Removed redundant overload of == operator in AssertionUtilities.h. Removed...

Removed redundant overload of == operator in AssertionUtilities.h. Removed extraneous version check for serialized integrators and state. Updated unit test to include more details. 

openmmapi/include/openmm/internal/AssertionUtilities.h

@@ -38,7 +38,6 @@
 
 #include "windowsExport.h"
 #include <cmath>
-#include <string>
 #include <sstream>
 
 namespace OpenMM {
@@ -47,16 +46,10 @@ void OPENMM_EXPORT throwException(const char* file, int line, const std::string&
 
 } // namespace OpenMM
 
-static inline bool operator==(const std::string& lhs, const std::string &rhs) {
-    if(lhs.compare(rhs) == 0)
-        return true;
-    return false;
-}
-
 #define ASSERT(cond) {if (!(cond)) throwException(__FILE__, __LINE__, "");};
 
 #define ASSERT_EQUAL(expected, found) {if (!((expected) == (found))) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
-
+ 
 #define ASSERT_EQUAL_TOL(expected, found, tol) {double _scale_ = std::abs(expected) > 1.0 ? std::abs(expected) : 1.0; if (!(std::abs((expected)-(found))/_scale_ <= (tol))) {std::stringstream details; details << "Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};
 
 #define ASSERT_EQUAL_VEC(expected, found, tol) {double _norm_ = std::sqrt((expected).dot(expected)); double _scale_ = _norm_ > 1.0 ? _norm_ : 1.0; if ((std::abs(((expected)[0])-((found)[0]))/_scale_ > (tol)) || (std::abs(((expected)[1])-((found)[1]))/_scale_ > (tol)) || (std::abs(((expected)[2])-((found)[2]))/_scale_ > (tol))) {std::stringstream details; details << " Expected "<<(expected)<<", found "<<(found); throwException(__FILE__, __LINE__, details.str());}};

serialization/src/BrownianIntegratorProxy.cpp

@@ -42,7 +42,7 @@ BrownianIntegratorProxy::BrownianIntegratorProxy() : SerializationProxy("Brownia
 void BrownianIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const BrownianIntegrator& integrator = *reinterpret_cast<const BrownianIntegrator*>(object);
-    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
     node.setDoubleProperty("temperature", integrator.getTemperature());
     node.setDoubleProperty("friction", integrator.getFriction());
@@ -50,11 +50,11 @@ void BrownianIntegratorProxy::serialize(const void* object, SerializationNode& n
 }
 
 void* BrownianIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
     BrownianIntegrator *integrator = new BrownianIntegrator(node.getDoubleProperty("temperature"),
                                                             node.getDoubleProperty("friction"),
-                                                            node.getDoubleProperty("stepSizeInPs"));
+                                                            node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
     return integrator;

serialization/src/CustomIntegratorProxy.cpp

@@ -65,14 +65,14 @@ void CustomIntegratorProxy::serialize(const void* object, SerializationNode& nod
     }
     node.setStringProperty("kineticEnergyExpression",integrator.getKineticEnergyExpression());
     node.setIntProperty("randomSeed",integrator.getRandomNumberSeed());
-    node.setDoubleProperty("stepSizeInPs",integrator.getStepSize());
+    node.setDoubleProperty("stepSize",integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance",integrator.getConstraintTolerance());
 }
 
 void* CustomIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
-    CustomIntegrator* integrator = new CustomIntegrator(node.getDoubleProperty("stepSizeInPs"));
+    CustomIntegrator* integrator = new CustomIntegrator(node.getDoubleProperty("stepSize"));
     const SerializationNode& globalVariablesNode = node.getChildNode("GlobalVariables");
     const map<string, string> &globalVariableProp = globalVariablesNode.getProperties();
     for(map<string, string>::const_iterator cit = globalVariableProp.begin(); cit != globalVariableProp.end(); cit++) {
@@ -95,25 +95,24 @@ void* CustomIntegratorProxy::deserialize(const SerializationNode& node) const {
     for(vector<SerializationNode>::const_iterator cit = computationsList.begin(); cit != computationsList.end(); cit++) {
         CustomIntegrator::ComputationType computationType = static_cast<CustomIntegrator::ComputationType>(cit->getIntProperty("computationType"));
         // make sure that the int casts to a valid enum
-        if(computationType == CustomIntegrator::ComputationType::ComputeGlobal) {
+        if(computationType == CustomIntegrator::ComputeGlobal) {
             integrator->addComputeGlobal(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::ComputationType::ComputePerDof) {
+        } else if(computationType == CustomIntegrator::ComputePerDof) {
             integrator->addComputePerDof(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::ComputationType::ComputeSum) {
+        } else if(computationType == CustomIntegrator::ComputeSum) {
             integrator->addComputeSum(cit->getStringProperty("computationVariable"), cit->getStringProperty("computationExpression"));
-        } else if(computationType == CustomIntegrator::ComputationType::ConstrainPositions) {
+        } else if(computationType == CustomIntegrator::ConstrainPositions) {
             integrator->addConstrainPositions();
-        } else if(computationType == CustomIntegrator::ComputationType::ConstrainVelocities) {
-            integrator->addConstrainVelocities();
-        } else if(computationType == CustomIntegrator::ComputationType::UpdateContextState) {
+        } else if(computationType == CustomIntegrator::ConstrainVelocities) {
             integrator->addConstrainVelocities();
+        } else if(computationType == CustomIntegrator::UpdateContextState) {
+            integrator->addUpdateContextState();
         } else {
             throw(OpenMMException("Custom Integrator Deserialization: Unknown computation type"));
         }
     }
     integrator->setKineticEnergyExpression(node.getStringProperty("kineticEnergyExpression"));
     integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
-    integrator->setStepSize(node.getDoubleProperty("stepSizeInPs"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     return integrator;
 }
\ No newline at end of file

serialization/src/LangevinIntegratorProxy.cpp

@@ -42,7 +42,7 @@ LangevinIntegratorProxy::LangevinIntegratorProxy() : SerializationProxy("Langevi
 void LangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const LangevinIntegrator& integrator = *reinterpret_cast<const LangevinIntegrator*>(object);
-    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
     node.setDoubleProperty("temperature", integrator.getTemperature());
     node.setDoubleProperty("friction", integrator.getFriction());
@@ -50,11 +50,11 @@ void LangevinIntegratorProxy::serialize(const void* object, SerializationNode& n
 }
 
 void* LangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
     LangevinIntegrator *integrator = new LangevinIntegrator(node.getDoubleProperty("temperature"),
                                                             node.getDoubleProperty("friction"),
-                                                            node.getDoubleProperty("stepSizeInPs"));
+                                                            node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
     return integrator;

serialization/src/StateProxy.cpp

@@ -102,7 +102,7 @@ void StateProxy::serialize(const void* object, SerializationNode& node) const {
 }
 
 void* StateProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
     double outTime = node.getDoubleProperty("time");
     const SerializationNode& boxVectorsNode = node.getChildNode("PeriodicBoxVectors");

serialization/src/VariableLangevinIntegratorProxy.cpp

@@ -42,7 +42,7 @@ VariableLangevinIntegratorProxy::VariableLangevinIntegratorProxy() : Serializati
 void VariableLangevinIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const VariableLangevinIntegrator& integrator = *reinterpret_cast<const VariableLangevinIntegrator*>(object);
-    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
     node.setDoubleProperty("temperature", integrator.getTemperature());
     node.setDoubleProperty("friction", integrator.getFriction());
@@ -51,12 +51,12 @@ void VariableLangevinIntegratorProxy::serialize(const void* object, Serializatio
 }
 
 void* VariableLangevinIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
     VariableLangevinIntegrator *integrator = new VariableLangevinIntegrator(node.getDoubleProperty("temperature"),
                                                             node.getDoubleProperty("friction"),
                                                             node.getDoubleProperty("errorTol"));
-    integrator->setStepSize(node.getDoubleProperty("stepSizeInPs"));
+    integrator->setStepSize(node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     integrator->setRandomNumberSeed(node.getIntProperty("randomSeed"));
     return integrator;

serialization/src/VariableVerletIntegratorProxy.cpp

@@ -43,15 +43,15 @@ void VariableVerletIntegratorProxy::serialize(const void* object, SerializationN
     node.setIntProperty("version", 1);
     const VariableVerletIntegrator& integrator = *reinterpret_cast<const VariableVerletIntegrator*>(object);
     node.setDoubleProperty("errorTol", integrator.getErrorTolerance());
-    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
 }
 
 void* VariableVerletIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
     VariableVerletIntegrator *integrator = new VariableVerletIntegrator(node.getDoubleProperty("errorTol"));
-    integrator->setStepSize(node.getDoubleProperty("stepSizeInPs"));
+    integrator->setStepSize(node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     return integrator;
 }
\ No newline at end of file

serialization/src/VerletIntegratorProxy.cpp

@@ -42,14 +42,14 @@ VerletIntegratorProxy::VerletIntegratorProxy() : SerializationProxy("VerletInteg
 void VerletIntegratorProxy::serialize(const void* object, SerializationNode& node) const {
     node.setIntProperty("version", 1);
     const VerletIntegrator& integrator = *reinterpret_cast<const VerletIntegrator*>(object);
-    node.setDoubleProperty("stepSizeInPs", integrator.getStepSize());
+    node.setDoubleProperty("stepSize", integrator.getStepSize());
     node.setDoubleProperty("constraintTolerance", integrator.getConstraintTolerance());
 }
 
 void* VerletIntegratorProxy::deserialize(const SerializationNode& node) const {
-    if (node.getIntProperty("version") != 1 && node.getIntProperty("version") != 2)
+    if (node.getIntProperty("version") != 1)
         throw OpenMMException("Unsupported version number");
-    VerletIntegrator *integrator = new VerletIntegrator(node.getDoubleProperty("stepSizeInPs"));
+    VerletIntegrator *integrator = new VerletIntegrator(node.getDoubleProperty("stepSize"));
     integrator->setConstraintTolerance(node.getDoubleProperty("constraintTolerance"));
     return integrator;
 }
\ No newline at end of file

serialization/tests/TestSerializeIntegrator.cpp

@@ -127,6 +127,9 @@ void testSerializeCustomIntegrator() {
     intg->addComputePerDof("x", "x+dt*v");
     intg->addConstrainPositions();
     intg->addComputePerDof("v", "(x-oldx)/dt");
+    intg->addUpdateContextState();
+    intg->addConstrainVelocities();
+    intg->addComputeSum("summand", "x*x+v*v");
     intg->addPerDofVariable("outf", 0);
     intg->addPerDofVariable("outf1", 0);
     intg->addPerDofVariable("outf2", 0);
@@ -139,6 +142,9 @@ void testSerializeCustomIntegrator() {
     intg->addComputeGlobal("oute", "energy");
     intg->addComputeGlobal("oute1", "energy1");
     intg->addComputeGlobal("oute2", "energy2");
+    intg->addUpdateContextState();
+    intg->addConstrainVelocities();
+    intg->addComputeSum("summand2", "v*v+f*f");
     intg->setConstraintTolerance(1e-5);
     intg->setKineticEnergyExpression("m*v1*v1/2; v1=v+0.5*dt*f/m");
     stringstream ss;