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Commit 52c04559 authored by Peter Eastman's avatar Peter Eastman
Browse files

Improved how matrices get calculated for reference C-SHAKE algorithm.

parent b6f21610
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Showing with 86 additions and 69 deletions
platforms/reference/src/ReferenceKernels.cpp
View file @ 52c04559
......@@ -609,7 +609,7 @@ void ReferenceIntegrateVerletStepKernel::execute(OpenMMContextImpl& context, con
delete constraints;
}
dynamics = new ReferenceVerletDynamics(context.getSystem().getNumParticles(), static_cast<RealOpenMM>(stepSize) );
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, (RealOpenMM)integrator.getConstraintTolerance());
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevStepSize = stepSize;
}
......@@ -668,7 +668,7 @@ void ReferenceIntegrateLangevinStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(tau),
static_cast<RealOpenMM>(temperature) );
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, (RealOpenMM)integrator.getConstraintTolerance());
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......@@ -728,7 +728,7 @@ void ReferenceIntegrateBrownianStepKernel::execute(OpenMMContextImpl& context, c
static_cast<RealOpenMM>(stepSize),
static_cast<RealOpenMM>(friction),
static_cast<RealOpenMM>(temperature) );
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, (RealOpenMM)integrator.getConstraintTolerance());
constraints = new ReferenceRigidShakeAlgorithm(context.getSystem().getNumParticles(), numConstraints, constraintIndices, constraintDistances, masses, (RealOpenMM)integrator.getConstraintTolerance());
dynamics->setReferenceConstraintAlgorithm(constraints);
prevTemp = temperature;
prevFriction = friction;
......
platforms/reference/src/SimTKReference/ReferenceRigidShakeAlgorithm.cpp
View file @ 52c04559
......@@ -57,6 +57,7 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms,
int numberOfConstraints,
int** atomIndices,
RealOpenMM* distance,
RealOpenMM* masses,
RealOpenMM tolerance){
// ---------------------------------------------------------------------------------------
......@@ -158,7 +159,88 @@ ReferenceRigidShakeAlgorithm::ReferenceRigidShakeAlgorithm( int numberOfAtoms,
atomConstraints[atom2->first].erase(*atom1);
atomConstraints[*atom1].clear();
}
// Compute the constraint coupling matrix for this cluster.
const vector<int>& cluster = _rigidClusters[i];
unsigned int size = cluster.size();
Array2D<double> matrix(size, size);
for (int j = 0; j < (int)size; j++) {
for (int k = 0; k < (int)size; k++) {
double scale;
int atomj0 = _atomIndices[cluster[j]][0];
int atomj1 = _atomIndices[cluster[j]][1];
int atomk0 = _atomIndices[cluster[k]][0];
int atomk1 = _atomIndices[cluster[k]][1];
RealOpenMM invMass0 = one/masses[atomj0];
RealOpenMM invMass1 = one/masses[atomj1];
int atoma, atomb;
if (atomj0 == atomk0) {
atoma = atomj1;
atomb = atomk1;
scale = invMass0/(invMass0+invMass1);
}
else if (atomj1 == atomk1) {
atoma = atomj0;
atomb = atomk0;
scale = invMass1/(invMass0+invMass1);
}
else if (atomj0 == atomk1) {
atoma = atomj1;
atomb = atomk0;
scale = invMass0/(invMass0+invMass1);
}
else if (atomj1 == atomk0) {
atoma = atomj0;
atomb = atomk1;
scale = invMass1/(invMass0+invMass1);
}
else {
matrix[j][k] = 0.0;
continue; // These constraints are not connected.
}
// Find the third constraint forming a triangle with these two.
for (int m = 0; m < size; m++) {
int other = cluster[m];
if ((_atomIndices[other][0] == atoma && _atomIndices[other][1] == atomb) || (_atomIndices[other][0] == atomb && _atomIndices[other][1] == atoma)) {
double d1 = _distance[cluster[j]];
double d2 = _distance[cluster[k]];
double d3 = _distance[other];
matrix[j][k] = scale*(d1*d1+d2*d2-d3*d3)/(2.0*d1*d2);
break;
}
}
}
matrix[j][j] = 1.0;
}
// Invert it using SVD.
Array2D<double> u, v;
Array1D<double> w;
SVD<double> svd(matrix);
svd.getU(u);
svd.getV(v);
svd.getSingularValues(w);
double singularValueCutoff = 0.01*w[0];
for (int j = 0; j < (int)size; j++)
w[j] = (w[j] < singularValueCutoff ? 0.0 : 1.0/w[j]);
for (int j = 0; j < (int)size; j++) {
for (int k = 0; k < (int)size; k++) {
matrix[j][k] = 0.0;
for (int m = 0; m < (int)size; m++)
matrix[j][k] += v[j][m]*w[m]*u[k][m];
}
}
// Record the inverted matrix.
_matrices.push_back(SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray(constraints.size(), constraints.size(), NULL, false, 0.0, ""));
for (int j = 0; j < (int)size; j++)
for (int k = 0; k < (int)size; k++)
_matrices[i][j][k] = (RealOpenMM)matrix[j][k]*_distance[cluster[k]]/_distance[cluster[j]];
}
}
......@@ -341,71 +423,6 @@ int ReferenceRigidShakeAlgorithm::apply( int numberOfAtoms, RealOpenMM** atomCoo
int atomJ = _atomIndices[ii][1];
reducedMasses[ii] = half/( inverseMasses[atomI] + inverseMasses[atomJ] );
}
for (unsigned int i = 0; i < _rigidClusters.size(); i++) {
// Compute the constraint coupling matrix for this cluster.
const vector<int>& cluster = _rigidClusters[i];
unsigned int size = cluster.size();
vector<Vec3> r(size);
for (unsigned int j = 0; j < cluster.size(); j++) {
int atom1 = _atomIndices[cluster[j]][0];
int atom2 = _atomIndices[cluster[j]][1];
r[j] = Vec3(atomCoordinates[atom1][0]-atomCoordinates[atom2][0],
atomCoordinates[atom1][1]-atomCoordinates[atom2][1],
atomCoordinates[atom1][2]-atomCoordinates[atom2][2]);
double invLength = 1.0/sqrt(r[j].dot(r[j]));
r[j][0] *= invLength;
r[j][1] *= invLength;
r[j][2] *= invLength;
}
Array2D<double> matrix(size, size);
for (int j = 0; j < (int)size; j++) {
for (int k = 0; k < (int)size; k++) {
double dot;
int atomj0 = _atomIndices[cluster[j]][0];
int atomj1 = _atomIndices[cluster[j]][1];
int atomk0 = _atomIndices[cluster[k]][0];
int atomk1 = _atomIndices[cluster[k]][1];
if (atomj0 == atomk0)
dot = r[j].dot(r[k])*inverseMasses[atomj0]/(inverseMasses[atomj0]+inverseMasses[atomj1]);
else if (atomj1 == atomk1)
dot = r[j].dot(r[k])*inverseMasses[atomj1]/(inverseMasses[atomj0]+inverseMasses[atomj1]);
else if (atomj0 == atomk1)
dot = -r[j].dot(r[k])*inverseMasses[atomj0]/(inverseMasses[atomj0]+inverseMasses[atomj1]);
else if (atomj1 == atomk0)
dot = -r[j].dot(r[k])*inverseMasses[atomj1]/(inverseMasses[atomj0]+inverseMasses[atomj1]);
else
dot = 0.0;
matrix[j][k] = dot;
}
matrix[j][j] = 1.0;
}
// Invert it using SVD.
Array2D<double> u, v;
Array1D<double> w;
SVD<double> svd(matrix);
svd.getU(u);
svd.getV(v);
svd.getSingularValues(w);
double singularValueCutoff = 0.01*w[0];
for (int j = 0; j < (int)size; j++)
w[j] = (w[j] < singularValueCutoff ? 0.0 : 1.0/w[j]);
for (int j = 0; j < (int)size; j++) {
for (int k = 0; k < (int)size; k++) {
matrix[j][k] = 0.0;
for (int m = 0; m < (int)size; m++)
matrix[j][k] += v[j][m]*w[m]*u[k][m];
}
}
// Record the inverted matrix.
for (int j = 0; j < (int)size; j++)
for (int k = 0; k < (int)size; k++)
_matrices[i][j][k] = (RealOpenMM)matrix[j][k]*_distance[cluster[k]]/_distance[cluster[j]];
}
}
// setup: r_ij for each (i,j) constraint
......
platforms/reference/src/SimTKReference/ReferenceRigidShakeAlgorithm.h
View file @ 52c04559
......@@ -64,7 +64,7 @@ class ReferenceRigidShakeAlgorithm : public ReferenceConstraintAlgorithm {
--------------------------------------------------------------------------------------- */
ReferenceRigidShakeAlgorithm( int numberOfAtoms, int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM tolerance );
ReferenceRigidShakeAlgorithm( int numberOfAtoms, int numberOfConstraints, int** atomIndices, RealOpenMM* distance, RealOpenMM* masses, RealOpenMM tolerance );
/**---------------------------------------------------------------------------------------
......
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