Skip to content

GitLab

"vscode:/vscode.git/clone" did not exist on "31d761d56e10672fd1b9efd4e8c5110b554ad655"
Commit 36762962 authored by Mark Friedrichs's avatar Mark Friedrichs
Browse files

Edits to remove some VC9 warnings

parent d5a7dd89
Hide whitespace changes
Inline Side-by-side
Showing with 90 additions and 83 deletions
platforms/cuda/src/kernels/kCalculateGBVIBornSum.cu
View file @ 36762962
......@@ -259,7 +259,7 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
int printOnlyOnNan = 1;
int foundNan = 0;
if( printOnlyOnNan ){
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms && foundNan == 0; ii++ ){
for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms && foundNan == 0; ii++ ){
foundNan += isNanOrInfinity( gpu->psBornRadii->_pSysData[ii] );
foundNan += isNanOrInfinity( gpu->psBornForce->_pSysData[ii] );
foundNan += isNanOrInfinity( gpu->psGBVISwitchDerivative->_pSysData[ii] );
......@@ -267,7 +267,7 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
if( foundNan ){
log = stderr;
(void) fprintf( log, "kPrintGBVI found nan \n", gpu->sim.paddedNumberOfAtoms );
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(void) fprintf( log, "%6d %15.7e %15.7e %15.7e\n", ii,
gpu->psPosq4->_pSysData[ii].x,
gpu->psPosq4->_pSysData[ii].y,
......@@ -281,7 +281,7 @@ void kPrintGBVI( gpuContext gpu, std::string callId, int call, FILE* log)
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
sizeof(Atom)*gpu->sim.nonbond_threads_per_block );
(void) fprintf( stderr, "bR bF swd r scR ...\n" );
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(void) fprintf( log, "%6d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e\n", ii,
gpu->psBornRadii->_pSysData[ii],
gpu->psBornForce->_pSysData[ii],
......
platforms/cuda/src/kernels/kCalculateObcGbsaBornSum.cu
View file @ 36762962
......@@ -149,7 +149,7 @@ void kPrintObc( gpuContext gpu, std::string callId, int call, FILE* log)
(void) fprintf( stderr, "bOutputWarp=%u blks=%u th/blk=%u wu=%u %u shrd=%u\n", gpu->bOutputBufferPerWarp,
gpu->sim.nonbond_blocks, gpu->sim.nonbond_threads_per_block, gpu->sim.workUnits, gpu->psWorkUnit->_pSysStream[0][0],
sizeof(Atom)*gpu->sim.nonbond_threads_per_block );
for( int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
for( unsigned int ii = 0; ii < gpu->sim.paddedNumberOfAtoms; ii++ ){
(void) fprintf( log, "%6d %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e %15.7e \n", ii,
gpu->psObcChain->_pSysData[ii],
gpu->psBornRadii->_pSysData[ii],
......
platforms/cuda/src/kernels/kForces.cu
View file @ 36762962
......@@ -291,7 +291,7 @@ double kReduceEnergy(gpuContext gpu)
//printf("kReduceEnergy\n");
gpu->psEnergy->Download();
double sum = 0.0;
for (int i = 0; i < gpu->sim.energyOutputBuffers; i++){
for (int i = 0; i < static_cast<int>(gpu->sim.energyOutputBuffers); i++){
sum += (*gpu->psEnergy)[i];
}
......
platforms/cuda/tests/TestCudaGBVIForce2.cpp
View file @ 36762962
......@@ -110,6 +110,7 @@ public:
int _particle2;
double _distance;
};
BondInfo_OpenMMTest::BondInfo_OpenMMTest( int particle1, int particle2, double distance ){
_particle1 = particle1;
_particle2 = particle2;
......@@ -279,13 +280,14 @@ public:
* @param boxDimensions box dimensions
* @param spacing spacing
* @param sfmt input random number generator
* @param bondDistance input bond distance
* @param array output vector of grid values
*
* @return -1 if particles will not fit on grid; 0 if they do
*/
int setParticlesOnGrid( const Vec3& origin, const Vec3& boxDimensions, const Vec3& spacing,
OpenMM_SFMT::SFMT& sfmt, std::vector<Vec3>& array ) const;
OpenMM_SFMT::SFMT& sfmt, double bondDistance, std::vector<Vec3>& array ) const;
/**
* Set bond distance
......@@ -525,9 +527,9 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
int errorFlag = 0;
positions.resize( _numParticles );
if( method == Random ){
for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){
positions[ii] = Vec3(_boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt));
for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++) {
for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++) {
positions[ii+jj] = positions[ii] + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
}
}
......@@ -540,7 +542,7 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
double particlesPerDimension = pow( static_cast<double>(_numMolecules), (1.0/3.0) );
int particlesPerDimensionI = static_cast<int>(particlesPerDimension+0.999999);
double boxSize = _boxSize;
double spacingPerDimension = boxSize/(particlesPerDimension+1.0);
double spacingPerDimension = (boxSize-_bondDistance)/(particlesPerDimension+1.0);
spacing = Vec3(spacingPerDimension, spacingPerDimension, spacingPerDimension );
boxDimensions = Vec3(boxSize, boxSize, boxSize );
......@@ -561,7 +563,7 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
(void) fprintf( _log, "SimpleGrid %s\n", msg.str().c_str() );
}
errorFlag = setParticlesOnGrid( origin, boxDimensions, spacing, sfmt, positions );
errorFlag = setParticlesOnGrid( origin, boxDimensions, spacing, sfmt, _bondDistance, positions );
}
return errorFlag;
......@@ -579,7 +581,7 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
*/
int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDimensions, const Vec3& spacing, OpenMM_SFMT::SFMT& sfmt,
std::vector<Vec3>& array ) const {
double bondDistance, std::vector<Vec3>& array ) const {
const double pi = 3.14159265358979323846;
const double pi2 = 2.0*pi;
......@@ -595,12 +597,12 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
// place molecule centers on grid
for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){
array[ii] = Vec3(start);
bool done = false;
for( unsigned int jj = 0; jj < 3 && !done; jj++ ){
start[jj] += spacing[jj];
if( start[jj] > boxDimensions[jj] ){
if( (start[jj]+4.0*bondDistance) > boxDimensions[jj] ){
start[jj] = origin[jj];
} else {
done = true;
......@@ -615,9 +617,9 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
// add molecule atoms
for( unsigned int ii = 0; ii < _numMolecules; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numMolecules); ii++ ){
int molecularIndex = ii*_numParticlesPerMolecule;
for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++ ){
for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++ ){
double theta = genrand_real2(sfmt)*pi2;
double phi = genrand_real2(sfmt)*pi;
array[molecularIndex+jj] = array[molecularIndex] + Vec3(_bondDistance*cos(theta)*cos(phi), _bondDistance*cos(theta)*sin(phi), _bondDistance*sin(theta) );
......@@ -688,12 +690,12 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
(box[1][0] - box[0][0]), (box[1][1] - box[0][1]), (box[1][2] - box[0][2]) );
for( unsigned int ii = 0; ii < positionIndexVector.size(); ii++ ){
if( positionIndexVector[ii] < positions.size() ){
if( positionIndexVector[ii] < static_cast<int>(positions.size()) ){
int positionIndex = positionIndexVector[ii];
IntDoublePairVector sortVector;
getSortedDistances( periodicBoundaryConditions, positionIndex, positions, sortVector );
(void) fprintf( _log, "Min/max distance from %6d:\n ", positionIndex );
for( unsigned int jj = 0; jj < sortVector.size() && jj < showIndex; jj++ ){
for( unsigned int jj = 0; jj < sortVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
IntDoublePair pair = sortVector[jj];
(void) fprintf( _log, "[%6d %15.7e] ", pair.first, pair.second);
}
......@@ -748,7 +750,7 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
std::sort( hitVector.begin(), hitVector.end(), TestIntDoublePair );
(void) fprintf( _log, "Min distances pbc=%d\n", periodicBoundaryConditions );
for( unsigned int jj = 0; jj < hitVector.size() && jj < showIndex; jj++ ){
for( unsigned int jj = 0; jj < hitVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
IntDoublePair pair = hitVector[jj];
int index = pair.first;
int iIndex = static_cast<int>(index/positions.size());
......@@ -798,7 +800,7 @@ void PositionGenerator::showParticlesWithinDistance( const std::vector<Vec3>& po
void PositionGenerator::showDistances( const IntIntPairVector& pairs, const std::vector<Vec3>& positions ) const {
for( IntIntPairVectorCI ii = pairs.begin(); ii != pairs.end(); ii++ ){
if( ii->first < positions.size() && ii->second < positions.size() ){
if( ii->first < static_cast<int>(positions.size()) && ii->second < static_cast<int>(positions.size()) ){
double d = getDistance( ii->first, ii->second, positions );
(void) fprintf( _log, "Distance %6d %6d %15.7e d2=%15.7e\n", ii->first, ii->second, d, d*d );
}
......@@ -976,7 +978,6 @@ static int setDoubleFromMapStringToDouble( MapStringToDouble& argumentMap, std::
return 0;
}
/**---------------------------------------------------------------------------------------
*
* Get relative difference between two forces
......@@ -2128,7 +2129,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
// add particle/mass
for( unsigned int ii = 0; ii < inputSystem.getNumParticles(); ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumParticles()); ii++ ){
systemCopy.addParticle( inputSystem.getParticleMass( static_cast<int>(ii) ) );
}
......@@ -2142,8 +2143,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
// copy constraints
for( unsigned int ii = 0; ii < inputSystem.getNumConstraints(); ii++ ){
int index;
for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumConstraints()); ii++ ){
int particle1, particle2;
double distance;
inputSystem.getConstraintParameters( ii, particle1, particle2, distance);
......@@ -2152,7 +2152,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
// copy forces
for( unsigned int ii = 0; ii < inputSystem.getNumForces(); ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumForces()); ii++ ){
systemCopy.addForce( copyForce( inputSystem.getForce(ii), log) );
}
......
platforms/opencl/tests/TestOpenCLGBSAOBCForce2.cpp
View file @ 36762962
......@@ -527,9 +527,9 @@ int PositionGenerator::setPositions( GenerationMethod method, OpenMM_SFMT::SFMT&
int errorFlag = 0;
positions.resize( _numParticles );
if( method == Random ){
for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){
positions[ii] = Vec3(_boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt), _boxSize*genrand_real2(sfmt));
for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++) {
for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++) {
positions[ii+jj] = positions[ii] + Vec3(_bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt), _bondDistance*genrand_real2(sfmt));
}
}
......@@ -597,13 +597,12 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
// place molecule centers on grid
for( unsigned int ii = 0; ii < _numParticles; ii += _numParticlesPerMolecule ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numParticles); ii += _numParticlesPerMolecule ){
array[ii] = Vec3(start);
bool done = false;
for( unsigned int jj = 0; jj < 3 && !done; jj++ ){
start[jj] += spacing[jj];
if( (start[jj]+4.0*bondDistance) > boxDimensions[jj] ){
//fprintf( stderr, "setParticlesOnGrid %6u %2u %15.7e %15.7e %15.7e\n", ii, jj, start[0], start[1], start[2] );
start[jj] = origin[jj];
} else {
done = true;
......@@ -618,9 +617,9 @@ int PositionGenerator::setParticlesOnGrid( const Vec3& origin, const Vec3& boxDi
// add molecule atoms
for( unsigned int ii = 0; ii < _numMolecules; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(_numMolecules); ii++ ){
int molecularIndex = ii*_numParticlesPerMolecule;
for( unsigned int jj = 1; jj < _numParticlesPerMolecule; jj++ ){
for( unsigned int jj = 1; jj < static_cast<unsigned int>(_numParticlesPerMolecule); jj++ ){
double theta = genrand_real2(sfmt)*pi2;
double phi = genrand_real2(sfmt)*pi;
array[molecularIndex+jj] = array[molecularIndex] + Vec3(_bondDistance*cos(theta)*cos(phi), _bondDistance*cos(theta)*sin(phi), _bondDistance*sin(theta) );
......@@ -691,12 +690,12 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
(box[1][0] - box[0][0]), (box[1][1] - box[0][1]), (box[1][2] - box[0][2]) );
for( unsigned int ii = 0; ii < positionIndexVector.size(); ii++ ){
if( positionIndexVector[ii] < positions.size() ){
if( positionIndexVector[ii] < static_cast<int>(positions.size()) ){
int positionIndex = positionIndexVector[ii];
IntDoublePairVector sortVector;
getSortedDistances( periodicBoundaryConditions, positionIndex, positions, sortVector );
(void) fprintf( _log, "Min/max distance from %6d:\n ", positionIndex );
for( unsigned int jj = 0; jj < sortVector.size() && jj < showIndex; jj++ ){
for( unsigned int jj = 0; jj < sortVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
IntDoublePair pair = sortVector[jj];
(void) fprintf( _log, "[%6d %15.7e] ", pair.first, pair.second);
}
......@@ -751,7 +750,7 @@ void PositionGenerator::showMinMaxDistances( const std::vector<Vec3>& positions,
std::sort( hitVector.begin(), hitVector.end(), TestIntDoublePair );
(void) fprintf( _log, "Min distances pbc=%d\n", periodicBoundaryConditions );
for( unsigned int jj = 0; jj < hitVector.size() && jj < showIndex; jj++ ){
for( unsigned int jj = 0; jj < hitVector.size() && jj < static_cast<unsigned int>(showIndex); jj++ ){
IntDoublePair pair = hitVector[jj];
int index = pair.first;
int iIndex = static_cast<int>(index/positions.size());
......@@ -801,7 +800,7 @@ void PositionGenerator::showParticlesWithinDistance( const std::vector<Vec3>& po
void PositionGenerator::showDistances( const IntIntPairVector& pairs, const std::vector<Vec3>& positions ) const {
for( IntIntPairVectorCI ii = pairs.begin(); ii != pairs.end(); ii++ ){
if( ii->first < positions.size() && ii->second < positions.size() ){
if( ii->first < static_cast<int>(positions.size()) && ii->second < static_cast<int>(positions.size()) ){
double d = getDistance( ii->first, ii->second, positions );
(void) fprintf( _log, "Distance %6d %6d %15.7e d2=%15.7e\n", ii->first, ii->second, d, d*d );
}
......@@ -1982,7 +1981,7 @@ static Force* copyForce( const Force& force, FILE* log ){
#ifdef INCLUDE_AMOEBA_FORCES
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaHarmonicBondForce& castForce = dynamic_cast<const AmoebaHarmonicBondForce&>(force);
......@@ -1991,7 +1990,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaHarmonicAngleForce& castForce = dynamic_cast<const AmoebaHarmonicAngleForce&>(force);
......@@ -2000,7 +1999,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaHarmonicInPlaneAngleForce& castForce = dynamic_cast<const AmoebaHarmonicInPlaneAngleForce&>(force);
......@@ -2009,7 +2008,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaMultipoleForce& castForce = dynamic_cast<const AmoebaMultipoleForce&>(force);
......@@ -2018,7 +2017,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaOutOfPlaneBendForce& castForce = dynamic_cast<const AmoebaOutOfPlaneBendForce&>(force);
......@@ -2027,7 +2026,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaPiTorsionForce& castForce = dynamic_cast<const AmoebaPiTorsionForce&>(force);
......@@ -2036,7 +2035,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaStretchBendForce& castForce = dynamic_cast<const AmoebaStretchBendForce&>(force);
......@@ -2045,7 +2044,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaTorsionForce& castForce = dynamic_cast<const AmoebaTorsionForce&>(force);
......@@ -2054,7 +2053,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaTorsionTorsionForce& castForce = dynamic_cast<const AmoebaTorsionTorsionForce&>(force);
......@@ -2063,7 +2062,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaUreyBradleyForce& castForce = dynamic_cast<const AmoebaUreyBradleyForce&>(force);
......@@ -2072,7 +2071,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaVdwForce& castForce = dynamic_cast<const AmoebaVdwForce&>(force);
......@@ -2081,7 +2080,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaWcaDispersionForce& castForce = dynamic_cast<const AmoebaWcaDispersionForce&>(force);
......@@ -2090,7 +2089,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaGeneralizedKirkwoodForce& castForce = dynamic_cast<const AmoebaGeneralizedKirkwoodForce&>(force);
......@@ -2099,7 +2098,7 @@ static Force* copyForce( const Force& force, FILE* log ){
}
}
if( forceCopy != NULL ){
if( forceCopy == NULL ){
try {
const AmoebaTorsionTorsionForce& castForce = dynamic_cast<const AmoebaTorsionTorsionForce&>(force);
......@@ -2130,7 +2129,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
// add particle/mass
for( unsigned int ii = 0; ii < inputSystem.getNumParticles(); ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumParticles()); ii++ ){
systemCopy.addParticle( inputSystem.getParticleMass( static_cast<int>(ii) ) );
}
......@@ -2144,8 +2143,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
// copy constraints
for( unsigned int ii = 0; ii < inputSystem.getNumConstraints(); ii++ ){
int index;
for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumConstraints()); ii++ ){
int particle1, particle2;
double distance;
inputSystem.getConstraintParameters( ii, particle1, particle2, distance);
......@@ -2154,7 +2152,7 @@ static void copySystem( const System& inputSystem, System& systemCopy, FILE* log
// copy forces
for( unsigned int ii = 0; ii < inputSystem.getNumForces(); ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(inputSystem.getNumForces()); ii++ ){
systemCopy.addForce( copyForce( inputSystem.getForce(ii), log) );
}
......@@ -3361,8 +3359,8 @@ int main() {
#endif
DoubleVector numberOfMolecules;
// numberOfMolecules.push_back( 10 );
// numberOfMolecules.push_back( 100 );
numberOfMolecules.push_back( 10 );
numberOfMolecules.push_back( 100 );
numberOfMolecules.push_back( 1000 );
numberOfMolecules.push_back( 2000 );
numberOfMolecules.push_back( 4000 );
......
plugins/amoeba/platforms/cuda/src/kernels/amoebaCudaGpu.cpp
View file @ 36762962
......@@ -1161,6 +1161,11 @@ static void testAmoebaTorsionTorsionGridLookup( amoebaGpuContext amoebaGpu, floa
values[i++] = grids[index++];
}
#if defined(_MSC_VER)
#pragma warning(push)
#pragma warning(disable: 4297)
#endif
extern "C"
void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext amoebaGpu, const std::vector< std::vector< std::vector< std::vector<float> > > >& floatGrids )
{
......@@ -1176,7 +1181,6 @@ void gpuSetAmoebaTorsionTorsionGrids(amoebaGpuContext amoebaGpu, const std::vect
throw OpenMM::OpenMMException( message.str() );
}
// 4 (grids) * (25 *25 grid)*(2 +4 a1, a2, f, f1,f2, f12) = 15000
// assumming uniform spacing of grid angle values, set offset in to memory, beginning angle, angle spacing (delta),
// and number of y-angles
......@@ -1779,7 +1783,7 @@ void gpuSetAmoebaMultipoleParameters(amoebaGpuContext amoebaGpu, const std::vect
int maxTorqueBufferIndex = 0;
int chargeSize = static_cast<int>(charges.size());
for( int ii = 0; ii < chargeSize; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(chargeSize); ii++ ){
// axis type & multipole particles ids
......@@ -2106,7 +2110,7 @@ void gpuSetAmoebaObcParameters( amoebaGpuContext amoebaGpu, float innerDielectri
}
// Dummy out extra particles data
for (unsigned int i = particles; i < paddedNumberOfAtoms; i++)
for (unsigned int i = particles; i < static_cast<unsigned int>(paddedNumberOfAtoms); i++)
{
(*gpu->psBornRadii)[i] = 0.2f;
(*gpu->psObcData)[i].x = 0.01f;
......@@ -2171,7 +2175,7 @@ void gpuSetAmoebaGrycukParameters( amoebaGpuContext amoebaGpu, float innerDielec
// Dummy out extra particles data
for (unsigned int i = particles; i < paddedNumberOfAtoms; i++)
for (unsigned int i = particles; i < static_cast<unsigned int>(paddedNumberOfAtoms); i++)
{
(*gpu->psBornRadii)[i] = 0.2f;
(*gpu->psObcData)[i].x = 0.01f;
......@@ -2398,7 +2402,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
psAmoebaVdwReduction->Upload();
amoebaGpu->vdwExclusions.resize( gpu->natoms );
for( unsigned int ii = 0; ii < gpu->natoms; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(gpu->natoms); ii++ ){
for (unsigned int jj = 0; jj < allExclusions[ii].size(); jj++){
amoebaGpu->vdwExclusions[ii].push_back( allExclusions[ii][jj] );
}
......@@ -2411,7 +2415,7 @@ void gpuSetAmoebaVdwParameters( amoebaGpuContext amoebaGpu,
(void) fprintf( amoebaGpu->log, "%s particles=%d numberOfNonReductions=%d numberOfReductionsi=%d\n",
methodName, particles, numberOfNonReductions, numberOfReductions );
#ifdef PARAMETER_PRINT
for( unsigned int ii = 0; ii < gpu->natoms; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(gpu->natoms); ii++ ){
(void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e %15.7e Ex[", ii, sigmas[ii], epsilons[ii], reductionFactors[ii] );
for( unsigned int jj = 0; jj < allExclusions[ii].size(); jj++ ){
(void) fprintf( amoebaGpu->log, "%6d ", allExclusions[ii][jj] );
......@@ -2850,7 +2854,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
// Dummy out extra particles data
for (unsigned int ii = particles; ii < paddedNumberOfAtoms; ii++)
for (unsigned int ii = particles; ii < static_cast<unsigned int>(paddedNumberOfAtoms); ii++)
{
amoebaGpu->psWcaDispersionRadiusEpsilon->_pSysData[ii].x = 1.0f;
amoebaGpu->psWcaDispersionRadiusEpsilon->_pSysData[ii].y = 0.0f;
......@@ -2870,7 +2874,7 @@ void gpuSetAmoebaWcaDispersionParameters( amoebaGpuContext amoebaGpu,
(void) fprintf( amoebaGpu->log, "%s particles=%u total max dispersion energy=%14.5e eps[%14.5e %14.5e] rmin[%14.5e %14.5e] awtr=%14.5e shctd=%14.5e dispoff=%14.5e\n",
methodName, static_cast<unsigned int>(radii.size()), totalMaxWcaDispersionEnergy, epso, epsh, rmino, rminh, awater, shctd, dispoff );
#ifdef PARAMETER_PRINT
for( unsigned int ii = 0; ii < gpu->natoms; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(gpu->natoms); ii++ ){
(void) fprintf( amoebaGpu->log, "%5u %15.7e %15.7e\n", ii, radii[ii], epsilons[ii] );
if( ii == maxPrint && ii < (paddedNumberOfAtoms - maxPrint) ){
(void) fprintf( amoebaGpu->log, "\n" );
......@@ -3089,7 +3093,7 @@ void amoebaGpuBuildOutputBuffers( amoebaGpuContext amoebaGpu, int hasAmoebaGener
// use the Cuda force output buffers for mapping torques onto forces, if max torque buffer count < number of buffers
amoebaGpu->amoebaSim.maxTorqueBufferIndex++;
if( amoebaGpu->amoebaSim.maxTorqueBufferIndex > outputBuffers ){
if( static_cast<unsigned int>(amoebaGpu->amoebaSim.maxTorqueBufferIndex) > outputBuffers ){
amoebaGpu->psTorqueMapForce4 = new CUDAStream<float4>(paddedNumberOfAtoms, amoebaGpu->amoebaSim.maxTorqueBufferIndex, "torqueMapForce");
amoebaGpu->torqueMapForce4Delete = 1;
} else {
......@@ -4714,7 +4718,7 @@ void initializeCudaFloatArray( int numberOfParticles, int entriesPerParticle,
void zeroCUDAStreamFloat4( CUDAStream<float4>* streamToCopy )
{
for( unsigned int ii = 0; ii < streamToCopy->_stride; ii++ ){
for( int jj = 0; jj < streamToCopy->_subStreams; jj++ ){
for( unsigned int jj = 0; jj < streamToCopy->_subStreams; jj++ ){
streamToCopy->_pSysStream[jj][ii].x = 0.0f;
streamToCopy->_pSysStream[jj][ii].y = 0.0f;
streamToCopy->_pSysStream[jj][ii].z = 0.0f;
......@@ -4743,7 +4747,7 @@ void reduceAndCopyCUDAStreamFloat4( CUDAStream<float4>* streamToCopy, CUDAStream
outputStream->_pSysData[indexOffset] = streamToCopy->_pSysStream[0][ii].x;
outputStream->_pSysData[indexOffset+1] = streamToCopy->_pSysStream[0][ii].y;
outputStream->_pSysData[indexOffset+2] = streamToCopy->_pSysStream[0][ii].z;
for( int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
for( unsigned int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
if( streamToCopy->_pSysStream[jj][ii].x != streamToCopy->_pSysStream[jj][ii].x ||
streamToCopy->_pSysStream[jj][ii].y != streamToCopy->_pSysStream[jj][ii].y ||
streamToCopy->_pSysStream[jj][ii].z != streamToCopy->_pSysStream[jj][ii].z ){
......@@ -4779,7 +4783,7 @@ void reduceAndCopyCUDAStreamFloat( CUDAStream<float>* streamToCopy, CUDAStream<f
for( unsigned int ii = 0; ii < streamToCopy->_stride; ii++ ){
outputStream->_pSysData[ii] = streamToCopy->_pSysStream[0][ii];
if( ii == 0 )(void) fprintf( stderr, "reduceAndCopyCUDAStreamFloat:%u %15.7e %u %u\n", ii, streamToCopy->_pSysStream[0][ii], streamToCopy->_stride, streamToCopy->_subStreams );
for( int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
for( unsigned int jj = 1; jj < streamToCopy->_subStreams; jj++ ){
if( streamToCopy->_pSysStream[jj][ii] != streamToCopy->_pSysStream[jj][ii] ){
(void) fprintf( stderr, "Nan at particle=%d stream=%d\n", ii, jj );
}
......@@ -4828,3 +4832,8 @@ double getTimeOfDay( void ){
#endif
}
#if defined(_MSC_VER)
#pragma warning(pop)
#endif
// 4 (grids) * (25 *25 grid)*(2 +4 a1, a2, f, f1,f2, f12) = 15000
plugins/amoeba/platforms/reference/tests/TestReferenceAmoebaOutOfPlaneBendForce.cpp
View file @ 36762962
......@@ -439,7 +439,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
Context context(system, integrator, Platform::getPlatformByName( "Reference"));
std::vector<Vec3> positions(numberOfParticles);
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(numberOfParticles); ii++ ){
if( coordinates.find( particleIndices[ii] ) == coordinates.end() ){
#ifdef AMOEBA_DEBUG
if( log ){
......@@ -480,7 +480,7 @@ void testOneOutOfPlaneBend2( FILE* log, int setId ) {
computeAmoebaOutOfPlaneBendForce( 0, positions, *amoebaOutOfPlaneBendForce, forces, &energy, log );
totalEnergy += energy;
for( unsigned int ii = 0; ii < numberOfParticles; ii++ ){
for( unsigned int ii = 0; ii < static_cast<unsigned int>(numberOfParticles); ii++ ){
for( unsigned int jj = 0; jj < 3; jj++ ){
totalForces[particleIndices[ii]][jj] += forces[ii][jj];
}
......
plugins/amoeba/serialization/src/AmoebaGeneralizedKirkwoodForceProxy.cpp
View file @ 36762962
......@@ -53,7 +53,7 @@ void AmoebaGeneralizedKirkwoodForceProxy::serialize(const void* object, Serializ
node.setIntProperty( "GeneralizedKirkwoodIncludeCavityTerm", force.getIncludeCavityTerm() );
SerializationNode& particles = node.createChildNode("GeneralizedKirkwoodParticles").setIntProperty( "size", force.getNumParticles() );
for (unsigned int ii = 0; ii < force.getNumParticles(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
double radius, charge, scalingFactor;
force.getParticleParameters( ii, charge, radius, scalingFactor );
particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("charge", charge).setDoubleProperty("radius", radius).setDoubleProperty("scaleFactor", scalingFactor);
......
plugins/amoeba/serialization/src/AmoebaHarmonicAngleForceProxy.cpp
View file @ 36762962
......@@ -52,7 +52,7 @@ void AmoebaHarmonicAngleForceProxy::serialize(const void* object, SerializationN
node.setDoubleProperty("HarmonicAngleSextic", force.getAmoebaGlobalHarmonicAngleSextic());
SerializationNode& bonds = node.createChildNode("Angles").setIntProperty( "size", force.getNumAngles() );
for (unsigned int ii = 0; ii < force.getNumAngles(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
int particle1, particle2, particle3;
double distance, k;
force.getAngleParameters(ii, particle1, particle2, particle3, distance, k);
......
plugins/amoeba/serialization/src/AmoebaHarmonicBondForceProxy.cpp
View file @ 36762962
......@@ -49,7 +49,7 @@ void AmoebaHarmonicBondForceProxy::serialize(const void* object, SerializationNo
node.setDoubleProperty("HarmonicBondQuartic", force.getAmoebaGlobalHarmonicBondQuartic());
SerializationNode& bonds = node.createChildNode("Bonds").setIntProperty( "size", force.getNumBonds() );
for (unsigned int ii = 0; ii < force.getNumBonds(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumBonds()); ii++) {
int particle1, particle2;
double distance, k;
force.getBondParameters(ii, particle1, particle2, distance, k);
......
plugins/amoeba/serialization/src/AmoebaHarmonicInPlaneAngleForceProxy.cpp
View file @ 36762962
......@@ -52,7 +52,7 @@ void AmoebaHarmonicInPlaneAngleForceProxy::serialize(const void* object, Seriali
node.setDoubleProperty("HarmonicInPlaneAngleSextic", force.getAmoebaGlobalHarmonicInPlaneAngleSextic());
SerializationNode& bonds = node.createChildNode("InPlaneAngles").setIntProperty( "size", force.getNumAngles() );
for ( unsigned int ii = 0; ii < force.getNumAngles(); ii++) {
for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumAngles()); ii++) {
int particle1, particle2, particle3, particle4;
double distance, k;
force.getAngleParameters(ii, particle1, particle2, particle3, particle4, distance, k);
......
plugins/amoeba/serialization/src/AmoebaMultipoleForceProxy.cpp
View file @ 36762962
......@@ -94,7 +94,7 @@ void AmoebaMultipoleForceProxy::serialize(const void* object, SerializationNode&
getCovalentTypes( covalentTypes );
SerializationNode& particles = node.createChildNode("MultipoleParticles").setIntProperty( "size", force.getNumMultipoles() );
for (unsigned int ii = 0; ii < force.getNumMultipoles(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumMultipoles()); ii++) {
int axisType, multipoleAtomZ, multipoleAtomX, multipoleAtomY;
double charge, thole, dampingFactor, polarity;
......
plugins/amoeba/serialization/src/AmoebaOutOfPlaneBendForceProxy.cpp
View file @ 36762962
......@@ -50,7 +50,7 @@ void AmoebaOutOfPlaneBendForceProxy::serialize(const void* object, Serialization
node.setDoubleProperty("OutOfPlaneBendSextic", force.getAmoebaGlobalOutOfPlaneBendSextic());
SerializationNode& bonds = node.createChildNode("OutOfPlaneBend").setIntProperty( "size", force.getNumOutOfPlaneBends() );
for (unsigned int ii = 0; ii < force.getNumOutOfPlaneBends(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumOutOfPlaneBends()); ii++) {
int particle1, particle2, particle3, particle4;
double k;
force.getOutOfPlaneBendParameters(ii, particle1, particle2, particle3, particle4, k);
......
plugins/amoeba/serialization/src/AmoebaPiTorsionForceProxy.cpp
View file @ 36762962
......@@ -45,7 +45,7 @@ void AmoebaPiTorsionForceProxy::serialize(const void* object, SerializationNode&
node.setIntProperty("version", 1);
const AmoebaPiTorsionForce& force = *reinterpret_cast<const AmoebaPiTorsionForce*>(object);
SerializationNode& bonds = node.createChildNode("PiTorsion").setIntProperty( "size", force.getNumPiTorsions() );
for ( unsigned int ii = 0; ii < force.getNumPiTorsions(); ii++) {
for ( unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumPiTorsions()); ii++) {
int particle1, particle2, particle3, particle4, particle5, particle6;
double k;
force.getPiTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, particle6, k);
......
plugins/amoeba/serialization/src/AmoebaStretchBendForceProxy.cpp
View file @ 36762962
......@@ -45,7 +45,7 @@ void AmoebaStretchBendForceProxy::serialize(const void* object, SerializationNod
node.setIntProperty("version", 1);
const AmoebaStretchBendForce& force = *reinterpret_cast<const AmoebaStretchBendForce*>(object);
SerializationNode& bonds = node.createChildNode("StretchBendAngles").setIntProperty( "size", force.getNumStretchBends() );
for (unsigned int ii = 0; ii < force.getNumStretchBends(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumStretchBends()); ii++) {
int particle1, particle2, particle3;
double distanceAB, distanceCB, angle, k;
force.getStretchBendParameters(ii, particle1, particle2, particle3, distanceAB, distanceCB, angle, k);
......
plugins/amoeba/serialization/src/AmoebaTorsionForceProxy.cpp
View file @ 36762962
......@@ -50,7 +50,7 @@ static void addTorsionValues( SerializationNode& torsion, const std::vector<doub
static void loadTorsionValues( SerializationNode& torsion, std::vector<double>& torsionValues ){
int size = torsion.getIntProperty("size");
torsionValues.resize(size);
for (unsigned int jj = 0; jj < size; jj++) {
for (unsigned int jj = 0; jj < static_cast<unsigned int>(size); jj++) {
torsionValues[jj] = ( torsion.getChildren()[jj].getDoubleProperty("v") );
}
}
......@@ -60,7 +60,7 @@ void AmoebaTorsionForceProxy::serialize(const void* object, SerializationNode& n
const AmoebaTorsionForce& force = *reinterpret_cast<const AmoebaTorsionForce*>(object);
SerializationNode& bonds = node.createChildNode("Torsion").setIntProperty("size", force.getNumTorsions() );
for (unsigned int ii = 0; ii < force.getNumTorsions(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsions()); ii++) {
int particle1, particle2, particle3, particle4;
std::vector<double> torsion1;
......
plugins/amoeba/serialization/src/AmoebaTorsionTorsionForceProxy.cpp
View file @ 36762962
......@@ -77,7 +77,7 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
SerializationNode& grids = node.createChildNode("TorsionTorsionGrids");
grids.setIntProperty("size", static_cast<int>(force.getNumTorsionTorsionGrids()));
for (unsigned int kk = 0; kk < force.getNumTorsionTorsionGrids(); kk++) {
for (unsigned int kk = 0; kk < static_cast<unsigned int>(force.getNumTorsionTorsionGrids()); kk++) {
const std::vector< std::vector< std::vector<double> > > grid = force.getTorsionTorsionGrid( kk );
......@@ -107,7 +107,7 @@ void AmoebaTorsionTorsionForceProxy::serialize(const void* object, Serialization
}
SerializationNode& bonds = node.createChildNode("TorsionTorsion");
for (unsigned int ii = 0; ii < force.getNumTorsionTorsions(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumTorsionTorsions()); ii++) {
int particle1, particle2, particle3, particle4, particle5;
int chiralCheckAtomIndex, gridIndex;
force.getTorsionTorsionParameters(ii, particle1, particle2, particle3, particle4, particle5, chiralCheckAtomIndex, gridIndex );
......
plugins/amoeba/serialization/src/AmoebaUreyBradleyForceProxy.cpp
View file @ 36762962
......@@ -49,7 +49,7 @@ void AmoebaUreyBradleyForceProxy::serialize(const void* object, SerializationNod
node.setDoubleProperty("UreyBradleyQuartic", force.getAmoebaGlobalUreyBradleyQuartic());
SerializationNode& bonds = node.createChildNode("UreyBradley").setIntProperty( "size", force.getNumInteractions() );
for (unsigned int ii = 0; ii < force.getNumInteractions(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumInteractions()); ii++) {
int particle1, particle2;
double distance, k;
force.getUreyBradleyParameters(ii, particle1, particle2, distance, k);
......
plugins/amoeba/serialization/src/AmoebaVdwForceProxy.cpp
View file @ 36762962
......@@ -53,7 +53,7 @@ void AmoebaVdwForceProxy::serialize(const void* object, SerializationNode& node)
node.setIntProperty( "VdwPBC", force.getPBC());
SerializationNode& particles = node.createChildNode("VdwParticles").setIntProperty("size", force.getNumParticles() );
for (unsigned int ii = 0; ii < force.getNumParticles(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
int ivIndex, classIndex;
double sigma, epsilon, reductionFactor;
......
plugins/amoeba/serialization/src/AmoebaWcaDispersionForceProxy.cpp
View file @ 36762962
......@@ -54,7 +54,7 @@ void AmoebaWcaDispersionForceProxy::serialize(const void* object, SerializationN
node.setDoubleProperty("Slevy", force.getSlevy());
SerializationNode& particles = node.createChildNode("WcaDispersionParticles").setIntProperty( "size", force.getNumParticles() );
for (unsigned int ii = 0; ii < force.getNumParticles(); ii++) {
for (unsigned int ii = 0; ii < static_cast<unsigned int>(force.getNumParticles()); ii++) {
double radius, epsilon;
force.getParticleParameters( ii, radius, epsilon );
particles.createChildNode("Particle").setIntProperty("index", ii).setDoubleProperty("radius", radius).setDoubleProperty("epsilon", epsilon);
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment