Homec4science
Diffusion akantu (features/joss-2021) Browse

rAKA/src/mesh/mesh_periodic.cc
033a8225e32afeatures/joss-2021

Last Change
Raw File

mesh_periodic.cc
View Options

/**
* @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 "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);
}
/* -------------------------------------------------------------------------- */
/* -------------------------------------------------------------------------- */
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.};
};
}
/* -------------------------------------------------------------------------- */
// 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;
/* ---------------------------------------------------------------------- */
auto extract_and_send_nodes = [&](const auto & bbox, const auto & node_list,
auto & send_buffers, auto proc,
auto cnt) {
send_buffers.emplace_back();
auto & buffer = send_buffers.back();
for (auto & info : node_list) {
if (bbox.contains(info.position) and isLocalOrMasterNode(info.node)) {
Vector<Real> pos = info.position;
pos(direction) = info.direction_position;
buffer << getNodeGlobalId(info.node);
buffer << pos;
buffer << ((*nodes_flags)(info.node) & NodeFlag::_periodic_mask);
// if is slave sends master info
if (isPeriodicSlave(info.node)) {
buffer << getNodeGlobalId(periodic_slave_master[info.node]);
}
// if is master sends list of slaves
if (isPeriodicMaster(info.node)) {
UInt nb_slaves = periodic_master_slave.count(info.node);
buffer << nb_slaves;
auto slaves = periodic_master_slave.equal_range(info.node);
for (auto it = slaves.first; it != slaves.second; ++it) {
UInt gslave = getNodeGlobalId(it->second);
buffer << gslave;
}
}
}
}
auto tag = Tag::genTag(prank, cnt, Tag::_PERIODIC_NODES);
return communicator->asyncSend(buffer, proc, tag);
};
/* ---------------------------------------------------------------------- */
auto recv_and_extract_nodes = [&](auto & bbox, auto & node_list,
const auto proc, auto cnt) {
if (not bbox)
return;
DynamicCommunicationBuffer buffer;
auto tag = Tag::genTag(proc, cnt, Tag::_PERIODIC_NODES);
communicator->receive(buffer, proc, tag);
while (not buffer.empty()) {
Vector<Real> pos(spatial_dimension);
UInt global_node;
NodeFlag flag;
buffer >> global_node;
buffer >> pos;
buffer >> flag;
auto local_node = getNodeLocalId(global_node);
// get the master info of is slave
if ((flag & NodeFlag::_periodic_mask) == NodeFlag::_periodic_slave) {
UInt master_node;
buffer >> master_node;
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;
for (auto ns[[gnu::unused]] : arange(nb_slaves)) {
UInt gslave_node;
buffer >> gslave_node;
auto lslave_node = getNodeLocalId(gslave_node);
AKANTU_DEBUG_ASSERT(lslave_node != UInt(-1),
"Should I know the slave node " << gslave_node);
}
}
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);
auto prank = communicator->whoAmI();
auto nb_proc = communicator->getNbProc();
using buffers_t = std::vector<DynamicCommunicationBuffer>;
std::vector<CommunicationRequest> send_requests;
buffers_t send_buffers;
for (auto && data : zip(arange(nb_proc), intersections_with_left,
intersections_with_right)) {
auto proc = std::get<0>(data);
if (proc == prank)
continue;
// Send nodes from local right side if intersects with remote left side
const auto & intersection_with_p_left = std::get<1>(data);
if (intersection_with_p_left) {
send_requests.push_back(extract_and_send_nodes(
intersection_with_p_left, nodes_right, send_buffers, proc, 0));
}
// Send nodes from local left side if intersects with remote right side
const auto & intersection_with_p_right = std::get<2>(data);
if (intersection_with_p_right) {
send_requests.push_back(extract_and_send_nodes(
intersection_with_p_right, nodes_left, send_buffers, proc, 1));
}
}
for (auto && data : zip(arange(nb_proc), intersections_with_left,
intersections_with_right)) {
auto proc = std::get<0>(data);
if (proc == prank)
continue;
// Receive remote left nodes to merge with local left nodes
const auto & intersections_with_left = std::get<1>(data);
recv_and_extract_nodes(intersections_with_left, nodes_left, proc, 1);
// Receive remote right nodes to merge with local right nodes
const auto & intersections_with_right = std::get<2>(data);
recv_and_extract_nodes(intersections_with_right, nodes_right, proc, 0);
}
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);
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(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);
}
};
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);
}
};
auto match_pairs = [&](auto & nodes_1, auto & nodes_2) {
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 (; it_cur != nodes_2.end(); ++it_cur) {
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 (this->is_distributed) {
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();
}
}
} // akantu
c4science · Help