void Integrator::initialize( ContextImpl &contextRef ) {
context = &contextRef;
if( context->getSystem().getNumConstraints() > 0 ) {
throw OpenMMException( "LTMD Integrator does not support constraints" );
}
kernel = context->getPlatform().createKernel( StepKernel::Name(), contextRef );
( ( StepKernel & )( kernel.getImpl() ) ).initialize( contextRef.getSystem(), *this );
//(dynamic_cast<StepKernel &>( kernel.getImpl() )).initialize( contextRef.getSystem(), *this );
}
void throwException(const char* file, int line, const std::string& details) {
std::string fn(file);
std::string::size_type pos = fn.find_last_of("/\\");
if (pos+1>=fn.size())
pos=0;
std::string filename(fn,(int)(pos+1),(int)(fn.size()-(pos+1)));
std::stringstream message;
message << "Assertion failure at "<<filename<<":"<<line;
if (details.size() > 0)
message << ". "<<details;
throw OpenMMException(message.str());
}
void StepKernel::ProjectionVectors( const Integrator &integrator ) {
//check if projection vectors changed
bool modesChanged = integrator.getProjVecChanged();
//projection vectors changed or never allocated
if( modesChanged || modes == NULL ) {
int numModes = integrator.getNumProjectionVectors();
//valid vectors?
if( numModes == 0 ) {
throw OpenMMException( "Projection vector size is zero." );
}
//if( modes != NULL && modes->_length != numModes * mParticles ) {
if( modes != NULL && modes->getSize() != numModes * mParticles ) {
delete modes;
delete modeWeights;
modes = NULL;
modeWeights = NULL;
}
if( modes == NULL ) {
/*modes = new CUDAStream<float4>( numModes * mParticles, 1, "NormalModes" );
modeWeights = new CUDAStream<float>( numModes > data.gpu->sim.blocks ? numModes : data.gpu->sim.blocks, 1, "NormalModeWeights" );*/
//cu->getNumThreadBlocks()*cu->ThreadBlockSize
modes = new CudaArray( *( data.contexts[0] ), numModes * mParticles, sizeof( float4 ), "NormalModes" );
modeWeights = new CudaArray( *( data.contexts[0] ), ( numModes > data.contexts[0]->getNumThreadBlocks()*data.contexts[0]->ThreadBlockSize ? numModes : data.contexts[0]->getNumThreadBlocks()*data.contexts[0]->ThreadBlockSize ), sizeof( float ), "NormalModeWeights" );
oldpos = new CudaArray( *( data.contexts[0] ), data.contexts[0]->getPaddedNumAtoms(), sizeof( float4 ), "OldPositions" );
pPosqP = new CudaArray( *( data.contexts[0] ), data.contexts[0]->getPaddedNumAtoms(), sizeof( float4 ), "MidIntegPositions" );
modesChanged = true;
}
if( modesChanged ) {
int index = 0;
const std::vector<std::vector<Vec3> > &modeVectors = integrator.getProjectionVectors();
std::vector<float4> tmp( numModes * mParticles );;
for( int i = 0; i < numModes; i++ ) {
for( int j = 0; j < mParticles; j++ ) {
tmp[index++] = make_float4( ( float ) modeVectors[i][j][0], ( float ) modeVectors[i][j][1], ( float ) modeVectors[i][j][2], 0.0f );
}
}
modes->upload( tmp );
}
}
}
