Commit 93497df6 authored by Lee-Ping Wang's avatar Lee-Ping Wang
Browse files

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

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

parent a0a0cac3
...@@ -38,7 +38,6 @@ ...@@ -38,7 +38,6 @@
#include <map> #include <map>
#include <sstream> #include <sstream>
#include <utility> #include <utility>
// #include <cstdio> // LPW Debug Printout
using namespace OpenMM; using namespace OpenMM;
using std::map; using std::map;
...@@ -131,8 +130,6 @@ void CustomNonbondedForce::setParticleParameters(int index, const vector<double> ...@@ -131,8 +130,6 @@ void CustomNonbondedForce::setParticleParameters(int index, const vector<double>
} }
int CustomNonbondedForce::addExclusion(int particle1, int particle2) { 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)); exclusions.push_back(ExclusionInfo(particle1, particle2));
return exclusions.size()-1; return exclusions.size()-1;
} }
......
...@@ -45,7 +45,6 @@ ...@@ -45,7 +45,6 @@
#include "lepton/ParsedExpression.h" #include "lepton/ParsedExpression.h"
#include "../src/SimTKUtilities/SimTKOpenMMRealType.h" #include "../src/SimTKUtilities/SimTKOpenMMRealType.h"
#include "../src/SimTKUtilities/SimTKOpenMMUtilities.h" #include "../src/SimTKUtilities/SimTKOpenMMUtilities.h"
#include <algorithm>
#include <cmath> #include <cmath>
#include <set> #include <set>
...@@ -1829,18 +1828,6 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const ...@@ -1829,18 +1828,6 @@ void CudaCalcCustomNonbondedForceKernel::initialize(const System& system, const
exclusionList[particle1].push_back(particle2); exclusionList[particle1].push_back(particle2);
exclusionList[particle2].push_back(particle1); 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); params->setParameterValues(paramVector);
// Record the tabulated functions. // Record the tabulated functions.
......
...@@ -32,7 +32,6 @@ ...@@ -32,7 +32,6 @@
#include <map> #include <map>
#include <set> #include <set>
#include <utility> #include <utility>
// #include <cstdio> // LPW Debug Printout
using namespace OpenMM; using namespace OpenMM;
using namespace std; using namespace std;
...@@ -106,37 +105,13 @@ void CudaNonbondedUtilities::addArgument(const ParameterInfo& parameter) { ...@@ -106,37 +105,13 @@ void CudaNonbondedUtilities::addArgument(const ParameterInfo& parameter) {
void CudaNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) { void CudaNonbondedUtilities::requestExclusions(const vector<vector<int> >& exclusionList) {
if (anyExclusions) { if (anyExclusions) {
bool sameExclusions = (exclusionList.size() == atomExclusions.size()); 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++) { for (int i = 0; i < (int) exclusionList.size() && sameExclusions; i++) {
if (exclusionList[i].size() != atomExclusions[i].size()) { 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; 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++) for (int j = 0; j < (int) exclusionList[i].size(); j++)
if (exclusionList[i][j] != atomExclusions[i][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]);
sameExclusions = false; 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) if (!sameExclusions)
throw OpenMMException("All Forces must have identical exceptions"); throw OpenMMException("All Forces must have identical exceptions");
} }
......
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