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Commit 047934e2 authored by Rafal P. Wiewiora's avatar Rafal P. Wiewiora
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Merge remote-tracking branch 'upstream/master'

parents ce3a5dc0 d12c9bd1
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platforms/reference/src/SimTKReference/ReferenceBondIxn.cpp
View file @ 047934e2
......@@ -39,13 +39,6 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceBondIxn::ReferenceBondIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceBondIxn::ReferenceBondIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -55,13 +48,6 @@ ReferenceBondIxn::ReferenceBondIxn() {
--------------------------------------------------------------------------------------- */
ReferenceBondIxn::~ReferenceBondIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceBondIxn::~ReferenceBondIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -76,15 +62,9 @@ ReferenceBondIxn::~ReferenceBondIxn() {
--------------------------------------------------------------------------------------- */
void ReferenceBondIxn::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::calculateBondIxn";
// ---------------------------------------------------------------------------------------
void ReferenceBondIxn::calculateBondIxn(int* atomIndices, vector<Vec3>& atomCoordinates,
double* parameters, vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
}
/**---------------------------------------------------------------------------------------
......@@ -102,67 +82,26 @@ ReferenceBondIxn::~ReferenceBondIxn() {
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getNormedDotProduct(RealOpenMM* vector1, RealOpenMM* vector2,
int hasREntry = 0) {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::getNormedDotProduct";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
// for angles near pi, double is required due to the 'steepness' of acos()
// in this regime.
//#define USE_DOUBLE_FOR_NORMED_DOT_PRODUCT
double ReferenceBondIxn::getNormedDotProduct(double* vector1, double* vector2,
int hasREntry = 0) {
#if defined USE_DOUBLE_FOR_NORMED_DOT_PRODUCT
double v1D[3];
double v2D[3];
v1D[0] = static_cast<double>(vector1[0]);
v1D[1] = static_cast<double>(vector1[1]);
v1D[2] = static_cast<double>(vector1[2]);
v2D[0] = static_cast<double>(vector2[0]);
v2D[1] = static_cast<double>(vector2[1]);
v2D[2] = static_cast<double>(vector2[2]);
double dotProductD = DOT3(v1D, v2D);
if (dotProductD != 0.0) {
if (hasREntry) {
dotProductD /= (static_cast<double>(vector1[ReferenceForce::RIndex])*static_cast<double>(vector2[ReferenceForce::RIndex]));
} else {
double norm1 = DOT3(v1D, v1D);
double norm2 = DOT3(v2D, v2D);
dotProductD /= sqrt(norm1*norm2);
}
}
RealOpenMM dotProduct = static_cast<RealOpenMM>(dotProductD);
#else
RealOpenMM dotProduct = DOT3(vector1, vector2);
if (dotProduct != zero) {
double dotProduct = DOT3(vector1, vector2);
if (dotProduct != 0.0) {
if (hasREntry) {
dotProduct /= (vector1[ReferenceForce::RIndex]*vector2[ReferenceForce::RIndex]);
} else {
RealOpenMM norm1 = DOT3(vector1, vector1);
RealOpenMM norm2 = DOT3(vector2, vector2);
dotProduct /= SQRT(norm1*norm2);
double norm1 = DOT3(vector1, vector1);
double norm2 = DOT3(vector2, vector2);
dotProduct /= sqrt(norm1*norm2);
}
}
#endif
#undef USE_DOUBLE_FOR_NORMED_DOT_PRODUCT
// clamp dot product to [-1,1]
if (dotProduct > one) {
dotProduct = one;
} else if (dotProduct < -one) {
dotProduct = -one;
if (dotProduct > 1.0) {
dotProduct = 1.0;
} else if (dotProduct < -1.0) {
dotProduct = -1.0;
}
return dotProduct;
......@@ -183,35 +122,26 @@ RealOpenMM ReferenceBondIxn::getNormedDotProduct(RealOpenMM* vector1, RealOpenMM
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors(RealOpenMM* vector1, RealOpenMM* vector2,
RealOpenMM* outputDotProduct = NULL,
int hasREntry = 0) {
double ReferenceBondIxn::getAngleBetweenTwoVectors(double* vector1, double* vector2,
double* outputDotProduct = NULL,
int hasREntry = 0) {
// ---------------------------------------------------------------------------------------
// get dot product betweenn vectors and then angle
// static const std::string methodName = "\nReferenceBondIxn::getAngle";
double dotProduct = getNormedDotProduct(vector1, vector2, hasREntry);
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
// get dot product betweenn vectors and then angle
RealOpenMM dotProduct = getNormedDotProduct(vector1, vector2, hasREntry);
RealOpenMM angle;
if (dotProduct > (RealOpenMM) 0.99 || dotProduct < (RealOpenMM) -0.99) {
double angle;
if (dotProduct > 0.99 || dotProduct < -0.99) {
// We're close to the singularity in acos(), so take the cross product and use asin() instead.
RealOpenMM cross[3];
double cross[3];
SimTKOpenMMUtilities::crossProductVector3(vector1, vector2, cross);
RealOpenMM scale = DOT3(vector1, vector1)*DOT3(vector2, vector2);
angle = ASIN(SQRT(DOT3(cross, cross)/scale));
if (dotProduct < zero)
angle = (RealOpenMM) (M_PI-angle);
double scale = DOT3(vector1, vector1)*DOT3(vector2, vector2);
angle = asin(sqrt(DOT3(cross, cross)/scale));
if (dotProduct < 0.0)
angle = M_PI-angle;
} else {
angle = ACOS(dotProduct);
angle = acos(dotProduct);
}
if (outputDotProduct) {
......@@ -240,29 +170,20 @@ RealOpenMM ReferenceBondIxn::getAngleBetweenTwoVectors(RealOpenMM* vector1, Real
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors(RealOpenMM* vector1,
RealOpenMM* vector2,
RealOpenMM* vector3,
RealOpenMM** outputCrossProduct = NULL,
RealOpenMM* cosineOfAngle = NULL,
RealOpenMM* signVector = NULL,
RealOpenMM* signOfAngle = NULL,
int hasREntry = 0) {
// ---------------------------------------------------------------------------------------
// static const std::string methodName = "\nReferenceBondIxn::getDihedralAngleBetweenThreeVectors";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
RealOpenMM tempVectors[6] = { zero, zero, zero, zero, zero, zero };
double ReferenceBondIxn::getDihedralAngleBetweenThreeVectors(double* vector1,
double* vector2,
double* vector3,
double** outputCrossProduct = NULL,
double* cosineOfAngle = NULL,
double* signVector = NULL,
double* signOfAngle = NULL,
int hasREntry = 0) {
// ---------------------------------------------------------------------------------------
double tempVectors[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 };
// get cross products between vectors and then angle between cross product vectors
RealOpenMM* crossProduct[2];
double* crossProduct[2];
if (outputCrossProduct) {
crossProduct[0] = outputCrossProduct[0];
crossProduct[1] = outputCrossProduct[1];
......@@ -274,13 +195,13 @@ RealOpenMM ReferenceBondIxn::getDihedralAngleBetweenThreeVectors(RealOpenMM* ve
SimTKOpenMMUtilities::crossProductVector3(vector1, vector2, crossProduct[0]);
SimTKOpenMMUtilities::crossProductVector3(vector2, vector3, crossProduct[1]);
RealOpenMM angle = getAngleBetweenTwoVectors(crossProduct[0], crossProduct[1], cosineOfAngle, 0);
double angle = getAngleBetweenTwoVectors(crossProduct[0], crossProduct[1], cosineOfAngle, 0);
// take care of sign of angle
if (signVector) {
RealOpenMM dotProduct = DOT3(signVector, crossProduct[1]);
RealOpenMM sign = dotProduct < zero ? -one : one;
double dotProduct = DOT3(signVector, crossProduct[1]);
double sign = dotProduct < 0.0 ? -1.0 : 1.0;
if (signOfAngle) {
*signOfAngle = sign;
}
......
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ 047934e2
......@@ -47,8 +47,8 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceBrownianDynamics::ReferenceBrownianDynamics(int numberOfAtoms,
RealOpenMM deltaT, RealOpenMM friction,
RealOpenMM temperature) :
double deltaT, double friction,
double temperature) :
ReferenceDynamics(numberOfAtoms, deltaT, temperature), friction(friction) {
if (friction <= 0) {
......@@ -67,13 +67,6 @@ ReferenceBrownianDynamics::ReferenceBrownianDynamics(int numberOfAtoms,
--------------------------------------------------------------------------------------- */
ReferenceBrownianDynamics::~ReferenceBrownianDynamics() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceBrownianDynamics::~ReferenceBrownianDynamics";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -84,14 +77,7 @@ ReferenceBrownianDynamics::~ReferenceBrownianDynamics() {
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceBrownianDynamics::getFriction() const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceBrownianDynamics::getFriction";
// ---------------------------------------------------------------------------------------
double ReferenceBrownianDynamics::getFriction() const {
return friction;
}
......@@ -108,18 +94,9 @@ RealOpenMM ReferenceBrownianDynamics::getFriction() const {
--------------------------------------------------------------------------------------- */
void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceBrownianDynamics::update";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities,
vector<Vec3>& forces, vector<double>& masses, double tolerance) {
// first-time-through initialization
......@@ -128,21 +105,21 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
// invert masses
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == zero)
inverseMasses[ii] = zero;
if (masses[ii] == 0.0)
inverseMasses[ii] = 0.0;
else
inverseMasses[ii] = one/masses[ii];
inverseMasses[ii] = 1.0/masses[ii];
}
}
// Perform the integration.
const RealOpenMM noiseAmplitude = static_cast<RealOpenMM>(sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction()));
const RealOpenMM forceScale = getDeltaT()/getFriction();
const double noiseAmplitude = sqrt(2.0*BOLTZ*getTemperature()*getDeltaT()/getFriction());
const double forceScale = getDeltaT()/getFriction();
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
xPrime[i][j] = atomCoordinates[i][j] + forceScale*inverseMasses[i]*forces[i][j] + noiseAmplitude*SQRT(inverseMasses[i])*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
xPrime[i][j] = atomCoordinates[i][j] + forceScale*inverseMasses[i]*forces[i][j] + noiseAmplitude*sqrt(inverseMasses[i])*SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
}
}
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
......@@ -151,9 +128,9 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
// Update the positions and velocities.
RealOpenMM velocityScale = static_cast<RealOpenMM>(1.0/getDeltaT());
double velocityScale = 1.0/getDeltaT();
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
if (masses[i] != 0.0)
for (int j = 0; j < 3; ++j) {
velocities[i][j] = velocityScale*(xPrime[i][j] - atomCoordinates[i][j]);
atomCoordinates[i][j] = xPrime[i][j];
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 047934e2
/* Portions copyright (c) 2006-2015 Stanford University and Simbios.
/* Portions copyright (c) 2006-2017 Stanford University and Simbios.
* Contributors: Peter Eastman, Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
......@@ -38,49 +38,13 @@
using namespace OpenMM;
using namespace std;
// This class extracts columns from the inverse matrix one at a time. It is done in parallel,
// since this can be very slow.
class ExtractMatrixTask : public ThreadPool::Task {
public:
ExtractMatrixTask(int numConstraints, vector<vector<pair<int, RealOpenMM> > >& transposedMatrix, const vector<RealOpenMM>& distance, RealOpenMM elementCutoff,
const int* qRowStart, const int* qColIndex, const int* rRowStart, const int* rColIndex, const double* qValue, const double* rValue) :
numConstraints(numConstraints), transposedMatrix(transposedMatrix), distance(distance), elementCutoff(elementCutoff), qRowStart(qRowStart), qColIndex(qColIndex),
rRowStart(rRowStart), rColIndex(rColIndex), qValue(qValue), rValue(rValue) {
}
void execute(ThreadPool& pool, int threadIndex) {
vector<double> rhs(numConstraints);
for (int i = threadIndex; i < numConstraints; i += pool.getNumThreads()) {
// Extract column i of the inverse matrix.
for (int j = 0; j < numConstraints; j++)
rhs[j] = (i == j ? 1.0 : 0.0);
QUERN_multiply_with_q_transpose(numConstraints, qRowStart, qColIndex, qValue, &rhs[0]);
QUERN_solve_with_r(numConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
for (int j = 0; j < numConstraints; j++) {
double value = rhs[j]*distance[i]/distance[j];
if (FABS((RealOpenMM) value) > elementCutoff)
transposedMatrix[i].push_back(pair<int, RealOpenMM>(j, (RealOpenMM) value));
}
}
}
private:
int numConstraints;
vector<vector<pair<int, RealOpenMM> > >& transposedMatrix;
const vector<RealOpenMM>& distance;
RealOpenMM elementCutoff;
const int *qRowStart, *qColIndex, *rRowStart, *rColIndex;
const double *qValue, *rValue;
};
ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
int numberOfConstraints,
const vector<pair<int, int> >& atomIndices,
const vector<RealOpenMM>& distance,
vector<RealOpenMM>& masses,
const vector<double>& distance,
vector<double>& masses,
vector<AngleInfo>& angles,
RealOpenMM elementCutoff) {
double elementCutoff) {
_numberOfConstraints = numberOfConstraints;
_elementCutoff = elementCutoff;
_atomIndices = atomIndices;
......@@ -116,8 +80,8 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
int atomj1 = _atomIndices[j].second;
int atomk0 = _atomIndices[k].first;
int atomk1 = _atomIndices[k].second;
RealOpenMM invMass0 = 1/masses[atomj0];
RealOpenMM invMass1 = 1/masses[atomj1];
double invMass0 = 1/masses[atomj0];
double invMass1 = 1/masses[atomj1];
int atoma, atomb, atomc;
if (atomj0 == atomk0) {
atoma = atomj1;
......@@ -192,18 +156,36 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
double *qValue, *rValue;
QUERN_compute_qr(numberOfConstraints, numberOfConstraints, &matrixRowStart[0], &matrixColIndex[0], &matrixValue[0], NULL,
&qRowStart, &qColIndex, &qValue, &rRowStart, &rColIndex, &rValue);
vector<vector<pair<int, RealOpenMM> > > transposedMatrix(numberOfConstraints);
vector<vector<pair<int, double> > > transposedMatrix(numberOfConstraints);
_matrix.resize(numberOfConstraints);
// Extract columns from the inverse matrix one at a time. It is done in parallel,
// since this can be very slow.
ThreadPool threads;
ExtractMatrixTask task(numberOfConstraints, transposedMatrix, _distance, _elementCutoff, qRowStart, qColIndex, rRowStart, rColIndex, qValue, rValue);
threads.execute(task);
threads.execute([&] (ThreadPool& pool, int threadIndex) {
vector<double> rhs(numberOfConstraints);
for (int i = threadIndex; i < numberOfConstraints; i += pool.getNumThreads()) {
// Extract column i of the inverse matrix.
for (int j = 0; j < numberOfConstraints; j++)
rhs[j] = (i == j ? 1.0 : 0.0);
QUERN_multiply_with_q_transpose(numberOfConstraints, qRowStart, qColIndex, qValue, &rhs[0]);
QUERN_solve_with_r(numberOfConstraints, rRowStart, rColIndex, rValue, &rhs[0], &rhs[0]);
for (int j = 0; j < numberOfConstraints; j++) {
double value = rhs[j]*distance[i]/distance[j];
if (fabs(value) > elementCutoff)
transposedMatrix[i].push_back(pair<int, double>(j, value));
}
}
});
threads.waitForThreads();
// For purposes of thread safety we extracted the matrix in transposed form, so we need to transpose it again.
for (int i = 0; i < numberOfConstraints; i++) {
for (int j = 0; j < transposedMatrix[i].size(); j++) {
pair<int, RealOpenMM> value = transposedMatrix[i][j];
pair<int, double> value = transposedMatrix[i][j];
_matrix[value.first].push_back(make_pair(i, value.second));
}
}
......@@ -232,25 +214,25 @@ void ReferenceCCMAAlgorithm::setMaximumNumberOfIterations(int maximumNumberOfIte
_maximumNumberOfIterations = maximumNumberOfIterations;
}
void ReferenceCCMAAlgorithm::apply(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
void ReferenceCCMAAlgorithm::apply(vector<Vec3>& atomCoordinates,
vector<Vec3>& atomCoordinatesP,
vector<double>& inverseMasses, double tolerance) {
applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false, tolerance);
}
void ReferenceCCMAAlgorithm::applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
void ReferenceCCMAAlgorithm::applyToVelocities(std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<double>& inverseMasses, double tolerance) {
applyConstraints(atomCoordinates, velocities, inverseMasses, true, tolerance);
}
void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses, bool constrainingVelocities, RealOpenMM tolerance) {
void ReferenceCCMAAlgorithm::applyConstraints(vector<Vec3>& atomCoordinates,
vector<Vec3>& atomCoordinatesP,
vector<double>& inverseMasses, bool constrainingVelocities, double tolerance) {
// temp arrays
vector<RealVec>& r_ij = _r_ij;
RealOpenMM* d_ij2 = _d_ij2;
RealOpenMM* reducedMasses = _reducedMasses;
vector<Vec3>& r_ij = _r_ij;
double* d_ij2 = _d_ij2;
double* reducedMasses = _reducedMasses;
// calculate reduced masses on 1st pass
......@@ -271,33 +253,33 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
r_ij[ii] = atomCoordinates[atomI] - atomCoordinates[atomJ];
d_ij2[ii] = r_ij[ii].dot(r_ij[ii]);
}
RealOpenMM lowerTol = 1-2*tolerance+tolerance*tolerance;
RealOpenMM upperTol = 1+2*tolerance+tolerance*tolerance;
double lowerTol = 1-2*tolerance+tolerance*tolerance;
double upperTol = 1+2*tolerance+tolerance*tolerance;
// main loop
int iterations = 0;
int numberConverged = 0;
vector<RealOpenMM> constraintDelta(_numberOfConstraints);
vector<RealOpenMM> tempDelta(_numberOfConstraints);
vector<double> constraintDelta(_numberOfConstraints);
vector<double> tempDelta(_numberOfConstraints);
while (iterations < getMaximumNumberOfIterations()) {
numberConverged = 0;
for (int ii = 0; ii < _numberOfConstraints; ii++) {
int atomI = _atomIndices[ii].first;
int atomJ = _atomIndices[ii].second;
RealVec rp_ij = atomCoordinatesP[atomI] - atomCoordinatesP[atomJ];
Vec3 rp_ij = atomCoordinatesP[atomI] - atomCoordinatesP[atomJ];
if (constrainingVelocities) {
RealOpenMM rrpr = rp_ij.dot(r_ij[ii]);
double rrpr = rp_ij.dot(r_ij[ii]);
constraintDelta[ii] = -2*reducedMasses[ii]*rrpr/d_ij2[ii];
if (fabs(constraintDelta[ii]) <= tolerance)
numberConverged++;
}
else {
RealOpenMM rp2 = rp_ij.dot(rp_ij);
RealOpenMM dist2 = _distance[ii]*_distance[ii];
RealOpenMM diff = dist2 - rp2;
double rp2 = rp_ij.dot(rp_ij);
double dist2 = _distance[ii]*_distance[ii];
double diff = dist2 - rp2;
constraintDelta[ii] = 0;
RealOpenMM rrpr = DOT3(rp_ij, r_ij[ii]);
double rrpr = DOT3(rp_ij, r_ij[ii]);
constraintDelta[ii] = reducedMasses[ii]*diff/rrpr;
if (rp2 >= lowerTol*dist2 && rp2 <= upperTol*dist2)
numberConverged++;
......@@ -309,9 +291,9 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
if (_matrix.size() > 0) {
for (int i = 0; i < _numberOfConstraints; i++) {
RealOpenMM sum = 0.0;
double sum = 0.0;
for (int j = 0; j < (int) _matrix[i].size(); j++) {
pair<int, RealOpenMM> element = _matrix[i][j];
pair<int, double> element = _matrix[i][j];
sum += element.second*constraintDelta[element.first];
}
tempDelta[i] = sum;
......@@ -321,13 +303,13 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
for (int ii = 0; ii < _numberOfConstraints; ii++) {
int atomI = _atomIndices[ii].first;
int atomJ = _atomIndices[ii].second;
RealVec dr = r_ij[ii]*constraintDelta[ii];
Vec3 dr = r_ij[ii]*constraintDelta[ii];
atomCoordinatesP[atomI] += dr*inverseMasses[atomI];
atomCoordinatesP[atomJ] -= dr*inverseMasses[atomJ];
}
}
}
const vector<vector<pair<int, RealOpenMM> > >& ReferenceCCMAAlgorithm::getMatrix() const {
const vector<vector<pair<int, double> > >& ReferenceCCMAAlgorithm::getMatrix() const {
return _matrix;
}
platforms/reference/src/SimTKReference/ReferenceCMAPTorsionIxn.cpp
View file @ 047934e2
......@@ -34,12 +34,12 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceCMAPTorsionIxn::ReferenceCMAPTorsionIxn(const vector<vector<vector<RealOpenMM> > >& coeff,
ReferenceCMAPTorsionIxn::ReferenceCMAPTorsionIxn(const vector<vector<vector<double> > >& coeff,
const vector<int>& torsionMaps, const vector<vector<int> >& torsionIndices) :
coeff(coeff), torsionMaps(torsionMaps), torsionIndices(torsionIndices), usePeriodic(false) {
}
void ReferenceCMAPTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCMAPTorsionIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -59,7 +59,7 @@ void ReferenceCMAPTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateIxn(vector<RealVec>& atomCoordinates, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
void ReferenceCMAPTorsionIxn::calculateIxn(vector<Vec3>& atomCoordinates, vector<Vec3>& forces, double* totalEnergy) const {
for (unsigned int i = 0; i < torsionMaps.size(); i++)
calculateOneIxn(i, atomCoordinates, forces, totalEnergy);
}
......@@ -75,8 +75,8 @@ void ReferenceCMAPTorsionIxn::calculateIxn(vector<RealVec>& atomCoordinates, vec
--------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<Vec3>& atomCoordinates, vector<Vec3>& forces,
double* totalEnergy) const {
int map = torsionMaps[index];
int a1 = torsionIndices[index][0];
int a2 = torsionIndices[index][1];
......@@ -89,8 +89,8 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
// Compute deltas between the various atoms involved.
RealOpenMM deltaA[3][ReferenceForce::LastDeltaRIndex];
RealOpenMM deltaB[3][ReferenceForce::LastDeltaRIndex];
double deltaA[3][ReferenceForce::LastDeltaRIndex];
double deltaB[3][ReferenceForce::LastDeltaRIndex];
if (usePeriodic) {
ReferenceForce::getDeltaRPeriodic(atomCoordinates[a2], atomCoordinates[a1], boxVectors, deltaA[0]);
ReferenceForce::getDeltaRPeriodic(atomCoordinates[a2], atomCoordinates[a3], boxVectors, deltaA[1]);
......@@ -110,40 +110,40 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
// Visual Studio complains if crossProduct declared as 'crossProduct[2][3]'
RealOpenMM crossProductMemory[12];
RealOpenMM* cpA[2];
double crossProductMemory[12];
double* cpA[2];
cpA[0] = crossProductMemory;
cpA[1] = crossProductMemory + 3;
RealOpenMM* cpB[2];
double* cpB[2];
cpB[0] = crossProductMemory + 6;
cpB[1] = crossProductMemory + 9;
// Compute the dihedral angles.
RealOpenMM dotDihedral;
RealOpenMM signOfAngle;
RealOpenMM angleA = getDihedralAngleBetweenThreeVectors(deltaA[0], deltaA[1], deltaA[2],
double dotDihedral;
double signOfAngle;
double angleA = getDihedralAngleBetweenThreeVectors(deltaA[0], deltaA[1], deltaA[2],
cpA, &dotDihedral, deltaA[0], &signOfAngle, 1);
RealOpenMM angleB = getDihedralAngleBetweenThreeVectors(deltaB[0], deltaB[1], deltaB[2],
double angleB = getDihedralAngleBetweenThreeVectors(deltaB[0], deltaB[1], deltaB[2],
cpB, &dotDihedral, deltaB[0], &signOfAngle, 1);
angleA = fmod(angleA+2.0*M_PI, 2.0*M_PI);
angleB = fmod(angleB+2.0*M_PI, 2.0*M_PI);
// Identify which patch this is in.
int size = (int) SQRT((RealOpenMM) coeff[map].size());
RealOpenMM delta = 2*M_PI/size;
int size = (int) sqrt(coeff[map].size());
double delta = 2*M_PI/size;
int s = (int) (angleA/delta);
int t = (int) (angleB/delta);
const vector<RealOpenMM>& c = coeff[map][s+size*t];
RealOpenMM da = angleA/delta-s;
RealOpenMM db = angleB/delta-t;
const vector<double>& c = coeff[map][s+size*t];
double da = angleA/delta-s;
double db = angleB/delta-t;
// Evaluate the spline to determine the energy and gradients.
RealOpenMM energy = 0;
RealOpenMM dEdA = 0;
RealOpenMM dEdB = 0;
double energy = 0;
double dEdA = 0;
double dEdB = 0;
for (int i = 3; i >= 0; i--) {
energy = da*energy + ((c[i*4+3]*db + c[i*4+2])*db + c[i*4+1])*db + c[i*4+0];
dEdA = db*dEdA + (3.0*c[i+3*4]*da + 2.0*c[i+2*4])*da + c[i+1*4];
......@@ -156,20 +156,20 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
// Apply the force to the first torsion.
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(cpA[0], cpA[0]);
RealOpenMM normBC = deltaA[1][ReferenceForce::RIndex];
double forceFactors[4];
double normCross1 = DOT3(cpA[0], cpA[0]);
double normBC = deltaA[1][ReferenceForce::RIndex];
forceFactors[0] = (-dEdA*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(cpA[1], cpA[1]);
double normCross2 = DOT3(cpA[1], cpA[1]);
forceFactors[3] = (dEdA*normBC)/normCross2;
forceFactors[1] = DOT3(deltaA[0], deltaA[1]);
forceFactors[1] /= deltaA[1][ReferenceForce::R2Index];
forceFactors[2] = DOT3(deltaA[2], deltaA[1]);
forceFactors[2] /= deltaA[1][ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
RealOpenMM f0 = forceFactors[0]*cpA[0][i];
RealOpenMM f3 = forceFactors[3]*cpA[1][i];
RealOpenMM s = forceFactors[1]*f0 - forceFactors[2]*f3;
double f0 = forceFactors[0]*cpA[0][i];
double f3 = forceFactors[3]*cpA[1][i];
double s = forceFactors[1]*f0 - forceFactors[2]*f3;
forces[a1][i] += f0;
forces[a2][i] -= f0-s;
forces[a3][i] -= f3+s;
......@@ -188,9 +188,9 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
forceFactors[2] = DOT3(deltaB[2], deltaB[1]);
forceFactors[2] /= deltaB[1][ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
RealOpenMM f0 = forceFactors[0]*cpB[0][i];
RealOpenMM f3 = forceFactors[3]*cpB[1][i];
RealOpenMM s = forceFactors[1]*f0 - forceFactors[2]*f3;
double f0 = forceFactors[0]*cpB[0][i];
double f3 = forceFactors[3]*cpB[1][i];
double s = forceFactors[1]*f0 - forceFactors[2]*f3;
forces[b1][i] += f0;
forces[b2][i] -= f0-s;
forces[b3][i] -= f3+s;
......@@ -206,6 +206,6 @@ void ReferenceCMAPTorsionIxn::calculateOneIxn(int index, vector<RealVec>& atomCo
--------------------------------------------------------------------------------------- */
void ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, vector<RealVec>& atomCoordinates,
RealOpenMM* parameters, vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCMAPTorsionIxn::calculateBondIxn(int* atomIndices, vector<Vec3>& atomCoordinates,
double* parameters, vector<Vec3>& forces, double* totalEnergy, double* energyParamDerivs) {
}
platforms/reference/src/SimTKReference/ReferenceConstraints.cpp
View file @ 047934e2
......@@ -43,9 +43,9 @@ using namespace std;
ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), settle(NULL) {
int numParticles = system.getNumParticles();
vector<RealOpenMM> masses(numParticles);
vector<double> masses(numParticles);
for (int i = 0; i < numParticles; ++i)
masses[i] = (RealOpenMM) system.getParticleMass(i);
masses[i] = system.getParticleMass(i);
// Record the set of constraints and how many constraints each atom is involved in.
......@@ -102,8 +102,8 @@ ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), s
vector<int> atom1;
vector<int> atom2;
vector<int> atom3;
vector<RealOpenMM> distance1;
vector<RealOpenMM> distance2;
vector<double> distance1;
vector<double> distance2;
for (int i = 0; i < settleClusters.size(); i++) {
int p1 = settleClusters[i];
int p2 = settleConstraints[p1].begin()->first;
......@@ -156,7 +156,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), s
// Record particles and distances for CCMA.
vector<pair<int, int> > ccmaIndices(numCCMA);
vector<RealOpenMM> ccmaDistance(numCCMA);
vector<double> ccmaDistance(numCCMA);
for (int i = 0; i < numCCMA; i++) {
int index = ccmaConstraints[i];
ccmaIndices[i] = make_pair(atom1[index], atom2[index]);
......@@ -173,7 +173,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), s
int atom1, atom2, atom3;
double angle, k;
force->getAngleParameters(j, atom1, atom2, atom3, angle, k);
angles.push_back(ReferenceCCMAAlgorithm::AngleInfo(atom1, atom2, atom3, (RealOpenMM) angle));
angles.push_back(ReferenceCCMAAlgorithm::AngleInfo(atom1, atom2, atom3, angle));
}
}
}
......@@ -191,14 +191,14 @@ ReferenceConstraints::~ReferenceConstraints() {
delete settle;
}
void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
void ReferenceConstraints::apply(vector<OpenMM::Vec3>& atomCoordinates, vector<OpenMM::Vec3>& atomCoordinatesP, vector<double>& inverseMasses, double tolerance) {
if (ccma != NULL)
ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
if (settle != NULL)
settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
}
void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
void ReferenceConstraints::applyToVelocities(vector<OpenMM::Vec3>& atomCoordinates, vector<OpenMM::Vec3>& velocities, vector<double>& inverseMasses, double tolerance) {
if (ccma != NULL)
ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
if (settle != NULL)
......
platforms/reference/src/SimTKReference/ReferenceCustomAngleIxn.cpp
View file @ 047934e2
......@@ -62,7 +62,7 @@ ReferenceCustomAngleIxn::ReferenceCustomAngleIxn(const Lepton::CompiledExpressio
ReferenceCustomAngleIxn::~ReferenceCustomAngleIxn() {
}
void ReferenceCustomAngleIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomAngleIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -82,11 +82,11 @@ void ReferenceCustomAngleIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
vector<Vec3>& atomCoordinates,
double* parameters,
vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
double deltaR[2][ReferenceForce::LastDeltaRIndex];
for (int i = 0; i < numParameters; i++)
expressionSet.setVariable(angleParamIndex[i], parameters[i]);
......@@ -105,30 +105,30 @@ void ReferenceCustomAngleIxn::calculateBondIxn(int* atomIndices,
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR[0]);
ReferenceForce::getDeltaR(atomCoordinates[atomCIndex], atomCoordinates[atomBIndex], deltaR[1]);
}
RealOpenMM pVector[3];
double pVector[3];
SimTKOpenMMUtilities::crossProductVector3(deltaR[0], deltaR[1], pVector);
RealOpenMM rp = SQRT(DOT3(pVector, pVector));
double rp = sqrt(DOT3(pVector, pVector));
if (rp < 1.0e-06)
rp = (RealOpenMM) 1.0e-06;
RealOpenMM dot = DOT3(deltaR[0], deltaR[1]);
RealOpenMM cosine = dot/SQRT((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
RealOpenMM angle;
rp = 1.0e-06;
double dot = DOT3(deltaR[0], deltaR[1]);
double cosine = dot/sqrt((deltaR[0][ReferenceForce::R2Index]*deltaR[1][ReferenceForce::R2Index]));
double angle;
if (cosine >= 1.0)
angle = 0.0;
else if (cosine <= -1.0)
angle = PI_M;
else
angle = ACOS(cosine);
angle = acos(cosine);
expressionSet.setVariable(thetaIndex, angle);
// Compute the force and energy, and apply them to the atoms.
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
RealOpenMM termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
RealOpenMM termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
double energy = energyExpression.evaluate();
double dEdR = forceExpression.evaluate();
double termA = dEdR/(deltaR[0][ReferenceForce::R2Index]*rp);
double termC = -dEdR/(deltaR[1][ReferenceForce::R2Index]*rp);
RealOpenMM deltaCrossP[3][3];
double deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(deltaR[0], pVector, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(deltaR[1], pVector, deltaCrossP[2]);
......
platforms/reference/src/SimTKReference/ReferenceCustomBondIxn.cpp
View file @ 047934e2
......@@ -63,7 +63,7 @@ ReferenceCustomBondIxn::ReferenceCustomBondIxn(const Lepton::CompiledExpression&
ReferenceCustomBondIxn::~ReferenceCustomBondIxn() {
}
void ReferenceCustomBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -83,11 +83,11 @@ void ReferenceCustomBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
vector<Vec3>& atomCoordinates,
double* parameters,
vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
double deltaR[ReferenceForce::LastDeltaRIndex];
for (int i = 0; i < numParameters; i++)
expressionSet.setVariable(bondParamIndex[i], parameters[i]);
......@@ -103,19 +103,19 @@ void ReferenceCustomBondIxn::calculateBondIxn(int* atomIndices,
ReferenceForce::getDeltaR(atomCoordinates[atomAIndex], atomCoordinates[atomBIndex], deltaR);
expressionSet.setVariable(rIndex, deltaR[ReferenceForce::RIndex]);
RealOpenMM dEdR = (RealOpenMM) forceExpression.evaluate();
dEdR = deltaR[ReferenceForce::RIndex] > 0 ? (dEdR/deltaR[ReferenceForce::RIndex]) : 0;
double dEdR = forceExpression.evaluate();
dEdR = deltaR[ReferenceForce::RIndex] > 0 ? (dEdR/deltaR[ReferenceForce::RIndex]) : 0;
forces[atomAIndex][0] += dEdR*deltaR[ReferenceForce::XIndex];
forces[atomAIndex][1] += dEdR*deltaR[ReferenceForce::YIndex];
forces[atomAIndex][2] += dEdR*deltaR[ReferenceForce::ZIndex];
forces[atomAIndex][0] += dEdR*deltaR[ReferenceForce::XIndex];
forces[atomAIndex][1] += dEdR*deltaR[ReferenceForce::YIndex];
forces[atomAIndex][2] += dEdR*deltaR[ReferenceForce::ZIndex];
forces[atomBIndex][0] -= dEdR*deltaR[ReferenceForce::XIndex];
forces[atomBIndex][1] -= dEdR*deltaR[ReferenceForce::YIndex];
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
forces[atomBIndex][0] -= dEdR*deltaR[ReferenceForce::XIndex];
forces[atomBIndex][1] -= dEdR*deltaR[ReferenceForce::YIndex];
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
*totalEnergy += energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceCustomCentroidBondIxn.cpp
View file @ 047934e2
......@@ -86,21 +86,21 @@ ReferenceCustomCentroidBondIxn::ReferenceCustomCentroidBondIxn(int numGroupsPerB
ReferenceCustomCentroidBondIxn::~ReferenceCustomCentroidBondIxn() {
}
void ReferenceCustomCentroidBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomCentroidBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
boxVectors[2] = vectors[2];
}
void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<Vec3>& atomCoordinates, double** bondParameters,
const map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
// First compute the center of each group.
int numGroups = groupAtoms.size();
vector<RealVec> groupCenters(numGroups);
vector<Vec3> groupCenters(numGroups);
for (int group = 0; group < numGroups; group++) {
for (int i = 0; i < groupAtoms[group].size(); i++)
groupCenters[group] += atomCoordinates[groupAtoms[group][i]]*normalizedWeights[group][i];
......@@ -110,7 +110,7 @@ void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
vector<RealVec> groupForces(numGroups);
vector<Vec3> groupForces(numGroups);
int numBonds = bondGroups.size();
for (int bond = 0; bond < numBonds; bond++) {
for (int i = 0; i < numParameters; i++)
......@@ -126,8 +126,8 @@ void ReferenceCustomCentroidBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
}
}
void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>& groupCenters,
vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<Vec3>& groupCenters,
vector<Vec3>& forces, double* totalEnergy, double* energyParamDerivs) {
// Compute all of the variables the energy can depend on.
const vector<int>& groups = bondGroups[bond];
......@@ -151,8 +151,8 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
computeDelta(groups[term.g2], groups[term.g1], term.delta1, groupCenters);
computeDelta(groups[term.g2], groups[term.g3], term.delta2, groupCenters);
computeDelta(groups[term.g4], groups[term.g3], term.delta3, groupCenters);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
double dotDihedral, signOfDihedral;
double* crossProduct[] = {term.cross1, term.cross2};
expressionSet.setVariable(term.index, getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1));
}
......@@ -167,9 +167,9 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]));
double dEdR = term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
double force = -dEdR*term.delta[i];
forces[groups[term.g1]][i] -= force;
forces[groups[term.g2]][i] += force;
}
......@@ -179,15 +179,15 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
double dEdTheta = term.forceExpression.evaluate();
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
double lengthThetaCross = sqrt(DOT3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-06)
lengthThetaCross = (RealOpenMM) 1.0e-06;
RealOpenMM termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM deltaCrossP[3][3];
lengthThetaCross = 1.0e-06;
double termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
double termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
double deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, thetaCross, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(term.delta2, thetaCross, deltaCrossP[2]);
for (int i = 0; i < 3; i++) {
......@@ -206,22 +206,22 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
RealOpenMM normBC = term.delta2[ReferenceForce::RIndex];
double dEdTheta = term.forceExpression.evaluate();
double internalF[4][3];
double forceFactors[4];
double normCross1 = DOT3(term.cross1, term.cross1);
double normBC = term.delta2[ReferenceForce::RIndex];
forceFactors[0] = (-dEdTheta*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
double normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
internalF[0][i] = forceFactors[0]*term.cross1[i];
internalF[3][i] = forceFactors[3]*term.cross2[i];
RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
double s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
internalF[1][i] = internalF[0][i] - s;
internalF[2][i] = internalF[3][i] + s;
}
......@@ -236,7 +236,7 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
*totalEnergy += energyExpression.evaluate();
// Compute derivatives of the energy.
......@@ -244,22 +244,22 @@ void ReferenceCustomCentroidBondIxn::calculateOneIxn(int bond, vector<RealVec>&
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
}
void ReferenceCustomCentroidBondIxn::computeDelta(int group1, int group2, RealOpenMM* delta, vector<RealVec>& groupCenters) const {
void ReferenceCustomCentroidBondIxn::computeDelta(int group1, int group2, double* delta, vector<Vec3>& groupCenters) const {
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(groupCenters[group1], groupCenters[group2], boxVectors, delta);
else
ReferenceForce::getDeltaR(groupCenters[group1], groupCenters[group2], delta);
}
RealOpenMM ReferenceCustomCentroidBondIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
RealOpenMM dot = DOT3(vec1, vec2);
RealOpenMM cosine = dot/SQRT((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
RealOpenMM angle;
double ReferenceCustomCentroidBondIxn::computeAngle(double* vec1, double* vec2) {
double dot = DOT3(vec1, vec2);
double cosine = dot/sqrt((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
double angle;
if (cosine >= 1)
angle = 0;
else if (cosine <= -1)
angle = PI_M;
else
angle = ACOS(cosine);
angle = acos(cosine);
return angle;
}
platforms/reference/src/SimTKReference/ReferenceCustomCompoundBondIxn.cpp
View file @ 047934e2
......@@ -97,7 +97,7 @@ ReferenceCustomCompoundBondIxn::ReferenceCustomCompoundBondIxn(int numParticlesP
ReferenceCustomCompoundBondIxn::~ReferenceCustomCompoundBondIxn() {
}
void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -116,9 +116,9 @@ void ReferenceCustomCompoundBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** bondParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<Vec3>& atomCoordinates, double** bondParameters,
const map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
int numBonds = bondAtoms.size();
......@@ -141,8 +141,8 @@ void ReferenceCustomCompoundBondIxn::calculatePairIxn(vector<RealVec>& atomCoord
--------------------------------------------------------------------------------------- */
void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>& atomCoordinates,
vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<Vec3>& atomCoordinates,
vector<Vec3>& forces, double* totalEnergy, double* energyParamDerivs) {
// Compute all of the variables the energy can depend on.
const vector<int>& atoms = bondAtoms[bond];
......@@ -166,8 +166,8 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
computeDelta(atoms[term.p2], atoms[term.p1], term.delta1, atomCoordinates);
computeDelta(atoms[term.p2], atoms[term.p3], term.delta2, atomCoordinates);
computeDelta(atoms[term.p4], atoms[term.p3], term.delta3, atomCoordinates);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
double dotDihedral, signOfDihedral;
double* crossProduct[] = {term.cross1, term.cross2};
expressionSet.setVariable(term.index,getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1));
}
......@@ -182,9 +182,9 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]));
double dEdR = term.forceExpression.evaluate()/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
double force = -dEdR*term.delta[i];
forces[atoms[term.p1]][i] -= force;
forces[atoms[term.p2]][i] += force;
}
......@@ -194,15 +194,15 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
double dEdTheta = term.forceExpression.evaluate();
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
double lengthThetaCross = sqrt(DOT3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-06)
lengthThetaCross = (RealOpenMM) 1.0e-06;
RealOpenMM termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM deltaCrossP[3][3];
lengthThetaCross = 1.0e-06;
double termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
double termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
double deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, thetaCross, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(term.delta2, thetaCross, deltaCrossP[2]);
for (int i = 0; i < 3; i++) {
......@@ -221,22 +221,22 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate();
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
RealOpenMM normBC = term.delta2[ReferenceForce::RIndex];
double dEdTheta = term.forceExpression.evaluate();
double internalF[4][3];
double forceFactors[4];
double normCross1 = DOT3(term.cross1, term.cross1);
double normBC = term.delta2[ReferenceForce::RIndex];
forceFactors[0] = (-dEdTheta*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
double normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
internalF[0][i] = forceFactors[0]*term.cross1[i];
internalF[3][i] = forceFactors[3]*term.cross2[i];
RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
double s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
internalF[1][i] = internalF[0][i] - s;
internalF[2][i] = internalF[3][i] + s;
}
......@@ -251,7 +251,7 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
*totalEnergy += energyExpression.evaluate();
// Compute derivatives of the energy.
......@@ -259,22 +259,22 @@ void ReferenceCustomCompoundBondIxn::calculateOneIxn(int bond, vector<RealVec>&
energyParamDerivs[i] += energyParamDerivExpressions[i].evaluate();
}
void ReferenceCustomCompoundBondIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
void ReferenceCustomCompoundBondIxn::computeDelta(int atom1, int atom2, double* delta, vector<Vec3>& atomCoordinates) const {
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom1], atomCoordinates[atom2], boxVectors, delta);
else
ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
}
RealOpenMM ReferenceCustomCompoundBondIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
RealOpenMM dot = DOT3(vec1, vec2);
RealOpenMM cosine = dot/SQRT((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
RealOpenMM angle;
double ReferenceCustomCompoundBondIxn::computeAngle(double* vec1, double* vec2) {
double dot = DOT3(vec1, vec2);
double cosine = dot/sqrt((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
double angle;
if (cosine >= 1)
angle = 0;
else if (cosine <= -1)
angle = PI_M;
else
angle = ACOS(cosine);
angle = acos(cosine);
return angle;
}
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 047934e2
......@@ -89,7 +89,7 @@ ReferenceCustomDynamics::ReferenceCustomDynamics(int numberOfAtoms, const Custom
ReferenceCustomDynamics::~ReferenceCustomDynamics() {
}
void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<RealOpenMM>& masses, map<string, RealOpenMM>& globals) {
void ReferenceCustomDynamics::initialize(ContextImpl& context, vector<double>& masses, map<string, double>& globals) {
// Some initialization can't be done in the constructor, since we need a ContextImpl from which to get the list of
// Context parameters. Instead, we do it the first time update() or computeKineticEnergy() is called.
......@@ -197,14 +197,14 @@ ExpressionTreeNode ReferenceCustomDynamics::replaceDerivFunctions(const Expressi
--------------------------------------------------------------------------------------- */
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance) {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& masses,
map<string, double>& globals, vector<vector<Vec3> >& perDof, bool& forcesAreValid, double tolerance) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
oldPos = atomCoordinates;
......@@ -217,7 +217,7 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
bool computeForce = needsForces[step] || computeBothForceAndEnergy[step];
bool computeEnergy = needsEnergy[step] || computeBothForceAndEnergy[step];
recordChangedParameters(context, globals);
RealOpenMM e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
double e = context.calcForcesAndEnergy(computeForce, computeEnergy, forceGroupFlags[step]);
if (computeEnergy) {
energy = e;
context.getEnergyParameterDerivatives(energyParamDerivs);
......@@ -232,13 +232,13 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
case CustomIntegrator::ComputeGlobal: {
uniform = SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber();
gaussian = SimTKOpenMMUtilities::getNormallyDistributedRandomNumber();
RealOpenMM result = stepExpressions[step][0].evaluate();
double result = stepExpressions[step][0].evaluate();
globals[stepVariable[step]] = result;
expressionSet.setVariable(stepVariableIndex[step], result);
break;
}
case CustomIntegrator::ComputePerDof: {
vector<RealVec>* results = NULL;
vector<Vec3>* results = NULL;
if (stepVariableIndex[step] == xIndex)
results = &atomCoordinates;
else if (stepVariableIndex[step] == vIndex)
......@@ -255,7 +255,7 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
}
case CustomIntegrator::ComputeSum: {
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, stepExpressions[step][0]);
RealOpenMM sum = 0.0;
double sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
......@@ -276,7 +276,7 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
recordChangedParameters(context, globals);
context.updateContextState();
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
break;
}
......@@ -305,9 +305,9 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
recordChangedParameters(context, globals);
}
void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<RealVec>& results, const vector<RealVec>& atomCoordinates,
const vector<RealVec>& velocities, const vector<RealVec>& forces, const vector<RealOpenMM>& masses,
const vector<vector<RealVec> >& perDof, const CompiledExpression& expression) {
void ReferenceCustomDynamics::computePerDof(int numberOfAtoms, vector<Vec3>& results, const vector<Vec3>& atomCoordinates,
const vector<Vec3>& velocities, const vector<Vec3>& forces, const vector<double>& masses,
const vector<vector<Vec3> >& perDof, const CompiledExpression& expression) {
// Loop over all degrees of freedom.
for (int i = 0; i < numberOfAtoms; i++) {
......@@ -354,7 +354,7 @@ bool ReferenceCustomDynamics::evaluateCondition(int step) {
/**
* Check which context parameters have changed and register them with the context.
*/
void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, RealOpenMM>& globals) {
void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& context, std::map<std::string, double>& globals) {
for (map<string, double>::const_iterator iter = context.getParameters().begin(); iter != context.getParameters().end(); ++iter) {
string name = iter->first;
double value = globals[name];
......@@ -379,20 +379,20 @@ void ReferenceCustomDynamics::recordChangedParameters(OpenMM::ContextImpl& conte
--------------------------------------------------------------------------------------- */
double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<OpenMM::RealVec>& forces, std::vector<RealOpenMM>& masses,
std::map<std::string, RealOpenMM>& globals, std::vector<std::vector<OpenMM::RealVec> >& perDof, bool& forcesAreValid) {
double ReferenceCustomDynamics::computeKineticEnergy(OpenMM::ContextImpl& context, int numberOfAtoms, std::vector<OpenMM::Vec3>& atomCoordinates,
std::vector<OpenMM::Vec3>& velocities, std::vector<OpenMM::Vec3>& forces, std::vector<double>& masses,
std::map<std::string, double>& globals, std::vector<std::vector<OpenMM::Vec3> >& perDof, bool& forcesAreValid) {
if (invalidatesForces.size() == 0)
initialize(context, masses, globals);
globals.insert(context.getParameters().begin(), context.getParameters().end());
for (map<string, RealOpenMM>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
for (map<string, double>::const_iterator iter = globals.begin(); iter != globals.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
if (kineticEnergyNeedsForce) {
energy = context.calcForcesAndEnergy(true, true, -1);
forcesAreValid = true;
}
computePerDof(numberOfAtoms, sumBuffer, atomCoordinates, velocities, forces, masses, perDof, kineticEnergyExpression);
RealOpenMM sum = 0.0;
double sum = 0.0;
for (int j = 0; j < numberOfAtoms; j++)
if (masses[j] != 0.0)
sum += sumBuffer[j][0]+sumBuffer[j][1]+sumBuffer[j][2];
......
platforms/reference/src/SimTKReference/ReferenceCustomExternalIxn.cpp
View file @ 047934e2
......@@ -78,13 +78,6 @@ ReferenceCustomExternalIxn::ReferenceCustomExternalIxn(const Lepton::CompiledExp
--------------------------------------------------------------------------------------- */
ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomExternalIxn::~ReferenceCustomExternalIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -100,12 +93,10 @@ ReferenceCustomExternalIxn::~ReferenceCustomExternalIxn() {
--------------------------------------------------------------------------------------- */
void ReferenceCustomExternalIxn::calculateForce(int atomIndex,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* energy) const {
static const std::string methodName = "\nReferenceCustomExternalIxn::calculateBondIxn";
vector<Vec3>& atomCoordinates,
double* parameters,
vector<Vec3>& forces,
double* energy) const {
for (int i = 0; i < numParameters; i++) {
ReferenceForce::setVariable(energyParams[i], parameters[i]);
......@@ -128,9 +119,9 @@ void ReferenceCustomExternalIxn::calculateForce(int atomIndex,
// ---------------------------------------------------------------------------------------
forces[atomIndex][0] -= (RealOpenMM) forceExpressionX.evaluate();
forces[atomIndex][1] -= (RealOpenMM) forceExpressionY.evaluate();
forces[atomIndex][2] -= (RealOpenMM) forceExpressionZ.evaluate();
forces[atomIndex][0] -= forceExpressionX.evaluate();
forces[atomIndex][1] -= forceExpressionY.evaluate();
forces[atomIndex][2] -= forceExpressionZ.evaluate();
if (energy != NULL)
*energy += (RealOpenMM) energyExpression.evaluate();
*energy += energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceCustomGBIxn.cpp
View file @ 047934e2
......@@ -120,7 +120,7 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
--------------------------------------------------------------------------------------- */
void ReferenceCustomGBIxn::setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors) {
void ReferenceCustomGBIxn::setUseCutoff(double distance, const OpenMM::NeighborList& neighbors) {
cutoff = true;
cutoffDistance = distance;
......@@ -137,7 +137,7 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
--------------------------------------------------------------------------------------- */
void ReferenceCustomGBIxn::setPeriodic(RealVec* vectors) {
void ReferenceCustomGBIxn::setPeriodic(Vec3* vectors) {
if (cutoff) {
assert(vectors[0][0] >= 2.0*cutoffDistance);
......@@ -150,9 +150,9 @@ ReferenceCustomGBIxn::~ReferenceCustomGBIxn() {
periodicBoxVectors[2] = vectors[2];
}
void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const vector<set<int> >& exclusions, map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<Vec3>& atomCoordinates, double** atomParameters,
const vector<set<int> >& exclusions, map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
......@@ -161,10 +161,10 @@ void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<RealVec>& atom
int numValues = valueTypes.size();
int numDerivs = valueParamDerivExpressions[0].size();
values.resize(numValues);
dEdV.resize(numValues, vector<RealOpenMM>(numberOfAtoms, 0.0));
dEdV.resize(numValues, vector<double>(numberOfAtoms, 0.0));
dValuedParam.resize(numValues);
for (int i = 0; i < numValues; i++)
dValuedParam[i].resize(numDerivs, vector<RealOpenMM>(numberOfAtoms, 0.0));
dValuedParam[i].resize(numDerivs, vector<double>(numberOfAtoms, 0.0));
// First calculate the computed values.
......@@ -193,7 +193,7 @@ void ReferenceCustomGBIxn::calculateIxn(int numberOfAtoms, vector<RealVec>& atom
calculateChainRuleForces(numberOfAtoms, atomCoordinates, atomParameters, exclusions, forces, energyParamDerivs);
}
void ReferenceCustomGBIxn::calculateSingleParticleValue(int index, int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters) {
void ReferenceCustomGBIxn::calculateSingleParticleValue(int index, int numAtoms, vector<Vec3>& atomCoordinates, double** atomParameters) {
values[index].resize(numAtoms);
for (int i = 0; i < numAtoms; i++) {
expressionSet.setVariable(xIndex, atomCoordinates[i][0]);
......@@ -203,25 +203,25 @@ void ReferenceCustomGBIxn::calculateSingleParticleValue(int index, int numAtoms,
expressionSet.setVariable(paramIndex[j], atomParameters[i][j]);
for (int j = 0; j < index; j++)
expressionSet.setVariable(valueIndex[j], values[j][i]);
values[index][i] = (RealOpenMM) valueExpressions[index].evaluate();
values[index][i] = valueExpressions[index].evaluate();
// Calculate derivatives with respect to parameters.
for (int j = 0; j < valueParamDerivExpressions[index].size(); j++)
dValuedParam[index][j][i] += valueParamDerivExpressions[index][j].evaluate();
for (int j = 0; j < index; j++) {
RealOpenMM dVdV = valueDerivExpressions[index][j].evaluate();
double dVdV = valueDerivExpressions[index][j].evaluate();
for (int k = 0; k < valueParamDerivExpressions[index].size(); k++)
dValuedParam[index][k][i] += dVdV*dValuedParam[j][k][i];
}
}
}
void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, vector<Vec3>& atomCoordinates, double** atomParameters,
const vector<set<int> >& exclusions, bool useExclusions) {
values[index].resize(numAtoms);
for (int i = 0; i < numAtoms; i++)
values[index][i] = (RealOpenMM) 0.0;
values[index][i] = 0.0;
if (cutoff) {
// Loop over all pairs in the neighbor list.
......@@ -247,13 +247,13 @@ void ReferenceCustomGBIxn::calculateParticlePairValue(int index, int numAtoms, v
}
}
void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2, vector<Vec3>& atomCoordinates, double** atomParameters) {
double deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom2], atomCoordinates[atom1], periodicBoxVectors, deltaR);
else
ReferenceForce::getDeltaR(atomCoordinates[atom2], atomCoordinates[atom1], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
double r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance)
return;
for (int i = 0; i < (int) paramIndex.size(); i++) {
......@@ -265,7 +265,7 @@ void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2
expressionSet.setVariable(particleValueIndex[i*2], values[i][atom1]);
expressionSet.setVariable(particleValueIndex[i*2+1], values[i][atom2]);
}
values[index][atom1] += (RealOpenMM) valueExpressions[index].evaluate();
values[index][atom1] += valueExpressions[index].evaluate();
// Calculate derivatives with respect to parameters.
......@@ -273,8 +273,8 @@ void ReferenceCustomGBIxn::calculateOnePairValue(int index, int atom1, int atom2
dValuedParam[index][i][atom1] += valueParamDerivExpressions[index][i].evaluate();
}
void ReferenceCustomGBIxn::calculateSingleParticleEnergyTerm(int index, int numAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomGBIxn::calculateSingleParticleEnergyTerm(int index, int numAtoms, vector<Vec3>& atomCoordinates,
double** atomParameters, vector<Vec3>& forces, double* totalEnergy, double* energyParamDerivs) {
for (int i = 0; i < numAtoms; i++) {
expressionSet.setVariable(xIndex, atomCoordinates[i][0]);
expressionSet.setVariable(yIndex, atomCoordinates[i][1]);
......@@ -287,12 +287,12 @@ void ReferenceCustomGBIxn::calculateSingleParticleEnergyTerm(int index, int numA
// Compute energy and force.
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpressions[index].evaluate();
*totalEnergy += energyExpressions[index].evaluate();
for (int j = 0; j < (int) valueIndex.size(); j++)
dEdV[j][i] += (RealOpenMM) energyDerivExpressions[index][j].evaluate();
forces[i][0] -= (RealOpenMM) energyGradientExpressions[index][0].evaluate();
forces[i][1] -= (RealOpenMM) energyGradientExpressions[index][1].evaluate();
forces[i][2] -= (RealOpenMM) energyGradientExpressions[index][2].evaluate();
dEdV[j][i] += energyDerivExpressions[index][j].evaluate();
forces[i][0] -= energyGradientExpressions[index][0].evaluate();
forces[i][1] -= energyGradientExpressions[index][1].evaluate();
forces[i][2] -= energyGradientExpressions[index][2].evaluate();
// Compute derivatives with respect to parameters.
......@@ -301,8 +301,8 @@ void ReferenceCustomGBIxn::calculateSingleParticleEnergyTerm(int index, int numA
}
}
void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const vector<set<int> >& exclusions, bool useExclusions, vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAtoms, vector<Vec3>& atomCoordinates, double** atomParameters,
const vector<set<int> >& exclusions, bool useExclusions, vector<Vec3>& forces, double* totalEnergy, double* energyParamDerivs) {
if (cutoff) {
// Loop over all pairs in the neighbor list.
......@@ -326,16 +326,16 @@ void ReferenceCustomGBIxn::calculateParticlePairEnergyTerm(int index, int numAto
}
}
void ReferenceCustomGBIxn::calculateOnePairEnergyTerm(int index, int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
vector<RealVec>& forces, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomGBIxn::calculateOnePairEnergyTerm(int index, int atom1, int atom2, vector<Vec3>& atomCoordinates, double** atomParameters,
vector<Vec3>& forces, double* totalEnergy, double* energyParamDerivs) {
// Compute the displacement.
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
double deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom2], atomCoordinates[atom1], periodicBoxVectors, deltaR);
else
ReferenceForce::getDeltaR(atomCoordinates[atom2], atomCoordinates[atom1], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
double r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance)
return;
......@@ -354,16 +354,16 @@ void ReferenceCustomGBIxn::calculateOnePairEnergyTerm(int index, int atom1, int
// Evaluate the energy and its derivatives.
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpressions[index].evaluate();
RealOpenMM dEdR = (RealOpenMM) energyDerivExpressions[index][0].evaluate();
*totalEnergy += energyExpressions[index].evaluate();
double dEdR = energyDerivExpressions[index][0].evaluate();
dEdR *= 1/r;
for (int i = 0; i < 3; i++) {
forces[atom1][i] -= dEdR*deltaR[i];
forces[atom2][i] += dEdR*deltaR[i];
}
for (int i = 0; i < (int) valueIndex.size(); i++) {
dEdV[i][atom1] += (RealOpenMM) energyDerivExpressions[index][2*i+1].evaluate();
dEdV[i][atom2] += (RealOpenMM) energyDerivExpressions[index][2*i+2].evaluate();
dEdV[i][atom1] += energyDerivExpressions[index][2*i+1].evaluate();
dEdV[i][atom2] += energyDerivExpressions[index][2*i+2].evaluate();
}
// Compute derivatives with respect to parameters.
......@@ -372,8 +372,8 @@ void ReferenceCustomGBIxn::calculateOnePairEnergyTerm(int index, int atom1, int
energyParamDerivs[i] += energyParamDerivExpressions[index][i].evaluate();
}
void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
const vector<set<int> >& exclusions, vector<RealVec>& forces, double* energyParamDerivs) {
void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<Vec3>& atomCoordinates, double** atomParameters,
const vector<set<int> >& exclusions, vector<Vec3>& forces, double* energyParamDerivs) {
if (cutoff) {
// Loop over all pairs in the neighbor list.
......@@ -402,22 +402,22 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec
expressionSet.setVariable(xIndex, atomCoordinates[i][0]);
expressionSet.setVariable(yIndex, atomCoordinates[i][1]);
expressionSet.setVariable(zIndex, atomCoordinates[i][2]);
vector<RealOpenMM> dVdX(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdY(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdZ(valueDerivExpressions.size(), 0.0);
vector<double> dVdX(valueDerivExpressions.size(), 0.0);
vector<double> dVdY(valueDerivExpressions.size(), 0.0);
vector<double> dVdZ(valueDerivExpressions.size(), 0.0);
for (int j = 0; j < (int) paramIndex.size(); j++)
expressionSet.setVariable(paramIndex[j], atomParameters[i][j]);
for (int j = 1; j < (int) valueIndex.size(); j++) {
expressionSet.setVariable(valueIndex[j-1], values[j-1][i]);
for (int k = 1; k < j; k++) {
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[j][k].evaluate();
double dVdV = valueDerivExpressions[j][k].evaluate();
dVdX[j] += dVdV*dVdX[k];
dVdY[j] += dVdV*dVdY[k];
dVdZ[j] += dVdV*dVdZ[k];
}
dVdX[j] += (RealOpenMM) valueGradientExpressions[j][0].evaluate();
dVdY[j] += (RealOpenMM) valueGradientExpressions[j][1].evaluate();
dVdZ[j] += (RealOpenMM) valueGradientExpressions[j][2].evaluate();
dVdX[j] += valueGradientExpressions[j][0].evaluate();
dVdY[j] += valueGradientExpressions[j][1].evaluate();
dVdZ[j] += valueGradientExpressions[j][2].evaluate();
forces[i][0] -= dEdV[j][i]*dVdX[j];
forces[i][1] -= dEdV[j][i]*dVdY[j];
forces[i][2] -= dEdV[j][i]*dVdZ[j];
......@@ -432,16 +432,16 @@ void ReferenceCustomGBIxn::calculateChainRuleForces(int numAtoms, vector<RealVec
energyParamDerivs[k] += dEdV[j][i]*dValuedParam[j][k][i];
}
void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vector<RealVec>& atomCoordinates, RealOpenMM** atomParameters,
vector<RealVec>& forces, bool isExcluded) {
void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vector<Vec3>& atomCoordinates, double** atomParameters,
vector<Vec3>& forces, bool isExcluded) {
// Compute the displacement.
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
double deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom2], atomCoordinates[atom1], periodicBoxVectors, deltaR);
else
ReferenceForce::getDeltaR(atomCoordinates[atom2], atomCoordinates[atom1], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
double r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance)
return;
......@@ -457,14 +457,14 @@ void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vecto
// Evaluate the derivative of each parameter with respect to position and apply forces.
RealOpenMM rinv = 1/r;
double rinv = 1/r;
deltaR[0] *= rinv;
deltaR[1] *= rinv;
deltaR[2] *= rinv;
vector<RealOpenMM> dVdR1(valueDerivExpressions.size(), 0.0);
vector<RealOpenMM> dVdR2(valueDerivExpressions.size(), 0.0);
vector<double> dVdR1(valueDerivExpressions.size(), 0.0);
vector<double> dVdR2(valueDerivExpressions.size(), 0.0);
if (!isExcluded || valueTypes[0] != OpenMM::CustomGBForce::ParticlePair) {
dVdR1[0] = (RealOpenMM) valueDerivExpressions[0][0].evaluate();
dVdR1[0] = valueDerivExpressions[0][0].evaluate();
dVdR2[0] = -dVdR1[0];
for (int i = 0; i < 3; i++) {
forces[atom1][i] -= dEdV[0][atom1]*dVdR1[0]*deltaR[i];
......@@ -480,7 +480,7 @@ void ReferenceCustomGBIxn::calculateOnePairChainRule(int atom1, int atom2, vecto
expressionSet.setVariable(yIndex, atomCoordinates[atom1][1]);
expressionSet.setVariable(zIndex, atomCoordinates[atom1][2]);
for (int j = 0; j < i; j++) {
RealOpenMM dVdV = (RealOpenMM) valueDerivExpressions[i][j].evaluate();
double dVdV = valueDerivExpressions[i][j].evaluate();
dVdR1[i] += dVdV*dVdR1[j];
dVdR2[i] += dVdV*dVdR2[j];
}
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
View file @ 047934e2
......@@ -74,7 +74,7 @@ ReferenceCustomHbondIxn::~ReferenceCustomHbondIxn() {
--------------------------------------------------------------------------------------- */
void ReferenceCustomHbondIxn::setUseCutoff(RealOpenMM distance) {
void ReferenceCustomHbondIxn::setUseCutoff(double distance) {
cutoff = true;
cutoffDistance = distance;
}
......@@ -89,7 +89,7 @@ void ReferenceCustomHbondIxn::setUseCutoff(RealOpenMM distance) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomHbondIxn::setPeriodic(RealVec* vectors) {
void ReferenceCustomHbondIxn::setPeriodic(Vec3* vectors) {
assert(cutoff);
assert(vectors[0][0] >= 2.0*cutoffDistance);
assert(vectors[1][1] >= 2.0*cutoffDistance);
......@@ -116,9 +116,9 @@ void ReferenceCustomHbondIxn::setPeriodic(RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** donorParameters, RealOpenMM** acceptorParameters,
vector<set<int> >& exclusions, const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
void ReferenceCustomHbondIxn::calculatePairIxn(vector<Vec3>& atomCoordinates, double** donorParameters, double** acceptorParameters,
vector<set<int> >& exclusions, const map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy) const {
map<string, double> variables = globalParameters;
......@@ -159,14 +159,8 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates,
--------------------------------------------------------------------------------------- */
void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<RealVec>& atomCoordinates,
map<string, double>& variables, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
// ---------------------------------------------------------------------------------------
static const std::string methodName = "\nReferenceCustomHbondIxn::calculateOneIxn";
// ---------------------------------------------------------------------------------------
void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Vec3>& atomCoordinates,
map<string, double>& variables, vector<Vec3>& forces, double* totalEnergy) const {
int atoms[6];
atoms[0] = acceptorAtoms[acceptor][0];
......@@ -179,7 +173,7 @@ void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Re
// Compute the distance between the primary donor and acceptor atoms, and compare to the cutoff.
if (cutoff) {
RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
double delta[ReferenceForce::LastDeltaRIndex];
computeDelta(atoms[0], atoms[3], delta, atomCoordinates);
if (delta[ReferenceForce::RIndex] >= cutoffDistance)
return;
......@@ -203,8 +197,8 @@ void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Re
computeDelta(atoms[term.p2], atoms[term.p1], term.delta1, atomCoordinates);
computeDelta(atoms[term.p2], atoms[term.p3], term.delta2, atomCoordinates);
computeDelta(atoms[term.p4], atoms[term.p3], term.delta3, atomCoordinates);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
double dotDihedral, signOfDihedral;
double* crossProduct[] = {term.cross1, term.cross2};
variables[term.name] = getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1);
}
......@@ -212,9 +206,9 @@ void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Re
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]));
double dEdR = term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
double force = -dEdR*term.delta[i];
forces[atoms[term.p1]][i] -= force;
forces[atoms[term.p2]][i] += force;
}
......@@ -224,15 +218,15 @@ void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Re
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
double dEdTheta = term.forceExpression.evaluate(variables);
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
double lengthThetaCross = sqrt(DOT3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-06)
lengthThetaCross = (RealOpenMM) 1.0e-06;
RealOpenMM termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM deltaCrossP[3][3];
lengthThetaCross = 1.0e-06;
double termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
double termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
double deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, thetaCross, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(term.delta2, thetaCross, deltaCrossP[2]);
for (int i = 0; i < 3; i++) {
......@@ -251,22 +245,22 @@ void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Re
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
RealOpenMM normBC = term.delta2[ReferenceForce::RIndex];
double dEdTheta = term.forceExpression.evaluate(variables);
double internalF[4][3];
double forceFactors[4];
double normCross1 = DOT3(term.cross1, term.cross1);
double normBC = term.delta2[ReferenceForce::RIndex];
forceFactors[0] = (-dEdTheta*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
double normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
internalF[0][i] = forceFactors[0]*term.cross1[i];
internalF[3][i] = forceFactors[3]*term.cross2[i];
RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
double s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
internalF[1][i] = internalF[0][i] - s;
internalF[2][i] = internalF[3][i] + s;
}
......@@ -281,25 +275,25 @@ void ReferenceCustomHbondIxn::calculateOneIxn(int donor, int acceptor, vector<Re
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
*totalEnergy += energyExpression.evaluate(variables);
}
void ReferenceCustomHbondIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
void ReferenceCustomHbondIxn::computeDelta(int atom1, int atom2, double* delta, vector<Vec3>& atomCoordinates) const {
if (periodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom1], atomCoordinates[atom2], periodicBoxVectors, delta);
else
ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
}
RealOpenMM ReferenceCustomHbondIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
RealOpenMM dot = DOT3(vec1, vec2);
RealOpenMM cosine = dot/SQRT((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
RealOpenMM angle;
double ReferenceCustomHbondIxn::computeAngle(double* vec1, double* vec2) {
double dot = DOT3(vec1, vec2);
double cosine = dot/sqrt((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
double angle;
if (cosine >= 1)
angle = 0;
else if (cosine <= -1)
angle = PI_M;
else
angle = ACOS(cosine);
angle = acos(cosine);
return angle;
}
platforms/reference/src/SimTKReference/ReferenceCustomManyParticleIxn.cpp
View file @ 047934e2
......@@ -105,20 +105,20 @@ ReferenceCustomManyParticleIxn::ReferenceCustomManyParticleIxn(const CustomManyP
ReferenceCustomManyParticleIxn::~ReferenceCustomManyParticleIxn() {
}
void ReferenceCustomManyParticleIxn::calculateIxn(vector<RealVec>& atomCoordinates, RealOpenMM** particleParameters,
const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
void ReferenceCustomManyParticleIxn::calculateIxn(vector<Vec3>& atomCoordinates, double** particleParameters,
const map<string, double>& globalParameters, vector<Vec3>& forces,
double* totalEnergy) const {
map<string, double> variables = globalParameters;
vector<int> particles(numParticlesPerSet);
loopOverInteractions(particles, 0, atomCoordinates, particleParameters, variables, forces, totalEnergy);
}
void ReferenceCustomManyParticleIxn::setUseCutoff(RealOpenMM distance) {
void ReferenceCustomManyParticleIxn::setUseCutoff(double distance) {
useCutoff = true;
cutoffDistance = distance;
}
void ReferenceCustomManyParticleIxn::setPeriodic(RealVec* vectors) {
void ReferenceCustomManyParticleIxn::setPeriodic(Vec3* vectors) {
assert(useCutoff);
assert(vectors[0][0] >= 2.0*cutoffDistance);
assert(vectors[1][1] >= 2.0*cutoffDistance);
......@@ -129,9 +129,9 @@ void ReferenceCustomManyParticleIxn::setPeriodic(RealVec* vectors) {
periodicBoxVectors[2] = vectors[2];
}
void ReferenceCustomManyParticleIxn::loopOverInteractions(vector<int>& particles, int loopIndex, vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** particleParameters, map<string, double>& variables, vector<OpenMM::RealVec>& forces,
RealOpenMM* totalEnergy) const {
void ReferenceCustomManyParticleIxn::loopOverInteractions(vector<int>& particles, int loopIndex, vector<OpenMM::Vec3>& atomCoordinates,
double** particleParameters, map<string, double>& variables, vector<OpenMM::Vec3>& forces,
double* totalEnergy) const {
int numParticles = atomCoordinates.size();
int firstPartialLoop = (centralParticleMode ? 2 : 1);
int start = (loopIndex < firstPartialLoop ? 0 : particles[loopIndex-1]+1);
......@@ -146,8 +146,8 @@ void ReferenceCustomManyParticleIxn::loopOverInteractions(vector<int>& particles
}
}
void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particles, vector<RealVec>& atomCoordinates,
RealOpenMM** particleParameters, map<string, double>& variables, vector<RealVec>& forces, RealOpenMM* totalEnergy) const {
void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particles, vector<Vec3>& atomCoordinates,
double** particleParameters, map<string, double>& variables, vector<Vec3>& forces, double* totalEnergy) const {
// Select the ordering to use for the particles.
vector<int> permutedParticles(numParticlesPerSet);
......@@ -176,7 +176,7 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
if (exclusions[p1].find(p2) != exclusions[p1].end())
return;
if (useCutoff && (i == 0 || !centralParticleMode)) {
RealOpenMM delta[ReferenceForce::LastDeltaRIndex];
double delta[ReferenceForce::LastDeltaRIndex];
computeDelta(p1, p2, delta, atomCoordinates);
if (delta[ReferenceForce::RIndex] >= cutoffDistance)
return;
......@@ -212,8 +212,8 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
computeDelta(permutedParticles[term.p2], permutedParticles[term.p1], term.delta1, atomCoordinates);
computeDelta(permutedParticles[term.p2], permutedParticles[term.p3], term.delta2, atomCoordinates);
computeDelta(permutedParticles[term.p4], permutedParticles[term.p3], term.delta3, atomCoordinates);
RealOpenMM dotDihedral, signOfDihedral;
RealOpenMM* crossProduct[] = {term.cross1, term.cross2};
double dotDihedral, signOfDihedral;
double* crossProduct[] = {term.cross1, term.cross2};
variables[term.name] = ReferenceBondIxn::getDihedralAngleBetweenThreeVectors(term.delta1, term.delta2, term.delta3, crossProduct, &dotDihedral, term.delta1, &signOfDihedral, 1);
}
......@@ -228,9 +228,9 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
for (int i = 0; i < (int) distanceTerms.size(); i++) {
const DistanceTermInfo& term = distanceTerms[i];
RealOpenMM dEdR = (RealOpenMM) (term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]));
double dEdR = term.forceExpression.evaluate(variables)/(term.delta[ReferenceForce::RIndex]);
for (int i = 0; i < 3; i++) {
RealOpenMM force = -dEdR*term.delta[i];
double force = -dEdR*term.delta[i];
forces[permutedParticles[term.p1]][i] -= force;
forces[permutedParticles[term.p2]][i] += force;
}
......@@ -240,15 +240,15 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
for (int i = 0; i < (int) angleTerms.size(); i++) {
const AngleTermInfo& term = angleTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM thetaCross[ReferenceForce::LastDeltaRIndex];
double dEdTheta = term.forceExpression.evaluate(variables);
double thetaCross[ReferenceForce::LastDeltaRIndex];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, term.delta2, thetaCross);
RealOpenMM lengthThetaCross = SQRT(DOT3(thetaCross, thetaCross));
double lengthThetaCross = sqrt(DOT3(thetaCross, thetaCross));
if (lengthThetaCross < 1.0e-06)
lengthThetaCross = (RealOpenMM) 1.0e-06;
RealOpenMM termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
RealOpenMM deltaCrossP[3][3];
lengthThetaCross = 1.0e-06;
double termA = dEdTheta/(term.delta1[ReferenceForce::R2Index]*lengthThetaCross);
double termC = -dEdTheta/(term.delta2[ReferenceForce::R2Index]*lengthThetaCross);
double deltaCrossP[3][3];
SimTKOpenMMUtilities::crossProductVector3(term.delta1, thetaCross, deltaCrossP[0]);
SimTKOpenMMUtilities::crossProductVector3(term.delta2, thetaCross, deltaCrossP[2]);
for (int i = 0; i < 3; i++) {
......@@ -267,22 +267,22 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
for (int i = 0; i < (int) dihedralTerms.size(); i++) {
const DihedralTermInfo& term = dihedralTerms[i];
RealOpenMM dEdTheta = (RealOpenMM) term.forceExpression.evaluate(variables);
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(term.cross1, term.cross1);
RealOpenMM normBC = term.delta2[ReferenceForce::RIndex];
double dEdTheta = term.forceExpression.evaluate(variables);
double internalF[4][3];
double forceFactors[4];
double normCross1 = DOT3(term.cross1, term.cross1);
double normBC = term.delta2[ReferenceForce::RIndex];
forceFactors[0] = (-dEdTheta*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
double normCross2 = DOT3(term.cross2, term.cross2);
forceFactors[3] = (dEdTheta*normBC)/normCross2;
forceFactors[1] = DOT3(term.delta1, term.delta2);
forceFactors[1] /= term.delta2[ReferenceForce::R2Index];
forceFactors[2] = DOT3(term.delta3, term.delta2);
forceFactors[2] /= term.delta2[ReferenceForce::R2Index];
for (int i = 0; i < 3; i++) {
internalF[0][i] = forceFactors[0]*term.cross1[i];
internalF[3][i] = forceFactors[3]*term.cross2[i];
RealOpenMM s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
double s = forceFactors[1]*internalF[0][i] - forceFactors[2]*internalF[3][i];
internalF[1][i] = internalF[0][i] - s;
internalF[2][i] = internalF[3][i] + s;
}
......@@ -297,25 +297,25 @@ void ReferenceCustomManyParticleIxn::calculateOneIxn(const vector<int>& particle
// Add the energy
if (totalEnergy)
*totalEnergy += (RealOpenMM) energyExpression.evaluate(variables);
*totalEnergy += energyExpression.evaluate(variables);
}
void ReferenceCustomManyParticleIxn::computeDelta(int atom1, int atom2, RealOpenMM* delta, vector<RealVec>& atomCoordinates) const {
void ReferenceCustomManyParticleIxn::computeDelta(int atom1, int atom2, double* delta, vector<Vec3>& atomCoordinates) const {
if (usePeriodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atom1], atomCoordinates[atom2], periodicBoxVectors, delta);
else
ReferenceForce::getDeltaR(atomCoordinates[atom1], atomCoordinates[atom2], delta);
}
RealOpenMM ReferenceCustomManyParticleIxn::computeAngle(RealOpenMM* vec1, RealOpenMM* vec2) {
RealOpenMM dot = DOT3(vec1, vec2);
RealOpenMM cosine = dot/SQRT((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
RealOpenMM angle;
double ReferenceCustomManyParticleIxn::computeAngle(double* vec1, double* vec2) {
double dot = DOT3(vec1, vec2);
double cosine = dot/sqrt((vec1[ReferenceForce::R2Index]*vec2[ReferenceForce::R2Index]));
double angle;
if (cosine >= 1)
angle = 0;
else if (cosine <= -1)
angle = PI_M;
else
angle = ACOS(cosine);
angle = acos(cosine);
return angle;
}
platforms/reference/src/SimTKReference/ReferenceCustomNonbondedIxn.cpp
View file @ 047934e2
......@@ -69,13 +69,6 @@ ReferenceCustomNonbondedIxn::ReferenceCustomNonbondedIxn(const Lepton::CompiledE
--------------------------------------------------------------------------------------- */
ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn";
// ---------------------------------------------------------------------------------------
}
/**---------------------------------------------------------------------------------------
......@@ -87,7 +80,7 @@ ReferenceCustomNonbondedIxn::~ReferenceCustomNonbondedIxn() {
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::setUseCutoff(RealOpenMM distance, const OpenMM::NeighborList& neighbors) {
void ReferenceCustomNonbondedIxn::setUseCutoff(double distance, const OpenMM::NeighborList& neighbors) {
cutoff = true;
cutoffDistance = distance;
......@@ -115,7 +108,7 @@ void ReferenceCustomNonbondedIxn::setInteractionGroups(const vector<pair<set<int
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(RealOpenMM distance) {
void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(double distance) {
useSwitch = true;
switchingDistance = distance;
}
......@@ -130,7 +123,7 @@ void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(RealOpenMM distance) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomNonbondedIxn::setPeriodic(OpenMM::Vec3* vectors) {
assert(cutoff);
assert(vectors[0][0] >= 2.0*cutoffDistance);
......@@ -161,10 +154,10 @@ void ReferenceCustomNonbondedIxn::setUseSwitchingFunction(RealOpenMM distance) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, vector<set<int> >& exclusions,
RealOpenMM* fixedParameters, const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Vec3>& atomCoordinates,
double** atomParameters, vector<set<int> >& exclusions,
double* fixedParameters, const map<string, double>& globalParameters, vector<Vec3>& forces,
double* energyByAtom, double* totalEnergy, double* energyParamDerivs) {
for (map<string, double>::const_iterator iter = globalParameters.begin(); iter != globalParameters.end(); ++iter)
expressionSet.setVariable(expressionSet.getVariableIndex(iter->first), iter->second);
......@@ -232,38 +225,38 @@ void ReferenceCustomNonbondedIxn::calculatePairIxn(int numberOfAtoms, vector<Rea
--------------------------------------------------------------------------------------- */
void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<RealVec>& atomCoordinates, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, double* energyParamDerivs) {
void ReferenceCustomNonbondedIxn::calculateOneIxn(int ii, int jj, vector<Vec3>& atomCoordinates, vector<Vec3>& forces,
double* energyByAtom, double* totalEnergy, double* energyParamDerivs) {
// get deltaR, R2, and R between 2 atoms
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
double deltaR[ReferenceForce::LastDeltaRIndex];
if (periodic)
ReferenceForce::getDeltaRPeriodic(atomCoordinates[jj], atomCoordinates[ii], periodicBoxVectors, deltaR);
else
ReferenceForce::getDeltaR(atomCoordinates[jj], atomCoordinates[ii], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
double r = deltaR[ReferenceForce::RIndex];
if (cutoff && r >= cutoffDistance)
return;
// accumulate forces
expressionSet.setVariable(rIndex, r);
RealOpenMM dEdR = (RealOpenMM) (forceExpression.evaluate()/(deltaR[ReferenceForce::RIndex]));
RealOpenMM energy = (RealOpenMM) energyExpression.evaluate();
RealOpenMM switchValue = 1.0;
double dEdR = forceExpression.evaluate()/(deltaR[ReferenceForce::RIndex]);
double energy = energyExpression.evaluate();
double switchValue = 1.0;
if (useSwitch) {
if (r > switchingDistance) {
RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
double t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
switchValue = 1+t*t*t*(-10+t*(15-t*6));
RealOpenMM switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
double switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
dEdR = switchValue*dEdR + energy*switchDeriv/r;
energy *= switchValue;
}
}
for (int kk = 0; kk < 3; kk++) {
RealOpenMM force = -dEdR*deltaR[kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
double force = -dEdR*deltaR[kk];
forces[ii][kk] += force;
forces[jj][kk] -= force;
}
for (int i = 0; i < energyParamDerivExpressions.size(); i++)
energyParamDerivs[i] += switchValue*energyParamDerivExpressions[i].evaluate();
......
platforms/reference/src/SimTKReference/ReferenceCustomTorsionIxn.cpp
View file @ 047934e2
......@@ -62,7 +62,7 @@ ReferenceCustomTorsionIxn::ReferenceCustomTorsionIxn(const Lepton::CompiledExpre
ReferenceCustomTorsionIxn::~ReferenceCustomTorsionIxn() {
}
void ReferenceCustomTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceCustomTorsionIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -82,11 +82,11 @@ void ReferenceCustomTorsionIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
RealOpenMM deltaR[3][ReferenceForce::LastDeltaRIndex];
vector<Vec3>& atomCoordinates,
double* parameters,
vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
double deltaR[3][ReferenceForce::LastDeltaRIndex];
for (int i = 0; i < numParameters; i++)
expressionSet.setVariable(torsionParamIndex[i], parameters[i]);
......@@ -111,45 +111,45 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
// Visual Studio complains if crossProduct declared as 'crossProduct[2][3]'
RealOpenMM crossProductMemory[6];
RealOpenMM* crossProduct[2];
double crossProductMemory[6];
double* crossProduct[2];
crossProduct[0] = crossProductMemory;
crossProduct[1] = crossProductMemory + 3;
// get dihedral angle
RealOpenMM dotDihedral;
RealOpenMM signOfAngle;
RealOpenMM angle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2], crossProduct, &dotDihedral, deltaR[0], &signOfAngle, 1);
double dotDihedral;
double signOfAngle;
double angle = getDihedralAngleBetweenThreeVectors(deltaR[0], deltaR[1], deltaR[2], crossProduct, &dotDihedral, deltaR[0], &signOfAngle, 1);
expressionSet.setVariable(thetaIndex, angle);
// evaluate delta angle, dE/d(angle)
RealOpenMM dEdAngle = (RealOpenMM) forceExpression.evaluate();
double dEdAngle = forceExpression.evaluate();
// compute force
RealOpenMM internalF[4][3];
RealOpenMM forceFactors[4];
RealOpenMM normCross1 = DOT3(crossProduct[0], crossProduct[0]);
RealOpenMM normBC = deltaR[1][ReferenceForce::RIndex];
forceFactors[0] = (-dEdAngle*normBC)/normCross1;
double internalF[4][3];
double forceFactors[4];
double normCross1 = DOT3(crossProduct[0], crossProduct[0]);
double normBC = deltaR[1][ReferenceForce::RIndex];
forceFactors[0] = (-dEdAngle*normBC)/normCross1;
RealOpenMM normCross2 = DOT3(crossProduct[1], crossProduct[1]);
forceFactors[3] = (dEdAngle*normBC)/normCross2;
double normCross2 = DOT3(crossProduct[1], crossProduct[1]);
forceFactors[3] = (dEdAngle*normBC)/normCross2;
forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
forceFactors[1] /= deltaR[1][ReferenceForce::R2Index];
forceFactors[1] = DOT3(deltaR[0], deltaR[1]);
forceFactors[1] /= deltaR[1][ReferenceForce::R2Index];
forceFactors[2] = DOT3(deltaR[2], deltaR[1]);
forceFactors[2] /= deltaR[1][ReferenceForce::R2Index];
forceFactors[2] = DOT3(deltaR[2], deltaR[1]);
forceFactors[2] /= deltaR[1][ReferenceForce::R2Index];
for (int ii = 0; ii < 3; ii++) {
internalF[0][ii] = forceFactors[0]*crossProduct[0][ii];
internalF[3][ii] = forceFactors[3]*crossProduct[1][ii];
RealOpenMM s = forceFactors[1]*internalF[0][ii] - forceFactors[2]*internalF[3][ii];
double s = forceFactors[1]*internalF[0][ii] - forceFactors[2]*internalF[3][ii];
internalF[1][ii] = internalF[0][ii] - s;
internalF[2][ii] = internalF[3][ii] + s;
......@@ -172,6 +172,6 @@ void ReferenceCustomTorsionIxn::calculateBondIxn(int* atomIndices,
// accumulate energies
if (totalEnergy != NULL)
*totalEnergy += (RealOpenMM) energyExpression.evaluate();
*totalEnergy += energyExpression.evaluate();
}
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ 047934e2
......@@ -44,19 +44,10 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceDynamics::ReferenceDynamics(int numberOfAtoms, RealOpenMM deltaT, RealOpenMM temperature) :
ReferenceDynamics::ReferenceDynamics(int numberOfAtoms, double deltaT, double temperature) :
_numberOfAtoms(numberOfAtoms), _deltaT(deltaT), _temperature(temperature) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::ReferenceDynamics";
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
_timeStep = 0;
_timeStep = 0;
_ownReferenceConstraint = false;
_referenceConstraint = NULL;
}
......@@ -68,13 +59,6 @@ ReferenceDynamics::ReferenceDynamics(int numberOfAtoms, RealOpenMM deltaT, Real
--------------------------------------------------------------------------------------- */
ReferenceDynamics::~ReferenceDynamics() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::~ReferenceDynamics";
// ---------------------------------------------------------------------------------------
if (_ownReferenceConstraint) {
delete _referenceConstraint;
}
......@@ -89,13 +73,6 @@ ReferenceDynamics::~ReferenceDynamics() {
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::getNumberOfAtoms() const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::getNumberOfAtoms";
// ---------------------------------------------------------------------------------------
return _numberOfAtoms;
}
......@@ -108,13 +85,6 @@ int ReferenceDynamics::getNumberOfAtoms() const {
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::getTimeStep() const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::getTimeStep";
// ---------------------------------------------------------------------------------------
return _timeStep;
}
......@@ -127,13 +97,6 @@ int ReferenceDynamics::getTimeStep() const {
--------------------------------------------------------------------------------------- */
int ReferenceDynamics::incrementTimeStep() {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::getTimeStep";
// ---------------------------------------------------------------------------------------
return (++_timeStep);
}
......@@ -145,14 +108,7 @@ int ReferenceDynamics::incrementTimeStep() {
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceDynamics::getDeltaT() const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::getDeltaT";
// ---------------------------------------------------------------------------------------
double ReferenceDynamics::getDeltaT() const {
return _deltaT;
}
......@@ -162,14 +118,7 @@ RealOpenMM ReferenceDynamics::getDeltaT() const {
--------------------------------------------------------------------------------------- */
void ReferenceDynamics::setDeltaT(RealOpenMM deltaT) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::setDeltaT";
// ---------------------------------------------------------------------------------------
void ReferenceDynamics::setDeltaT(double deltaT) {
_deltaT = deltaT;
}
......@@ -181,14 +130,7 @@ void ReferenceDynamics::setDeltaT(RealOpenMM deltaT) {
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceDynamics::getTemperature() const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::getTemperature";
// ---------------------------------------------------------------------------------------
double ReferenceDynamics::getTemperature() const {
return _temperature;
}
......@@ -201,13 +143,6 @@ RealOpenMM ReferenceDynamics::getTemperature() const {
--------------------------------------------------------------------------------------- */
ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm() const {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::getReferenceConstraint";
// ---------------------------------------------------------------------------------------
return _referenceConstraint;
}
......@@ -220,13 +155,6 @@ ReferenceConstraintAlgorithm* ReferenceDynamics::getReferenceConstraintAlgorithm
--------------------------------------------------------------------------------------- */
void ReferenceDynamics::setReferenceConstraintAlgorithm(ReferenceConstraintAlgorithm* referenceConstraint) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "\nReferenceDynamics::setReferenceConstraint";
// ---------------------------------------------------------------------------------------
// delete if own
if (_referenceConstraint && _ownReferenceConstraint) {
......@@ -251,15 +179,6 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm(ReferenceConstraintAlgor
--------------------------------------------------------------------------------------- */
void ReferenceDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceDynamics::update";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
// ---------------------------------------------------------------------------------------
void ReferenceDynamics::update(const OpenMM::System& system, vector<Vec3>& atomCoordinates,
vector<Vec3>& velocities, vector<Vec3>& forces, vector<double>& masses, double tolerance) {
}
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ 047934e2
......@@ -56,40 +56,40 @@ ReferenceForce::~ReferenceForce() {
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceForce::periodicDifference(RealOpenMM val1, RealOpenMM val2, RealOpenMM period) {
RealOpenMM diff = val1-val2;
RealOpenMM base = (RealOpenMM) (floor(diff/period+0.5)*period);
double ReferenceForce::periodicDifference(double val1, double val2, double period) {
double diff = val1-val2;
double base = floor(diff/period+0.5)*period;
return diff-base;
}
void ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
RealOpenMM* deltaR) {
void ReferenceForce::getDeltaR(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
double* deltaR) {
deltaR[XIndex] = atomCoordinatesJ[0] - atomCoordinatesI[0];
deltaR[YIndex] = atomCoordinatesJ[1] - atomCoordinatesI[1];
deltaR[ZIndex] = atomCoordinatesJ[2] - atomCoordinatesI[2];
deltaR[R2Index] = DOT3(deltaR, deltaR);
deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
deltaR[RIndex] = sqrt(deltaR[R2Index]);
}
RealVec ReferenceForce::getDeltaR(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ) {
Vec3 ReferenceForce::getDeltaR(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ) {
return atomCoordinatesJ-atomCoordinatesI;
}
void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealOpenMM* boxSize, RealOpenMM* deltaR) {
void ReferenceForce::getDeltaRPeriodic(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
const double* boxSize, double* deltaR) {
deltaR[XIndex] = periodicDifference(atomCoordinatesJ[0], atomCoordinatesI[0], boxSize[0]);
deltaR[YIndex] = periodicDifference(atomCoordinatesJ[1], atomCoordinatesI[1], boxSize[1]);
deltaR[ZIndex] = periodicDifference(atomCoordinatesJ[2], atomCoordinatesI[2], boxSize[2]);
deltaR[R2Index] = DOT3(deltaR, deltaR);
deltaR[RIndex] = (RealOpenMM) SQRT(deltaR[R2Index]);
deltaR[RIndex] = sqrt(deltaR[R2Index]);
}
void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealVec* boxVectors, RealOpenMM* deltaR) {
RealVec diff = atomCoordinatesJ-atomCoordinatesI;
void ReferenceForce::getDeltaRPeriodic(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
const Vec3* boxVectors, double* deltaR) {
Vec3 diff = atomCoordinatesJ-atomCoordinatesI;
diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5);
diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5);
diff -= boxVectors[0]*floor(diff[0]/boxVectors[0][0]+0.5);
......@@ -97,12 +97,12 @@ void ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const Re
deltaR[YIndex] = diff[1];
deltaR[ZIndex] = diff[2];
deltaR[R2Index] = diff.dot(diff);
deltaR[RIndex] = SQRT(deltaR[R2Index]);
deltaR[RIndex] = sqrt(deltaR[R2Index]);
}
RealVec ReferenceForce::getDeltaRPeriodic(const RealVec& atomCoordinatesI, const RealVec& atomCoordinatesJ,
const RealVec* boxVectors) {
RealVec diff = atomCoordinatesJ-atomCoordinatesI;
Vec3 ReferenceForce::getDeltaRPeriodic(const Vec3& atomCoordinatesI, const Vec3& atomCoordinatesJ,
const Vec3* boxVectors) {
Vec3 diff = atomCoordinatesJ-atomCoordinatesI;
diff -= boxVectors[2]*floor(diff[2]/boxVectors[2][2]+0.5);
diff -= boxVectors[1]*floor(diff[1]/boxVectors[1][1]+0.5);
diff -= boxVectors[0]*floor(diff[0]/boxVectors[0][0]+0.5);
......
platforms/reference/src/SimTKReference/ReferenceGayBerneForce.cpp
View file @ 047934e2
......@@ -78,11 +78,11 @@ ReferenceGayBerneForce::ReferenceGayBerneForce(const GayBerneForce& force) {
for (int i = 0; i < numParticles; i++) {
ParticleInfo& p = particles[i];
s[i] = (p.rx*p.ry + p.rz*p.rz)*SQRT(p.rx*p.ry);
s[i] = (p.rx*p.ry + p.rz*p.rz)*sqrt(p.rx*p.ry);
}
}
RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positions, vector<RealVec>& forces, const RealVec* boxVectors) {
double ReferenceGayBerneForce::calculateForce(const vector<Vec3>& positions, vector<Vec3>& forces, const Vec3* boxVectors) {
if (nonbondedMethod == GayBerneForce::CutoffPeriodic) {
double minAllowedSize = 1.999999*cutoffDistance;
if (boxVectors[0][0] < minAllowedSize || boxVectors[1][1] < minAllowedSize || boxVectors[2][2] < minAllowedSize)
......@@ -95,9 +95,9 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
// Compute standard interactions.
RealOpenMM energy = 0;
double energy = 0;
int numParticles = particles.size();
vector<RealVec> torques(numParticles, Vec3());
vector<Vec3> torques(numParticles, Vec3());
for (int i = 1; i < numParticles; i++) {
if (particles[i].epsilon == 0.0)
continue;
......@@ -106,8 +106,8 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
continue;
if (exclusions.find(make_pair(j, i)) != exclusions.end())
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);
double sigma = 0.5*(particles[i].sigma+particles[j].sigma);
double epsilon = sqrt(particles[i].epsilon*particles[j].epsilon);
energy += computeOneInteraction(i, j, sigma, epsilon, positions, forces, torques, boxVectors);
}
}
......@@ -126,39 +126,39 @@ RealOpenMM ReferenceGayBerneForce::calculateForce(const vector<RealVec>& positio
return energy;
}
void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<RealVec>& positions) {
void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<Vec3>& positions) {
int numParticles = particles.size();
for (int particle = 0; particle < numParticles; particle++) {
ParticleInfo& p = particles[particle];
// Compute the local coordinate system of the ellipsoid;
RealVec xdir, ydir, zdir;
Vec3 xdir, ydir, zdir;
if (p.xparticle == -1) {
xdir = RealVec(1, 0, 0);
ydir = RealVec(0, 1, 0);
xdir = Vec3(1, 0, 0);
ydir = Vec3(0, 1, 0);
}
else {
xdir = positions[particle]-positions[p.xparticle];
xdir /= SQRT(xdir.dot(xdir));
xdir /= sqrt(xdir.dot(xdir));
if (p.yparticle == -1) {
if (xdir[1] > -0.5 && xdir[1] < 0.5)
ydir = RealVec(0, 1, 0);
ydir = Vec3(0, 1, 0);
else
ydir = RealVec(1, 0, 0);
ydir = Vec3(1, 0, 0);
}
else
ydir = positions[particle]-positions[p.yparticle];
ydir -= xdir*(xdir.dot(ydir));
ydir /= SQRT(ydir.dot(ydir));
ydir /= sqrt(ydir.dot(ydir));
}
zdir = xdir.cross(ydir);
// Compute matrices we will need later.
RealOpenMM (&a)[3][3] = A[particle].v;
RealOpenMM (&b)[3][3] = B[particle].v;
RealOpenMM (&g)[3][3] = G[particle].v;
double (&a)[3][3] = A[particle].v;
double (&b)[3][3] = B[particle].v;
double (&g)[3][3] = G[particle].v;
a[0][0] = xdir[0];
a[0][1] = xdir[1];
a[0][2] = xdir[2];
......@@ -168,8 +168,8 @@ void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<RealVec>& posit
a[2][0] = zdir[0];
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(1/sqrt(p.ex), 1/sqrt(p.ey), 1/sqrt(p.ez));
Vec3 r2(p.rx*p.rx, p.ry*p.ry, p.rz*p.rz);
Vec3 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;
......@@ -182,26 +182,26 @@ void ReferenceGayBerneForce::computeEllipsoidFrames(const vector<RealVec>& posit
}
}
void ReferenceGayBerneForce::applyTorques(const vector<RealVec>& positions, vector<RealVec>& forces, const vector<RealVec>& torques) {
void ReferenceGayBerneForce::applyTorques(const vector<Vec3>& positions, vector<Vec3>& forces, const vector<Vec3>& torques) {
int numParticles = particles.size();
for (int particle = 0; particle < numParticles; particle++) {
ParticleInfo& p = particles[particle];
RealVec pos = positions[particle];
Vec3 pos = positions[particle];
if (p.xparticle != -1) {
// Apply a force to the x particle.
RealVec dx = positions[p.xparticle]-pos;
Vec3 dx = positions[p.xparticle]-pos;
double dx2 = dx.dot(dx);
RealVec f = torques[particle].cross(dx)/dx2;
Vec3 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;
Vec3 dy = positions[p.yparticle]-pos;
double dy2 = dy.dot(dy);
RealVec torque = dx*(torques[particle].dot(dx)/dx2);
Vec3 torque = dx*(torques[particle].dot(dx)/dx2);
f = torque.cross(dy)/dy2;
forces[p.yparticle] += f;
forces[particle] -= f;
......@@ -210,62 +210,62 @@ void ReferenceGayBerneForce::applyTorques(const vector<RealVec>& positions, vect
}
}
RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int particle2, RealOpenMM sigma, RealOpenMM epsilon, const vector<RealVec>& positions,
vector<RealVec>& forces, vector<RealVec>& torques, const RealVec* boxVectors) {
double ReferenceGayBerneForce::computeOneInteraction(int particle1, int particle2, double sigma, double epsilon, const vector<Vec3>& positions,
vector<Vec3>& forces, vector<Vec3>& torques, const Vec3* boxVectors) {
// Compute the displacement and check against the cutoff.
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
double deltaR[ReferenceForce::LastDeltaRIndex];
if (nonbondedMethod == GayBerneForce::CutoffPeriodic)
ReferenceForce::getDeltaRPeriodic(positions[particle2], positions[particle1], boxVectors, deltaR);
else
ReferenceForce::getDeltaR(positions[particle2], positions[particle1], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
double r = deltaR[ReferenceForce::RIndex];
if (nonbondedMethod != GayBerneForce::NoCutoff && r >= cutoffDistance)
return 0;
// Compute vectors and matrices we'll be needing.
RealOpenMM rInv = 1/r;
RealVec dr(deltaR[ReferenceForce::XIndex], deltaR[ReferenceForce::YIndex], deltaR[ReferenceForce::ZIndex]);
RealVec drUnit = dr*rInv;
double rInv = 1/r;
Vec3 dr(deltaR[ReferenceForce::XIndex], deltaR[ReferenceForce::YIndex], deltaR[ReferenceForce::ZIndex]);
Vec3 drUnit = dr*rInv;
Matrix B12 = B[particle1]+B[particle2];
Matrix G12 = G[particle1]+G[particle2];
Matrix B12inv = B12.inverse();
Matrix G12inv = G12.inverse();
RealOpenMM detG12 = G12.determinant();
double detG12 = G12.determinant();
// Compute the switching function.
RealOpenMM switchValue = 1, switchDeriv = 0;
double switchValue = 1, switchDeriv = 0;
if (useSwitchingFunction && r > switchingDistance) {
RealOpenMM t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
double t = (r-switchingDistance)/(cutoffDistance-switchingDistance);
switchValue = 1+t*t*t*(-10+t*(15-t*6));
switchDeriv = t*t*(-30+t*(60-t*30))/(cutoffDistance-switchingDistance);
}
// Estimate the distance between the ellipsoids and compute the first terms needed for the energy.
RealOpenMM sigma12 = 1/SQRT(0.5*drUnit.dot(G12inv*drUnit));
RealOpenMM h12 = r - sigma12;
RealOpenMM rho = sigma/(h12+sigma);
RealOpenMM rho2 = rho*rho;
RealOpenMM rho6 = rho2*rho2*rho2;
RealOpenMM u = 4*epsilon*(rho6*rho6-rho6);
RealOpenMM eta = SQRT(2*s[particle1]*s[particle2]/detG12);
RealOpenMM chi = 2*drUnit.dot(B12inv*drUnit);
double sigma12 = 1/sqrt(0.5*drUnit.dot(G12inv*drUnit));
double h12 = r - sigma12;
double rho = sigma/(h12+sigma);
double rho2 = rho*rho;
double rho6 = rho2*rho2*rho2;
double u = 4*epsilon*(rho6*rho6-rho6);
double eta = sqrt(2*s[particle1]*s[particle2]/detG12);
double chi = 2*drUnit.dot(B12inv*drUnit);
chi *= chi;
RealOpenMM energy = u*eta*chi;
double energy = u*eta*chi;
// Compute the terms needed for the force.
RealVec kappa = G12inv*dr;
RealVec iota = B12inv*dr;
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*switchValue) - drUnit*(energy*switchDeriv);
Vec3 kappa = G12inv*dr;
Vec3 iota = B12inv*dr;
double rInv2 = rInv*rInv;
double dUSLJdr = 24*epsilon*(2*rho6-1)*rho6*rho/sigma;
double temp = 0.5*sigma12*sigma12*sigma12*rInv2;
Vec3 dudr = (drUnit + (kappa-drUnit*kappa.dot(drUnit))*temp)*dUSLJdr;
Vec3 dchidr = (iota-drUnit*iota.dot(drUnit))*(-8*rInv2*sqrt(chi));
Vec3 force = (dchidr*u + dudr*chi)*(eta*switchValue) - drUnit*(energy*switchDeriv);
forces[particle1] += force;
forces[particle2] -= force;
......@@ -273,14 +273,14 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
for (int j = 0; j < 2; j++) {
int particle = (j == 0 ? particle1 : particle2);
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;
Vec3 dudq = (kappa*G[particle]).cross(kappa*(temp*dUSLJdr));
Vec3 dchidq = (iota*B[particle]).cross(iota)*(-4*rInv2);
double (&g12)[3][3] = G12.v;
double (&a)[3][3] = A[particle].v;
ParticleInfo& p = particles[particle];
RealVec scale = RealVec(p.rx*p.rx, p.ry*p.ry, p.rz*p.rz)*(-0.5*eta/detG12);
Vec3 scale = Vec3(p.rx*p.rx, p.ry*p.ry, p.rz*p.rz)*(-0.5*eta/detG12);
Matrix D;
RealOpenMM (&d)[3][3] = D.v;
double (&d)[3][3] = D.v;
d[0][0] = scale[0]*(2*a[0][0]*(g12[1][1]*g12[2][2] - g12[1][2]*g12[2][1]) +
a[0][2]*(g12[1][2]*g12[0][1] + g12[1][0]*g12[2][1] - g12[1][1]*(g12[0][2] + g12[2][0])) +
a[0][1]*(g12[0][2]*g12[2][1] + g12[2][0]*g12[1][2] - g12[2][2]*(g12[0][1] + g12[1][0])));
......@@ -308,10 +308,10 @@ RealOpenMM ReferenceGayBerneForce::computeOneInteraction(int particle1, int part
d[2][2] = scale[2]*( a[2][0]*(g12[0][1]*g12[1][2] + g12[2][1]*g12[1][0] - g12[1][1]*(g12[0][2] + g12[2][0])) +
a[2][1]*(g12[1][0]*g12[0][2] + g12[2][0]*g12[0][1] - g12[0][0]*(g12[1][2] + g12[2][1])) +
2*a[2][2]*(g12[1][1]*g12[0][0] - g12[1][0]*g12[0][1]));
RealVec detadq;
Vec3 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))*switchValue;
detadq += Vec3(a[i][0], a[i][1], a[i][2]).cross(Vec3(d[i][0], d[i][1], d[i][2]));
Vec3 torque = (dchidq*(u*eta) + detadq*(u*chi) + dudq*(eta*chi))*switchValue;
torques[particle] -= torque;
}
return switchValue*energy;
......
platforms/reference/src/SimTKReference/ReferenceHarmonicBondIxn.cpp
View file @ 047934e2
......@@ -50,7 +50,7 @@ ReferenceHarmonicBondIxn::ReferenceHarmonicBondIxn() : usePeriodic(false) {
ReferenceHarmonicBondIxn::~ReferenceHarmonicBondIxn() {
}
void ReferenceHarmonicBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
void ReferenceHarmonicBondIxn::setPeriodic(OpenMM::Vec3* vectors) {
usePeriodic = true;
boxVectors[0] = vectors[0];
boxVectors[1] = vectors[1];
......@@ -71,20 +71,11 @@ void ReferenceHarmonicBondIxn::setPeriodic(OpenMM::RealVec* vectors) {
--------------------------------------------------------------------------------------- */
void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
vector<RealVec>& atomCoordinates,
RealOpenMM* parameters,
vector<RealVec>& forces,
RealOpenMM* totalEnergy, double* energyParamDerivs) {
static const std::string methodName = "\nReferenceHarmonicBondIxn::calculateBondIxn";
static const int twoI = 2;
static const RealOpenMM zero = 0.0;
static const RealOpenMM two = 2.0;
static const RealOpenMM half = 0.5;
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
vector<Vec3>& atomCoordinates,
double* parameters,
vector<Vec3>& forces,
double* totalEnergy, double* energyParamDerivs) {
double deltaR[ReferenceForce::LastDeltaRIndex];
// ---------------------------------------------------------------------------------------
......@@ -99,14 +90,14 @@ void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
// deltaIdeal = r - r_0
RealOpenMM deltaIdeal = deltaR[ReferenceForce::RIndex] - parameters[0];
RealOpenMM deltaIdeal2 = deltaIdeal*deltaIdeal;
double deltaIdeal = deltaR[ReferenceForce::RIndex] - parameters[0];
double deltaIdeal2 = deltaIdeal*deltaIdeal;
RealOpenMM dEdR = parameters[1]*deltaIdeal;
double dEdR = parameters[1]*deltaIdeal;
// chain rule
dEdR = deltaR[ReferenceForce::RIndex] > zero ? (dEdR/deltaR[ReferenceForce::RIndex]) : zero;
dEdR = deltaR[ReferenceForce::RIndex] > 0.0 ? (dEdR/deltaR[ReferenceForce::RIndex]) : 0.0;
forces[atomAIndex][0] += dEdR*deltaR[ReferenceForce::XIndex];
forces[atomAIndex][1] += dEdR*deltaR[ReferenceForce::YIndex];
......@@ -117,5 +108,5 @@ void ReferenceHarmonicBondIxn::calculateBondIxn(int* atomIndices,
forces[atomBIndex][2] -= dEdR*deltaR[ReferenceForce::ZIndex];
if (totalEnergy != NULL)
*totalEnergy += half*parameters[1]*deltaIdeal2;
*totalEnergy += 0.5*parameters[1]*deltaIdeal2;
}
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