/** * 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; } }