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DataBase.cc
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//---------------------------------Spheral++----------------------------------//
// DataBase -- The central point to store NodeLists and fields, to serve the
// Spheral++ physics modules.
//
// Created by JMO, Sun Feb 6 13:44:49 PST 2000
//----------------------------------------------------------------------------//
#include "DataBase.hh"
#include "Geometry/Dimension.hh"
#include "Field/NodeIterators.hh"
#include "Field/Field.hh"
#include "Field/FieldList.hh"
#include "Kernel/TableKernel.hh"
#include "Material/EquationOfState.hh"
#include "Utilities/testBoxIntersection.hh"
#include "Utilities/safeInv.hh"
#include "Hydro/HydroFieldNames.hh"
#include "Utilities/globalBoundingVolumes.hh"
#include "Utilities/globalNodeIDs.hh"
#include "Distributed/allReduce.hh"
#include "Distributed/Communicator.hh"
#include "Utilities/DBC.hh"
#ifdef USE_MPI
extern "C" {
#include <mpi.h>
}
#endif
#include <algorithm>
#include <memory>
using std::vector;
using std::cout;
using std::cerr;
using std::endl;
using std::min;
using std::max;
using std::abs;
using std::shared_ptr;
namespace Spheral {
//------------------------------------------------------------------------------
// Empty constructor.
//------------------------------------------------------------------------------
template<typename Dimension>
DataBase<Dimension>::DataBase():
mNodeListPtrs(0),
mFluidNodeListPtrs(0),
mFluidNodeListAsNodeListPtrs(0),
mSolidNodeListPtrs(0),
mSolidNodeListAsNodeListPtrs(0),
mDEMNodeListPtrs(0),
mDEMNodeListAsNodeListPtrs(0),
mConnectivityMapPtr(new ConnectivityMap<Dimension>()) {
}
//------------------------------------------------------------------------------
// Destructor.
//------------------------------------------------------------------------------
template<typename Dimension>
DataBase<Dimension>::~DataBase() {
}
//------------------------------------------------------------------------------
// Assignment.
//------------------------------------------------------------------------------
template<typename Dimension>
DataBase<Dimension>&
DataBase<Dimension>::
operator=(const DataBase<Dimension>& rhs) {
REQUIRE(rhs.valid());
if (this != &rhs) {
mNodeListPtrs = rhs.mNodeListPtrs;
mFluidNodeListPtrs = rhs.mFluidNodeListPtrs;
mFluidNodeListAsNodeListPtrs = rhs.mFluidNodeListAsNodeListPtrs;
mSolidNodeListPtrs = rhs.mSolidNodeListPtrs;
mSolidNodeListAsNodeListPtrs = rhs.mSolidNodeListAsNodeListPtrs;
mDEMNodeListPtrs = rhs.mDEMNodeListPtrs;
mDEMNodeListAsNodeListPtrs = rhs.mDEMNodeListAsNodeListPtrs;
mConnectivityMapPtr = std::shared_ptr<ConnectivityMap<Dimension> >(new ConnectivityMap<Dimension>());
}
ENSURE(valid());
return *this;
}
//------------------------------------------------------------------------------
// Global numbers of nodes in the DataBase.
//------------------------------------------------------------------------------
template<typename Dimension>
int
DataBase<Dimension>::globalNumInternalNodes() const {
int localResult = numInternalNodes();
int result = localResult;
result = allReduce(result, SPHERAL_OP_SUM);
return result;
}
template<typename Dimension>
int
DataBase<Dimension>::globalNumGhostNodes() const {
int localResult = numGhostNodes();
int result = localResult;
result = allReduce(result, SPHERAL_OP_SUM);
return result;
}
template<typename Dimension>
int
DataBase<Dimension>::globalNumNodes() const {
int localResult = numNodes();
int result = localResult;
result = allReduce(result, SPHERAL_OP_SUM);
return result;
}
//------------------------------------------------------------------------------
// Global numbers of fluid nodes in the DataBase.
//------------------------------------------------------------------------------
template<typename Dimension>
int
DataBase<Dimension>::globalNumFluidInternalNodes() const {
int localResult = numFluidInternalNodes();
int result = localResult;
result = allReduce(result, SPHERAL_OP_SUM);
return result;
}
template<typename Dimension>
int
DataBase<Dimension>::globalNumFluidGhostNodes() const {
int localResult = numFluidGhostNodes();
int result = localResult;
result = allReduce(result, SPHERAL_OP_SUM);
return result;
}
template<typename Dimension>
int
DataBase<Dimension>::globalNumFluidNodes() const {
int localResult = numFluidNodes();
int result = localResult;
result = allReduce(result, SPHERAL_OP_SUM);
return result;
}
//------------------------------------------------------------------------------
// Node iterators for all node IDs.
//------------------------------------------------------------------------------
template<typename Dimension>
AllNodeIterator<Dimension>
DataBase<Dimension>::nodeBegin() const {
ConstNodeListIterator nodeListItr = nodeListBegin();
while (nodeListItr < nodeListEnd() &&
(*nodeListItr)->numNodes() < 1) ++nodeListItr;
CHECK(nodeListItr >= nodeListBegin() && nodeListItr <= nodeListEnd());
return AllNodeIterator<Dimension>(nodeListItr,
nodeListBegin(),
nodeListEnd());
}
template<typename Dimension>
AllNodeIterator<Dimension>
DataBase<Dimension>::nodeEnd() const {
return AllNodeIterator<Dimension>(nodeListEnd(),
nodeListBegin(),
nodeListEnd());
}
//------------------------------------------------------------------------------
// Node iterators for internal nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
InternalNodeIterator<Dimension>
DataBase<Dimension>::internalNodeBegin() const {
ConstNodeListIterator nodeListItr = nodeListBegin();
while (nodeListItr < nodeListEnd() &&
(*nodeListItr)->numInternalNodes() < 1) ++nodeListItr;
CHECK(nodeListItr >= nodeListBegin() && nodeListItr <= nodeListEnd());
return InternalNodeIterator<Dimension>(nodeListItr,
nodeListBegin(),
nodeListEnd());
}
template<typename Dimension>
InternalNodeIterator<Dimension>
DataBase<Dimension>::internalNodeEnd() const {
return InternalNodeIterator<Dimension>(nodeListEnd(),
nodeListBegin(),
nodeListEnd());
}
//------------------------------------------------------------------------------
// Node iterators for ghost nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
GhostNodeIterator<Dimension>
DataBase<Dimension>::ghostNodeBegin() const {
ConstNodeListIterator nodeListItr = nodeListBegin();
while (nodeListItr < nodeListEnd() &&
(*nodeListItr)->numGhostNodes() < 1) ++nodeListItr;
if (nodeListItr < nodeListEnd()) {
return GhostNodeIterator<Dimension>(nodeListItr,
nodeListBegin(),
nodeListEnd(),
(*nodeListItr)->firstGhostNode());
} else {
return this->ghostNodeEnd();
}
}
template<typename Dimension>
GhostNodeIterator<Dimension>
DataBase<Dimension>::ghostNodeEnd() const {
return GhostNodeIterator<Dimension>(nodeListEnd(),
nodeListBegin(),
nodeListEnd());
}
//------------------------------------------------------------------------------
// Node iterators for master neighbor nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
MasterNodeIterator<Dimension>
DataBase<Dimension>::masterNodeBegin(const std::vector<std::vector<int>>& masterLists) const {
ConstNodeListIterator nodeListItr = nodeListBegin();
unsigned iNodeList = 0;
while (nodeListItr < nodeListEnd() &&
masterLists[iNodeList].empty()) {
++nodeListItr;
++iNodeList;
}
if (nodeListItr < nodeListEnd()) {
return MasterNodeIterator<Dimension>(nodeListItr,
nodeListBegin(),
nodeListEnd(),
masterLists[iNodeList].begin(),
masterLists);
} else {
return this->masterNodeEnd();
}
}
template<typename Dimension>
MasterNodeIterator<Dimension>
DataBase<Dimension>::masterNodeEnd() const {
return MasterNodeIterator<Dimension>(nodeListEnd(),
nodeListBegin(),
nodeListEnd(),
std::vector<std::vector<int>>());
}
//------------------------------------------------------------------------------
// Node iterators for coarse neighbor nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
CoarseNodeIterator<Dimension>
DataBase<Dimension>::coarseNodeBegin(const std::vector<std::vector<int>>& coarseNeighbors) const {
ConstNodeListIterator nodeListItr = nodeListBegin();
unsigned iNodeList = 0;
while (nodeListItr < nodeListEnd() &&
coarseNeighbors[iNodeList].empty()) {
++nodeListItr;
++iNodeList;
}
if (nodeListItr < nodeListEnd()) {
return CoarseNodeIterator<Dimension>(nodeListItr,
nodeListBegin(),
nodeListEnd(),
coarseNeighbors[iNodeList].begin(),
coarseNeighbors);
} else {
return this->coarseNodeEnd();
}
}
template<typename Dimension>
CoarseNodeIterator<Dimension>
DataBase<Dimension>::coarseNodeEnd() const {
return CoarseNodeIterator<Dimension>(nodeListEnd(),
nodeListBegin(),
nodeListEnd(),
std::vector<std::vector<int>>());
}
//------------------------------------------------------------------------------
// Node iterators for refine neighbor nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
RefineNodeIterator<Dimension>
DataBase<Dimension>::refineNodeBegin(const std::vector<std::vector<int>>& refineNeighbors) const {
ConstNodeListIterator nodeListItr = nodeListBegin();
unsigned iNodeList = 0;
while (nodeListItr < nodeListEnd() &&
refineNeighbors[iNodeList].empty()) {
++nodeListItr;
++iNodeList;
}
if (nodeListItr < nodeListEnd()) {
return RefineNodeIterator<Dimension>(nodeListItr,
nodeListBegin(),
nodeListEnd(),
refineNeighbors[iNodeList].begin(),
refineNeighbors);
} else {
return this->refineNodeEnd();
}
}
template<typename Dimension>
RefineNodeIterator<Dimension>
DataBase<Dimension>::refineNodeEnd() const {
return RefineNodeIterator<Dimension>(nodeListEnd(),
nodeListBegin(),
nodeListEnd(),
std::vector<std::vector<int>>());
}
//------------------------------------------------------------------------------
// Node iterators for all fluid node IDs.
//------------------------------------------------------------------------------
template<typename Dimension>
AllNodeIterator<Dimension>
DataBase<Dimension>::fluidNodeBegin() const {
ConstNodeListIterator nodeListItr = fluidNodeListAsNodeListBegin();
while (nodeListItr < fluidNodeListAsNodeListEnd() &&
(*nodeListItr)->numNodes() < 1) ++nodeListItr;
return AllNodeIterator<Dimension>(nodeListItr,
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd());
}
template<typename Dimension>
AllNodeIterator<Dimension>
DataBase<Dimension>::fluidNodeEnd() const {
return AllNodeIterator<Dimension>(fluidNodeListAsNodeListEnd(),
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd());
}
//------------------------------------------------------------------------------
// Node iterators for fluid internal nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
InternalNodeIterator<Dimension>
DataBase<Dimension>::fluidInternalNodeBegin() const {
ConstNodeListIterator nodeListItr = fluidNodeListAsNodeListBegin();
while (nodeListItr < fluidNodeListAsNodeListEnd() &&
(*nodeListItr)->numInternalNodes() < 1) ++nodeListItr;
return InternalNodeIterator<Dimension>(nodeListItr,
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd());
}
template<typename Dimension>
InternalNodeIterator<Dimension>
DataBase<Dimension>::fluidInternalNodeEnd() const {
return InternalNodeIterator<Dimension>(fluidNodeListAsNodeListEnd(),
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd());
}
//------------------------------------------------------------------------------
// Node iterators for fluid ghost nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
GhostNodeIterator<Dimension>
DataBase<Dimension>::fluidGhostNodeBegin() const {
ConstNodeListIterator nodeListItr = fluidNodeListAsNodeListBegin();
while (nodeListItr < fluidNodeListAsNodeListEnd() &&
(*nodeListItr)->numGhostNodes() < 1) ++nodeListItr;
CHECK(nodeListItr >= fluidNodeListAsNodeListBegin() &&
nodeListItr <= fluidNodeListAsNodeListEnd());
if (nodeListItr < fluidNodeListAsNodeListEnd()) {
return GhostNodeIterator<Dimension>(nodeListItr,
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
(*nodeListItr)->firstGhostNode());
} else {
return this->fluidGhostNodeEnd();
}
}
template<typename Dimension>
GhostNodeIterator<Dimension>
DataBase<Dimension>::fluidGhostNodeEnd() const {
return GhostNodeIterator<Dimension>(fluidNodeListAsNodeListEnd(),
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd());
}
//------------------------------------------------------------------------------
// Node iterators for fluid master neighbor nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
MasterNodeIterator<Dimension>
DataBase<Dimension>::fluidMasterNodeBegin(const std::vector<std::vector<int>>& masterLists) const {
ConstNodeListIterator nodeListItr = fluidNodeListAsNodeListBegin();
unsigned iNodeList = 0;
while (nodeListItr < fluidNodeListAsNodeListEnd() &&
masterLists[iNodeList].empty()) {
++nodeListItr;
++iNodeList;
}
CHECK(nodeListItr >= fluidNodeListAsNodeListBegin() &&
nodeListItr <= fluidNodeListAsNodeListEnd());
if (nodeListItr < fluidNodeListAsNodeListEnd()) {
return MasterNodeIterator<Dimension>(nodeListItr,
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
masterLists[iNodeList].begin(),
masterLists);
} else {
return this->fluidMasterNodeEnd();
}
}
template<typename Dimension>
MasterNodeIterator<Dimension>
DataBase<Dimension>::fluidMasterNodeEnd() const {
return MasterNodeIterator<Dimension>(fluidNodeListAsNodeListEnd(),
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
std::vector<std::vector<int>>());
}
//------------------------------------------------------------------------------
// Node iterators for fluid coarse neighbor nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
CoarseNodeIterator<Dimension>
DataBase<Dimension>::fluidCoarseNodeBegin(const std::vector<std::vector<int>>& coarseNeighbors) const {
ConstNodeListIterator nodeListItr = fluidNodeListAsNodeListBegin();
unsigned iNodeList = 0;
while (nodeListItr < fluidNodeListAsNodeListEnd() &&
coarseNeighbors[iNodeList].empty()) {
++nodeListItr;
++iNodeList;
}
CHECK(nodeListItr >= fluidNodeListAsNodeListBegin() &&
nodeListItr <= fluidNodeListAsNodeListEnd());
if (nodeListItr < fluidNodeListAsNodeListEnd()) {
return CoarseNodeIterator<Dimension>(nodeListItr,
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
coarseNeighbors[iNodeList].begin(),
coarseNeighbors);
} else {
return this->fluidCoarseNodeEnd();
}
}
template<typename Dimension>
CoarseNodeIterator<Dimension>
DataBase<Dimension>::fluidCoarseNodeEnd() const {
return CoarseNodeIterator<Dimension>(fluidNodeListAsNodeListEnd(),
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
std::vector<std::vector<int>>());
}
//------------------------------------------------------------------------------
// Node iterators for fluid refine neighbor nodes.
//------------------------------------------------------------------------------
template<typename Dimension>
RefineNodeIterator<Dimension>
DataBase<Dimension>::fluidRefineNodeBegin(const std::vector<std::vector<int>>& refineNeighbors) const {
ConstNodeListIterator nodeListItr = fluidNodeListAsNodeListBegin();
unsigned iNodeList = 0;
while (nodeListItr < fluidNodeListAsNodeListEnd() &&
refineNeighbors[iNodeList].empty()) {
++nodeListItr;
++iNodeList;
}
CHECK(nodeListItr >= fluidNodeListAsNodeListBegin() &&
nodeListItr <= fluidNodeListAsNodeListEnd());
if (nodeListItr < fluidNodeListAsNodeListEnd()) {
return RefineNodeIterator<Dimension>(nodeListItr,
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
refineNeighbors[iNodeList].begin(),
refineNeighbors);
} else {
return this->fluidRefineNodeEnd();
}
}
template<typename Dimension>
RefineNodeIterator<Dimension>
DataBase<Dimension>::fluidRefineNodeEnd() const {
return RefineNodeIterator<Dimension>(fluidNodeListAsNodeListEnd(),
fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
std::vector<std::vector<int>>());
}
//------------------------------------------------------------------------------
// Optimize neighbor objects.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
reinitializeNeighbors() const {
// Find the current bounding box and average node extent in one loop.
// Compute the average node extent.
auto xmin = Vector(0.1*std::numeric_limits<Scalar>::max()), xmax = 0.1*Vector(std::numeric_limits<Scalar>::lowest());
unsigned ntot = 0;
Scalar havg = 0.0, hmax = 0.0, maxExtent = 0.0;
for (auto itr = this->nodeListBegin(); itr != this->nodeListEnd(); ++itr) {
const auto positions = (*itr)->positions();
const auto n = (*itr)->numInternalNodes();
const auto& neighbor = (*itr)->neighbor();
const auto etaMax = neighbor.kernelExtent();
maxExtent = std::max(maxExtent, etaMax);
ntot += n;
for (auto i = 0u; i < n; ++i) {
const auto& xi = positions(i);
xmin = elementWiseMin(xmin, xi);
xmax = elementWiseMax(xmax, xi);
const auto hi = neighbor.nodeExtent(i).maxElement()/etaMax;
havg += hi;
hmax = std::max(hmax, hi);
}
}
// Find the global result across all processors.
auto box = 0.0;
for (auto i = 0; i != Dimension::nDim; ++i) {
xmin(i) = allReduce(xmin(i), SPHERAL_OP_MIN);
xmax(i) = allReduce(xmax(i), SPHERAL_OP_MAX);
box = std::max(box, xmax(i) - xmin(i));
}
havg = allReduce(havg, SPHERAL_OP_SUM);
ntot = allReduce(ntot, SPHERAL_OP_SUM);
hmax = allReduce(hmax, SPHERAL_OP_MAX);
if (ntot > 0) {
havg /= ntot;
box = std::max(box, maxExtent*hmax);
for (auto i = 0; i < Dimension::nDim; ++i) {
xmin(i) -= box;
xmax(i) += box;
}
// Now initialize the neighbors.
for (auto itr = this->nodeListBegin(); itr != this->nodeListEnd(); ++itr) {
auto& neighbor = (*itr)->neighbor();
neighbor.reinitialize(xmin, xmax, havg);
neighbor.updateNodes();
}
}
}
//------------------------------------------------------------------------------
// Update the connectivity map.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
updateConnectivityMap(const bool computeGhostConnectivity,
const bool computeOverlapConnectivity,
const bool computeIntersectionConnectivity) const {
REQUIRE(mConnectivityMapPtr != 0 and
mConnectivityMapPtr.get() != 0);
mConnectivityMapPtr->rebuild(nodeListBegin(), nodeListEnd(),
computeGhostConnectivity, computeOverlapConnectivity, computeIntersectionConnectivity);
}
//------------------------------------------------------------------------------
// Patch the connectivity map.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
patchConnectivityMap(const FieldList<Dimension, int>& flags,
const FieldList<Dimension, int>& old2new) const {
REQUIRE(mConnectivityMapPtr != 0 and
mConnectivityMapPtr.get() != 0);
mConnectivityMapPtr->patchConnectivity(flags, old2new);
}
//------------------------------------------------------------------------------
// Add a NodeList to this DataBase.
//------------------------------------------------------------------------------
// DEMNodeList
template<typename Dimension>
void
DataBase<Dimension>::
appendNodeList(DEMNodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (haveNodeList(nodeList)) {
cerr << "DataBase::appendNodeList() Warning: attempt to add DEMNodeList "
<< &nodeList << " to DataBase " << this
<< ", which already has it." << endl;
} else {
const NodeListRegistrar<Dimension>& nlr = NodeListRegistrar<Dimension>::instance();
NodeListIterator orderItr = nlr.findInsertionPoint((NodeList<Dimension>*) &nodeList,
nodeListBegin(),
nodeListEnd());
mNodeListPtrs.insert(orderItr, &nodeList);
DEMNodeListIterator DEMOrderItr = nlr.findInsertionPoint(&nodeList,
DEMNodeListBegin(),
DEMNodeListEnd());
const size_t delta = distance(DEMNodeListBegin(), DEMOrderItr);
mDEMNodeListPtrs.insert(DEMOrderItr, &nodeList);
mDEMNodeListAsNodeListPtrs.insert(DEMNodeListAsNodeListBegin() + delta,
&nodeList);
}
ENSURE(valid());
}
// SolidNodeList
template<typename Dimension>
void
DataBase<Dimension>::
appendNodeList(SolidNodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (haveNodeList(nodeList)) {
cerr << "DataBase::appendNodeList() Warning: attempt to add SolidNodeList "
<< &nodeList << " to DataBase " << this
<< ", which already has it." << endl;
} else {
const NodeListRegistrar<Dimension>& nlr = NodeListRegistrar<Dimension>::instance();
NodeListIterator orderItr = nlr.findInsertionPoint((NodeList<Dimension>*) &nodeList,
nodeListBegin(),
nodeListEnd());
mNodeListPtrs.insert(orderItr, &nodeList);
SolidNodeListIterator solidOrderItr = nlr.findInsertionPoint(&nodeList,
solidNodeListBegin(),
solidNodeListEnd());
size_t delta = distance(solidNodeListBegin(), solidOrderItr);
mSolidNodeListPtrs.insert(solidOrderItr, &nodeList);
mSolidNodeListAsNodeListPtrs.insert(solidNodeListAsNodeListBegin() + delta,
&nodeList);
FluidNodeListIterator fluidOrderItr = nlr.findInsertionPoint(&nodeList,
fluidNodeListBegin(),
fluidNodeListEnd());
delta = distance(fluidNodeListBegin(), fluidOrderItr);
mFluidNodeListPtrs.insert(fluidOrderItr, &nodeList);
mFluidNodeListAsNodeListPtrs.insert(fluidNodeListAsNodeListBegin() + delta,
&nodeList);
}
ENSURE(valid());
}
// FluidNodeList
template<typename Dimension>
void
DataBase<Dimension>::
appendNodeList(FluidNodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (haveNodeList(nodeList)) {
cerr << "DataBase::appendNodeList() Warning: attempt to add FluidNodeList "
<< &nodeList << " to DataBase " << this
<< ", which already has it." << endl;
} else {
const NodeListRegistrar<Dimension>& nlr = NodeListRegistrar<Dimension>::instance();
NodeListIterator orderItr = nlr.findInsertionPoint((NodeList<Dimension>*) &nodeList,
nodeListBegin(),
nodeListEnd());
mNodeListPtrs.insert(orderItr, &nodeList);
FluidNodeListIterator fluidOrderItr = nlr.findInsertionPoint(&nodeList,
fluidNodeListBegin(),
fluidNodeListEnd());
const size_t delta = distance(fluidNodeListBegin(), fluidOrderItr);
mFluidNodeListPtrs.insert(fluidOrderItr, &nodeList);
mFluidNodeListAsNodeListPtrs.insert(fluidNodeListAsNodeListBegin() + delta,
&nodeList);
}
ENSURE(valid());
}
// NodeList
template<typename Dimension>
void
DataBase<Dimension>::
appendNodeList(NodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (haveNodeList(nodeList)) {
cerr << "DataBase::appendNodeList() Warning: attempt to add NodeList "
<< &nodeList << " to DataBase " << this
<< ", which already has it." << endl;
} else {
const NodeListRegistrar<Dimension>& nlr = NodeListRegistrar<Dimension>::instance();
NodeListIterator orderItr = nlr.findInsertionPoint(&nodeList,
nodeListBegin(),
nodeListEnd());
mNodeListPtrs.insert(orderItr, &nodeList);
}
ENSURE(valid());
}
//------------------------------------------------------------------------------
// Delete a NodeList from this DataBase.
//------------------------------------------------------------------------------
// DEMNodeList
template<typename Dimension>
void
DataBase<Dimension>::
deleteNodeList(DEMNodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (!haveNodeList(nodeList)) {
cerr << "DataBase::deleteNodeList() Warning: attempt to remove DEMNodeList "
<< &nodeList << " from DataBase " << this
<< ", which does not have it." << endl;
} else {
// Erase from the NodeList vector.
NodeListIterator nodeListItr = find(nodeListBegin(), nodeListEnd(),
&nodeList);
CHECK(nodeListItr != nodeListEnd());
mNodeListPtrs.erase(nodeListItr);
// Erase from the DEMNodeList vector.
DEMNodeListIterator DEMItr = find(DEMNodeListBegin(), DEMNodeListEnd(), &nodeList);
CHECK(DEMItr != DEMNodeListEnd());
mDEMNodeListPtrs.erase(DEMItr);
// Erase from the DEMNodeListAsNodeList vector.
nodeListItr = find(DEMNodeListAsNodeListBegin(),
DEMNodeListAsNodeListEnd(),
&nodeList);
CHECK(nodeListItr != DEMNodeListAsNodeListEnd());
mDEMNodeListAsNodeListPtrs.erase(nodeListItr);
}
ENSURE(valid());
}
// SolidNodeList
template<typename Dimension>
void
DataBase<Dimension>::
deleteNodeList(SolidNodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (!haveNodeList(nodeList)) {
cerr << "DataBase::deleteNodeList() Warning: attempt to remove SolidNodeList "
<< &nodeList << " from DataBase " << this
<< ", which does not have it." << endl;
} else {
// Erase from the NodeList vector.
NodeListIterator nodeListItr = find(nodeListBegin(), nodeListEnd(),
&nodeList);
CHECK(nodeListItr != nodeListEnd());
mNodeListPtrs.erase(nodeListItr);
// Erase from the SolidNodeList vector.
SolidNodeListIterator solidItr = find(solidNodeListBegin(), solidNodeListEnd(), &nodeList);
CHECK(solidItr != solidNodeListEnd());
mSolidNodeListPtrs.erase(solidItr);
// Erase from the SolidNodeListAsNodeList vector.
nodeListItr = find(solidNodeListAsNodeListBegin(),
solidNodeListAsNodeListEnd(),
&nodeList);
CHECK(nodeListItr != solidNodeListAsNodeListEnd());
mSolidNodeListAsNodeListPtrs.erase(nodeListItr);
// Erase from the FluidNodeList vector.
FluidNodeListIterator fluidItr = find(fluidNodeListBegin(), fluidNodeListEnd(), &nodeList);
CHECK(fluidItr != fluidNodeListEnd());
mFluidNodeListPtrs.erase(fluidItr);
// Erase from the FluidNodeListAsNodeList vector.
nodeListItr = find(fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
&nodeList);
CHECK(nodeListItr != fluidNodeListAsNodeListEnd());
mFluidNodeListAsNodeListPtrs.erase(nodeListItr);
}
ENSURE(valid());
}
// FluidNodeList
template<typename Dimension>
void
DataBase<Dimension>::
deleteNodeList(FluidNodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (!haveNodeList(nodeList)) {
cerr << "DataBase::deleteNodeList() Warning: attempt to remove FluidNodeList "
<< &nodeList << " from DataBase " << this
<< ", which does not have it." << endl;
} else {
// Erase from the NodeList vector.
NodeListIterator nodeListItr = find(nodeListBegin(), nodeListEnd(),
&nodeList);
CHECK(nodeListItr != nodeListEnd());
mNodeListPtrs.erase(nodeListItr);
// Erase from the FluidNodeList vector.
FluidNodeListIterator fluidItr = find(fluidNodeListBegin(), fluidNodeListEnd(), &nodeList);
CHECK(fluidItr != fluidNodeListEnd());
mFluidNodeListPtrs.erase(fluidItr);
// Erase from the FluidNodeListAsNodeList vector.
nodeListItr = find(fluidNodeListAsNodeListBegin(),
fluidNodeListAsNodeListEnd(),
&nodeList);
CHECK(nodeListItr != fluidNodeListAsNodeListEnd());
mFluidNodeListAsNodeListPtrs.erase(nodeListItr);
}
ENSURE(valid());
}
// NodeList
template<typename Dimension>
void
DataBase<Dimension>::
deleteNodeList(NodeList<Dimension>& nodeList) {
REQUIRE(valid());
if (!haveNodeList(nodeList)) {
cerr << "DataBase::deleteNodeList() Warning: attempt to remove NodeList "
<< &nodeList << " from DataBase " << this
<< ", which does not have it." << endl;
} else {
// Erase from the NodeList vector.
NodeListIterator nodeListItr = find(nodeListBegin(), nodeListEnd(),
&nodeList);
CHECK(nodeListItr != nodeListEnd());
mNodeListPtrs.erase(nodeListItr);
}
ENSURE(valid());
}
//------------------------------------------------------------------------------
// Test if the given NodeList is registered with this DataBase.
//------------------------------------------------------------------------------
template<typename Dimension>
bool
DataBase<Dimension>::
haveNodeList(const NodeList<Dimension>& nodeList) const {
ConstNodeListIterator itr = find(nodeListBegin(),
nodeListEnd(),
&nodeList);
return itr != nodeListEnd();
}
//------------------------------------------------------------------------------
// Return the const list of NodeList pointers.
//------------------------------------------------------------------------------
template<typename Dimension>
const vector<NodeList<Dimension>*>&
DataBase<Dimension>::nodeListPtrs() const {
return mNodeListPtrs;
}
//------------------------------------------------------------------------------
// Return the const list of FluidNodeList pointers.
//------------------------------------------------------------------------------
template<typename Dimension>
const vector<FluidNodeList<Dimension>*>&
DataBase<Dimension>::fluidNodeListPtrs() const {
return mFluidNodeListPtrs;
}
//------------------------------------------------------------------------------
// Return the const list of SolidNodeList pointers.
//------------------------------------------------------------------------------
template<typename Dimension>
const vector<SolidNodeList<Dimension>*>&
DataBase<Dimension>::solidNodeListPtrs() const {
return mSolidNodeListPtrs;
}
//------------------------------------------------------------------------------
// Return the const list of DEMNodeList pointers.
//------------------------------------------------------------------------------
template<typename Dimension>
const vector<DEMNodeList<Dimension>*>&
DataBase<Dimension>::DEMNodeListPtrs() const {
return mDEMNodeListPtrs;
}
//------------------------------------------------------------------------------
// Set the master neighbor information for the NodeLists.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
setMasterNodeLists(const typename Dimension::Vector& position,
const typename Dimension::SymTensor& H,
std::vector<std::vector<int>>& masterLists,
std::vector<std::vector<int>>& coarseNeighbors,
const bool computeGhostConnectivity) const {
Neighbor<Dimension>::setMasterNeighborGroup(position, H,
nodeListBegin(),
nodeListEnd(),
maxKernelExtent(),
masterLists,
coarseNeighbors,
computeGhostConnectivity);
}
//------------------------------------------------------------------------------
// Set the master neighbor information for the FluidNodeLists.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
setMasterFluidNodeLists(const typename Dimension::Vector& position,
const typename Dimension::SymTensor& H,
std::vector<std::vector<int>>& masterLists,
std::vector<std::vector<int>>& coarseNeighbors,
const bool computeGhostConnectivity) const {
Neighbor<Dimension>::setMasterNeighborGroup(position, H,
fluidNodeListBegin(),
fluidNodeListEnd(),
maxKernelExtent(),
masterLists,
coarseNeighbors,
computeGhostConnectivity);
}
//------------------------------------------------------------------------------
// Set the refine neighbor information for the NodeLists.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
setRefineNodeLists(const typename Dimension::Vector& position,
const typename Dimension::SymTensor& H,
const std::vector<std::vector<int>>& coarseNeighbors,
std::vector<std::vector<int>>& refineNeighbors) const {
REQUIRE(coarseNeighbors.size() == this->numNodeLists());
refineNeighbors = std::vector<std::vector<int>>(this->numNodeLists());
size_t iNodeList = 0;
for (ConstNodeListIterator nodeListItr = nodeListBegin();
nodeListItr < nodeListEnd();
++nodeListItr, ++iNodeList) {
(*nodeListItr)->neighbor().setRefineNeighborList(position, H,
coarseNeighbors[iNodeList],
refineNeighbors[iNodeList]);
}
}
//------------------------------------------------------------------------------
// Set the refine neighbor information for the FluidNodeLists.
//------------------------------------------------------------------------------
template<typename Dimension>
void
DataBase<Dimension>::
setRefineFluidNodeLists(const typename Dimension::Vector& position,
const typename Dimension::SymTensor& H,
const std::vector<std::vector<int>>& coarseNeighbors,
std::vector<std::vector<int>>& refineNeighbors) const {
REQUIRE(coarseNeighbors.size() == this->numFluidNodeLists());
refineNeighbors = std::vector<std::vector<int>>(this->numFluidNodeLists());
size_t iNodeList = 0;
for (ConstFluidNodeListIterator nodeListItr = fluidNodeListBegin();
nodeListItr < fluidNodeListEnd();
++nodeListItr, ++iNodeList) {
(*nodeListItr)->neighbor().setRefineNeighborList(position, H,
coarseNeighbors[iNodeList],
refineNeighbors[iNodeList]);
}
}
//------------------------------------------------------------------------------
// Return the global mass field.
//------------------------------------------------------------------------------
template<typename Dimension>
FieldList<Dimension, typename Dimension::Scalar>
DataBase<Dimension>::globalMass() const {
REQUIRE(valid());
FieldList<Dimension, Scalar> result;
for (ConstNodeListIterator nodeListItr = nodeListBegin();
nodeListItr < nodeListEnd(); ++nodeListItr) {
result.appendField((*nodeListItr)->mass());
}
return result;
}
//------------------------------------------------------------------------------
// Return the global position field.
//------------------------------------------------------------------------------
template<typename Dimension>
FieldList<Dimension, typename Dimension::Vector>
DataBase<Dimension>::globalPosition() const {
REQUIRE(valid());
FieldList<Dimension, Vector> result;
for (ConstNodeListIterator nodeListItr = nodeListBegin();
nodeListItr < nodeListEnd(); ++nodeListItr) {
result.appendField((*nodeListItr)->positions());
}
return result;
}
//------------------------------------------------------------------------------
// Return the global velocity field.
//------------------------------------------------------------------------------
template<typename Dimension>
FieldList<Dimension, typename Dimension::Vector>
DataBase<Dimension>::globalVelocity() const {
REQUIRE(valid());
FieldList<Dimension, Vector> result;