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Commit a4020466 authored by Peter Eastman's avatar Peter Eastman
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Renamed OpenMMContext to Context

parent 95b8dbd6
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Showing with 89 additions and 89 deletions
platforms/cuda/src/CudaStreamFactory.cpp
View file @ a4020466
......@@ -28,12 +28,12 @@
#include "CudaStreamFactory.h"
#include "CudaStreamImpl.h"
#include "openmm/OpenMMException.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "kernels/gputypes.h"
using namespace OpenMM;
StreamImpl* CudaStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, OpenMMContextImpl& context) const {
StreamImpl* CudaStreamFactory::createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, ContextImpl& context) const {
CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(context.getPlatformData());
if (name == "particlePositions") {
float padding[] = {100000.0f, 100000.0f, 100000.0f, 0.2f};
......
platforms/cuda/tests/TestCudaAndersenThermostat.cpp
View file @ a4020466
......@@ -35,7 +35,7 @@
#include "../../../tests/AssertionUtilities.h"
#include "openmm/AndersenThermostat.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -63,7 +63,7 @@ void testTemperature() {
system.addForce(forceField);
AndersenThermostat* thermstat = new AndersenThermostat(temp, collisionFreq);
system.addForce(thermstat);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
......@@ -111,7 +111,7 @@ void testRandomSeed() {
// Try twice with the same random seed.
thermostat->setRandomNumberSeed(5);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
......
platforms/cuda/tests/TestCudaBrownianIntegrator.cpp
View file @ a4020466
......@@ -37,7 +37,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
......@@ -63,7 +63,7 @@ void testSingleBond() {
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
......@@ -100,7 +100,7 @@ void testTemperature() {
for (int i = 0; i < numBonds; ++i)
forceField->addBond(i, i+1, 1.0, 5.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3(i, 0, 0);
......@@ -143,7 +143,7 @@ void testConstraints() {
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......@@ -194,7 +194,7 @@ void testRandomSeed() {
// Try twice with the same random seed.
integrator.setRandomNumberSeed(5);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
......
platforms/cuda/tests/TestCudaCMMotionRemover.cpp
View file @ a4020466
......@@ -35,7 +35,7 @@
#include "../../../tests/AssertionUtilities.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
......@@ -75,7 +75,7 @@ void testMotionRemoval(Integrator& integrator) {
system.addForce(nonbonded);
CMMotionRemover* remover = new CMMotionRemover();
system.addForce(remover);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......
platforms/cuda/tests/TestCudaGBSAOBCForce.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/GBSAOBCForce.h"
......@@ -62,7 +62,7 @@ void testSingleParticle() {
nonbonded->addParticle(0.5, 1, 0);
system.addForce(gbsa);
system.addForce(nonbonded);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
positions[0] = Vec3(0, 0, 0);
context.setPositions(positions);
......@@ -100,7 +100,7 @@ void testCutoffAndPeriodic() {
// Calculate the forces for both cutoff and periodic with two different atom positions.
nonbonded->setNonbondedMethod(NonbondedForce::CutoffNonPeriodic);
OpenMMContext context(system, integrator, cuda);
Context context(system, integrator, cuda);
context.setPositions(positions);
State state1 = context.getState(State::Forces);
nonbonded->setNonbondedMethod(NonbondedForce::CutoffPeriodic);
......@@ -149,8 +149,8 @@ void testForce(int numParticles, NonbondedForce::NonbondedMethod method) {
}
system.addForce(gbsa);
system.addForce(nonbonded);
OpenMMContext context(system, integrator, cuda);
OpenMMContext refContext(system, integrator, reference);
Context context(system, integrator, cuda);
Context refContext(system, integrator, reference);
// Set random (but uniformly distributed) positions for all the particles.
......
platforms/cuda/tests/TestCudaHarmonicAngleForce.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicAngleForce.h"
#include "openmm/System.h"
......@@ -60,7 +60,7 @@ void testAngles() {
forceField->addAngle(0, 1, 2, PI_M/3, 1.1);
forceField->addAngle(1, 2, 3, PI_M/2, 1.2);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
......
platforms/cuda/tests/TestCudaHarmonicBondForce.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/System.h"
......@@ -59,7 +59,7 @@ void testBonds() {
forceField->addBond(0, 1, 1.5, 0.8);
forceField->addBond(1, 2, 1.2, 0.7);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
......
platforms/cuda/tests/TestCudaLangevinIntegrator.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
......@@ -59,7 +59,7 @@ void testSingleBond() {
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
......@@ -106,7 +106,7 @@ void testTemperature() {
forceField->addParticle((i%2 == 0 ? 1.0 : -1.0), 1.0, 5.0);
}
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; ++i)
positions[i] = Vec3((i%2 == 0 ? 2 : -2), (i%4 < 2 ? 2 : -2), (i < 4 ? 2 : -2));
......@@ -148,7 +148,7 @@ void testConstraints() {
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......@@ -199,7 +199,7 @@ void testRandomSeed() {
// Try twice with the same random seed.
integrator.setRandomNumberSeed(5);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
context.setPositions(positions);
context.setVelocities(velocities);
integrator.step(10);
......
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "ReferencePlatform.h"
#include "openmm/HarmonicBondForce.h"
......@@ -42,7 +42,7 @@
#include "openmm/System.h"
#include "openmm/LangevinIntegrator.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "kernels/gputypes.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/sfmt/SFMT.h"
......@@ -64,7 +64,7 @@ void testCoulomb() {
forceField->addParticle(0.5, 1, 0);
forceField->addParticle(-1.5, 1, 0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
......@@ -87,7 +87,7 @@ void testLJ() {
forceField->addParticle(0, 1.2, 1);
forceField->addParticle(0, 1.4, 2);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
......@@ -143,7 +143,7 @@ void testExclusionsAnd14() {
nonbonded->setExceptionParameters(first14, 0, 3, 0, 1.5, i == 3 ? 0.5 : 0.0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0.0);
positions[i] = Vec3(r, 0, 0);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
......@@ -169,7 +169,7 @@ void testExclusionsAnd14() {
nonbonded->setParticleParameters(i, 2, 1.5, 0);
nonbonded->setExceptionParameters(first14, 0, 3, i == 3 ? 4/1.2 : 0, 1.5, 0);
nonbonded->setExceptionParameters(second14, 1, 4, 0, 1.5, 0);
OpenMMContext context2(system, integrator, platform);
Context context2(system, integrator, platform);
context2.setPositions(positions);
state = context2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces2 = state.getForces();
......@@ -206,7 +206,7 @@ void testCutoff() {
const double eps = 50.0;
forceField->setReactionFieldDielectric(eps);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2, 0);
......@@ -257,7 +257,7 @@ void testCutoff14() {
second14 = i;
}
system.addForce(nonbonded);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(5);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
......@@ -341,7 +341,7 @@ void testPeriodic() {
nonbonded->setCutoffDistance(cutoff);
nonbonded->setPeriodicBoxVectors(Vec3(4, 0, 0), Vec3(0, 4, 0), Vec3(0, 0, 4));
system.addForce(nonbonded);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(2, 0, 0);
......@@ -374,7 +374,7 @@ void testEwald() {
nonbonded->setEwaldErrorTolerance(TOL);
nonbonded->setPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(0, 6, 0), Vec3(0, 0, 6));
system.addForce(nonbonded);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(3.048000,2.764000,3.156000);
positions[1] = Vec3(2.809000,2.888000,2.571000);
......@@ -428,8 +428,8 @@ void testLargeSystem() {
nonbonded->setCutoffDistance(cutoff);
system.addForce(nonbonded);
system.addForce(bonds);
OpenMMContext cudaContext(system, integrator, cuda);
OpenMMContext referenceContext(system, integrator, reference);
Context cudaContext(system, integrator, cuda);
Context referenceContext(system, integrator, reference);
cudaContext.setPositions(positions);
cudaContext.setVelocities(velocities);
referenceContext.setPositions(positions);
......@@ -484,10 +484,10 @@ void testBlockInteractions(bool periodic) {
nonbonded->setCutoffDistance(cutoff);
nonbonded->setPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
system.addForce(nonbonded);
OpenMMContext context(system, integrator, cuda);
Context context(system, integrator, cuda);
context.setPositions(positions);
State state = context.getState(State::Positions | State::Velocities | State::Forces);
OpenMMContextImpl* contextImpl = *reinterpret_cast<OpenMMContextImpl**>(&context);
ContextImpl* contextImpl = *reinterpret_cast<ContextImpl**>(&context);
CudaPlatform::PlatformData& data = *static_cast<CudaPlatform::PlatformData*>(contextImpl->getPlatformData());
// Verify that the bounds of each block were calculated correctly.
......
platforms/cuda/tests/TestCudaPeriodicTorsionForce.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/PeriodicTorsionForce.h"
#include "openmm/System.h"
......@@ -59,7 +59,7 @@ void testPeriodicTorsions() {
PeriodicTorsionForce* forceField = new PeriodicTorsionForce();
forceField->addTorsion(0, 1, 2, 3, 2, PI_M/3, 1.1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
......
platforms/cuda/tests/TestCudaRBTorsionForce.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/RBTorsionForce.h"
#include "openmm/System.h"
......@@ -59,7 +59,7 @@ void testRBTorsions() {
RBTorsionForce* forceField = new RBTorsionForce();
forceField->addTorsion(0, 1, 2, 3, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 1, 0);
positions[1] = Vec3(0, 0, 0);
......
platforms/cuda/tests/TestCudaSettle.cpp
View file @ a4020466
......@@ -35,7 +35,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/NonbondedForce.h"
#include "openmm/System.h"
......@@ -69,7 +69,7 @@ void testConstraints() {
system.addConstraint(i*3+1, i*3+2, 0.163);
}
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......
platforms/cuda/tests/TestCudaStreams.cpp
View file @ a4020466
......@@ -35,7 +35,7 @@
#include "../../../tests/AssertionUtilities.h"
#include "CudaPlatform.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "openmm/Stream.h"
#include "openmm/VerletIntegrator.h"
#include <iostream>
......@@ -53,8 +53,8 @@ void testStream(Stream::DataType type, T scale) {
for (int i = 0; i < size; i++)
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
OpenMMContext context(system, integrator, platform);
OpenMMContextImpl* impl = *reinterpret_cast<OpenMMContextImpl**>(&context);
Context context(system, integrator, platform);
ContextImpl* impl = *reinterpret_cast<ContextImpl**>(&context);
Stream stream = platform.createStream("", size, type, *impl);
const int length = size*WIDTH;
T array[size*WIDTH+1];
......
platforms/cuda/tests/TestCudaVariableVerletIntegrator.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
......@@ -59,7 +59,7 @@ void testSingleBond() {
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
......@@ -104,7 +104,7 @@ void testConstraints() {
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......@@ -169,7 +169,7 @@ void testConstrainedClusters() {
system.addConstraint(3, 4, sqrt(2.0));
system.addConstraint(5, 6, sqrt(2.0));
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
......
platforms/cuda/tests/TestCudaVerletIntegrator.cpp
View file @ a4020466
......@@ -34,7 +34,7 @@
*/
#include "../../../tests/AssertionUtilities.h"
#include "openmm/OpenMMContext.h"
#include "openmm/Context.h"
#include "CudaPlatform.h"
#include "openmm/HarmonicBondForce.h"
#include "openmm/NonbondedForce.h"
......@@ -59,7 +59,7 @@ void testSingleBond() {
HarmonicBondForce* forceField = new HarmonicBondForce();
forceField->addBond(0, 1, 1.5, 1);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(-1, 0, 0);
positions[1] = Vec3(1, 0, 0);
......@@ -104,7 +104,7 @@ void testConstraints() {
system.addConstraint(4, 5, 1.0);
system.addConstraint(6, 7, 1.0);
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
vector<Vec3> velocities(numParticles);
init_gen_rand(0);
......@@ -161,7 +161,7 @@ void testConstrainedClusters() {
system.addConstraint(3, 4, sqrt(2.0));
system.addConstraint(5, 6, sqrt(2.0));
system.addForce(forceField);
OpenMMContext context(system, integrator, platform);
Context context(system, integrator, platform);
vector<Vec3> positions(numParticles);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
......
platforms/reference/include/ReferenceKernelFactory.h
View file @ a4020466
......@@ -42,7 +42,7 @@ namespace OpenMM {
class ReferenceKernelFactory : public KernelFactory {
public:
KernelImpl* createKernelImpl(std::string name, const Platform& platform, OpenMMContextImpl& context) const;
KernelImpl* createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const;
};
} // namespace OpenMM
......
platforms/reference/include/ReferencePlatform.h
View file @ a4020466
......@@ -55,8 +55,8 @@ public:
}
bool supportsDoublePrecision() const;
const StreamFactory& getDefaultStreamFactory() const;
void contextCreated(OpenMMContextImpl& context) const;
void contextDestroyed(OpenMMContextImpl& context) const;
void contextCreated(ContextImpl& context) const;
void contextDestroyed(ContextImpl& context) const;
private:
ReferenceStreamFactory defaultStreamFactory;
};
......
platforms/reference/include/ReferenceStreamFactory.h
View file @ a4020466
......@@ -43,7 +43,7 @@ namespace OpenMM {
class OPENMM_EXPORT ReferenceStreamFactory : public StreamFactory {
public:
StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, OpenMMContextImpl& context) const;
StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, ContextImpl& context) const;
};
} // namespace OpenMM
......
platforms/reference/src/ReferenceKernelFactory.cpp
View file @ a4020466
......@@ -31,12 +31,12 @@
#include "ReferenceKernelFactory.h"
#include "ReferenceKernels.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/OpenMMException.h"
using namespace OpenMM;
KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Platform& platform, OpenMMContextImpl& context) const {
KernelImpl* ReferenceKernelFactory::createKernelImpl(std::string name, const Platform& platform, ContextImpl& context) const {
ReferencePlatform::PlatformData& data = *static_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
if (name == InitializeForcesKernel::Name())
return new ReferenceInitializeForcesKernel(name, platform);
......
platforms/reference/src/ReferenceKernels.cpp
View file @ a4020466
......@@ -49,7 +49,7 @@
#include "SimTKReference/ReferenceVerletDynamics.h"
#include "openmm/CMMotionRemover.h"
#include "openmm/System.h"
#include "openmm/internal/OpenMMContextImpl.h"
#include "openmm/internal/ContextImpl.h"
#include "openmm/Integrator.h"
#include "SimTKUtilities/SimTKOpenMMUtilities.h"
#include <cmath>
......@@ -125,7 +125,7 @@ static void findAnglesForCCMA(const System& system, vector<ReferenceCCMAAlgorith
void ReferenceInitializeForcesKernel::initialize(const System& system) {
}
void ReferenceInitializeForcesKernel::execute(OpenMMContextImpl& context) {
void ReferenceInitializeForcesKernel::execute(ContextImpl& context) {
double zero[] = {0.0, 0.0, 0.0};
context.getForces().fillWithValue(zero);
}
......@@ -133,11 +133,11 @@ void ReferenceInitializeForcesKernel::execute(OpenMMContextImpl& context) {
void ReferenceUpdateTimeKernel::initialize(const System& system) {
}
double ReferenceUpdateTimeKernel::getTime(const OpenMMContextImpl& context) const {
double ReferenceUpdateTimeKernel::getTime(const ContextImpl& context) const {
return data.time;
}
void ReferenceUpdateTimeKernel::setTime(OpenMMContextImpl& context, double time) {
void ReferenceUpdateTimeKernel::setTime(ContextImpl& context, double time) {
data.time = time;
}
......@@ -161,7 +161,7 @@ void ReferenceCalcHarmonicBondForceKernel::initialize(const System& system, cons
}
}
void ReferenceCalcHarmonicBondForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcHarmonicBondForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
ReferenceBondForce refBondForce;
......@@ -169,7 +169,7 @@ void ReferenceCalcHarmonicBondForceKernel::executeForces(OpenMMContextImpl& cont
refBondForce.calculateForce(numBonds, bondIndexArray, posData, bondParamArray, forceData, 0, 0, 0, harmonicBond);
}
double ReferenceCalcHarmonicBondForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcHarmonicBondForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numBonds];
......@@ -205,7 +205,7 @@ void ReferenceCalcHarmonicAngleForceKernel::initialize(const System& system, con
}
}
void ReferenceCalcHarmonicAngleForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcHarmonicAngleForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
ReferenceBondForce refBondForce;
......@@ -213,7 +213,7 @@ void ReferenceCalcHarmonicAngleForceKernel::executeForces(OpenMMContextImpl& con
refBondForce.calculateForce(numAngles, angleIndexArray, posData, angleParamArray, forceData, 0, 0, 0, angleBond);
}
double ReferenceCalcHarmonicAngleForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcHarmonicAngleForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numAngles];
......@@ -251,7 +251,7 @@ void ReferenceCalcPeriodicTorsionForceKernel::initialize(const System& system, c
}
}
void ReferenceCalcPeriodicTorsionForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcPeriodicTorsionForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
ReferenceBondForce refBondForce;
......@@ -259,7 +259,7 @@ void ReferenceCalcPeriodicTorsionForceKernel::executeForces(OpenMMContextImpl& c
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, periodicTorsionBond);
}
double ReferenceCalcPeriodicTorsionForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcPeriodicTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
......@@ -300,7 +300,7 @@ void ReferenceCalcRBTorsionForceKernel::initialize(const System& system, const R
}
}
void ReferenceCalcRBTorsionForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcRBTorsionForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
ReferenceBondForce refBondForce;
......@@ -308,7 +308,7 @@ void ReferenceCalcRBTorsionForceKernel::executeForces(OpenMMContextImpl& context
refBondForce.calculateForce(numTorsions, torsionIndexArray, posData, torsionParamArray, forceData, 0, 0, 0, rbTorsionBond);
}
double ReferenceCalcRBTorsionForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcRBTorsionForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
RealOpenMM* energyArray = new RealOpenMM[numTorsions];
......@@ -413,7 +413,7 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
rfDielectric = force.getReactionFieldDielectric();
}
void ReferenceCalcNonbondedForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcNonbondedForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
ReferenceLJCoulombIxn clj;
......@@ -438,7 +438,7 @@ void ReferenceCalcNonbondedForceKernel::executeForces(OpenMMContextImpl& context
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0, 0, nonbonded14);
}
double ReferenceCalcNonbondedForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcNonbondedForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = allocateRealArray(numParticles, 3);
RealOpenMM energy = 0;
......@@ -518,13 +518,13 @@ void ReferenceCalcGBSAOBCForceKernel::initialize(const System& system, const GBS
obc->setIncludeAceApproximation(true);
}
void ReferenceCalcGBSAOBCForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcGBSAOBCForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
}
double ReferenceCalcGBSAOBCForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcGBSAOBCForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = allocateRealArray(context.getSystem().getNumParticles(), 3);
obc->computeImplicitSolventForces(posData, &charges[0], forceData, 1);
......@@ -586,7 +586,7 @@ void ReferenceCalcGBVIForceKernel::initialize(const System& system, const GBVIFo
}
void ReferenceCalcGBVIForceKernel::executeForces(OpenMMContextImpl& context) {
void ReferenceCalcGBVIForceKernel::executeForces(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM** forceData = ((ReferenceFloatStreamImpl&) context.getForces().getImpl()).getData();
......@@ -596,7 +596,7 @@ void ReferenceCalcGBVIForceKernel::executeForces(OpenMMContextImpl& context) {
delete[] bornRadii;
}
double ReferenceCalcGBVIForceKernel::executeEnergy(OpenMMContextImpl& context) {
double ReferenceCalcGBVIForceKernel::executeEnergy(ContextImpl& context) {
RealOpenMM** posData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData()); // Reference code needs to be made const correct
RealOpenMM* bornRadii = new RealOpenMM[context.getSystem().getNumParticles()];
gbvi->computeBornRadii(posData, bornRadii, NULL );
......@@ -636,7 +636,7 @@ void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const
}
}
void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, const VerletIntegrator& integrator) {
void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
double stepSize = integrator.getStepSize();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
......@@ -692,7 +692,7 @@ void ReferenceIntegrateLangevinStepKernel::initialize(const System& system, cons
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, const LangevinIntegrator& integrator) {
void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -757,7 +757,7 @@ void ReferenceIntegrateBrownianStepKernel::initialize(const System& system, cons
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, const BrownianIntegrator& integrator) {
void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const BrownianIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
......@@ -821,7 +821,7 @@ void ReferenceIntegrateVariableLangevinStepKernel::initialize(const System& syst
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
}
void ReferenceIntegrateVariableLangevinStepKernel::execute(OpenMMContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double errorTol = integrator.getErrorTolerance();
......@@ -884,7 +884,7 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system
}
}
void ReferenceIntegrateVariableVerletStepKernel::execute(OpenMMContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
double errorTol = integrator.getErrorTolerance();
RealOpenMM** posData = ((ReferenceFloatStreamImpl&) context.getPositions().getImpl()).getData();
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
......@@ -927,7 +927,7 @@ void ReferenceApplyAndersenThermostatKernel::initialize(const System& system, co
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) thermostat.getRandomNumberSeed());
}
void ReferenceApplyAndersenThermostatKernel::execute(OpenMMContextImpl& context) {
void ReferenceApplyAndersenThermostatKernel::execute(ContextImpl& context) {
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
thermostat->applyThermostat(
context.getVelocities().getSize(),
......@@ -945,7 +945,7 @@ void ReferenceCalcKineticEnergyKernel::initialize(const System& system) {
masses[i] = system.getParticleMass(i);
}
double ReferenceCalcKineticEnergyKernel::execute(OpenMMContextImpl& context) {
double ReferenceCalcKineticEnergyKernel::execute(ContextImpl& context) {
RealOpenMM** velData = const_cast<RealOpenMM**>(((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData()); // Reference code needs to be made const correct
double energy = 0.0;
for (size_t i = 0; i < masses.size(); ++i)
......@@ -960,7 +960,7 @@ void ReferenceRemoveCMMotionKernel::initialize(const System& system, const CMMot
masses[i] = system.getParticleMass(i);
}
void ReferenceRemoveCMMotionKernel::execute(OpenMMContextImpl& context) {
void ReferenceRemoveCMMotionKernel::execute(ContextImpl& context) {
if (data.stepCount%frequency != 0)
return;
RealOpenMM** velData = ((ReferenceFloatStreamImpl&) context.getVelocities().getImpl()).getData();
......
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