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velocity_mesh_amr.h
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velocity_mesh_amr.h
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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.
*/
#ifndef VELOCITY_MESH_AMR_H
#define VELOCITY_MESH_AMR_H
#include <iostream>
#include <stdint.h>
#include <vector>
#include <map>
#include <unordered_map>
#include <set>
#include <cmath>
#include <algorithm>
#ifndef NDEBUG
#define DEBUG_VAMR_MESH
#endif
#include "velocity_mesh_parameters.h"
namespace vmesh {
template<typename GID,typename LID>
class VelocityMesh {
public:
//VelocityMesh();
//~VelocityMesh();
size_t capacityInBytes() const;
bool check() const;
void clear();
bool coarsenAllowed(const GID& globalID) const;
bool copy(const LID& sourceLocalID,const LID& targetLocalID);
size_t count(const GID& globalID) const;
GID findBlockDown(uint8_t& refLevel,GID cellIndices[3]) const;
GID findBlock(uint8_t& refLevel,GID cellIndices[3]) const;
bool getBlockCoordinates(const GID& globalID,Real coords[3]) const;
void getBlockInfo(const GID& globalID,Real* array) const;
const Real* getBlockSize(const uint8_t& refLevel) const;
bool getBlockSize(const GID& globalID,Real size[3]) const;
const Real* getCellSize(const uint8_t& refLevel) const;
bool getCellSize(const GID& globalID,Real size[3]) const;
void getChildren(const GID& globalID,std::vector<GID>& children) const;
GID getGlobalID(const LID& localID) const;
GID getGlobalID(const uint8_t& refLevel,const Real* coords) const;
GID getGlobalID(const uint8_t& refLevel,LID indices[3]) const;
GID getGlobalID(const uint32_t& refLevel,const LID& i,const LID& j,const LID& k) const;
GID getGlobalIndexOffset(const uint8_t& refLevel) const;
std::vector<GID>& getGrid();
const LID* getGridLength(const uint8_t& refLevel) const;
void getIndices(const GID& globalID,uint8_t& refLevel,LID& i,LID& j,LID& k) const;
LID getLocalID(const GID& globalID) const;
uint8_t getMaxAllowedRefinementLevel() const;
GID getMaxVelocityBlocks() const;
size_t getMesh() const;
const Real* getMeshMaxLimits() const;
const Real* getMeshMinLimits() const;
void getNeighborsAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs) const;
void getNeighborsExistingAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs) const;
void getNeighborsExistingAtOffset(const GID& globalID,const int& i,const int& j,const int& k,std::vector<LID>& neighborLIDs,int32_t& refLevelDifference) const;
int getOctant(const GID& globalID) const;
GID getParent(const GID& globalID) const;
uint8_t getRefinementLevel(const GID& globalID) const;
void getSiblingNeighbors(const GID& globalID,std::vector<GID>& nbrs) const;
void getSiblings(const GID& globalID,std::vector<GID>& siblings) const;
bool hasChildren(const GID& globalID) const;
GID hasGrandParent(const GID& globalID) const;
bool initialize(const size_t& meshID,std::vector<vmesh::MeshParameters>& meshParameters);
bool initialize(const size_t& meshID);
static LID invalidBlockIndex();
static GID invalidGlobalID();
static LID invalidLocalID();
bool isInitialized() const;
void pop();
bool push_back(const GID& globalID);
uint8_t push_back(const std::vector<GID>& blocks);
bool refine(const GID& globalID,std::set<GID>& erasedBlocks,std::map<GID,LID>& insertedBlocks);
void setGrid();
bool setGrid(const std::vector<GID>& globalIDs);
bool setMesh(const size_t& meshID);
void setNewSize(const LID& newSize);
size_t size() const;
size_t sizeInBytes() const;
void swap(VelocityMesh& vm);
private:
bool initialized; /**< If true, velocity mesh has been successfully initialized.*/
static std::vector<vmesh::MeshParameters> meshParameters;
size_t meshID;
//std::vector<GID> offsets; /**< Block global ID offsets for each refinement level.*/
//Real* blockSizes;
//Real* cellSizes;
//LID* gridLengths;
std::vector<GID> localToGlobalMap;
std::unordered_map<GID,LID> globalToLocalMap;
bool checkChildren(const GID& globalID) const;
bool checkParent(const GID& globalID) const;
};
// ***** INITIALIZERS FOR STATIC MEMBER VARIABLES ***** //
template<typename GID,typename LID> std::vector<vmesh::MeshParameters> VelocityMesh<GID,LID>::meshParameters;
// ***** DEFINITIONS OF TEMPLATE MEMBER FUNCTIONS ***** //
//template<typename GID,typename LID> inline
//VelocityMesh<GID,LID>::VelocityMesh() { }
//template<typename GID,typename LID> inline
//VelocityMesh<GID,LID>::~VelocityMesh() { }
template<typename GID,typename LID> inline
size_t VelocityMesh<GID,LID>::capacityInBytes() const {
return localToGlobalMap.capacity()*sizeof(GID)
+ globalToLocalMap.bucket_count()*(sizeof(GID)+sizeof(LID));
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::check() const {
bool ok = true;
if (localToGlobalMap.size() != globalToLocalMap.size()) {
std::cerr << "VMO ERROR: sizes differ, " << localToGlobalMap.size() << " vs " << globalToLocalMap.size() << std::endl;
ok = false;
}
for (size_t b=0; b<size(); ++b) {
const LID globalID = localToGlobalMap[b];
typename std::unordered_map<GID,LID>::const_iterator it = globalToLocalMap.find(globalID);
const GID localID = it->second;
if (localID != b) {
ok = false;
std::cerr << "VMO ERROR: localToGlobalMap[" << b << "] = " << globalID << " but ";
std::cerr << "globalToLocalMap[" << globalID << "] = " << localID << std::endl;
}
// Recursively check that none of the possible children exist:
std::vector<GID> children;
getChildren(globalID,children);
bool hasChildren = false;
for (size_t c=0; c<children.size(); ++c) {
if (children[c] == invalidGlobalID()) continue;
if (checkChildren(children[c]) == true) hasChildren = true;
}
if (hasChildren == true) {
std::cerr << "VM AMR ERROR: block " << globalID << " at refinement level " << (int)getRefinementLevel(globalID);
std::cerr << " exists and has children or grandchildren" << std::endl;
std::cerr << "\t ERROR from " << __FILE__ << ':' << __LINE__ << std::endl;
ok = false;
}
/*
// Recursively check that parents do not exist:
bool hasParents = false;
if (checkParent(globalID) == true) hasParents=true;
if (hasParents == true) {
std::cerr << "VM AMR ERROR: block " << globalID << " at refinement level " << (int)getRefinementLevel(globalID);
std::cerr << " exists and has a parent or a grandparent" << std::endl;
std::cerr << "\t ERROR from " << __FILE__ << ':' << __LINE__ << std::endl;
ok = false;
}*/
}
return ok;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::checkChildren(const GID& globalID) const {
// Check that none of the children exist:
std::vector<GID> children;
getChildren(globalID,children);
for (size_t c=0; c<children.size(); ++c) {
if (getLocalID(children[c]) != invalidLocalID()) {
return true;
}
}
// Recursively check that none of the grandchildren exist:
for (size_t c=0; c<children.size(); ++c) {
if (checkChildren(children[c]) == true) return true;
}
return false;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::checkParent(const GID& globalID) const {
GID parent = getParent(globalID);
if (parent == globalID) return false;
if (getLocalID(parent) != invalidLocalID()) return true;
return checkParent(parent);
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::clear() {
std::vector<GID>().swap(localToGlobalMap);
std::unordered_map<GID,LID>().swap(globalToLocalMap);
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::coarsenAllowed(const GID& globalID) const {
if (globalToLocalMap.count(globalID) == 0) return false;
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
if (refLevel == 0) return false;
// Coarsen not allowed if any of the siblings have children
std::vector<GID> siblings;
getSiblings(globalID,siblings);
for (size_t s=0; s<siblings.size(); ++s) {
std::vector<GID> children;
getChildren(siblings[s],children);
for (size_t c=0; c<children.size(); ++c) {
if (globalToLocalMap.count(children[c]) > 0) return false;
}
}
// Get all neighbors of the blocks in this octant
std::vector<GID> octantNeighbors;
getSiblingNeighbors(globalID,octantNeighbors);
// Block cannot be coarsened if any of the octant neighbors have children
for (size_t n=0; n<octantNeighbors.size(); ++n) {
std::vector<GlobalID> children;
getChildren(octantNeighbors[n],children);
for (size_t c=0; c<children.size(); ++c) {
if (globalToLocalMap.count(children[c]) != 0) return false;
}
}
// Block can be coarsened
return true;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::copy(const LID& sourceLID,const LID& targetLID) {
#ifdef DEBUG_VAMR_MESH
bool ok=true;
if (sourceLID >= localToGlobalMap.size()) ok=false;
if (targetLID >= localToGlobalMap.size()) ok=false;
if (ok == false) {
std::cerr << "ERROR in copy, source/target LIDs are " << sourceLID << ' ' << targetLID << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
const GID sourceGID = localToGlobalMap[sourceLID]; // block at the end of list
const GID targetGID = localToGlobalMap[targetLID]; // removed block
#ifdef DEBUG_VAMR_MESH
if (globalToLocalMap.find(sourceGID) == globalToLocalMap.end()) ok=false;
if (globalToLocalMap.find(targetGID) == globalToLocalMap.end()) ok=false;
if (ok == false) {
std::cerr << "ERROR in copy, source/target LIDs are " << sourceLID << ' ' << targetLID << std::endl;
std::cerr << " GIDs are " << sourceGID << ' ' << targetGID << std::endl;
std::cerr << "\t sourceGID valid? ";
if (globalToLocalMap.find(sourceGID) != globalToLocalMap.end()) std::cerr << "yes" << std::endl;
else std::cerr << "no" << std::endl;
std::cerr << "\t targetGID valid? ";
if (globalToLocalMap.find(targetGID) != globalToLocalMap.end()) std::cerr << "yes" << std::endl;
else std::cerr << "no" << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
// at-function will throw out_of_range exception for non-existing global ID:
globalToLocalMap.at(sourceGID) = targetLID;
localToGlobalMap[targetLID] = sourceGID;
globalToLocalMap.at(targetGID) = sourceLID; // These are needed to make pop() work
localToGlobalMap[sourceLID] = targetGID;
return true;
}
template<typename GID,typename LID> inline
size_t VelocityMesh<GID,LID>::count(const GID& globalID) const {
return globalToLocalMap.count(globalID);
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::findBlockDown(uint8_t& refLevel,GID cellIndices[3]) const {
GID rvalue = invalidGlobalID();
int refMul = std::pow(2,getMaxAllowedRefinementLevel()-refLevel);
while (refLevel <= getMaxAllowedRefinementLevel()) {
// Calculate i/j/k indices of the block that would own the cell at refinement level r:
GID i_block = cellIndices[0] / (meshParameters[meshID].blockLength[0] * refMul);
GID j_block = cellIndices[1] / (meshParameters[meshID].blockLength[1] * refMul);
GID k_block = cellIndices[2] / (meshParameters[meshID].blockLength[2] * refMul);
// Calculate block global ID:
GID blockGID = getGlobalID(refLevel,i_block,j_block,k_block);
// If the block exists, return it:
if (globalToLocalMap.find(blockGID) != globalToLocalMap.end()) {
return blockGID;
}
refMul *= 2;
--refLevel;
}
refLevel = 0;
return invalidGlobalID();
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::findBlock(uint8_t& refLevel,GID cellIndices[3]) const {
GID rvalue = invalidGlobalID();
if (refLevel > getMaxAllowedRefinementLevel()) return invalidGlobalID();
int refMul = std::pow(2,getMaxAllowedRefinementLevel()-refLevel);
for (uint8_t r=refLevel; r<=getMaxAllowedRefinementLevel(); ++r) {
// Calculate i/j/k indices of the block that would own the cell at refinement level r:
GID i_block = cellIndices[0] / (meshParameters[meshID].blockLength[0] * refMul);
GID j_block = cellIndices[1] / (meshParameters[meshID].blockLength[1] * refMul);
GID k_block = cellIndices[2] / (meshParameters[meshID].blockLength[2] * refMul);
// Calculate block global ID:
GID blockGID = getGlobalID(r,i_block,j_block,k_block);
// If the block exists, return it:
if (globalToLocalMap.find(blockGID) != globalToLocalMap.end()) {
refLevel = r;
return blockGID;
}
refMul /= 2;
}
return invalidGlobalID();
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::getBlockCoordinates(const GID& globalID,Real coords[3]) const {
if (globalID == invalidGlobalID()) {
for (int i=0; i<3; ++i) coords[i] = std::numeric_limits<Real>::quiet_NaN();
return false;
}
// Calculate block's refinement level and (i,j,k) indices:
uint8_t refLevel;
LID indices[3];
getIndices(globalID,refLevel,indices[0],indices[1],indices[2]);
if (indices[0] == invalidBlockIndex()) {
for (int i=0; i<3; ++i) coords[i] = std::numeric_limits<Real>::quiet_NaN();
return false;
}
// NUmber of blocks per coordinate at this refinement level:
const GlobalID multiplier = std::pow(2,refLevel);
coords[0] = meshParameters[meshID].meshMinLimits[0] + indices[0]*meshParameters[meshID].blockSize[0]/multiplier;
coords[1] = meshParameters[meshID].meshMinLimits[1] + indices[1]*meshParameters[meshID].blockSize[1]/multiplier;
coords[2] = meshParameters[meshID].meshMinLimits[2] + indices[2]*meshParameters[meshID].blockSize[2]/multiplier;
return true;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getBlockInfo(const GID& globalID,Real* array) const {
#ifdef DEBUG_VAMR_MESH
if (globalID == invalidGlobalID()) {
for (int i=0; i<6; ++i) array[i] = std::numeric_limits<Real>::infinity();
}
#endif
getBlockCoordinates(globalID,array+0);
getCellSize(globalID,array+3);
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getBlockSize(const uint8_t& refLevel) const {
return meshParameters[meshID].blockSizes.data() + refLevel*3;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::getBlockSize(const GID& globalID,Real size[3]) const {
// Calculate block's refinement level and (i,j,k) indices:
uint8_t refLevel;
LID indices[3];
getIndices(globalID,refLevel,indices[0],indices[1],indices[2]);
// NUmber of blocks per coordinate at this refinement level:
const GlobalID multiplier = std::pow(2,refLevel);
// Calculate the number of blocks in each coordinate direction at this refinement level:
size[0] = meshParameters[meshID].blockSize[0] / multiplier;
size[1] = meshParameters[meshID].blockSize[1] / multiplier;
size[2] = meshParameters[meshID].blockSize[2] / multiplier;
return true;
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getCellSize(const uint8_t& refLevel) const {
return meshParameters[meshID].cellSizes.data() + refLevel*3;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::getCellSize(const GID& globalID,Real size[3]) const {
// Calculate block size and divide it by the number of cells in block
getBlockSize(globalID,size);
size[0] /= meshParameters[meshID].blockLength[0];
size[1] /= meshParameters[meshID].blockLength[1];
size[2] /= meshParameters[meshID].blockLength[2];
return true;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getChildren(const GID& globalID,std::vector<GID>& children) const {
children.clear();
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
if (refLevel == getMaxAllowedRefinementLevel()) return;
i *= 2;
j *= 2;
k *= 2;
children.push_back(getGlobalID(refLevel+1,i ,j ,k ));
children.push_back(getGlobalID(refLevel+1,i+1,j ,k ));
children.push_back(getGlobalID(refLevel+1,i ,j+1,k ));
children.push_back(getGlobalID(refLevel+1,i+1,j+1,k ));
children.push_back(getGlobalID(refLevel+1,i ,j ,k+1));
children.push_back(getGlobalID(refLevel+1,i+1,j ,k+1));
children.push_back(getGlobalID(refLevel+1,i ,j+1,k+1));
children.push_back(getGlobalID(refLevel+1,i+1,j+1,k+1));
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const LID& localID) const {
if (localID >= localToGlobalMap.size()) return invalidGlobalID();
#ifdef DEBUG_VAMR_MESH
bool ok=true;
const GID globalID = localToGlobalMap[localID];
if (globalToLocalMap.find(globalID) == globalToLocalMap.end()) ok=false;
if (ok == false) {
std::cerr << "ERROR in getGlobalID, localID=" << localID << " and globalID=" << globalID;
std::cerr << " but globalToLocalMap does not contain the block" << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
return localToGlobalMap[localID];
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const uint8_t& refLevel,LID indices[3]) const {
const uint8_t multiplier = std::pow(2,refLevel);
if (indices[0] >= meshParameters[meshID].gridLength[0]*multiplier) return invalidGlobalID();
if (indices[1] >= meshParameters[meshID].gridLength[1]*multiplier) return invalidGlobalID();
if (indices[2] >= meshParameters[meshID].gridLength[2]*multiplier) return invalidGlobalID();
return
meshParameters[meshID].offsets[refLevel]
+ indices[2]*meshParameters[meshID].gridLength[1]*meshParameters[meshID].gridLength[0]*multiplier*multiplier
+ indices[1]*meshParameters[meshID].gridLength[0]*multiplier + indices[0];
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const uint32_t& refLevel,const LID& i,const LID& j,const LID& k) const {
const uint32_t multiplier = std::pow(2,refLevel);
if (i >= meshParameters[meshID].gridLength[0]*multiplier) return invalidGlobalID();
if (j >= meshParameters[meshID].gridLength[1]*multiplier) return invalidGlobalID();
if (k >= meshParameters[meshID].gridLength[2]*multiplier) return invalidGlobalID();
return
meshParameters[meshID].offsets[refLevel]
+ k*meshParameters[meshID].gridLength[1]*meshParameters[meshID].gridLength[0]*multiplier*multiplier
+ j*meshParameters[meshID].gridLength[0]*multiplier + i;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalID(const uint8_t& refLevel,const Real* coords) const {
if (coords[0] < meshParameters[meshID].meshMinLimits[0] || coords[0] >= meshParameters[meshID].meshMaxLimits[0] ||
(coords[1] < meshParameters[meshID].meshMinLimits[1] || coords[1] >= meshParameters[meshID].meshMaxLimits[1] ||
coords[2] < meshParameters[meshID].meshMinLimits[2] || coords[2] >= meshParameters[meshID].meshMaxLimits[2])) {
return invalidGlobalID();
}
const LID multiplier = std::pow(2,refLevel);
const LID indices[3] = {
static_cast<LID>(floor((coords[0] - meshParameters[meshID].meshMinLimits[0])*multiplier / meshParameters[meshID].blockSize[0])),
static_cast<LID>(floor((coords[1] - meshParameters[meshID].meshMinLimits[1])*multiplier / meshParameters[meshID].blockSize[1])),
static_cast<LID>(floor((coords[2] - meshParameters[meshID].meshMinLimits[2])*multiplier / meshParameters[meshID].blockSize[2]))
};
return
meshParameters[meshID].offsets[refLevel]
+ indices[2]*meshParameters[meshID].gridLength[1]*meshParameters[meshID].gridLength[0]*multiplier*multiplier
+ indices[1]*meshParameters[meshID].gridLength[0]*multiplier + indices[0];
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getGlobalIndexOffset(const uint8_t& refLevel) const {
return meshParameters[meshID].offsets[refLevel];
}
template<typename GID,typename LID> inline
std::vector<GID>& VelocityMesh<GID,LID>::getGrid() {
return localToGlobalMap;
}
template<typename GID,typename LID> inline
const LID* VelocityMesh<GID,LID>::getGridLength(const uint8_t& refLevel) const {
return meshParameters[meshID].gridLengths.data() + refLevel*3;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getIndices(const GID& globalID,uint8_t& refLevel,LID& i,LID& j,LID& k) const {
refLevel = std::upper_bound(meshParameters[meshID].offsets.begin(),meshParameters[meshID].offsets.end(),globalID)
- meshParameters[meshID].offsets.begin()-1;
const GID cellOffset = meshParameters[meshID].offsets[refLevel];
const GID multiplier = std::pow(2,refLevel);
const GID Nx = meshParameters[meshID].gridLength[0] * multiplier;
const GID Ny = meshParameters[meshID].gridLength[1] * multiplier;
GID index = globalID - cellOffset;
k = index / (Ny*Nx);
index -= k*Ny*Nx;
j = index / Nx;
i = index - j*Nx;
}
template<typename GID,typename LID> inline
LID VelocityMesh<GID,LID>::getLocalID(const GID& globalID) const {
typename std::unordered_map<GID,LID>::const_iterator it = globalToLocalMap.find(globalID);
if (it != globalToLocalMap.end()) return it->second;
return invalidLocalID();
}
template<typename GID,typename LID> inline
uint8_t VelocityMesh<GID,LID>::getMaxAllowedRefinementLevel() const {
return meshParameters[meshID].refLevelMaxAllowed;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getMaxVelocityBlocks() const {
return meshParameters[meshID].max_velocity_blocks;
}
template<typename GID,typename LID> inline
size_t VelocityMesh<GID,LID>::getMesh() const {return meshID;}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getMeshMaxLimits() const {
return meshParameters[meshID].meshMaxLimits;
}
template<typename GID,typename LID> inline
const Real* VelocityMesh<GID,LID>::getMeshMinLimits() const {
return meshParameters[meshID].meshMinLimits;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getNeighborsAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs) const {
neighborIDs.resize(27);
// Calculate block refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Calculate global IDs of all 27 blocks:
const LID Nx_max = meshParameters[meshID].gridLength[0] * std::pow(2,refLevel);
const LID Ny_max = meshParameters[meshID].gridLength[1] * std::pow(2,refLevel);
const LID Nz_max = meshParameters[meshID].gridLength[2] * std::pow(2,refLevel);
int nbr = 0;
for (int k_off=-1; k_off<2; ++k_off) for (int j_off=-1; j_off<2; ++j_off) for (int i_off=-1; i_off<2; ++i_off) {
if (i+i_off < Nx_max && (j+j_off < Ny_max && k+k_off < Nz_max)) neighborIDs[nbr] = getGlobalID(refLevel,i+i_off,j+j_off,k+k_off);
else neighborIDs[nbr] = invalidGlobalID();
++nbr;
}
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getNeighborsExistingAtSameLevel(const GID& globalID,std::vector<GID>& neighborIDs) const {
neighborIDs.clear();
// Calculate block refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Calculate global IDs of all 26 neighbors. Note that
// some of the neighbors may not actually exist.
const LID Nx_max = meshParameters[meshID].gridLength[0] * std::pow(2,refLevel);
const LID Ny_max = meshParameters[meshID].gridLength[1] * std::pow(2,refLevel);
const LID Nz_max = meshParameters[meshID].gridLength[2] * std::pow(2,refLevel);
for (int k_off=-1; k_off<2; ++k_off) {
if (k+k_off >= Nz_max) continue;
for (int j_off=-1; j_off<2; ++j_off) {
if (j+j_off >= Ny_max) continue;
for (int i_off=-1; i_off<2; ++i_off) {
if (i+i_off >= Nx_max) continue;
if (i_off == 0 && (j_off == 0 && k_off == 0)) continue;
neighborIDs.push_back(getGlobalID(refLevel,i+i_off,j+j_off,k+k_off));
}
}
}
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getNeighborsExistingAtOffset(const GID& globalID,const int& i_off,const int& j_off,const int& k_off,std::vector<LID>& neighborLocalIDs,int32_t& refLevelDifference) const {
#ifdef DEBUG_VAMR_MESH
if (abs(i_off) > 1 || (abs(j_off) > 1 || abs(k_off) > 1)) {
std::stringstream ss;
ss << "VelocityMesh ERROR: invalid offsets in getNeighborsExistingAtOffset " << i_off << ' ' << j_off << ' ' << k_off << std::endl;
std::cerr << ss.str();
exit(1);
}
#endif
refLevelDifference = 0;
neighborLocalIDs.clear();
// Calculate block refinement level and indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// First check if the neighbor at same refinement level exists
typename std::unordered_map<GID,LID>::const_iterator nbr;
GID nbrGlobalID = getGlobalID(refLevel,i+i_off,j+j_off,k+k_off);
if (nbrGlobalID == invalidGlobalID()) return;
nbr = globalToLocalMap.find(nbrGlobalID);
if (nbr != globalToLocalMap.end()) {
neighborLocalIDs.push_back(nbr->second);
refLevelDifference = 0;
return;
}
// Check if parent of the neighbor exists
nbr = globalToLocalMap.find(getParent(nbrGlobalID));
if (nbr != globalToLocalMap.end()) {
neighborLocalIDs.push_back(nbr->second);
refLevelDifference = -1;
return;
}
// Exit if neighbor cannot have children:
if (refLevel == getMaxAllowedRefinementLevel()) return;
refLevelDifference = +1;
// Check if neighbor's children exist:
std::vector<GID> nbrChildren;
getChildren(nbrGlobalID,nbrChildren);
// Block can have zero to four face neighbors because of the sparse grid.
// We need to return four neighbors so that the code calling this function
// indexes neighborLocalIDs correctly, non-existing neighbors have an invalid local ID.
neighborLocalIDs.resize(4);
for (size_t n=0; n<4; ++n) neighborLocalIDs[n] = invalidLocalID();
const int nbrTypeID = (k_off+1)*9+(j_off+1)*3+(i_off+1);
switch (nbrTypeID) {
case 4: // -z face neighbor
nbr = globalToLocalMap.find(nbrChildren[4]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[5]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[6]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[7]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 10: // -y face neighbor
nbr = globalToLocalMap.find(nbrChildren[2]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[3]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[6]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[7]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 12: // -x face neighbor
nbr = globalToLocalMap.find(nbrChildren[1]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[3]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[5]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[7]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 14: // +x face neighbor
nbr = globalToLocalMap.find(nbrChildren[0]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[2]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[4]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[6]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 16: // +y face neighbor
nbr = globalToLocalMap.find(nbrChildren[0]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[1]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[4]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[5]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
case 22: // +z face neighbor
nbr = globalToLocalMap.find(nbrChildren[0]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[0] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[1]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[1] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[2]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[2] = nbr->second;}
nbr = globalToLocalMap.find(nbrChildren[3]); if (nbr != globalToLocalMap.end()) {neighborLocalIDs[3] = nbr->second;}
break;
default:
break;
}
}
template<typename GID,typename LID> inline
int VelocityMesh<GID,LID>::getOctant(const GID& globalID) const {
// Calculate block indices and refinement level
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
const int i_oct = i % 2;
const int j_oct = j % 2;
const int k_oct = k % 2;
return k_oct*2*2 + j_oct*2 + i_oct;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::getParent(const GID& globalID) const {
// Calculate block indices and refinement level
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Blocks at base grid level don't have a parent
if (refLevel == 0) return globalID;
// Calculate parent's global ID
i /= 2;
j /= 2;
k /= 2;
return getGlobalID(refLevel-1,i,j,k);
}
template<typename GID,typename LID> inline
uint8_t VelocityMesh<GID,LID>::getRefinementLevel(const GID& globalID) const {
for (size_t i=1; i<meshParameters[meshID].refLevelMaxAllowed+1; ++i) {
if (globalID < meshParameters[meshID].offsets[i]) return i-1;
}
return meshParameters[meshID].refLevelMaxAllowed;
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getSiblingNeighbors(const GID& globalID,std::vector<GID>& nbrs) const {
nbrs.clear();
// Get block indices
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
// Shift indices to bottom lower left corner in the octant
i -= (i % 2);
j -= (j % 2);
k -= (k % 2);
// Calculate the global IDs of all common neighbors of the blocks in the octant
for (LID k_off=-1; k_off<3; ++k_off) {
for (LID j_off=-1; j_off<3; ++j_off) {
for (LID i_off=-1; i_off<3; ++i_off) {
int cntr=0;
if (i_off == 0 || i_off == 1) ++cntr;
if (j_off == 0 || j_off == 1) ++cntr;
if (k_off == 0 || k_off == 1) ++cntr;
if (cntr == 3) continue;
nbrs.push_back(getGlobalID(refLevel,i+i_off,j+j_off,k+k_off));
}
}
}
}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::getSiblings(const GID& globalID,std::vector<GID>& siblings) const {
uint8_t refLevel;
LID i,j,k;
getIndices(globalID,refLevel,i,j,k);
siblings.resize(8);
i -= (i % 2);
j -= (j % 2);
k -= (k % 2);
siblings[0] = getGlobalID(refLevel,i ,j ,k );
siblings[1] = getGlobalID(refLevel,i+1,j ,k );
siblings[2] = getGlobalID(refLevel,i ,j+1,k );
siblings[3] = getGlobalID(refLevel,i+1,j+1,k );
siblings[4] = getGlobalID(refLevel,i ,j ,k+1);
siblings[5] = getGlobalID(refLevel,i+1,j ,k+1);
siblings[6] = getGlobalID(refLevel,i ,j+1,k+1);
siblings[7] = getGlobalID(refLevel,i+1,j+1,k+1);
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::hasChildren(const GID& globalID) const {
std::vector<GID> children;
getChildren(globalID,children);
// If children.size() is zero, block is at max refinement level:
if (children.size() == 0) return false;
// Check all children, if even one exists return 'true':
for (size_t c=0; c<children.size(); ++c) {
if (getLocalID(children[c]) != invalidLocalID()) return true;
}
return false;
}
/** Check if the block has any existing grandparents.
* @param globalID Global ID of the block.
* @return INVALID_GLOBALID if block has no existing grandparents, otherwise
* the global ID of the grandparent is returned.*/
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::hasGrandParent(const GID& globalID) const {
// Exit if the block cannot have grandparents
uint8_t refLevel = getRefinementLevel(globalID);
if (refLevel <= 1) return invalidGlobalID();
// Calculate the global ID of the first possible grandparent
GID parentGID = getParent(globalID);
parentGID = getParent(parentGID);
do {
// Grandparent exists, return its global ID
if (getLocalID(parentGID) != invalidLocalID()) return parentGID;
// Move down one refinement level
GID tmp = parentGID;
parentGID = getParent(parentGID);
if (tmp == parentGID) break;
} while (true);
return invalidGlobalID();
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::initialize(const size_t& meshID) {
this->meshID = meshID;
return true;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::initialize(const size_t& meshID,std::vector<vmesh::MeshParameters>& meshParameters) {
meshParameters[meshID].initialized = false;
meshParameters[meshID].meshMinLimits[0] = meshParameters[meshID].meshLimits[0];
meshParameters[meshID].meshMinLimits[1] = meshParameters[meshID].meshLimits[2];
meshParameters[meshID].meshMinLimits[2] = meshParameters[meshID].meshLimits[4];
meshParameters[meshID].meshMaxLimits[0] = meshParameters[meshID].meshLimits[1];
meshParameters[meshID].meshMaxLimits[1] = meshParameters[meshID].meshLimits[3];
meshParameters[meshID].meshMaxLimits[2] = meshParameters[meshID].meshLimits[5];
// Calculate derived mesh parameters:
meshParameters[meshID].gridSize[0] = meshParameters[meshID].meshMaxLimits[0] - meshParameters[meshID].meshMinLimits[0];
meshParameters[meshID].gridSize[1] = meshParameters[meshID].meshMaxLimits[1] - meshParameters[meshID].meshMinLimits[1];
meshParameters[meshID].gridSize[2] = meshParameters[meshID].meshMaxLimits[2] - meshParameters[meshID].meshMinLimits[2];
meshParameters[meshID].blockSize[0] = meshParameters[meshID].gridSize[0] / meshParameters[meshID].gridLength[0];
meshParameters[meshID].blockSize[1] = meshParameters[meshID].gridSize[1] / meshParameters[meshID].gridLength[1];
meshParameters[meshID].blockSize[2] = meshParameters[meshID].gridSize[2] / meshParameters[meshID].gridLength[2];
meshParameters[meshID].cellSize[0] = meshParameters[meshID].blockSize[0] / meshParameters[meshID].blockLength[0];
meshParameters[meshID].cellSize[1] = meshParameters[meshID].blockSize[1] / meshParameters[meshID].blockLength[1];
meshParameters[meshID].cellSize[2] = meshParameters[meshID].blockSize[2] / meshParameters[meshID].blockLength[2];
/*meshParameters[meshID].max_velocity_blocks
= meshParameters[meshID].gridLength[0]
* meshParameters[meshID].gridLength[1]
* meshParameters[meshID].gridLength[2];*/
meshParameters[meshID].max_velocity_blocks = 1000000;
meshParameters[meshID].initialized = true;
// Calculate global ID offsets for all possible refinement levels:
const GID N_blocks0 = meshParameters[meshID].gridLength[0]*meshParameters[meshID].gridLength[1]*meshParameters[meshID].gridLength[2];
meshParameters[meshID].offsets.resize(meshParameters[meshID].refLevelMaxAllowed+1);
meshParameters[meshID].offsets[0] = 0;
for (size_t i=1; i<meshParameters[meshID].refLevelMaxAllowed+1; ++i) {
meshParameters[meshID].offsets[i] = meshParameters[meshID].offsets[i-1] + N_blocks0 * std::pow(8,i-1);
}
meshParameters[meshID].gridLengths.resize(3*(meshParameters[meshID].refLevelMaxAllowed+1));
meshParameters[meshID].blockSizes.resize(3*(meshParameters[meshID].refLevelMaxAllowed+1));
meshParameters[meshID].cellSizes.resize(3*(meshParameters[meshID].refLevelMaxAllowed+1));
uint32_t mul = 1;
for (uint8_t r=0; r<meshParameters[meshID].refLevelMaxAllowed+1; ++r) {
for (int i=0; i<3; ++i) meshParameters[meshID].gridLengths[3*r+i] = meshParameters[meshID].gridLength[i] * mul;
for (int i=0; i<3; ++i) meshParameters[meshID].blockSizes[3*r+i] = meshParameters[meshID].blockSize[i] / mul;
for (int i=0; i<3; ++i) meshParameters[meshID].cellSizes[3*r+i] = meshParameters[meshID].blockSize[i] / (mul * meshParameters[meshID].blockLength[i]);
mul *= 2;
}
vmesh::VelocityMesh<GID,LID>::meshParameters = meshParameters;
return meshParameters[meshID].initialized;
}
template<typename GID,typename LID> inline
LID VelocityMesh<GID,LID>::invalidBlockIndex() {
return INVALID_VEL_BLOCK_INDEX;
}
template<typename GID,typename LID> inline
GID VelocityMesh<GID,LID>::invalidGlobalID() {
return INVALID_GLOBALID;
}
template<typename GID,typename LID> inline
LID VelocityMesh<GID,LID>::invalidLocalID() {
return INVALID_LOCALID;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::isInitialized() const {return initialized;}
template<typename GID,typename LID> inline
void VelocityMesh<GID,LID>::pop() {
if (size() == 0) return;
const LID lastLID = size()-1;
const GID lastGID = localToGlobalMap[lastLID];
#ifdef DEBUG_VAMR_MESH
bool ok = true;
if (globalToLocalMap.find(lastGID) == globalToLocalMap.end()) ok = false;
if (ok == false) {
std::cerr << "ERROR in pop(): last localID=" << lastLID << " globalID=" << lastGID;
std::cerr << " but globalToLocalMap does not contain that block" << std::endl;
std::cerr << "\t exiting from " << __FILE__ << ':' << __LINE__ << std::endl;
exit(1);
}
#endif
typename std::unordered_map<GID,LID>::iterator last = globalToLocalMap.find(lastGID);
globalToLocalMap.erase(last);
localToGlobalMap.pop_back();
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::push_back(const GID& globalID) {
if (globalID == invalidGlobalID()) return false;
if (size() >= meshParameters[meshID].max_velocity_blocks) {
std::cerr << "vmesh-amr: too many blocks, current size is " << size() << " max " << meshParameters[meshID].max_velocity_blocks << std::endl;
return false;
}
std::pair<typename std::unordered_map<GID,LID>::iterator,bool> position
= globalToLocalMap.insert(std::make_pair(globalID,localToGlobalMap.size()));
if (position.second == true) {
localToGlobalMap.push_back(globalID);
}
return position.second;
}
template<typename GID,typename LID> inline
uint8_t VelocityMesh<GID,LID>::push_back(const std::vector<GID>& blocks) {
if (size()+blocks.size() >= meshParameters[meshID].max_velocity_blocks) {
std::cerr << "vmesh-amr: too many blocks, current size is " << size() << " max " << meshParameters[meshID].max_velocity_blocks << std::endl;
return 0;
}
// Attempt to add the given blocks
uint8_t adds=0;
for (size_t b=0; b<blocks.size(); ++b) {
const GID globalID = blocks[b];
std::pair<typename std::unordered_map<GID,LID>::iterator,bool> position
= globalToLocalMap.insert(std::make_pair(globalID,localToGlobalMap.size()+b));
if (position.second == true) {
localToGlobalMap.push_back(globalID);
++adds;
}
}
return adds;
}
template<typename GID,typename LID> inline
bool VelocityMesh<GID,LID>::refine(const GID& globalID,std::set<GID>& erasedBlocks,std::map<GID,LID>& insertedBlocks) {
// Check that the block exists
typename std::unordered_map<GID,LID>::iterator it = globalToLocalMap.find(globalID);
if (it == globalToLocalMap.end()) {
return false;
}