static void copyFrameToBodyState(FrameType& frame, Body& body)
{
const BodyMotion& motion = frame.motion();
int numJoints = std::min(body.numJoints(), motion.numJoints());
const MultiValueSeq::Frame q = motion.jointPosSeq()->frame(frame.frame());
for(int i=0; i < numJoints; ++i){
body.joint(i)->q() = q[i];
}
int numLinks = std::min(body.numLinks(), motion.numLinks());
const MultiSE3Seq::Frame p = motion.linkPosSeq()->frame(frame.frame());
for(int i=0; i < numLinks; ++i){
Link* link = body.link(i);
link->p() = p[i].translation();
link->R() = p[i].rotation().toRotationMatrix();
}
}
bool IPv6Packet <FrameType>::frame(const FrameType& frame) {
if (frame.datagramType() != DATAGRAM_IPV6) {
return false;
}
_frame = frame;
return true;
}
HINLINE void operator()(
ThreadParams* params,
FrameType& frame,
const std::string subGroup,
const uint64_t particlesOffset,
const uint64_t elements)
{
typedef T_Identifier Identifier;
typedef typename PMacc::traits::Resolve<Identifier>::type::type ValueType;
const uint32_t components = GetNComponents<ValueType>::value;
typedef typename GetComponentsType<ValueType>::type ComponentType;
typedef typename PICToSplash<ComponentType>::type SplashType;
log<picLog::INPUT_OUTPUT > ("HDF5: ( begin ) load species attribute: %1%") % Identifier::getName();
const std::string name_lookup[] = {"x", "y", "z"};
ComponentType* tmpArray = nullptr;
if( elements > 0 )
tmpArray = new ComponentType[elements];
ParallelDomainCollector* dataCollector = params->dataCollector;
for (uint32_t d = 0; d < components; d++)
{
OpenPMDName<T_Identifier> openPMDName;
std::stringstream datasetName;
datasetName << subGroup << "/" << openPMDName();
if (components > 1)
datasetName << "/" << name_lookup[d];
ValueType* dataPtr = frame.getIdentifier(Identifier()).getPointer();
Dimensions sizeRead(0, 0, 0);
// read one component from file to temporary array
dataCollector->read(params->currentStep,
Dimensions(elements, 1, 1),
Dimensions(particlesOffset, 0, 0),
datasetName.str().c_str(),
sizeRead,
tmpArray
);
PMACC_ASSERT(sizeRead[0] == elements);
/* copy component from temporary array to array of structs */
#pragma omp parallel for
for (size_t i = 0; i < elements; ++i)
{
ComponentType& ref = ((ComponentType*) dataPtr)[i * components + d];
ref = tmpArray[i];
}
}
__deleteArray(tmpArray);
log<picLog::INPUT_OUTPUT > ("HDF5: ( end ) load species attribute: %1%") %
Identifier::getName();
}
HINLINE void operator()(
ThreadParams* params,
FrameType& frame,
const std::string particlePath,
const uint64_t particlesOffset,
const uint64_t elements)
{
typedef T_Identifier Identifier;
typedef typename PMacc::traits::Resolve<Identifier>::type::type ValueType;
const uint32_t components = GetNComponents<ValueType>::value;
typedef typename GetComponentsType<ValueType>::type ComponentType;
log<picLog::INPUT_OUTPUT > ("ADIOS: ( begin ) load species attribute: %1%") % Identifier::getName();
const std::string name_lookup[] = {"x", "y", "z"};
ComponentType* tmpArray = NULL;
if( elements > 0 )
tmpArray = new ComponentType[elements];
// dev assert!
if( elements > 0 )
assert(tmpArray);
for (uint32_t n = 0; n < components; ++n)
{
OpenPMDName<T_Identifier> openPMDName;
std::stringstream datasetName;
datasetName << particlePath << openPMDName();
if (components > 1)
datasetName << "/" << name_lookup[n];
ValueType* dataPtr = frame.getIdentifier(Identifier()).getPointer();
ADIOS_VARINFO* varInfo = adios_inq_var( params->fp, datasetName.str().c_str() );
// it's possible to aquire the local block with that call again and
// the local elements to-be-read, but the block-ID must be known (MPI rank?)
//ADIOS_CMD(adios_inq_var_blockinfo( params->fp, varInfo ));
ADIOS_SELECTION* sel = adios_selection_boundingbox( 1, &particlesOffset, &elements );
/** Note: adios_schedule_read is not a collective call in any
* ADIOS method and can therefore be skipped for empty reads */
if( elements > 0 )
{
ADIOS_CMD(adios_schedule_read( params->fp,
sel,
datasetName.str().c_str(),
0, /* from_step (not used in streams) */
1, /* nsteps to read (must be 1 for stream) */
(void*)tmpArray ));
}
/** start a blocking read of all scheduled variables
* (this is collective call in many ADIOS methods) */
ADIOS_CMD(adios_perform_reads( params->fp, 1 ));
log<picLog::INPUT_OUTPUT > ("ADIOS: Did read %1% local of %2% global elements for %3%") %
elements % varInfo->dims[0] % datasetName.str();
/* copy component from temporary array to array of structs */
#pragma omp parallel for
for (size_t i = 0; i < elements; ++i)
{
ComponentType& ref = ((ComponentType*) dataPtr)[i * components + n];
ref = tmpArray[i];
}
adios_selection_delete( sel );
adios_free_varinfo( varInfo );
}
__deleteArray(tmpArray);
log<picLog::INPUT_OUTPUT > ("ADIOS: ( end ) load species attribute: %1%") %
Identifier::getName();
}
