Fixed another case where the exclusions for CustomGBForce could be handled incorrectly

platforms/opencl/src/OpenCLKernels.cpp

@@ -2074,6 +2074,8 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
             file = OpenCLKernelSources::customGBValueN2_default;
         cl::Program program = cl.createProgram(cl.replaceStrings(file, replacements), defines);
         pairValueKernel = cl::Kernel(program, "computeN2Value");
+        if (useExclusionsForValue)
+            cl.getNonbondedUtilities().requestExclusions(exclusionList);
     }
     {
         // Create the kernel to reduce the N2 value and calculate other values.

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -93,7 +93,24 @@ void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic
         if (cutoffDistance != cutoff)
             throw OpenMMException("All Forces must use the same cutoff distance");
     }
-    if (usesExclusions && anyExclusions) {
+    if (usesExclusions)
+        requestExclusions(exclusionList);
+    useCutoff = usesCutoff;
+    usePeriodic = usesPeriodic;
+    cutoff = cutoffDistance;
+    kernelSource += kernel+"\n";
+}
+
+void OpenCLNonbondedUtilities::addParameter(const ParameterInfo& parameter) {
+    parameters.push_back(parameter);
+}
+
+void OpenCLNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
+    arguments.push_back(parameter);
+}
+
+void OpenCLNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) {
+    if (anyExclusions) {
         bool sameExclusions = (exclusionList.size() == atomExclusions.size());
         for (int i = 0; i < (int) exclusionList.size() && sameExclusions; i++) {
             if (exclusionList[i].size() != atomExclusions[i].size())
@@ -105,24 +122,12 @@ void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic
         if (!sameExclusions)
             throw OpenMMException("All Forces must have identical exceptions");
     }
-    useCutoff = usesCutoff;
-    usePeriodic = usesPeriodic;
-    cutoff = cutoffDistance;
-    kernelSource += kernel+"\n";
-    if (usesExclusions && !anyExclusions) {
+    else {
         atomExclusions = exclusionList;
         anyExclusions = true;
     }
 }
 
-void OpenCLNonbondedUtilities::addParameter(const ParameterInfo& parameter) {
-    parameters.push_back(parameter);
-}
-
-void OpenCLNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
-    arguments.push_back(parameter);
-}
-
 void OpenCLNonbondedUtilities::initialize(const System& system) {
     if (cutoff == -1.0)
         return; // There are no nonbonded interactions in the System.

platforms/opencl/src/OpenCLNonbondedUtilities.h

@@ -84,6 +84,12 @@ public:
      * Add an array (other than a per-atom parameter) that should be passed as an argument to the default interaction kernel.
      */
     void addArgument(const ParameterInfo& parameter);
+    /**
+     * Specify the list of exclusions that an interaction outside the default kernel will depend on.
+     * 
+     * @param exclusionList  for each atom, specifies the list of other atoms whose interactions should be excluded
+     */
+    void requestExclusions(const std::vector<std::vector<int> >& exclusionList);
     /**
      * Initialize this object in preparation for a simulation.
      */