Fixed bug when CustomGBForce was told to use exclusions, but didn't have any...

Fixed bug when CustomGBForce was told to use exclusions, but didn't have any exclusions.  (See bug 1519.)

platforms/opencl/src/OpenCLKernels.cpp

@@ -2136,15 +2136,14 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
         for (int i = 0; i < force.getNumGlobalParameters(); i++)
             variables[force.getGlobalParameterName(i)] = "globals["+intToString(i)+"]";
         stringstream n2EnergySource;
-        bool anyExclusions = false;
+        bool anyExclusions = (force.getNumExclusions() > 0);
         for (int i = 0; i < force.getNumEnergyTerms(); i++) {
             string expression;
             CustomGBForce::ComputationType type;
             force.getEnergyTermParameters(i, expression, type);
             if (type == CustomGBForce::SingleParticle)
                 continue;
-            bool exclude = (type == CustomGBForce::ParticlePair);
-            anyExclusions |= exclude;
+            bool exclude = (anyExclusions && type == CustomGBForce::ParticlePair);
             map<string, Lepton::ParsedExpression> n2EnergyExpressions;
             n2EnergyExpressions["tempEnergy += "] = Lepton::Parser::parse(expression, functions).optimize();
             n2EnergyExpressions["dEdR += "] = Lepton::Parser::parse(expression, functions).differentiate("r").optimize();

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -35,7 +35,7 @@
 using namespace OpenMM;
 using namespace std;
 
-OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), cutoff(-1.0), useCutoff(false),
+OpenCLNonbondedUtilities::OpenCLNonbondedUtilities(OpenCLContext& context) : context(context), cutoff(-1.0), useCutoff(false), anyExclusions(false),
         numForceBuffers(0), exclusionIndices(NULL), exclusionRowIndices(NULL), exclusions(NULL), interactingTiles(NULL), interactionFlags(NULL),
         interactionCount(NULL), blockCenter(NULL), blockBoundingBox(NULL) {
     // Decide how many thread blocks and force buffers to use.
@@ -93,7 +93,7 @@ void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic
         if (cutoffDistance != cutoff)
             throw OpenMMException("All Forces must use the same cutoff distance");
     }
-    if (usesExclusions && atomExclusions.size() != 0) {
+    if (usesExclusions && anyExclusions) {
         bool sameExclusions = (exclusionList.size() == atomExclusions.size());
         for (int i = 0; i < (int) exclusionList.size() && sameExclusions; i++) {
             if (exclusionList[i].size() != atomExclusions[i].size())
@@ -109,8 +109,10 @@ void OpenCLNonbondedUtilities::addInteraction(bool usesCutoff, bool usesPeriodic
     usePeriodic = usesPeriodic;
     cutoff = cutoffDistance;
     kernelSource += kernel+"\n";
-    if (usesExclusions)
+    if (usesExclusions && !anyExclusions) {
         atomExclusions = exclusionList;
+        anyExclusions = true;
+    }
 }
 
 void OpenCLNonbondedUtilities::addParameter(const ParameterInfo& parameter) {

platforms/opencl/src/OpenCLNonbondedUtilities.h

@@ -245,7 +245,7 @@ private:
     std::string kernelSource;
     std::map<std::string, std::string> kernelDefines;
     double cutoff;
-    bool useCutoff, usePeriodic, forceBufferPerAtomBlock, deviceIsCpu;
+    bool useCutoff, usePeriodic, forceBufferPerAtomBlock, deviceIsCpu, anyExclusions;
     int numForceBuffers, startTileIndex, numTiles, numForceThreadBlocks, forceThreadBlockSize;
 };