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Commit d1793e5a authored by Peter Eastman's avatar Peter Eastman
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Eliminated nested classes, since SWIG didn't handle them well

parent f728d2f6
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Showing with 42 additions and 44 deletions
openmmapi/include/OpenMM.h
View file @ d1793e5a
......@@ -65,6 +65,7 @@
#include "openmm/VariableVerletIntegrator.h"
#include "openmm/Vec3.h"
#include "openmm/VerletIntegrator.h"
#include "openmm/VirtualSite.h"
#include "openmm/Platform.h"
#endif /*OPENMM_H_*/
openmmapi/include/openmm/VirtualSite.h
View file @ d1793e5a
......@@ -46,9 +46,6 @@ namespace OpenMM {
class OPENMM_EXPORT VirtualSite {
public:
class TwoParticleAverage;
class ThreeParticleAverage;
class OutOfPlane;
virtual ~VirtualSite() {
}
/**
......@@ -75,10 +72,10 @@ private:
* of two other particle's locations. Assuming the weights add up to 1, this means
* the virtual site is on the line passing through the two particles.
*/
class VirtualSite::TwoParticleAverage : public VirtualSite {
class TwoParticleAverageSite : public VirtualSite {
public:
/**
* Create a new TwoParticleAverage virtual site. Normally weight1 and weight2
* Create a new TwoParticleAverageSite virtual site. Normally weight1 and weight2
* should add up to 1, although this is not strictly required.
*
* @param particle1 the index of the first particle
......@@ -86,7 +83,7 @@ public:
* @param weight1 the weight factor (between 0 and 1) for the first particle
* @param weight2 the weight factor (between 0 and 1) for the second particle
*/
TwoParticleAverage(int particle1, int particle2, double weight1, double weight2);
TwoParticleAverageSite(int particle1, int particle2, double weight1, double weight2);
/**
* Get the weight factor used for a particle this virtual site depends on.
*
......@@ -103,10 +100,10 @@ private:
* of three other particle's locations. Assuming the weights add up to 1, this means
* the virtual site is in the plane of the three particles.
*/
class VirtualSite::ThreeParticleAverage : public VirtualSite {
class ThreeParticleAverageSite : public VirtualSite {
public:
/**
* Create a new ThreeParticleAverage virtual site. Normally the weights
* Create a new ThreeParticleAverageSite virtual site. Normally the weights
* should add up to 1, although this is not strictly required.
*
* @param particle1 the index of the first particle
......@@ -116,7 +113,7 @@ public:
* @param weight2 the weight factor (between 0 and 1) for the second particle
* @param weight2 the weight factor (between 0 and 1) for the third particle
*/
ThreeParticleAverage(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3);
ThreeParticleAverageSite(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3);
/**
* Get the weight factor used for a particle this virtual site depends on.
*
......@@ -140,10 +137,10 @@ private:
* The three weight factors are user-specified. This allows the virtual site location
* to be out of the plane of the three particles.
*/
class VirtualSite::OutOfPlane : public VirtualSite {
class OutOfPlaneSite : public VirtualSite {
public:
/**
* Create a new OutOfPlane virtual site.
* Create a new OutOfPlaneSite virtual site.
*
* @param particle1 the index of the first particle
* @param particle2 the index of the second particle
......@@ -152,7 +149,7 @@ public:
* @param weight13 the weight factor for the vector from particle1 to particle3
* @param weightCross the weight factor for the cross product
*/
OutOfPlane(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross);
OutOfPlaneSite(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross);
/**
* Get the weight factor for the vector from particle1 to particle2.
*/
......
openmmapi/src/VirtualSite.cpp
View file @ d1793e5a
......@@ -48,7 +48,7 @@ int VirtualSite::getParticle(int particle) const {
return particles[particle];
}
VirtualSite::TwoParticleAverage::TwoParticleAverage(int particle1, int particle2, double weight1, double weight2) :
TwoParticleAverageSite::TwoParticleAverageSite(int particle1, int particle2, double weight1, double weight2) :
weight1(weight1), weight2(weight2) {
vector<int> particles(2);
particles[0] = particle1;
......@@ -56,7 +56,7 @@ VirtualSite::TwoParticleAverage::TwoParticleAverage(int particle1, int particle2
setParticles(particles);
}
double VirtualSite::TwoParticleAverage::getWeight(int particle) const {
double TwoParticleAverageSite::getWeight(int particle) const {
if (particle == 0)
return weight1;
if (particle == 1)
......@@ -64,7 +64,7 @@ double VirtualSite::TwoParticleAverage::getWeight(int particle) const {
throw OpenMMException("Illegal index for particle");
}
VirtualSite::ThreeParticleAverage::ThreeParticleAverage(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3) :
ThreeParticleAverageSite::ThreeParticleAverageSite(int particle1, int particle2, int particle3, double weight1, double weight2, double weight3) :
weight1(weight1), weight2(weight2), weight3(weight3) {
vector<int> particles(3);
particles[0] = particle1;
......@@ -73,7 +73,7 @@ VirtualSite::ThreeParticleAverage::ThreeParticleAverage(int particle1, int parti
setParticles(particles);
}
double VirtualSite::ThreeParticleAverage::getWeight(int particle) const {
double ThreeParticleAverageSite::getWeight(int particle) const {
if (particle == 0)
return weight1;
if (particle == 1)
......@@ -83,7 +83,7 @@ double VirtualSite::ThreeParticleAverage::getWeight(int particle) const {
throw OpenMMException("Illegal index for particle");
}
VirtualSite::OutOfPlane::OutOfPlane(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross) :
OutOfPlaneSite::OutOfPlaneSite(int particle1, int particle2, int particle3, double weight12, double weight13, double weightCross) :
weight12(weight12), weight13(weight13), weightCross(weightCross) {
vector<int> particles(3);
particles[0] = particle1;
......@@ -92,14 +92,14 @@ VirtualSite::OutOfPlane::OutOfPlane(int particle1, int particle2, int particle3,
setParticles(particles);
}
double VirtualSite::OutOfPlane::getWeight12() const {
double OutOfPlaneSite::getWeight12() const {
return weight12;
}
double VirtualSite::OutOfPlane::getWeight13() const {
double OutOfPlaneSite::getWeight13() const {
return weight13;
}
double VirtualSite::OutOfPlane::getWeightCross() const {
double OutOfPlaneSite::getWeightCross() const {
return weightCross;
}
platforms/reference/src/SimTKReference/ReferenceVirtualSites.cpp
View file @ d1793e5a
......@@ -38,26 +38,26 @@ using namespace std;
void ReferenceVirtualSites::computePositions(const OpenMM::System& system, vector<OpenMM::RealVec>& atomCoordinates) {
for (int i = 0; i < system.getNumParticles(); i++)
if (system.isVirtualSite(i)) {
if (dynamic_cast<const VirtualSite::TwoParticleAverage*>(&system.getVirtualSite(i)) != NULL) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A two particle average.
const VirtualSite::TwoParticleAverage& site = dynamic_cast<const VirtualSite::TwoParticleAverage&>(system.getVirtualSite(i));
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1);
RealOpenMM w1 = site.getWeight(0), w2 = site.getWeight(1);
atomCoordinates[i] = atomCoordinates[p1]*w1 + atomCoordinates[p2]*w2;
}
else if (dynamic_cast<const VirtualSite::ThreeParticleAverage*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A three particle average.
const VirtualSite::ThreeParticleAverage& site = dynamic_cast<const VirtualSite::ThreeParticleAverage&>(system.getVirtualSite(i));
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2);
RealOpenMM w1 = site.getWeight(0), w2 = site.getWeight(1), w3 = site.getWeight(2);
atomCoordinates[i] = atomCoordinates[p1]*w1 + atomCoordinates[p2]*w2 + atomCoordinates[p3]*w3;
}
else if (dynamic_cast<const VirtualSite::OutOfPlane*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site.
const VirtualSite::OutOfPlane& site = dynamic_cast<const VirtualSite::OutOfPlane&>(system.getVirtualSite(i));
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2);
RealOpenMM w12 = site.getWeight12(), w13 = site.getWeight13(), wcross = site.getWeightCross();
RealVec v12 = atomCoordinates[p2]-atomCoordinates[p1];
......@@ -73,29 +73,29 @@ void ReferenceVirtualSites::distributeForces(const OpenMM::System& system, const
for (int i = 0; i < system.getNumParticles(); i++)
if (system.isVirtualSite(i)) {
RealVec f = forces[i];
if (dynamic_cast<const VirtualSite::TwoParticleAverage*>(&system.getVirtualSite(i)) != NULL) {
if (dynamic_cast<const TwoParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A two particle average.
const VirtualSite::TwoParticleAverage& site = dynamic_cast<const VirtualSite::TwoParticleAverage&>(system.getVirtualSite(i));
const TwoParticleAverageSite& site = dynamic_cast<const TwoParticleAverageSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1);
RealOpenMM w1 = site.getWeight(0), w2 = site.getWeight(1);
forces[p1] += f*w1;
forces[p2] += f*w2;
}
else if (dynamic_cast<const VirtualSite::ThreeParticleAverage*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const ThreeParticleAverageSite*>(&system.getVirtualSite(i)) != NULL) {
// A three particle average.
const VirtualSite::ThreeParticleAverage& site = dynamic_cast<const VirtualSite::ThreeParticleAverage&>(system.getVirtualSite(i));
const ThreeParticleAverageSite& site = dynamic_cast<const ThreeParticleAverageSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2);
RealOpenMM w1 = site.getWeight(0), w2 = site.getWeight(1), w3 = site.getWeight(2);
forces[p1] += f*w1;
forces[p2] += f*w2;
forces[p3] += f*w3;
}
else if (dynamic_cast<const VirtualSite::OutOfPlane*>(&system.getVirtualSite(i)) != NULL) {
else if (dynamic_cast<const OutOfPlaneSite*>(&system.getVirtualSite(i)) != NULL) {
// An out of plane site.
const VirtualSite::OutOfPlane& site = dynamic_cast<const VirtualSite::OutOfPlane&>(system.getVirtualSite(i));
const OutOfPlaneSite& site = dynamic_cast<const OutOfPlaneSite&>(system.getVirtualSite(i));
int p1 = site.getParticle(0), p2 = site.getParticle(1), p3 = site.getParticle(2);
RealOpenMM w12 = site.getWeight12(), w13 = site.getWeight13(), wcross = site.getWeightCross();
RealVec v12 = atomCoordinates[p2]-atomCoordinates[p1];
......
platforms/reference/tests/TestReferenceVirtualSites.cpp
View file @ d1793e5a
......@@ -88,7 +88,7 @@ void testMasslessParticle() {
}
/**
* Test a TwoParticleAverage virtual site.
* Test a TwoParticleAverageSite virtual site.
*/
void testTwoParticleAverage() {
ReferencePlatform platform;
......@@ -96,7 +96,7 @@ void testTwoParticleAverage() {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(2, new VirtualSite::TwoParticleAverage(0, 1, 0.8, 0.2));
system.setVirtualSite(2, new TwoParticleAverageSite(0, 1, 0.8, 0.2));
CustomExternalForce* forceField = new CustomExternalForce("-a*x");
system.addForce(forceField);
forceField->addPerParticleParameter("a");
......@@ -124,7 +124,7 @@ void testTwoParticleAverage() {
}
/**
* Test a ThreeParticleAverage virtual site.
* Test a ThreeParticleAverageSite virtual site.
*/
void testThreeParticleAverage() {
ReferencePlatform platform;
......@@ -133,7 +133,7 @@ void testThreeParticleAverage() {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(3, new VirtualSite::ThreeParticleAverage(0, 1, 2, 0.2, 0.3, 0.5));
system.setVirtualSite(3, new ThreeParticleAverageSite(0, 1, 2, 0.2, 0.3, 0.5));
CustomExternalForce* forceField = new CustomExternalForce("-a*x");
system.addForce(forceField);
forceField->addPerParticleParameter("a");
......@@ -165,7 +165,7 @@ void testThreeParticleAverage() {
}
/**
* Test an OutOfPlane virtual site.
* Test an OutOfPlaneSite virtual site.
*/
void testOutOfPlane() {
ReferencePlatform platform;
......@@ -174,7 +174,7 @@ void testOutOfPlane() {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(3, new VirtualSite::OutOfPlane(0, 1, 2, 0.3, 0.4, 0.5));
system.setVirtualSite(3, new OutOfPlaneSite(0, 1, 2, 0.3, 0.4, 0.5));
CustomExternalForce* forceField = new CustomExternalForce("-a*x");
system.addForce(forceField);
forceField->addPerParticleParameter("a");
......@@ -228,7 +228,7 @@ void testConservationLaws() {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(2, new VirtualSite::TwoParticleAverage(0, 1, 0.4, 0.6));
system.setVirtualSite(2, new TwoParticleAverageSite(0, 1, 0.4, 0.6));
system.addConstraint(0, 1, 2.0);
for (int i = 0; i < 3; i++) {
forceField->addParticle(0, 1, 10);
......@@ -245,7 +245,7 @@ void testConservationLaws() {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(6, new VirtualSite::ThreeParticleAverage(3, 4, 5, 0.3, 0.5, 0.2));
system.setVirtualSite(6, new ThreeParticleAverageSite(3, 4, 5, 0.3, 0.5, 0.2));
system.addConstraint(3, 4, 1.0);
system.addConstraint(3, 5, 1.0);
system.addConstraint(4, 5, sqrt(2.0));
......@@ -265,7 +265,7 @@ void testConservationLaws() {
system.addParticle(1.0);
system.addParticle(1.0);
system.addParticle(0.0);
system.setVirtualSite(10, new VirtualSite::OutOfPlane(7, 8, 9, 0.3, 0.5, 0.2));
system.setVirtualSite(10, new OutOfPlaneSite(7, 8, 9, 0.3, 0.5, 0.2));
system.addConstraint(7, 8, 1.0);
system.addConstraint(7, 9, 1.0);
system.addConstraint(8, 9, sqrt(2.0));
......@@ -294,9 +294,9 @@ void testConservationLaws() {
const vector<Vec3>& vel = state.getVelocities();
const vector<Vec3>& f = state.getForces();
double energy = state.getPotentialEnergy();
for (int i = 0; i < numParticles; i++) {
Vec3 v = vel[i] + f[i]*0.5*integrator.getStepSize();
energy += 0.5*system.getParticleMass(i)*v.dot(v);
for (int j = 0; j < numParticles; j++) {
Vec3 v = vel[j] + f[j]*0.5*integrator.getStepSize();
energy += 0.5*system.getParticleMass(j)*v.dot(v);
}
if (i == 0)
initialEnergy = energy;
......
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