Eliminated nested classes, since SWIG didn't handle them well

openmmapi/include/OpenMM.h

@@ -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

@@ -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

@@ -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

@@ -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

@@ -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;