Undo changes.

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

-#ifndef OPENMM_ASSERTIONUTILITIES_H_
-#define OPENMM_ASSERTIONUTILITIES_H_
-
-/* -------------------------------------------------------------------------- *
- *                                   OpenMM                                   *
- * -------------------------------------------------------------------------- *
- * This is part of the OpenMM molecular simulation toolkit originating from   *
- * Simbios, the NIH National Center for Physics-Based Simulation of           *
- * Biological Structures at Stanford, funded under the NIH Roadmap for        *
- * Medical Research, grant U54 GM072970. See https://simtk.org.               *
- *                                                                            *
- * Portions copyright (c) 2008-2013 Stanford University and the Authors.      *
- * Authors: Peter Eastman                                                     *
- * Contributors:                                                              *
- *                                                                            *
- * Permission is hereby granted, free of charge, to any person obtaining a    *
- * copy of this software and associated documentation files (the "Software"), *
- * to deal in the Software without restriction, including without limitation  *
- * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
- * and/or sell copies of the Software, and to permit persons to whom the      *
- * Software is furnished to do so, subject to the following conditions:       *
- *                                                                            *
- * The above copyright notice and this permission notice shall be included in *
- * all copies or substantial portions of the Software.                        *
- *                                                                            *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
- * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
- * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
- * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
- * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
- * -------------------------------------------------------------------------- */
-
-/**
- * This file provides a variety of macros useful in test cases.
- */
-
-#include "windowsExport.h"
-#include <cmath>
-#include <sstream>
-
-namespace OpenMM {
-
-void OPENMM_EXPORT throwException(const char* file, int line, const std::string& details);
-
-} // namespace OpenMM
-
-#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());}};
-
-#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());}};
-
-#define ASSERT_USUALLY_TRUE(cond) {if (!(cond)) throwException(__FILE__, __LINE__, "(This test is stochastic and may occasionally fail)");};
-
-#define ASSERT_USUALLY_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)<<" (This test is stochastic and may occasionally fail)"; throwException(__FILE__, __LINE__, details.str());}};
-
-#define ASSERT_VALID_INDEX(index, vector) {if (index < 0 || index >= (int) vector.size()) throwException(__FILE__, __LINE__, "Index out of range");};
-
-#endif /*OPENMM_ASSERTIONUTILITIES_H_*/

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", false));
-        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance", -1.0));
-        force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection", false));
+        force->setUseSwitchingFunction(node.getBoolProperty("useSwitchingFunction"));
+        force->setSwitchingDistance(node.getDoubleProperty("switchingDistance"));
+        force->setUseLongRangeCorrection(node.getBoolProperty("useLongRangeCorrection"));
         const SerializationNode& perParticleParams = node.getChildNode("PerParticleParameters");
         for (int i = 0; i < (int) perParticleParams.getChildren().size(); i++) {
             const SerializationNode& parameter = perParticleParams.getChildren()[i];
@@ -149,8 +149,6 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
                 force->addTabulatedFunction(function.getStringProperty("name"), new Continuous1DFunction(values, function.getDoubleProperty("min"), function.getDoubleProperty("max")));
             }
         }
-        // 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];
@@ -166,9 +164,6 @@ void* CustomNonbondedForceProxy::deserialize(const SerializationNode& node) cons
               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;
     }
     catch (...) {

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", 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));
+        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"));
         double alpha;
         int nx, ny, nz;
-        alpha = node.getDoubleProperty("alpha", 0.0);
-        nx = node.getIntProperty("nx", 0);
-        ny = node.getIntProperty("ny", 0);
-        nz = node.getIntProperty("nz", 0);
+        alpha = node.getDoubleProperty("alpha");
+        nx = node.getIntProperty("nx");
+        ny = node.getIntProperty("ny");
+        nz = node.getIntProperty("nz");
         force->setPMEParameters(alpha, nx, ny, nz);
-        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup", -1));
+        force->setReciprocalSpaceForceGroup(node.getIntProperty("recipForceGroup"));
         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               = NO
+WARNINGS               = YES
 
 # 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      = NO
+WARN_IF_DOC_ERROR      = YES
 
 # This WARN_NO_PARAMDOC option can be abled to get warnings for 
 # functions that are documented, but have no documentation for their parameters 
@@ -564,14 +564,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories 
 # with spaces.
 
-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"
+INPUT                  = "$(OPENMM_INCLUDE_PATH)/OpenMM.h" \
+                         "$(OPENMM_INCLUDE_PATH)/openmm"
 
 # 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 
@@ -600,7 +594,7 @@ 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                = *Impl.h
+EXCLUDE                = 
 
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or 
 # directories that are symbolic links (a Unix filesystem feature) are excluded 
@@ -614,15 +608,11 @@ 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/* \
-                         */openmmapi/src/* \
-                         */internal/* \
-                         */.svn/* \
-                         *amoebaKernels.h \
-                         *DrudeKernels.h \
-                         *RpmdKernels.h \
-                         *OpenMMFortranModule.f90 \
-                         *OpenMMCWrapper.h
+                         */.svn/*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names 
 # (namespaces, classes, functions, etc.) that should be excluded from the