Implemented updateParametersInContext() for five more Force classes

olla/include/openmm/kernels.h

@@ -596,6 +596,13 @@ 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 CustomNonbondedForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomNonbondedForce& force) = 0;
 };
 
 /**
@@ -693,6 +700,13 @@ 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 CustomGBForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomGBForce& force) = 0;
 };
 
 /**
@@ -721,6 +735,13 @@ 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 CustomExternalForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomExternalForce& force) = 0;
 };
 
 /**
@@ -754,6 +775,13 @@ 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 CustomHbondForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomHbondForce& force) = 0;
 };
 
 /**
@@ -782,6 +810,13 @@ 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 CustomCompoundBondForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const CustomCompoundBondForce& force) = 0;
 };
 
 /**

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -257,6 +257,17 @@ public:
      * @param max            the value of the independent variable corresponding to the last element of values
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
+    /**
+     * 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/CustomExternalForce.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 force field term
      */
     void setParticleParameters(int index, int particle, const std::vector<double>& parameters);
+    /**
+     * Update the per-particle 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 setParticleParameters() 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-particle parameters.
+     * All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing
+     * the Context.  Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

openmmapi/include/openmm/CustomGBForce.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:                                                              *
  *                                                                            *
@@ -483,6 +483,17 @@ public:
      * @param max            the value of the independent variable corresponding to the last element of values
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
+    /**
+     * Update the per-particle 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 setParticleParameters() 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-particle parameters.
+     * All other aspects of the Force (such as the energy function) are unaffected and can only be changed by reinitializing
+     * the Context.  Also, this method cannot be used to add new particles, only to change the parameters of existing ones.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

openmmapi/include/openmm/CustomHbondForce.h

@@ -403,6 +403,18 @@ public:
      * @param max            the value of the independent variable corresponding to the last element of values
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
+    /**
+     * Update the per-donor and per-acceptor 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 setDonorParameters() and setAcceptorParameters() 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-donor and per-acceptor parameters.
+     * All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can only
+     * be changed by reinitializing the Context.  The set of particles involved in a donor or acceptor cannot be changed, nor can
+     * new donors or acceptors be added.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

openmmapi/include/openmm/CustomNonbondedForce.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:                                                              *
  *                                                                            *
@@ -307,6 +307,18 @@ public:
      * @param max            the value of the independent variable corresponding to the last element of values
      */
     void setFunctionParameters(int index, const std::string& name, const std::vector<double>& values, double min, double max);
+    /**
+     * Update the per-particle 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 setParticleParameters() 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-particle parameters.
+     * All other aspects of the Force (the energy function, nonbonded method, cutoff distance, etc.) are unaffected and can
+     * only be changed by reinitializing the Context.  Also, this method cannot be used to add new particles, only to change
+     * the parameters of existing ones.
+     */
+    void updateParametersInContext(Context& context);
 protected:
     ForceImpl* createImpl();
 private:

openmmapi/include/openmm/internal/CustomCompoundBondForceImpl.h

@@ -62,6 +62,7 @@ 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);
     /**
      * This is a utility routine that parses the energy expression, identifies the angles and dihedrals
      * in it, and replaces them with variables.

openmmapi/include/openmm/internal/CustomExternalForceImpl.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:                                                              *
  *                                                                            *
@@ -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:
     CustomExternalForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/CustomGBForceImpl.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:                                                              *
  *                                                                            *
@@ -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:
     CustomGBForce& owner;
     Kernel kernel;

openmmapi/include/openmm/internal/CustomHbondForceImpl.h

@@ -62,6 +62,7 @@ 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);
     /**
      * This is a utility routine that parses the energy expression, identifies the angles and dihedrals
      * in it, and replaces them with variables.  The particle indices returned in the maps are defined

openmmapi/include/openmm/internal/CustomNonbondedForceImpl.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:                                                              *
  *                                                                            *
@@ -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:
     CustomNonbondedForce& owner;
     Kernel kernel;

openmmapi/src/CustomCompoundBondForce.cpp

@@ -153,3 +153,6 @@ ForceImpl* CustomCompoundBondForce::createImpl() {
     return new CustomCompoundBondForceImpl(*this);
 }
 
+void CustomCompoundBondForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomCompoundBondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomCompoundBondForceImpl.cpp

@@ -192,3 +192,7 @@ ExpressionTreeNode CustomCompoundBondForceImpl::replaceFunctions(const Expressio
     
     return ExpressionTreeNode(new Operation::Variable(name));
 }
+
+void CustomCompoundBondForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomCompoundBondForceKernel>().copyParametersToContext(context, owner);
+}

openmmapi/src/CustomExternalForce.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:                                                              *
  *                                                                            *
@@ -115,3 +115,7 @@ void CustomExternalForce::setParticleParameters(int index, int particle, const v
 ForceImpl* CustomExternalForce::createImpl() {
     return new CustomExternalForceImpl(*this);
 }
+
+void CustomExternalForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomExternalForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomExternalForceImpl.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:                                                              *
  *                                                                            *
@@ -95,4 +95,6 @@ map<string, double> CustomExternalForceImpl::getDefaultParameters() {
     return parameters;
 }
 
-
+void CustomExternalForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomExternalForceKernel>().copyParametersToContext(context, owner);
+}

openmmapi/src/CustomGBForce.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:                                                              *
  *                                                                            *
@@ -206,3 +206,6 @@ ForceImpl* CustomGBForce::createImpl() {
     return new CustomGBForceImpl(*this);
 }
 
+void CustomGBForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomGBForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomGBForceImpl.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:                                                              *
  *                                                                            *
@@ -124,3 +124,6 @@ map<string, double> CustomGBForceImpl::getDefaultParameters() {
     return parameters;
 }
 
+void CustomGBForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomGBForceKernel>().copyParametersToContext(context, owner);
+}

openmmapi/src/CustomHbondForce.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) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -220,3 +220,6 @@ ForceImpl* CustomHbondForce::createImpl() {
     return new CustomHbondForceImpl(*this);
 }
 
+void CustomHbondForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomHbondForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}

openmmapi/src/CustomHbondForceImpl.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) 2008-2010 Stanford University and the Authors.      *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors: Peter Eastman                                                     *
  * Contributors:                                                              *
  *                                                                            *
@@ -266,3 +266,7 @@ ExpressionTreeNode CustomHbondForceImpl::replaceFunctions(const ExpressionTreeNo
     
     return ExpressionTreeNode(new Operation::Variable(name));
 }
+
+void CustomHbondForceImpl::updateParametersInContext(ContextImpl& context) {
+    kernel.getAs<CalcCustomHbondForceKernel>().copyParametersToContext(context, owner);
+}

openmmapi/src/CustomNonbondedForce.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:                                                              *
  *                                                                            *
@@ -177,3 +177,7 @@ void CustomNonbondedForce::setFunctionParameters(int index, const std::string& n
 ForceImpl* CustomNonbondedForce::createImpl() {
     return new CustomNonbondedForceImpl(*this);
 }
+
+void CustomNonbondedForce::updateParametersInContext(Context& context) {
+    dynamic_cast<CustomNonbondedForceImpl&>(getImplInContext(context)).updateParametersInContext(getContextImpl(context));
+}