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Commit 37b86c10 authored by Peter Eastman's avatar Peter Eastman
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Fixed bug that prevented constraints being applied when computing kinetic energy

parent 29256dfe
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Showing with 20 additions and 30 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ 37b86c10
......@@ -1701,6 +1701,9 @@ void ReferenceIntegrateVerletStepKernel::initialize(const System& system, const
constraintIndices[i][1] = particle2;
constraintDistances[i] = static_cast<RealOpenMM>(distance);
}
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
}
void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const VerletIntegrator& integrator) {
......@@ -1711,14 +1714,9 @@ void ReferenceIntegrateVerletStepKernel::execute(ContextImpl& context, const Ver
if (dynamics == 0 || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
if (dynamics) {
if (dynamics)
delete dynamics;
delete constraints;
}
dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevStepSize = stepSize;
}
......@@ -1760,6 +1758,9 @@ void ReferenceIntegrateLangevinStepKernel::initialize(const System& system, cons
constraintDistances[i] = static_cast<RealOpenMM>(distance);
}
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
}
void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const LangevinIntegrator& integrator) {
......@@ -1772,19 +1773,14 @@ void ReferenceIntegrateLangevinStepKernel::execute(ContextImpl& context, const L
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
if (dynamics) {
if (dynamics)
delete dynamics;
delete constraints;
}
RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction );
dynamics = new ReferenceStochasticDynamics(
context.getSystem().getNumParticles(),
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau),
static_cast<RealOpenMM>(temperature) );
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......@@ -1828,6 +1824,9 @@ void ReferenceIntegrateBrownianStepKernel::initialize(const System& system, cons
constraintDistances[i] = static_cast<RealOpenMM>(distance);
}
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
}
void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const BrownianIntegrator& integrator) {
......@@ -1840,18 +1839,13 @@ void ReferenceIntegrateBrownianStepKernel::execute(ContextImpl& context, const B
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || stepSize != prevStepSize) {
// Recreate the computation objects with the new parameters.
if (dynamics) {
if (dynamics)
delete dynamics;
delete constraints;
}
dynamics = new ReferenceBrownianDynamics(
context.getSystem().getNumParticles(),
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(friction),
static_cast<RealOpenMM>(temperature) );
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......@@ -1895,6 +1889,9 @@ void ReferenceIntegrateVariableLangevinStepKernel::initialize(const System& syst
constraintDistances[i] = static_cast<RealOpenMM>(distance);
}
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
}
double ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
......@@ -1907,15 +1904,10 @@ double ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& contex
if (dynamics == 0 || temperature != prevTemp || friction != prevFriction || errorTol != prevErrorTol) {
// Recreate the computation objects with the new parameters.
if (dynamics) {
if (dynamics)
delete dynamics;
delete constraints;
}
RealOpenMM tau = static_cast<RealOpenMM>( friction == 0.0 ? 0.0 : 1.0/friction );
dynamics = new ReferenceVariableStochasticDynamics(context.getSystem().getNumParticles(), (RealOpenMM) tau, (RealOpenMM) temperature, (RealOpenMM) errorTol);
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......@@ -1962,6 +1954,9 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system
constraintIndices[i][1] = particle2;
constraintDistances[i] = static_cast<RealOpenMM>(distance);
}
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(system, angles);
constraints = new ReferenceCCMAAlgorithm(system.getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
}
double ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
......@@ -1972,14 +1967,9 @@ double ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context,
if (dynamics == 0 || errorTol != prevErrorTol) {
// Recreate the computation objects with the new parameters.
if (dynamics) {
if (dynamics)
delete dynamics;
delete constraints;
}
dynamics = new ReferenceVariableVerletDynamics(context.getSystem().getNumParticles(), (RealOpenMM) errorTol);
vector<ReferenceCCMAAlgorithm::AngleInfo> angles;
findAnglesForCCMA(context.getSystem(), angles);
constraints = new ReferenceCCMAAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, angles, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevErrorTol = errorTol;
}
......
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