Merged fork with latest original master

libraries/irrxml/include/CXMLReaderImpl.h

@@ -2,6 +2,8 @@
 // This file is part of the "Irrlicht Engine" and the "irrXML" project.
 // For conditions of distribution and use, see copyright notice in irrlicht.h and/or irrXML.h
 
+// MODIFIED by Peter Eastman, Feb. 4, 2016, to support numeric escape sequences
+
 #ifndef __ICXML_READER_IMPL_H_INCLUDED__
 #define __ICXML_READER_IMPL_H_INCLUDED__
 
@@ -529,10 +531,37 @@ private:
 				pos += SpecialCharacters[specialChar].size();
 			}
 			else
+			{
+				int semicolonPos = origstr.findNext(L';', pos);
+				if (semicolonPos != -1 && origstr.c_str()[pos+1] == L'#')
+				{
+					// it is a numeric character reference
+					int number;
+					core::string<char> numberString;
+					if (origstr.c_str()[pos+2] == L'x')
+					{
+						// hex value
+						for (int i=pos+3; i<semicolonPos; ++i)
+							numberString.append((char) origstr[i]);
+						sscanf(numberString.c_str(), "%x", &number);
+					}
+					else
+					{
+						// decimal value
+						for (int i=pos+2; i<semicolonPos; ++i)
+							numberString.append((char) origstr[i]);
+						sscanf(numberString.c_str(), "%d", &number);
+					}
+					newstr.append(origstr.subString(oldPos, pos - oldPos));
+					newstr.append((char_type) number);
+					pos = semicolonPos+1;
+				}
+				else
 				{
 					newstr.append(origstr.subString(oldPos, pos - oldPos + 1));
 					pos += 1;
 				}
+			}
 
 			// find next &
 			oldPos = pos;

libraries/lepton/src/CompiledExpression.cpp

@@ -78,6 +78,7 @@ CompiledExpression& CompiledExpression::operator=(const CompiledExpression& expr
     for (int i = 0; i < (int) operation.size(); i++)
         operation[i] = expression.operation[i]->clone();
 #ifdef LEPTON_USE_JIT
+    if (workspace.size() > 0)
         generateJitCode();
 #endif
     return *this;

libraries/sfmt/src/SFMT.cpp

@@ -124,14 +124,12 @@ public:
 };
 
 void SFMT::createCheckpoint(std::ostream& stream) {
-    stream.write((char*) &data->baseData, sizeof(data->baseData));
-    stream.write((char*) &data->sfmt, sizeof(data->sfmt));
+    stream.write((char*) data->sfmt, N*sizeof(w128_t));
     stream.write((char*) &data->idx, sizeof(data->idx));
 }
 
 void SFMT::loadCheckpoint(std::istream& stream) {
-    stream.read((char*) &data->baseData, sizeof(data->baseData));
-    stream.read((char*) &data->sfmt, sizeof(data->sfmt));
+    stream.read((char*) data->sfmt, N*sizeof(w128_t));
     stream.read((char*) &data->idx, sizeof(data->idx));
 }
 

olla/include/openmm/Kernel.h

@@ -62,7 +62,7 @@ public:
     /**
      * Create a Kernel that wraps a KernelImpl.
      *
-     * @param name the name of the kernel to create
+     * @param KernelImpl the KernelImpl to wrap
      */
     Kernel(KernelImpl* impl);
     ~Kernel();

olla/include/openmm/Platform.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -53,7 +53,7 @@ class KernelFactory;
  * To get a Platform object, call
  *
  * <pre>
- * Platform& platform Platform::findPlatform(kernelNames);
+ * Platform& platform = Platform::findPlatform(kernelNames);
  * </pre>
  *
  * passing in the names of all kernels that will be required for the calculation you plan to perform.  It
@@ -78,6 +78,9 @@ public:
     /**
      * Get whether this Platform supports double precision arithmetic.  If this returns false, the platform
      * is permitted to represent double precision values internally as single precision.
+     *
+     * @deprecated This method is not well defined, and is too simplistic to describe the actual behavior of
+     * some Platforms, such as ones that offer multiple precision modes.  It will be removed in a future release.
      */
     virtual bool supportsDoublePrecision() const = 0;
     /**
@@ -233,7 +236,9 @@ protected:
      */
     const ContextImpl& getContextImpl(const Context& context) const;
     std::vector<std::string> platformProperties;
+    std::map<std::string, std::string> deprecatedPropertyReplacements;
 private:
+    friend class ContextImpl;
     std::map<std::string, KernelFactory*> kernelFactories;
     std::map<std::string, std::string> defaultProperties;
     static std::vector<Platform*>& getPlatforms();

olla/include/openmm/kernels.h

@@ -187,7 +187,7 @@ public:
      * @param b      the vector defining the second edge of the periodic box
      * @param c      the vector defining the third edge of the periodic box
      */
-    virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) const = 0;
+    virtual void setPeriodicBoxVectors(ContextImpl& context, const Vec3& a, const Vec3& b, const Vec3& c) = 0;
     /**
      * Create a checkpoint recording the current state of the Context.
      * 

olla/src/Platform.cpp

@@ -6,7 +6,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -89,15 +89,21 @@ void Platform::setPropertyValue(Context& context, const string& property, const
 }
 
 const string& Platform::getPropertyDefaultValue(const string& property) const {
-    map<string, string>::const_iterator value = defaultProperties.find(property);
+    string propertyName = property;
+    if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
+        propertyName = deprecatedPropertyReplacements.find(property)->second;
+    map<string, string>::const_iterator value = defaultProperties.find(propertyName);
     if (value == defaultProperties.end())
         throw OpenMMException("getPropertyDefaultValue: Illegal property name");
     return value->second;
 }
 
 void Platform::setPropertyDefaultValue(const string& property, const string& value) {
+    string propertyName = property;
+    if (deprecatedPropertyReplacements.find(property) != deprecatedPropertyReplacements.end())
+        propertyName = deprecatedPropertyReplacements.find(property)->second;
     for (int i = 0; i < (int) platformProperties.size(); i++)
-        if (platformProperties[i] == property) {
+        if (platformProperties[i] == propertyName) {
             defaultProperties[property] = value;
             return;
         }
@@ -314,7 +320,11 @@ const string& Platform::getDefaultPluginsDirectory() {
 #define STRING(x) STRING1(x)
 
 const string& Platform::getOpenMMVersion() {
+#if OPENMM_BUILD_VERSION == 0
     static const string version = STRING(OPENMM_MAJOR_VERSION) "." STRING(OPENMM_MINOR_VERSION);
+#else
+    static const string version = STRING(OPENMM_MAJOR_VERSION) "." STRING(OPENMM_MINOR_VERSION) "." STRING(OPENMM_BUILD_VERSION);
+#endif
     return version;
 }
 

openmmapi/include/openmm/CMAPTorsionForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -159,15 +159,18 @@ public:
      * new bonds and torsions cannot be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -175,6 +178,7 @@ private:
     class CMAPTorsionInfo;
     std::vector<MapInfo> maps;
     std::vector<CMAPTorsionInfo> torsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomAngleForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -203,15 +203,18 @@ public:
      * the Context.  The set of particles involved in a angle cannot be changed, nor can new angles be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -222,6 +225,7 @@ private:
     std::vector<AngleParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<AngleInfo> angles;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -200,15 +200,18 @@ public:
      * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -219,6 +222,7 @@ private:
     std::vector<BondParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<BondInfo> bonds;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomCentroidBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -324,15 +324,18 @@ public:
      * bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -348,6 +351,7 @@ private:
     std::vector<GroupInfo> groups;
     std::vector<BondInfo> bonds;
     std::vector<FunctionInfo> functions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -298,15 +298,18 @@ public:
      * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
      */
     void updateParametersInContext(Context& context);
+    /**
+     * Set whether this force should apply periodic boundary conditions when calculating displacements.
+     * Usually this is not appropriate for bonded forces, but there are situations when it can be useful.
+     */
+    void setUsesPeriodicBoundaryConditions(bool periodic);
     /**
      * Returns whether or not this force makes use of periodic boundary
      * conditions.
      *
-     * @returns false
+     * @returns true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -320,6 +323,7 @@ private:
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<BondInfo> bonds;
     std::vector<FunctionInfo> functions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/CustomHbondForce.h

@@ -369,8 +369,8 @@ public:
      * Get the donor and acceptor in a pair whose interaction should be excluded.
      *
      * @param index           the index of the exclusion for which to get donor and acceptor indices
-     * @param[out] particle1  the index of the donor
-     * @param[out] particle2  the index of the acceptor
+     * @param[out] donor      the index of the donor
+     * @param[out] acceptor   the index of the acceptor
      */
     void getExclusionParticles(int index, int& donor, int& acceptor) const;
     /**

openmmapi/include/openmm/CustomIntegrator.h

@@ -9,7 +9,7 @@
  * Biological Structures at Stanford, funded under the NIH Roadmap for        *
  * Medical Research, grant U54 GM072970. See https://simtk.org.               *
  *                                                                            *
- * Portions copyright (c) 2011-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2011-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -266,15 +266,15 @@ public:
         /**
          * Begin an "if" block.
          */
-        BeginIfBlock = 6,
+        IfBlockStart = 6,
         /**
          * Begin a while" block.
          */
-        BeginWhileBlock = 7,
+        WhileBlockStart = 7,
         /**
          * End an "if" or "while" block.
          */
-        EndBlock = 8
+        BlockEnd = 8
     };
     /**
      * Create a CustomIntegrator.