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Commit 37b86c10 authored by Peter Eastman's avatar Peter Eastman
Browse files

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