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Commit 19d2885a authored by Lee-Ping's avatar Lee-Ping
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Merge github.com:SimTk/openmm

parents 99ef4344 57a6768e
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Showing with 92 additions and 144 deletions
platforms/reference/src/SimTKReference/ReferenceBrownianDynamics.cpp
View file @ 19d2885a
...@@ -125,7 +125,7 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const { ...@@ -125,7 +125,7 @@ RealOpenMM ReferenceBrownianDynamics::getFriction( void ) const {
void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates, void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){ vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -162,7 +162,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real ...@@ -162,7 +162,7 @@ void ReferenceBrownianDynamics::update(const OpenMM::System& system, vector<Real
} }
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm(); ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm) if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses); referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities. // Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceCCMAAlgorithm.cpp
View file @ 19d2885a
...@@ -48,14 +48,12 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms, ...@@ -48,14 +48,12 @@ ReferenceCCMAAlgorithm::ReferenceCCMAAlgorithm(int numberOfAtoms,
const vector<pair<int, int> >& atomIndices, const vector<pair<int, int> >& atomIndices,
const vector<RealOpenMM>& distance, const vector<RealOpenMM>& distance,
vector<RealOpenMM>& masses, vector<RealOpenMM>& masses,
vector<AngleInfo>& angles, vector<AngleInfo>& angles) {
RealOpenMM tolerance) {
_numberOfConstraints = numberOfConstraints; _numberOfConstraints = numberOfConstraints;
_atomIndices = atomIndices; _atomIndices = atomIndices;
_distance = distance; _distance = distance;
_maximumNumberOfIterations = 150; _maximumNumberOfIterations = 150;
_tolerance = tolerance;
_hasInitializedMasses = false; _hasInitializedMasses = false;
// work arrays // work arrays
...@@ -201,28 +199,20 @@ void ReferenceCCMAAlgorithm::setMaximumNumberOfIterations(int maximumNumberOfIte ...@@ -201,28 +199,20 @@ void ReferenceCCMAAlgorithm::setMaximumNumberOfIterations(int maximumNumberOfIte
_maximumNumberOfIterations = maximumNumberOfIterations; _maximumNumberOfIterations = maximumNumberOfIterations;
} }
RealOpenMM ReferenceCCMAAlgorithm::getTolerance() const {
return _tolerance;
}
void ReferenceCCMAAlgorithm::setTolerance(RealOpenMM tolerance) {
_tolerance = tolerance;
}
void ReferenceCCMAAlgorithm::apply(vector<RealVec>& atomCoordinates, void ReferenceCCMAAlgorithm::apply(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP, vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses) { vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false); applyConstraints(atomCoordinates, atomCoordinatesP, inverseMasses, false, tolerance);
} }
void ReferenceCCMAAlgorithm::applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates, void ReferenceCCMAAlgorithm::applyToVelocities(std::vector<OpenMM::RealVec>& atomCoordinates,
std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses) { std::vector<OpenMM::RealVec>& velocities, std::vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
applyConstraints(atomCoordinates, velocities, inverseMasses, true); applyConstraints(atomCoordinates, velocities, inverseMasses, true, tolerance);
} }
void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates, void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
vector<RealVec>& atomCoordinatesP, vector<RealVec>& atomCoordinatesP,
vector<RealOpenMM>& inverseMasses, bool constrainingVelocities) { vector<RealOpenMM>& inverseMasses, bool constrainingVelocities, RealOpenMM tolerance) {
// temp arrays // temp arrays
vector<RealVec>& r_ij = _r_ij; vector<RealVec>& r_ij = _r_ij;
...@@ -242,15 +232,14 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates, ...@@ -242,15 +232,14 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
// setup: r_ij for each (i,j) constraint // setup: r_ij for each (i,j) constraint
RealOpenMM tolerance = getTolerance()*2;
for (int ii = 0; ii < _numberOfConstraints; ii++) { for (int ii = 0; ii < _numberOfConstraints; ii++) {
int atomI = _atomIndices[ii].first; int atomI = _atomIndices[ii].first;
int atomJ = _atomIndices[ii].second; int atomJ = _atomIndices[ii].second;
r_ij[ii] = atomCoordinates[atomI] - atomCoordinates[atomJ]; r_ij[ii] = atomCoordinates[atomI] - atomCoordinates[atomJ];
d_ij2[ii] = r_ij[ii].dot(r_ij[ii]); d_ij2[ii] = r_ij[ii].dot(r_ij[ii]);
} }
RealOpenMM lowerTol = 1-2*getTolerance()+getTolerance()*getTolerance(); RealOpenMM lowerTol = 1-2*tolerance+tolerance*tolerance;
RealOpenMM upperTol = 1+2*getTolerance()+getTolerance()*getTolerance(); RealOpenMM upperTol = 1+2*tolerance+tolerance*tolerance;
// main loop // main loop
...@@ -267,7 +256,7 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates, ...@@ -267,7 +256,7 @@ void ReferenceCCMAAlgorithm::applyConstraints(vector<RealVec>& atomCoordinates,
if (constrainingVelocities) { if (constrainingVelocities) {
RealOpenMM rrpr = rp_ij.dot(r_ij[ii]); RealOpenMM rrpr = rp_ij.dot(r_ij[ii]);
constraintDelta[ii] = -2*reducedMasses[ii]*rrpr/d_ij2[ii]; constraintDelta[ii] = -2*reducedMasses[ii]*rrpr/d_ij2[ii];
if (fabs(constraintDelta[ii]) <= getTolerance()) if (fabs(constraintDelta[ii]) <= tolerance)
numberConverged++; numberConverged++;
} }
else { else {
......
platforms/reference/src/SimTKReference/ReferenceConstraints.cpp
View file @ 19d2885a
...@@ -30,6 +30,8 @@ ...@@ -30,6 +30,8 @@
* -------------------------------------------------------------------------- */ * -------------------------------------------------------------------------- */
#include "ReferenceConstraints.h" #include "ReferenceConstraints.h"
#include "ReferenceCCMAAlgorithm.h"
#include "ReferenceSETTLEAlgorithm.h"
#include "openmm/HarmonicAngleForce.h" #include "openmm/HarmonicAngleForce.h"
#include "openmm/OpenMMException.h" #include "openmm/OpenMMException.h"
#include <map> #include <map>
...@@ -39,8 +41,7 @@ ...@@ -39,8 +41,7 @@
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tolerance) : ccma(NULL), settle(NULL) { ReferenceConstraints::ReferenceConstraints(const System& system) : ccma(NULL), settle(NULL) {
this->tolerance = tolerance;
int numParticles = system.getNumParticles(); int numParticles = system.getNumParticles();
vector<RealOpenMM> masses(numParticles); vector<RealOpenMM> masses(numParticles);
for (int i = 0; i < numParticles; ++i) for (int i = 0; i < numParticles; ++i)
...@@ -141,7 +142,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole ...@@ -141,7 +142,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole
isSettleAtom[p2] = true; isSettleAtom[p2] = true;
isSettleAtom[p3] = true; isSettleAtom[p3] = true;
} }
settle = new ReferenceSETTLEAlgorithm(atom1, atom2, atom3, distance1, distance2, masses, tolerance); settle = new ReferenceSETTLEAlgorithm(atom1, atom2, atom3, distance1, distance2, masses);
} }
// All other constraints are handled with CCMA. // All other constraints are handled with CCMA.
...@@ -179,7 +180,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole ...@@ -179,7 +180,7 @@ ReferenceConstraints::ReferenceConstraints(const System& system, RealOpenMM tole
// Create the CCMA object. // Create the CCMA object.
ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles, tolerance); ccma = new ReferenceCCMAAlgorithm(numParticles, numCCMA, ccmaIndices, ccmaDistance, masses, angles);
} }
} }
...@@ -190,28 +191,16 @@ ReferenceConstraints::~ReferenceConstraints() { ...@@ -190,28 +191,16 @@ ReferenceConstraints::~ReferenceConstraints() {
delete settle; delete settle;
} }
RealOpenMM ReferenceConstraints::getTolerance() const { void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
return tolerance;
}
void ReferenceConstraints::setTolerance(RealOpenMM tolerance) {
this->tolerance = tolerance;
if (ccma != NULL)
ccma->setTolerance(tolerance);
if (settle != NULL)
settle->setTolerance(tolerance);
}
void ReferenceConstraints::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) {
if (ccma != NULL) if (ccma != NULL)
ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses); ccma->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
if (settle != NULL) if (settle != NULL)
settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses); settle->apply(atomCoordinates, atomCoordinatesP, inverseMasses, tolerance);
} }
void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) { void ReferenceConstraints::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
if (ccma != NULL) if (ccma != NULL)
ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses); ccma->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
if (settle != NULL) if (settle != NULL)
settle->applyToVelocities(atomCoordinates, velocities, inverseMasses); settle->applyToVelocities(atomCoordinates, velocities, inverseMasses, tolerance);
} }
platforms/reference/src/SimTKReference/ReferenceCustomDynamics.cpp
View file @ 19d2885a
...@@ -97,7 +97,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() { ...@@ -97,7 +97,7 @@ ReferenceCustomDynamics::~ReferenceCustomDynamics() {
void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates, void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses,
map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid){ map<string, RealOpenMM>& globals, vector<vector<RealVec> >& perDof, bool& forcesAreValid, RealOpenMM tolerance){
int numSteps = stepType.size(); int numSteps = stepType.size();
globals.insert(context.getParameters().begin(), context.getParameters().end()); globals.insert(context.getParameters().begin(), context.getParameters().end());
oldPos = atomCoordinates; oldPos = atomCoordinates;
...@@ -252,12 +252,12 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve ...@@ -252,12 +252,12 @@ void ReferenceCustomDynamics::update(ContextImpl& context, int numberOfAtoms, ve
break; break;
} }
case CustomIntegrator::ConstrainPositions: { case CustomIntegrator::ConstrainPositions: {
getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses); getReferenceConstraintAlgorithm()->apply(oldPos, atomCoordinates, inverseMasses, tolerance);
oldPos = atomCoordinates; oldPos = atomCoordinates;
break; break;
} }
case CustomIntegrator::ConstrainVelocities: { case CustomIntegrator::ConstrainVelocities: {
getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses); getReferenceConstraintAlgorithm()->applyToVelocities(oldPos, velocities, inverseMasses, tolerance);
break; break;
} }
case CustomIntegrator::UpdateContextState: { case CustomIntegrator::UpdateContextState: {
......
platforms/reference/src/SimTKReference/ReferenceDynamics.cpp
View file @ 19d2885a
...@@ -249,11 +249,12 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgo ...@@ -249,11 +249,12 @@ void ReferenceDynamics::setReferenceConstraintAlgorithm( ReferenceConstraintAlgo
@param velocities velocities @param velocities velocities
@param forces forces @param forces forces
@param masses atom masses @param masses atom masses
@param tolerance the constraint tolerance
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates, void ReferenceDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){ vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferencePME.cpp
View file @ 19d2885a
...@@ -195,7 +195,7 @@ pme_calculate_bsplines_moduli(pme_t pme) ...@@ -195,7 +195,7 @@ pme_calculate_bsplines_moduli(pme_t pme)
static void static void
pme_update_grid_index_and_fraction(pme_t pme, pme_update_grid_index_and_fraction(pme_t pme,
vector<RealVec>& atomCoordinates, const vector<RealVec>& atomCoordinates,
const RealOpenMM periodicBoxSize[3]) const RealOpenMM periodicBoxSize[3])
{ {
int i; int i;
...@@ -317,7 +317,7 @@ pme_update_bsplines(pme_t pme) ...@@ -317,7 +317,7 @@ pme_update_bsplines(pme_t pme)
static void static void
pme_grid_spread_charge(pme_t pme, vector<RealOpenMM>& charges) pme_grid_spread_charge(pme_t pme, const vector<RealOpenMM>& charges)
{ {
int order; int order;
int i; int i;
...@@ -519,10 +519,10 @@ pme_reciprocal_convolution(pme_t pme, ...@@ -519,10 +519,10 @@ pme_reciprocal_convolution(pme_t pme,
static void static void
pme_grid_interpolate_force(pme_t pme, pme_grid_interpolate_force(pme_t pme,
const RealOpenMM periodicBoxSize[3], const RealOpenMM periodicBoxSize[3],
vector<RealOpenMM>& charges, const vector<RealOpenMM>& charges,
vector<RealVec>& forces) vector<RealVec>& forces)
{ {
int i; int i;
int ix,iy,iz; int ix,iy,iz;
...@@ -666,12 +666,12 @@ pme_init(pme_t * ppme, ...@@ -666,12 +666,12 @@ pme_init(pme_t * ppme,
int pme_exec(pme_t pme, int pme_exec(pme_t pme,
vector<RealVec>& atomCoordinates, const vector<RealVec>& atomCoordinates,
vector<RealVec>& forces, vector<RealVec>& forces,
vector<RealOpenMM>& charges, const vector<RealOpenMM>& charges,
const RealOpenMM periodicBoxSize[3], const RealOpenMM periodicBoxSize[3],
RealOpenMM * energy, RealOpenMM* energy,
RealOpenMM pme_virial[3][3]) RealOpenMM pme_virial[3][3])
{ {
/* Routine is called with coordinates in x, a box, and charges in q */ /* Routine is called with coordinates in x, a box, and charges in q */
......
platforms/reference/src/SimTKReference/ReferenceSETTLEAlgorithm.cpp
View file @ 19d2885a
...@@ -35,19 +35,23 @@ using namespace OpenMM; ...@@ -35,19 +35,23 @@ using namespace OpenMM;
using namespace std; using namespace std;
ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const vector<int>& atom1, const vector<int>& atom2, const vector<int>& atom3, ReferenceSETTLEAlgorithm::ReferenceSETTLEAlgorithm(const vector<int>& atom1, const vector<int>& atom2, const vector<int>& atom3,
const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses, RealOpenMM tolerance) : const vector<RealOpenMM>& distance1, const vector<RealOpenMM>& distance2, vector<RealOpenMM>& masses) :
atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses), tolerance(tolerance) { atom1(atom1), atom2(atom2), atom3(atom3), distance1(distance1), distance2(distance2), masses(masses) {
} }
RealOpenMM ReferenceSETTLEAlgorithm::getTolerance() const { int ReferenceSETTLEAlgorithm::getNumClusters() const {
return tolerance; return atom1.size();
} }
void ReferenceSETTLEAlgorithm::setTolerance(RealOpenMM tolerance) { void ReferenceSETTLEAlgorithm::getClusterParameters(int index, int& atom1, int& atom2, int& atom3, RealOpenMM& distance1, RealOpenMM& distance2) const {
this->tolerance = tolerance; atom1 = this->atom1[index];
atom2 = this->atom2[index];
atom3 = this->atom3[index];
distance1 = this->distance1[index];
distance2 = this->distance2[index];
} }
void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses) { void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& atomCoordinatesP, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) { for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]]; RealVec apos0 = atomCoordinates[atom1[index]];
RealVec xp0 = atomCoordinatesP[atom1[index]]-apos0; RealVec xp0 = atomCoordinatesP[atom1[index]]-apos0;
...@@ -190,7 +194,7 @@ void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, v ...@@ -190,7 +194,7 @@ void ReferenceSETTLEAlgorithm::apply(vector<OpenMM::RealVec>& atomCoordinates, v
} }
} }
void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses) { void ReferenceSETTLEAlgorithm::applyToVelocities(vector<OpenMM::RealVec>& atomCoordinates, vector<OpenMM::RealVec>& velocities, vector<RealOpenMM>& inverseMasses, RealOpenMM tolerance) {
for (int index = 0; index < (int) atom1.size(); ++index) { for (int index = 0; index < (int) atom1.size(); ++index) {
RealVec apos0 = atomCoordinates[atom1[index]]; RealVec apos0 = atomCoordinates[atom1[index]];
RealVec apos1 = atomCoordinates[atom2[index]]; RealVec apos1 = atomCoordinates[atom2[index]];
......
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ 19d2885a
...@@ -200,7 +200,7 @@ void ReferenceStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec ...@@ -200,7 +200,7 @@ void ReferenceStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec
--------------------------------------------------------------------------------------- */ --------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates, void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses ){ vector<RealVec>& velocities, vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -235,7 +235,7 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re ...@@ -235,7 +235,7 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm(); ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm) if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses); referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates // copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 19d2885a
...@@ -260,7 +260,7 @@ void ReferenceVariableStochasticDynamics::updatePart2( int numberOfAtoms, vector ...@@ -260,7 +260,7 @@ void ReferenceVariableStochasticDynamics::updatePart2( int numberOfAtoms, vector
void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates, void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){ vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -279,7 +279,7 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v ...@@ -279,7 +279,7 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm(); ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm) if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses); referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// copy xPrime -> atomCoordinates // copy xPrime -> atomCoordinates
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ 19d2885a
...@@ -104,7 +104,7 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) { ...@@ -104,7 +104,7 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates, void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize ){ vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM maxStepSize, RealOpenMM tolerance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -155,7 +155,7 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto ...@@ -155,7 +155,7 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto
} }
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm(); ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm) if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses); referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities. // Update the positions and velocities.
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 19d2885a
...@@ -95,7 +95,7 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){ ...@@ -95,7 +95,7 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){
void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates, void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities, vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses ){ vector<RealVec>& forces, vector<RealOpenMM>& masses, RealOpenMM tolerance) {
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
...@@ -131,7 +131,7 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe ...@@ -131,7 +131,7 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
} }
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm(); ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm) if (referenceConstraintAlgorithm)
referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses); referenceConstraintAlgorithm->apply(atomCoordinates, xPrime, inverseMasses, tolerance);
// Update the positions and velocities. // Update the positions and velocities.
......
platforms/reference/tests/CMakeLists.txt
View file @ 19d2885a
...@@ -12,6 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS}) ...@@ -12,6 +12,7 @@ FOREACH(TEST_PROG ${TEST_PROGS})
# All tests use shared libraries # All tests use shared libraries
ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG}) ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET}) TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT}) ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
ENDFOREACH(TEST_PROG ${TEST_PROGS}) ENDFOREACH(TEST_PROG ${TEST_PROGS})
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ 19d2885a
...@@ -251,7 +251,7 @@ void testMembrane() { ...@@ -251,7 +251,7 @@ void testMembrane() {
for (int i = 0; i < (int) forces.size(); ++i) for (int i = 0; i < (int) forces.size(); ++i)
norm += forces[i].dot(forces[i]); norm += forces[i].dot(forces[i]);
norm = std::sqrt(norm); norm = std::sqrt(norm);
const double stepSize = 1e-3; const double stepSize = 1e-2;
double step = 0.5*stepSize/norm; double step = 0.5*stepSize/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles); vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < (int) positions.size(); ++i) { for (int i = 0; i < (int) positions.size(); ++i) {
......
platforms/reference/tests/TestReferenceGBSAOBCForce.cpp
View file @ 19d2885a
...@@ -66,7 +66,7 @@ void testSingleParticle() { ...@@ -66,7 +66,7 @@ void testSingleParticle() {
double bornRadius = 0.15-0.009; // dielectric offset double bornRadius = 0.15-0.009; // dielectric offset
double eps0 = EPSILON0; double eps0 = EPSILON0;
double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius; double bornEnergy = (-0.5*0.5/(8*PI_M*eps0))*(1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric())/bornRadius;
double extendedRadius = bornRadius+0.14; // probe radius double extendedRadius = 0.15+0.14; // probe radius
double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from? Just copied it from CpuImplicitSolvent.cpp double nonpolarEnergy = CAL2JOULE*PI_M*0.0216*(10*extendedRadius)*(10*extendedRadius)*std::pow(0.15/bornRadius, 6.0); // Where did this formula come from? Just copied it from CpuImplicitSolvent.cpp
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01); ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
...@@ -171,7 +171,7 @@ void testForce() { ...@@ -171,7 +171,7 @@ void testForce() {
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2]; norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
} }
norm = std::sqrt(norm); norm = std::sqrt(norm);
const double delta = 1e-3; const double delta = 1e-2;
double step = 0.5*delta/norm; double step = 0.5*delta/norm;
vector<Vec3> positions2(numParticles), positions3(numParticles); vector<Vec3> positions2(numParticles), positions3(numParticles);
for (int i = 0; i < numParticles; ++i) { for (int i = 0; i < numParticles; ++i) {
......
plugins/amoeba/CMakeLists.txt
View file @ 19d2885a
...@@ -16,15 +16,9 @@ ...@@ -16,15 +16,9 @@
#INCLUDE(Dart) #INCLUDE(Dart)
# ----------------------------------------------------------------------------
#SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA OFF CACHE BOOL "Build verison of OpenMMAmoeba w/ backdoor serialization capability")
#SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA TRUE )
SET(CREATE_SERIALIZABLE_OPENMM_AMOEBA FALSE )
# ----------------------------------------------------------------------------
# The source is organized into subdirectories, but we handle them all from # The source is organized into subdirectories, but we handle them all from
# this CMakeLists file rather than letting CMake visit them as SUBDIRS. # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi platforms/reference) SET(OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS . openmmapi serialization)
# Collect up information about the version of the OpenMM library we're building # Collect up information about the version of the OpenMM library we're building
# and make it available to the code so it can be built into the binaries. # and make it available to the code so it can be built into the binaries.
...@@ -41,17 +35,11 @@ ADD_DEFINITIONS(-DOPENMM_AMOEBA_LIBRARY_NAME=${OPENMM_AMOEBA_LIBRARY_NAME} ...@@ -41,17 +35,11 @@ ADD_DEFINITIONS(-DOPENMM_AMOEBA_LIBRARY_NAME=${OPENMM_AMOEBA_LIBRARY_NAME}
SET(SHARED_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}) SET(SHARED_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME})
SET(STATIC_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_static) SET(STATIC_AMOEBA_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_static)
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
SET(SHARED_AMOEBA_SERIALIZABLE_TARGET ${OPENMM_AMOEBA_LIBRARY_NAME}_serializable)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
# But on Unix or Cygwin we have to add the suffix manually # But on Unix or Cygwin we have to add the suffix manually
IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
SET(SHARED_AMOEBA_TARGET ${SHARED_AMOEBA_TARGET}_d) SET(SHARED_AMOEBA_TARGET ${SHARED_AMOEBA_TARGET}_d)
SET(STATIC_AMOEBA_TARGET ${STATIC_AMOEBA_TARGET}_d) SET(STATIC_AMOEBA_TARGET ${STATIC_AMOEBA_TARGET}_d)
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
SET(SHARED_AMOEBA_SERIALIZABLE_TARGET ${SHARED_AMOEBA_SERIALIZABLE_TARGET}_d)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
# These are all the places to search for header files which are # These are all the places to search for header files which are
...@@ -94,11 +82,6 @@ FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS}) ...@@ -94,11 +82,6 @@ FOREACH(subdir ${OPENMM_AMOEBA_PLUGIN_SOURCE_SUBDIRS})
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
ENDFOREACH(subdir) ENDFOREACH(subdir)
INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${OPENMM_DIR}/platforms/reference/src/SimTKReference)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/platforms/reference/src/SimTKReference)
# ---------------------------------------------------------------------------- # ----------------------------------------------------------------------------
# If API_AMOEBA wrappers are being generated, and add them to the build. # If API_AMOEBA wrappers are being generated, and add them to the build.
...@@ -111,24 +94,18 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS) ...@@ -111,24 +94,18 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src) INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
ADD_LIBRARY(${SHARED_AMOEBA_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES}) ADD_LIBRARY(${SHARED_AMOEBA_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY") SET_TARGET_PROPERTIES(${SHARED_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY")
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA ) FILE(GLOB serialization_files ${CMAKE_CUURENT_SOURCE_DIR}/serialization/src/*.cpp)
ADD_LIBRARY(${SHARED_AMOEBA_SERIALIZABLE_TARGET} SHARED ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES}) SET_SOURCE_FILES_PROPERTIES(${serialization_files} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DTIXML_USE_STL")
SET_TARGET_PROPERTIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_AMOEBA_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_SERIALIZE")
INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/../../serialization/include)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
ADD_LIBRARY(${STATIC_AMOEBA_TARGET} STATIC ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES}) ADD_LIBRARY(${STATIC_AMOEBA_TARGET} STATIC ${SOURCE_AMOEBA_FILES} ${SOURCE_AMOEBA_INCLUDE_FILES} ${API_AMOEBA_ABS_INCLUDE_FILES})
SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY") SET_TARGET_PROPERTIES(${STATIC_AMOEBA_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES -DOPENMM_BUILDING_STATIC_LIBRARY -DLEPTON_USE_STATIC_LIBRARIES -DLEPTON_BUILDING_STATIC_LIBRARY")
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS) IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
ADD_DEPENDENCIES(${SHARED_AMOEBA_TARGET} AmoebaApiWrappers) ADD_DEPENDENCIES(${SHARED_AMOEBA_TARGET} AmoebaApiWrappers)
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
ADD_DEPENDENCIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} AmoebaApiWrappers)
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
ADD_DEPENDENCIES(${STATIC_AMOEBA_TARGET} AmoebaApiWrappers) ADD_DEPENDENCIES(${STATIC_AMOEBA_TARGET} AmoebaApiWrappers)
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
...@@ -140,9 +117,6 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS) ...@@ -140,9 +117,6 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
FIND_LIBRARY(DL_LIBRARY dl) FIND_LIBRARY(DL_LIBRARY dl)
IF(DL_LIBRARY) IF(DL_LIBRARY)
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TARGET} ${DL_LIBRARY}) TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_TARGET} ${DL_LIBRARY})
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
TARGET_LINK_LIBRARIES(${SHARED_AMOEBA_SERIALIZABLE_TARGET} ${DL_LIBRARY})
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES(${STATIC_AMOEBA_TARGET} ${DL_LIBRARY}) TARGET_LINK_LIBRARIES(${STATIC_AMOEBA_TARGET} ${DL_LIBRARY})
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
...@@ -155,16 +129,14 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) ...@@ -155,16 +129,14 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug) ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET} ) TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_TARGET} ${SHARED_TARGET} )
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
TARGET_LINK_LIBRARIES( ${SHARED_AMOEBA_SERIALIZABLE_TARGET} ${SHARED_TARGET} )
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} ) TARGET_LINK_LIBRARIES( ${STATIC_AMOEBA_TARGET} ${STATIC_TARGET} )
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
ADD_SUBDIRECTORY(platforms/reference/tests)
# Which hardware platforms to build # Which hardware platforms to build
ADD_SUBDIRECTORY(platforms/reference)
IF(CUDA_FOUND) IF(CUDA_FOUND)
SET(OPENMM_BUILD_AMOEBA_CUDA_LIB ON CACHE BOOL "Build OpenMMAmoebaCuda library for Nvidia GPUs") SET(OPENMM_BUILD_AMOEBA_CUDA_LIB ON CACHE BOOL "Build OpenMMAmoebaCuda library for Nvidia GPUs")
ELSE(CUDA_FOUND) ELSE(CUDA_FOUND)
...@@ -175,20 +147,11 @@ SET(OPENMM_BUILD_AMOEBA_PATH) ...@@ -175,20 +147,11 @@ SET(OPENMM_BUILD_AMOEBA_PATH)
SET(OPENMM_BUILD_AMOEBA_CUDA_PATH) SET(OPENMM_BUILD_AMOEBA_CUDA_PATH)
IF(OPENMM_BUILD_AMOEBA_CUDA_LIB) IF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
ADD_SUBDIRECTORY(platforms/cuda) ADD_SUBDIRECTORY(platforms/cuda)
SET(OPENMM_BUILD_AMOEBA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
SET(OPENMM_BUILD_AMOEBA_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda) SET(OPENMM_BUILD_AMOEBA_CUDA_PATH ${CMAKE_CURRENT_SOURCE_DIR}/platforms/cuda)
SET(OPENMM_AMOEBA_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda) SET(OPENMM_AMOEBA_CUDA_SOURCE_SUBDIRS . openmmapi olla platforms/cuda)
ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB) ENDIF(OPENMM_BUILD_AMOEBA_CUDA_LIB)
#SET(OPENMM_BUILD_OPENCL_LIB OFF CACHE BOOL "Build OpenMMOpenCL library for Nvidia GPUs")
#IF(OPENMM_BUILD_OPENCL_LIB)
# ADD_SUBDIRECTORY(platforms/opencl)
#ENDIF(OPENMM_BUILD_OPENCL_LIB)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_AMOEBA_TARGET}) INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_AMOEBA_TARGET})
IF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_AMOEBA_SERIALIZABLE_TARGET})
ENDIF( CREATE_SERIALIZABLE_OPENMM_AMOEBA )
IF(OPENMM_BUILD_STATIC_LIB) IF(OPENMM_BUILD_STATIC_LIB)
INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_AMOEBA_TARGET}) INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_AMOEBA_TARGET})
ENDIF(OPENMM_BUILD_STATIC_LIB) ENDIF(OPENMM_BUILD_STATIC_LIB)
...@@ -199,18 +162,6 @@ INSTALL_FILES(/include FILES ${CORE_HEADERS}) ...@@ -199,18 +162,6 @@ INSTALL_FILES(/include FILES ${CORE_HEADERS})
INSTALL_FILES(/include/openmm FILES ${TOP_HEADERS}) INSTALL_FILES(/include/openmm FILES ${TOP_HEADERS})
INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS}) INSTALL_FILES(/include/openmm/internal FILES ${INTERNAL_HEADERS})
#
# Allow automated build and dashboard.
#
#INCLUDE (Dart)
#IF (UNIX AND NOT CYGWIN AND NOT APPLE)
# IF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
# ADD_DEFINITIONS(-fprofile-arcs -ftest-coverage)
# LINK_LIBRARIES(gcov)
# ENDIF (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE MATCHES Debug)
#ENDIF (UNIX AND NOT CYGWIN AND NOT APPLE)
# #
# Testing # Testing
# #
...@@ -223,11 +174,4 @@ ELSE (EXECUTABLE_OUTPUT_PATH) ...@@ -223,11 +174,4 @@ ELSE (EXECUTABLE_OUTPUT_PATH)
SET (TEST_PATH .) SET (TEST_PATH .)
ENDIF (EXECUTABLE_OUTPUT_PATH) ENDIF (EXECUTABLE_OUTPUT_PATH)
IF (OPENMM_BUILD_SERIALIZATION_SUPPORT) ADD_SUBDIRECTORY(serialization/tests)
ADD_SUBDIRECTORY(serialization)
ENDIF (OPENMM_BUILD_SERIALIZATION_SUPPORT)
#INCLUDE(ApiDoxygen.cmake)
#ADD_SUBDIRECTORY(tests)
#ADD_SUBDIRECTORY(examples)
plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h
View file @ 19d2885a
...@@ -175,6 +175,10 @@ private: ...@@ -175,6 +175,10 @@ private:
std::vector<AngleInfo> angles; std::vector<AngleInfo> angles;
}; };
/**
* This is an internal class used to record information about an angle.
* @private
*/
class AmoebaAngleForce::AngleInfo { class AmoebaAngleForce::AngleInfo {
public: public:
int particle1, particle2, particle3; int particle1, particle2, particle3;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h
View file @ 19d2885a
...@@ -147,6 +147,10 @@ private: ...@@ -147,6 +147,10 @@ private:
std::vector<BondInfo> bonds; std::vector<BondInfo> bonds;
}; };
/**
* This is an internal class used to record information about a bond.
* @private
*/
class AmoebaBondForce::BondInfo { class AmoebaBondForce::BondInfo {
public: public:
int particle1, particle2; int particle1, particle2;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h
View file @ 19d2885a
...@@ -174,6 +174,10 @@ private: ...@@ -174,6 +174,10 @@ private:
std::vector<ParticleInfo> particles; std::vector<ParticleInfo> particles;
}; };
/**
* This is an internal class used to record information about a particle.
* @private
*/
class AmoebaGeneralizedKirkwoodForce::ParticleInfo { class AmoebaGeneralizedKirkwoodForce::ParticleInfo {
public: public:
double charge, radius, scalingFactor; double charge, radius, scalingFactor;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h
View file @ 19d2885a
...@@ -180,6 +180,10 @@ private: ...@@ -180,6 +180,10 @@ private:
std::vector<AngleInfo> angles; std::vector<AngleInfo> angles;
}; };
/**
* This is an internal class used to record information about an angle.
* @private
*/
class AmoebaInPlaneAngleForce::AngleInfo { class AmoebaInPlaneAngleForce::AngleInfo {
public: public:
int particle1, particle2, particle3, particle4; int particle1, particle2, particle3, particle4;
......
plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h
View file @ 19d2885a
...@@ -368,6 +368,10 @@ private: ...@@ -368,6 +368,10 @@ private:
std::vector<MultipoleInfo> multipoles; std::vector<MultipoleInfo> multipoles;
}; };
/**
* This is an internal class used to record information about a multipole.
* @private
*/
class AmoebaMultipoleForce::MultipoleInfo { class AmoebaMultipoleForce::MultipoleInfo {
public: public:
......
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