mesh_periodic.cc
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mesh_periodic.cc
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	/**
	* @file mesh_periodic.cc
	*
	* @author Nicolas Richart <nicolas.richart@epfl.ch>
	*
	* @date creation: Mon Feb 12 2018
	* @date last modification: Sun Mar 15 2020
	*
	* @brief Implementation of the perdiodicity capabilities in the mesh
	*
	*
	* @section LICENSE
	*
	* Copyright (©) 2016-2021 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 "communication_tag.hh"
	#include "communicator.hh"
	#include "element_group.hh"
	#include "mesh.hh"
	#include "periodic_node_synchronizer.hh"
	/* -------------------------------------------------------------------------- */

	namespace akantu {

	/* -------------------------------------------------------------------------- */
	void Mesh::makePeriodic(const SpatialDirection & direction) {
	Array<UInt> list_1;
	Array<UInt> list_2;
	Real tolerance = 1e-10;

	auto lower_bound = this->getLowerBounds();
	auto upper_bound = this->getUpperBounds();
	auto length = upper_bound(direction) - lower_bound(direction);

	const auto & positions = *nodes;

	for (auto && data : enumerate(make_view(positions, spatial_dimension))) {
	UInt node = std::get<0>(data);
	const auto & pos = std::get<1>(data);

	if (std::abs((pos(direction) - lower_bound(direction)) / length) <
	tolerance) {
	list_1.push_back(node);
	}

	if (std::abs((pos(direction) - upper_bound(direction)) / length) <
	tolerance) {
	list_2.push_back(node);
	}
	}

	this->makePeriodic(direction, list_1, list_2);
	}

	/* -------------------------------------------------------------------------- */
	void Mesh::makePeriodic(const SpatialDirection & direction, const ID & list_1,
	const ID & list_2) {
	const auto & list_nodes_1 =
	mesh.getElementGroup(list_1).getNodeGroup().getNodes();
	const auto & list_nodes_2 =
	mesh.getElementGroup(list_2).getNodeGroup().getNodes();

	this->makePeriodic(direction, list_nodes_1, list_nodes_2);
	}

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

	namespace {
	struct NodeInfo {
	NodeInfo() = default;
	NodeInfo(UInt spatial_dimension) : position(spatial_dimension) {}
	NodeInfo(UInt node, const Vector<Real> & position,
	const SpatialDirection & direction)
	: node(node), position(position) {
	this->direction_position = position(direction);
	this->position(direction) = 0.;
	}

	NodeInfo(const NodeInfo & other) = default;
	NodeInfo(NodeInfo && other) noexcept = default;
	NodeInfo & operator=(const NodeInfo & other) = default;
	NodeInfo & operator=(NodeInfo && other) = default;

	UInt node{0};
	Vector<Real> position;
	Real direction_position{0.};
	};
	} // namespace

	/* -------------------------------------------------------------------------- */
	// left is for lower values on direction and right for highest values
	void Mesh::makePeriodic(const SpatialDirection & direction,
	const Array<UInt> & list_left,
	const Array<UInt> & list_right) {
	Real tolerance = 1e-10;

	const auto & positions = *nodes;
	auto lower_bound = this->getLowerBounds();
	auto upper_bound = this->getUpperBounds();
	auto length = upper_bound(direction) - lower_bound(direction);

	lower_bound(direction) = 0;
	upper_bound(direction) = 0;

	auto prank = communicator->whoAmI();

	std::vector<NodeInfo> nodes_left(list_left.size());
	std::vector<NodeInfo> nodes_right(list_right.size());

	BBox bbox(spatial_dimension);
	auto to_position = [&](UInt node) {
	Vector<Real> pos(spatial_dimension);
	for (UInt s : arange(spatial_dimension)) {
	pos(s) = positions(node, s);
	}
	auto && info = NodeInfo(node, pos, direction);
	bbox += info.position;
	return std::move(info);
	};

	std::transform(list_left.begin(), list_left.end(), nodes_left.begin(),
	to_position);
	BBox bbox_left = bbox;

	bbox.reset();
	std::transform(list_right.begin(), list_right.end(), nodes_right.begin(),
	to_position);
	BBox bbox_right = bbox;

	std::vector<UInt> new_nodes;
	if (is_distributed) {
	NewNodesEvent event(AKANTU_CURRENT_FUNCTION);

	/* ---------------------------------------------------------------------- */
	// function to send nodes in bboxes intersections
	auto extract_and_send_nodes = [&](const auto & bbox, const auto & node_list,
	auto & buffers, auto proc, auto cnt) {
	// buffers.resize(buffers.size() + 1);
	buffers.push_back(std::make_unique<DynamicCommunicationBuffer>());
	auto & buffer = *buffers.back();

	// std::cout << "Sending to " << proc << std::endl;
	for (auto & info : node_list) {
	if (bbox.contains(info.position) and isLocalOrMasterNode(info.node)) {
	Vector<Real> pos = info.position;
	pos(direction) = info.direction_position;

	NodeFlag flag = (*nodes_flags)(info.node) & NodeFlag::_periodic_mask;
	UInt gnode = getNodeGlobalId(info.node);
	buffer << gnode;
	buffer << pos;
	buffer << flag;

	// std::cout << " - node " << getNodeGlobalId(info.node);

	// if is slave sends master info
	if (flag == NodeFlag::_periodic_slave) {
	UInt master = getNodeGlobalId(periodic_slave_master[info.node]);
	// std::cout << " slave of " << master << std::endl;
	buffer << master;
	}

	// if is master sends list of slaves
	if (flag == NodeFlag::_periodic_master) {
	UInt nb_slaves = periodic_master_slave.count(info.node);
	buffer << nb_slaves;

	// std::cout << " master of " << nb_slaves << " nodes : [";
	auto slaves = periodic_master_slave.equal_range(info.node);
	for (auto it = slaves.first; it != slaves.second; ++it) {
	UInt gslave = getNodeGlobalId(it->second);
	// std::cout << (it == slaves.first ? "" : ", ") << gslave;
	buffer << gslave;
	}
	// std::cout << "]";
	}
	// std::cout << std::endl;
	}
	}

	auto tag = Tag::genTag(prank, 10 * direction + cnt, Tag::_periodic_nodes);
	// std::cout << "SBuffer size " << buffer.size() << " " << tag <<
	// std::endl;
	return communicator->asyncSend(buffer, proc, tag);
	};

	/* ---------------------------------------------------------------------- */
	// function to receive nodes in bboxes intersections
	auto recv_and_extract_nodes = [&](auto & node_list, const auto proc,
	auto cnt) {
	DynamicCommunicationBuffer buffer;
	auto tag = Tag::genTag(proc, 10 * direction + cnt, Tag::_periodic_nodes);
	communicator->receive(buffer, proc, tag);
	// std::cout << "RBuffer size " << buffer.size() << " " << tag <<
	// std::endl; std::cout << "Receiving from " << proc << std::endl;

	while (not buffer.empty()) {
	Vector<Real> pos(spatial_dimension);
	UInt global_node;
	NodeFlag flag;
	buffer >> global_node;
	buffer >> pos;
	buffer >> flag;

	// std::cout << " - node " << global_node;
	auto local_node = getNodeLocalId(global_node);

	// get the master info of is slave
	if (flag == NodeFlag::_periodic_slave) {
	UInt master_node;
	buffer >> master_node;
	// std::cout << " slave of " << master_node << std::endl;
	// auto local_master_node = getNodeLocalId(master_node);
	// AKANTU_DEBUG_ASSERT(local_master_node != UInt(-1),
	//"Should I know the master node " << master_node);
	}

	// get the list of slaves if is master
	if ((flag & NodeFlag::_periodic_mask) == NodeFlag::_periodic_master) {
	UInt nb_slaves;
	buffer >> nb_slaves;
	// std::cout << " master of " << nb_slaves << " nodes : [";
	for (auto ns [[gnu::unused]] : arange(nb_slaves)) {
	UInt gslave_node;
	buffer >> gslave_node;
	// std::cout << (ns == 0 ? "" : ", ") << gslave_node;
	// auto lslave_node = getNodeLocalId(gslave_node);
	// AKANTU_DEBUG_ASSERT(lslave_node != UInt(-1),
	// "Should I know the slave node " <<
	// gslave_node);
	}
	// std::cout << "]";
	}
	// std::cout << std::endl;
	if (local_node != UInt(-1)) {
	continue;
	}

	local_node = nodes->size();

	NodeInfo info(local_node, pos, direction);
	nodes->push_back(pos);
	nodes_global_ids->push_back(global_node);
	nodes_flags->push_back(flag \| NodeFlag::_pure_ghost);
	new_nodes.push_back(info.node);
	node_list.push_back(info);

	nodes_prank[info.node] = proc;
	event.getList().push_back(local_node);
	}
	};

	/* ---------------------------------------------------------------------- */
	auto && intersections_with_right =
	bbox_left.intersection(bbox_right, *communicator);
	auto && intersections_with_left =
	bbox_right.intersection(bbox_left, *communicator);

	std::vector<CommunicationRequest> send_requests;
	std::vector<std::unique_ptr<DynamicCommunicationBuffer>> send_buffers;

	// sending nodes in the common zones
	auto send_intersections = [&](auto & intersections, auto send_count) {
	for (auto && data : intersections) {
	auto proc = std::get<0>(data);

	// Send local nodes if intersects with remote
	const auto & intersection_with_proc = std::get<1>(data);
	if (intersection_with_proc) {
	send_requests.push_back(
	extract_and_send_nodes(intersection_with_proc, nodes_right,
	send_buffers, proc, send_count));
	}

	send_count += 2;
	}
	};

	auto recv_intersections = [&](auto & intersections, auto recv_count) {
	for (auto && data : intersections) {
	auto proc = std::get<0>(data);

	// receive remote nodes if intersects with local
	const auto & intersection_with_proc = std::get<1>(data);
	if (intersection_with_proc) {
	recv_and_extract_nodes(nodes_right, proc, recv_count);
	}

	recv_count += 2;
	}
	};

	send_intersections(intersections_with_left, 0);
	send_intersections(intersections_with_right, 1);

	recv_intersections(intersections_with_right, 0);
	recv_intersections(intersections_with_right, 1);

	Communicator::waitAll(send_requests);
	Communicator::freeCommunicationRequest(send_requests);

	this->sendEvent(event);
	} // end distributed work

	auto to_sort = [&](auto && info1, auto && info2) -> bool {
	return info1.position < info2.position;
	};

	// sort nodes based on their distance to lower corner
	std::sort(nodes_left.begin(), nodes_left.end(), to_sort);
	std::sort(nodes_right.begin(), nodes_right.end(), to_sort);

	// function to change the master of nodes
	auto updating_master = [&](auto & old_master, auto & new_master) {
	if (old_master == new_master) {
	return;
	}

	auto slaves = periodic_master_slave.equal_range(old_master);
	AKANTU_DEBUG_ASSERT(
	isPeriodicMaster(
	old_master), // slaves.first != periodic_master_slave.end(),
	"Cannot update master " << old_master << ", its not a master node!");
	decltype(periodic_master_slave) tmp_master_slave;
	for (auto it = slaves.first; it != slaves.second; ++it) {
	auto slave = it->second;
	tmp_master_slave.insert(std::make_pair(new_master, slave));
	periodic_slave_master[slave] = new_master;
	}

	periodic_master_slave.erase(old_master);
	(*nodes_flags)[old_master] &= ~NodeFlag::_periodic_master;
	addPeriodicSlave(old_master, new_master);

	for (auto && data : tmp_master_slave) {
	addPeriodicSlave(data.second, data.first);
	}
	};

	// handling 2 nodes that are periodic
	auto match_found = [&](auto & info1, auto & info2) {
	const auto & node1 = info1.node;
	const auto & node2 = info2.node;

	auto master = node1;
	bool node1_side_master = false;
	if (isPeriodicMaster(node1)) {
	node1_side_master = true;
	} else if (isPeriodicSlave(node1)) {
	node1_side_master = true;
	master = periodic_slave_master[node1];
	}

	auto node2_master = node2;
	if (isPeriodicSlave(node2)) {
	node2_master = periodic_slave_master[node2];
	}

	if (node1_side_master) {
	if (isPeriodicSlave(node2)) {
	updating_master(node2_master, master);
	return;
	}

	if (isPeriodicMaster(node2)) {
	updating_master(node2, master);
	return;
	}

	addPeriodicSlave(node2, master);
	} else {
	if (isPeriodicSlave(node2)) {
	addPeriodicSlave(node1, node2_master);
	return;
	}

	if (isPeriodicMaster(node2)) {
	addPeriodicSlave(node1, node2);
	return;
	}

	addPeriodicSlave(node2, node1);
	}
	};

	// matching the nodes from 2 lists
	auto match_pairs = [&](auto & nodes_1, auto & nodes_2) {
	// Guillaume to Nico: It seems that the list of nodes is not sorted
	// as it was: therefore the loop cannot be truncated anymore.
	// Otherwise many pairs are missing.
	// I replaced (temporarily?) for the N^2 loop so as not to miss
	// any pbc pair.
	//

	// auto it = nodes_2.begin();
	// for every nodes in 1st list
	for (auto && info1 : nodes_1) {
	auto & pos1 = info1.position;
	// auto it_cur = it;

	// try to find a match in 2nd list
	for (auto && info2 : nodes_2) {
	// auto & info2 = *it_cur;
	auto & pos2 = info2.position;

	auto dist = pos1.distance(pos2) / length;
	if (dist < tolerance) {
	// handles the found matches
	match_found(info1, info2);
	// it = it_cur;
	break;
	}
	}
	}
	};

	match_pairs(nodes_left, nodes_right);
	// match_pairs(nodes_right, nodes_left);

	this->updatePeriodicSynchronizer();

	this->is_periodic = true;
	}

	/* -------------------------------------------------------------------------- */
	void Mesh::wipePeriodicInfo() {
	this->is_periodic = false;

	this->periodic_slave_master.clear();
	this->periodic_master_slave.clear();

	for (auto && flags : *nodes_flags) {
	flags &= ~NodeFlag::_periodic_mask;
	}
	}

	/* -------------------------------------------------------------------------- */
	void Mesh::updatePeriodicSynchronizer() {
	if (not this->periodic_node_synchronizer) {
	this->periodic_node_synchronizer =
	std::make_unique<PeriodicNodeSynchronizer>(
	*this, this->getID() + ":periodic_synchronizer", false);
	}

	this->periodic_node_synchronizer->update();
	}

	} // namespace akantu

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