Homec4science
Diffusion akantu (bugfixes/python_interface_energy_computations) Browse

rAKA/src/common/aka_grid_dynamic.hh
63db325b3a31bugfixes/python_interfa…

Last Change
Raw File

aka_grid_dynamic.hh
View Options

/**
* @file aka_grid_dynamic.hh
*
* @author Aurelia Isabel Cuba Ramos <aurelia.cubaramos@epfl.ch>
* @author Nicolas Richart <nicolas.richart@epfl.ch>
*
* @date creation: Thu Feb 21 2013
* @date last modification: Wed Nov 08 2017
*
* @brief Grid that is auto balanced
*
*
* Copyright (©) 2014-2018 EPFL (Ecole Polytechnique Fédérale de Lausanne)
* Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)
*
* Akantu is free software: you can redistribute it and/or modify it under the
* terms of the GNU Lesser General Public License as published by the Free
* Software Foundation, either version 3 of the License, or (at your option) any
* later version.
*
* Akantu 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 Lesser General Public License for more
* details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with Akantu. If not, see <http://www.gnu.org/licenses/>.
*
*/
/* -------------------------------------------------------------------------- */
#include "aka_array.hh"
#include "aka_common.hh"
#include "aka_types.hh"
#include "mesh_accessor.hh"
#include <iostream>
/* -------------------------------------------------------------------------- */
#include <map>
/* -------------------------------------------------------------------------- */
#ifndef AKANTU_AKA_GRID_DYNAMIC_HH_
#define AKANTU_AKA_GRID_DYNAMIC_HH_
namespace akantu {
class Mesh;
template <typename T> class SpatialGrid {
public:
explicit SpatialGrid(UInt dimension)
: dimension(dimension), spacing(dimension), center(dimension),
lower(dimension), upper(dimension), empty_cell() {}
SpatialGrid(UInt dimension, const Vector<Real> & spacing,
const Vector<Real> & center)
: dimension(dimension), spacing(spacing), center(center),
lower(dimension), upper(dimension), empty_cell() {
for (UInt i = 0; i < dimension; ++i) {
lower(i) = std::numeric_limits<Real>::max();
upper(i) = -std::numeric_limits<Real>::max();
}
}
virtual ~SpatialGrid() = default;
class neighbor_cells_iterator;
class cells_iterator;
class CellID {
public:
CellID() = default;
explicit CellID(UInt dimention) : ids(dimention) {}
void setID(UInt dir, Int id) { ids(dir) = id; }
Int getID(UInt dir) const { return ids(dir); }
bool operator<(const CellID & id) const {
return std::lexicographical_compare(
ids.storage(), ids.storage() + ids.size(), id.ids.storage(),
id.ids.storage() + id.ids.size());
}
bool operator==(const CellID & id) const {
return std::equal(ids.storage(), ids.storage() + ids.size(),
id.ids.storage());
}
bool operator!=(const CellID & id) const { return !(operator==(id)); }
class neighbor_cells_iterator
: private std::iterator<std::forward_iterator_tag, UInt> {
public:
neighbor_cells_iterator(const CellID & cell_id, bool end)
: cell_id(cell_id), position(cell_id.ids.size(), end ? 1 : -1) {
this->updateIt();
if (end) {
this->it++;
}
}
neighbor_cells_iterator & operator++() {
UInt i = 0;
for (; i < position.size() && position(i) == 1; ++i) {
;
}
if (i == position.size()) {
++it;
return *this;
}
for (UInt j = 0; j < i; ++j) {
position(j) = -1;
}
position(i)++;
updateIt();
return *this;
}
neighbor_cells_iterator operator++(int) {
neighbor_cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const neighbor_cells_iterator & rhs) const {
return cell_id == rhs.cell_id && it == rhs.it;
};
bool operator!=(const neighbor_cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(cell_id);
cur_cell_id.ids += position;
return cur_cell_id;
};
private:
void updateIt() {
it = 0;
for (UInt i = 0; i < position.size(); ++i) {
it = it * 3 + (position(i) + 1);
}
}
private:
/// central cell id
const CellID & cell_id;
// number representing the current neighbor in base 3;
UInt it;
// current cell shift
Vector<Int> position;
};
class Neighbors {
public:
explicit Neighbors(const CellID & cell_id) : cell_id(cell_id) {}
decltype(auto) begin() { return neighbor_cells_iterator(cell_id, false); }
decltype(auto) end() { return neighbor_cells_iterator(cell_id, true); }
private:
const CellID & cell_id;
};
decltype(auto) neighbors() { return Neighbors(*this); }
private:
friend class cells_iterator;
Vector<Int> ids;
};
/* ------------------------------------------------------------------------ */
class Cell {
public:
using iterator = typename std::vector<T>::iterator;
using const_iterator = typename std::vector<T>::const_iterator;
Cell() : id(), data() {}
explicit Cell(const CellID & cell_id) : id(cell_id), data() {}
bool operator==(const Cell & cell) const { return id == cell.id; }
bool operator!=(const Cell & cell) const { return id != cell.id; }
Cell & add(const T & d) {
data.push_back(d);
return *this;
}
iterator begin() { return data.begin(); }
const_iterator begin() const { return data.begin(); }
iterator end() { return data.end(); }
const_iterator end() const { return data.end(); }
private:
CellID id;
std::vector<T> data;
};
private:
using cells_container = std::map<CellID, Cell>;
public:
const Cell & getCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second;
}
return empty_cell;
}
decltype(auto) beginCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.begin();
}
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.end();
}
return empty_cell.end();
}
decltype(auto) beginCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.begin();
}
return empty_cell.begin();
}
decltype(auto) endCell(const CellID & cell_id) const {
auto it = cells.find(cell_id);
if (it != cells.end()) {
return it->second.end();
}
return empty_cell.end();
}
/* ------------------------------------------------------------------------ */
class cells_iterator
: private std::iterator<std::forward_iterator_tag, CellID> {
public:
explicit cells_iterator(typename std::map<CellID, Cell>::const_iterator it)
: it(it) {}
cells_iterator & operator++() {
this->it++;
return *this;
}
cells_iterator operator++(int /*unused*/) {
cells_iterator tmp(*this);
operator++();
return tmp;
};
bool operator==(const cells_iterator & rhs) const { return it == rhs.it; };
bool operator!=(const cells_iterator & rhs) const {
return !operator==(rhs);
};
CellID operator*() const {
CellID cur_cell_id(this->it->first);
return cur_cell_id;
};
private:
/// map iterator
typename std::map<CellID, Cell>::const_iterator it;
};
public:
template <class vector_type>
Cell & insert(const T & d, const vector_type & position) {
auto && cell_id = getCellID(position);
auto && it = cells.find(cell_id);
if (it == cells.end()) {
Cell cell(cell_id);
auto & tmp = (cells[cell_id] = cell).add(d);
for (UInt i = 0; i < dimension; ++i) {
Real posl = center(i) + cell_id.getID(i) * spacing(i);
Real posu = posl + spacing(i);
if (posl < lower(i)) {
lower(i) = posl;
}
if (posu > upper(i)) {
upper(i) = posu;
}
}
return tmp;
}
return it->second.add(d);
}
/* ------------------------------------------------------------------------ */
inline decltype(auto) begin() const {
auto begin = this->cells.begin();
return cells_iterator(begin);
}
inline decltype(auto) end() const {
auto end = this->cells.end();
return cells_iterator(end);
}
template <class vector_type>
CellID getCellID(const vector_type & position) const {
CellID cell_id(dimension);
for (UInt i = 0; i < dimension; ++i) {
cell_id.setID(i, getCellID(position(i), i));
}
return cell_id;
}
void printself(std::ostream & stream, int indent = 0) const {
std::string space(indent, AKANTU_INDENT);
std::streamsize prec = stream.precision();
std::ios_base::fmtflags ff = stream.flags();
stream.setf(std::ios_base::showbase);
stream.precision(5);
stream << space << "SpatialGrid<" << debug::demangle(typeid(T).name())
<< "> [" << std::endl;
stream << space << " + dimension : " << this->dimension << std::endl;
stream << space << " + lower bounds : {";
for (UInt i = 0; i < lower.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << lower(i);
};
stream << "}" << std::endl;
stream << space << " + upper bounds : {";
for (UInt i = 0; i < upper.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << upper(i);
};
stream << "}" << std::endl;
stream << space << " + spacing : {";
for (UInt i = 0; i < spacing.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << spacing(i);
};
stream << "}" << std::endl;
stream << space << " + center : {";
for (UInt i = 0; i < center.size(); ++i) {
if (i != 0) {
stream << ", ";
}
stream << center(i);
};
stream << "}" << std::endl;
stream << space << " + nb_cells : " << this->cells.size() << "/";
Vector<Real> dist(this->dimension);
dist = upper;
dist -= lower;
for (UInt i = 0; i < this->dimension; ++i) {
dist(i) /= spacing(i);
}
UInt nb_cells = std::ceil(dist(0));
for (UInt i = 1; i < this->dimension; ++i) {
nb_cells *= std::ceil(dist(i));
}
stream << nb_cells << std::endl;
stream << space << "]" << std::endl;
stream.precision(prec);
stream.flags(ff);
}
void saveAsMesh(Mesh & mesh) const;
private:
/* --------------------------------------------------------------------------
*/
inline UInt getCellID(Real position, UInt direction) const {
AKANTU_DEBUG_ASSERT(direction < center.size(), "The direction asked ("
<< direction
<< ") is out of range "
<< center.size());
Real dist_center = position - center(direction);
Int id = std::floor(dist_center / spacing(direction));
// if(dist_center < 0) id--;
return id;
}
friend class GridSynchronizer;
public:
AKANTU_GET_MACRO(LowerBounds, lower, const Vector<Real> &);
AKANTU_GET_MACRO(UpperBounds, upper, const Vector<Real> &);
AKANTU_GET_MACRO(Spacing, spacing, const Vector<Real> &);
protected:
UInt dimension;
cells_container cells;
Vector<Real> spacing;
Vector<Real> center;
Vector<Real> lower;
Vector<Real> upper;
Cell empty_cell;
};
/// standard output stream operator
template <typename T>
inline std::ostream & operator<<(std::ostream & stream,
const SpatialGrid<T> & _this) {
_this.printself(stream);
return stream;
}
} // namespace akantu
#include "mesh.hh"
namespace akantu {
/* -------------------------------------------------------------------------- */
template <typename T> void SpatialGrid<T>::saveAsMesh(Mesh & mesh) const {
ElementType type = _not_defined;
switch (dimension) {
case 1:
type = _segment_2;
break;
case 2:
type = _quadrangle_4;
break;
case 3:
type = _hexahedron_8;
break;
}
MeshAccessor mesh_accessor(mesh);
auto & connectivity = mesh_accessor.getConnectivity(type);
auto & nodes = mesh_accessor.getNodes();
auto & uint_data = mesh.getDataPointer<UInt>("tag_1", type);
Vector<Real> pos(dimension);
UInt global_id = 0;
for (auto & cell_pair : cells) {
UInt cur_node = nodes.size();
UInt cur_elem = connectivity.size();
const CellID & cell_id = cell_pair.first;
for (UInt i = 0; i < dimension; ++i) {
pos(i) = center(i) + cell_id.getID(i) * spacing(i);
}
nodes.push_back(pos);
for (UInt i = 0; i < dimension; ++i) {
pos(i) += spacing(i);
}
nodes.push_back(pos);
connectivity.push_back(cur_node);
switch (dimension) {
case 1:
connectivity(cur_elem, 1) = cur_node + 1;
break;
case 2:
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(0) += spacing(0);
pos(1) -= spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 3;
connectivity(cur_elem, 2) = cur_node + 1;
connectivity(cur_elem, 3) = cur_node + 2;
break;
case 3:
pos(1) -= spacing(1);
pos(2) -= spacing(2);
nodes.push_back(pos);
pos(1) += spacing(1);
nodes.push_back(pos);
pos(0) -= spacing(0);
nodes.push_back(pos);
pos(1) -= spacing(1);
pos(2) += spacing(2);
nodes.push_back(pos);
pos(0) += spacing(0);
nodes.push_back(pos);
pos(0) -= spacing(0);
pos(1) += spacing(1);
nodes.push_back(pos);
connectivity(cur_elem, 1) = cur_node + 2;
connectivity(cur_elem, 2) = cur_node + 3;
connectivity(cur_elem, 3) = cur_node + 4;
connectivity(cur_elem, 4) = cur_node + 5;
connectivity(cur_elem, 5) = cur_node + 6;
connectivity(cur_elem, 6) = cur_node + 1;
connectivity(cur_elem, 7) = cur_node + 7;
break;
}
uint_data.push_back(global_id);
++global_id;
}
}
} // namespace akantu
#endif /* AKANTU_AKA_GRID_DYNAMIC_HH_ */
c4science · Help