Bonded forces ok

platforms/brook/src/OpenMMBrookInterface.h

@@ -99,6 +99,17 @@ class OpenMMBrookInterface {
       
       int getNumberOfParticles( void ) const;
       
+      /** 
+       * Set number of particles
+       * 
+       * @param numberOfParticles number of particles
+       *
+       * @return DefaultReturnValue
+       *
+       */
+      
+      int setNumberOfParticles( int numberOfParticles );
+      
       /** 
        * Get particle stream width
        * 
@@ -166,10 +177,13 @@ class OpenMMBrookInterface {
        * Compute energy
        *
        * @param context OpenMMContextImpl context 
+       * @param system  system reference
+       *
+       * @return potential energy
        *
        */
       
-      double computeEnergy( OpenMMContextImpl& context );
+      double computeEnergy( OpenMMContextImpl& context, System& system );
       
       /** 
        * Set trigger Force Kernel
@@ -207,6 +221,24 @@ class OpenMMBrookInterface {
       
       void* getTriggerEnergyKernel( void ) const;
       
+      /** 
+       * Get BrookNonBonded reference
+       * 
+       * @return BrookNonBonded reference
+       *
+       */
+      
+      BrookNonBonded& getBrookNonBonded( void );
+      
+      /** 
+       * Get BrookGbsa reference
+       * 
+       * @return BrookGbsa reference
+       *
+       */
+      
+      BrookGbsa& getBrookGbsa( void );
+      
       /** 
        * Get BrookBondParameters for harmonic bond force
        * 
@@ -392,9 +424,9 @@ class OpenMMBrookInterface {
 
        // Brook bonded, nonbonded, Gbsa
 
-       BrookBonded* _brookBonded;
-       BrookNonBonded* _brookNonBonded;
-       BrookGbsa* _brookGbsa;
+       BrookBonded     _brookBonded;
+       BrookNonBonded  _brookNonBonded;
+       BrookGbsa       _brookGbsa;
 
        void* _triggerForceKernel;
        void* _triggerEnergyKernel;

platforms/brook/src/gpu/kinvmap_gather.br

@@ -304,7 +304,6 @@ kernel void kinvmap_gather3_4(
 	outforce += do_gather_nobranch( strwidth, invmap4_4, forces4 );
 }
 
-
 //Takes three + five inverse maps
 kernel void kinvmap_gather3_5(
 		float strwidth,    //stream width of the dihedral forces
@@ -337,6 +336,25 @@ kernel void kinvmap_gather3_5(
 }
 
 
+//Takes one + one inverse maps
+kernel void kinvmap_gather1_1(
+		float strwidth,    //stream width of the dihedral forces
+		float4 invmap3_1[][],   //indices into the dihedral forces
+		float3 forces3[][], //dihedral forces
+		float4 invmap5_1[][],   //indices into the dihedral forces
+		float3 forces5[][], //dihedral forces
+		float3 inforce<>,  //particle forces before
+		out float3 outforce<> //particle forces after
+		)
+{
+	float2 idx = indexof(outforce);
+	outforce = inforce;
+
+	outforce += do_gather_nobranch( strwidth, invmap3_1[idx], forces3 );
+	outforce += do_gather_nobranch( strwidth, invmap5_1[idx], forces5 );
+}
+
+
 //Takes five + two inverse maps
 kernel void kinvmap_gather5_2(
 		float strwidth,    //stream width of the dihedral forces

platforms/brook/src/gpu/kinvmap_gather.h

@@ -121,6 +121,15 @@ void  kinvmap_gather3_5 (const float  strwidth,
 		::brook::stream outforce);
 
 
+void  kinvmap_gather1_1 (const float  strwidth,
+		::brook::stream invmap3_1,
+		::brook::stream forces3,
+		::brook::stream invmap5_1,
+		::brook::stream forces5,
+		::brook::stream inforce,
+		::brook::stream outforce);
+
+
 void  kinvmap_gather5_2 (const float  strwidth,
 		::brook::stream invmap5_1,
 		::brook::stream invmap5_2,