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Commit 505824d6 authored by peastman's avatar peastman
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Finished reference implementation of GayBerneForce

parent 4452d437
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openmmapi/include/openmm/GayBerneForce.h
View file @ 505824d6
......@@ -44,20 +44,19 @@ namespace OpenMM {
/**
* This class implements the Gay-Berne anisotropic potential. This is similar to a Lennard-Jones potential,
* but it represents the particles as ellipsoids rather than point particles. In addition to the standard
* sigma and epsilon parameters, each particle has three radii r_x, r_y, and r_z that give the size of the
* ellipsoid along each axis. It also has three scale factors e_x, e_y, and e_z that scale the strength
* sigma and epsilon parameters, each particle has three widths sx, sy, and sz that give the diameter of the
* ellipsoid along each axis. It also has three scale factors ex, ey, and ez that scale the strength
* of the interaction along each axis. You can think of this force as a Lennard-Jones interaction computed
* based on the distance between the nearest points on two ellipsoids. The interpretation of the scale
* factors is slightly complicated, but roughly speaking, the strength of the interaction along the ellipsoid's
* x axis is divided by e_x^2, and likewise for the other axes. If two particles each have all their
* radii set to sigma/2 and all their scale factors set 1, the interaction simplifies to a standard Lennard-Jones
* force between point particles.
* based on the distance between the nearest points on two ellipsoids. The scale factors act as multipliers
* for epsilon along each axis, so the strength of the interaction along the ellipsoid's x axis is multiplied by
* ex, and likewise for the other axes. If two particles each have all their widths set to sigma and all their
* scale factors set to 1, the interaction simplifies to a standard Lennard-Jones force between point particles.
*
* The orientation of a particle's ellipsoid is determined based on the positions of two other particles.
* The vector to the first particle sets the direction of the x axis. The vector to the second particle
* (after subtracting out any x component) sets the direction of the y axis. If the ellipsoid is axially
* symmetric (r_y=r_z and e_y=e_z), you can omit the second particle and define only an x axis direction.
* If the ellipsoid is a sphere (all three radii and all three scale factors are equal), both particles
* symmetric (sy=sz and ey=ez), you can omit the second particle and define only an x axis direction.
* If the ellipsoid is a sphere (all three widths and all three scale factors are equal), both particles
* can be omitted.
*
* To determine the values of sigma and epsilon for an interaction, this class uses Lorentz-Berthelot
......@@ -166,15 +165,15 @@ public:
* @param epsilon the epsilon parameter (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
* @param xparticle the index of the particle whose position defines the ellipsoid's x axis, or -1 if the ellipsoid is a sphere
* @param yparticle the index of the particle whose position defines the ellipsoid's y axis, or -1 if the ellipsoid is axially symmetric
* @param rx the radius of the ellipsoid along its x axis
* @param ry the radius of the ellipsoid along its y axis
* @param rz the radius of the ellipsoid along its z axis
* @param sx the diameter of the ellipsoid along its x axis
* @param sy the diameter of the ellipsoid along its y axis
* @param sz the diameter of the ellipsoid along its z axis
* @param ex the factor by which epsilon is scaled along the ellipsoid's x axis
* @param ey the factor by which epsilon is scaled along the ellipsoid's y axis
* @param ez the factor by which epsilon is scaled along the ellipsoid's z axis
* @return the index of the particle that was added
*/
int addParticle(double sigma, double epsilon, int xparticle, int yparticle, double rx, double ry, double rz, double ex, double ey, double ez);
int addParticle(double sigma, double epsilon, int xparticle, int yparticle, double sx, double sy, double sz, double ex, double ey, double ez);
/**
* Get the parameters for a particle.
*
......@@ -183,14 +182,14 @@ public:
* @param[out] epsilon the epsilon parameter (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
* @param[out] xparticle the index of the particle whose position defines the ellipsoid's x axis, or -1 if the ellipsoid is a sphere
* @param[out] yparticle the index of the particle whose position defines the ellipsoid's y axis, or -1 if the ellipsoid is axially symmetric
* @param[out] rx the radius of the ellipsoid along its x axis
* @param[out] ry the radius of the ellipsoid along its y axis
* @param[out] rz the radius of the ellipsoid along its z axis
* @param[out] sx the diameter of the ellipsoid along its x axis
* @param[out] sy the diameter of the ellipsoid along its y axis
* @param[out] sz the diameter of the ellipsoid along its z axis
* @param[out] ex the factor by which epsilon is scaled along the ellipsoid's x axis
* @param[out] ey the factor by which epsilon is scaled along the ellipsoid's y axis
* @param[out] ez the factor by which epsilon is scaled along the ellipsoid's z axis
*/
void getParticleParameters(int index, double& sigma, double& epsilon, int& xparticle, int& yparticle, double& rx, double& ry, double& rz, double& ex, double& ey, double& ez) const;
void getParticleParameters(int index, double& sigma, double& epsilon, int& xparticle, int& yparticle, double& sx, double& sy, double& sz, double& ex, double& ey, double& ez) const;
/**
* Set the parameters for a particle.
*
......@@ -199,14 +198,14 @@ public:
* @param epsilon the epsilon parameter (corresponding to the well depth of the van der Waals interaction), measured in kJ/mol
* @param xparticle the index of the particle whose position defines the ellipsoid's x axis, or -1 if the ellipsoid is a sphere
* @param yparticle the index of the particle whose position defines the ellipsoid's y axis, or -1 if the ellipsoid is axially symmetric
* @param rx the radius of the ellipsoid along its x axis
* @param ry the radius of the ellipsoid along its y axis
* @param rz the radius of the ellipsoid along its z axis
* @param sx the diameter of the ellipsoid along its x axis
* @param sy the diameter of the ellipsoid along its y axis
* @param sz the diameter of the ellipsoid along its z axis
* @param ex the factor by which epsilon is scaled along the ellipsoid's x axis
* @param ey the factor by which epsilon is scaled along the ellipsoid's y axis
* @param ez the factor by which epsilon is scaled along the ellipsoid's z axis
*/
void setParticleParameters(int index, double sigma, double epsilon, int xparticle, int yparticle, double rx, double ry, double rz, double ex, double ey, double ez);
void setParticleParameters(int index, double sigma, double epsilon, int xparticle, int yparticle, double sx, double sy, double sz, double ex, double ey, double ez);
/**
* Add an interaction to the list of exceptions that should be calculated differently from other interactions. If
* epsilon is equal to 0, this will cause the interaction to be completely omitted from force and energy calculations.
......@@ -284,13 +283,13 @@ private:
class GayBerneForce::ParticleInfo {
public:
int xparticle, yparticle;
double sigma, epsilon, rx, ry, rz, ex, ey, ez;
double sigma, epsilon, sx, sy, sz, ex, ey, ez;
ParticleInfo() {
xparticle = yparticle = -1;
sigma = epsilon = rx = ry = rz = ex = ey = ez = 0.0;
sigma = epsilon = sx = sy = sz = ex = ey = ez = 0.0;
}
ParticleInfo(double sigma, double epsilon, int xparticle, int yparticle, double rx, double ry, double rz, double ex, double ey, double ez) :
sigma(sigma), epsilon(epsilon), xparticle(xparticle), yparticle(yparticle), rx(rx), ry(ry), rz(rz), ex(ex), ey(ey), ez(ez) {
ParticleInfo(double sigma, double epsilon, int xparticle, int yparticle, double sx, double sy, double sz, double ex, double ey, double ez) :
sigma(sigma), epsilon(epsilon), xparticle(xparticle), yparticle(yparticle), sx(sx), sy(sy), sz(sz), ex(ex), ey(ey), ez(ez) {
}
};
......
openmmapi/src/GayBerneForce.cpp
View file @ 505824d6
......@@ -82,36 +82,36 @@ void GayBerneForce::setSwitchingDistance(double distance) {
switchingDistance = distance;
}
int GayBerneForce::addParticle(double sigma, double epsilon, int xparticle, int yparticle, double rx, double ry, double rz, double ex, double ey, double ez) {
if (yparticle == -1 && (ry != rz || ey != ez))
int GayBerneForce::addParticle(double sigma, double epsilon, int xparticle, int yparticle, double sx, double sy, double sz, double ex, double ey, double ez) {
if (yparticle == -1 && (sy != sz || ey != ez))
throw OpenMMException("GayBerneForce: yparticle is -1 for a particle that is not axially symmetric");
if (xparticle == -1 && (rx != rz || ex != ez))
if (xparticle == -1 && (sx != sz || ex != ez))
throw OpenMMException("GayBerneForce: xparticle is -1 for a particle that is not spherical");
if (xparticle == -1 && yparticle != -1)
throw OpenMMException("GayBerneForce: xparticle cannot be -1 if yparticle is not also -1");
particles.push_back(ParticleInfo(sigma, epsilon, xparticle, yparticle, rx, ry, rz, ex, ey, ez));
particles.push_back(ParticleInfo(sigma, epsilon, xparticle, yparticle, sx, sy, sz, ex, ey, ez));
return particles.size()-1;
}
void GayBerneForce::getParticleParameters(int index, double& sigma, double& epsilon, int& xparticle, int& yparticle, double& rx, double& ry, double& rz, double& ex, double& ey, double& ez) const {
void GayBerneForce::getParticleParameters(int index, double& sigma, double& epsilon, int& xparticle, int& yparticle, double& sx, double& sy, double& sz, double& ex, double& ey, double& ez) const {
ASSERT_VALID_INDEX(index, particles);
sigma = particles[index].sigma;
epsilon = particles[index].epsilon;
xparticle = particles[index].xparticle;
yparticle = particles[index].yparticle;
rx = particles[index].rx;
ry = particles[index].ry;
rz = particles[index].rz;
sx = particles[index].sx;
sy = particles[index].sy;
sz = particles[index].sz;
ex = particles[index].ex;
ey = particles[index].ey;
ez = particles[index].ez;
}
void GayBerneForce::setParticleParameters(int index, double sigma, double epsilon, int xparticle, int yparticle, double rx, double ry, double rz, double ex, double ey, double ez) {
void GayBerneForce::setParticleParameters(int index, double sigma, double epsilon, int xparticle, int yparticle, double sx, double sy, double sz, double ex, double ey, double ez) {
ASSERT_VALID_INDEX(index, particles);
if (yparticle == -1 && (ry != rz || ey != ez))
if (yparticle == -1 && (sy != sz || ey != ez))
throw OpenMMException("GayBerneForce: yparticle is -1 for a particle that is not axially symmetric");
if (xparticle == -1 && (rx != rz || ex != ez))
if (xparticle == -1 && (sx != sz || ex != ez))
throw OpenMMException("GayBerneForce: xparticle is -1 for a particle that is not spherical");
if (xparticle == -1 && yparticle != -1)
throw OpenMMException("GayBerneForce: xparticle cannot be -1 if yparticle is not also -1");
......@@ -119,9 +119,9 @@ void GayBerneForce::setParticleParameters(int index, double sigma, double epsilo
particles[index].epsilon = epsilon;
particles[index].xparticle = xparticle;
particles[index].yparticle = yparticle;
particles[index].rx = rx;
particles[index].ry = ry;
particles[index].rz = rx;
particles[index].sx = sx;
particles[index].sy = sy;
particles[index].sz = sz;
particles[index].ex = ex;
particles[index].ey = ey;
particles[index].ez = ez;
......
platforms/reference/include/ReferenceGayBerneForce.h
View file @ 505824d6
......@@ -70,6 +70,8 @@ private:
std::vector<Matrix> A, B, G;
void computeEllipsoidFrames(const std::vector<RealVec>& positions);
void applyTorques(const std::vector<RealVec>& positions, std::vector<RealVec>& forces, const std::vector<RealVec>& torques);
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);
......@@ -134,7 +136,7 @@ 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],
return RealVec(m.v[0][0]*r[0] + m.v[1][0]*r[1] + m.v[2][0]*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]);
}
......
platforms/reference/src/SimTKReference/ReferenceGayBerneForce.cpp
View file @ 505824d6
......@@ -44,7 +44,11 @@ ReferenceGayBerneForce::ReferenceGayBerneForce(const GayBerneForce& force) {
particles.resize(numParticles);
for (int i = 0; i < numParticles; i++) {
ParticleInfo& p = particles[i];
force.getParticleParameters(i, p.sigma, p.epsilon, p.xparticle, p.yparticle, p.rx, p.ry, p.rz, p.ex, p.ey, p.ez);
double sx, sy, sz;
force.getParticleParameters(i, p.sigma, p.epsilon, p.xparticle, p.yparticle, sx, sy, sz, p.ex, p.ey, p.ez);
p.rx = 0.5*sx;
p.ry = 0.5*sy;
p.rz = 0.5*sz;
}
int numExceptions = force.getNumExceptions();
exceptions.resize(numExceptions);
......@@ -110,6 +114,10 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
ExceptionInfo& e = exceptions[i];
energy += computeOneInteraction(e.particle1, e.particle2, e.sigma, e.epsilon, positions, forces, torques, boxVectors);
}
// Apply torques.
applyTorques(positions, forces, torques);
return energy;
}
......@@ -156,7 +164,7 @@ void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<RealVec>& posit
a[2][1] = zdir[1];
a[2][2] = zdir[2];
RealVec r2(p.rx*p.rx, p.ry*p.ry, p.rz*p.rz);
RealVec e2(p.ex*p.ex, p.ey*p.ey, p.ez*p.ez);
RealVec e2(1/sqrt(p.ex), 1/sqrt(p.ey), 1/sqrt(p.ez));
for (int i = 0; i < 3; i++)
for (int j = 0; j < 3; j++) {
b[i][j] = 0;
......@@ -169,6 +177,34 @@ void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<RealVec>& posit
}
}
void ReferenceGayBerneForce::applyTorques(const vector<RealVec>& positions, vector<RealVec>& forces, const vector<RealVec>& torques) {
int numParticles = particles.size();
for (int particle = 0; particle < numParticles; particle++) {
ParticleInfo& p = particles[particle];
RealVec pos = positions[particle];
if (p.xparticle != -1) {
// Apply a force to the x particle.
RealVec dx = positions[p.xparticle]-pos;
double dx2 = dx.dot(dx);
RealVec f = torques[particle].cross(dx)/dx2;
forces[p.xparticle] += f;
forces[particle] -= f;
if (p.yparticle != -1) {
// Apply a force to the y particle. This is based on the component of the torque
// that was not already applied to the x particle.
RealVec dy = positions[p.yparticle]-pos;
double dy2 = dy.dot(dy);
RealVec torque = dx*(torques[particle].dot(dx)/dx2);
f = torque.cross(dy)/dy2;
forces[p.yparticle] += f;
forces[particle] -= f;
}
}
}
}
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.
......@@ -195,8 +231,6 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
// Estimate the distance between the ellipsoids and compute the first terms needed for the energy.
ParticleInfo& p1 = particles[particle1];
ParticleInfo& p2 = particles[particle2];
RealOpenMM sigma12 = 1/SQRT(0.5*drUnit.dot(G12inv*drUnit));
RealOpenMM h12 = r - sigma12;
RealOpenMM rho = sigma/(h12+sigma);
......@@ -224,11 +258,12 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
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);
RealVec dudq = (kappa*G[particle]).cross(kappa*(temp*dUSLJdr));
RealVec dchidq = (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);
ParticleInfo& p = particles[particle];
RealVec scale = RealVec(p.rx*p.rx, p.ry*p.ry, p.rz*p.rz)*(-0.5*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] -
......@@ -280,7 +315,7 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
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;
torques[particle] -= torque;
}
return u*eta*chi;
}
tests/TestGayBerneForce.h
View file @ 505824d6
......@@ -64,7 +64,7 @@ void testPointParticles() {
init_gen_rand(0, sfmt);
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
gb->addParticle(sigma, epsilon, -1, -1, sigma/2, sigma/2, sigma/2, 1, 1, 1);
gb->addParticle(sigma, epsilon, -1, -1, sigma, sigma, sigma, 1, 1, 1);
nb->addParticle(0, sigma, epsilon);
positions.push_back(Vec3(2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt), 2.0*genrand_real2(sfmt)));
}
......@@ -91,10 +91,10 @@ void testEnergyScales() {
system.addParticle(1.0);
GayBerneForce* gb = new GayBerneForce();
system.addForce(gb);
gb->addParticle(sigma, epsilon, 1, 2, sigma/2, sigma/2, sigma/2, 1.1, 1.5, 1.8);
gb->addParticle(sigma, epsilon, 1, 2, sigma, sigma, sigma, 1.1, 1.5, 1.8);
gb->addParticle(1, 0, -1, -1, 1, 1, 1, 1, 1, 1);
gb->addParticle(1, 0, -1, -1, 1, 1, 1, 1, 1, 1);
gb->addParticle(sigma, epsilon, 4, 5, sigma/2, sigma/2, sigma/2, 1.2, 1.6, 1.7);
gb->addParticle(sigma, epsilon, 4, 5, sigma, sigma, sigma, 1.2, 1.6, 1.7);
gb->addParticle(1, 0, -1, -1, 1, 1, 1, 1, 1, 1);
gb->addParticle(1, 0, -1, -1, 1, 1, 1, 1, 1, 1);
vector<Vec3> positions(6);
......@@ -113,7 +113,7 @@ void testEnergyScales() {
double expectedEnergy = 4*epsilon*(pow(sigma, 12.0)-pow(sigma, 6.0));
double expectedForce = 4*epsilon*(12*pow(sigma, 12.0)-6*pow(sigma, 6.0));
double expectedScale = pow(2.0/(1.1*1.1+1.2*1.2), 2.0);
double expectedScale = pow(2.0/(1/sqrt(1.1) + 1/sqrt(1.2)), 2.0);
State state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(expectedForce*expectedScale, 0, 0), state.getForces()[3], 1e-5);
......@@ -121,7 +121,7 @@ void testEnergyScales() {
positions[4] = Vec3(1, 1, 0);
positions[5] = Vec3(0, 2, 0);
context.setPositions(positions);
expectedScale = pow(2.0/(1.5*1.5+1.6*1.6), 2.0);
expectedScale = pow(2.0/(1/sqrt(1.5) + 1/sqrt(1.6)), 2.0);
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(0, expectedForce*expectedScale, 0), state.getForces()[3], 1e-5);
......@@ -129,7 +129,7 @@ void testEnergyScales() {
positions[4] = Vec3(1, 1, 0);
positions[5] = Vec3(0, 1, 1);
context.setPositions(positions);
expectedScale = pow(2.0/(1.5*1.5+1.7*1.7), 2.0);
expectedScale = pow(2.0/(1/sqrt(1.5) + 1/sqrt(1.7)), 2.0);
state = context.getState(State::Forces | State::Energy);
ASSERT_EQUAL_TOL(expectedEnergy*expectedScale, state.getPotentialEnergy(), 1e-5);
ASSERT_EQUAL_VEC(Vec3(0, expectedForce*expectedScale, 0), state.getForces()[3], 1e-5);
......@@ -154,7 +154,7 @@ void testEnergyConservation() {
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(0.2, 10.0, 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));
......@@ -166,22 +166,19 @@ void testEnergyConservation() {
}
}
}
VerletIntegrator integ(0.001);
VerletIntegrator integ(0.0005);
Context context(system, integ, platform);
context.setPositions(positions);
context.setVelocitiesToTemperature(300.0);
double initialEnergy;
for (int i = 0; i < 100; i++) {
integ.step(5);
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]);
double energy = state.getPotentialEnergy()+state.getKineticEnergy();
if (i == 0)
initialEnergy = energy;
else
ASSERT_EQUAL_TOL(initialEnergy, energy, 1e-3);
}
}
......
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