Removed fiels that didn't below.

openmmapi/include/openmm/internal/AssertionUtilities.h~

@@ -49,6 +49,8 @@ void OPENMM_EXPORT throwException(const char* file, int line, const std::string&
 #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_CONTAINERS(expected, found) {if (!((expected) == (found))) {std::stringstream details; details << "Containers not equal"; 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());}};
 

serialization/src/CustomNonbondedForceProxy.cpp

@@ -103,9 +103,9 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
         CustomNonbondedForce* force = new CustomNonbondedForce(node.getStringProperty("energy"));
         force->setNonbondedMethod((CustomNonbondedForce::NonbondedMethod) node.getIntProperty("method"));
         force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction"));
-        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance"));
-        force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection"));
+        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction", false));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
+        force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
         for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perParticleParams.getChildren()[i];
@@ -149,8 +149,10 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
-        const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
-        for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
+        // Look for interaction group definitions in a backward-compatible way.
+        try {
+          const SerializationNode& interactionGroups = node.getChildNode("InteractionGroups");
+          for (int i = 0; i < (int) interactionGroups.getChildren().size(); i++) {
             const SerializationNode& interactionGroup = interactionGroups.getChildren()[i];
             // Get set 1.
             const SerializationNode& set1node = interactionGroup.getChildNode("Set1");
@@ -163,6 +165,9 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
             for (int j = 0; j < (int) set2node.getChildren().size(); j++)
               set2.insert(set2node.getChildren()[j].getIntProperty("index"));
             force->addInteractionGroup(set1, set2);
+          }
+        } catch (exception &e) {
+          // Do nothing, since we have to assume that InteractionGroups is not present and allow for this possibility.
         }
         return force;
     }

serialization/src/NonbondedForceProxy.cpp

@@ -80,20 +80,20 @@ void* NonbondedForceProxy::deserialize(const SerializationNode& node) const {
     NonbondedForce* force = new NonbondedForce();
     try {
         force->setNonbondedMethod((NonbondedForce::NonbondedMethod) node.getIntProperty("method"));
-        force->setCutoffDistance(node.getDoubleProperty("cutoff"));
-        force->setUseSwitchingFunction(node.getDoubleProperty("useSwitchingFunction"));
-        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance"));
-        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance"));
-        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric"));
-        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection"));
+        force->setCutoffDistance(node.getDoubleProperty("cutoff", 1.0));
+        force->setUseSwitchingFunction(node.getDoubleProperty("useSwitchingFunction", false));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
+        force->setEwaldErrorTolerance(node.getDoubleProperty("ewaldTolerance", 5e-4));
+        force->setReactionFieldDielectric(node.getDoubleProperty("rfDielectric", 78.3));
+        force->setUseDispersionCorrection(node.getIntProperty("dispersionCorrection",true));
         double alpha;
         int nx, ny, nz;
-        alpha = node.getDoubleProperty("alpha");
-        nx = node.getIntProperty("nx");
-        ny = node.getIntProperty("ny");
-        nz = node.getIntProperty("nz");
+        alpha = node.getDoubleProperty("alpha", 0.0);
+        nx = node.getIntProperty("nx", 0);
+        ny = node.getIntProperty("ny", 0);
+        nz = node.getIntProperty("nz", 0);
         force->setPMEParameters(alpha, nx, ny, nz);
-        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup"));
+        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
         const SerializationNode& particles = node.getChildNode("Particles");
         for (int i = 0; i < (int) particles.getChildren().size(); i++) {
             const SerializationNode& particle = particles.getChildren()[i];

wrappers/python/src/swig_doxygen/doxygen/Doxyfile

@@ -517,7 +517,7 @@ QUIET                  = NO
 # generated by doxygen. Possible values are YES and NO. If left blank 
 # NO is used.
 
-WARNINGS               = YES
+WARNINGS               = NO
 
 # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings 
 # for undocumented members. If EXTRACT_ALL is set to YES then this flag will 
@@ -530,7 +530,7 @@ WARN_IF_UNDOCUMENTED   = NO
 # parameters in a documented function, or documenting parameters that 
 # don't exist or using markup commands wrongly.
 
-WARN_IF_DOC_ERROR      = YES
+WARN_IF_DOC_ERROR      = NO
 
 # This WARN_NO_PARAMDOC option can be abled to get warnings for 
 # functions that are documented, but have no documentation for their parameters 
@@ -564,8 +564,14 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-INPUT                  = "$(OPENMM_INCLUDE_PATH)/OpenMM.h" \
-                         "$(OPENMM_INCLUDE_PATH)/openmm"
+INPUT                  = "/Users/choderaj/code/openmm/openmm.jchodera/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/olla/include/openmm/Platform.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/SerializationNode.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/SerializationProxy.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/serialization/include/openmm/serialization/XmlSerializer.h" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/amoeba/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/rpmd/openmmapi" \
+                         "/Users/choderaj/code/openmm/openmm.jchodera/plugins/drude/openmmapi"
 
 # This tag can be used to specify the character encoding of the source files 
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is 
@@ -594,7 +600,7 @@ RECURSIVE              = YES
 # excluded from the INPUT source files. This way you can easily exclude a 
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 
-EXCLUDE                = 
+EXCLUDE                = *Impl.h
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
@@ -608,11 +614,15 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories 
 # for example use the pattern */test/*
 
-#EXCLUDE_PATTERNS       = */tests/* \
-#                         */src/* \
-#                         */.svn/*
 EXCLUDE_PATTERNS       = */tests/* \
-                         */.svn/*
+                         */openmmapi/src/* \
+                         */internal/* \
+                         */.svn/* \
+                         *amoebaKernels.h \
+                         *DrudeKernels.h \
+                         *RpmdKernels.h \
+                         *OpenMMFortranModule.f90 \
+                         *OpenMMCWrapper.h
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
 # (namespaces, classes, functions, etc.) that should be excluded from the