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Commit 04ea8ce9 authored by Peter Eastman's avatar Peter Eastman
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Fixed lots of errors and warnings compiling under Windows

parent a01da386
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Showing with 751 additions and 69 deletions
CMakeLists.txt
View file @ 04ea8ce9
......@@ -41,11 +41,11 @@ SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla platforms/reference)
# SET(LIB64) # nothing
#ENDIF (ARCH64)
IF( ${CMAKE_SIZEOF_VOID_P} EQUAL 8 )
IF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
SET( LIB64 64 )
ELSE( ${CMAKE_SIZEOF_VOID_P} EQUAL 8 )
ELSE( CMAKE_SIZEOF_VOID_P EQUAL 8 )
SET( LIB64 )
ENDIF( ${CMAKE_SIZEOF_VOID_P} EQUAL 8 )
ENDIF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
IF(UNIX AND NOT CMAKE_BUILD_TYPE)
......
olla/include/Stream.h
View file @ 04ea8ce9
......@@ -68,7 +68,7 @@ class OPENMM_EXPORT StreamImpl;
* may choose to implement it internally with single precision values.
*/
class Stream {
class OPENMM_EXPORT Stream {
public:
Stream();
Stream(const Stream& copy);
......
olla/include/StreamImpl.h
View file @ 04ea8ce9
......@@ -43,7 +43,7 @@ namespace OpenMM {
* A StreamImpl defines the internal implementation of a Stream object.
*/
class StreamImpl {
class OPENMM_EXPORT StreamImpl {
public:
/**
* Create a StreamImpl.
......
openmmapi/include/internal/OpenMMContextImpl.h
View file @ 04ea8ce9
......@@ -49,7 +49,7 @@ class System;
* This is the internal implementation of an OpenMMContext.
*/
class OpenMMContextImpl {
class OPENMM_EXPORT OpenMMContextImpl {
public:
/**
* Create an OpenMMContextImpl for an OpenMMContext;
......
platforms/cuda/include/CudaPlatform.h
View file @ 04ea8ce9
......@@ -41,7 +41,7 @@ namespace OpenMM {
* This Platform subclass uses CUDA implementations of the OpenMM kernels to run on NVidia GPUs.
*/
class CudaPlatform : public Platform {
class OPENMM_EXPORT CudaPlatform : public Platform {
public:
CudaPlatform();
std::string getName() const {
......
platforms/cuda/include/CudaStreamFactory.h
View file @ 04ea8ce9
......@@ -40,7 +40,7 @@ namespace OpenMM {
* This StreamFactory creates all streams for CudaPlatform.
*/
class CudaStreamFactory : public StreamFactory {
class OPENMM_EXPORT CudaStreamFactory : public StreamFactory {
public:
StreamImpl* createStreamImpl(std::string name, int size, Stream::DataType type, const Platform& platform, OpenMMContextImpl& context) const;
};
......
platforms/cuda/src/CudaKernels.cpp
View file @ 04ea8ce9
......@@ -70,8 +70,8 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
psBondID->_pSysStream[0][i].y = bondIndices[i][1];
psBondID->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psBondID->_pSysStream[0][i].x]++;
psBondID->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psBondID->_pSysStream[0][i].y]++;
psBondParameter->_pSysStream[0][i].x = bondParameters[i][0];
psBondParameter->_pSysStream[0][i].y = bondParameters[i][1];
psBondParameter->_pSysStream[0][i].x = (float) bondParameters[i][0];
psBondParameter->_pSysStream[0][i].y = (float) bondParameters[i][1];
}
psBondID->Upload();
psBondParameter->Upload();
......@@ -95,8 +95,8 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
psBondAngleID1->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psBondAngleID1->_pSysStream[0][i].x]++;
psBondAngleID2->_pSysStream[0][i].x = gpu->pOutputBufferCounter[psBondAngleID1->_pSysStream[0][i].y]++;
psBondAngleID2->_pSysStream[0][i].y = gpu->pOutputBufferCounter[psBondAngleID1->_pSysStream[0][i].z]++;
psBondAngleParameter->_pSysStream[0][i].x = angleParameters[i][0]*180.0/M_PI;
psBondAngleParameter->_pSysStream[0][i].y = angleParameters[i][1];
psBondAngleParameter->_pSysStream[0][i].x = (float) (angleParameters[i][0]*180.0/3.14159265);
psBondAngleParameter->_pSysStream[0][i].y = (float) angleParameters[i][1];
}
psBondAngleID1->Upload();
psBondAngleID2->Upload();
......@@ -123,9 +123,9 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
psDihedralID2->_pSysStream[0][i].y = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].y]++;
psDihedralID2->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].z]++;
psDihedralID2->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].w]++;
psDihedralParameter->_pSysStream[0][i].x = periodicTorsionParameters[i][0];
psDihedralParameter->_pSysStream[0][i].y = periodicTorsionParameters[i][1];
psDihedralParameter->_pSysStream[0][i].z = periodicTorsionParameters[i][2];
psDihedralParameter->_pSysStream[0][i].x = (float) periodicTorsionParameters[i][0];
psDihedralParameter->_pSysStream[0][i].y = (float) periodicTorsionParameters[i][1];
psDihedralParameter->_pSysStream[0][i].z = (float) periodicTorsionParameters[i][2];
psDihedralParameter->_pSysStream[0][i].w = 0.0f;
}
psDihedralID1->Upload();
......@@ -156,12 +156,12 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
psRbDihedralID2->_pSysStream[0][i].y = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].y]++;
psRbDihedralID2->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].z]++;
psRbDihedralID2->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].w]++;
psRbDihedralParameter1->_pSysStream[0][i].x = rbTorsionParameters[i][0];
psRbDihedralParameter1->_pSysStream[0][i].y = rbTorsionParameters[i][1];
psRbDihedralParameter1->_pSysStream[0][i].z = rbTorsionParameters[i][2];
psRbDihedralParameter1->_pSysStream[0][i].w = rbTorsionParameters[i][3];
psRbDihedralParameter2->_pSysStream[0][i].x = rbTorsionParameters[i][4];
psRbDihedralParameter2->_pSysStream[0][i].y = rbTorsionParameters[i][5];
psRbDihedralParameter1->_pSysStream[0][i].x = (float) rbTorsionParameters[i][0];
psRbDihedralParameter1->_pSysStream[0][i].y = (float) rbTorsionParameters[i][1];
psRbDihedralParameter1->_pSysStream[0][i].z = (float) rbTorsionParameters[i][2];
psRbDihedralParameter1->_pSysStream[0][i].w = (float) rbTorsionParameters[i][3];
psRbDihedralParameter2->_pSysStream[0][i].x = (float) rbTorsionParameters[i][4];
psRbDihedralParameter2->_pSysStream[0][i].y = (float) rbTorsionParameters[i][5];
}
psRbDihedralID1->Upload();
psRbDihedralID2->Upload();
......@@ -171,9 +171,9 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
// Initialize nonbonded interactions.
for (int i = 0; i < numAtoms; i++) {
gpu->psPosq4->_pSysStream[0][i].w = nonbondedParameters[i][0];
gpu->psSigEps2->_pSysStream[0][i].x = nonbondedParameters[i][1];
gpu->psSigEps2->_pSysStream[0][i].y = nonbondedParameters[i][2];
gpu->psPosq4->_pSysStream[0][i].w = (float) nonbondedParameters[i][0];
gpu->psSigEps2->_pSysStream[0][i].x = (float) nonbondedParameters[i][1];
gpu->psSigEps2->_pSysStream[0][i].y = (float) nonbondedParameters[i][2];
}
gpu->psPosq4->Upload();
gpu->psSigEps2->Upload();
......@@ -197,9 +197,9 @@ void CudaCalcStandardMMForceFieldKernel::initialize(const vector<vector<int> >&
psLJ14ID->_pSysStream[0][i].y = atom2;
psLJ14ID->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psLJ14ID->_pSysStream[0][i].x]++;
psLJ14ID->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psLJ14ID->_pSysStream[0][i].y]++;
psLJ14Parameter->_pSysStream[0][i].x = atom1params[0]+atom2params[0];
psLJ14Parameter->_pSysStream[0][i].y = lj14Scale*(atom1params[1]*atom2params[1]);
psLJ14Parameter->_pSysStream[0][i].z = coulomb14Scale*(atom1params[2]*atom2params[2]);
psLJ14Parameter->_pSysStream[0][i].x = (float) (atom1params[0]+atom2params[0]);
psLJ14Parameter->_pSysStream[0][i].y = (float) (lj14Scale*(atom1params[1]*atom2params[1]));
psLJ14Parameter->_pSysStream[0][i].z = (float) (coulomb14Scale*(atom1params[2]*atom2params[2]));
}
psLJ14ID->Upload();
psLJ14Parameter->Upload();
......@@ -217,6 +217,7 @@ void CudaCalcStandardMMForceFieldKernel::executeForces(const Stream& positions,
}
double CudaCalcStandardMMForceFieldKernel::executeEnergy(const Stream& positions) {
return 0.0;
}
//CudaCalcGBSAOBCForceFieldKernel::~CudaCalcGBSAOBCForceFieldKernel() {
......
platforms/cuda/src/CudaStreamImpl.h
View file @ 04ea8ce9
......@@ -141,15 +141,15 @@ void CudaStreamImpl<T>::loadFromArray(const void* array) {
double* arrayData = (double*) array;
for (int i = 0; i < getSize(); ++i)
for (int j = 0; j < width; ++j)
data[i*rowOffset+j] = arrayData[i*width+j];
data[i*rowOffset+j] = (float) arrayData[i*width+j];
}
else {
int* arrayData = (int*) array;
for (int i = 0; i < getSize(); ++i)
for (int j = 0; j < width; ++j)
data[i*rowOffset+j] = arrayData[i*width+j];
data[i*rowOffset+j] = (float) arrayData[i*width+j];
}
for (int i = getSize(); i < stream->_length; ++i)
for (int i = getSize(); i < (int) stream->_length; ++i)
for (int j = 0; j < rowOffset; ++j)
data[i*rowOffset+j] = paddingValues[j];
stream->Upload();
......@@ -174,7 +174,7 @@ void CudaStreamImpl<T>::saveToArray(void* array) {
int* arrayData = (int*) array;
for (int i = 0; i < getSize(); ++i)
for (int j = 0; j < width; ++j)
arrayData[i*width+j] = data[i*rowOffset+j];
arrayData[i*width+j] = (int) data[i*rowOffset+j];
}
stream->Download();
}
......@@ -192,15 +192,15 @@ void CudaStreamImpl<T>::fillWithValue(void* value) {
double valueData = *((double*) value);
for (int i = 0; i < getSize(); ++i)
for (int j = 0; j < width; ++j)
data[i*rowOffset+j] = valueData;
data[i*rowOffset+j] = (float) valueData;
}
else {
int valueData = *((int*) value);
for (int i = 0; i < getSize(); ++i)
for (int j = 0; j < width; ++j)
data[i*rowOffset+j] = valueData;
data[i*rowOffset+j] = (float) valueData;
}
for (int i = getSize(); i < stream->_length; ++i)
for (int i = getSize(); i < (int) stream->_length; ++i)
for (int j = 0; j < rowOffset; ++j)
data[i*rowOffset+j] = paddingValues[j];
stream->Upload();
......
platforms/cuda/tests/TestCudaStreams.cpp
View file @ 04ea8ce9
......@@ -71,16 +71,16 @@ void testStream(Stream::DataType type, T scale) {
array[i] = 0;
stream.saveToArray(array);
for (int i = 0; i < length; ++i)
ASSERT_EQUAL_TOL((i*scale), array[i], TOL);
ASSERT_EQUAL_TOL(0, array[length], TOL);
ASSERT_EQUAL_TOL((double) (i*scale), array[i], TOL);
ASSERT_EQUAL_TOL(0.0, (double) array[length], TOL);
}
int main() {
try {
testStream<float, 1>(Stream::Float, 0.1);
testStream<float, 2>(Stream::Float2, 0.1);
testStream<float, 3>(Stream::Float3, 0.1);
testStream<float, 4>(Stream::Float4, 0.1);
testStream<float, 1>(Stream::Float, 0.1f);
testStream<float, 2>(Stream::Float2, 0.1f);
testStream<float, 3>(Stream::Float3, 0.1f);
testStream<float, 4>(Stream::Float4, 0.1f);
testStream<double, 1>(Stream::Double, 0.1);
testStream<double, 2>(Stream::Double2, 0.1);
testStream<double, 3>(Stream::Double3, 0.1);
......
platforms/reference/src/ReferenceKernels.cpp
View file @ 04ea8ce9
......@@ -164,10 +164,10 @@ void ReferenceCalcStandardMMForceFieldKernel::initialize(const vector<vector<int
bonded14ParamArray[i][2] = static_cast<RealOpenMM>( coulomb14Scale*(atomParamArray[atom1][2]*atomParamArray[atom2][2]) );
}
this->nonbondedMethod = nonbondedMethod;
this->nonbondedCutoff = nonbondedCutoff;
this->periodicBoxSize[0] = periodicBoxSize[0];
this->periodicBoxSize[1] = periodicBoxSize[1];
this->periodicBoxSize[2] = periodicBoxSize[2];
this->nonbondedCutoff = (RealOpenMM) nonbondedCutoff;
this->periodicBoxSize[0] = (RealOpenMM) periodicBoxSize[0];
this->periodicBoxSize[1] = (RealOpenMM) periodicBoxSize[1];
this->periodicBoxSize[2] = (RealOpenMM) periodicBoxSize[2];
if (nonbondedMethod == NoCutoff)
neighborList = NULL;
else
......@@ -191,14 +191,14 @@ void ReferenceCalcStandardMMForceFieldKernel::executeForces(const Stream& positi
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numAtoms, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, 78.3);
clj.setUseCutoff(nonbondedCutoff, *neighborList, 78.3f);
}
if (periodic)
clj.setPeriodic(periodicBoxSize);
clj.calculatePairIxn(numAtoms, posData, atomParamArray, exclusionArray, 0, forceData, 0, 0);
ReferenceLJCoulomb14 nonbonded14;
if (nonbondedMethod != NoCutoff)
nonbonded14.setUseCutoff(nonbondedCutoff, 78.3);
nonbonded14.setUseCutoff(nonbondedCutoff, 78.3f);
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, 0, 0, 0, nonbonded14);
}
......@@ -229,14 +229,14 @@ double ReferenceCalcStandardMMForceFieldKernel::executeEnergy(const Stream& posi
bool periodic = (nonbondedMethod == CutoffPeriodic);
if (nonbondedMethod != NoCutoff) {
computeNeighborListVoxelHash(*neighborList, numAtoms, posData, exclusions, periodic ? periodicBoxSize : NULL, nonbondedCutoff, 0.0);
clj.setUseCutoff(nonbondedCutoff, *neighborList, 78.3);
clj.setUseCutoff(nonbondedCutoff, *neighborList, 78.3f);
}
if (periodic)
clj.setPeriodic(periodicBoxSize);
clj.calculatePairIxn(numAtoms, posData, atomParamArray, exclusionArray, 0, forceData, 0, &energy);
ReferenceLJCoulomb14 nonbonded14;
if (nonbondedMethod != NoCutoff)
nonbonded14.setUseCutoff(nonbondedCutoff, 78.3);
nonbonded14.setUseCutoff(nonbondedCutoff, 78.3f);
for (int i = 0; i < arraySize; ++i)
energyArray[i] = 0;
refBondForce.calculateForce(num14, bonded14IndexArray, posData, bonded14ParamArray, forceData, energyArray, 0, &energy, nonbonded14);
......
platforms/reference/src/SimTKReference/ReferenceForce.cpp
View file @ 04ea8ce9
......@@ -70,7 +70,7 @@ ReferenceForce::~ReferenceForce( ){
RealOpenMM ReferenceForce::periodicDifference(RealOpenMM val1, RealOpenMM val2, RealOpenMM period) {
RealOpenMM diff = val1-val2;
RealOpenMM base = floor(diff/period+0.5)*period;
RealOpenMM base = (RealOpenMM) (floor(diff/period+0.5)*period);
return diff-base;
}
......
platforms/reference/src/SimTKReference/ReferenceLJCoulomb14.cpp
View file @ 04ea8ce9
......@@ -78,8 +78,8 @@ ReferenceLJCoulomb14::~ReferenceLJCoulomb14( ){
cutoff = true;
cutoffDistance = distance;
krf = pow(cutoffDistance, -3.0)*(solventDielectric-1.0)/(2.0*solventDielectric+1.0);
crf = (1.0/cutoffDistance)*(3.0*solventDielectric)/(2.0*solventDielectric+1.0);
krf = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0f)/(2.0f*solventDielectric+1.0f);
crf = (1.0f/cutoffDistance)*(3.0f*solventDielectric)/(2.0f*solventDielectric+1.0f);
return ReferenceForce::DefaultReturn;
}
......@@ -202,7 +202,7 @@ int ReferenceLJCoulomb14::calculateBondIxn( int* atomIndices, RealOpenMM** atomC
RealOpenMM dEdR = parameters[1]*( twelve*sig6 - six )*sig6;
if (cutoff)
dEdR += parameters[2]*(inverseR-2.0*krf*r2);
dEdR += parameters[2]*(inverseR-2.0f*krf*r2);
else
dEdR += parameters[2]*inverseR;
dEdR *= inverseR*inverseR;
......
platforms/reference/src/SimTKReference/ReferenceLJCoulombIxn.cpp
View file @ 04ea8ce9
......@@ -80,8 +80,8 @@ ReferenceLJCoulombIxn::~ReferenceLJCoulombIxn( ){
cutoff = true;
cutoffDistance = distance;
neighborList = &neighbors;
krf = pow(cutoffDistance, -3.0)*(solventDielectric-1.0)/(2.0*solventDielectric+1.0);
crf = (1.0/cutoffDistance)*(3.0*solventDielectric)/(2.0*solventDielectric+1.0);
krf = pow(cutoffDistance, -3.0f)*(solventDielectric-1.0f)/(2.0f*solventDielectric+1.0f);
crf = (1.0f/cutoffDistance)*(3.0f*solventDielectric)/(2.0f*solventDielectric+1.0f);
return ReferenceForce::DefaultReturn;
}
......@@ -190,7 +190,7 @@ int ReferenceLJCoulombIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM** ato
RealOpenMM* energyByAtom, RealOpenMM* totalEnergy ) const {
if (cutoff) {
for (int i = 0; i < neighborList->size(); i++) {
for (int i = 0; i < (int) neighborList->size(); i++) {
OpenMM::AtomPair pair = (*neighborList)[i];
calculateOneIxn(pair.first, pair.second, atomCoordinates, atomParameters, forces, energyByAtom, totalEnergy);
}
......@@ -290,7 +290,7 @@ int ReferenceLJCoulombIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM** ato
RealOpenMM eps = atomParameters[ii][EpsIndex]*atomParameters[jj][EpsIndex];
RealOpenMM dEdR = eps*( twelve*sig6 - six )*sig6;
if (cutoff)
dEdR += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0*krf*r2);
dEdR += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*(inverseR-2.0f*krf*r2);
else
dEdR += atomParameters[ii][QIndex]*atomParameters[jj][QIndex]*inverseR;
dEdR *= inverseR*inverseR;
......@@ -373,5 +373,6 @@ int ReferenceLJCoulombIxn::calculatePairIxn( int numberOfAtoms, RealOpenMM** ato
SimTKOpenMMLog::printMessage( message );
}
return ReferenceForce::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceNeighborList.H 0 → 100755
View file @ 04ea8ce9
#ifndef OPENMM_REFERENCE_NEIGHBORLIST_H_
#define OPENMM_REFERENCE_NEIGHBORLIST_H_
#include "../SimTKUtilities/SimTKOpenMMRealType.h"
#include "internal/windowsExport.h"
#include <set>
#include <vector>
namespace OpenMM {
typedef RealOpenMM** AtomLocationList;
typedef unsigned int AtomIndex;
typedef std::pair<AtomIndex, AtomIndex> AtomPair;
typedef std::vector<AtomPair> NeighborList;
// Ridiculous O(n^2) version of neighbor list
// for pedagogical purposes and simplicity
// parameter neighborList is automatically clear()ed before
// neighbors are added
void OPENMM_EXPORT computeNeighborListNaive(
NeighborList& neighborList,
int nAtoms,
const AtomLocationList& atomLocations,
const std::vector<std::set<int> >& exclusions,
const RealOpenMM* periodicBoxSize,
double maxDistance,
double minDistance = 0.0,
bool reportSymmetricPairs = false
);
// O(n) neighbor list method using voxel hash data structure
// parameter neighborList is automatically clear()ed before
// neighbors are added
void OPENMM_EXPORT computeNeighborListVoxelHash(
NeighborList& neighborList,
int nAtoms,
const AtomLocationList& atomLocations,
const std::vector<std::set<int> >& exclusions,
const RealOpenMM* periodicBoxSize,
double maxDistance,
double minDistance = 0.0,
bool reportSymmetricPairs = false
);
} // namespace OpenMM
#endif // OPENMM_REFERENCE_NEIGHBORLIST_H_
platforms/reference/src/SimTKReference/ReferenceNeighborList.cpp
View file @ 04ea8ce9
......@@ -3,6 +3,7 @@
#include <map>
#include <cmath>
#include <iostream>
#include <cassert>
using namespace std;
......@@ -34,7 +35,7 @@ static double compPairDistanceSquared(const RealOpenMM* pos1, const RealOpenMM*
// Ridiculous O(n^2) version of neighbor list
// for pedagogical purposes and simplicity
void computeNeighborListNaive(
void OPENMM_EXPORT computeNeighborListNaive(
NeighborList& neighborList,
int nAtoms,
const AtomLocationList& atomLocations,
......@@ -50,9 +51,9 @@ void computeNeighborListNaive(
double maxDistanceSquared = maxDistance * maxDistance;
double minDistanceSquared = minDistance * minDistance;
for (AtomIndex atomI = 0; atomI < (nAtoms - 1); ++atomI)
for (AtomIndex atomI = 0; atomI < (AtomIndex) (nAtoms - 1); ++atomI)
{
for (AtomIndex atomJ = atomI + 1; atomJ < nAtoms; ++atomJ)
for (AtomIndex atomJ = atomI + 1; atomJ < (AtomIndex) nAtoms; ++atomJ)
{
double pairDistanceSquared = compPairDistanceSquared(atomLocations[atomI], atomLocations[atomJ], periodicBoxSize);
if ( (pairDistanceSquared <= maxDistanceSquared) && (pairDistanceSquared >= minDistanceSquared))
......@@ -97,9 +98,9 @@ public:
VoxelHash(double vsx, double vsy, double vsz, const RealOpenMM* periodicBoxSize) :
voxelSizeX(vsx), voxelSizeY(vsy), voxelSizeZ(vsz), periodicBoxSize(periodicBoxSize) {
if (periodicBoxSize != NULL) {
nx = floor(periodicBoxSize[0]/voxelSizeX+0.5);
ny = floor(periodicBoxSize[1]/voxelSizeY+0.5);
nz = floor(periodicBoxSize[2]/voxelSizeZ+0.5);
nx = (int) floor(periodicBoxSize[0]/voxelSizeX+0.5);
ny = (int) floor(periodicBoxSize[1]/voxelSizeY+0.5);
nz = (int) floor(periodicBoxSize[2]/voxelSizeZ+0.5);
}
}
......@@ -213,7 +214,7 @@ private:
// O(n) neighbor list method using voxel hash data structure
void computeNeighborListVoxelHash(
void OPENMM_EXPORT computeNeighborListVoxelHash(
NeighborList& neighborList,
int nAtoms,
const AtomLocationList& atomLocations,
......@@ -235,7 +236,7 @@ void computeNeighborListVoxelHash(
edgeSizeZ = periodicBoxSize[2]/floor(periodicBoxSize[2]/maxDistance);
}
VoxelHash voxelHash(edgeSizeX, edgeSizeY, edgeSizeZ, periodicBoxSize);
for (AtomIndex atomJ = 0; atomJ < nAtoms; ++atomJ) // use "j", because j > i for pairs
for (AtomIndex atomJ = 0; atomJ < (AtomIndex) nAtoms; ++atomJ) // use "j", because j > i for pairs
{
// 1) Find other atoms that are close to this one
const RealOpenMM* location = atomLocations[atomJ];
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.H 0 → 100644
View file @ 04ea8ce9
This diff is collapsed.
platforms/reference/tests/TestReferenceNeighborList.cpp
View file @ 04ea8ce9
......@@ -13,7 +13,7 @@ void testNeighborList()
atomList[0] = new RealOpenMM[3];
atomList[1] = new RealOpenMM[3];
atomList[2] = new RealOpenMM[3];
atomList[0][0] = 13.6;
atomList[0][0] = 13.6f;
atomList[0][1] = 0;
atomList[0][2] = 0;
atomList[1][0] = 0;
......@@ -54,7 +54,7 @@ double distance2(RealOpenMM* pos1, RealOpenMM* pos2, const RealOpenMM* periodicB
}
void verifyNeighborList(NeighborList& list, int numAtoms, RealOpenMM** positions, const RealOpenMM* periodicBoxSize, double cutoff) {
for (int i = 0; i < list.size(); i++) {
for (int i = 0; i < (int) list.size(); i++) {
int atom1 = list[i].first;
int atom2 = list[i].second;
ASSERT(distance2(positions[atom1], positions[atom2], periodicBoxSize) <= cutoff*cutoff);
......@@ -75,9 +75,9 @@ void testPeriodic() {
init_gen_rand(0);
for (int i = 0; i <numAtoms; i++) {
atomList[i] = new RealOpenMM[3];
atomList[i][0] = genrand_real2()*periodicBoxSize[0]*3;
atomList[i][1] = genrand_real2()*periodicBoxSize[1]*3;
atomList[i][2] = genrand_real2()*periodicBoxSize[2]*3;
atomList[i][0] = (RealOpenMM) (genrand_real2()*periodicBoxSize[0]*3);
atomList[i][1] = (RealOpenMM) (genrand_real2()*periodicBoxSize[1]*3);
atomList[i][2] = (RealOpenMM) (genrand_real2()*periodicBoxSize[2]*3);
}
vector<set<int> > exclusions(numAtoms);
NeighborList neighborList;
......
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