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Commit 4c5e01a1 authored by peastman's avatar peastman
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Merge pull request #230 from peastman/master 

Major simplification to constraint handling in reference platform
parents 6caf992a 4d25f4e7
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Showing with 25 additions and 73 deletions
platforms/reference/src/SimTKReference/ReferenceSETTLEAlgorithm.cpp
View file @ 4c5e01a1
......@@ -35,19 +35,11 @@ using namespace OpenMM;
using namespace std;
ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const vector<int>& atom1, const vector<int>& atom2, const vector<int>& atom3,
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses, RealOpenMM tolerance) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses), tolerance(tolerance) {
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses) {
}
RealOpenMM ReferenceSETTLEAlgorithm::getTolerance() const {
return tolerance;
}
void ReferenceSETTLEAlgorithm::setTolerance(RealOpenMM tolerance) {
this->tolerance = tolerance;
}
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) {
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]];
RealVec xp0 = atomCoordinatesP[atom1[index]]-apos0;
......@@ -190,7 +182,7 @@ void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, v
}
}
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) {
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]];
RealVec apos1 = atomCoordinates[atom2[index]];
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ 4c5e01a1
......@@ -200,7 +200,7 @@ void ReferenceStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -235,7 +235,7 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 4c5e01a1
......@@ -260,7 +260,7 @@ void ReferenceVariableStochasticDynamics::updatePart2( int numberOfAtoms, vector
void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -279,7 +279,7 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ 4c5e01a1
......@@ -104,7 +104,7 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -155,7 +155,7 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 4c5e01a1
......@@ -95,7 +95,7 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){
void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
......@@ -131,7 +131,7 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses);
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities.
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.cpp
View file @ 4c5e01a1
......@@ -56,7 +56,12 @@ static vector<RealVec>& extractForces(ContextImpl& context) {
return *((vector<RealVec>*) data->forces);
}
static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift, ReferenceConstraintAlgorithm* constraints) {
static ReferenceConstraints& extractConstraints(ContextImpl& context) {
ReferencePlatform::PlatformData* data = reinterpret_cast<ReferencePlatform::PlatformData*>(context.getPlatformData());
return *(ReferenceConstraints*) data->constraints;
}
static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>& inverseMasses, double timeShift) {
const System& system = context.getSystem();
int numParticles = system.getNumParticles();
vector<RealVec>& posData = extractPositions(context);
......@@ -75,10 +80,7 @@ static double computeShiftedKineticEnergy(ContextImpl& context, vector<double>&
// Apply constraints to them.
if (constraints != NULL) {
constraints->setTolerance(1e-4);
constraints->applyToVelocities(posData, shiftedVel, inverseMasses);
}
extractConstraints(context).applyToVelocities(posData, shiftedVel, inverseMasses, 1e-4);
// Compute the kinetic energy.
......@@ -224,8 +226,6 @@ void ReferenceCalcDrudeForceKernel::copyParametersToContext(ContextImpl& context
}
ReferenceIntegrateDrudeLangevinStepKernel::~ReferenceIntegrateDrudeLangevinStepKernel() {
if (constraints != NULL)
delete constraints;
}
void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system, const DrudeLangevinIntegrator& integrator, const DrudeForce& force) {
......@@ -254,23 +254,6 @@ void ReferenceIntegrateDrudeLangevinStepKernel::initialize(const System& system,
pairInvReducedMass.push_back((m1+m2)/(m1*m2));
}
normalParticles.insert(normalParticles.begin(), particles.begin(), particles.end());
// Prepare constraints.
if (system.getNumConstraints() > 0) {
vector<pair<int, int> > constraintIndices;
vector<RealOpenMM> constraintDistances;
for (int i = 0; i < system.getNumConstraints(); ++i) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
constraintIndices.push_back(make_pair(particle1, particle2));
constraintDistances.push_back(distance);
}
}
constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
}
}
void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
......@@ -330,8 +313,7 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
// Apply constraints.
if (constraints != NULL)
constraints->apply(pos, xPrime, particleInvMass);
extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
// Record the constrained positions and velocities.
......@@ -348,12 +330,10 @@ void ReferenceIntegrateDrudeLangevinStepKernel::execute(ContextImpl& context, co
}
double ReferenceIntegrateDrudeLangevinStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeLangevinIntegrator& integrator) {
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize());
}
ReferenceIntegrateDrudeSCFStepKernel::~ReferenceIntegrateDrudeSCFStepKernel() {
if (constraints != NULL)
delete constraints;
if (minimizerPos != NULL)
lbfgs_free(minimizerPos);
}
......@@ -377,23 +357,6 @@ void ReferenceIntegrateDrudeSCFStepKernel::initialize(const System& system, cons
particleInvMass.push_back(mass == 0.0 ? 0.0 : 1.0/mass);
}
// Prepare constraints.
if (system.getNumConstraints() > 0) {
vector<pair<int, int> > constraintIndices;
vector<RealOpenMM> constraintDistances;
for (int i = 0; i < system.getNumConstraints(); ++i) {
int particle1, particle2;
double distance;
system.getConstraintParameters(i, particle1, particle2, distance);
if (system.getParticleMass(particle1) != 0 || system.getParticleMass(particle2) != 0) {
constraintIndices.push_back(make_pair(particle1, particle2));
constraintDistances.push_back(distance);
}
}
constraints = new ReferenceConstraints(system, (RealOpenMM) integrator.getConstraintTolerance());
}
// Initialize the energy minimizer.
minimizerPos = lbfgs_malloc(drudeParticles.size()*3);
......@@ -424,8 +387,7 @@ void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const D
// Apply constraints.
if (constraints != NULL)
constraints->apply(pos, xPrime, particleInvMass);
extractConstraints(context).apply(pos, xPrime, particleInvMass, integrator.getConstraintTolerance());
// Record the constrained positions and velocities.
......@@ -446,7 +408,7 @@ void ReferenceIntegrateDrudeSCFStepKernel::execute(ContextImpl& context, const D
}
double ReferenceIntegrateDrudeSCFStepKernel::computeKineticEnergy(ContextImpl& context, const DrudeSCFIntegrator& integrator) {
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize(), constraints);
return computeShiftedKineticEnergy(context, particleInvMass, 0.5*integrator.getStepSize());
}
struct MinimizerData {
......
plugins/drude/platforms/reference/src/ReferenceDrudeKernels.h
View file @ 4c5e01a1
......@@ -86,7 +86,7 @@ private:
class ReferenceIntegrateDrudeLangevinStepKernel : public IntegrateDrudeLangevinStepKernel {
public:
ReferenceIntegrateDrudeLangevinStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
IntegrateDrudeLangevinStepKernel(name, platform), data(data), constraints(NULL) {
IntegrateDrudeLangevinStepKernel(name, platform), data(data) {
}
~ReferenceIntegrateDrudeLangevinStepKernel();
/**
......@@ -118,7 +118,6 @@ private:
std::vector<double> particleInvMass;
std::vector<double> pairInvTotalMass;
std::vector<double> pairInvReducedMass;
ReferenceConstraintAlgorithm* constraints;
};
/**
......@@ -127,7 +126,7 @@ private:
class ReferenceIntegrateDrudeSCFStepKernel : public IntegrateDrudeSCFStepKernel {
public:
ReferenceIntegrateDrudeSCFStepKernel(std::string name, const Platform& platform, ReferencePlatform::PlatformData& data) :
IntegrateDrudeSCFStepKernel(name, platform), data(data), constraints(NULL), minimizerPos(NULL) {
IntegrateDrudeSCFStepKernel(name, platform), data(data), minimizerPos(NULL) {
}
~ReferenceIntegrateDrudeSCFStepKernel();
/**
......@@ -157,7 +156,6 @@ private:
ReferencePlatform::PlatformData& data;
std::vector<int> drudeParticles;
std::vector<double> particleInvMass;
ReferenceConstraintAlgorithm* constraints;
lbfgsfloatval_t *minimizerPos;
lbfgs_parameter_t minimizerParams;
};
......
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