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Unverified Commit b28d2e66 authored by Peter Eastman's avatar Peter Eastman Committed by GitHub
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Merged parallel code (#4649) 

* Unified lots of parallel computation code between platforms

* Unified test code between platforms

* Eliminated duplicated timing code
parent 78902bed
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tests/TestHarmonicAngleForce.h
View file @ b28d2e66
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors.s *
* Portions copyright (c) 2008-2024 Stanford University and the Authors.s *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -120,6 +120,49 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(0.5*1.1*(PI_M/6)*(PI_M/6), state.getPotentialEnergy(), TOL);
}
void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
HarmonicAngleForce* force = new HarmonicAngleForce();
for (int i = 2; i < numParticles; i++)
force->addAngle(i-2, i-1, i, 1.1, i);
system.addForce(force);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(i, i%2, 0);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
VerletIntegrator integrator2(0.01);
string deviceIndex = platform.getPropertyValue(context1, "DeviceIndex");
map<string, string> props;
props["DeviceIndex"] = deviceIndex+","+deviceIndex;
Context context2(system, integrator2, platform, props);
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
// Try updating some parameters and see if they still match.
for (int i = 95; i < 102; i++) {
int p1, p2, p3;
double angle, k;
force->getAngleParameters(i, p1, p2, p3, angle, k);
force->setAngleParameters(i, p1, p2, p3, angle+0.1, 2*k);
}
force->updateParametersInContext(context1);
force->updateParametersInContext(context2);
State state3 = context1.getState(State::Energy);
State state4 = context2.getState(State::Energy);
ASSERT_EQUAL_TOL(state3.getPotentialEnergy(), state4.getPotentialEnergy(), 1e-5);
ASSERT(fabs(state1.getPotentialEnergy()-state3.getPotentialEnergy()) > 0.1);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......
tests/TestHarmonicBondForce.h
View file @ b28d2e66
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -106,6 +106,49 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(0.5*0.8*0.2*0.2, state.getPotentialEnergy(), TOL);
}
void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
HarmonicBondForce* force = new HarmonicBondForce();
for (int i = 1; i < numParticles; i++)
force->addBond(i-1, i, 1.1, i);
system.addForce(force);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(i, 0, 0);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
VerletIntegrator integrator2(0.01);
string deviceIndex = platform.getPropertyValue(context1, "DeviceIndex");
map<string, string> props;
props["DeviceIndex"] = deviceIndex+","+deviceIndex;
Context context2(system, integrator2, platform, props);
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
// Try updating some parameters and see if they still match.
for (int i = 95; i < 102; i++) {
int p1, p2;
double length, k;
force->getBondParameters(i, p1, p2, length, k);
force->setBondParameters(i, p1, p2, length+0.1, 2*k);
}
force->updateParametersInContext(context1);
force->updateParametersInContext(context2);
State state3 = context1.getState(State::Energy);
State state4 = context2.getState(State::Energy);
ASSERT_EQUAL_TOL(state3.getPotentialEnergy(), state4.getPotentialEnergy(), 1e-5);
ASSERT(fabs(state1.getPotentialEnergy()-state3.getPotentialEnergy()) > 0.1);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......
tests/TestNonbondedForce.h
View file @ b28d2e66
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2021 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -987,6 +987,105 @@ void testDirectAndReciprocal() {
ASSERT_EQUAL_TOL(e3, e4, 1e-5);
}
void testParallelComputation(NonbondedForce::NonbondedMethod method) {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
NonbondedForce* force = new NonbondedForce();
for (int i = 0; i < numParticles; i++)
force->addParticle(i%2-0.5, 0.5, 1.0);
force->setNonbondedMethod(method);
system.addForce(force);
system.setDefaultPeriodicBoxVectors(Vec3(5,0,0), Vec3(0,5,0), Vec3(0,0,5));
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(5*genrand_real2(sfmt), 5*genrand_real2(sfmt), 5*genrand_real2(sfmt));
force->addGlobalParameter("scale", 0.5);
for (int i = 0; i < numParticles; ++i)
for (int j = 0; j < i; ++j) {
Vec3 delta = positions[i]-positions[j];
if (delta.dot(delta) < 0.1) {
force->addException(i, j, 0, 1, 0);
}
else if (delta.dot(delta) < 0.2) {
int index = force->addException(i, j, 0.5, 1, 1.0);
force->addExceptionParameterOffset("scale", index, 0.5, 0.4, 0.3);
}
}
// Create two contexts, one with a single device and one with two devices.
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
VerletIntegrator integrator2(0.01);
string deviceIndex = platform.getPropertyValue(context1, "DeviceIndex");
map<string, string> props;
props["DeviceIndex"] = deviceIndex+","+deviceIndex;
Context context2(system, integrator2, platform, props);
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
// See if they agree.
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
// Modify some parameters and see if they still agree.
for (int i = 0; i < numParticles; i += 5) {
double charge, sigma, epsilon;
force->getParticleParameters(i, charge, sigma, epsilon);
force->setParticleParameters(i, 0.9*charge, sigma, epsilon);
}
for (int i = force->getNumExceptions()/2-10; i < force->getNumExceptions()/2+10; i++) {
int p1, p2;
double charge, sigma, epsilon;
force->getExceptionParameters(i, p1, p2, charge, sigma, epsilon);
if (epsilon != 0)
force->setExceptionParameters(i, p1, p2, charge, sigma, 2*epsilon);
}
force->updateParametersInContext(context1);
force->updateParametersInContext(context2);
state1 = context1.getState(State::Forces | State::Energy);
state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
void testReordering() {
// Check that reordering of atoms doesn't alter their positions.
const int numParticles = 200;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(6, 0, 0), Vec3(2.1, 6, 0), Vec3(-1.5, -0.5, 6));
NonbondedForce *nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::PME);
system.addForce(nonbonded);
vector<Vec3> positions;
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
nonbonded->addParticle(0.0, 0.0, 0.0);
positions.push_back(Vec3(genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5, genrand_real2(sfmt)-0.5)*20);
}
VerletIntegrator integrator(0.001);
Context context(system, integrator, platform);
context.setPositions(positions);
integrator.step(1);
State state = context.getState(State::Positions | State::Velocities);
for (int i = 0; i < numParticles; i++) {
ASSERT_EQUAL_VEC(positions[i], state.getPositions()[i], 1e-6);
}
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......
tests/TestPeriodicTorsionForce.h
View file @ b28d2e66
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -118,6 +118,49 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(1.1*(1+std::cos(2*PI_M/3)), state.getPotentialEnergy(), TOL);
}
void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
PeriodicTorsionForce* force = new PeriodicTorsionForce();
for (int i = 3; i < numParticles; i++)
force->addTorsion(i-3, i-2, i-1, i, 2, 1.1, i);
system.addForce(force);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(i, i%2, i%3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
VerletIntegrator integrator2(0.01);
string deviceIndex = platform.getPropertyValue(context1, "DeviceIndex");
map<string, string> props;
props["DeviceIndex"] = deviceIndex+","+deviceIndex;
Context context2(system, integrator2, platform, props);
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
// Try updating some parameters and see if they still match.
for (int i = 95; i < 102; i++) {
int p1, p2, p3, p4, periodicity;
double phase, k;
force->getTorsionParameters(i, p1, p2, p3, p4, periodicity, phase, k);
force->setTorsionParameters(i, p1, p2, p3, p4, periodicity, phase+0.1, 2*k);
}
force->updateParametersInContext(context1);
force->updateParametersInContext(context2);
State state3 = context1.getState(State::Energy);
State state4 = context2.getState(State::Energy);
ASSERT_EQUAL_TOL(state3.getPotentialEnergy(), state4.getPotentialEnergy(), 1e-5);
ASSERT(fabs(state1.getPotentialEnergy()-state3.getPotentialEnergy()) > 0.1);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......
tests/TestRBTorsionForce.h
View file @ b28d2e66
......@@ -6,7 +6,7 @@
* Biological Structures at Stanford, funded under the NIH Roadmap for *
* Medical Research, grant U54 GM072970. See https://simtk.org. *
* *
* Portions copyright (c) 2008-2016 Stanford University and the Authors. *
* Portions copyright (c) 2008-2024 Stanford University and the Authors. *
* Authors: Peter Eastman *
* Contributors: *
* *
......@@ -147,6 +147,34 @@ void testPeriodic() {
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), TOL);
}
void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
RBTorsionForce* force = new RBTorsionForce();
for (int i = 3; i < numParticles; i++)
force->addTorsion(i-3, i-2, i-1, i, 2, 0.1*i, 0.5*i, i, 1, 1);
system.addForce(force);
vector<Vec3> positions(numParticles);
for (int i = 0; i < numParticles; i++)
positions[i] = Vec3(i, i%2, i%3);
VerletIntegrator integrator1(0.01);
Context context1(system, integrator1, platform);
context1.setPositions(positions);
State state1 = context1.getState(State::Forces | State::Energy);
VerletIntegrator integrator2(0.01);
string deviceIndex = platform.getPropertyValue(context1, "DeviceIndex");
map<string, string> props;
props["DeviceIndex"] = deviceIndex+","+deviceIndex;
Context context2(system, integrator2, platform, props);
context2.setPositions(positions);
State state2 = context2.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), 1e-5);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], 1e-5);
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......
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