CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are...

CustomNonbondedForce.cpp, CudaNonbondedUtilities.cpp and CudaKernels.cpp are now fully reverted to 3478.

openmmapi/src/CustomNonbondedForce.cpp

@@ -38,7 +38,6 @@
 #include <map>
 #include <sstream>
 #include <utility>
-// #include <cstdio> // LPW Debug Printout
 
 using namespace OpenMM;
 using std::map;
@@ -131,8 +130,6 @@ void CustomNonbondedForce::setParticleParameters(int index, const vector<double>
 }
 
 int CustomNonbondedForce::addExclusion(int particle1, int particle2) {
-  // LPW Debug Printout
-  // printf("Pushing Exclusion particle1 = %i particle2 = %i\n",particle1,particle2);
     exclusions.push_back(ExclusionInfo(particle1, particle2));
     return exclusions.size()-1;
 }

platforms/cuda/src/CudaKernels.cpp

@@ -45,7 +45,6 @@
 #include "lepton/ParsedExpression.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
 #include "../src/SimTKUtilities/SimTKOpenMMUtilities.h"
-#include <algorithm>
 #include <cmath>
 #include <set>
 
@@ -1829,18 +1828,6 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
         exclusionList[particle1].push_back(particle2);
         exclusionList[particle2].push_back(particle1);
     }
-    // In JDC's 2012-10 program, the exclusionList can be out of order while the atomExclusions are in order,
-    // causing OpenMM to throw an exception.  Keeping debug printout for now.
-    /*
-    for (int i = 0; i < numParticles; i++) {
-      stable_sort(exclusionList[i].begin(), exclusionList[i].end());
-      printf("Exclusion list for particle %i is: ",i);
-      for (int j = 0; j < (int) exclusionList[i].size() ; j++) {
-	printf(" %i",exclusionList[i][j]);
-      }
-      printf("\n");
-    }
-    */
     params->setParameterValues(paramVector);
 
     // Record the tabulated functions.

platforms/cuda/src/CudaNonbondedUtilities.cpp

@@ -32,7 +32,6 @@
 #include <map>
 #include <set>
 #include <utility>
-// #include <cstdio> // LPW Debug Printout
 
 using namespace OpenMM;
 using namespace std;
@@ -106,37 +105,13 @@ void CudaNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
 void CudaNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) {
     if (anyExclusions) {
         bool sameExclusions = (exclusionList.size() == atomExclusions.size());
-	// LPW Debug Printout
-	// printf("LPW Debug Printout 1\n");
-	// printf("exclusionList.size() = %i, atomExclusions.size() = %i, sameExclusions = %i\n",(int)exclusionList.size(),(int)atomExclusions.size(),sameExclusions);
-	
-	// LPW Debug Printout
-	//for (int i = 0; i < (int) exclusionList.size(); i++) {
         for (int i = 0; i < (int) exclusionList.size() && sameExclusions; i++) {
-	  if (exclusionList[i].size() != atomExclusions[i].size()) {
-	    // LPW Debug Printout
-	    // printf("exclusionList[%i].size() != atomExclusions[%i].size() [%i != %i]\n",i,i,(int)exclusionList[i].size(),(int)atomExclusions[i].size());
+	     if (exclusionList[i].size() != atomExclusions[i].size())
 	         sameExclusions = false;
-	  }
-	  /*
-	  else {
-	    // LPW Debug Printout
-	    printf("exclusionList[%i].size() = atomExclusions[%i].size() [%i = %i]\n",i,i,(int)exclusionList[i].size(),(int)atomExclusions[i].size());
-	  }
-	  */
 	     for (int j = 0; j < (int) exclusionList[i].size(); j++)
-	      if (exclusionList[i][j] != atomExclusions[i][j]) {
-		// LPW Debug Printout
-		// printf("exclusionList[%i][%i] != atomExclusions[%i][%i] {%i != %i}\n",i,j,i,j,exclusionList[i][j],atomExclusions[i][j]);
+	         if (exclusionList[i][j] != atomExclusions[i][j])
 		     sameExclusions = false;
         }
-	    /*
-	      else {
-		// LPW Debug Printout
-		printf("exclusionList[%i][%i] = atomExclusions[%i][%i] {%i = %i}\n",i,j,i,j,exclusionList[i][j],atomExclusions[i][j]);
-	      }
-	    */
-        }
         if (!sameExclusions)
             throw OpenMMException("All Forces must have identical exceptions");
     }