @@ void testSingleBond() { ...@@ -56,7 +56,7 @@ void testSingleBond() {
system.setAtomMass(1, 2.0); system.setAtomMass(1, 2.0);
double dt = 0.01; double dt = 0.01;
BrownianIntegrator integrator(0, 0.1, dt); BrownianIntegrator integrator(0, 0.1, dt);
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); forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField); system.addForce(forceField);
OpenMMContext context(system, integrator, platform); OpenMMContext context(system, integrator, platform);
...@@ -90,7 +90,7 @@ void testTemperature() { ...@@ -90,7 +90,7 @@ void testTemperature() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, 0); System system(numAtoms, 0);
BrownianIntegrator integrator(temp, 2.0, 0.01); BrownianIntegrator integrator(temp, 2.0, 0.01);
StandardMMForceField* forceField = new StandardMMForceField(numAtoms, numBonds, 0, 0, 0); StandardMMForceField* forceField = new StandardMMForceField(numAtoms, numBonds, 0, 0, 0, 0);
for (int i = 0; i < numAtoms; ++i) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 2.0); system.setAtomMass(i, 2.0);
// forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0); // forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
...@@ -127,7 +127,7 @@ void testConstraints() { ...@@ -127,7 +127,7 @@ void testConstraints() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, numAtoms-1); System system(numAtoms, numAtoms-1);
BrownianIntegrator integrator(temp, 2.0, 0.001); BrownianIntegrator integrator(temp, 2.0, 0.001);
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) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 10.0); system.setAtomMass(i, 10.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0); forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
......
platforms/reference/tests/TestReferenceCMMotionRemover.cpp
View file @ a138663d
...@@ -65,7 +65,7 @@ void testMotionRemoval() { ...@@ -65,7 +65,7 @@ void testMotionRemoval() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, 0); System system(numAtoms, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, i+1); system.setAtomMass(i, i+1);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0); forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
......
platforms/reference/tests/TestReferenceLangevinIntegrator.cpp
View file @ a138663d
...@@ -55,7 +55,7 @@ void testSingleBond() { ...@@ -55,7 +55,7 @@ void testSingleBond() {
system.setAtomMass(0, 2.0); system.setAtomMass(0, 2.0);
system.setAtomMass(1, 2.0); system.setAtomMass(1, 2.0);
LangevinIntegrator integrator(0, 0.1, 0.01); 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); forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField); system.addForce(forceField);
OpenMMContext context(system, integrator, platform); OpenMMContext context(system, integrator, platform);
...@@ -99,7 +99,7 @@ void testTemperature() { ...@@ -99,7 +99,7 @@ void testTemperature() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, 0); System system(numAtoms, 0);
LangevinIntegrator integrator(temp, 2.0, 0.01); 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) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 2.0); system.setAtomMass(i, 2.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0); forceField->setAtomParameters(i, (i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
...@@ -134,7 +134,7 @@ void testConstraints() { ...@@ -134,7 +134,7 @@ void testConstraints() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, numAtoms-1); System system(numAtoms, numAtoms-1);
LangevinIntegrator integrator(temp, 2.0, 0.01); 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) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 10.0); system.setAtomMass(i, 10.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0); forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
......
platforms/reference/tests/TestReferenceStandardMMForceField.cpp
View file @ a138663d
...@@ -52,7 +52,7 @@ void testBonds() { ...@@ -52,7 +52,7 @@ void testBonds() {
ReferencePlatform platform; ReferencePlatform platform;
System system(3, 0); System system(3, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 0, 1, 1.5, 0.8);
forceField->setBondParameters(1, 1, 2, 1.2, 0.7); forceField->setBondParameters(1, 1, 2, 1.2, 0.7);
system.addForce(forceField); system.addForce(forceField);
...@@ -74,7 +74,7 @@ void testAngles() { ...@@ -74,7 +74,7 @@ void testAngles() {
ReferencePlatform platform; ReferencePlatform platform;
System system(4, 0); System system(4, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 0, 1, 2, PI_M/3, 1.1);
forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2); forceField->setAngleParameters(1, 1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField); system.addForce(forceField);
...@@ -99,7 +99,7 @@ void testPeriodicTorsions() { ...@@ -99,7 +99,7 @@ void testPeriodicTorsions() {
ReferencePlatform platform; ReferencePlatform platform;
System system(4, 0); System system(4, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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); forceField->setPeriodicTorsionParameters(0, 0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField); system.addForce(forceField);
OpenMMContext context(system, integrator, platform); OpenMMContext context(system, integrator, platform);
...@@ -122,7 +122,7 @@ void testRBTorsions() { ...@@ -122,7 +122,7 @@ void testRBTorsions() {
ReferencePlatform platform; ReferencePlatform platform;
System system(4, 0); System system(4, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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); forceField->setRBTorsionParameters(0, 0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField); system.addForce(forceField);
OpenMMContext context(system, integrator, platform); OpenMMContext context(system, integrator, platform);
...@@ -155,7 +155,7 @@ void testCoulomb() { ...@@ -155,7 +155,7 @@ void testCoulomb() {
ReferencePlatform platform; ReferencePlatform platform;
System system(2, 0); System system(2, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 0.5, 1, 0);
forceField->setAtomParameters(1, -1.5, 1, 0); forceField->setAtomParameters(1, -1.5, 1, 0);
system.addForce(forceField); system.addForce(forceField);
...@@ -176,7 +176,7 @@ void testLJ() { ...@@ -176,7 +176,7 @@ void testLJ() {
ReferencePlatform platform; ReferencePlatform platform;
System system(2, 0); System system(2, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 0, 1.2, 1);
forceField->setAtomParameters(1, 0, 1.4, 2); forceField->setAtomParameters(1, 0, 1.4, 2);
system.addForce(forceField); system.addForce(forceField);
...@@ -199,7 +199,7 @@ void testExclusionsAnd14() { ...@@ -199,7 +199,7 @@ void testExclusionsAnd14() {
ReferencePlatform platform; ReferencePlatform platform;
System system(5, 0); System system(5, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 0, 1, 1, 0);
forceField->setBondParameters(1, 1, 2, 1, 0); forceField->setBondParameters(1, 1, 2, 1, 0);
forceField->setBondParameters(2, 2, 3, 1, 0); forceField->setBondParameters(2, 2, 3, 1, 0);
...@@ -218,6 +218,8 @@ void testExclusionsAnd14() { ...@@ -218,6 +218,8 @@ void testExclusionsAnd14() {
} }
forceField->setAtomParameters(0, 0, 1.5, 1); forceField->setAtomParameters(0, 0, 1.5, 1);
forceField->setAtomParameters(i, 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); positions[i] = Vec3(r, 0, 0);
context.reinitialize(); context.reinitialize();
context.setPositions(positions); context.setPositions(positions);
...@@ -243,6 +245,8 @@ void testExclusionsAnd14() { ...@@ -243,6 +245,8 @@ void testExclusionsAnd14() {
forceField->setAtomParameters(0, 2, 1.5, 0); forceField->setAtomParameters(0, 2, 1.5, 0);
forceField->setAtomParameters(i, 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);
context.reinitialize(); context.reinitialize();
context.setPositions(positions); context.setPositions(positions);
state = context.getState(State::Forces | State::Energy); state = context.getState(State::Forces | State::Energy);
...@@ -267,7 +271,7 @@ void testCutoff() { ...@@ -267,7 +271,7 @@ void testCutoff() {
ReferencePlatform platform; ReferencePlatform platform;
System system(3, 0); System system(3, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 1.0, 1, 0);
forceField->setAtomParameters(1, 1.0, 1, 0); forceField->setAtomParameters(1, 1.0, 1, 0);
forceField->setAtomParameters(2, 1.0, 1, 0); forceField->setAtomParameters(2, 1.0, 1, 0);
...@@ -300,7 +304,7 @@ void testCutoff14() { ...@@ -300,7 +304,7 @@ void testCutoff14() {
ReferencePlatform platform; ReferencePlatform platform;
System system(5, 0); System system(5, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 0, 1, 1, 0);
forceField->setBondParameters(1, 1, 2, 1, 0); forceField->setBondParameters(1, 1, 2, 1, 0);
forceField->setBondParameters(2, 2, 3, 1, 0); forceField->setBondParameters(2, 2, 3, 1, 0);
...@@ -324,6 +328,8 @@ void testCutoff14() { ...@@ -324,6 +328,8 @@ void testCutoff14() {
for (int j = 1; j < 5; ++j) for (int j = 1; j < 5; ++j)
forceField->setAtomParameters(j, 0, 1.5, 0); forceField->setAtomParameters(j, 0, 1.5, 0);
forceField->setAtomParameters(i, 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);
context.reinitialize(); context.reinitialize();
context.setPositions(positions); context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy); State state = context.getState(State::Forces | State::Energy);
...@@ -350,6 +356,8 @@ void testCutoff14() { ...@@ -350,6 +356,8 @@ void testCutoff14() {
const double q = 0.7; const double q = 0.7;
forceField->setAtomParameters(0, q, 1.5, 0); forceField->setAtomParameters(0, q, 1.5, 0);
forceField->setAtomParameters(i, 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.reinitialize();
context.setPositions(positions); context.setPositions(positions);
state = context.getState(State::Forces | State::Energy); state = context.getState(State::Forces | State::Energy);
...@@ -377,7 +385,7 @@ void testPeriodic() { ...@@ -377,7 +385,7 @@ void testPeriodic() {
ReferencePlatform platform; ReferencePlatform platform;
System system(3, 0); System system(3, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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(0, 1.0, 1, 0);
forceField->setAtomParameters(1, 1.0, 1, 0); forceField->setAtomParameters(1, 1.0, 1, 0);
forceField->setAtomParameters(2, 1.0, 1, 0); forceField->setAtomParameters(2, 1.0, 1, 0);
......
platforms/reference/tests/TestReferenceVerletIntegrator.cpp
View file @ a138663d
...@@ -55,7 +55,7 @@ void testSingleBond() { ...@@ -55,7 +55,7 @@ void testSingleBond() {
system.setAtomMass(0, 2.0); system.setAtomMass(0, 2.0);
system.setAtomMass(1, 2.0); system.setAtomMass(1, 2.0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(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); forceField->setBondParameters(0, 0, 1, 1.5, 1);
system.addForce(forceField); system.addForce(forceField);
OpenMMContext context(system, integrator, platform); OpenMMContext context(system, integrator, platform);
...@@ -90,7 +90,7 @@ void testConstraints() { ...@@ -90,7 +90,7 @@ void testConstraints() {
ReferencePlatform platform; ReferencePlatform platform;
System system(numAtoms, numAtoms-1); System system(numAtoms, numAtoms-1);
VerletIntegrator integrator(0.002); VerletIntegrator integrator(0.002);
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) { for (int i = 0; i < numAtoms; ++i) {
system.setAtomMass(i, 10.0); system.setAtomMass(i, 10.0);
forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0); forceField->setAtomParameters(i, (i%2 == 0 ? 0.2 : -0.2), 0.5, 5.0);
......
tests/TestFindExclusions.cpp
View file @ a138663d
...@@ -140,19 +140,13 @@ class DummyForceKernel : public CalcStandardMMForceFieldKernel { ...@@ -140,19 +140,13 @@ class DummyForceKernel : public CalcStandardMMForceFieldKernel {
public: public:
DummyForceKernel(string name, const Platform& platform) : CalcStandardMMForceFieldKernel(name, platform) { DummyForceKernel(string name, const Platform& platform) : CalcStandardMMForceFieldKernel(name, platform) {
} }
void initialize(const vector<vector<int> >& bondIndices, const vector<vector<double> >& bondParameters, void initialize(const System& system, const StandardMMForceField& force, const std::vector<std::set<int> >& exclusions) {
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]) {
verifyExclusions(exclusions); verifyExclusions(exclusions);
verify14(bonded14Indices); // verify14(bonded14Indices);
} }
void executeForces(const Stream& positions, Stream& forces) { void executeForces(OpenMMContextImpl& context) {
} }
double executeEnergy(const Stream& positions) { double executeEnergy(OpenMMContextImpl& context) {
return 0.0; return 0.0;
} }
}; };
...@@ -161,9 +155,9 @@ class DummyIntegratorKernel : public IntegrateVerletStepKernel { ...@@ -161,9 +155,9 @@ class DummyIntegratorKernel : public IntegrateVerletStepKernel {
public: public:
DummyIntegratorKernel(string name, const Platform& platform) : IntegrateVerletStepKernel(name, platform) { DummyIntegratorKernel(string name, const Platform& platform) : IntegrateVerletStepKernel(name, platform) {
} }
void initialize(const vector<double>& masses, const vector<vector<int> >& constraintIndices, const vector<double>& constraintLengths) { void initialize(const System& system, const VerletIntegrator& integrator) {
} }
void execute(Stream& positions, Stream& velocities, const Stream& forces, double stepSize) { void execute(OpenMMContextImpl& context, const VerletIntegrator& integrator) {
} }
}; };
...@@ -171,9 +165,9 @@ class DummyKEKernel : public CalcKineticEnergyKernel { ...@@ -171,9 +165,9 @@ class DummyKEKernel : public CalcKineticEnergyKernel {
public: public:
DummyKEKernel(string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) { DummyKEKernel(string name, const Platform& platform) : CalcKineticEnergyKernel(name, platform) {
} }
void initialize(const vector<double>& masses) { void initialize(const System& system) {
} }
double execute(const Stream& positions) { double execute(OpenMMContextImpl& context) {
return 0.0; return 0.0;
} }
}; };
...@@ -238,7 +232,7 @@ int main() { ...@@ -238,7 +232,7 @@ int main() {
DummyPlatform platform; DummyPlatform platform;
System system(NUM_ATOMS, 0); System system(NUM_ATOMS, 0);
VerletIntegrator integrator(0.01); VerletIntegrator integrator(0.01);
StandardMMForceField* forces = new StandardMMForceField(NUM_ATOMS, NUM_ATOMS-1, 0, 0, 0); StandardMMForceField* forces = new StandardMMForceField(NUM_ATOMS, NUM_ATOMS-1, 0, 0, 0, 0);
// loop over all main-chain atoms (even numbered atoms) // loop over all main-chain atoms (even numbered atoms)
for (int i = 0; i < NUM_ATOMS-1; i += 2) for (int i = 0; i < NUM_ATOMS-1; i += 2)
......
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