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structured data has been modified for new changes in version (1.0)

This commit is contained in:
Hamidreza Norouzi 2024-03-24 02:02:48 -07:00
parent 22405db699
commit 6b3a4f017b
19 changed files with 251 additions and 133 deletions
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85
src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.cpp
View File

@ -21,57 +21,25 @@ Licence:
#include "boundaryBase.hpp"
#include "dictionary.hpp"
#include "internalPoints.hpp"
#include "anyList.hpp"
#include "Time.hpp"
#include "boundaryBaseKernels.hpp"
/*pFlow::boundaryBase::boundaryBase
(
const plane& bplane,
uint32 mirrorProc,
const word& name,
const word& type,
internalPoints& internal
)
:
subscriber(groupNames(name,type)),
boundaryPlane_(bplane),
name_(name),
type_(type),
mirrorProcessoNo_(mirrorProc),
internal_(internal)
{
}*/
void pFlow::boundaryBase::setNewIndices
(
deviceViewType1D<uint32> newIndices
const uint32Vector_D& newIndices
)
{
auto newSize = newIndices.size();
setSize(static_cast<uint32>(newSize));
if(newSize>0u)
{
copy(indexList_.deviceView(), newIndices);
}
indexList_.assign(newIndices, false);
}
void pFlow::boundaryBase::appendNewIndices
(
deviceViewType1D<uint32> newIndices
const uint32Vector_D& newIndices
)
{
auto s = static_cast<uint32>(newIndices.size());
if(s == 0) return;
uint32 oldS = size();
uint32 newSize = oldS + s;
setSize(newSize);
auto appendView = Kokkos::subview(
indexList_.deviceViewAll(),
Kokkos::make_pair<uint32>(oldS, newSize));
copy(appendView, newIndices);
indexList_.append(newIndices);
// TODO: notify observers about this change
@ -79,12 +47,10 @@ void pFlow::boundaryBase::appendNewIndices
//sort(indexList_.deviceViewAll(), 0, newSize);
}
bool pFlow::boundaryBase::removeIndices
(
uint32 numRemove,
deviceViewType1D<uint32> removeMask
const uint32Vector_D& removeMask
)
{
if(removeMask.size() != size()+1 )
@ -93,12 +59,12 @@ bool pFlow::boundaryBase::removeIndices
return false;
}
deviceViewType1D<uint32> removeIndices("removeIndices", 1);
deviceViewType1D<uint32> keepIndices("keepIndices",1);
uint32Vector_D removeIndices("removeIndices");
uint32Vector_D keepIndices("keepIndices");
pFlow::boundaryBaseKernels::createRemoveKeepIndices
(
indexList_.deviceView(),
indexList_,
numRemove,
removeMask,
removeIndices,
@ -114,15 +80,32 @@ bool pFlow::boundaryBase::removeIndices
setNewIndices(keepIndices);
//TODO: notify observers about changes
anyList aList;
aList.emplaceBack(
message::eventName(message::BNDR_RESET),
std::move(keepIndices));
message msgBndry = message::BNDR_RESET;
uint32 iter = internal_.time().currentIter();
real t = internal_.time().currentTime();
real dt = internal_.time().dt();
if( !this->notify(iter, t, dt, msgBndry, aList) )
{
fatalErrorInFunction<<"Error in notify operation in boundary "<<
name_ <<endl;
return false;
}
return true;
}
bool pFlow::boundaryBase::transferPoints
(
uint32 numTransfer,
deviceViewType1D<uint32> transferMask,
const uint32Vector_D& transferMask,
uint32 transferBoundaryIndex,
realx3 transferVector
)
@ -133,12 +116,12 @@ bool pFlow::boundaryBase::transferPoints
return false;
}
deviceViewType1D<uint32> transferIndices("transferIndices",1);
deviceViewType1D<uint32> keepIndices("keepIndices",1);
uint32Vector_D transferIndices("transferIndices");
uint32Vector_D keepIndices("keepIndices");
pFlow::boundaryBaseKernels::createRemoveKeepIndices
(
indexList_.deviceView(),
indexList_,
numTransfer,
transferMask,
transferIndices,
@ -150,7 +133,7 @@ bool pFlow::boundaryBase::transferPoints
// first, change the flags in the internalPoints
if( !internal_.changePointsFlag(
transferIndices,
transferIndices.deviceView(),
transferBoundaryIndex) )
{
return false;
@ -158,7 +141,7 @@ bool pFlow::boundaryBase::transferPoints
// second, change the position of points
if(!internal_.changePointsPoisition(
transferIndices,
transferIndices.deviceView(),
transferVector))
{
return false;

16
src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.hpp
View File

@ -53,6 +53,10 @@ private:
/// list of particles indices on device
uint32Vector_D indexList_;
uint32Vector_H indexListH_;
bool indexSync_ = false;
/// The length defined for creating neighbor list
real neighborLength_;
@ -67,17 +71,17 @@ private:
protected:
void setNewIndices(deviceViewType1D<uint32> newIndices);
void setNewIndices(const uint32Vector_D& newIndices);
void appendNewIndices(deviceViewType1D<uint32> newIndices);
void appendNewIndices(const uint32Vector_D& newIndices);
bool removeIndices(
uint32 numRemove,
deviceViewType1D<uint32> removeMask);
const uint32Vector_D& removeMask);
bool transferPoints(
uint32 numTransfer,
deviceViewType1D<uint32> transferMask,
const uint32Vector_D& transferMask,
uint32 transferBoundaryIndex,
realx3 transferVector);
@ -176,10 +180,10 @@ public:
bool beforeIteration(uint32 iterNum, real t, real dt) = 0 ;
virtual
bool iterate(uint32 iterNum, real t) = 0;
bool iterate(uint32 iterNum, real t, real dt) = 0;
virtual
bool afterIteration(uint32 iterNum, real t) = 0;
bool afterIteration(uint32 iterNum, real t, real dt) = 0;
const auto& indexList()const

59
src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBaseKernels.cpp
View File

@ -24,16 +24,25 @@ void pFlow::boundaryBaseKernels::createRemoveKeepLists
(
uint32 numTotal,
uint32 numRemove,
deviceViewType1D<uint32> removeMask,
deviceViewType1D<uint32>& removeList,
deviceViewType1D<uint32>& keepList
const uint32Vector_D& removeMask,
uint32Vector_D& removeList,
uint32Vector_D& keepList
)
{
uint32 numKeep = numTotal - numRemove;
deviceViewType1D<uint32> rList("rList",numRemove);
deviceViewType1D<uint32> kList("kList",numKeep);
removeList.reallocate(numRemove,numRemove);
keepList.reallocate(numKeep,numKeep);
exclusiveScan(removeMask, 0u, numTotal+1, removeMask, 0u);
auto maskD = removeMask.deviceViewAll();
const auto& removeD = removeList.deviceViewAll();
const auto& keepD = keepList.deviceViewAll();
exclusiveScan(
maskD,
0u,
numTotal+1,
maskD,
0u);
Kokkos::parallel_for
(
@ -41,35 +50,38 @@ void pFlow::boundaryBaseKernels::createRemoveKeepLists
deviceRPolicyStatic(0, numTotal),
LAMBDA_HD(uint32 i)
{
if(removeMask(i)!= removeMask(i+1))
rList(removeMask(i)) = i;
if(maskD(i)!= maskD(i+1))
removeD(maskD(i)) = i;
else
kList(i-removeMask(i)) = i;
keepD(i-maskD(i)) = i;
}
);
Kokkos::fence();
removeList = rList;
keepList = kList;
}
void pFlow::boundaryBaseKernels::createRemoveKeepIndices
(
deviceViewType1D<uint32> indices,
const uint32Vector_D& indices,
uint32 numRemove,
deviceViewType1D<uint32> removeMask,
deviceViewType1D<uint32>& removeIndices,
deviceViewType1D<uint32>& keepIndices
const uint32Vector_D& removeMask,
uint32Vector_D& removeIndices,
uint32Vector_D& keepIndices
)
{
uint32 numTotal = indices.size();
uint32 numKeep = numTotal - numRemove;
deviceViewType1D<uint32> rIndices("rIndices",numRemove);
deviceViewType1D<uint32> kIndices("kIndices",numKeep);
exclusiveScan(removeMask, 0u, numTotal+1, removeMask, 0u);
removeIndices.reallocate(numRemove, numRemove);
keepIndices.reallocate(numKeep, numKeep);
auto maskD = removeMask.deviceViewAll();
const auto& removeD = removeIndices.deviceViewAll();
const auto& keepD = keepIndices.deviceViewAll();
const auto& indicesD = indices.deviceViewAll();
exclusiveScan(maskD, 0u, numTotal+1, maskD, 0u);
Kokkos::parallel_for
(
@ -77,14 +89,11 @@ void pFlow::boundaryBaseKernels::createRemoveKeepIndices
deviceRPolicyStatic(0, numTotal),
LAMBDA_HD(uint32 i)
{
if(removeMask(i)!= removeMask(i+1))
rIndices(removeMask(i)) = indices(i);
if(maskD(i)!= maskD(i+1))
removeD(maskD(i)) = indicesD(i);
else
kIndices(i-removeMask(i)) = indices(i);
keepD(i-maskD(i)) = indicesD(i);
}
);
Kokkos::fence();
removeIndices = rIndices;
keepIndices = kIndices;
}

16
src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBaseKernels.hpp
View File

@ -21,7 +21,7 @@ Licence:
#ifndef __boundaryBaseKernels_hpp__
#define __boundaryBaseKernels_hpp__
#include "phasicFlowKokkos.hpp"
#include "VectorSingles.hpp"
namespace pFlow::boundaryBaseKernels
{
@ -29,16 +29,16 @@ namespace pFlow::boundaryBaseKernels
void createRemoveKeepLists(
uint32 numTotal,
uint32 numRemove,
deviceViewType1D<uint32> removeMask,
deviceViewType1D<uint32>& removeList,
deviceViewType1D<uint32>& keepList);
const uint32Vector_D& removeMask,
uint32Vector_D& removeList,
uint32Vector_D& keepList);
void createRemoveKeepIndices(
deviceViewType1D<uint32> indices,
const uint32Vector_D& indices,
uint32 numRemove,
deviceViewType1D<uint32> removeMask,
deviceViewType1D<uint32>& removeIndices,
deviceViewType1D<uint32>& keepIndices);
const uint32Vector_D& removeMask,
uint32Vector_D& removeIndices,
uint32Vector_D& keepIndices);
}

15
src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.cpp
View File

@ -33,7 +33,7 @@ pFlow::boundaryExit::boundaryExit
boundaryBase(dict, bplane, internal)
{
exitMarginLength_ = max(
dict.getValOrSet("exitMarginLength",0.0), 0.0);
dict.getValOrSet("exitMarginLength",(real)0.0), (real)0.0);
checkForExitInterval_ = max(
dict.getValOrSet("checkForExitInterval", 1), 1);
}
@ -52,9 +52,10 @@ bool pFlow::boundaryExit::beforeIteration
}
uint32 s = size();
deviceViewType1D<uint32> deleteFlags("deleteFlags",s+1);
fill(deleteFlags, 0, s+1, 0u);
uint32Vector_D deleteFlags("deleteFlags",s+1, s+1, RESERVE());
deleteFlags.fill(0u);
const auto& deleteD = deleteFlags.deviceViewAll();
auto points = thisPoints();
auto p = boundaryPlane().infPlane();
@ -68,7 +69,7 @@ bool pFlow::boundaryExit::beforeIteration
{
if(p.pointInNegativeSide(points(i)))
{
deleteFlags(i)=1;
deleteD(i)=1;
delToUpdate++;
}
},
@ -87,7 +88,8 @@ bool pFlow::boundaryExit::beforeIteration
bool pFlow::boundaryExit::iterate
(
uint32 iterNum,
real t
real t,
real dt
)
{
return true;
@ -96,7 +98,8 @@ bool pFlow::boundaryExit::iterate
bool pFlow::boundaryExit::afterIteration
(
uint32 iterNum,
real t
real t,
real dt
)
{
return true;

4
src/phasicFlow/structuredData/boundaries/boundaryExit/boundaryExit.hpp
View File

@ -63,9 +63,9 @@ public:
bool beforeIteration(uint32 iterNum, real t, real dt) override;
bool iterate(uint32 iterNum, real t) override;
bool iterate(uint32 iterNum, real t, real dt) override;
bool afterIteration(uint32 iterNum, real t) override;
bool afterIteration(uint32 iterNum, real t, real dt) override;
};

18
src/phasicFlow/structuredData/boundaries/boundaryList.cpp
View File

@ -155,6 +155,15 @@ bool pFlow::boundaryList::iterate
real dt
)
{
for(auto& bdry:*this)
{
if( !bdry->iterate(iter, t, dt))
{
fatalErrorInFunction<<
"Error in iterate in boundary "<<bdry->name()<<endl;
return false;
}
}
return true;
}
@ -165,5 +174,14 @@ bool pFlow::boundaryList::afterIteration
real dt
)
{
for(auto& bdry:*this)
{
if( !bdry->afterIteration(iter, t, dt))
{
fatalErrorInFunction<<
"Error in afterIteration in boundary "<<bdry->name()<<endl;
return false;
}
}
return true;
}

6
src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.cpp
View File

@ -43,7 +43,8 @@ bool pFlow::boundaryNone::beforeIteration
bool pFlow::boundaryNone::iterate
(
uint32 iterNum,
real t
real t,
real dt
)
{
return true;
@ -52,7 +53,8 @@ bool pFlow::boundaryNone::iterate
bool pFlow::boundaryNone::afterIteration
(
uint32 iterNum,
real t
real t,
real dt
)
{
return true;

4
src/phasicFlow/structuredData/boundaries/boundaryNone/boundaryNone.hpp
View File

@ -52,9 +52,9 @@ public:
bool beforeIteration(uint32 iterNum, real t, real dt) override;
bool iterate(uint32 iterNum, real t) override;
bool iterate(uint32 iterNum, real t, real dt) override;
bool afterIteration(uint32 iterNum, real t) override;
bool afterIteration(uint32 iterNum, real t, real dt) override;
};

13
src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.cpp
View File

@ -63,11 +63,12 @@ bool pFlow::boundaryPeriodic::beforeIteration(
}
uint32 s = size();
deviceViewType1D<uint32> transferFlags("transferFlags",s+1);
fill(transferFlags, 0, s+1, 0u);
uint32Vector_D transferFlags("transferFlags",s+1, s+1, RESERVE());
transferFlags.fill(0u);
auto points = thisPoints();
auto p = boundaryPlane().infPlane();
const auto & transferD = transferFlags.deviceViewAll();
uint32 numTransfered = 0;
Kokkos::parallel_reduce
@ -78,7 +79,7 @@ bool pFlow::boundaryPeriodic::beforeIteration(
{
if(p.pointInNegativeSide(points(i)))
{
transferFlags(i)=1;
transferD(i)=1;
trnasToUpdate++;
}
},
@ -109,7 +110,8 @@ bool pFlow::boundaryPeriodic::beforeIteration(
bool pFlow::boundaryPeriodic::iterate
(
uint32 iterNum,
real t
real t,
real dt
)
{
return true;
@ -118,7 +120,8 @@ bool pFlow::boundaryPeriodic::iterate
bool pFlow::boundaryPeriodic::afterIteration
(
uint32 iterNum,
real t
real t,
real dt
)
{
return true;

6
src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.hpp
View File

@ -46,7 +46,7 @@ public:
const plane& bplane,
internalPoints& internal);
virtual
~boundaryPeriodic() override= default;
add_vCtor
@ -64,9 +64,9 @@ public:
bool beforeIteration(uint32 iterNum, real t, real dt) override;
bool iterate(uint32 iterNum, real t) override;
bool iterate(uint32 iterNum, real t, real dt) override;
bool afterIteration(uint32 iterNum, real t) override;
bool afterIteration(uint32 iterNum, real t, real dt) override;
};

2
src/phasicFlow/structuredData/domain/simulationDomain.cpp
View File

@ -53,7 +53,7 @@ pFlow::domain pFlow::simulationDomain::extendThisDomain
}
pFlow::uniquePtr<pFlow::simulationDomain>
pFlow::simulationDomain::create(systemControl &control)
pFlow::simulationDomain::create(systemControl &control)
{
word sType = angleBracketsNames(
"simulationDomain",

2
src/phasicFlow/structuredData/iBox/iBox.hpp
View File

@ -43,7 +43,7 @@ protected:
public:
// - type info
TypeInfoTemplateNV("iBox", intType);
TypeInfoTemplateNV11("iBox", intType);
//// - Constructors
INLINE_FUNCTION_HD

54
src/phasicFlow/structuredData/pointStructure/internalPoints.cpp
View File

@ -18,10 +18,11 @@ Licence:
-----------------------------------------------------------------------------*/
#include "Time.hpp"
#include "internalPoints.hpp"
#include "domain.hpp"
#include "Vectors.hpp"
#include "anyList.hpp"
#include "internalPointsKernels.hpp"
void pFlow::internalPoints::syncPFlag()const
@ -33,16 +34,57 @@ void pFlow::internalPoints::syncPFlag()const
}
}
bool pFlow::internalPoints::deletePoints(deviceViewType1D<uint32> delPoints)
bool pFlow::internalPoints::deletePoints(const uint32Vector_D& delPoints)
{
if(!pFlagsD_.deletePoints(delPoints))
if(delPoints.empty())return true;
auto oldRange = pFlagsD_.activeRange();
auto oldSize = size();
if(!pFlagsD_.deletePoints(delPoints.deviceView()))
{
fatalErrorInFunction<<
"Error in deleting points from internal points"<<endl;
return false;
}
pFlagSync_ = false;
WARNING<<"Notify the observersin in internalPoints"<<END_WARNING;
auto newRange = pFlagsD_.activeRange();
auto newSize = size();
anyList varList;
varList.emplaceBack(
message::eventName(message::ITEM_DELETE),
delPoints);
message msg(message::ITEM_DELETE);
if(oldSize!= newSize)
{
msg.add(message::SIZE_CHANGED);
varList.emplaceBack(
message::eventName(message::SIZE_CHANGED),
newSize);
}
if(oldRange!=newRange)
{
msg.add(message::RANGE_CHANGED);
varList.emplaceBack(
message::eventName(message::RANGE_CHANGED),
newRange);
}
auto iter = time().currentIter();
auto t = time().currentTime();
auto dt = time().dt();
if( !notify(iter, t, dt, msg, varList) )
{
fatalErrorInFunction;
return false;
}
return true;
}
@ -247,7 +289,7 @@ bool pFlow::internalPoints::read
return false;
}
pointPosition_.assign(fRead);
pointPosition_.assignFromHost(fRead);
pFlagsD_ = pFlagTypeDevice(pointPosition_.capacity(), 0, pointPosition_.size());
pFlagSync_ = false;
@ -284,7 +326,7 @@ bool pFlow::internalPoints::read
return false;
}
pointPosition_.assign(fRead);
pointPosition_.assignFromHost(fRead);
pFlagsD_ = pFlagTypeDevice(pointPosition_.capacity(), 0, pointPosition_.size());
pFlagSync_ = false;

9
src/phasicFlow/structuredData/pointStructure/internalPoints.hpp
View File

@ -22,6 +22,7 @@ Licence:
#include "subscriber.hpp"
#include "Vectors.hpp"
#include "VectorSingles.hpp"
#include "Fields.hpp"
#include "pointFlag.hpp"
@ -75,7 +76,7 @@ protected:
friend boundaryBase;
bool deletePoints(deviceViewType1D<uint32> delPoints);
bool deletePoints(const uint32Vector_D& delPoints);
bool changePointsFlag(
deviceViewType1D<uint32> changePoints,
@ -161,6 +162,12 @@ public:
return pointPosition_.capacity();
}
INLINE_FUNCTION_H
bool empty()const
{
return size()==0u;
}
// - number of active points
INLINE_FUNCTION_H
uint32 numActive() const

3
src/phasicFlow/structuredData/pointStructure/pointFlag.hpp
View File

@ -277,6 +277,9 @@ public:
isAllActive_);
}
ViewType1D<uint32, memory_space> getActivePoints();
/// @brief Loop over the active points and mark those out of the box
/// and return number of deleted points
/// @param validBox the box whose inside is valid

31
src/phasicFlow/structuredData/pointStructure/pointFlagKernels.hpp
View File

@ -20,7 +20,36 @@ Licence:
#ifndef __pointFlagKernels_hpp__
#define __pointFlagKernels_hpp__
#include "streams.hpp"
template<typename ExecutionSpace>
pFlow::ViewType1D<pFlow::uint32, typename pFlow::pointFlag<ExecutionSpace>::memory_space>
pFlow::pointFlag<ExecutionSpace>::getActivePoints()
{
using rpAPoints = Kokkos::RangePolicy<execution_space,
Kokkos::IndexType<uint32>>;
ViewType1D<pFlow::uint32,memory_space>
aPoints("activePoints", activeRange_.end()+1);
Kokkos::parallel_for(
"pFlow::pointFlag<ExecutionSpace>::getActivePoints",
rpAPoints(0,activeRange_.end()),
CLASS_LAMBDA_HD(uint32 i)
{
if( isActive(i))
{
aPoints[i] = 1;
}
else
{
aPoints[i] = 0;
}
}
);
Kokkos::fence();
return aPoints;
}
template<typename ExecutionSpace>
pFlow::uint32 pFlow::pointFlag<ExecutionSpace>::markOutOfBoxDelete

17
src/phasicFlow/structuredData/pointStructure/pointStructure.cpp
View File

@ -80,7 +80,7 @@ bool pFlow::pointStructure::setupPointStructure(const PointsTypeHost &points)
bool pFlow::pointStructure::initializePoints(const PointsTypeHost &points)
{
pointPosition_.assign(points);
pointPosition_.assignFromHost(points);
pFlagsD_ = pFlagTypeDevice(pointPosition_.capacity(), 0, pointPosition_.size());
pFlagSync_ = false;
@ -117,7 +117,7 @@ pFlow::pointStructure::pointStructure
*this
)
{
REPORT(0)<< "Reading "<< Green_Text("point structure")<<
REPORT(1)<< "Reading "<< Green_Text("pointStructure")<<
" from "<<IOobject::path()<<END_REPORT;
if( !IOobject::readObject() )
@ -177,11 +177,24 @@ bool pFlow::pointStructure::beforeIteration()
bool pFlow::pointStructure::iterate()
{
if( !boundaries_.iterate(currentIter(), currentTime(), dt()) )
{
fatalErrorInFunction<<
"Unable to perform iterate for boundaries"<<endl;
return false;
}
return true;
}
bool pFlow::pointStructure::afterIteration()
{
if( !boundaries_.afterIteration(currentIter(), currentTime(), dt()) )
{
fatalErrorInFunction<<
"Unable to perform afterIteration for boundaries"<<endl;
return false;
}
return true;
}

12
src/phasicFlow/structuredData/pointStructure/pointStructure.hpp
View File

@ -27,12 +27,9 @@ Licence:
#include "boundaryList.hpp"
#include "streams.hpp"
namespace pFlow
{
class pointStructure
:
public IOobject,
@ -74,7 +71,7 @@ public:
//// - Constructors
/// an empty pointStructure, good for reading from file
pointStructure(systemControl& control);
explicit pointStructure(systemControl& control);
/// construct from point positions, assume all points are active
pointStructure(
@ -119,7 +116,6 @@ public:
return boundaries_;
}
Time& time() override
{
return demComponent::time();
@ -140,11 +136,17 @@ public:
return boundaries_[i];
}
inline
const auto& simDomain()const
{
return simulationDomain_();
}
inline
const auto& thisDomain()const
{
return simulationDomain_().thisDomain();
}
// - IO methods