Added code to calculate electrostatic potential given vector of grid points

plugins/amoeba/platforms/reference/src/AmoebaReferenceKernels.h

@@ -384,6 +384,15 @@ public:
      * @return the potential energy due to the force
      */
     double execute(ContextImpl& context, bool includeForces, bool includeEnergy);
+    /** 
+     * Execute the kernel to calculate the electrostatic potential
+     *
+     * @param context        the context in which to execute this kernel
+     * @param inputGrid      input grid coordinates
+     * @param outputElectrostaticPotential output potential 
+     */
+    void getElectrostaticPotential(ContextImpl& context, const std::vector< Vec3 >& inputGrid,
+                                   std::vector< double >& outputElectrostaticPotential );
 private:
     int numMultipoles;
     int polarizationType;

plugins/amoeba/wrappers/CWrapper_Header.xslt

@@ -21,7 +21,7 @@
 <xsl:variable name="vector_tortor_type_id" select="/GCC_XML/Class[starts-with(@name, 'vector&lt;std::vector&lt;std::vector&lt;double')]/@id"/>
 
 <!-- Do not generate functions for the following classes -->
-<xsl:variable name="skip_classes" select="('Vec3', 'Kernel', 'System', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory', 'ContextImpl', 'OpenMMException', 'Force', 'ForceImpl')"/>
+<xsl:variable name="skip_classes" select="('Vec3', 'Context', 'Kernel', 'System', 'Stream', 'KernelImpl', 'StreamImpl', 'KernelFactory', 'StreamFactory', 'ContextImpl', 'OpenMMException', 'Force', 'ForceImpl')"/>
 <!-- Do not generate the following functions -->
 <xsl:variable name="skip_methods" select="('OpenMM_Context_getState', 'OpenMM_Platform_loadPluginsFromDirectory')"/>
 <!-- Suppress any function which references any of the following classes -->
@@ -46,7 +46,6 @@ static <xsl:call-template name="wrap_type"><xsl:with-param name="type_id" select
 typedef struct OpenMM_<xsl:value-of select="concat(@name, '_struct OpenMM_', @name, ';')"/>
  </xsl:for-each>
 
-typedef struct OpenMM_IntArray_struct OpenMM_IntArray;
 typedef struct OpenMM_2D_IntArray_struct OpenMM_2D_IntArray;
 typedef struct OpenMM_3D_DoubleArray_struct OpenMM_3D_DoubleArray;
 

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -286,8 +286,10 @@ UNITS = {
 ("AmoebaMultipoleForce",                 "getCovalentMap")                                :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getCovalentMaps")                               :  ( None, ()),
 ("AmoebaMultipoleForce",                 "getScalingDistanceCutoff")                      :  ( 'unit.nanometer', ()),
-#("AmoebaMultipoleForce",                 "getElectricConstant")                           :  ( '1/(unit.nanometer*unit.kilojoule_per_mole)', ()),
 ("AmoebaMultipoleForce",                 "getElectricConstant")                           :  ( None, ()),
+#("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( None, ('unit.kilojoule_per_mole')),
+#("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( ('unit.kilojoule_per_mole'), ()),
+("AmoebaMultipoleForce",                 "getElectrostaticPotential")                     :  ( None, ()),
 
 ("AmoebaOutOfPlaneBendForce",            "getNumOutOfPlaneBends")                         :  ( None, ()),
 ("AmoebaOutOfPlaneBendForce",            "getAmoebaGlobalOutOfPlaneBendCubic")            :  ( None,()),