resolved conflict

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 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)
+     * @param defaultPressure     The default pressure acting on each axis (in bar)
+     * @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 frequency         the frequency at which Monte Carlo pressure changes should be attempted (in time steps)
+     * @param defaultPressure     the default pressure acting on the system (in bar)
+     * @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;
+}

openmmapi/src/CustomCentroidBondForce.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) 2015 Stanford University and the Authors.           *
+ * Portions copyright (c) 2015-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,7 +48,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy) {
+CustomCentroidBondForce::CustomCentroidBondForce(int numGroups, const string& energy) : groupsPerBond(numGroups), energyExpression(energy), usePeriodic(false) {
 }
 
 CustomCentroidBondForce::~CustomCentroidBondForce() {
@@ -173,3 +173,11 @@ ForceImpl* CustomCentroidBondForce::createImpl() const {
 void CustomCentroidBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomCentroidBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomCentroidBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomCentroidBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomCompoundBondForce.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) 2008-2014 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -48,7 +48,7 @@ using std::string;
 using std::stringstream;
 using std::vector;
 
-CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy) {
+CustomCompoundBondForce::CustomCompoundBondForce(int numParticles, const string& energy) : particlesPerBond(numParticles), energyExpression(energy), usePeriodic(false) {
 }
 
 
@@ -176,3 +176,11 @@ ForceImpl* CustomCompoundBondForce::createImpl() const {
 void CustomCompoundBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomCompoundBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomCompoundBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/CustomIntegrator.cpp

@@ -248,21 +248,21 @@ int CustomIntegrator::addUpdateContextState() {
 int CustomIntegrator::beginIfBlock(const string& expression) {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(BeginIfBlock, "", expression));
+    computations.push_back(ComputationInfo(IfBlockStart, "", expression));
     return computations.size()-1;
 }
 
 int CustomIntegrator::beginWhileBlock(const string& expression) {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(BeginWhileBlock, "", expression));
+    computations.push_back(ComputationInfo(WhileBlockStart, "", expression));
     return computations.size()-1;
 }
 
 int CustomIntegrator::endBlock() {
     if (owner != NULL)
         throw OpenMMException("The integrator cannot be modified after it is bound to a context");
-    computations.push_back(ComputationInfo(EndBlock, "", ""));
+    computations.push_back(ComputationInfo(BlockEnd, "", ""));
     return computations.size()-1;
 }
 

openmmapi/src/CustomIntegratorUtilities.cpp

@@ -87,7 +87,7 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
     for (int step = 0; step < numSteps; step++) {
         string expression;
         integrator.getComputationStep(step, stepType[step], stepVariable[step], expression);
-        if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock) {
+        if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart) {
             // This step involves a condition.
 
             string lhs, rhs;
@@ -158,9 +158,9 @@ void CustomIntegratorUtilities::analyzeComputations(const ContextImpl& context,
     vector<int> blockStart;
     blockEnd.resize(numSteps, -1);
     for (int step = 0; step < numSteps; step++) {
-        if (stepType[step] == CustomIntegrator::BeginIfBlock || stepType[step] == CustomIntegrator::BeginWhileBlock)
+        if (stepType[step] == CustomIntegrator::IfBlockStart || stepType[step] == CustomIntegrator::WhileBlockStart)
             blockStart.push_back(step);
-        else if (stepType[step] == CustomIntegrator::EndBlock) {
+        else if (stepType[step] == CustomIntegrator::BlockEnd) {
             if (blockStart.size() == 0) {
                 stringstream error("CustomIntegrator: Unexpected end of block at computation ");
                 error << step;
@@ -207,7 +207,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
             jumps[step] = -1;
             step = nextStep;
         }
-        else if (stepType[step] == CustomIntegrator::BeginIfBlock) {
+        else if (stepType[step] == CustomIntegrator::IfBlockStart) {
             // Consider skipping the block.
 
             enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);
@@ -216,7 +216,7 @@ void CustomIntegratorUtilities::enumeratePaths(int firstStep, vector<int> steps,
 
             step++;
         }
-        else if (stepType[step] == CustomIntegrator::BeginWhileBlock && jumps[step] != -2) {
+        else if (stepType[step] == CustomIntegrator::WhileBlockStart && jumps[step] != -2) {
             // Consider skipping the block.
 
             enumeratePaths(blockEnd[step]+1, steps, jumps, blockEnd, stepType, needsForces, needsEnergy, invalidatesForces, forceGroup, computeBoth);

openmmapi/src/CustomTorsionForce.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;
 
-CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy) {
+CustomTorsionForce::CustomTorsionForce(const string& energy) : energyExpression(energy), usePeriodic(false) {
 }
 
 const string& CustomTorsionForce::getEnergyFunction() const {
@@ -125,3 +125,11 @@ ForceImpl* CustomTorsionForce::createImpl() const {
 void CustomTorsionForce::updateParametersInContext(Context& context) {
     dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void CustomTorsionForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool CustomTorsionForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/HarmonicAngleForce.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:                                                              *
  *                                                                            *
@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-HarmonicAngleForce::HarmonicAngleForce() {
+HarmonicAngleForce::HarmonicAngleForce() : usePeriodic(false) {
 }
 
 int HarmonicAngleForce::addAngle(int particle1, int particle2, int particle3, double angle, double k) {
@@ -70,3 +70,11 @@ ForceImpl* HarmonicAngleForce::createImpl() const {
 void HarmonicAngleForce::updateParametersInContext(Context& context) {
     dynamic_cast<HarmonicAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void HarmonicAngleForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool HarmonicAngleForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/HarmonicBondForce.cpp

@@ -37,7 +37,7 @@
 
 using namespace OpenMM;
 
-HarmonicBondForce::HarmonicBondForce() {
+HarmonicBondForce::HarmonicBondForce() : usePeriodic(false) {
 }
 
 int HarmonicBondForce::addBond(int particle1, int particle2, double length, double k) {
@@ -68,3 +68,11 @@ ForceImpl* HarmonicBondForce::createImpl() const {
 void HarmonicBondForce::updateParametersInContext(Context& context) {
     dynamic_cast<HarmonicBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
 }
+
+void HarmonicBondForce::setUsesPeriodicBoundaryConditions(bool periodic) {
+    usePeriodic = periodic;
+}
+
+bool HarmonicBondForce::usesPeriodicBoundaryConditions() const {
+    return usePeriodic;
+}

openmmapi/src/LocalEnergyMinimizer.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) 2010-2012 Stanford University and the Authors.      *
+ * Portions copyright (c) 2010-2016 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -108,7 +108,8 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
     if (x == NULL)
         throw OpenMMException("LocalEnergyMinimizer: Failed to allocate memory");
     double constraintTol = context.getIntegrator().getConstraintTolerance();
-    double k = tolerance/constraintTol;
+    double workingConstraintTol = max(1e-4, constraintTol);
+    double k = tolerance/workingConstraintTol;
 
     // Initialize the minimizer.
 
@@ -121,7 +122,7 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
 
     // Make sure the initial configuration satisfies all constraints.
 
-    context.applyConstraints(constraintTol);
+    context.applyConstraints(workingConstraintTol);
 
     // Record the initial positions and determine a normalization constant for scaling the tolerance.
 
@@ -162,14 +163,14 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
             if (error > maxError)
                 maxError = error;
         }
-        if (maxError <= constraintTol)
+        if (maxError <= workingConstraintTol)
             break; // All constraints are satisfied.
         context.setPositions(initialPos);
         if (maxError >= prevMaxError)
             break; // Further tightening the springs doesn't seem to be helping, so just give up.
         prevMaxError = maxError;
         k *= 10;
-        if (maxError > 100*constraintTol) {
+        if (maxError > 100*workingConstraintTol) {
             // We've gotten far enough from a valid state that we might have trouble getting
             // back, so reset to the original positions.
             
@@ -181,5 +182,11 @@ void LocalEnergyMinimizer::minimize(Context& context, double tolerance, int maxI
         }
     }
     lbfgs_free(x);
+    
+    // If necessary, do a final constraint projection to make sure they are satisfied
+    // to the full precision requested by the user.
+    
+    if (constraintTol < workingConstraintTol)
+        context.applyConstraints(workingConstraintTol);
 }