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spatial_cell_cpu.cpp
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spatial_cell_cpu.cpp
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/*
* This file is part of Vlasiator.
* Copyright 2010-2016 Finnish Meteorological Institute
*
* For details of usage, see the COPYING file and read the "Rules of the Road"
* at http://www.physics.helsinki.fi/vlasiator/
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
*/
#include <unordered_set>
#include "spatial_cell_wrapper.hpp"
#include "velocity_blocks.h"
#include "object_wrapper.h"
#ifndef NDEBUG
#define DEBUG_SPATIAL_CELL
#endif
using namespace std;
namespace spatial_cell {
int SpatialCell::activePopID = 0;
uint64_t SpatialCell::mpi_transfer_type = 0;
bool SpatialCell::mpiTransferAtSysBoundaries = false;
bool SpatialCell::mpiTransferInAMRTranslation = false;
int SpatialCell::mpiTransferXYZTranslation = 0;
SpatialCell::SpatialCell() {
// Block list and cache always have room for all blocks
this->sysBoundaryLayer=0; // Default value, layer not yet initialized
for (unsigned int i=0; i<WID3; ++i) null_block_data[i] = 0.0;
// reset spatial cell parameters
for (unsigned int i = 0; i < CellParams::N_SPATIAL_CELL_PARAMS; i++) {
this->parameters[i]=0.0;
}
// reset BVOL derivatives
for (unsigned int i = 0; i < bvolderivatives::N_BVOL_DERIVATIVES; i++) {
this->derivativesBVOL[i]=0;
}
for (unsigned int i = 0; i < MAX_NEIGHBORS_PER_DIM; ++i) {
this->neighbor_number_of_blocks[i] = 0;
this->neighbor_block_data[i] = NULL;
}
//is transferred by default
this->mpiTransferEnabled=true;
// Set correct number of populations
populations.resize(getObjectWrapper().particleSpecies.size());
// Set velocity meshes
for (uint popID=0; popID<populations.size(); ++popID) {
const species::Species& spec = getObjectWrapper().particleSpecies[popID];
populations[popID].vmesh.initialize(spec.velocityMesh);
populations[popID].velocityBlockMinValue = spec.sparseMinValue;
populations[popID].N_blocks = 0;
}
}
/** Adds "important" and removes "unimportant" velocity blocks
* to/from this cell.
*
* velocity_block_with_content_list needs to be up to date in local and remote cells.
* velocity_block_with_no_content_list needs to be up to date in local cells.
*
* update_velocity_block_with_content_lists() should have
* been called with the current distribution function values, and then the contetn list transferred.
*
* Removes all velocity blocks from this spatial cell which don't
* have content and don't have spatial or velocity neighbors with
* content. Adds neighbors for all velocity blocks which do have
* content (including spatial neighbors). All cells in
* spatial_neighbors are assumed to be neighbors of this cell.
*
* This function is thread-safe when called for different cells
* per thread. We need the block_has_content vector from
* neighbouring cells, but these are not written to here. We only
* modify local cell.
*
* NOTE: The VAMR mesh must be valid, otherwise this function will
* remove some blocks that should not be removed.*/
#ifndef VAMR
void SpatialCell::adjust_velocity_blocks(const std::vector<SpatialCell*>& spatial_neighbors,
const uint popID,bool doDeleteEmptyBlocks) {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
// This set contains all those cellids which have neighbors in any
// of the 6-dimensions Actually, we would only need to add
// local blocks with no content here, as blocks with content
// do not need to be created and also will not be removed as
// we only check for removal for blocks with no content
std::unordered_set<vmesh::GlobalID> neighbors_have_content;
//add neighbor content info for velocity space neighbors to map. We loop over blocks
//with content and raise the neighbors_have_content for
//itself, and for all its neighbors
for (vmesh::LocalID block_index=0; block_index<velocity_block_with_content_list.size(); ++block_index) {
vmesh::GlobalID block = velocity_block_with_content_list[block_index];
const uint8_t refLevel=0;
const velocity_block_indices_t indices = SpatialCell::get_velocity_block_indices(popID,block);
neighbors_have_content.insert(block); //also add the cell itself
int addWidthV = getObjectWrapper().particleSpecies[popID].sparseBlockAddWidthV;
for (int offset_vx=-addWidthV;offset_vx<=addWidthV;offset_vx++) {
for (int offset_vy=-addWidthV;offset_vy<=addWidthV;offset_vy++) {
for (int offset_vz=-addWidthV;offset_vz<=addWidthV;offset_vz++) {
const vmesh::GlobalID neighbor_block
= get_velocity_block(popID,{{indices[0]+offset_vx,indices[1]+offset_vy,indices[2]+offset_vz}},refLevel);
neighbors_have_content.insert(neighbor_block); //add all potential ngbrs of this block with content
}
}
}
}
//add neighbor content info for spatial space neighbors to map. We loop over
//neighbor cell lists with existing blocks, and raise the
//flag for the local block with same block id
for (std::vector<SpatialCell*>::const_iterator neighbor=spatial_neighbors.begin();
neighbor != spatial_neighbors.end(); ++neighbor) {
for (vmesh::LocalID block_index=0; block_index<(*neighbor)->velocity_block_with_content_list.size(); ++block_index) {
vmesh::GlobalID block = (*neighbor)->velocity_block_with_content_list[block_index];
neighbors_have_content.insert(block);
}
}
// REMOVE all blocks in this cell without content + without neighbors with content
// better to do it in the reverse order, as then blocks at the
// end are removed first, and we may avoid copying extra data.
if (doDeleteEmptyBlocks) {
for (int block_index= this->velocity_block_with_no_content_list.size()-1; block_index>=0; --block_index) {
const vmesh::GlobalID blockGID = velocity_block_with_no_content_list[block_index];
#ifdef DEBUG_SPATIAL_CELL
if (blockGID == invalid_global_id()) {
cerr << "Got invalid block at " << __FILE__ << ' ' << __LINE__ << endl;
exit(1);
}
#endif
const vmesh::LocalID blockLID = get_velocity_block_local_id(blockGID,popID);
#ifdef DEBUG_SPATIAL_CELL
if (blockLID == invalid_local_id()) {
cerr << "Could not find block in " << __FILE__ << ' ' << __LINE__ << endl;
exit(1);
}
#endif
bool removeBlock = false;
std::unordered_set<vmesh::GlobalID>::iterator it = neighbors_have_content.find(blockGID);
if (it == neighbors_have_content.end()) removeBlock = true;
if (removeBlock == true) {
//No content, and also no neighbor have content -> remove
//and increment rho loss counters
const Real* block_parameters = get_block_parameters(popID)+blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS;
const Real DV3 = block_parameters[BlockParams::DVX]
* block_parameters[BlockParams::DVY]
* block_parameters[BlockParams::DVZ];
Real sum=0;
for (unsigned int i=0; i<WID3; ++i) sum += get_data(popID)[blockLID*SIZE_VELBLOCK+i];
this->populations[popID].RHOLOSSADJUST += DV3*sum;
// and finally remove block
this->remove_velocity_block(blockGID,popID);
}
}
}
// ADD all blocks with neighbors in spatial or velocity space (if it exists then the block is unchanged)
for (std::unordered_set<vmesh::GlobalID>::iterator it=neighbors_have_content.begin(); it != neighbors_have_content.end(); ++it) {
this->add_velocity_block(*it,popID);
}
}
#else // VAMR version
void SpatialCell::adjust_velocity_blocks(const std::vector<SpatialCell*>& spatial_neighbors,
const uint popID,bool doDeleteEmptyBlocks) {
// This set contains all those cell ids which have neighbors in any
// of the 6-dimensions Actually, we would only need to add
// local blocks with no content here, as blocks with content
// do not need to be created and also will not be removed as
// we only check for removal for blocks with no content
std::unordered_set<vmesh::GlobalID> neighbors_have_content;
for (vmesh::LocalID block_index=0; block_index<velocity_block_with_content_list.size(); ++block_index) {
vmesh::GlobalID blockGID = velocity_block_with_content_list[block_index];
vector<vmesh::GlobalID> neighborGIDs;
populations[popID].vmesh.getNeighborsExistingAtSameLevel(blockGID,neighborGIDs);
neighbors_have_content.insert(neighborGIDs.begin(),neighborGIDs.end());
neighbors_have_content.insert(blockGID);
}
//add neighbor content info for spatial space neighbors to map. We loop over
//neighbor cell lists with existing blocks, and raise the
//flag for the local block with same block id
unordered_set<vmesh::GlobalID> spat_nbr_has_content;
for (std::vector<SpatialCell*>::const_iterator neighbor=spatial_neighbors.begin();
neighbor != spatial_neighbors.end(); ++neighbor) {
for (vmesh::LocalID block_index=0; block_index<(*neighbor)->velocity_block_with_content_list.size(); ++block_index) {
vmesh::GlobalID block = (*neighbor)->velocity_block_with_content_list[block_index];
spat_nbr_has_content.insert(block);
}
}
// REMOVE all blocks in this cell without content + without neighbors with content
// better to do it in the reverse order, as then blocks at the
// end are removed first, and we may avoid copying extra data.
if (doDeleteEmptyBlocks) {
for (int block_index= this->velocity_block_with_no_content_list.size()-1; block_index>=0; --block_index) {
const vmesh::GlobalID blockGID = this->velocity_block_with_no_content_list[block_index];
#ifdef DEBUG_SPATIAL_CELL
if (blockGID == invalid_global_id()) {
cerr << "Got invalid block at " << __FILE__ << ' ' << __LINE__ << endl;
exit(1);
}
#endif
const vmesh::LocalID blockLID = get_velocity_block_local_id(blockGID,popID);
#ifdef DEBUG_SPATIAL_CELL
if (blockLID == invalid_local_id()) {
cerr << "Could not find block in " << __FILE__ << ' ' << __LINE__ << endl;
exit(1);
}
#endif
bool removeBlock = false;
// Check this block in the neighbor cells
if (neighbors_have_content.find(blockGID) != neighbors_have_content.end()) continue;
// Check the parent of this block in the neighbor cells
if (neighbors_have_content.find(populations[popID].vmesh.getParent(blockGID)) != neighbors_have_content.end()) continue;
// Check all the children of this block in the neighbor cells
std::vector<vmesh::GlobalID> children;
populations[popID].vmesh.getChildren(blockGID,children);
int counter = 0;
for (size_t c=0; c<children.size(); ++c) {
if (neighbors_have_content.find(children[c]) != neighbors_have_content.end()) ++counter;
}
if (counter > 0) continue;
// It is safe to remove this block
removeBlock = true;
if (removeBlock == true) {
//No content, and also no neighbor have content -> remove
//and increment rho loss counters
const Real* block_parameters = get_block_parameters(popID)+blockLID*BlockParams::N_VELOCITY_BLOCK_PARAMS;
const Real DV3 = block_parameters[BlockParams::DVX]
* block_parameters[BlockParams::DVY]
* block_parameters[BlockParams::DVZ];
Real sum=0;
for (unsigned int i=0; i<WID3; ++i) sum += get_data(popID)[blockLID*SIZE_VELBLOCK+i];
this->populations[popID].RHOLOSSADJUST += DV3*sum;
// and finally remove block
this->remove_velocity_block(blockGID,popID);
}
}
}
// Filter the spat_nbr_has_content list so that it doesn't
// contain overlapping blocks
unordered_set<vmesh::GlobalID> ghostBlockList;
vector<vector<vmesh::GlobalID> > sorted(populations[popID].vmesh.getMaxAllowedRefinementLevel()+1);
// First sort the list according to refinement levels. This allows
// us to skip checking the existence of children and grandchildren below.
for (unordered_set<vmesh::GlobalID>::const_iterator it=spat_nbr_has_content.begin();
it!=spat_nbr_has_content.end(); ++it) {
sorted[populations[popID].vmesh.getRefinementLevel(*it)].push_back(*it);
}
// Iterate through the sorted block list, and determine the no-content
// blocks and their correct refinement levels that must exist
for (int r=sorted.size()-1; r >= 0; --r) {
for (size_t b=0; b<sorted[r].size(); ++b) {
// If parent exists, all siblings must exist
if (r > 0) {
if (spat_nbr_has_content.find(populations[popID].vmesh.getParent(sorted[r][b])) != spat_nbr_has_content.end()) {
vector<vmesh::GlobalID> siblings;
populations[popID].vmesh.getSiblings(sorted[r][b],siblings);
ghostBlockList.insert(siblings.begin(),siblings.end());
continue;
}
}
// If grandparent exists, parent octant must exist
if (r > 1) {
vmesh::GlobalID grandParentGID = populations[popID].vmesh.getParent(populations[popID].vmesh.getParent(sorted[r][b]));
if (spat_nbr_has_content.find(grandParentGID) != spat_nbr_has_content.end()) {
vector<vmesh::GlobalID> siblings;
populations[popID].vmesh.getSiblings(populations[popID].vmesh.getParent(sorted[r][b]),siblings);
ghostBlockList.insert(siblings.begin(),siblings.end());
continue;
}
}
// Parent or grandparent does not exist, add this block
ghostBlockList.insert(sorted[r][b]);
}
}
// Add missing no-content blocks
for (unordered_set<vmesh::GlobalID>::const_iterator it=ghostBlockList.begin();
it != ghostBlockList.end(); ++it) {
// Parent already exists
if (populations[popID].vmesh.getLocalID(populations[popID].vmesh.getParent(*it)) != vmesh::VelocityMesh<vmesh::GlobalID,vmesh::LocalID>::invalidLocalID()) continue;
// If any children exist, make sure they all exist
std::vector<vmesh::GlobalID> children;
populations[popID].vmesh.getChildren(*it,children);
bool childrensExist = false;
for (size_t c=0; c<children.size(); ++c) {
if (populations[popID].vmesh.getLocalID(children[c]) != vmesh::VelocityMesh<vmesh::GlobalID,vmesh::LocalID>::invalidLocalID()) {
childrensExist = true;
break;
}
}
if (childrensExist == true) {
// Attempt to add all children, only succeeds if the
// children does not exist
for (size_t c=0; c<children.size(); ++c) add_velocity_block(children[c],popID);
continue;
}
add_velocity_block(*it,popID);
}
}
#endif
void SpatialCell::adjustSingleCellVelocityBlocks(const uint popID, bool doDeleteEmpty) {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
//neighbor_ptrs is empty as we do not have any consistent
//data in neighbours yet, adjustments done only based on velocity
//space. TODO: should this delete blocks or not? Now not
std::vector<SpatialCell*> neighbor_ptrs;
update_velocity_block_content_lists(popID);
adjust_velocity_blocks(neighbor_ptrs,popID,doDeleteEmpty);
}
void SpatialCell::coarsen_block(const vmesh::GlobalID& parent,const std::vector<vmesh::GlobalID>& children,const uint popID) {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
// First create the parent (coarse) block and grab pointer to its data.
// add_velocity_block initializes data to zero values.
if (add_velocity_block(parent,popID) == false) return;
vmesh::LocalID parentLID = populations[popID].vmesh.getLocalID(parent);
Realf* parent_data = get_data(popID)+parentLID*SIZE_VELBLOCK;
// Calculate children (fine) block local IDs, some of the children may not exist
for (size_t c=0; c<children.size(); ++c) {
vmesh::LocalID childrenLID = populations[popID].vmesh.getLocalID(children[c]);
if (childrenLID == SpatialCell::invalid_local_id()) continue;
Realf* data = get_data(popID)+childrenLID*SIZE_VELBLOCK;
const int i_oct = c % 2;
const int j_oct = (c/2) % 2;
const int k_oct = c / 4;
/*for (int k=0; k<WID; k+=2) for (int j=0; j<WID; j+=2) for (int i=0; i<WID; i+=2) {
cerr << "\t" << i_oct*2+i/2 << ' ' << j_oct*2+j/2 << ' ' << k_oct*2+k/2 << " gets values from" << endl;
// Sum the values in 8 cells that correspond to the same call in parent block
Realf sum = 0;
for (int kk=0; kk<2; ++kk) for (int jj=0; jj<2; ++jj) for (int ii=0; ii<2; ++ii) {
cerr << "\t\t" << i+ii << ' ' << j+jj << ' ' << k+kk << endl;
sum += data[vblock::index(i+ii,j+jj,k+kk)];
}
parent_data[vblock::index(i_oct*2+i/2,j_oct*2+j/2,k_oct*2+k/2)] = sum/8;
}*/
for (uint k=0; k<WID; ++k) for (uint j=0; j<WID; ++j) for (uint i=0; i<WID; ++i) {
parent_data[vblock::index(i_oct*2+i/2,j_oct*2+j/2,k_oct*2+k/2)] += data[vblock::index(i,j,k)]/8.0;
}
}
// Remove the children
for (size_t c=0; c<children.size(); ++c) {
remove_velocity_block(children[c],popID);
}
}
void SpatialCell::coarsen_blocks(vamr_ref_criteria::Base* refCriterion,const uint popID) {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
// Sort blocks according to their refinement levels
vector<vector<vmesh::GlobalID> > blocks(populations[popID].vmesh.getMaxAllowedRefinementLevel()+1);
for (vmesh::LocalID blockLID=0; blockLID<get_number_of_velocity_blocks(popID); ++blockLID) {
vmesh::GlobalID blockGID = populations[popID].vmesh.getGlobalID(blockLID);
uint8_t r = populations[popID].vmesh.getRefinementLevel(blockGID);
blocks[r].push_back(blockGID);
}
// This is how much neighbor data we use when evaluating refinement criteria
const int PAD=1;
Realf array[(WID+2*PAD)*(WID+2*PAD)*(WID+2*PAD)];
// Evaluate refinement criterion for velocity blocks, starting from
// the highest refinement level blocks
for (size_t r=blocks.size()-1; r>=1; --r) {
// List of blocks that can be coarsened
//vector<vmesh::GlobalID> coarsenList;
unordered_set<vmesh::GlobalID> coarsenList;
// Evaluate refinement criterion for all blocks
for (size_t b=0; b<blocks[r].size(); ++b) {
const vmesh::GlobalID blockGID = blocks[r][b];
fetch_data<1>(blockGID,populations[popID].vmesh,get_data(popID),array);
if (refCriterion->evaluate(array,popID) < Parameters::vamrCoarsenLimit) coarsenList.insert(blockGID);
}
// List of blocks created and removed during the coarsening. The first element (=key)
// is the global ID of the parent block that is created, the vector (=value) contains
// the global IDs of the children that will be removed
unordered_map<vmesh::GlobalID,vector<vmesh::GlobalID> > allowCoarsen;
// A block can refined only if all blocks in the octant allow it,
// and only if the octant (in which the block belongs to) neighbors
// do not have children
for (unordered_set<vmesh::GlobalID>::const_iterator it=coarsenList.begin(); it!=coarsenList.end(); ++it) {
vector<vmesh::GlobalID> siblings;
populations[popID].vmesh.getSiblings(*it,siblings);
bool allows=true;
for (size_t s=0; s<siblings.size(); ++s) {
// Skip non-existing blocks
if (populations[popID].vmesh.getLocalID(siblings[s]) == invalid_local_id()) {
continue;
}
// Check that the sibling allows coarsening
if (coarsenList.find(siblings[s]) == coarsenList.end()) {
allows = false;
break;
}
}
// Check that the mesh structure allows coarsening
if (populations[popID].vmesh.coarsenAllowed(*it) == false) continue;
// If all siblings allow coarsening, add block to coarsen list
if (allows == true) {
allowCoarsen.insert(make_pair(populations[popID].vmesh.getParent(*it),siblings));
}
}
cerr << "ref level " << r << " has " << allowCoarsen.size() << " blocks for coarsening" << endl;
for (unordered_map<vmesh::GlobalID,vector<vmesh::GlobalID> >::const_iterator it=allowCoarsen.begin(); it!=allowCoarsen.end(); ++it) {
coarsen_block(it->first,it->second,popID);
}
}
}
/*!
Returns true if given velocity block has enough of a distribution function.
Returns false if the value of the distribution function is too low in every
sense in given block.
Also returns false if given block doesn't exist or is an error block.
*/
bool SpatialCell::compute_block_has_content(const vmesh::GlobalID& blockGID,const uint popID) const {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
if (blockGID == invalid_global_id()) return false;
const vmesh::LocalID blockLID = get_velocity_block_local_id(blockGID,popID);
if (blockLID == invalid_local_id()) return false;
bool has_content = false;
const Real velocity_block_min_value = getVelocityBlockMinValue(popID);
const Realf* block_data = populations[popID].blockContainer.getData(blockLID);
for (unsigned int i=0; i<VELOCITY_BLOCK_LENGTH; ++i) {
if (block_data[i] >= velocity_block_min_value) {
has_content = true;
break;
}
}
return has_content;
}
/** Get maximum translation timestep for the given species.
* @param popID ID of the particle species.
* @return Maximum timestep calculated by the Vlasov translation.*/
const Real& SpatialCell::get_max_r_dt(const uint popID) const {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
return populations[popID].max_dt[species::MAXRDT];
}
/** Get maximum acceleration timestep for the given species.
* @param popID ID of the particle species.
* @return Maximum timestep calculated by Vlasov acceleration.*/
const Real& SpatialCell::get_max_v_dt(const uint popID) const {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
return populations[popID].max_dt[species::MAXVDT];
}
/** Get MPI datatype for sending the cell data.
* @param cellID Spatial cell (dccrg) ID.
* @param sender_rank Rank of the MPI process sending data from this cell.
* @param receiver_rank Rank of the MPI process receiving data to this cell.
* @param receiving If true, this process is receiving data.
* @param neighborhood Neighborhood ID.
* @return MPI datatype that transfers the requested data.*/
std::tuple<void*, int, MPI_Datatype> SpatialCell::get_mpi_datatype(
const CellID cellID,
const int sender_rank,
const int receiver_rank,
const bool receiving,
const int neighborhood
) {
std::vector<MPI_Aint> displacements;
std::vector<int> block_lengths;
// create datatype for actual data if we are in the first two
// layers around a boundary, or if we send for the whole system
// in AMR translation, only send the necessary cells
if (this->mpiTransferEnabled && ((SpatialCell::mpiTransferAtSysBoundaries==false && SpatialCell::mpiTransferInAMRTranslation==false) ||
(SpatialCell::mpiTransferAtSysBoundaries==true && (this->sysBoundaryLayer ==1 || this->sysBoundaryLayer ==2)) ||
(SpatialCell::mpiTransferInAMRTranslation==true &&
this->parameters[CellParams::AMR_TRANSLATE_COMM_X+SpatialCell::mpiTransferXYZTranslation]==true ))) {
//add data to send/recv to displacement and block length lists
if ((SpatialCell::mpi_transfer_type & Transfer::VEL_BLOCK_LIST_STAGE1) != 0) {
//first copy values in case this is the send operation
populations[activePopID].N_blocks = populations[activePopID].blockContainer.size();
// send velocity block list size
displacements.push_back((uint8_t*) &(populations[activePopID].N_blocks) - (uint8_t*) this);
block_lengths.push_back(sizeof(vmesh::LocalID));
}
if ((SpatialCell::mpi_transfer_type & Transfer::VEL_BLOCK_LIST_STAGE2) != 0) {
// STAGE1 should have been done, otherwise we have problems...
if (receiving) {
//mpi_number_of_blocks transferred earlier
populations[activePopID].vmesh.setNewSize(populations[activePopID].N_blocks);
} else {
//resize to correct size (it will avoid reallocation if it is big enough, I assume)
populations[activePopID].N_blocks = populations[activePopID].blockContainer.size();
}
// send velocity block list
displacements.push_back((uint8_t*) &(populations[activePopID].vmesh.getGrid()[0]) - (uint8_t*) this);
block_lengths.push_back(sizeof(vmesh::GlobalID) * populations[activePopID].vmesh.size());
}
if ((SpatialCell::mpi_transfer_type & Transfer::VEL_BLOCK_WITH_CONTENT_STAGE1) !=0) {
//Communicate size of list so that buffers can be allocated on receiving side
if (!receiving) this->velocity_block_with_content_list_size = this->velocity_block_with_content_list.size();
displacements.push_back((uint8_t*) &(this->velocity_block_with_content_list_size) - (uint8_t*) this);
block_lengths.push_back(sizeof(vmesh::LocalID));
}
if ((SpatialCell::mpi_transfer_type & Transfer::VEL_BLOCK_WITH_CONTENT_STAGE2) !=0) {
if (receiving) {
this->velocity_block_with_content_list.resize(this->velocity_block_with_content_list_size);
}
//velocity_block_with_content_list_size should first be updated, before this can be done (STAGE1)
displacements.push_back((uint8_t*) &(this->velocity_block_with_content_list[0]) - (uint8_t*) this);
block_lengths.push_back(sizeof(vmesh::GlobalID)*this->velocity_block_with_content_list_size);
}
if ((SpatialCell::mpi_transfer_type & Transfer::VEL_BLOCK_DATA) !=0) {
displacements.push_back((uint8_t*) get_data(activePopID) - (uint8_t*) this);
block_lengths.push_back(sizeof(Realf) * VELOCITY_BLOCK_LENGTH * populations[activePopID].blockContainer.size());
}
if ((SpatialCell::mpi_transfer_type & Transfer::NEIGHBOR_VEL_BLOCK_DATA) != 0) {
/*We are actually transferring the data of a
* neighbor. The values of neighbor_block_data
* and neighbor_number_of_blocks should be set in
* solver.*/
// Send this data only to ranks that contain face neighbors
// this->neighbor_number_of_blocks has been initialized to 0, on other ranks it can stay that way.
const set<int>& ranks = this->face_neighbor_ranks[neighborhood];
if ( P::amrMaxSpatialRefLevel == 0 || receiving || ranks.find(receiver_rank) != ranks.end()) {
for ( int i = 0; i < MAX_NEIGHBORS_PER_DIM; ++i) {
displacements.push_back((uint8_t*) this->neighbor_block_data[i] - (uint8_t*) this);
block_lengths.push_back(sizeof(Realf) * VELOCITY_BLOCK_LENGTH * this->neighbor_number_of_blocks[i]);
}
}
}
// send spatial cell parameters
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_PARAMETERS)!=0){
displacements.push_back((uint8_t*) &(this->parameters[0]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * CellParams::N_SPATIAL_CELL_PARAMS);
}
// send spatial cell dimensions and coordinates
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_DIMENSIONS)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::XCRD]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 6);
}
// send BGBXVOL BGBYVOL BGBZVOL PERBXVOL PERBYVOL PERBZVOL
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_BVOL)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::BGBXVOL]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 6);
}
// send RHOM, VX, VY, VZ
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_RHOM_V)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::RHOM]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 4);
}
// send RHOM_DT2, VX_DT2, VY_DT2, VZ_DT2
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_RHOMDT2_VDT2)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::RHOM_DT2]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 4);
}
// send RHOQ
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_RHOQ)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::RHOQ]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real));
}
// send RHOQ_DT2
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_RHOQDT2)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::RHOQ_DT2]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real));
}
// send spatial cell BVOL derivatives
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_BVOL_DERIVATIVES)!=0){
displacements.push_back((uint8_t*) &(this->derivativesBVOL[0]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * bvolderivatives::N_BVOL_DERIVATIVES);
}
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_IOLOCALCELLID)!=0){
displacements.push_back((uint8_t*) &(this->ioLocalCellId) - (uint8_t*) this);
block_lengths.push_back(sizeof(uint64_t));
}
// send electron pressure gradient term components
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_GRADPE_TERM)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::EXGRADPE]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 3);
}
// send P tensor diagonal components
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_P)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::P_11]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 3);
}
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_PDT2)!=0){
displacements.push_back((uint8_t*) &(this->parameters[CellParams::P_11_DT2]) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * 3);
}
// send sysBoundaryFlag
if ((SpatialCell::mpi_transfer_type & Transfer::CELL_SYSBOUNDARYFLAG)!=0){
displacements.push_back((uint8_t*) &(this->sysBoundaryFlag) - (uint8_t*) this);
block_lengths.push_back(sizeof(uint));
displacements.push_back((uint8_t*) &(this->sysBoundaryLayer) - (uint8_t*) this);
block_lengths.push_back(sizeof(uint));
}
if ((SpatialCell::mpi_transfer_type & Transfer::VEL_BLOCK_PARAMETERS) !=0) {
displacements.push_back((uint8_t*) get_block_parameters(activePopID) - (uint8_t*) this);
block_lengths.push_back(sizeof(Real) * size(activePopID) * BlockParams::N_VELOCITY_BLOCK_PARAMS);
}
// Copy particle species metadata
if ((SpatialCell::mpi_transfer_type & Transfer::POP_METADATA) != 0) {
for (uint popID=0; popID<populations.size(); ++popID) {
displacements.push_back((uint8_t*) &(populations[popID].RHO) - (uint8_t*)this);
block_lengths.push_back(offsetof(spatial_cell::Population, N_blocks));
}
}
// Refinement parameters
if ((SpatialCell::mpi_transfer_type & Transfer::REFINEMENT_PARAMETERS)){
displacements.push_back(reinterpret_cast<uint8_t*>(this->parameters.data() + CellParams::AMR_ALPHA1) - reinterpret_cast<uint8_t*>(this));
block_lengths.push_back(sizeof(Real) * (CellParams::AMR_ALPHA2 - CellParams::AMR_ALPHA1 + 1)); // This is just 2, but let's be explicit
}
// Copy random number generator state variables
//if ((SpatialCell::mpi_transfer_type & Transfer::RANDOMGEN) != 0) {
// displacements.push_back((uint8_t*)get_rng_state_buffer() - (uint8_t*)this);
// block_lengths.push_back(256/8);
// displacements.push_back((uint8_t*)get_rng_data_buffer() - (uint8_t*)this);
// block_lengths.push_back(sizeof(random_data));
//}
}
void* address = this;
int count;
MPI_Datatype datatype;
if (displacements.size() > 0) {
count = 1;
MPI_Type_create_hindexed(
displacements.size(),
&block_lengths[0],
&displacements[0],
MPI_BYTE,
&datatype
);
} else {
count = 0;
datatype = MPI_BYTE;
}
const bool printMpiDatatype = false;
if(printMpiDatatype) {
int mpiSize;
int myRank;
MPI_Type_size(datatype,&mpiSize);
MPI_Comm_rank(MPI_COMM_WORLD,&myRank);
cout << myRank << " get_mpi_datatype: " << cellID << " " << sender_rank << " " << receiver_rank << " " << mpiSize << ", Nblocks = " << populations[activePopID].N_blocks << ", nbr Nblocks =";
for (uint i = 0; i < MAX_NEIGHBORS_PER_DIM; ++i) {
const set<int>& ranks = this->face_neighbor_ranks[neighborhood];
if ( receiving || ranks.find(receiver_rank) != ranks.end()) {
cout << " " << this->neighbor_number_of_blocks[i];
} else {
cout << " " << 0;
}
}
cout << " face_neighbor_ranks =";
for (const auto& rank : this->face_neighbor_ranks[neighborhood]) {
cout << " " << rank;
}
cout << endl;
}
return std::make_tuple(address,count,datatype);
}
/** Get random number generator data buffer.
* @return Random number generator data buffer.*/
//random_data* SpatialCell::get_rng_data_buffer() {
// return &rngDataBuffer;
//}
/** Get random number generator state buffer.
* @return Random number generator state buffer.*/
//char* SpatialCell::get_rng_state_buffer() {
// return rngStateBuffer;
//}
/**< Minimum value of distribution function in any phase space cell
* of a velocity block for the block to be considered to have content.
* @param popID ID of the particle species.
* @return Sparse min value for this species.*/
Real SpatialCell::getVelocityBlockMinValue(const uint popID) const {
return populations[popID].velocityBlockMinValue;
}
void SpatialCell::merge_values_recursive(const uint popID,vmesh::GlobalID parentGID,vmesh::GlobalID blockGID,
uint8_t refLevel,bool recursive,const Realf* data,
std::set<vmesh::GlobalID>& blockRemovalList) {
#ifdef DEBUG_SPATIAL_CELL
if (blockGID == invalid_global_id()) {
cerr << "merge_values_recursive called for GID=" << blockGID << " at r=" << (int)refLevel << " parent=" << parentGID << endl;
}
#endif
// Get all possible children:
vector<vmesh::GlobalID> childrenGIDs;
populations[popID].vmesh.getChildren(blockGID,childrenGIDs);
#ifdef VAMR
#warning FIXME activePopID is not correct here (VAMR, hence TBD)
#endif
// Check if any of block's children exist:
bool hasChildren = false;
for (size_t c=0; c<childrenGIDs.size(); ++c) {
if (populations[activePopID].vmesh.getLocalID(childrenGIDs[c]) != invalid_local_id()) {
hasChildren = true;
break;
}
}
/* // TEST
for (size_t c=0; c<childrenGIDs.size(); ++c) {
bool hasGrandChildren=false;
vector<vmesh::GlobalID> grandChildren;
if (vmesh.getLocalID(childrenGIDs[c]) != vmesh.invalidLocalID()) continue;
vmesh::VelocityMesh<vmesh::GlobalID,vmesh::LocalID>::getChildren(childrenGIDs[c],grandChildren);
for (size_t cc=0; cc<grandChildren.size(); ++cc) {
if (vmesh.getLocalID(grandChildren[cc]) != vmesh.invalidLocalID()) {
hasGrandChildren = true;
break;
}
}
if (hasGrandChildren==true) {
std::cerr << "block at r=" << (int)refLevel << " has lost grand children" << std::endl;
}
}
// END TEST */
// No children, try to merge values to this block:
if (hasChildren == false) {
vmesh::LocalID blockLID = populations[activePopID].vmesh.getLocalID(blockGID);
#ifdef DEBUG_SPATIAL_CELL
if (blockLID == invalid_local_id()) {
cerr << "ERROR: Failed to merge values, block does not exist!" << endl;
cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << endl;
exit(1);
}
#endif
Realf* myData = populations[activePopID].blockContainer.getData(blockLID);
if (parentGID == blockGID) {
// If we enter here, the block is at the lowest refinement level.
// If the block does not have enough content, flag it for removal
//#warning REMOVED for debugging
/*for (unsigned int i=0; i<WID3; ++i) {
if (myData[i] >= SpatialCell::velocity_block_min_value) return;
}
blockRemovalList.insert(blockGID);*/
} else {
// Merge values to this block
for (uint i=0; i<WID3; ++i) myData[i] += data[i];
}
return;
}
// Iterate over all octants, each octant corresponds to a different child:
for (int k_oct=0; k_oct<2; ++k_oct) for (int j_oct=0; j_oct<2; ++j_oct) for (int i_oct=0; i_oct<2; ++i_oct) {
// Copy data belonging to the octant to a temporary array:
Realf array[WID3];
for (uint k=0; k<WID; ++k) for (uint j=0; j<WID; ++j) for (uint i=0; i<WID; ++i) {
array[vblock::index(i,j,k)] = data[vblock::index(i_oct*2+i/2,j_oct*2+j/2,k_oct*2+k/2)];
}
// Send the data to the child:
const int octant = k_oct*4 + j_oct*2 + i_oct;
merge_values_recursive(popID,blockGID,childrenGIDs[octant],refLevel+1,true,array,blockRemovalList);
}
// Data merged to children, block can be removed
blockRemovalList.insert(blockGID);
}
void SpatialCell::merge_values(const uint popID) {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
const uint8_t maxRefLevel = populations[popID].vmesh.getMaxAllowedRefinementLevel();
for (uint i=0; i<WID3; ++i) null_block_data[i] = 0;
// Sort blocks according to their refinement levels:
vector<vector<vmesh::GlobalID> > blocks(maxRefLevel+1);
for (vmesh::LocalID blockLID=0; blockLID<get_number_of_velocity_blocks(popID); ++blockLID) {
const vmesh::GlobalID blockGID = populations[popID].vmesh.getGlobalID(blockLID);
if (blockGID == SpatialCell::invalid_global_id()) {
cerr << "got invalid global id from mesh!" << endl;
continue;
}
uint8_t refLevel = populations[popID].vmesh.getRefinementLevel(blockGID);
blocks[refLevel].push_back(blockGID);
}
set<vmesh::GlobalID> blockRemovalList;
for (uint8_t refLevel=0; refLevel<blocks.size()-1; ++refLevel) {
for (size_t b=0; b<blocks[refLevel].size(); ++b) {
const vmesh::GlobalID blockGID = blocks[refLevel][b];
const vmesh::LocalID blockLID = populations[popID].vmesh.getLocalID(blockGID);
if (blockLID == invalid_local_id()) continue;
const Realf* data = populations[popID].blockContainer.getData(blockLID);
merge_values_recursive(popID,blockGID,blockGID,refLevel,true,data,blockRemovalList);
}
}
cerr << "should remove " << blockRemovalList.size() << " blocks" << endl;
for (set<vmesh::GlobalID>::const_iterator it=blockRemovalList.begin(); it!=blockRemovalList.end(); ++it) {
//remove_velocity_block(*it);
}
}
void SpatialCell::add_values(const vmesh::GlobalID& targetGID,
std::unordered_map<vmesh::GlobalID,Realf[(WID+2)*(WID+2)*(WID+2)]>& sourceData,
const uint popID) {
#ifdef DEBUG_SPATIAL_CELL
if (popID >= populations.size()) {
std::cerr << "ERROR, popID " << popID << " exceeds populations.size() " << populations.size() << " in ";
std::cerr << __FILE__ << ":" << __LINE__ << std::endl;
exit(1);
}
#endif
vmesh::LocalID targetLID = get_velocity_block_local_id(targetGID,popID);
if (targetLID == SpatialCell::invalid_local_id()) {
std::cerr << "error has occurred" << std::endl;
return;
}
Realf* targetData = get_data(popID)+targetLID*SIZE_VELBLOCK;
// Add data from all same level blocks
vector<vmesh::GlobalID> neighborIDs;
populations[popID].vmesh.getNeighborsAtSameLevel(targetGID,neighborIDs);
std::unordered_map<vmesh::GlobalID,Realf[(WID+2)*(WID+2)*(WID+2)]>::iterator it;
it = sourceData.find(neighborIDs[vblock::nbrIndex( 0, 0, 0)]); // This block
if (it != sourceData.end()) {
Realf* source = it->second;
for (uint k=0; k<WID; ++k) for (uint j=0; j<WID; ++j) for (uint i=0; i<WID; ++i) {
targetData[vblock::index(i,j,k)] += source[vblock::padIndex<1>(i+1,j+1,k+1)];
}
}
// ***** face neighbors ***** //
for (int i_off=-1; i_off<2; i_off+=2) {
it = sourceData.find(neighborIDs[vblock::nbrIndex(i_off,0,0)]);
if (it == sourceData.end()) continue;
uint i_trgt = 0;
uint i_src = WID+1;
if (i_off > 0) {i_trgt = WID-1; i_src=0;}
Realf* source = it->second;
for (uint k=0; k<WID; ++k) for (uint j=0; j<WID; ++j) {
targetData[vblock::index(i_trgt,j,k)] += source[vblock::padIndex<1>(i_src,j+1,k+1)];
}
}