LPW attempted bugfixes: (1) Changed unit multipliers in...

LPW attempted bugfixes: (1) Changed unit multipliers in AmoebaVdwForce::getParticleParameters (2) Sorted vectors in exclusionLists so it agrees with atomExclusions

openmmapi/src/CustomNonbondedForce.cpp

@@ -38,6 +38,7 @@
 #include <map>
 #include <sstream>
 #include <utility>
+// #include <cstdio> // LPW Debug Printout
 
 using namespace OpenMM;
 using std::map;
@@ -130,6 +131,8 @@ 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

@@ -45,6 +45,7 @@
 #include "lepton/ParsedExpression.h"
 #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
 #include "../src/SimTKUtilities/SimTKOpenMMUtilities.h"
+#include <algorithm>
 #include <cmath>
 #include <set>
 
@@ -1828,6 +1829,19 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
         exclusionList[particle1].push_back(particle2);
         exclusionList[particle2].push_back(particle1);
     }
+    // LPW Sort the exclusion list.  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.
+    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

@@ -32,6 +32,7 @@
 #include <map>
 #include <set>
 #include <utility>
+// #include <cstdio> // LPW Debug Printout
 
 using namespace OpenMM;
 using namespace std;
@@ -105,12 +106,36 @@ 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())
-                sameExclusions = false;
+	  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());
+	    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])
-                    sameExclusions = false;
+	      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]);
+		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");

wrappers/python/src/swig_doxygen/swigInputConfig.py

@@ -301,13 +301,16 @@ UNITS = {
 ("AmoebaTorsionTorsionForce",             "getTorsionTorsionParameters")                   :  ( None, ()),
 ("AmoebaTorsionTorsionForce",             "getTorsionTorsionGrid")                         :  ( None, ()),
 
-("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
+# LPW 2012-10 : Is this a duplicate entry?
+#("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
 ("AmoebaVdwForce",                        "getSigmaCombiningRule")                         :  ( None, ()),
 ("AmoebaVdwForce",                        "getEpsilonCombiningRule")                       :  ( None, ()),
 ("AmoebaVdwForce",                        "getParticleExclusions")                         :  ( None, ()),
 ("AmoebaVdwForce",                        "getCutoff")                                     :  ( 'unit.nanometer', ()),
 ("AmoebaVdwForce",                        "getNonbondedMethod")                            :  ( None, ()),
-("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
+# LPW 2012-10 Modified because it no longer returns ivIndex and classIndex.
+# ("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
+("AmoebaVdwForce",                        "getParticleParameters")                         :  ( None, (None, 'unit.nanometer', 'unit.kilojoule_per_mole', None)),
 
 ("AmoebaWcaDispersionForce",              "getParticleParameters")                         :  ( None, ('unit.nanometer', 'unit.kilojoule_per_mole')),
 ("AmoebaWcaDispersionForce",              "getAwater")                                     :  ( '1/(unit.nanometer*unit.nanometer*unit.nanometer)',()),