Added updateParametersInContext() methods to most AMOEBA forces.

plugins/amoeba/openmmapi/include/openmm/AmoebaAngleForce.h

@@ -155,6 +155,16 @@ public:
      * @param quadratic k   the quadratic force constant for the angle, measured in kJ/mol/radian^2
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, double length, double quadraticK );
+    /**
+     * 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 an angle cannot be changed, nor can new angles be added.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaBondForce.h

@@ -127,6 +127,16 @@ public:
      * @param k         the quadratic force constant for the bond
      */
     void setBondParameters(int index, int particle1, int particle2, double length, double quadraticK );
+    /**
+     * 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:
     double _globalQuarticK, _globalCubicK;

plugins/amoeba/openmmapi/include/openmm/AmoebaGeneralizedKirkwoodForce.h

@@ -152,6 +152,16 @@ public:
      * Set the surface area factor kJ/(nm*nm) used in SASA contribution
      */
     void setSurfaceAreaFactor( double surfaceAreaFactor );
+    /**
+     * 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.
+     * 
+     * The only information this method updates is the values of per-particle parameters.  All other aspects of the Force
+     * (the probe radius, the surface area factor, etc.) are unaffected and can only be changed by reinitializing the Context.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaInPlaneAngleForce.h

@@ -160,6 +160,16 @@ public:
      * @param quadratic k   the quadratic force constant for the angle, measured in kJ/mol/radian^2
      */
     void setAngleParameters(int index, int particle1, int particle2, int particle3, int particle4, double length, double quadraticK );
+    /**
+     * 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 an angle cannot be changed, nor can new angles be added.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaMultipoleForce.h

@@ -328,6 +328,18 @@ public:
                                       quadrupole_zx, quadrupole_zy, quadrupole_zz)
      */
     void getSystemMultipoleMoments(Context& context, std::vector< double >& outputMultipoleMoments);
+    /**
+     * Update the multipole 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 setMultipoleParameters() 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 parameters of multipoles.
+     * All other aspects of the Force (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be
+     * changed by reinitializing the Context.  Furthermore, this method cannot be used to add new multipoles,
+     * only to change the parameters of existing ones.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaOutOfPlaneBendForce.h

@@ -152,6 +152,16 @@ public:
      * @param k             the force constant for the out-of-plane bend
      */
     void setOutOfPlaneBendParameters(int index, int particle1, int particle2, int particle3, int particle4, double k);
+    /**
+     * Update the per-bend term 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 setOutOfPlaneBendParameters() 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-bend term parameters.  The set of particles involved
+     * in a term cannot be changed, nor can new terms be added.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaPiTorsionForce.h

@@ -102,6 +102,16 @@ public:
      * @param k             the force constant for the torsion
      */
     void setPiTorsionParameters(int index, int particle1, int particle2, int particle3, int particle4, int particle5, int particle6, 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 setPiTorsionParameters() 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();

plugins/amoeba/openmmapi/include/openmm/AmoebaStretchBendForce.h

@@ -105,6 +105,16 @@ public:
      */
     void setStretchBendParameters(int index, int particle1, int particle2, int particle3, 
                                   double lengthAB,  double lengthCB, double angle, double k );
+    /**
+     * Update the per-stretch-bend term 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 setStretchBendParameters() 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-stretch-bend term parameters.  The set of particles involved
+     * in a term cannot be changed, nor can new terms be added.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaVdwForce.h

@@ -201,6 +201,16 @@ public:
      * Set the method used for handling long range nonbonded interactions.
      */
     void setNonbondedMethod(NonbondedMethod method);
+    /**
+     * 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.
+     * 
+     * The only information this method updates is the values of per-particle parameters.  All other aspects of the Force
+     * (the nonbonded method, the cutoff distance, etc.) are unaffected and can only be changed by reinitializing the Context.
+     */
+    void updateParametersInContext(Context& context);
 
 protected:
     ForceImpl* createImpl();

plugins/amoeba/openmmapi/include/openmm/AmoebaWcaDispersionForce.h

@@ -88,6 +88,16 @@ public:
      * @return index of added particle
      */
     int addParticle(double radius, double epsilon);
+    /**
+     * 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.
+     * 
+     * The only information this method updates is the values of per-particle parameters.  All other aspects of the Force
+     * are unaffected and can only be changed by reinitializing the Context.
+     */
+    void updateParametersInContext(Context& context);
 
     /* 
      * Constants

plugins/amoeba/openmmapi/include/openmm/amoebaKernels.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 Stanford University and the Authors.           *
+ * Portions copyright (c) 2008-2012 Stanford University and the Authors.      *
  * Authors:                                                                   *
  * Contributors:                                                              *
  *                                                                            *
@@ -74,7 +74,13 @@ 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 AmoebaBondForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaBondForce& force) = 0;
 };
 
 /**
@@ -108,6 +114,13 @@ 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 AmoebaAngleForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaAngleForce& force) = 0;
 };
 
 /**
@@ -141,6 +154,13 @@ 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 AmoebaInPlaneAngleForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaInPlaneAngleForce& force) = 0;
 };
 
 /**
@@ -174,6 +194,13 @@ 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 AmoebaPiTorsionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaPiTorsionForce& force) = 0;
 };
 
 /**
@@ -207,6 +234,13 @@ 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 AmoebaStretchBendForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaStretchBendForce& force) = 0;
 };
 
 /**
@@ -240,6 +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 AmoebaOutOfPlaneBendForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaOutOfPlaneBendForce& force) = 0;
 };
 
 /**
@@ -311,7 +352,13 @@ public:
                                             std::vector< double >& outputElectrostaticPotential ) = 0;
 
     virtual void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMonents ) = 0;
-
+    /**
+     * Copy changed parameters over to a context.
+     *
+     * @param context    the context to copy parameters to
+     * @param force      the AmoebaMultipoleForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaMultipoleForce& force) = 0;
 };
 
 /**
@@ -345,6 +392,13 @@ 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 AmoebaGeneralizedKirkwoodForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaGeneralizedKirkwoodForce& force) = 0;
 };
 
 
@@ -378,6 +432,13 @@ 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 AmoebaVdwForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaVdwForce& force) = 0;
 };
 
 /**
@@ -411,6 +472,13 @@ 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 AmoebaWcaDispersionForce to copy the parameters from
+     */
+    virtual void copyParametersToContext(ContextImpl& context, const AmoebaWcaDispersionForce& force) = 0;
 };
 
 } // namespace OpenMM

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaAngleForceImpl.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:
     AmoebaAngleForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaBondForceImpl.h

@@ -64,6 +64,7 @@ public:
     std::vector<std::string> getKernelNames();
 
     std::vector< std::pair<int, int> > getBondedParticles() const;
+    void updateParametersInContext(ContextImpl& context);
 private:
     AmoebaBondForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaGeneralizedKirkwoodForceImpl.h

@@ -61,6 +61,7 @@ public:
     Kernel& getKernel() {
         return kernel;
     }
+    void updateParametersInContext(ContextImpl& context);
 private:
     AmoebaGeneralizedKirkwoodForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaInPlaneAngleForceImpl.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:
     AmoebaInPlaneAngleForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaMultipoleForceImpl.h

@@ -86,6 +86,7 @@ public:
                                     std::vector< double >& outputElectrostaticPotential );
 
     void getSystemMultipoleMoments( ContextImpl& context, std::vector< double >& outputMultipoleMonents );
+    void updateParametersInContext(ContextImpl& context);
  
 
 private:

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaOutOfPlaneBendForceImpl.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:
     AmoebaOutOfPlaneBendForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaPiTorsionForceImpl.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:
     AmoebaPiTorsionForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaStretchBendForceImpl.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:
     AmoebaStretchBendForce& owner;
     Kernel kernel;

plugins/amoeba/openmmapi/include/openmm/internal/AmoebaVdwForceImpl.h

@@ -68,6 +68,7 @@ public:
      * long range dispersion correction to the energy.
      */
     static double calcDispersionCorrection(const System& system, const AmoebaVdwForce& force);
+    void updateParametersInContext(ContextImpl& context);
 private:
     AmoebaVdwForce& owner;
     Kernel kernel;