Merge branch 'master' into gayberne

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;
         }

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/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.

openmmapi/include/openmm/CustomTorsionForce.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:                                                              *
  *                                                                            *
@@ -206,15 +206,18 @@ public:
      * the Context.  The set of particles involved in a torsion cannot be changed, nor can new torsions 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 true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
@@ -225,6 +228,7 @@ private:
     std::vector<TorsionParameterInfo> parameters;
     std::vector<GlobalParameterInfo> globalParameters;
     std::vector<TorsionInfo> torsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/HarmonicAngleForce.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:                                                              *
  *                                                                            *
@@ -102,20 +102,23 @@ public:
      * 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 true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
-protected:
+    bool usesPeriodicBoundaryConditions() const;protected:
     ForceImpl* createImpl() const;
 private:
     class AngleInfo;
     std::vector<AngleInfo> angles;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/HarmonicBondForce.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:                                                              *
  *                                                                            *
@@ -99,20 +99,24 @@ public:
      * 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 true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class BondInfo;
     std::vector<BondInfo> bonds;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/MonteCarloAnisotropicBarostat.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) 2010-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman, Lee-Ping Wang                                      *
  * Contributors:                                                              *
  *                                                                            *
@@ -81,17 +81,25 @@ public:
         static const std::string key = "MonteCarloPressureZ";
         return key;
     }
+    /**
+     * This is the name of the parameter which stores the current temperature at which the
+     * system is being maintained (in Kelvin)
+     */
+    static const std::string& Temperature() {
+        static const std::string key = "AnisotropicMonteCarloTemperature";
+        return key;
+    }
     /**
      * Create a MonteCarloAnisotropicBarostat.
      *
      * @param defaultPressure     The default pressure acting on each axis (in bar)
-     * @param temperature       the temperature at which the system is being maintained (in Kelvin)
+     * @param defaultTemperature  the default temperature at which the system is being maintained (in Kelvin)
      * @param scaleX              whether to allow the X dimension of the periodic box to change size
      * @param scaleY              whether to allow the Y dimension of the periodic box to change size
      * @param scaleZ              whether to allow the Z dimension of the periodic box to change size
      * @param frequency           the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
      */
-    MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double temperature, bool scaleX = true, bool scaleY = true, bool scaleZ = true, int frequency = 25);
+    MonteCarloAnisotropicBarostat(const Vec3& defaultPressure, double defaultTemperature, bool scaleX = true, bool scaleY = true, bool scaleZ = true, int frequency = 25);
     /**
      * Get the default pressure (in bar).
      *
@@ -142,18 +150,19 @@ public:
         frequency = freq;
     }
     /**
-     * Get the temperature at which the system is being maintained, measured in Kelvin.
+     * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
-    double getTemperature() const {
-        return temperature;
+    double getDefaultTemperature() const {
+        return defaultTemperature;
     }
     /**
-     * Set the temperature at which the system is being maintained.
+     * Set the default temperature at which the system is being maintained.  This will affect any new Contexts you create,
+     * but not ones that already exist.
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setTemperature(double temp) {
-        temperature = temp;
+    void setDefaultTemperature(double temp) {
+        defaultTemperature = temp;
     }
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
@@ -188,7 +197,7 @@ protected:
     ForceImpl* createImpl() const;
 private:
     Vec3 defaultPressure;
-    double temperature;
+    double defaultTemperature;
     bool scaleX, scaleY, scaleZ;
     int frequency, randomNumberSeed;
 };

openmmapi/include/openmm/MonteCarloBarostat.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -58,14 +58,22 @@ public:
         static const std::string key = "MonteCarloPressure";
         return key;
     }
+    /**
+     * This is the name of the parameter which stores the current temperature at which the
+     * system is being maintained (in Kelvin)
+     */
+    static const std::string& Temperature() {
+        static const std::string key = "MonteCarloTemperature";
+        return key;
+    }
     /**
      * Create a MonteCarloBarostat.
      *
      * @param defaultPressure     the default pressure acting on the system (in bar)
-     * @param temperature       the temperature at which the system is being maintained (in Kelvin)
+     * @param defaultTemperature  the default temperature at which the system is being maintained (in Kelvin)
      * @param frequency           the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
      */
-    MonteCarloBarostat(double defaultPressure, double temperature, int frequency = 25);
+    MonteCarloBarostat(double defaultPressure, double defaultTemperature, int frequency = 25);
     /**
      * Get the default pressure acting on the system (in bar).
      *
@@ -98,18 +106,19 @@ public:
         frequency = freq;
     }
     /**
-     * Get the temperature at which the system is being maintained, measured in Kelvin.
+     * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
-    double getTemperature() const {
-        return temperature;
+    double getDefaultTemperature() const {
+        return defaultTemperature;
     }
     /**
-     * Set the temperature at which the system is being maintained.
+     * Set the default temperature at which the system is being maintained.  This will affect any new Contexts you create,
+     * but not ones that already exist.
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setTemperature(double temp) {
-        temperature = temp;
+    void setDefaultTemperature(double temp) {
+        defaultTemperature = temp;
     }
     /**
      * Get the random number seed.  See setRandomNumberSeed() for details.
@@ -143,7 +152,7 @@ public:
 protected:
     ForceImpl* createImpl() const;
 private:
-    double defaultPressure, temperature;
+    double defaultPressure, defaultTemperature;
     int frequency, randomNumberSeed;
 };
 

openmmapi/include/openmm/MonteCarloMembraneBarostat.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) 2010-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -111,17 +111,25 @@ public:
         static const std::string key = "MembraneMonteCarloSurfaceTension";
         return key;
     }
+    /**
+     * This is the name of the parameter which stores the current temperature at which the
+     * system is being maintained (in Kelvin)
+     */
+    static const std::string& Temperature() {
+        static const std::string key = "MembraneMonteCarloTemperature";
+        return key;
+    }
     /**
      * Create a MonteCarloMembraneBarostat.
      *
      * @param defaultPressure        the default pressure acting on the system (in bar)
      * @param defaultSurfaceTension  the default surface tension acting on the system (in bar*nm)
-     * @param temperature            the temperature at which the system is being maintained (in Kelvin)
+     * @param defaultTemperature     the default temperature at which the system is being maintained (in Kelvin)
      * @param xymode                 the mode specifying the behavior of the X and Y axes
      * @param zmode                  the mode specifying the behavior of the Z axis
      * @param frequency              the frequency at which Monte Carlo volume changes should be attempted (in time steps)
      */
-    MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double temperature, XYMode xymode, ZMode zmode, int frequency = 25);
+    MonteCarloMembraneBarostat(double defaultPressure, double defaultSurfaceTension, double defaultTemperature, XYMode xymode, ZMode zmode, int frequency = 25);
     /**
      * Get the default pressure acting on the system (in bar).
      *
@@ -171,18 +179,19 @@ public:
         frequency = freq;
     }
     /**
-     * Get the temperature at which the system is being maintained, measured in Kelvin.
+     * Get the default temperature at which the system is being maintained, measured in Kelvin.
      */
-    double getTemperature() const {
-        return temperature;
+    double getDefaultTemperature() const {
+        return defaultTemperature;
     }
     /**
-     * Set the temperature at which the system is being maintained.
+     * Set the default temperature at which the system is being maintained.  This will affect any new Contexts you create,
+     * but not ones that already exist.
      *
      * @param temp     the system temperature, measured in Kelvin.
      */
-    void setTemperature(double temp) {
-        temperature = temp;
+    void setDefaultTemperature(double temp) {
+        defaultTemperature = temp;
     }
     /**
      * Get the mode specifying the behavior of the X and Y axes.
@@ -240,7 +249,7 @@ public:
 protected:
     ForceImpl* createImpl() const;
 private:
-    double defaultPressure, defaultSurfaceTension, temperature;
+    double defaultPressure, defaultSurfaceTension, defaultTemperature;
     XYMode xymode;
     ZMode zmode;
     int frequency, randomNumberSeed;

openmmapi/include/openmm/PeriodicTorsionForce.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:                                                              *
  *                                                                            *
@@ -108,20 +108,24 @@ public:
      * in a torsion cannot be changed, nor can new torsions 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 true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class PeriodicTorsionInfo;
     std::vector<PeriodicTorsionInfo> periodicTorsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/RBTorsionForce.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:                                                              *
  *                                                                            *
@@ -117,20 +117,24 @@ public:
      * in a torsion cannot be changed, nor can new torsions 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 true if force uses PBC and false otherwise
      */
-    bool usesPeriodicBoundaryConditions() const {
-        return false;
-    }
+    bool usesPeriodicBoundaryConditions() const;
 protected:
     ForceImpl* createImpl() const;
 private:
     class RBTorsionInfo;
     std::vector<RBTorsionInfo> rbTorsions;
+    bool usePeriodic;
 };
 
 /**

openmmapi/include/openmm/internal/OSRngSeed.h

-#ifndef OPENMM_OSRNGSEED_H_
+#ifndef OPENMM_OSRNGSEED_H_
 #define OPENMM_OSRNGSEED_H_
 
 

openmmapi/src/CMAPTorsionForce.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) 2010-2015 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-CMAPTorsionForce::CMAPTorsionForce() {
+CMAPTorsionForce::CMAPTorsionForce() : usePeriodic(false) {
 }
 
 int CMAPTorsionForce::addMap(int size, const std::vector<double>& energy) {
@@ -99,3 +99,11 @@ ForceImpl* CMAPTorsionForce::createImpl() const {
 void CMAPTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<CMAPTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CMAPTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CMAPTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/ContextImpl.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) 2008-2013 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -84,15 +84,20 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     // Validate the list of properties.
 
     const vector<string>& platformProperties = platform->getPropertyNames();
+    map<string, string> validatedProperties;
     for (map<string, string>::const_iterator iter = properties.begin(); iter != properties.end(); ++iter) {
+        string property = iter->first;
+        if (platform->deprecatedPropertyReplacements.find(property) != platform->deprecatedPropertyReplacements.end())
+            property = platform->deprecatedPropertyReplacements[property];
         bool valid = false;
         for (int i = 0; i < (int) platformProperties.size(); i++)
-            if (platformProperties[i] == iter->first) {
+            if (platformProperties[i] == property) {
                 valid = true;
                 break;
             }
         if (!valid)
             throw OpenMMException("Illegal property name: "+iter->first);
+        validatedProperties[property] = iter->second;
     }
     
     // Find the list of kernels required.
@@ -139,7 +144,7 @@ ContextImpl::ContextImpl(Context& owner, const System& system, Integrator& integ
     for (int i = candidatePlatforms.size()-1; i >= 0; i--) {
         try {
             this->platform = platform = candidatePlatforms[i].second;
-            platform->contextCreated(*this, properties);
+            platform->contextCreated(*this, validatedProperties);
             break;
         }
         catch (...) {

openmmapi/src/CustomAngleForce.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) 2010 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,7 +44,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy) {
+CustomAngleForce::CustomAngleForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomAngleForce::getEnergyFunction() const {
@@ -123,3 +123,11 @@ ForceImpl* CustomAngleForce::createImpl() const {
 void CustomAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomBondForce.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -44,7 +44,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy) {
+CustomBondForce::CustomBondForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomBondForce::getEnergyFunction() const {
@@ -121,3 +121,11 @@ ForceImpl* CustomBondForce::createImpl() const {
 void CustomBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}