Implemented updateParametersInContext() for seven more Force classes

olla/include/openmm/kernels.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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -274,6 +274,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the HarmonicBondForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const HarmonicBondForce& force) = 0;
 };
 
 /**
@@ -302,6 +309,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomBondForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomBondForce& force) = 0;
 };
 
 /**
@@ -330,6 +344,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the HarmonicAngleForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const HarmonicAngleForce& force) = 0;
 };
 
 /**
@@ -358,6 +379,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomAngleForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomAngleForce& force) = 0;
 };
 
 /**
@@ -386,6 +414,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the PeriodicTorsionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const PeriodicTorsionForce& force) = 0;
 };
 
 /**
@@ -414,6 +449,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the RBTorsionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const RBTorsionForce& force) = 0;
 };
 
 /**
@@ -470,6 +512,13 @@ public:
      * @return the potential energy due to the force
      */
     virtual double execute(ContextImpl& context, bool includeForces, bool includeEnergy) = 0;
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the CustomTorsionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomTorsionForce& force) = 0;
 };
 
 /**

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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -190,6 +190,17 @@ public:
      * @param parameters    the list of parameters for the angle
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, const std::vector<double>& parameters);
+    /**
+     * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * This method has several limitations.  The only information it updates is the values of per-angle parameters.
+     * All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing
+     * the Context.  The set of particles involved in a angle cannot be changed, nor can new angles be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -187,6 +187,17 @@ public:
      * @param parameters    the list of parameters for the bond
      */
     void setBondParameters(int index, int particle1, int particle2, const std::vector<double>& parameters);
+    /**
+     * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * This method has several limitations.  The only information it updates is the values of per-bond parameters.
+     * All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing
+     * the Context.  The set of particles involved in a bond cannot be changed, nor can new bonds be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2010-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -193,6 +193,17 @@ public:
      * @param parameters    the list of parameters for the torsion
      */
     void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, const std::vector<double>& parameters);
+    /**
+     * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * This method has several limitations.  The only information it updates is the values of per-torsion parameters.
+     * All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing
+     * the Context.  The set of particles involved in a torsion cannot be changed, nor can new torsions be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -91,6 +91,16 @@ public:
      * @param k         the harmonic force constant for the angle, measured in kJ/mol/radian^2
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, double angle, double k);
+    /**
+     * Update the per-angle parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setAngleParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * The only information this method updates is the values of per-angle parameters.  The set of particles involved
+     * in a angle cannot be changed, nor can new angles be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -88,6 +88,16 @@ public:
      * @param k         the harmonic force constant for the bond, measured in kJ/mol/nm^2
      */
     void setBondParameters(int index, int particle1, int particle2, double length, double k);
+    /**
+     * Update the per-bond parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setBondParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * The only information this method updates is the values of per-bond parameters.  The set of particles involved
+     * in a bond cannot be changed, nor can new bonds be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -97,6 +97,16 @@ public:
      * @param k            the force constant for the torsion
      */
     void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int periodicity, double phase, double k);
+    /**
+     * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * The only information this method updates is the values of per-torsion parameters.  The set of particles involved
+     * in a torsion cannot be changed, nor can new torsions be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

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) 2008-2009 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -106,6 +106,16 @@ public:
      * @param c5           the coefficient of the 5th order term, measured in kJ/mol
      */
     void setTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, double c0, double c1, double c2, double c3, double c4, double c5);
+    /**
+     * Update the per-torsion parameters in a Context to match those stored in this Force object.  This method provides
+     * an efficient method to update certain parameters in an existing Context without needing to reinitialize it.
+     * Simply call setTorsionParameters() to modify this object's parameters, then call updateParametersInState()
+     * to copy them over to the Context.
+     * 
+     * The only information this method updates is the values of per-torsion parameters.  The set of particles involved
+     * in a torsion cannot be changed, nor can new torsions be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

openmmapi/include/openmm/internal/CustomAngleForceImpl.h

@@ -59,6 +59,7 @@ public:
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     std::map<std::string, double> getDefaultParameters();
     std::vector<std::string> getKernelNames();
+    void updateParametersInContext(ContextImpl& context);
 private:
     CustomAngleForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/CustomBondForceImpl.h

@@ -60,6 +60,7 @@ public:
     std::map<std::string, double> getDefaultParameters();
     std::vector<std::string> getKernelNames();
     std::vector<std::pair<int, int> > getBondedParticles() const;
+    void updateParametersInContext(ContextImpl& context);
 private:
     CustomBondForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/CustomTorsionForceImpl.h

@@ -59,6 +59,7 @@ public:
     double calcForcesAndEnergy(ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
     std::map<std::string, double> getDefaultParameters();
     std::vector<std::string> getKernelNames();
+    void updateParametersInContext(ContextImpl& context);
 private:
     CustomTorsionForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/HarmonicAngleForceImpl.h

@@ -61,6 +61,7 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
+    void updateParametersInContext(ContextImpl& context);
 private:
     HarmonicAngleForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/HarmonicBondForceImpl.h

@@ -62,6 +62,7 @@ public:
     }
     std::vector<std::string> getKernelNames();
     std::vector<std::pair<int, int> > getBondedParticles() const;
+    void updateParametersInContext(ContextImpl& context);
 private:
     HarmonicBondForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/PeriodicTorsionForceImpl.h

@@ -61,6 +61,7 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
+    void updateParametersInContext(ContextImpl& context);
 private:
     PeriodicTorsionForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/RBTorsionForceImpl.h

@@ -61,6 +61,7 @@ public:
         return std::map<std::string, double>(); // This force field doesn't define any parameters.
     }
     std::vector<std::string> getKernelNames();
+    void updateParametersInContext(ContextImpl& context);
 private:
     RBTorsionForce& owner;
     Kernel kernel;

openmmapi/src/CustomAngleForce.cpp

@@ -120,3 +120,6 @@ ForceImpl* CustomAngleForce::createImpl() {
     return new CustomAngleForceImpl(*this);
 }
 
+void CustomAngleForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomAngleForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomAngleForceImpl.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) 2010-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -107,3 +107,6 @@ map<string, double> CustomAngleForceImpl::getDefaultParameters() {
     return parameters;
 }
 
+void CustomAngleForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomAngleForceKernel>().copyParametersToContext(context, owner);
+}

openmmapi/src/CustomBondForce.cpp

@@ -118,3 +118,6 @@ ForceImpl* CustomBondForce::createImpl() {
     return new CustomBondForceImpl(*this);
 }
 
+void CustomBondForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomBondForceImpl.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) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -110,3 +110,7 @@ vector<pair<int, int> > CustomBondForceImpl::getBondedParticles() const {
     }
     return bonds;
 }
+
+void CustomBondForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomBondForceKernel>().copyParametersToContext(context, owner);
+}

openmmapi/src/CustomTorsionForce.cpp

@@ -122,3 +122,6 @@ ForceImpl* CustomTorsionForce::createImpl() {
     return new CustomTorsionForceImpl(*this);
 }
 
+void CustomTorsionForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomTorsionForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}