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* 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; } }
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; } }