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Commit 4452d437 authored by peastman's avatar peastman
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Continuing reference implementation of Gay-Berne force

parent 4d3b7319
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Showing with 135 additions and 8 deletions
platforms/reference/include/ReferenceGayBerneForce.h
View file @ 4452d437
......@@ -41,6 +41,7 @@ namespace OpenMM {
class OPENMM_EXPORT ReferenceGayBerneForce {
public:
struct Matrix;
/**
* Constructor.
*/
......@@ -59,7 +60,6 @@ public:
private:
struct ParticleInfo;
struct ExceptionInfo;
struct Matrix;
std::vector<ParticleInfo> particles;
std::vector<ExceptionInfo> exceptions;
std::set<std::pair<int, int> > exclusions;
......@@ -71,7 +71,8 @@ private:
void computeEllipsoidFrames(const std::vector<RealVec>& positions);
RealOpenMM computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const std::vector<RealVec>& positions, std::vector<RealVec>& forces, const RealVec* boxVectors);
RealOpenMM computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const std::vector<RealVec>& positions,
std::vector<RealVec>& forces, std::vector<RealVec>& torques, const RealVec* boxVectors);
};
struct ReferenceGayBerneForce::ParticleInfo {
......@@ -132,6 +133,12 @@ struct ReferenceGayBerneForce::Matrix {
}
};
static RealVec operator*(const RealVec& r, ReferenceGayBerneForce::Matrix& m) {
return RealVec(m.v[0][0]*r[0] + m.v[1][1]*r[1] + m.v[2][2]*r[2],
m.v[0][1]*r[0] + m.v[1][1]*r[1] + m.v[2][1]*r[2],
m.v[0][2]*r[0] + m.v[1][2]*r[1] + m.v[2][2]*r[2]);
}
} // namespace OpenMM
#endif // __ReferenceGayBerneForce_H__
platforms/reference/src/SimTKReference/ReferenceGayBerneForce.cpp
View file @ 4452d437
......@@ -88,6 +88,7 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
RealOpenMM energy = 0;
int numParticles = particles.size();
vector<RealVec> torques(numParticles, Vec3());
for (int i = 1; i < numParticles; i++) {
if (particles[i].epsilon == 0.0)
continue;
......@@ -98,7 +99,7 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
continue; // This interaction will be handled by an exception.
RealOpenMM sigma = 0.5*(particles[i].sigma+particles[j].sigma);
RealOpenMM epsilon = SQRT(particles[i].epsilon*particles[j].epsilon);
energy += computeOneInteraction(i, j, sigma, epsilon, positions, forces, boxVectors);
energy += computeOneInteraction(i, j, sigma, epsilon, positions, forces, torques, boxVectors);
}
}
......@@ -107,7 +108,7 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
int numExceptions = exceptions.size();
for (int i = 0; i < numExceptions; i++) {
ExceptionInfo& e = exceptions[i];
energy += computeOneInteraction(e.particle1, e.particle2, e.sigma, e.epsilon, positions, forces, boxVectors);
energy += computeOneInteraction(e.particle1, e.particle2, e.sigma, e.epsilon, positions, forces, torques, boxVectors);
}
return energy;
}
......@@ -168,7 +169,8 @@ void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<RealVec>& posit
}
}
RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const vector<RealVec>& positions, vector<RealVec>& forces, const RealVec* boxVectors) {
RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const vector<RealVec>& positions,
vector<RealVec>& forces, vector<RealVec>& torques, const RealVec* boxVectors) {
// Compute the displacement and check against the cutoff.
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
......@@ -189,6 +191,7 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
Matrix G12 = G[particle1]+G[particle2];
Matrix B12inv = B12.inverse();
Matrix G12inv = G12.inverse();
RealOpenMM detG12 = G12.determinant();
// Estimate the distance between the ellipsoids and compute the first terms needed for the energy.
......@@ -200,7 +203,7 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
RealOpenMM rho2 = rho*rho;
RealOpenMM rho6 = rho2*rho2*rho2;
RealOpenMM u = 4*epsilon*(rho6*rho6-rho6);
RealOpenMM eta = SQRT(2*s[particle1]*s[particle2]/G12.determinant());
RealOpenMM eta = SQRT(2*s[particle1]*s[particle2]/detG12);
RealOpenMM chi = 2*drUnit.dot(B12inv*drUnit);
chi *= chi;
......@@ -208,10 +211,76 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
RealVec kappa = G12inv*dr;
RealVec iota = B12inv*dr;
RealVec dudr = (drUnit + (kappa-drUnit*kappa.dot(drUnit))*(0.5*sigma12*sigma12*sigma12*rInv*rInv))*(24*epsilon*(2*rho6-1)*rho6*rho/sigma);
RealVec dchidr = (iota-drUnit*iota.dot(drUnit))*(-8*rInv*rInv*SQRT(chi));
RealOpenMM rInv2 = rInv*rInv;
RealOpenMM dUSLJdr = 24*epsilon*(2*rho6-1)*rho6*rho/sigma;
RealOpenMM temp = 0.5*sigma12*sigma12*sigma12*rInv2;
RealVec dudr = (drUnit + (kappa-drUnit*kappa.dot(drUnit))*temp)*dUSLJdr;
RealVec dchidr = (iota-drUnit*iota.dot(drUnit))*(-8*rInv2*SQRT(chi));
RealVec force = (dchidr*u + dudr*chi)*eta;
forces[particle1] += force;
forces[particle2] -= force;
// Compute the terms needed for the torque.
for (int j = 0; j < 2; j++) {
int particle = (j == 0 ? particle1 : particle2);
RealVec dudq = A[particle]*((kappa*G[particle]).cross(kappa*temp));
RealVec dchidq = (A[particle]*((iota*B[particle]).cross(iota)))*(-4*rInv2);
RealOpenMM (&g12)[3][3] = G12.v;
RealOpenMM (&a)[3][3] = A[particle].v;
RealVec scale = RealVec(particles[particle].rx, particles[particle].ry, particles[particle].rz)*(-eta/detG12);
Matrix D;
RealOpenMM (&d)[3][3] = D.v;
d[0][0] = scale[0]*(g12[1][2]*g12[0][1]*a[0][2] + 2*g12[1][1]*g12[2][2]*a[0][0] -
g12[1][1]*a[0][2]*g12[0][2] - 2*g12[1][2]*a[0][0]*g12[2][1] +
a[0][1]*g12[0][2]*g12[2][1] - a[0][1]*g12[0][1]*g12[2][2] -
g12[1][0]*g12[2][2]*a[0][1] + g12[2][0]*g12[1][2]*a[0][1] +
g12[1][0]*a[0][2]*g12[2][1] - a[0][2]*g12[2][0]*g12[1][1]);
d[0][1] = scale[0]*( g12[0][2]*a[0][0]*g12[2][1] - g12[2][2]*a[0][0]*g12[0][1] +
2*g12[0][0]*g12[2][2]*a[0][1] - g12[0][0]*a[0][2]*g12[1][2] -
2*g12[2][0]*g12[0][2]*a[0][1] + a[0][2]*g12[1][0]*g12[0][2] -
g12[2][2]*g12[1][0]*a[0][0] + g12[2][0]*a[0][0]*g12[1][2] +
g12[2][0]*a[0][2]*g12[0][1] - a[0][2]*g12[0][0]*g12[2][1]);
d[0][2] = scale[0]*( g12[0][1]*g12[1][2]*a[0][0] - g12[0][2]*a[0][0]*g12[1][1] -
g12[0][0]*g12[1][2]*a[0][1] + g12[1][0]*g12[0][2]*a[0][1] -
a[0][1]*g12[0][0]*g12[2][1] - g12[2][0]*g12[1][1]*a[0][0] +
2*g12[1][1]*g12[0][0]*a[0][2] - 2*g12[1][0]*a[0][2]*g12[0][1] +
g12[1][0]*g12[2][1]*a[0][0] + g12[2][0]*a[0][1]*g12[0][1]);
d[1][0] = scale[1]*(-g12[1][1]*a[1][2]*g12[0][2] + 2*g12[1][1]*g12[2][2]*a[1][0] +
g12[1][2]*g12[0][1]*a[1][2] - 2*g12[1][2]*a[1][0]*g12[2][1] +
a[1][1]*g12[0][2]*g12[2][1] - a[1][1]*g12[0][1]*g12[2][2] -
g12[1][0]*g12[2][2]*a[1][1] + g12[2][0]*g12[1][2]*a[1][1] -
a[1][2]*g12[2][0]*g12[1][1] + g12[1][0]*a[1][2]*g12[2][1]);
d[1][1] = scale[1]*( g12[0][2]*a[1][0]*g12[2][1] - g12[0][1]*g12[2][2]*a[1][0] +
2*g12[2][2]*g12[0][0]*a[1][1] - a[1][2]*g12[0][0]*g12[1][2] -
2*g12[2][0]*a[1][1]*g12[0][2] - g12[1][0]*g12[2][2]*a[1][0] +
g12[2][0]*g12[1][2]*a[1][0] + g12[1][0]*a[1][2]*g12[0][2] -
g12[0][0]*a[1][2]*g12[2][1] + a[1][2]*g12[0][1]*g12[2][0]);
d[1][2] = scale[1]*( g12[0][1]*g12[1][2]*a[1][0] - g12[0][2]*a[1][0]*g12[1][1] -
g12[0][0]*g12[1][2]*a[1][1] + g12[1][0]*g12[0][2]*a[1][1] +
2*g12[1][1]*g12[0][0]*a[1][2] - g12[0][0]*a[1][1]*g12[2][1] +
g12[0][1]*g12[2][0]*a[1][1] - a[1][0]*g12[2][0]*g12[1][1] -
2*g12[1][0]*g12[0][1]*a[1][2] + g12[1][0]*a[1][0]*g12[2][1]);
d[2][0] = scale[2]*( -g12[1][1]*g12[0][2]*a[2][2] + g12[0][1]*g12[1][2]*a[2][2] +
2*g12[1][1]*a[2][0]*g12[2][2] - g12[0][1]*a[2][1]*g12[2][2] +
g12[0][2]*g12[2][1]*a[2][1] - 2*a[2][0]*g12[2][1]*g12[1][2] -
g12[1][0]*a[2][1]*g12[2][2] + g12[1][2]*g12[2][0]*a[2][1] -
g12[1][1]*g12[2][0]*a[2][2] + g12[2][1]*g12[1][0]*a[2][2]);
d[2][1] = scale[2]*( -g12[0][1]*g12[2][2]*a[2][0] + g12[0][2]*a[2][0]*g12[2][1] +
2*a[2][1]*g12[0][0]*g12[2][2] - g12[1][2]*a[2][2]*g12[0][0] -
2*a[2][1]*g12[0][2]*g12[2][0] - g12[1][0]*a[2][0]*g12[2][2] +
g12[1][0]*g12[0][2]*a[2][2] + g12[1][2]*g12[2][0]*a[2][0] -
g12[0][0]*a[2][2]*g12[2][1] + a[2][2]*g12[0][1]*g12[2][0]);
d[2][2] = scale[2]*( g12[0][1]*g12[1][2]*a[2][0] - g12[0][2]*a[2][0]*g12[1][1] -
g12[0][0]*g12[1][2]*a[2][1] + g12[1][0]*g12[0][2]*a[2][1] -
g12[1][1]*g12[2][0]*a[2][0] - g12[2][1]*a[2][1]*g12[0][0] +
2*g12[1][1]*a[2][2]*g12[0][0] + g12[2][1]*g12[1][0]*a[2][0] +
g12[2][0]*g12[0][1]*a[2][1] - 2*a[2][2]*g12[1][0]*g12[0][1]);
RealVec detadq;
for (int i = 0; i < 3; i++)
detadq += RealVec(a[i][0], a[i][1], a[i][2]).cross(RealVec(d[i][0], d[i][1], d[i][2]));
RealVec torque = dchidq*(u*eta) + detadq*(u*chi) + dudq*(eta*chi);
torques[particle] += torque;
}
return u*eta*chi;
}
tests/TestGayBerneForce.h
View file @ 4452d437
......@@ -135,6 +135,56 @@ void testEnergyScales() {
ASSERT_EQUAL_VEC(Vec3(0, expectedForce*expectedScale, 0), state.getForces()[3], 1e-5);
}
void testEnergyConservation() {
// Create a box of ellipsoids and make sure a simulation conserves energy.
// That verifies that forces and energies are consistent.
const double boxSize = 3.0;
System system;
system.setDefaultPeriodicBoxVectors(Vec3(boxSize, 0, 0), Vec3(0, boxSize, 0), Vec3(0, 0, boxSize));
GayBerneForce* gb = new GayBerneForce();
system.addForce(gb);
gb->setNonbondedMethod(GayBerneForce::CutoffPeriodic);
gb->setCutoffDistance(1.0);
vector<Vec3> positions;
for (int x = 0; x < 3; x++) {
for (int y = 0; y < 3; y++) {
for (int z = 0; z < 3; z++) {
int first = system.getNumParticles();
system.addParticle(10.0);
system.addParticle(1.0);
system.addParticle(1.0);
gb->addParticle(0.2, 2.0, first+1, first+2, 0.2, 0.25, 0.3, 0.9, 1.0, 1.1);
gb->addParticle(1.0, 0.0, -1, -1, 1, 1, 1, 1, 1, 1);
gb->addParticle(1.0, 0.0, -1, -1, 1, 1, 1, 1, 1, 1);
positions.push_back(Vec3(x, y, z));
positions.push_back(Vec3(x+0.1, y, z));
positions.push_back(Vec3(x, y+0.1, z));
system.addConstraint(first, first+1, 0.1);
system.addConstraint(first, first+2, 0.1);
system.addConstraint(first+1, first+2, 0.1*sqrt(2.0));
}
}
}
VerletIntegrator integ(0.001);
Context context(system, integ, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
for (int i = 0; i < 100; i++) {
State state = context.getState(State::Energy);
printf("%d %g\n", i, state.getPotentialEnergy()+state.getKineticEnergy());
integ.step(10);
}
State state = context.getState(State::Positions);
for (int i = 0; i < 9; i++) {
Vec3 p1 = state.getPositions()[3*i];
Vec3 p2 = state.getPositions()[3*i+1];
Vec3 p3 = state.getPositions()[3*i+2];
printf("%g %g %g, %g %g %g, %g %g %g\n", p1[0], p1[1], p1[2], p2[0]-p1[0], p2[1]-p1[1], p2[2]-p1[2], p3[0]-p1[0], p3[1]-p1[1], p3[2]-p1[2]);
}
}
void runPlatformTests();
int main(int argc, char* argv[]) {
......@@ -142,6 +192,7 @@ int main(int argc, char* argv[]) {
initializeTests(argc, argv);
testPointParticles();
testEnergyScales();
testEnergyConservation();
runPlatformTests();
}
catch(const exception& e) {
......
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