Added System::getNumDegreesOfFreedom()

openmmapi/include/openmm/System.h

@@ -224,6 +224,12 @@ public:
      * @param c      the vector defining the third edge of the periodic box
      */
     void setDefaultPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Vec3& c);
+    /**
+     * Get the total number of degrees of freedom in this system.  This is equal to
+     * 3*(number of massive particles)-(number of constraints), where massive particles
+     * are ones whose mass does not equal zero.
+     */
+    int getNumDegreesOfFreedom() const;
 private:
     class ConstraintInfo;
     Vec3 periodicBoxVectors[3];

openmmapi/src/System.cpp

@@ -119,3 +119,11 @@ void System::setDefaultPeriodicBoxVectors(const Vec3& a, const Vec3& b, const Ve
     periodicBoxVectors[1] = b;
     periodicBoxVectors[2] = c;
 }
+
+int System::getNumDegreesOfFreedom() const {
+    int numMassiveParticles = 0;
+    for (int i = 0; i < (int) masses.size(); i++)
+        if (masses[i] != 0.0)
+            numMassiveParticles++;
+    return 3*numMassiveParticles-constraints.size();
+}

platforms/cuda/tests/TestCudaAndersenThermostat.cpp

@@ -138,7 +138,7 @@ void testConstraints() {
         integrator.step(1);
     }
     ke /= numSteps;
-    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temp;
+    double expected = 0.5*system.getNumDegreesOfFreedom()*BOLTZ*temp;
     ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
 }
 

platforms/cuda/tests/TestCudaRandom.cpp

@@ -128,7 +128,7 @@ void testRandomVelocities() {
         Vec3 v = state.getVelocities()[i];
         ke += 0.5*system.getParticleMass(i)*v.dot(v);
     }
-    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temperture;
+    double expected = 0.5*system.getNumDegreesOfFreedom()*BOLTZ*temperture;
     ASSERT_USUALLY_EQUAL_TOL(expected, ke, 4/sqrt((double) numParticles));
 }
 

platforms/opencl/tests/TestOpenCLAndersenThermostat.cpp

@@ -138,7 +138,7 @@ void testConstraints() {
         integrator.step(1);
     }
     ke /= numSteps;
-    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temp;
+    double expected = 0.5*system.getNumDegreesOfFreedom()*BOLTZ*temp;
     ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
 }
 

platforms/opencl/tests/TestOpenCLRandom.cpp

@@ -126,7 +126,7 @@ void testRandomVelocities() {
         Vec3 v = state.getVelocities()[i];
         ke += 0.5*system.getParticleMass(i)*v.dot(v);
     }
-    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temperture;
+    double expected = 0.5*system.getNumDegreesOfFreedom()*BOLTZ*temperture;
     ASSERT_USUALLY_EQUAL_TOL(expected, ke, 4/sqrt((double) numParticles));
 }
 

platforms/reference/tests/TestReferenceAndersenThermostat.cpp

@@ -138,7 +138,7 @@ void testConstraints() {
         integrator.step(1);
     }
     ke /= numSteps;
-    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temp;
+    double expected = 0.5*system.getNumDegreesOfFreedom()*BOLTZ*temp;
     ASSERT_USUALLY_EQUAL_TOL(expected, ke, 0.1);
 }
 

platforms/reference/tests/TestReferenceRandom.cpp

@@ -108,7 +108,7 @@ void testRandomVelocities() {
         Vec3 v = state.getVelocities()[i];
         ke += 0.5*system.getParticleMass(i)*v.dot(v);
     }
-    double expected = 0.5*(numParticles*3-system.getNumConstraints())*BOLTZ*temperture;
+    double expected = 0.5*system.getNumDegreesOfFreedom()*BOLTZ*temperture;
     ASSERT_USUALLY_EQUAL_TOL(expected, ke, 4/sqrt((double) numParticles));
 }