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rAKA/src/mesh/mesh_periodic.cc
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mesh_periodic.cc
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/**
* @file mesh_pbc.cc
*
* @author Nicolas Richart
*
* @date creation Sat Feb 10 2018
*
* @brief Implementation of the perdiodicity capabilities in the mesh
*
* @section LICENSE
*
* Copyright (©) 2010-2011 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() {}
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)
: node(other.node), position(other.position),
direction_position(other.direction_position) {}
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 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",
this->getMemoryID(), false);
}
this->periodic_node_synchronizer->update();
}
} // namespace akantu
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