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Commit 761b4bbf authored by Peter Eastman's avatar Peter Eastman
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Variable time step integrators correctly report the size of the last step... 

Variable time step integrators correctly report the size of the last step taken.  Also improved accuracy of integration unit tests.
parent 420fac9c
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Showing with 182 additions and 66 deletions
olla/include/openmm/kernels.h
View file @ 761b4bbf
...@@ -780,8 +780,9 @@ public: ...@@ -780,8 +780,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the LangevinIntegrator this kernel is being used for * @param integrator the LangevinIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
virtual void execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) = 0; virtual double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) = 0;
}; };
/** /**
...@@ -807,8 +808,9 @@ public: ...@@ -807,8 +808,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for * @param integrator the VerletIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
virtual void execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) = 0; virtual double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) = 0;
}; };
/** /**
......
openmmapi/src/VariableLangevinIntegrator.cpp
View file @ 761b4bbf
...@@ -69,7 +69,7 @@ void VariableLangevinIntegrator::step(int steps) { ...@@ -69,7 +69,7 @@ void VariableLangevinIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) { for (int i = 0; i < steps; ++i) {
context->updateContextState(); context->updateContextState();
context->calcForcesAndEnergy(true, false); context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this, std::numeric_limits<double>::infinity()); setStepSize(dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this, std::numeric_limits<double>::infinity()));
} }
} }
...@@ -77,6 +77,6 @@ void VariableLangevinIntegrator::stepTo(double time) { ...@@ -77,6 +77,6 @@ void VariableLangevinIntegrator::stepTo(double time) {
while (time > context->getTime()) { while (time > context->getTime()) {
context->updateContextState(); context->updateContextState();
context->calcForcesAndEnergy(true, false); context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this, time); setStepSize(dynamic_cast<IntegrateVariableLangevinStepKernel&>(kernel.getImpl()).execute(*context, *this, time));
} }
} }
openmmapi/src/VariableVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -64,7 +64,7 @@ void VariableVerletIntegrator::step(int steps) { ...@@ -64,7 +64,7 @@ void VariableVerletIntegrator::step(int steps) {
for (int i = 0; i < steps; ++i) { for (int i = 0; i < steps; ++i) {
context->updateContextState(); context->updateContextState();
context->calcForcesAndEnergy(true, false); context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this, std::numeric_limits<double>::infinity()); setStepSize(dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this, std::numeric_limits<double>::infinity()));
} }
} }
...@@ -72,6 +72,6 @@ void VariableVerletIntegrator::stepTo(double time) { ...@@ -72,6 +72,6 @@ void VariableVerletIntegrator::stepTo(double time) {
while (time > context->getTime()) { while (time > context->getTime()) {
context->updateContextState(); context->updateContextState();
context->calcForcesAndEnergy(true, false); context->calcForcesAndEnergy(true, false);
dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this, time); setStepSize(dynamic_cast<IntegrateVariableVerletStepKernel&>(kernel.getImpl()).execute(*context, *this, time));
} }
} }
platforms/cuda/src/CudaKernels.cpp
View file @ 761b4bbf
...@@ -1343,7 +1343,7 @@ void CudaIntegrateVariableVerletStepKernel::initialize(const System& system, con ...@@ -1343,7 +1343,7 @@ void CudaIntegrateVariableVerletStepKernel::initialize(const System& system, con
prevErrorTol = -1.0; prevErrorTol = -1.0;
} }
void CudaIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) { double CudaIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
_gpuContext* gpu = data.gpu; _gpuContext* gpu = data.gpu;
double errorTol = integrator.getErrorTolerance(); double errorTol = integrator.getErrorTolerance();
if (errorTol != prevErrorTol) { if (errorTol != prevErrorTol) {
...@@ -1368,6 +1368,7 @@ void CudaIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const ...@@ -1368,6 +1368,7 @@ void CudaIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const
if ((*gpu->psStepSize)[0].y == maxStepSize) if ((*gpu->psStepSize)[0].y == maxStepSize)
data.time = maxTime; // Avoid round-off error data.time = maxTime; // Avoid round-off error
data.stepCount++; data.stepCount++;
return (*gpu->psStepSize)[0].y;
} }
CudaIntegrateVariableLangevinStepKernel::~CudaIntegrateVariableLangevinStepKernel() { CudaIntegrateVariableLangevinStepKernel::~CudaIntegrateVariableLangevinStepKernel() {
...@@ -1383,7 +1384,7 @@ void CudaIntegrateVariableLangevinStepKernel::initialize(const System& system, c ...@@ -1383,7 +1384,7 @@ void CudaIntegrateVariableLangevinStepKernel::initialize(const System& system, c
prevErrorTol = -1.0; prevErrorTol = -1.0;
} }
void CudaIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) { double CudaIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
_gpuContext* gpu = data.gpu; _gpuContext* gpu = data.gpu;
double temperature = integrator.getTemperature(); double temperature = integrator.getTemperature();
double friction = integrator.getFriction(); double friction = integrator.getFriction();
...@@ -1415,6 +1416,7 @@ void CudaIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, cons ...@@ -1415,6 +1416,7 @@ void CudaIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, cons
if ((*gpu->psStepSize)[0].y == maxStepSize) if ((*gpu->psStepSize)[0].y == maxStepSize)
data.time = maxTime; // Avoid round-off error data.time = maxTime; // Avoid round-off error
data.stepCount++; data.stepCount++;
return (*gpu->psStepSize)[0].y;
} }
CudaApplyAndersenThermostatKernel::~CudaApplyAndersenThermostatKernel() { CudaApplyAndersenThermostatKernel::~CudaApplyAndersenThermostatKernel() {
......
platforms/cuda/src/CudaKernels.h
View file @ 761b4bbf
...@@ -734,8 +734,9 @@ public: ...@@ -734,8 +734,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for * @param integrator the VerletIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
void execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime); double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
private: private:
CudaPlatform::PlatformData& data; CudaPlatform::PlatformData& data;
double prevErrorTol; double prevErrorTol;
...@@ -762,8 +763,9 @@ public: ...@@ -762,8 +763,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the VariableLangevinIntegrator this kernel is being used for * @param integrator the VariableLangevinIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
void execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime); double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime);
private: private:
CudaPlatform::PlatformData& data; CudaPlatform::PlatformData& data;
double prevTemp, prevFriction, prevErrorTol; double prevTemp, prevFriction, prevErrorTol;
......
platforms/cuda/tests/TestCudaVariableVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -50,6 +50,23 @@ using namespace std; ...@@ -50,6 +50,23 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
/**
* Compute the energy of a state, taking into account the half step offset between
* positions and velocities.
*/
static double computeEnergy(const State& state, const System& system, double dt) {
const vector<Vec3>& v = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = 0.0;
for (int i = 0; i < system.getNumParticles(); i++) {
double m = system.getParticleMass(i);
Vec3 vel = v[i]+f[i]*(0.5*dt/m);
energy += 0.5*m*vel.dot(vel);
}
return energy+state.getPotentialEnergy();
}
void testSingleBond() { void testSingleBond() {
CudaPlatform platform; CudaPlatform platform;
System system; System system;
...@@ -121,21 +138,21 @@ void testConstraints() { ...@@ -121,21 +138,21 @@ void testConstraints() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < numConstraints; ++j) { for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
system.getConstraintParameters(j, particle1, particle2, distance); system.getConstraintParameters(j, particle1, particle2, distance);
Vec3 p1 = state.getPositions()[particle1]; Vec3 p1 = state.getPositions()[particle1];
Vec3 p2 = state.getPositions()[particle2]; Vec3 p2 = state.getPositions()[particle2];
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4); ASSERT_EQUAL_TOL(distance, dist, 1e-4);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.1); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
double finalTime = context.getState(State::Positions).getTime(); double finalTime = context.getState(State::Positions).getTime();
...@@ -193,7 +210,7 @@ void testConstrainedClusters() { ...@@ -193,7 +210,7 @@ void testConstrainedClusters() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -203,11 +220,11 @@ void testConstrainedClusters() { ...@@ -203,11 +220,11 @@ void testConstrainedClusters() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
ASSERT(context.getState(State::Positions).getTime() > 0.1); ASSERT(context.getState(State::Positions).getTime() > 0.1);
......
platforms/cuda/tests/TestCudaVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -50,6 +50,23 @@ using namespace std; ...@@ -50,6 +50,23 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
/**
* Compute the energy of a state, taking into account the half step offset between
* positions and velocities.
*/
static double computeEnergy(const State& state, const System& system, double dt) {
const vector<Vec3>& v = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = 0.0;
for (int i = 0; i < system.getNumParticles(); i++) {
double m = system.getParticleMass(i);
Vec3 vel = v[i]+f[i]*(0.5*dt/m);
energy += 0.5*m*vel.dot(vel);
}
return energy+state.getPotentialEnergy();
}
void testSingleBond() { void testSingleBond() {
CudaPlatform platform; CudaPlatform platform;
System system; System system;
...@@ -121,7 +138,7 @@ void testConstraints() { ...@@ -121,7 +138,7 @@ void testConstraints() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < numConstraints; ++j) { for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -131,11 +148,11 @@ void testConstraints() { ...@@ -131,11 +148,11 @@ void testConstraints() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4); ASSERT_EQUAL_TOL(distance, dist, 1e-4);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
} }
...@@ -145,7 +162,7 @@ void testConstrainedClusters() { ...@@ -145,7 +162,7 @@ void testConstrainedClusters() {
const double temp = 500.0; const double temp = 500.0;
CudaPlatform platform; CudaPlatform platform;
System system; System system;
VerletIntegrator integrator(0.002); VerletIntegrator integrator(0.001);
integrator.setConstraintTolerance(1e-5); integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce(); NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
...@@ -185,7 +202,7 @@ void testConstrainedClusters() { ...@@ -185,7 +202,7 @@ void testConstrainedClusters() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -195,11 +212,11 @@ void testConstrainedClusters() { ...@@ -195,11 +212,11 @@ void testConstrainedClusters() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
} }
......
platforms/opencl/src/OpenCLKernels.cpp
View file @ 761b4bbf
...@@ -3400,7 +3400,7 @@ void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, c ...@@ -3400,7 +3400,7 @@ void OpenCLIntegrateVariableVerletStepKernel::initialize(const System& system, c
blockSize = std::min(std::min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>()); blockSize = std::min(std::min(256, system.getNumParticles()), (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
} }
void OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) { double OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities(); OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms(); int numAtoms = cl.getNumAtoms();
if (!hasInitializedKernels) { if (!hasInitializedKernels) {
...@@ -3452,6 +3452,7 @@ void OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, cons ...@@ -3452,6 +3452,7 @@ void OpenCLIntegrateVariableVerletStepKernel::execute(ContextImpl& context, cons
time = maxTime; // Avoid round-off error time = maxTime; // Avoid round-off error
cl.setTime(time); cl.setTime(time);
cl.setStepCount(cl.getStepCount()+1); cl.setStepCount(cl.getStepCount()+1);
return dt;
} }
OpenCLIntegrateVariableLangevinStepKernel::~OpenCLIntegrateVariableLangevinStepKernel() { OpenCLIntegrateVariableLangevinStepKernel::~OpenCLIntegrateVariableLangevinStepKernel() {
...@@ -3475,7 +3476,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system, ...@@ -3475,7 +3476,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::initialize(const System& system,
blockSize = std::min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>()); blockSize = std::min(blockSize, (int) cl.getDevice().getInfo<CL_DEVICE_MAX_WORK_GROUP_SIZE>());
} }
void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) { double OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities(); OpenCLIntegrationUtilities& integration = cl.getIntegrationUtilities();
int numAtoms = cl.getNumAtoms(); int numAtoms = cl.getNumAtoms();
if (!hasInitializedKernels) { if (!hasInitializedKernels) {
...@@ -3530,6 +3531,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co ...@@ -3530,6 +3531,7 @@ void OpenCLIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, co
time = maxTime; // Avoid round-off error time = maxTime; // Avoid round-off error
cl.setTime(time); cl.setTime(time);
cl.setStepCount(cl.getStepCount()+1); cl.setStepCount(cl.getStepCount()+1);
return dt;
} }
class OpenCLIntegrateCustomStepKernel::ReorderListener : public OpenCLContext::ReorderListener { class OpenCLIntegrateCustomStepKernel::ReorderListener : public OpenCLContext::ReorderListener {
......
platforms/opencl/src/OpenCLKernels.h
View file @ 761b4bbf
...@@ -875,8 +875,9 @@ public: ...@@ -875,8 +875,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for * @param integrator the VerletIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
void execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime); double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
private: private:
OpenCLContext& cl; OpenCLContext& cl;
bool hasInitializedKernels; bool hasInitializedKernels;
...@@ -906,8 +907,9 @@ public: ...@@ -906,8 +907,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the VariableLangevinIntegrator this kernel is being used for * @param integrator the VariableLangevinIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
void execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime); double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime);
private: private:
OpenCLContext& cl; OpenCLContext& cl;
bool hasInitializedKernels; bool hasInitializedKernels;
......
platforms/opencl/tests/TestOpenCLVariableVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -50,6 +50,23 @@ using namespace std; ...@@ -50,6 +50,23 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
/**
* Compute the energy of a state, taking into account the half step offset between
* positions and velocities.
*/
static double computeEnergy(const State& state, const System& system, double dt) {
const vector<Vec3>& v = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = 0.0;
for (int i = 0; i < system.getNumParticles(); i++) {
double m = system.getParticleMass(i);
Vec3 vel = v[i]+f[i]*(0.5*dt/m);
energy += 0.5*m*vel.dot(vel);
}
return energy+state.getPotentialEnergy();
}
void testSingleBond() { void testSingleBond() {
OpenCLPlatform platform; OpenCLPlatform platform;
System system; System system;
...@@ -121,7 +138,7 @@ void testConstraints() { ...@@ -121,7 +138,7 @@ void testConstraints() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < numConstraints; ++j) { for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -131,11 +148,11 @@ void testConstraints() { ...@@ -131,11 +148,11 @@ void testConstraints() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4); ASSERT_EQUAL_TOL(distance, dist, 1e-4);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.1); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
double finalTime = context.getState(State::Positions).getTime(); double finalTime = context.getState(State::Positions).getTime();
...@@ -193,7 +210,7 @@ void testConstrainedClusters() { ...@@ -193,7 +210,7 @@ void testConstrainedClusters() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -203,11 +220,11 @@ void testConstrainedClusters() { ...@@ -203,11 +220,11 @@ void testConstrainedClusters() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
ASSERT(context.getState(State::Positions).getTime() > 0.1); ASSERT(context.getState(State::Positions).getTime() > 0.1);
......
platforms/opencl/tests/TestOpenCLVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -50,6 +50,23 @@ using namespace std; ...@@ -50,6 +50,23 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
/**
* Compute the energy of a state, taking into account the half step offset between
* positions and velocities.
*/
static double computeEnergy(const State& state, const System& system, double dt) {
const vector<Vec3>& v = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = 0.0;
for (int i = 0; i < system.getNumParticles(); i++) {
double m = system.getParticleMass(i);
Vec3 vel = v[i]+f[i]*(0.5*dt/m);
energy += 0.5*m*vel.dot(vel);
}
return energy+state.getPotentialEnergy();
}
void testSingleBond() { void testSingleBond() {
OpenCLPlatform platform; OpenCLPlatform platform;
System system; System system;
...@@ -121,7 +138,7 @@ void testConstraints() { ...@@ -121,7 +138,7 @@ void testConstraints() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < numConstraints; ++j) { for (int j = 0; j < numConstraints; ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -131,11 +148,11 @@ void testConstraints() { ...@@ -131,11 +148,11 @@ void testConstraints() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 1e-4); ASSERT_EQUAL_TOL(distance, dist, 1e-4);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
} }
...@@ -145,7 +162,7 @@ void testConstrainedClusters() { ...@@ -145,7 +162,7 @@ void testConstrainedClusters() {
const double temp = 500.0; const double temp = 500.0;
OpenCLPlatform platform; OpenCLPlatform platform;
System system; System system;
VerletIntegrator integrator(0.002); VerletIntegrator integrator(0.001);
integrator.setConstraintTolerance(1e-5); integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce(); NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
...@@ -185,7 +202,7 @@ void testConstrainedClusters() { ...@@ -185,7 +202,7 @@ void testConstrainedClusters() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -195,11 +212,11 @@ void testConstrainedClusters() { ...@@ -195,11 +212,11 @@ void testConstrainedClusters() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
} }
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 761b4bbf
...@@ -1447,7 +1447,7 @@ void ReferenceIntegrateVariableLangevinStepKernel::initialize(const System& syst ...@@ -1447,7 +1447,7 @@ void ReferenceIntegrateVariableLangevinStepKernel::initialize(const System& syst
SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed()); SimTKOpenMMUtilities::setRandomNumberSeed((unsigned int) integrator.getRandomNumberSeed());
} }
void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) { double ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime) {
double temperature = integrator.getTemperature(); double temperature = integrator.getTemperature();
double friction = integrator.getFriction(); double friction = integrator.getFriction();
double errorTol = integrator.getErrorTolerance(); double errorTol = integrator.getErrorTolerance();
...@@ -1478,6 +1478,7 @@ void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context, ...@@ -1478,6 +1478,7 @@ void ReferenceIntegrateVariableLangevinStepKernel::execute(ContextImpl& context,
if (dynamics->getDeltaT() == maxStepSize) if (dynamics->getDeltaT() == maxStepSize)
data.time = maxTime; // Avoid round-off error data.time = maxTime; // Avoid round-off error
data.stepCount++; data.stepCount++;
return dynamics->getDeltaT();
} }
ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletStepKernel() { ReferenceIntegrateVariableVerletStepKernel::~ReferenceIntegrateVariableVerletStepKernel() {
...@@ -1509,7 +1510,7 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system ...@@ -1509,7 +1510,7 @@ void ReferenceIntegrateVariableVerletStepKernel::initialize(const System& system
} }
} }
void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) { double ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime) {
double errorTol = integrator.getErrorTolerance(); double errorTol = integrator.getErrorTolerance();
vector<RealVec>& posData = extractPositions(context); vector<RealVec>& posData = extractPositions(context);
vector<RealVec>& velData = extractVelocities(context); vector<RealVec>& velData = extractVelocities(context);
...@@ -1535,6 +1536,7 @@ void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, c ...@@ -1535,6 +1536,7 @@ void ReferenceIntegrateVariableVerletStepKernel::execute(ContextImpl& context, c
if (dynamics->getDeltaT() == maxStepSize) if (dynamics->getDeltaT() == maxStepSize)
data.time = maxTime; // Avoid round-off error data.time = maxTime; // Avoid round-off error
data.stepCount++; data.stepCount++;
return dynamics->getDeltaT();
} }
ReferenceIntegrateCustomStepKernel::~ReferenceIntegrateCustomStepKernel() { ReferenceIntegrateCustomStepKernel::~ReferenceIntegrateCustomStepKernel() {
......
platforms/reference/src/ReferenceKernels.h
View file @ 761b4bbf
...@@ -836,8 +836,9 @@ public: ...@@ -836,8 +836,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the LangevinIntegrator this kernel is being used for * @param integrator the LangevinIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
void execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime); double execute(ContextImpl& context, const VariableLangevinIntegrator& integrator, double maxTime);
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVariableStochasticDynamics* dynamics; ReferenceVariableStochasticDynamics* dynamics;
...@@ -871,8 +872,9 @@ public: ...@@ -871,8 +872,9 @@ public:
* @param context the context in which to execute this kernel * @param context the context in which to execute this kernel
* @param integrator the VerletIntegrator this kernel is being used for * @param integrator the VerletIntegrator this kernel is being used for
* @param maxTime the maximum time beyond which the simulation should not be advanced * @param maxTime the maximum time beyond which the simulation should not be advanced
* @return the size of the step that was taken
*/ */
void execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime); double execute(ContextImpl& context, const VariableVerletIntegrator& integrator, double maxTime);
private: private:
ReferencePlatform::PlatformData& data; ReferencePlatform::PlatformData& data;
ReferenceVariableVerletDynamics* dynamics; ReferenceVariableVerletDynamics* dynamics;
......
platforms/reference/tests/TestReferenceVariableVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -50,6 +50,23 @@ using namespace std; ...@@ -50,6 +50,23 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
/**
* Compute the energy of a state, taking into account the half step offset between
* positions and velocities.
*/
static double computeEnergy(const State& state, const System& system, double dt) {
const vector<Vec3>& v = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = 0.0;
for (int i = 0; i < system.getNumParticles(); i++) {
double m = system.getParticleMass(i);
Vec3 vel = v[i]+f[i]*(0.5*dt/m);
energy += 0.5*m*vel.dot(vel);
}
return energy+state.getPotentialEnergy();
}
void testSingleBond() { void testSingleBond() {
ReferencePlatform platform; ReferencePlatform platform;
System system; System system;
...@@ -118,7 +135,7 @@ void testConstraints() { ...@@ -118,7 +135,7 @@ void testConstraints() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -128,11 +145,11 @@ void testConstraints() { ...@@ -128,11 +145,11 @@ void testConstraints() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.1); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
double finalTime = context.getState(State::Positions).getTime(); double finalTime = context.getState(State::Positions).getTime();
...@@ -190,7 +207,7 @@ void testConstrainedClusters() { ...@@ -190,7 +207,7 @@ void testConstrainedClusters() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -200,11 +217,11 @@ void testConstrainedClusters() { ...@@ -200,11 +217,11 @@ void testConstrainedClusters() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
ASSERT(context.getState(State::Positions).getTime() > 0.1); ASSERT(context.getState(State::Positions).getTime() > 0.1);
......
platforms/reference/tests/TestReferenceVerletIntegrator.cpp
View file @ 761b4bbf
...@@ -50,6 +50,23 @@ using namespace std; ...@@ -50,6 +50,23 @@ using namespace std;
const double TOL = 1e-5; const double TOL = 1e-5;
/**
* Compute the energy of a state, taking into account the half step offset between
* positions and velocities.
*/
static double computeEnergy(const State& state, const System& system, double dt) {
const vector<Vec3>& v = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = 0.0;
for (int i = 0; i < system.getNumParticles(); i++) {
double m = system.getParticleMass(i);
Vec3 vel = v[i]+f[i]*(0.5*dt/m);
energy += 0.5*m*vel.dot(vel);
}
return energy+state.getPotentialEnergy();
}
void testSingleBond() { void testSingleBond() {
ReferencePlatform platform; ReferencePlatform platform;
System system; System system;
...@@ -117,7 +134,7 @@ void testConstraints() { ...@@ -117,7 +134,7 @@ void testConstraints() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -127,11 +144,11 @@ void testConstraints() { ...@@ -127,11 +144,11 @@ void testConstraints() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
} }
...@@ -141,7 +158,7 @@ void testConstrainedClusters() { ...@@ -141,7 +158,7 @@ void testConstrainedClusters() {
const double temp = 500.0; const double temp = 500.0;
ReferencePlatform platform; ReferencePlatform platform;
System system; System system;
VerletIntegrator integrator(0.002); VerletIntegrator integrator(0.001);
integrator.setConstraintTolerance(1e-5); integrator.setConstraintTolerance(1e-5);
NonbondedForce* forceField = new NonbondedForce(); NonbondedForce* forceField = new NonbondedForce();
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
...@@ -181,7 +198,7 @@ void testConstrainedClusters() { ...@@ -181,7 +198,7 @@ void testConstrainedClusters() {
double initialEnergy = 0.0; double initialEnergy = 0.0;
for (int i = 0; i < 1000; ++i) { for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Energy); State state = context.getState(State::Positions | State::Energy | State::Velocities | State::Forces);
for (int j = 0; j < system.getNumConstraints(); ++j) { for (int j = 0; j < system.getNumConstraints(); ++j) {
int particle1, particle2; int particle1, particle2;
double distance; double distance;
...@@ -191,11 +208,11 @@ void testConstrainedClusters() { ...@@ -191,11 +208,11 @@ void testConstrainedClusters() {
double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); double dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2]));
ASSERT_EQUAL_TOL(distance, dist, 2e-5); ASSERT_EQUAL_TOL(distance, dist, 2e-5);
} }
double energy = state.getKineticEnergy()+state.getPotentialEnergy(); double energy = computeEnergy(state, system, integrator.getStepSize());
if (i == 1) if (i == 1)
initialEnergy = energy; initialEnergy = energy;
else if (i > 1) else if (i > 1)
ASSERT_EQUAL_TOL(initialEnergy, energy, 0.05); ASSERT_EQUAL_TOL(initialEnergy, energy, 0.01);
integrator.step(1); integrator.step(1);
} }
} }
......
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