Merge pull request #2176 from peastman/offsets

Fixed bugs in particle parameter offsets

platforms/cpu/src/CpuKernels.cpp

@@ -494,6 +494,14 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
 
     // Identify which exceptions are 1-4 interactions.
 
+    set<int> exceptionsWithOffsets;
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        string param;
+        int exception;
+        double charge, sigma, epsilon;
+        force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
+        exceptionsWithOffsets.insert(exception);
+    }
     numParticles = force.getNumParticles();
     exclusions.resize(numParticles);
     vector<int> nb14s;
@@ -503,7 +511,7 @@ void CpuCalcNonbondedForceKernel::initialize(const System& system, const Nonbond
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
         exclusions[particle1].insert(particle2);
         exclusions[particle2].insert(particle1);
-        if (chargeProd != 0.0 || epsilon != 0.0)
+        if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
             nb14s.push_back(i);
     }
 

platforms/cuda/src/CudaKernels.cpp

@@ -1574,6 +1574,14 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
 
     // Identify which exceptions are 1-4 interactions.
 
+    set<int> exceptionsWithOffsets;
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        string param;
+        int exception;
+        double charge, sigma, epsilon;
+        force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
+        exceptionsWithOffsets.insert(exception);
+    }
     vector<pair<int, int> > exclusions;
     vector<int> exceptions;
     for (int i = 0; i < force.getNumExceptions(); i++) {
@@ -1581,7 +1589,7 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         double chargeProd, sigma, epsilon;
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
         exclusions.push_back(pair<int, int>(particle1, particle2));
-        if (chargeProd != 0.0 || epsilon != 0.0)
+        if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
             exceptions.push_back(i);
     }
 
@@ -1602,6 +1610,16 @@ void CudaCalcNonbondedForceKernel::initialize(const System& system, const Nonbon
         if (epsilon != 0.0)
             hasLJ = true;
     }
+    for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
+        string param;
+        int particle;
+        double charge, sigma, epsilon;
+        force.getParticleParameterOffset(i, param, particle, charge, sigma, epsilon);
+        if (charge != 0.0)
+            hasCoulomb = true;
+        if (epsilon != 0.0)
+            hasLJ = true;
+    }
     for (auto exclusion : exclusions) {
         exclusionList[exclusion.first].push_back(exclusion.second);
         exclusionList[exclusion.second].push_back(exclusion.first);

platforms/opencl/src/OpenCLKernels.cpp

@@ -1566,6 +1566,14 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
 
     // Identify which exceptions are 1-4 interactions.
 
+    set<int> exceptionsWithOffsets;
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        string param;
+        int exception;
+        double charge, sigma, epsilon;
+        force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
+        exceptionsWithOffsets.insert(exception);
+    }
     vector<pair<int, int> > exclusions;
     vector<int> exceptions;
     for (int i = 0; i < force.getNumExceptions(); i++) {
@@ -1573,7 +1581,7 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         double chargeProd, sigma, epsilon;
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
         exclusions.push_back(pair<int, int>(particle1, particle2));
-        if (chargeProd != 0.0 || epsilon != 0.0)
+        if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
             exceptions.push_back(i);
     }
 
@@ -1594,6 +1602,16 @@ void OpenCLCalcNonbondedForceKernel::initialize(const System& system, const Nonb
         if (epsilon != 0.0)
             hasLJ = true;
     }
+    for (int i = 0; i < force.getNumParticleParameterOffsets(); i++) {
+        string param;
+        int particle;
+        double charge, sigma, epsilon;
+        force.getParticleParameterOffset(i, param, particle, charge, sigma, epsilon);
+        if (charge != 0.0)
+            hasCoulomb = true;
+        if (epsilon != 0.0)
+            hasLJ = true;
+    }
     for (auto exclusion : exclusions) {
         exclusionList[exclusion.first].push_back(exclusion.second);
         exclusionList[exclusion.second].push_back(exclusion.first);

platforms/reference/src/ReferenceKernels.cpp

@@ -866,6 +866,14 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
 
     // Identify which exceptions are 1-4 interactions.
 
+    set<int> exceptionsWithOffsets;
+    for (int i = 0; i < force.getNumExceptionParameterOffsets(); i++) {
+        string param;
+        int exception;
+        double charge, sigma, epsilon;
+        force.getExceptionParameterOffset(i, param, exception, charge, sigma, epsilon);
+        exceptionsWithOffsets.insert(exception);
+    }
     numParticles = force.getNumParticles();
     exclusions.resize(numParticles);
     vector<int> nb14s;
@@ -875,7 +883,7 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
         force.getExceptionParameters(i, particle1, particle2, chargeProd, sigma, epsilon);
         exclusions[particle1].insert(particle2);
         exclusions[particle2].insert(particle1);
-        if (chargeProd != 0.0 || epsilon != 0.0)
+        if (chargeProd != 0.0 || epsilon != 0.0 || exceptionsWithOffsets.find(i) != exceptionsWithOffsets.end())
             nb14s.push_back(i);
     }