Skip to content

GitLab

Commit 15ffd4af authored by Peter Eastman's avatar Peter Eastman
Browse files

Fixed RPMD test cases

parent 84f5e008
Hide whitespace changes
Inline Side-by-side
Showing with 53 additions and 71 deletions
plugins/rpmd/platforms/opencl/tests/TestOpenCLRpmd.cpp
View file @ 15ffd4af
...@@ -47,20 +47,15 @@ ...@@ -47,20 +47,15 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
void testIntegration() { void testFreeParticles() {
const int numParticles = 1; const int numParticles = 100;
const int numCopies = 25; const int numCopies = 30;
const double temperature = 300.0; const double temperature = 300.0;
const double mass = 1.0;
System system; System system;
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
system.addParticle(i+1); system.addParticle(mass);
if (numParticles > 1) { RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
HarmonicBondForce* bonds = new HarmonicBondForce();
system.addForce(bonds);
for (int i = 0; i < numParticles-1; i++)
bonds->addBond(i, i+1, 1.0, 100.0);
}
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
Platform& platform = Platform::getPlatformByName("OpenCL"); Platform& platform = Platform::getPlatformByName("OpenCL");
Context context(system, integ, platform); Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt; OpenMM_SFMT::SFMT sfmt;
...@@ -69,7 +64,7 @@ void testIntegration() { ...@@ -69,7 +64,7 @@ void testIntegration() {
for (int i = 0; i < numCopies; i++) for (int i = 0; i < numCopies; i++)
{ {
for (int j = 0; j < numParticles; j++) for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(j+0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt)); positions[j] = Vec3(0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt));
integ.setPositions(i, positions); integ.setPositions(i, positions);
} }
const int numSteps = 1000; const int numSteps = 1000;
...@@ -82,43 +77,38 @@ void testIntegration() { ...@@ -82,43 +77,38 @@ void testIntegration() {
integ.step(1); integ.step(1);
vector<State> state(numCopies); vector<State> state(numCopies);
for (int j = 0; j < numCopies; j++) for (int j = 0; j < numCopies; j++)
state[j] = integ.getState(j, State::Positions | State::Velocities | State::Energy); state[j] = integ.getState(j, State::Positions | State::Velocities);
for (int j = 0; j < numCopies; j++)
ke[j] += state[j].getKineticEnergy();
double totalEnergy = 0.0;
for (int j = 0; j < numCopies; j++) {
totalEnergy += state[j].getKineticEnergy()+state[j].getPotentialEnergy();
for (int k = 0; k < numParticles; k++) {
Vec3 delta = state[j].getPositions()[k]-state[j == 0 ? numCopies-1 : j-1].getPositions()[k];
totalEnergy += 0.5*system.getParticleMass(k)*wn*wn*delta.dot(delta);
}
}
for (int j = 0; j < numParticles; j++) { for (int j = 0; j < numParticles; j++) {
double rg2 = 0.0; double rg2 = 0.0;
for (int k = 0; k < numCopies; k++) for (int k = 0; k < numCopies; k++) {
Vec3 v = state[k].getVelocities()[j];
ke[k] += 0.5*mass*v.dot(v);
for (int m = 0; m < numCopies; m++) { for (int m = 0; m < numCopies; m++) {
Vec3 delta = state[k].getPositions()[j]-state[m].getPositions()[j]; Vec3 delta = state[k].getPositions()[j]-state[m].getPositions()[j];
rg2 += delta.dot(delta); rg2 += delta.dot(delta);
} }
rg[j] += sqrt(rg2/(2*numCopies*numCopies)); }
rg[j] += rg2/(2*numCopies*numCopies);
} }
} }
for (int i = 0; i < numCopies; i++) { double meanKE = 0.0;
double value = ke[i]/numSteps; for (int i = 0; i < numCopies; i++)
double expected = 0.5*numCopies*numParticles*3*BOLTZ*temperature; meanKE += ke[i];
printf("%d: %g %g %g\n", i, value, expected, value/expected); meanKE /= numSteps*numCopies;
} double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
for (int i = 0; i < numParticles; i++) { ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
double value = rg[i]/numSteps; double meanRg2 = 0.0;
double expected = hbar/(2*sqrt(system.getParticleMass(i)*BOLTZ*temperature)); for (int i = 0; i < numParticles; i++)
printf("%d: %g %g %g\n", i, value, expected, value/expected); meanRg2 += rg[i];
} meanRg2 /= numSteps*numParticles;
double expectedRg = hbar/(2*sqrt(mass*BOLTZ*temperature));
ASSERT_USUALLY_EQUAL_TOL(expectedRg, sqrt(meanRg2), 1e-3);
} }
int main() { int main() {
try { try {
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory()); Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
testIntegration(); testFreeParticles();
} }
catch(const std::exception& e) { catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl; std::cout << "exception: " << e.what() << std::endl;
......
plugins/rpmd/platforms/reference/tests/TestReferenceRpmd.cpp
View file @ 15ffd4af
...@@ -47,18 +47,15 @@ ...@@ -47,18 +47,15 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
void testIntegration() { void testFreeParticles() {
const int numParticles = 1; const int numParticles = 100;
const int numCopies = 30; const int numCopies = 30;
const double temperature = 300.0; const double temperature = 300.0;
const double mass = 1.0;
System system; System system;
for (int i = 0; i < numParticles; i++) for (int i = 0; i < numParticles; i++)
system.addParticle(i+1); system.addParticle(mass);
HarmonicBondForce* bonds = new HarmonicBondForce(); RPMDIntegrator integ(numCopies, temperature, 10.0, 0.001);
system.addForce(bonds);
for (int i = 0; i < numParticles-1; i++)
bonds->addBond(i, i+1, 1.0, 100.0);
RPMDIntegrator integ(numCopies, temperature, 1.0, 0.001);
Platform& platform = Platform::getPlatformByName("Reference"); Platform& platform = Platform::getPlatformByName("Reference");
Context context(system, integ, platform); Context context(system, integ, platform);
OpenMM_SFMT::SFMT sfmt; OpenMM_SFMT::SFMT sfmt;
...@@ -67,11 +64,11 @@ void testIntegration() { ...@@ -67,11 +64,11 @@ void testIntegration() {
for (int i = 0; i < numCopies; i++) for (int i = 0; i < numCopies; i++)
{ {
for (int j = 0; j < numParticles; j++) for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(j+0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt), 0.01*genrand_real2(sfmt)); positions[j] = Vec3(0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt), 0.02*genrand_real2(sfmt));
integ.setPositions(i, positions); integ.setPositions(i, positions);
} }
const int numSteps = 100000; const int numSteps = 1000;
integ.step(10000); integ.step(1000);
vector<double> ke(numCopies, 0.0); vector<double> ke(numCopies, 0.0);
vector<double> rg(numParticles, 0.0); vector<double> rg(numParticles, 0.0);
const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12); const RealOpenMM hbar = 1.054571628e-34*AVOGADRO/(1000*1e-12);
...@@ -80,43 +77,38 @@ void testIntegration() { ...@@ -80,43 +77,38 @@ void testIntegration() {
integ.step(1); integ.step(1);
vector<State> state(numCopies); vector<State> state(numCopies);
for (int j = 0; j < numCopies; j++) for (int j = 0; j < numCopies; j++)
state[j] = integ.getState(j, State::Positions | State::Velocities | State::Energy); state[j] = integ.getState(j, State::Positions | State::Velocities);
for (int j = 0; j < numCopies; j++)
ke[j] += state[j].getKineticEnergy();
double totalEnergy = 0.0;
for (int j = 0; j < numCopies; j++) {
totalEnergy += state[j].getKineticEnergy()+state[j].getPotentialEnergy();
for (int k = 0; k < numParticles; k++) {
Vec3 delta = state[j].getPositions()[k]-state[j == 0 ? numCopies-1 : j-1].getPositions()[k];
totalEnergy += 0.5*system.getParticleMass(k)*wn*wn*delta.dot(delta);
}
}
for (int j = 0; j < numParticles; j++) { for (int j = 0; j < numParticles; j++) {
double rg2 = 0.0; double rg2 = 0.0;
for (int k = 0; k < numCopies; k++) for (int k = 0; k < numCopies; k++) {
Vec3 v = state[k].getVelocities()[j];
ke[k] += 0.5*mass*v.dot(v);
for (int m = 0; m < numCopies; m++) { for (int m = 0; m < numCopies; m++) {
Vec3 delta = state[k].getPositions()[j]-state[m].getPositions()[j]; Vec3 delta = state[k].getPositions()[j]-state[m].getPositions()[j];
rg2 += delta.dot(delta); rg2 += delta.dot(delta);
} }
rg[j] += sqrt(rg2/(2*numCopies*numCopies)); }
rg[j] += rg2/(2*numCopies*numCopies);
} }
} }
for (int i = 0; i < numCopies; i++) { double meanKE = 0.0;
double value = ke[i]/numSteps; for (int i = 0; i < numCopies; i++)
double expected = 0.5*numCopies*numParticles*3*BOLTZ*temperature; meanKE += ke[i];
printf("%d: %g %g %g\n", i, value, expected, value/expected); meanKE /= numSteps*numCopies;
} double expectedKE = 0.5*numCopies*numParticles*3*BOLTZ*temperature;
for (int i = 0; i < numParticles; i++) { ASSERT_USUALLY_EQUAL_TOL(expectedKE, meanKE, 1e-2);
double value = rg[i]/numSteps; double meanRg2 = 0.0;
double expected = hbar/(2*sqrt(system.getParticleMass(i)*BOLTZ*temperature)); for (int i = 0; i < numParticles; i++)
printf("%d: %g %g %g\n", i, value, expected, value/expected); meanRg2 += rg[i];
} meanRg2 /= numSteps*numParticles;
double expectedRg = hbar/(2*sqrt(mass*BOLTZ*temperature));
ASSERT_USUALLY_EQUAL_TOL(expectedRg, sqrt(meanRg2), 1e-3);
} }
int main() { int main() {
try { try {
Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory()); Platform::loadPluginsFromDirectory(Platform::getDefaultPluginsDirectory());
testIntegration(); testFreeParticles();
} }
catch(const std::exception& e) { catch(const std::exception& e) {
std::cout << "exception: " << e.what() << std::endl; std::cout << "exception: " << e.what() << std::endl;
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment