void* CMAPTorsionForceProxy::deserialize(const SerializationNode& node) const { if (node.getIntProperty("version") != 1) throw OpenMMException("Unsupported version number"); CMAPTorsionForce* force = new CMAPTorsionForce(); try { const SerializationNode& maps = node.getChildNode("Maps"); for (int i = 0; i < (int) maps.getChildren().size(); i++) { const SerializationNode& map = maps.getChildren()[i]; int size = map.getIntProperty("size"); if (size*size != map.getChildren().size()) throw OpenMMException("Wrong number of values specified for CMAP"); vector<double> energy(size*size); for (int j = 0; j < (int) energy.size(); j++) energy[j] = map.getChildren()[j].getDoubleProperty("e"); force->addMap(size, energy); } const SerializationNode& torsions = node.getChildNode("Torsions"); for (int i = 0; i < (int) torsions.getChildren().size(); i++) { const SerializationNode& torsion = torsions.getChildren()[i]; force->addTorsion(torsion.getIntProperty("map"), torsion.getIntProperty("a1"), torsion.getIntProperty("a2"), torsion.getIntProperty("a3"), torsion.getIntProperty("a4"), torsion.getIntProperty("b1"), torsion.getIntProperty("b2"), torsion.getIntProperty("b3"), torsion.getIntProperty("b4")); } } catch (...) { delete force; throw; } return force; }
void testChangingParameters() { // Create a system with two maps and one torsion. const int mapSize = 8; System system; for (int i = 0; i < 5; i++) system.addParticle(1.0); CMAPTorsionForce* cmap = new CMAPTorsionForce(); vector<double> mapEnergy1(mapSize*mapSize); vector<double> mapEnergy2(mapSize*mapSize); for (int i = 0; i < mapSize; i++) { double angle1 = i*2*M_PI/mapSize; double energy1 = cos(angle1); for (int j = 0; j < mapSize; j++) { double angle2 = j*2*M_PI/mapSize; double energy2 = 10*sin(angle2); mapEnergy1[i+j*mapSize] = energy1+energy2; mapEnergy2[i+j*mapSize] = energy1-energy2; } } cmap->addMap(mapSize, mapEnergy1); cmap->addMap(mapSize, mapEnergy2); cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4); system.addForce(cmap); // Set particle positions so angle1=0 and angle2=PI/4. vector<Vec3> positions(5); positions[0] = Vec3(0, 0, 1); positions[1] = Vec3(0, 0, 0); positions[2] = Vec3(1, 0, 0); positions[3] = Vec3(1, 0, 1); positions[4] = Vec3(0.5, -0.5, 1); VerletIntegrator integrator(0.01); Context context(system, integrator, platform); context.setPositions(positions); // Check that the energy is correct. double energy = context.getState(State::Energy).getPotentialEnergy(); ASSERT_EQUAL_TOL(1+10*sin(M_PI/4), energy, 1e-5); // Modify the parameters. cmap->setTorsionParameters(0, 1, 0, 1, 2, 3, 1, 2, 3, 4); for (int i = 0; i < mapSize*mapSize; i++) mapEnergy2[i] *= 2.0; cmap->setMapParameters(1, mapSize, mapEnergy2); cmap->updateParametersInContext(context); // See if the results are correct. energy = context.getState(State::Energy).getPotentialEnergy(); ASSERT_EQUAL_TOL(2-20*sin(M_PI/4), energy, 1e-5); }
void testCMAPTorsions() { const int mapSize = 36; // Create two systems: one with a pair of periodic torsions, and one with a CMAP torsion // that approximates the same force. System system1; for (int i = 0; i < 5; i++) system1.addParticle(1.0); PeriodicTorsionForce* periodic = new PeriodicTorsionForce(); periodic->addTorsion(0, 1, 2, 3, 2, M_PI/4, 1.5); periodic->addTorsion(1, 2, 3, 4, 3, M_PI/3, 2.0); system1.addForce(periodic); System system2; for (int i = 0; i < 5; i++) system2.addParticle(1.0); CMAPTorsionForce* cmap = new CMAPTorsionForce(); vector<double> mapEnergy(mapSize*mapSize); for (int i = 0; i < mapSize; i++) { double angle1 = i*2*M_PI/mapSize; double energy1 = 1.5*(1+cos(2*angle1-M_PI/4)); for (int j = 0; j < mapSize; j++) { double angle2 = j*2*M_PI/mapSize; double energy2 = 2.0*(1+cos(3*angle2-M_PI/3)); mapEnergy[i+j*mapSize] = energy1+energy2; } } cmap->addMap(mapSize, mapEnergy); cmap->addTorsion(0, 0, 1, 2, 3, 1, 2, 3, 4); system2.addForce(cmap); // Set the atoms in various positions, and verify that both systems give equal forces and energy. OpenMM_SFMT::SFMT sfmt; init_gen_rand(0, sfmt); vector<Vec3> positions(5); VerletIntegrator integrator1(0.01); VerletIntegrator integrator2(0.01); Context c1(system1, integrator1, platform); Context c2(system2, integrator2, platform); for (int i = 0; i < 50; i++) { for (int j = 0; j < (int) positions.size(); j++) positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt)); c1.setPositions(positions); c2.setPositions(positions); State s1 = c1.getState(State::Forces | State::Energy); State s2 = c2.getState(State::Forces | State::Energy); for (int i = 0; i < system1.getNumParticles(); i++) ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], 0.05); ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), 1e-3); } }