mesh_partition.cc
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mesh_partition.cc
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	/**
	* @file mesh_partition.cc
	*
	* @author David Simon Kammer <david.kammer@epfl.ch>
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	*
	* @date creation: Tue Aug 17 2010
	* @date last modification: Fri Jul 24 2020
	*
	* @brief implementation of common part of all partitioner
	*
	*
	* @section LICENSE
	*
	* Copyright (©) 2010-2021 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 "mesh_partition.hh"
	#include "aka_iterators.hh"
	#include "aka_types.hh"
	#include "mesh_accessor.hh"
	#include "mesh_iterators.hh"
	#include "mesh_utils.hh"
	/* -------------------------------------------------------------------------- */
	#include <algorithm>
	#include <numeric>
	#include <unordered_map>
	/* -------------------------------------------------------------------------- */

	namespace akantu {

	/* -------------------------------------------------------------------------- */
	MeshPartition::MeshPartition(Mesh & mesh, UInt spatial_dimension, const ID & id)
	: mesh(mesh), spatial_dimension(spatial_dimension),
	partitions("partition", id), ghost_partitions("ghost_partition", id),
	ghost_partitions_offset("ghost_partition_offset", id),
	saved_connectivity("saved_connectivity", id) {
	AKANTU_DEBUG_IN();

	UInt nb_total_element = 0;
	for (auto && type :
	mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
	linearized_offsets.emplace_back(type, nb_total_element);
	nb_total_element += mesh.getConnectivity(type).size();
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	MeshPartition::~MeshPartition() = default;

	/* -------------------------------------------------------------------------- */
	UInt MeshPartition::linearized(const Element & element) {
	auto it =
	std::find_if(linearized_offsets.begin(), linearized_offsets.end(),
	[&element](auto & a) { return a.first == element.type; });
	AKANTU_DEBUG_ASSERT(it != linearized_offsets.end(),
	"A bug might be crawling around this corner...");
	return (it->second + element.element);
	}

	/* -------------------------------------------------------------------------- */
	Element MeshPartition::unlinearized(UInt lin_element) {
	ElementType type{_not_defined};
	UInt offset{0};
	for (auto & pair : linearized_offsets) {
	if (lin_element < pair.second) {
	continue;
	}
	std::tie(type, offset) = pair;
	}

	return Element{type, lin_element - offset, _not_ghost};
	}

	/* -------------------------------------------------------------------------- */
	/**
	* conversion in c++ of the METIS_MeshToDual (mesh.c) function wrote by George
	* in Metis (University of Minnesota)
	*/
	void MeshPartition::buildDualGraph(
	Array<Int> & dxadj, Array<Int> & dadjncy, Array<Int> & edge_loads,
	const std::function<Int(const Element &, const Element &)> & edge_load_func,
	Array<Int> & vertex_loads,
	const std::function<Int(const Element &)> & vertex_load_func) {

	CSR<Element> nodes_to_elements;
	MeshUtils::buildNode2Elements(mesh, nodes_to_elements);

	std::unordered_map<UInt, std::vector<UInt>> adjacent_elements;

	// for each elements look for its connected elements
	for_each_element(
	mesh,
	[&](auto && element) {
	const auto & conn =
	const_cast<const Mesh &>(mesh).getConnectivity(element);
	std::map<Element, UInt> hits;

	// count the number of nodes shared with a given element
	for (auto && node : conn) {
	for (auto && connected_element : nodes_to_elements.getRow(node)) {
	++hits[connected_element];
	}
	}

	// define a minumum number of nodes to share to be considered as a
	// ajacent element
	UInt magic_number{conn.size()};
	for (auto n : arange(mesh.getNbFacetTypes(element.type))) {
	magic_number = std::min(
	mesh.getNbNodesPerElement(mesh.getFacetType(element.type, n)),
	magic_number);
	}

	// check all neighbors to see which ones are "adjacent"
	for (auto && data : hits) {
	const auto & adjacent_element = data.first;
	// not adjacent to miself
	if (adjacent_element == element) {
	continue;
	}

	// not enough shared nodes
	if (data.second < magic_number) {
	continue;
	}

	/// Patch in order to prevent neighboring cohesive elements
	/// from detecting each other
	#if defined(AKANTU_COHESIVE_ELEMENT)
	auto element_kind = element.kind();
	auto adjacent_element_kind = adjacent_element.kind();

	if (element_kind == adjacent_element_kind &&
	element_kind == _ek_cohesive) {
	continue;
	}
	#endif

	adjacent_elements[this->linearized(element)].push_back(
	this->linearized(adjacent_element));
	}
	},
	_spatial_dimension = mesh.getSpatialDimension(),
	_element_kind = _ek_not_defined);

	// prepare the arrays
	auto nb_elements{adjacent_elements.size()};
	dxadj.resize(nb_elements + 1);
	vertex_loads.resize(nb_elements);

	for (auto && data : adjacent_elements) {
	const auto & element{data.first};
	const auto & neighbors{data.second};
	dxadj[element] = neighbors.size();
	}

	/// convert the dxadj array of sizes in a csr one of offsets
	for (UInt i = 1; i < nb_elements; ++i) {
	dxadj(i) += dxadj(i - 1);
	}
	for (UInt i = nb_elements; i > 0; --i) {
	dxadj(i) = dxadj(i - 1);
	}
	dxadj(0) = 0;

	dadjncy.resize(dxadj(nb_elements));
	edge_loads.resize(dadjncy.size());

	// fill the different arrays
	for (auto && data : adjacent_elements) {
	const auto & element{data.first};
	const auto & neighbors{data.second};

	auto unlinearized_element = unlinearized(element);
	vertex_loads(element) = vertex_load_func(unlinearized_element);

	auto pos = dxadj(element);

	for (auto && neighbor : neighbors) {
	dadjncy(pos) = neighbor;
	edge_loads(pos) =
	edge_load_func(unlinearized_element, unlinearized(neighbor));
	++pos;
	}
	}
	}

	/* -------------------------------------------------------------------------- */
	void MeshPartition::fillPartitionInformation(
	const Mesh & mesh, const Int * linearized_partitions) {
	AKANTU_DEBUG_IN();

	CSR<Element> node_to_elem;

	MeshUtils::buildNode2Elements(mesh, node_to_elem);

	UInt linearized_el = 0;
	for (const auto & type :
	mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
	UInt nb_element = mesh.getNbElement(type);
	UInt nb_nodes_per_element = Mesh::getNbNodesPerElement(type);

	auto & partition = partitions.alloc(nb_element, 1, type, _not_ghost);
	auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
	ghost_part_csr.resizeRows(nb_element);

	auto & ghost_partition_offset =
	ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
	auto & ghost_partition = ghost_partitions.alloc(0, 1, type, _ghost);

	const auto & connectivity = mesh.getConnectivity(type, _not_ghost);
	auto conn_it = connectivity.begin(connectivity.getNbComponent());

	for (UInt el = 0; el < nb_element; ++el, ++linearized_el) {
	UInt part = linearized_partitions[linearized_el];

	partition(el) = part;
	std::list<UInt> list_adj_part;
	for (UInt n = 0; n < nb_nodes_per_element; ++n) {
	auto conn = Vector<UInt>(*(conn_it + el));
	UInt node = conn(n);
	for (const auto & adj_element : node_to_elem.getRow(node)) {
	UInt adj_el = linearized(adj_element);
	UInt adj_part = linearized_partitions[adj_el];
	if (part != adj_part) {
	list_adj_part.push_back(adj_part);
	}
	}
	}

	list_adj_part.sort();
	list_adj_part.unique();

	for (auto & adj_part : list_adj_part) {
	ghost_part_csr.getRows().push_back(adj_part);
	ghost_part_csr.rowOffset(el)++;

	ghost_partition.push_back(adj_part);
	ghost_partition_offset(el)++;
	}
	}

	ghost_part_csr.countToCSR();

	/// convert the ghost_partitions_offset array in an offset array
	auto & ghost_partitions_offset_ptr = ghost_partitions_offset(type, _ghost);
	for (UInt i = 1; i < nb_element; ++i) {
	ghost_partitions_offset_ptr(i) += ghost_partitions_offset_ptr(i - 1);
	}
	for (UInt i = nb_element; i > 0; --i) {
	ghost_partitions_offset_ptr(i) = ghost_partitions_offset_ptr(i - 1);
	}
	ghost_partitions_offset_ptr(0) = 0;
	}

	// All Facets
	for (Int sp = spatial_dimension - 1; sp >= 0; --sp) {
	for (const auto & type :
	mesh.elementTypes(sp, _not_ghost, _ek_not_defined)) {
	UInt nb_element = mesh.getNbElement(type);

	auto & partition = partitions.alloc(nb_element, 1, type, _not_ghost);
	AKANTU_DEBUG_INFO("Allocating partitions for " << type);
	auto & ghost_part_csr = ghost_partitions_csr(type, _not_ghost);
	ghost_part_csr.resizeRows(nb_element);

	auto & ghost_partition_offset =
	ghost_partitions_offset.alloc(nb_element + 1, 1, type, _ghost);
	auto & ghost_partition = ghost_partitions.alloc(0, 1, type, _ghost);
	AKANTU_DEBUG_INFO("Allocating ghost_partitions for " << type);
	const Array<std::vector<Element>> & elem_to_subelem =
	mesh.getElementToSubelement(type, _not_ghost);

	// Facet loop
	for (UInt i(0); i < mesh.getNbElement(type, _not_ghost); ++i) {
	const auto & adjacent_elems = elem_to_subelem(i);
	if (adjacent_elems.empty()) {
	partition(i) = 0;
	continue;
	}
	Element min_elem{_max_element_type, std::numeric_limits<UInt>::max(),
	*(ghost_type_t{}.end())};
	UInt min_part(std::numeric_limits<UInt>::max());
	std::set<UInt> adjacent_parts;

	for (auto adj_elem : adjacent_elems) {
	if (adj_elem == ElementNull) { // case of boundary elements
	continue;
	}

	auto adjacent_elem_part = partitions(adj_elem);
	if (adjacent_elem_part < min_part) {
	min_part = adjacent_elem_part;
	min_elem = adj_elem;
	}
	adjacent_parts.insert(adjacent_elem_part);
	}
	partition(i) = min_part;

	auto git = ghost_partitions_csr(min_elem.type, _not_ghost)
	.begin(min_elem.element);
	auto gend = ghost_partitions_csr(min_elem.type, _not_ghost)
	.end(min_elem.element);
	for (; git != gend; ++git) {
	adjacent_parts.insert(*git);
	}

	adjacent_parts.erase(min_part);
	for (const auto & part : adjacent_parts) {
	ghost_part_csr.getRows().push_back(part);
	ghost_part_csr.rowOffset(i)++;
	ghost_partition.push_back(part);
	}

	ghost_partition_offset(i + 1) =
	ghost_partition_offset(i + 1) + adjacent_elems.size();
	}
	ghost_part_csr.countToCSR();
	}
	}
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void MeshPartition::tweakConnectivity() {
	AKANTU_DEBUG_IN();

	MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));

	for (auto && type :
	mesh.elementTypes(spatial_dimension, _not_ghost, _ek_not_defined)) {
	auto & connectivity = mesh_accessor.getConnectivity(type, _not_ghost);

	auto & saved_conn = saved_connectivity.alloc(
	connectivity.size(), connectivity.getNbComponent(), type, _not_ghost);
	saved_conn.copy(connectivity);

	for (auto && conn :
	make_view(connectivity, connectivity.getNbComponent())) {
	for (auto && node : conn) {
	if (mesh.isPeriodicSlave(node)) {
	node = mesh.getPeriodicMaster(node);
	}
	}
	}
	}

	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	void MeshPartition::restoreConnectivity() {
	AKANTU_DEBUG_IN();
	MeshAccessor mesh_accessor(const_cast<Mesh &>(mesh));
	for (auto && type : saved_connectivity.elementTypes(
	spatial_dimension, _not_ghost, _ek_not_defined)) {
	auto & conn = mesh_accessor.getConnectivity(type, _not_ghost);
	auto & saved_conn = saved_connectivity(type, _not_ghost);
	conn.copy(saved_conn);
	}
	AKANTU_DEBUG_OUT();
	}

	/* -------------------------------------------------------------------------- */
	bool MeshPartition::hasPartitions(ElementType type, GhostType ghost_type) {
	return partitions.exists(type, ghost_type);
	}

	/* -------------------------------------------------------------------------- */
	void MeshPartition::printself(std::ostream & stream, int indent) const {
	std::string space(indent, AKANTU_INDENT);
	stream << space << "MeshPartition ["
	<< "\n";
	stream << space << " + id : " << id << "\n";
	stream << space << " + nb partitions: " << nb_partitions << "\n";
	stream << space << " + partitions [ "
	<< "\n";
	partitions.printself(stream, indent + 2);
	stream << space << " ]"
	<< "\n";
	stream << space << "]"
	<< "\n";
	}

	/* -------------------------------------------------------------------------- */

	} // namespace akantu

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