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SetResumeFrom.hpp
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Stéphane Del Pino authored
It allows to simply manipulate checkpoint files - get list of available checkpoints - change resuming checkpoint - get the script that was used to produce a given checkpoint
Stéphane Del Pino authoredIt allows to simply manipulate checkpoint files - get list of available checkpoints - change resuming checkpoint - get the script that was used to produce a given checkpoint
MeshNodeBoundary.hpp 15.13 KiB
#ifndef MESH_NODE_BOUNDARY_HPP
#define MESH_NODE_BOUNDARY_HPP
#include <Kokkos_Vector.hpp>
#include <algebra/TinyVector.hpp>
#include <mesh/ConnectivityMatrix.hpp>
#include <mesh/IConnectivity.hpp>
#include <mesh/ItemValue.hpp>
#include <mesh/RefItemList.hpp>
#include <utils/Array.hpp>
#include <utils/Exceptions.hpp>
#include <utils/Messenger.hpp>
template <size_t Dimension>
class MeshNodeBoundary // clazy:exclude=copyable-polymorphic
{
protected:
Array<const NodeId> m_node_list;
std::string m_boundary_name;
public:
MeshNodeBoundary& operator=(const MeshNodeBoundary&) = default;
MeshNodeBoundary& operator=(MeshNodeBoundary&&) = default;
const Array<const NodeId>&
nodeList() const
{
return m_node_list;
}
template <typename MeshType>
MeshNodeBoundary(const MeshType& mesh, const RefFaceList& ref_face_list)
: m_boundary_name(ref_face_list.refId().tagName())
{
static_assert(Dimension == MeshType::Dimension);
const auto& face_to_cell_matrix = mesh.connectivity().faceToCellMatrix();
const Array<const FaceId>& face_list = ref_face_list.list();
parallel_for(
face_list.size(), PUGS_LAMBDA(int l) {
const auto& face_cells = face_to_cell_matrix[face_list[l]];
if (face_cells.size() > 1) {
std::ostringstream ost;
ost << "invalid boundary " << rang::fgB::yellow << this->m_boundary_name << rang::style::reset
<< ": inner faces cannot be used to define mesh boundaries";
throw NormalError(ost.str());
}
});
Kokkos::vector<unsigned int> node_ids;
// not enough but should reduce significantly the number of resizing
node_ids.reserve(Dimension * face_list.size());
const auto& face_to_node_matrix = mesh.connectivity().faceToNodeMatrix();
for (size_t l = 0; l < face_list.size(); ++l) {
const FaceId face_number = face_list[l];
const auto& face_nodes = face_to_node_matrix[face_number];
for (size_t r = 0; r < face_nodes.size(); ++r) {
node_ids.push_back(face_nodes[r]);
}
}
std::sort(node_ids.begin(), node_ids.end());
auto last = std::unique(node_ids.begin(), node_ids.end());
node_ids.resize(std::distance(node_ids.begin(), last));
Array<NodeId> node_list(node_ids.size());
parallel_for(
node_ids.size(), PUGS_LAMBDA(int r) { node_list[r] = node_ids[r]; });
m_node_list = node_list;
}
template <typename MeshType>
MeshNodeBoundary(const MeshType&, const RefNodeList& ref_node_list)
: m_node_list(ref_node_list.list()), m_boundary_name(ref_node_list.refId().tagName())
{
static_assert(Dimension == MeshType::Dimension);
}
MeshNodeBoundary() = default;
virtual ~MeshNodeBoundary() = default;
protected:
MeshNodeBoundary(const MeshNodeBoundary&) = default;
MeshNodeBoundary(MeshNodeBoundary&&) = default;
};
template <size_t Dimension>
class MeshFlatNodeBoundary : public MeshNodeBoundary<Dimension> // clazy:exclude=copyable-polymorphic
{
public:
using Rd = TinyVector<Dimension, double>;
private:
const Rd m_outgoing_normal;
template <typename MeshType>
PUGS_INLINE Rd _getNormal(const MeshType& mesh);
template <typename MeshType>
PUGS_INLINE void
_checkBoundaryIsFlat(const TinyVector<Dimension, double>& normal,
const TinyVector<Dimension, double>& origin,
const double length,
const MeshType& mesh) const
{
static_assert(MeshType::Dimension == Dimension);
const NodeValue<const Rd>& xr = mesh.xr();
parallel_for(
this->m_node_list.size(), PUGS_LAMBDA(const size_t r) {
const Rd& x = xr[this->m_node_list[r]];
if (dot(x - origin, normal) > 1E-13 * length) {
std::ostringstream ost;
ost << "invalid boundary " << rang::fgB::yellow << this->m_boundary_name << rang::style::reset
<< ": boundary is not flat!";
throw NormalError(ost.str());
}
});
}
template <typename MeshType>
PUGS_INLINE Rd _getOutgoingNormal(const MeshType& mesh);
public:
const Rd&
outgoingNormal() const
{
return m_outgoing_normal;
}
MeshFlatNodeBoundary& operator=(const MeshFlatNodeBoundary&) = default;
MeshFlatNodeBoundary& operator=(MeshFlatNodeBoundary&&) = default;
template <typename MeshType>
MeshFlatNodeBoundary(const MeshType& mesh, const RefFaceList& ref_face_list)
: MeshNodeBoundary<Dimension>(mesh, ref_face_list), m_outgoing_normal(_getOutgoingNormal(mesh))
{
;
}
template <typename MeshType>
MeshFlatNodeBoundary(const MeshType& mesh, const RefNodeList& ref_node_list)
: MeshNodeBoundary<Dimension>(mesh, ref_node_list), m_outgoing_normal(_getOutgoingNormal(mesh))
{
;
}
MeshFlatNodeBoundary() = default;
MeshFlatNodeBoundary(const MeshFlatNodeBoundary&) = default;
MeshFlatNodeBoundary(MeshFlatNodeBoundary&&) = default;
virtual ~MeshFlatNodeBoundary() = default;
};
template <>
template <typename MeshType>
PUGS_INLINE TinyVector<1, double>
MeshFlatNodeBoundary<1>::_getNormal(const MeshType& mesh)
{
static_assert(MeshType::Dimension == 1);
using R = TinyVector<1, double>;
const size_t number_of_bc_nodes = [&]() {
size_t number_of_bc_nodes = 0;
auto node_is_owned = mesh.connectivity().nodeIsOwned();
for (size_t i_node = 0; i_node < m_node_list.size(); ++i_node) {
number_of_bc_nodes += (node_is_owned[m_node_list[i_node]]);
}
return parallel::allReduceMax(number_of_bc_nodes);
}();
if (number_of_bc_nodes != 1) {
std::ostringstream ost;
ost << "invalid boundary " << rang::fgB::yellow << m_boundary_name << rang::style::reset
<< ": node boundaries in 1D require to have exactly 1 node";
throw NormalError(ost.str());
}
return R{1};
}
template <>
template <typename MeshType>
PUGS_INLINE TinyVector<2, double>
MeshFlatNodeBoundary<2>::_getNormal(const MeshType& mesh)
{
static_assert(MeshType::Dimension == 2);
using R2 = TinyVector<2, double>;
const NodeValue<const R2>& xr = mesh.xr();
R2 xmin(std::numeric_limits<double>::max(), std::numeric_limits<double>::max());
R2 xmax(-std::numeric_limits<double>::max(), -std::numeric_limits<double>::max());
auto update_xmin = [](const R2& x, R2& xmin) {
if ((x[0] < xmin[0]) or ((x[0] == xmin[0]) and (x[1] < xmin[1]))) {
xmin = x;
}
};
auto update_xmax = [](const R2& x, R2& xmax) {
if ((x[0] > xmax[0]) or ((x[0] == xmax[0]) and (x[1] > xmax[1]))) {
xmax = x;
}
};
for (size_t r = 0; r < m_node_list.size(); ++r) {
const R2& x = xr[m_node_list[r]];
update_xmin(x, xmin);
update_xmax(x, xmax);
}
if (parallel::size() > 1) {
Array<R2> xmin_array = parallel::allGather(xmin);
Array<R2> xmax_array = parallel::allGather(xmax);
for (size_t i = 0; i < xmin_array.size(); ++i) {
update_xmin(xmin_array[i], xmin);
}
for (size_t i = 0; i < xmax_array.size(); ++i) {
update_xmax(xmax_array[i], xmax);
}
}
if (xmin == xmax) {
std::ostringstream ost;
ost << "invalid boundary " << rang::fgB::yellow << this->m_boundary_name << rang::style::reset
<< ": unable to compute normal";
throw NormalError(ost.str());
}
R2 dx = xmax - xmin;
dx *= 1. / l2Norm(dx);
const R2 normal(-dx[1], dx[0]);
this->_checkBoundaryIsFlat(normal, 0.5 * (xmin + xmax), l2Norm(xmax - xmin), mesh);
return normal;
}
template <>
template <typename MeshType>
PUGS_INLINE TinyVector<3, double>
MeshFlatNodeBoundary<3>::_getNormal(const MeshType& mesh)
{
static_assert(MeshType::Dimension == 3);
using R3 = TinyVector<3, double>;
auto update_xmin = [](const R3& x, R3& xmin) {
// XMIN: X.xmin X.ymax X.zmax
if ((x[0] < xmin[0]) or ((x[0] == xmin[0]) and (x[1] > xmin[1])) or
((x[0] == xmin[0]) and (x[1] == xmin[1]) and (x[2] > xmin[2]))) {
xmin = x;
}
};
auto update_xmax = [](const R3& x, R3& xmax) {
// XMAX: X.xmax X.ymin X.zmin
if ((x[0] > xmax[0]) or ((x[0] == xmax[0]) and (x[1] < xmax[1])) or
((x[0] == xmax[0]) and (x[1] == xmax[1]) and (x[2] < xmax[2]))) {
xmax = x;
}
};
auto update_ymin = [](const R3& x, R3& ymin) {
// YMIN: X.ymin X.zmax X.xmin
if ((x[1] < ymin[1]) or ((x[1] == ymin[1]) and (x[2] > ymin[2])) or
((x[1] == ymin[1]) and (x[2] == ymin[2]) and (x[0] < ymin[0]))) {
ymin = x;
}
};
auto update_ymax = [](const R3& x, R3& ymax) {
// YMAX: X.ymax X.zmin X.xmax
if ((x[1] > ymax[1]) or ((x[1] == ymax[1]) and (x[2] < ymax[2])) or
((x[1] == ymax[1]) and (x[2] == ymax[1]) and (x[0] > ymax[0]))) {
ymax = x;
}
};
auto update_zmin = [](const R3& x, R3& zmin) {
// ZMIN: X.zmin X.xmin X.ymin
if ((x[2] < zmin[2]) or ((x[2] == zmin[2]) and (x[2] < zmin[2])) or
((x[1] == zmin[1]) and (x[2] == zmin[1]) and (x[0] < zmin[0]))) {
zmin = x;
}
};
auto update_zmax = [](const R3& x, R3& zmax) {
// ZMAX: X.zmax X.xmax X.ymax
if ((x[2] > zmax[2]) or ((x[2] == zmax[2]) and (x[2] > zmax[2])) or
((x[1] == zmax[1]) and (x[2] == zmax[1]) and (x[0] > zmax[0]))) {
zmax = x;
}
};
R3 xmin(std::numeric_limits<double>::max(), std::numeric_limits<double>::max(), std::numeric_limits<double>::max());
R3 ymin = xmin;
R3 zmin = xmin;
R3 xmax = -xmin;
R3 ymax = xmax;
R3 zmax = xmax;
const NodeValue<const R3>& xr = mesh.xr();
for (size_t r = 0; r < m_node_list.size(); ++r) {
const R3& x = xr[m_node_list[r]];
update_xmin(x, xmin);
update_xmax(x, xmax);
update_ymin(x, ymin);
update_ymax(x, ymax);
update_zmin(x, zmin);
update_zmax(x, zmax);
}
if (parallel::size() > 0) {
Array<const R3> xmin_array = parallel::allGather(xmin);
Array<const R3> xmax_array = parallel::allGather(xmax);
Array<const R3> ymin_array = parallel::allGather(ymin);
Array<const R3> ymax_array = parallel::allGather(ymax);
Array<const R3> zmin_array = parallel::allGather(zmin);
Array<const R3> zmax_array = parallel::allGather(zmax);
for (size_t i = 0; i < xmin_array.size(); ++i) {
update_xmin(xmin_array[i], xmin);
}
for (size_t i = 0; i < ymin_array.size(); ++i) {
update_ymin(ymin_array[i], ymin);
}
for (size_t i = 0; i < zmin_array.size(); ++i) {
update_zmin(zmin_array[i], zmin);
}
for (size_t i = 0; i < xmax_array.size(); ++i) {
update_xmax(xmax_array[i], xmax);
}
for (size_t i = 0; i < ymax_array.size(); ++i) {
update_ymax(ymax_array[i], ymax);
}
for (size_t i = 0; i < zmax_array.size(); ++i) {
update_zmax(zmax_array[i], zmax);
}
}
const R3 u = xmax - xmin;
const R3 v = ymax - ymin;
const R3 w = zmax - zmin;
const R3 uv = crossProduct(u, v);
const double uv_l2 = dot(uv, uv);
R3 normal = uv;
double normal_l2 = uv_l2;
const R3 uw = crossProduct(u, w);
const double uw_l2 = dot(uw, uw);
if (uw_l2 > uv_l2) {
normal = uw;
normal_l2 = uw_l2;
}
const R3 vw = crossProduct(v, w);
const double vw_l2 = dot(vw, vw);
if (vw_l2 > normal_l2) {
normal = vw;
normal_l2 = vw_l2;
}
if (normal_l2 == 0) {
std::ostringstream ost;
ost << "invalid boundary " << rang::fgB::yellow << this->m_boundary_name << rang::style::reset
<< ": unable to compute normal";
throw NormalError(ost.str());
}
const double length = sqrt(normal_l2);
normal *= 1. / length;
this->_checkBoundaryIsFlat(normal, 1. / 6. * (xmin + xmax + ymin + ymax + zmin + zmax), length, mesh);
return normal;
}
template <>
template <typename MeshType>
PUGS_INLINE TinyVector<1, double>
MeshFlatNodeBoundary<1>::_getOutgoingNormal(const MeshType& mesh)
{
static_assert(MeshType::Dimension == 1);
using R = TinyVector<1, double>;
const R normal = this->_getNormal(mesh);
double max_height = 0;
if (m_node_list.size() > 0) {
const NodeValue<const R>& xr = mesh.xr();
const auto& cell_to_node_matrix = mesh.connectivity().cellToNodeMatrix();
const auto& node_to_cell_matrix = mesh.connectivity().nodeToCellMatrix();
const NodeId r0 = m_node_list[0];
const CellId j0 = node_to_cell_matrix[r0][0];
const auto& j0_nodes = cell_to_node_matrix[j0];
for (size_t r = 0; r < j0_nodes.size(); ++r) {
const double height = dot(xr[j0_nodes[r]] - xr[r0], normal);
if (std::abs(height) > std::abs(max_height)) {
max_height = height;
}
}
}
Array<double> max_height_array = parallel::allGather(max_height);
for (size_t i = 0; i < max_height_array.size(); ++i) {
const double height = max_height_array[i];
if (std::abs(height) > std::abs(max_height)) {
max_height = height;
}
}
if (max_height > 0) {
return -normal;
} else {
return normal;
}
}
template <>
template <typename MeshType>
PUGS_INLINE TinyVector<2, double>
MeshFlatNodeBoundary<2>::_getOutgoingNormal(const MeshType& mesh)
{
static_assert(MeshType::Dimension == 2);
using R2 = TinyVector<2, double>;
const R2 normal = this->_getNormal(mesh);
double max_height = 0;
if (m_node_list.size() > 0) {
const NodeValue<const R2>& xr = mesh.xr();
const auto& cell_to_node_matrix = mesh.connectivity().cellToNodeMatrix();
const auto& node_to_cell_matrix = mesh.connectivity().nodeToCellMatrix();
const NodeId r0 = m_node_list[0];
const CellId j0 = node_to_cell_matrix[r0][0];
const auto& j0_nodes = cell_to_node_matrix[j0];
for (size_t r = 0; r < j0_nodes.size(); ++r) {
const double height = dot(xr[j0_nodes[r]] - xr[r0], normal);
if (std::abs(height) > std::abs(max_height)) {
max_height = height;
}
}
}
Array<double> max_height_array = parallel::allGather(max_height);
for (size_t i = 0; i < max_height_array.size(); ++i) {
const double height = max_height_array[i];
if (std::abs(height) > std::abs(max_height)) {
max_height = height;
}
}
if (max_height > 0) {
return -normal;
} else {
return normal;
}
}
template <>
template <typename MeshType>
PUGS_INLINE TinyVector<3, double>
MeshFlatNodeBoundary<3>::_getOutgoingNormal(const MeshType& mesh)
{
static_assert(MeshType::Dimension == 3);
using R3 = TinyVector<3, double>;
const R3 normal = this->_getNormal(mesh);
double max_height = 0;
if (m_node_list.size() > 0) {
const NodeValue<const R3>& xr = mesh.xr();
const auto& cell_to_node_matrix = mesh.connectivity().cellToNodeMatrix();
const auto& node_to_cell_matrix = mesh.connectivity().nodeToCellMatrix();
const NodeId r0 = m_node_list[0];
const CellId j0 = node_to_cell_matrix[r0][0];
const auto& j0_nodes = cell_to_node_matrix[j0];
for (size_t r = 0; r < j0_nodes.size(); ++r) {
const double height = dot(xr[j0_nodes[r]] - xr[r0], normal);
if (std::abs(height) > std::abs(max_height)) {
max_height = height;
}
}
}
Array<double> max_height_array = parallel::allGather(max_height);
for (size_t i = 0; i < max_height_array.size(); ++i) {
const double height = max_height_array[i];
if (std::abs(height) > std::abs(max_height)) {
max_height = height;
}
}
if (max_height > 0) {
return -normal;
} else {
return normal;
}
}
#endif // MESH_NODE_BOUNDARY_HPP