/**
* Check that massless particles are handled correctly.
*/
void testMasslessParticle() {
System system;
system.addParticle(0.0);
system.addParticle(1.0);
CustomBondForce* bonds = new CustomBondForce("-1/r");
system.addForce(bonds);
vector<double> params;
bonds->addBond(0, 1, params);
VerletIntegrator integrator(0.002);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(1, 0, 0);
context.setPositions(positions);
vector<Vec3> velocities(2);
velocities[0] = Vec3(0, 0, 0);
velocities[1] = Vec3(0, 1, 0);
context.setVelocities(velocities);
// The second particle should move in a circular orbit around the first one.
// Compare it to the analytical solution.
for (int i = 0; i < 1000; ++i) {
State state = context.getState(State::Positions | State::Velocities | State::Forces);
double time = state.getTime();
ASSERT_EQUAL_VEC(Vec3(), state.getPositions()[0], 0.0);
ASSERT_EQUAL_VEC(Vec3(), state.getVelocities()[0], 0.0);
ASSERT_EQUAL_VEC(Vec3(cos(time), sin(time), 0), state.getPositions()[1], 0.01);
ASSERT_EQUAL_VEC(Vec3(-sin(time), cos(time), 0), state.getVelocities()[1], 0.01);
integrator.step(1);
}
}
void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomBondForce* force = new CustomBondForce(("(r-1.1)^2"));
vector<double> params;
for (int i = 1; i < numParticles; i++)
force->addBond(i-1, i, params);
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, OpenCLPlatform::OpenCLDeviceIndex());
map<string, string> props;
props[OpenCLPlatform::OpenCLDeviceIndex()] = 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 testBonds() {
ReferencePlatform platform;
System system;
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("scale*k*(r-r0)^2");
forceField->addPerBondParameter("r0");
forceField->addPerBondParameter("k");
forceField->addGlobalParameter("scale", 0.5);
vector<double> parameters(2);
parameters[0] = 1.5;
parameters[1] = 0.8;
forceField->addBond(0, 1, parameters);
parameters[0] = 1.2;
parameters[1] = 0.7;
forceField->addBond(1, 2, parameters);
system.addForce(forceField);
ASSERT(!forceField->usesPeriodicBoundaryConditions());
ASSERT(!system.usesPeriodicBoundaryConditions());
Context context(system, integrator, platform);
vector<Vec3> positions(3);
positions[0] = Vec3(0, 2, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(1, 0, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.8*0.5, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.7*0.2, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.8*0.5*0.5 + 0.5*0.7*0.2*0.2, state.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[1] = 0.9;
forceField->setBondParameters(0, 0, 1, parameters);
parameters[0] = 1.3;
parameters[1] = 0.8;
forceField->setBondParameters(1, 1, 2, parameters);
forceField->updateParametersInContext(context);
state = context.getState(State::Forces | State::Energy);
{
const vector<Vec3>& forces = state.getForces();
ASSERT_EQUAL_VEC(Vec3(0, -0.9*0.4, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0.8*0.3, 0, 0), forces[2], TOL);
ASSERT_EQUAL_VEC(Vec3(-forces[0][0]-forces[2][0], -forces[0][1]-forces[2][1], -forces[0][2]-forces[2][2]), forces[1], TOL);
ASSERT_EQUAL_TOL(0.5*0.9*0.4*0.4 + 0.5*0.8*0.3*0.3, state.getPotentialEnergy(), TOL);
}
}
void testManyParameters() {
System system;
system.addParticle(1.0);
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomBondForce* forceField = new CustomBondForce("(a+b+c+d+e+f+g+h+i)*r");
forceField->addPerBondParameter("a");
forceField->addPerBondParameter("b");
forceField->addPerBondParameter("c");
forceField->addPerBondParameter("d");
forceField->addPerBondParameter("e");
forceField->addPerBondParameter("f");
forceField->addPerBondParameter("g");
forceField->addPerBondParameter("h");
forceField->addPerBondParameter("i");
vector<double> parameters(forceField->getNumPerBondParameters());
for (int i = 0; i < (int) parameters.size(); i++)
parameters[i] = i;
forceField->addBond(0, 1, parameters);
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(2);
positions[0] = Vec3(0, 0, 0);
positions[1] = Vec3(0, 2.5, 0);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double f = 1+2+3+4+5+6+7+8;
ASSERT_EQUAL_VEC(Vec3(0, f, 0), forces[0], TOL);
ASSERT_EQUAL_VEC(Vec3(0, -f, 0), forces[1], TOL);
ASSERT_EQUAL_TOL(f*2.5, state.getPotentialEnergy(), TOL);
}
void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
if (node.getIntProperty("version") != 1)
throw OpenMMException("Unsupported version number");
CustomBondForce* force = NULL;
try {
CustomBondForce* force = new CustomBondForce(node.getStringProperty("energy"));
const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
for (int i = 0; i < (int) perBondParams.getChildren().size(); i++) {
const SerializationNode& parameter = perBondParams.getChildren()[i];
force->addPerBondParameter(parameter.getStringProperty("name"));
}
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (int i = 0; i < (int) globalParams.getChildren().size(); i++) {
const SerializationNode& parameter = globalParams.getChildren()[i];
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
}
const SerializationNode& bonds = node.getChildNode("Bonds");
vector<double> params(force->getNumPerBondParameters());
for (int i = 0; i < (int) bonds.getChildren().size(); i++) {
const SerializationNode& bond = bonds.getChildren()[i];
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
params[j] = bond.getDoubleProperty(key.str());
}
force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), params);
}
return force;
}
catch (...) {
if (force != NULL)
delete force;
throw;
}
}
void* CustomBondForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 3)
throw OpenMMException("Unsupported version number");
CustomBondForce* force = NULL;
try {
CustomBondForce* force = new CustomBondForce(node.getStringProperty("energy"));
force->setForceGroup(node.getIntProperty("forceGroup", 0));
if (version > 1)
force->setUsesPeriodicBoundaryConditions(node.getBoolProperty("usesPeriodic"));
const SerializationNode& perBondParams = node.getChildNode("PerBondParameters");
for (auto& parameter : perBondParams.getChildren())
force->addPerBondParameter(parameter.getStringProperty("name"));
const SerializationNode& globalParams = node.getChildNode("GlobalParameters");
for (auto& parameter : globalParams.getChildren())
force->addGlobalParameter(parameter.getStringProperty("name"), parameter.getDoubleProperty("default"));
if (version > 2) {
const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives");
for (auto& parameter : energyDerivs.getChildren())
force->addEnergyParameterDerivative(parameter.getStringProperty("name"));
}
const SerializationNode& bonds = node.getChildNode("Bonds");
vector<double> params(force->getNumPerBondParameters());
for (auto& bond : bonds.getChildren()) {
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
params[j] = bond.getDoubleProperty(key.str());
}
force->addBond(bond.getIntProperty("p1"), bond.getIntProperty("p2"), params);
}
return force;
}
catch (...) {
if (force != NULL)
delete force;
throw;
}
}
