void* CustomGBForceProxy::deserialize(const SerializationNode& node) const { int version = node.getIntProperty("version"); if (version < 1 || version > 2) throw OpenMMException("Unsupported version number"); CustomGBForce* force = NULL; try { CustomGBForce* force = new CustomGBForce(); force->setForceGroup(node.getIntProperty("forceGroup", 0)); force->setNonbondedMethod((CustomGBForce::NonbondedMethod) node.getIntProperty("method")); force->setCutoffDistance(node.getDoubleProperty("cutoff")); const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters"); for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) { const SerializationNode& parameter = perParticleParams.getChildren()[i]; force->addPerParticleParameter(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")); } if (version > 1) { const SerializationNode& energyDerivs = node.getChildNode("EnergyParameterDerivatives"); for (int i = 0; i < (int) energyDerivs.getChildren().size(); i++) { const SerializationNode& parameter = energyDerivs.getChildren()[i]; force->addEnergyParameterDerivative(parameter.getStringProperty("name")); } } const SerializationNode& computedValues = node.getChildNode("ComputedValues"); for (int i = 0; i < (int) computedValues.getChildren().size(); i++) { const SerializationNode& value = computedValues.getChildren()[i]; force->addComputedValue(value.getStringProperty("name"), value.getStringProperty("expression"), (CustomGBForce::ComputationType) value.getIntProperty("type")); } const SerializationNode& energyTerms = node.getChildNode("EnergyTerms"); for (int i = 0; i < (int) energyTerms.getChildren().size(); i++) { const SerializationNode& term = energyTerms.getChildren()[i]; force->addEnergyTerm(term.getStringProperty("expression"), (CustomGBForce::ComputationType) term.getIntProperty("type")); } const SerializationNode& particles = node.getChildNode("Particles"); vector<double> params(force->getNumPerParticleParameters()); for (int i = 0; i < (int) particles.getChildren().size(); i++) { const SerializationNode& particle = particles.getChildren()[i]; for (int j = 0; j < (int) params.size(); j++) { stringstream key; key << "param"; key << j+1; params[j] = particle.getDoubleProperty(key.str()); } force->addParticle(params); } const SerializationNode& exclusions = node.getChildNode("Exclusions"); for (int i = 0; i < (int) exclusions.getChildren().size(); i++) { const SerializationNode& exclusion = exclusions.getChildren()[i]; force->addExclusion(exclusion.getIntProperty("p1"), exclusion.getIntProperty("p2")); } const SerializationNode& functions = node.getChildNode("Functions"); for (int i = 0; i < (int) functions.getChildren().size(); i++) { const SerializationNode& function = functions.getChildren()[i]; if (function.hasProperty("type")) { force->addTabulatedFunction(function.getStringProperty("name"), function.decodeObject<TabulatedFunction>()); } else { // This is an old file created before TabulatedFunction existed. const SerializationNode& valuesNode = function.getChildNode("Values"); vector<double> values; for (int j = 0; j < (int) valuesNode.getChildren().size(); j++) values.push_back(valuesNode.getChildren()[j].getDoubleProperty("v")); force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max"))); } } return force; } catch (...) { if (force != NULL) delete force; throw; } }
void testExclusions() { ReferencePlatform platform; for (int i = 3; i < 4; i++) { System system; system.addParticle(1.0); system.addParticle(1.0); VerletIntegrator integrator(0.01); CustomGBForce* force = new CustomGBForce(); force->addComputedValue("a", "r", i < 2 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions); force->addEnergyTerm("a", CustomGBForce::SingleParticle); force->addEnergyTerm("(1+a1+a2)*r", i%2 == 0 ? CustomGBForce::ParticlePair : CustomGBForce::ParticlePairNoExclusions); force->addParticle(vector<double>()); force->addParticle(vector<double>()); force->addExclusion(0, 1); system.addForce(force); Context context(system, integrator, platform); vector<Vec3> positions(2); positions[0] = Vec3(0, 0, 0); positions[1] = Vec3(1, 0, 0); context.setPositions(positions); State state = context.getState(State::Forces | State::Energy); const vector<Vec3>& forces = state.getForces(); double f, energy; switch (i) { case 0: // e = 0 f = 0; energy = 0; break; case 1: // e = r f = 1; energy = 1; break; case 2: // e = 2r f = 2; energy = 2; break; case 3: // e = 3r + 2r^2 f = 7; energy = 5; break; default: ASSERT(false); } ASSERT_EQUAL_VEC(Vec3(f, 0, 0), forces[0], 1e-4); ASSERT_EQUAL_VEC(Vec3(-f, 0, 0), forces[1], 1e-4); ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 1e-4); // Take a small step in the direction of the energy gradient and see whether the potential energy changes by the expected amount. double norm = 0.0; for (int i = 0; i < (int) forces.size(); ++i) norm += forces[i].dot(forces[i]); norm = std::sqrt(norm); const double stepSize = 1e-3; double step = stepSize/norm; for (int i = 0; i < (int) positions.size(); ++i) { Vec3 p = positions[i]; Vec3 f = forces[i]; positions[i] = Vec3(p[0]-f[0]*step, p[1]-f[1]*step, p[2]-f[2]*step); } context.setPositions(positions); State state2 = context.getState(State::Energy); ASSERT_EQUAL_TOL(norm, (state2.getPotentialEnergy()-state.getPotentialEnergy())/stepSize, 1e-3*abs(state.getPotentialEnergy())); } }