void testParallelComputation() {
System system;
const int numParticles = 200;
for (int i = 0; i < numParticles; i++)
system.addParticle(1.0);
CustomCompoundBondForce* force = new CustomCompoundBondForce(2, ("(distance(p1,p2)-1.1)^2"));
vector<int> particles(2);
vector<double> params;
for (int i = 1; i < numParticles; i++) {
particles[0] = i-1;
particles[1] = i;
force->addBond(particles, 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, CudaPlatform::CudaDeviceIndex());
map<string, string> props;
props[CudaPlatform::CudaDeviceIndex()] = 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 testPositionDependence() {
ReferencePlatform platform;
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(2, "scale1*distance(p1,p2)+scale2*x1+2*y2");
custom->addGlobalParameter("scale1", 0.3);
custom->addGlobalParameter("scale2", 0.2);
vector<int> particles(2);
particles[0] = 0;
particles[1] = 1;
vector<double> parameters;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(2);
positions[0] = Vec3(0.5, 1, 0);
positions[1] = Vec3(1.5, 1, 0);
VerletIntegrator integrator(0.01);
Context context(customSystem, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.3*1.0+0.2*0.5+2*1, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(0.3-0.2, 0, 0), state.getForces()[0], 1e-5);
ASSERT_EQUAL_VEC(Vec3(-0.3, -2, 0), state.getForces()[1], 1e-5);
}
void testContinuous3DFunction() {
const int xsize = 10;
const int ysize = 11;
const int zsize = 12;
const double xmin = 0.4;
const double xmax = 1.1;
const double ymin = 0.0;
const double ymax = 0.9;
const double zmin = 0.2;
const double zmax = 1.3;
ReferencePlatform platform;
System system;
system.addParticle(1.0);
VerletIntegrator integrator(0.01);
CustomCompoundBondForce* forceField = new CustomCompoundBondForce(1, "fn(x1,y1,z1)+1");
vector<int> particles(1, 0);
forceField->addBond(particles, vector<double>());
vector<double> table(xsize*ysize*zsize);
for (int i = 0; i < xsize; i++) {
for (int j = 0; j < ysize; j++) {
for (int k = 0; k < zsize; k++) {
double x = xmin + i*(xmax-xmin)/xsize;
double y = ymin + j*(ymax-ymin)/ysize;
double z = zmin + k*(zmax-zmin)/zsize;
table[i+xsize*j+xsize*ysize*k] = sin(0.25*x)*cos(0.33*y)*(1+z);
}
}
}
forceField->addTabulatedFunction("fn", new Continuous3DFunction(xsize, ysize, zsize, table, xmin, xmax, ymin, ymax, zmin, zmax));
system.addForce(forceField);
Context context(system, integrator, platform);
vector<Vec3> positions(1);
for (double x = xmin-0.15; x < xmax+0.2; x += 0.1) {
for (double y = ymin-0.15; y < ymax+0.2; y += 0.1) {
for (double z = zmin-0.15; z < zmax+0.2; z += 0.1) {
positions[0] = Vec3(x, y, z);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = state.getForces();
double energy = 1;
Vec3 force(0, 0, 0);
if (x >= xmin && x <= xmax && y >= ymin && y <= ymax && z >= zmin && z <= zmax) {
energy = sin(0.25*x)*cos(0.33*y)*(1.0+z)+1;
force[0] = -0.25*cos(0.25*x)*cos(0.33*y)*(1.0+z);
force[1] = 0.3*sin(0.25*x)*sin(0.33*y)*(1.0+z);
force[2] = -sin(0.25*x)*cos(0.33*y);
}
ASSERT_EQUAL_VEC(force, forces[0], 0.1);
ASSERT_EQUAL_TOL(energy, state.getPotentialEnergy(), 0.05);
}
}
}
}
void testMultipleBonds() {
// Two compound bonds using Urey-Bradley example from API doc
ReferencePlatform platform;
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(3,
"0.5*(kangle*(angle(p1,p2,p3)-theta0)^2+kbond*(distance(p1,p3)-r0)^2)");
custom->addPerBondParameter("kangle");
custom->addPerBondParameter("kbond");
custom->addPerBondParameter("theta0");
custom->addPerBondParameter("r0");
vector<double> parameters(4);
parameters[0] = 1.0;
parameters[1] = 1.0;
parameters[2] = 2 * M_PI / 3;
parameters[3] = sqrt(3.0) / 2;
vector<int> particles0(3);
particles0[0] = 0;
particles0[1] = 1;
particles0[2] = 2;
vector<int> particles1(3);
particles1[0] = 1;
particles1[1] = 2;
particles1[2] = 3;
custom->addBond(particles0, parameters);
custom->addBond(particles1, parameters);
customSystem.addForce(custom);
vector<Vec3> positions(4);
positions[0] = Vec3(0, 0.5, 0);
positions[1] = Vec3(0, 0, 0);
positions[2] = Vec3(0.5, 0, 0);
positions[3] = Vec3(0.6, 0, 0.4);
VerletIntegrator integrator(0.01);
Context context(customSystem, integrator, platform);
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(0.199, state.getPotentialEnergy(), 1e-3);
vector<Vec3> forces(state.getForces());
ASSERT_EQUAL_VEC(Vec3(-1.160, 0.112, 0.0), forces[0], 1e-3);
ASSERT_EQUAL_VEC(Vec3(0.927, 1.047, -0.638), forces[1], 1e-3);
ASSERT_EQUAL_VEC(Vec3(-0.543, -1.160, 0.721), forces[2], 1e-3);
ASSERT_EQUAL_VEC(Vec3(0.776, 0.0, -0.084), forces[3], 1e-3);
}
void testBond() {
// Create a system using a CustomCompoundBondForce.
System customSystem;
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
customSystem.addParticle(1.0);
CustomCompoundBondForce* custom = new CustomCompoundBondForce(4, "0.5*kb*((distance(p1,p2)-b0)^2+(distance(p2,p3)-b0)^2)+0.5*ka*(angle(p2,p3,p4)-a0)^2+kt*(1+cos(dihedral(p1,p2,p3,p4)-t0))");
custom->addPerBondParameter("kb");
custom->addPerBondParameter("ka");
custom->addPerBondParameter("kt");
custom->addPerBondParameter("b0");
custom->addPerBondParameter("a0");
custom->addPerBondParameter("t0");
vector<int> particles(4);
particles[0] = 0;
particles[1] = 1;
particles[2] = 3;
particles[3] = 2;
vector<double> parameters(6);
parameters[0] = 1.5;
parameters[1] = 0.8;
parameters[2] = 0.6;
parameters[3] = 1.1;
parameters[4] = 2.9;
parameters[5] = 1.3;
custom->addBond(particles, parameters);
customSystem.addForce(custom);
// Create an identical system using standard forces.
System standardSystem;
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
standardSystem.addParticle(1.0);
HarmonicBondForce* bonds = new HarmonicBondForce();
bonds->addBond(0, 1, 1.1, 1.5);
bonds->addBond(1, 3, 1.1, 1.5);
standardSystem.addForce(bonds);
HarmonicAngleForce* angles = new HarmonicAngleForce();
angles->addAngle(1, 3, 2, 2.9, 0.8);
standardSystem.addForce(angles);
PeriodicTorsionForce* torsions = new PeriodicTorsionForce();
torsions->addTorsion(0, 1, 3, 2, 1, 1.3, 0.6);
standardSystem.addForce(torsions);
// Set the atoms in various positions, and verify that both systems give identical forces and energy.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
VerletIntegrator integrator1(0.01);
VerletIntegrator integrator2(0.01);
Context c1(customSystem, integrator1, platform);
Context c2(standardSystem, integrator2, platform);
vector<Vec3> positions(4);
for (int i = 0; i < 10; 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 < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
// Try changing the bond parameters and make sure it's still correct.
parameters[0] = 1.6;
parameters[3] = 1.3;
custom->setBondParameters(0, particles, parameters);
custom->updateParametersInContext(c1);
bonds->setBondParameters(0, 0, 1, 1.3, 1.6);
bonds->setBondParameters(1, 1, 3, 1.3, 1.6);
bonds->updateParametersInContext(c2);
{
State s1 = c1.getState(State::Forces | State::Energy);
State s2 = c2.getState(State::Forces | State::Energy);
const vector<Vec3>& forces = s1.getForces();
for (int i = 0; i < customSystem.getNumParticles(); i++)
ASSERT_EQUAL_VEC(s1.getForces()[i], s2.getForces()[i], TOL);
ASSERT_EQUAL_TOL(s1.getPotentialEnergy(), s2.getPotentialEnergy(), TOL);
}
}
void testComplexFunction() {
int numParticles = 5;
System system;
for (int i = 0; i < numParticles; i++)
system.addParticle(2.0);
vector<double> table(20);
for (int i = 0; i < 20; i++)
table[i] = sin(0.11*i);
// When every group contains only one particle, a CustomCentroidBondForce is identical to a
// CustomCompoundBondForce. Use that to test a complicated energy function with lots of terms.
CustomCompoundBondForce* compound = new CustomCompoundBondForce(4, "x1+y2+z4+fn(distance(p1,p2))*angle(p3,p2,p4)+scale*dihedral(p2,p1,p4,p3)");
CustomCentroidBondForce* centroid = new CustomCentroidBondForce(4, "x1+y2+z4+fn(distance(g1,g2))*angle(g3,g2,g4)+scale*dihedral(g2,g1,g4,g3)");
compound->addGlobalParameter("scale", 0.5);
centroid->addGlobalParameter("scale", 0.5);
compound->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
centroid->addTabulatedFunction("fn", new Continuous1DFunction(table, -1, 10));
// Add two bonds to the CustomCompoundBondForce.
vector<int> particles(4);
vector<double> parameters;
particles[0] = 0;
particles[1] = 1;
particles[2] = 2;
particles[3] = 3;
compound->addBond(particles, parameters);
particles[0] = 2;
particles[1] = 4;
particles[2] = 3;
particles[3] = 1;
compound->addBond(particles, parameters);
// Add identical bonds to the CustomCentroidBondForce. As a stronger test, make sure that
// group number is different from particle number.
vector<int> groupMembers(1);
groupMembers[0] = 3;
centroid->addGroup(groupMembers);
groupMembers[0] = 0;
centroid->addGroup(groupMembers);
groupMembers[0] = 1;
centroid->addGroup(groupMembers);
groupMembers[0] = 2;
centroid->addGroup(groupMembers);
groupMembers[0] = 4;
centroid->addGroup(groupMembers);
vector<int> groups(4);
groups[0] = 1;
groups[1] = 2;
groups[2] = 3;
groups[3] = 0;
centroid->addBond(groups, parameters);
groups[0] = 3;
groups[1] = 4;
groups[2] = 0;
groups[3] = 2;
centroid->addBond(groups, parameters);
// Add both forces as different force groups, and create a context.
centroid->setForceGroup(1);
system.addForce(compound);
system.addForce(centroid);
VerletIntegrator integrator(0.01);
Context context(system, integrator, platform);
// Evaluate the force and energy for various positions and see if they match.
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
vector<Vec3> positions(numParticles);
for (int i = 0; i < 10; i++) {
for (int j = 0; j < numParticles; j++)
positions[j] = Vec3(5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt), 5.0*genrand_real2(sfmt));
context.setPositions(positions);
State state1 = context.getState(State::Forces | State::Energy, false, 1<<0);
State state2 = context.getState(State::Forces | State::Energy, false, 1<<1);
ASSERT_EQUAL_TOL(state1.getPotentialEnergy(), state2.getPotentialEnergy(), TOL);
for (int i = 0; i < numParticles; i++)
ASSERT_EQUAL_VEC(state1.getForces()[i], state2.getForces()[i], TOL);
}
}
void* CustomCompoundBondForceProxy::deserialize(const SerializationNode& node) const {
int version = node.getIntProperty("version");
if (version < 1 || version > 3)
throw OpenMMException("Unsupported version number");
CustomCompoundBondForce* force = NULL;
try {
CustomCompoundBondForce* force = new CustomCompoundBondForce(node.getIntProperty("particles"), 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<int> particles(force->getNumParticlesPerBond());
vector<double> params(force->getNumPerBondParameters());
for (auto& bond : bonds.getChildren()) {
for (int j = 0; j < (int) particles.size(); j++) {
stringstream key;
key << "p";
key << j+1;
particles[j] = bond.getIntProperty(key.str());
}
for (int j = 0; j < (int) params.size(); j++) {
stringstream key;
key << "param";
key << j+1;
params[j] = bond.getDoubleProperty(key.str());
}
force->addBond(particles, params);
}
const SerializationNode& functions = node.getChildNode("Functions");
for (auto& function : functions.getChildren()) {
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 (auto& child : valuesNode.getChildren())
values.push_back(child.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;
}
}
