void CpuIntegrateLangevinStepKernel::initialize(const System& system, const LangevinIntegrator& integrator) {
int numParticles = system.getNumParticles();
masses.resize(numParticles);
for (int i = 0; i < numParticles; ++i)
masses[i] = static_cast<RealOpenMM>(system.getParticleMass(i));
data.random.initialize(integrator.getRandomNumberSeed(), data.threads.getNumThreads());
}
void CpuIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
double temperature = integrator.getTemperature();
double friction = integrator.getFriction();
double stepSize = integrator.getStepSize();
vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& velData = extractVelocities(context);
vector<RealVec>& forceData = extractForces(context);
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
if (dynamics)
delete dynamics;
RealOpenMM tau = (friction == 0.0 ? 0.0 : 1.0/friction);
dynamics = new CpuLangevinDynamics(context.getSystem().getNumParticles(), stepSize, tau, temperature, data.threads, data.random);
dynamics->setReferenceConstraintAlgorithm(&extractConstraints(context));
prevTemp = temperature;
prevFriction = friction;
prevStepSize = stepSize;
}
dynamics->update(context.getSystem(), posData, velData, forceData, masses, integrator.getConstraintTolerance());
ReferencePlatform::PlatformData* refData = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
refData->time += stepSize;
refData->stepCount++;
}
void testSerializeLangevinIntegrator() {
LangevinIntegrator *intg = new LangevinIntegrator(372.4, 1.234, 0.0018);
stringstream ss;
XmlSerializer::serialize<Integrator>(intg, "LangevinIntegrator", ss);
LangevinIntegrator *intg2 = dynamic_cast<LangevinIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
ASSERT_EQUAL(intg->getConstraintTolerance(), intg2->getConstraintTolerance());
ASSERT_EQUAL(intg->getStepSize(), intg2->getStepSize());
ASSERT_EQUAL(intg->getTemperature(), intg2->getTemperature());
ASSERT_EQUAL(intg->getFriction(), intg2->getFriction());
ASSERT_EQUAL(intg->getRandomNumberSeed(), intg2->getRandomNumberSeed());
delete intg;
delete intg2;
}
double CpuIntegrateLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const LangevinIntegrator& integrator) {
return computeShiftedKineticEnergy(context, masses, 0.5*integrator.getStepSize());
}
void ValidateOpenMM::writeIntegrator( FILE* filePtr, const Integrator& integrator ) const {
// LangevinIntegrator
try {
const LangevinIntegrator langevinIntegrator = dynamic_cast<const LangevinIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator LangevinIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", langevinIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", langevinIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "Temperature %14.7e\n", langevinIntegrator.getTemperature() );
(void) fprintf( filePtr, "Friction %14.7e\n", langevinIntegrator.getFriction() );
(void) fprintf( filePtr, "RandomNumberSeed %d\n", langevinIntegrator.getRandomNumberSeed() );
return;
} catch( std::bad_cast ){
}
// VariableLangevinIntegrator
try {
const VariableLangevinIntegrator& langevinIntegrator = dynamic_cast<const VariableLangevinIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator VariableLangevinIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", langevinIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", langevinIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "Temperature %14.7e\n", langevinIntegrator.getTemperature() );
(void) fprintf( filePtr, "Friction %14.7e\n", langevinIntegrator.getFriction() );
(void) fprintf( filePtr, "RandomNumberSeed %d\n", langevinIntegrator.getRandomNumberSeed() );
(void) fprintf( filePtr, "ErrorTolerance %14.7e\n", langevinIntegrator.getErrorTolerance() );
return;
} catch( std::bad_cast ){
}
// VerletIntegrator
try {
const VerletIntegrator& verletIntegrator = dynamic_cast<const VerletIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator VerletIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", verletIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", verletIntegrator.getConstraintTolerance() );
return;
} catch( std::bad_cast ){
}
// VariableVerletIntegrator
try {
const VariableVerletIntegrator & variableVerletIntegrator = dynamic_cast<const VariableVerletIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator VariableVerletIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", variableVerletIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", variableVerletIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "ErrorTolerance %14.7e\n", variableVerletIntegrator.getErrorTolerance() );
return;
} catch( std::bad_cast ){
}
// BrownianIntegrator
try {
const BrownianIntegrator& brownianIntegrator = dynamic_cast<const BrownianIntegrator&>(integrator);
(void) fprintf( filePtr, "Integrator BrownianIntegrator\n" );
(void) fprintf( filePtr, "StepSize %14.7e\n", brownianIntegrator.getStepSize() );
(void) fprintf( filePtr, "ConstraintTolerance %14.7e\n", brownianIntegrator.getConstraintTolerance() );
(void) fprintf( filePtr, "Temperature %14.7e\n", brownianIntegrator.getTemperature() );
(void) fprintf( filePtr, "Friction %14.7e\n", brownianIntegrator.getFriction() );
(void) fprintf( filePtr, "RandomNumberSeed %d\n", brownianIntegrator.getRandomNumberSeed() );
return;
} catch( std::bad_cast ){
}
if( getLog() ){
(void) fprintf( getLog(), "Integrator not recognized." );
(void) fflush( getLog() );
}
return;
}
