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Commit 4b129949 authored by peastman's avatar peastman
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Simplified reference platform code for processing nonbonded exclusions

parent 21fc406b
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Showing with 32 additions and 91 deletions
platforms/reference/include/ReferenceCustomHbondIxn.h
View file @ 4b129949
......@@ -29,6 +29,7 @@
#include "lepton/ExpressionProgram.h"
#include "lepton/ParsedExpression.h"
#include <map>
#include <set>
#include <vector>
// ---------------------------------------------------------------------------------------
......@@ -143,10 +144,8 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
@param atomCoordinates atom coordinates
@param donorParameters donor parameters values donorParameters[donorIndex][parameterIndex]
@param acceptorParameters acceptor parameters values acceptorParameters[acceptorIndex][parameterIndex]
@param exclusions exclusion indices exclusions[donorIndex][acceptorToExcludeIndex]
exclusions[donorIndex][0] = number of exclusions
exclusions[donorIndex][no.-1] = indices of acceptors to excluded from
interacting w/ donor donorIndex
@param exclusions exclusion indices
exclusions[donorIndex] contains the list of excluded acceptors for that donor
@param globalParameters the values of global parameters
@param forces force array (forces added)
@param totalEnergy total energy
......@@ -154,7 +153,7 @@ class ReferenceCustomHbondIxn : public ReferenceBondIxn {
--------------------------------------------------------------------------------------- */
void calculatePairIxn(std::vector<OpenMM::RealVec>& atomCoordinates, RealOpenMM** donorParameters, RealOpenMM** acceptorParameters,
int** exclusions, const std::map<std::string, double>& globalParameters,
std::vector<std::set<int> >& exclusions, const std::map<std::string, double>& globalParameters,
std::vector<OpenMM::RealVec>& forces, RealOpenMM* totalEnergy) const;
// ---------------------------------------------------------------------------------------
......
platforms/reference/include/ReferenceKernels.h
View file @ 4b129949
......@@ -572,7 +572,7 @@ public:
void copyParametersToContext(ContextImpl& context, const NonbondedForce& force);
private:
int numParticles, num14;
int **exclusionArray, **bonded14IndexArray;
int **bonded14IndexArray;
RealOpenMM **particleParamArray, **bonded14ParamArray;
RealOpenMM nonbondedCutoff, switchingDistance, rfDielectric, ewaldAlpha, dispersionCoefficient;
int kmax[3], gridSize[3];
......@@ -819,7 +819,6 @@ public:
private:
int numDonors, numAcceptors, numParticles;
bool isPeriodic;
int **exclusionArray;
RealOpenMM **donorParamArray, **acceptorParamArray;
RealOpenMM nonbondedCutoff;
ReferenceCustomHbondIxn* ixn;
......
platforms/reference/include/ReferenceLJCoulombIxn.h
View file @ 4b129949
......@@ -156,10 +156,8 @@ class ReferenceLJCoulombIxn {
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
......@@ -170,7 +168,7 @@ class ReferenceLJCoulombIxn {
--------------------------------------------------------------------------------------- */
void calculatePairIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const;
......@@ -182,10 +180,8 @@ private:
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters (charges, c6, c12, ...) atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
......@@ -196,7 +192,7 @@ private:
--------------------------------------------------------------------------------------- */
void calculateEwaldIxn(int numberOfAtoms, std::vector<OpenMM::RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM** atomParameters, std::vector<std::set<int> >& exclusions,
RealOpenMM* fixedParameters, std::vector<OpenMM::RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const;
};
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 4b129949
......@@ -805,7 +805,6 @@ void ReferenceCalcCustomTorsionForceKernel::copyParametersToContext(ContextImpl&
ReferenceCalcNonbondedForceKernel::~ReferenceCalcNonbondedForceKernel() {
disposeRealArray(particleParamArray, numParticles);
disposeIntArray(exclusionArray, numParticles);
disposeIntArray(bonded14IndexArray, num14);
disposeRealArray(bonded14ParamArray, num14);
if (neighborList != NULL)
......@@ -843,14 +842,6 @@ void ReferenceCalcNonbondedForceKernel::initialize(const System& system, const N
particleParamArray[i][2] = static_cast<RealOpenMM>(charge);
}
this->exclusions = exclusions;
exclusionArray = new int*[numParticles];
for (int i = 0; i < numParticles; ++i) {
exclusionArray[i] = new int[exclusions[i].size()+1];
exclusionArray[i][0] = exclusions[i].size();
int index = 0;
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
exclusionArray[i][++index] = *iter;
}
for (int i = 0; i < num14; ++i) {
int particle1, particle2;
double charge, radius, depth;
......@@ -914,7 +905,7 @@ double ReferenceCalcNonbondedForceKernel::execute(ContextImpl& context, bool inc
clj.setUsePME(ewaldAlpha, gridSize);
if (useSwitchingFunction)
clj.setUseSwitchingFunction(switchingDistance);
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusionArray, 0, forceData, 0, includeEnergy ? &energy : NULL, includeDirect, includeReciprocal);
clj.calculatePairIxn(numParticles, posData, particleParamArray, exclusions, 0, forceData, 0, includeEnergy ? &energy : NULL, includeDirect, includeReciprocal);
if (includeDirect) {
ReferenceBondForce refBondForce;
ReferenceLJCoulomb14 nonbonded14;
......@@ -1500,7 +1491,6 @@ void ReferenceCalcCustomExternalForceKernel::copyParametersToContext(ContextImpl
ReferenceCalcCustomHbondForceKernel::~ReferenceCalcCustomHbondForceKernel() {
disposeRealArray(donorParamArray, numDonors);
disposeRealArray(acceptorParamArray, numAcceptors);
disposeIntArray(exclusionArray, numDonors);
if (ixn != NULL)
delete ixn;
}
......@@ -1547,14 +1537,6 @@ void ReferenceCalcCustomHbondForceKernel::initialize(const System& system, const
for (int j = 0; j < numAcceptorParameters; j++)
acceptorParamArray[i][j] = static_cast<RealOpenMM>(parameters[j]);
}
exclusionArray = new int*[numDonors];
for (int i = 0; i < numDonors; ++i) {
exclusionArray[i] = new int[exclusions[i].size()+1];
exclusionArray[i][0] = exclusions[i].size();
int index = 0;
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter)
exclusionArray[i][++index] = *iter;
}
NonbondedMethod nonbondedMethod = CalcCustomHbondForceKernel::NonbondedMethod(force.getNonbondedMethod());
nonbondedCutoff = (RealOpenMM) force.getCutoffDistance();
......@@ -1603,7 +1585,7 @@ double ReferenceCalcCustomHbondForceKernel::execute(ContextImpl& context, bool i
map<string, double> globalParameters;
for (int i = 0; i < (int) globalParameterNames.size(); i++)
globalParameters[globalParameterNames[i]] = context.getParameter(globalParameterNames[i]);
ixn->calculatePairIxn(posData, donorParamArray, acceptorParamArray, exclusionArray, globalParameters, forceData, includeEnergy ? &energy : NULL);
ixn->calculatePairIxn(posData, donorParamArray, acceptorParamArray, exclusions, globalParameters, forceData, includeEnergy ? &energy : NULL);
return energy;
}
......
platforms/reference/src/SimTKReference/ReferenceCustomHbondIxn.cpp
View file @ 4b129949
......@@ -34,6 +34,7 @@
using std::map;
using std::pair;
using std::set;
using std::string;
using std::stringstream;
using std::vector;
......@@ -109,10 +110,8 @@ void ReferenceCustomHbondIxn::setPeriodic(RealVec& boxSize) {
@param atomCoordinates atom coordinates
@param donorParameters donor parameters values donorParameters[donorIndex][parameterIndex]
@param acceptorParameters acceptor parameters values acceptorParameters[acceptorIndex][parameterIndex]
@param exclusions exclusion indices exclusions[donorIndex][acceptorToExcludeIndex]
exclusions[donorIndex][0] = number of exclusions
exclusions[donorIndex][no.-1] = indices of acceptors to excluded from
interacting w/ donor donorIndex
@param exclusions exclusion indices
exclusions[donorIndex] contains the list of excluded acceptors for that donor
@param globalParameters the values of global parameters
@param forces force array (forces added)
@param totalEnergy total energy
......@@ -120,7 +119,7 @@ void ReferenceCustomHbondIxn::setPeriodic(RealVec& boxSize) {
--------------------------------------------------------------------------------------- */
void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates, RealOpenMM** donorParameters, RealOpenMM** acceptorParameters,
int** exclusions, const map<string, double>& globalParameters, vector<RealVec>& forces,
vector<set<int> >& exclusions, const map<string, double>& globalParameters, vector<RealVec>& forces,
RealOpenMM* totalEnergy) const {
map<string, double> variables = globalParameters;
......@@ -129,18 +128,8 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates,
int numDonors = donorAtoms.size();
int numAcceptors = acceptorAtoms.size();
int* exclusionIndices = new int[numAcceptors];
for( int ii = 0; ii < numAcceptors; ii++ ){
exclusionIndices[ii] = -1;
}
for( int donor = 0; donor < numDonors; donor++ ){
// set exclusions
for (int j = 1; j <= exclusions[donor][0]; j++)
exclusionIndices[exclusions[donor][j]] = donor;
// Initialize per-donor parameters.
for (int j = 0; j < (int) donorParamNames.size(); j++)
......@@ -149,16 +138,13 @@ void ReferenceCustomHbondIxn::calculatePairIxn(vector<RealVec>& atomCoordinates,
// loop over atom pairs
for( int acceptor = 0; acceptor < numAcceptors; acceptor++ ){
if( exclusionIndices[acceptor] != donor ){
if (exclusions[donor].find(acceptor) == exclusions[donor].end()) {
for (int j = 0; j < (int) acceptorParamNames.size(); j++)
variables[acceptorParamNames[j]] = acceptorParameters[acceptor][j];
calculateOneIxn(donor, acceptor, atomCoordinates, variables, forces, totalEnergy);
}
}
}
delete[] exclusionIndices;
}
/**---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ 4b129949
......@@ -37,6 +37,7 @@
// make sure that erf() and erfc() are defined.
#include "openmm/internal/MSVC_erfc.h"
using std::set;
using std::vector;
using OpenMM::RealVec;
......@@ -169,10 +170,8 @@ void ReferenceLJCoulombIxn::setUseSwitchingFunction( RealOpenMM distance ) {
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
......@@ -183,7 +182,7 @@ void ReferenceLJCoulombIxn::setUseSwitchingFunction( RealOpenMM distance ) {
--------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM** atomParameters, vector<set<int> >& exclusions,
RealOpenMM* fixedParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const {
typedef std::complex<RealOpenMM> d_complex;
......@@ -423,10 +422,10 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
RealOpenMM totalExclusionEnergy = 0.0f;
for (int i = 0; i < numberOfAtoms; i++)
for (int j = 1; j <= exclusions[i][0]; j++)
if (exclusions[i][j] > i) {
for (set<int>::const_iterator iter = exclusions[i].begin(); iter != exclusions[i].end(); ++iter) {
if (*iter > i) {
int ii = i;
int jj = exclusions[i][j];
int jj = *iter;
RealOpenMM deltaR[2][ReferenceForce::LastDeltaRIndex];
ReferenceForce::getDeltaR( atomCoordinates[jj], atomCoordinates[ii], deltaR[0] );
......@@ -454,6 +453,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
energyByAtom[jj] -= realSpaceEwaldEnergy;
}
}
}
if( totalEnergy )
*totalEnergy -= totalExclusionEnergy;
......@@ -467,10 +467,8 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param atomParameters atom parameters atomParameters[atomIndex][paramterIndex]
@param exclusions atom exclusion indices exclusions[atomIndex][atomToExcludeIndex]
exclusions[atomIndex][0] = number of exclusions
exclusions[atomIndex][1-no.] = atom indices of atoms to excluded from
interacting w/ atom atomIndex
@param exclusions atom exclusion indices
exclusions[atomIndex] contains the list of exclusions for that atom
@param fixedParameters non atom parameters (not currently used)
@param forces force array (forces added)
@param energyByAtom atom energy
......@@ -481,7 +479,7 @@ void ReferenceLJCoulombIxn::calculateEwaldIxn(int numberOfAtoms, vector<RealVec>
--------------------------------------------------------------------------------------- */
void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>& atomCoordinates,
RealOpenMM** atomParameters, int** exclusions,
RealOpenMM** atomParameters, vector<set<int> >& exclusions,
RealOpenMM* fixedParameters, vector<RealVec>& forces,
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy, bool includeDirect, bool includeReciprocal) const {
......@@ -499,33 +497,14 @@ void ReferenceLJCoulombIxn::calculatePairIxn(int numberOfAtoms, vector<RealVec>&
}
}
else {
// allocate and initialize exclusion array
int* exclusionIndices = new int[numberOfAtoms];
for( int ii = 0; ii < numberOfAtoms; ii++ ){
exclusionIndices[ii] = -1;
}
for( int ii = 0; ii < numberOfAtoms; ii++ ){
// set exclusions
for( int jj = 1; jj <= exclusions[ii][0]; jj++ ){
exclusionIndices[exclusions[ii][jj]] = ii;
}
// loop over atom pairs
for( int jj = ii+1; jj < numberOfAtoms; jj++ ){
if( exclusionIndices[jj] != ii ){
for( int jj = ii+1; jj < numberOfAtoms; jj++ )
if (exclusions[jj].find(ii) == exclusions[jj].end())
calculateOneIxn(ii, jj, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy);
}
}
}
delete[] exclusionIndices;
}
}
/**---------------------------------------------------------------------------------------
......
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