mesh_block.cpp File Reference

Mesh blocks: generated meshes, HDF5 mesh files. More...

#include "mesh_block.h"
#include <algorithm>
#include <cmath>
#include <filesystem>
#include <stdexcept>
#include <Kokkos_Core.hpp>
#include "comm.h"
#include "input.h"
#include "hdf5_util.h"

Functions
std::array< rtype, 2 >	wedge_node (rtype x, rtype y, rtype Ly)
	Node (x, y) of the supersonic wedge mesh, moved from the box node (x, y).
rtype	stretched_coordinate (uint32_t i, uint32_t n, rtype L, rtype beta)
	Node i of n along a side of length L of a generated mesh, clustered toward both ends by the tanh stretching factor beta > 0: L / 2 (1 + tanh(beta (2 i / n - 1)) / tanh(beta)).
Stretching	mesh_stretching (const toml::value &input)
	[mesh] stretching: the tanh factor of each direction, 0 (uniform) if not given.
MeshBlock	cartesian_2d_block (uint32_t nx, uint32_t ny, rtype Lx, rtype Ly, MeshType kind, int r, int p, const Stretching &stretching)
	Part r of p of a generated 2D mesh (cartesian, cartesian_tri or wedge): near-equal blocks of its cells and nodes, numbered as Mesh::init_cart, init_cart_tri and init_wedge number them, and the boundary faces of those cells.
std::array< uint64_t, 2 >	cartesian_3d_size (uint32_t nx, uint32_t ny, uint32_t nz, MeshType kind)
	Total cell and node counts of a generated 3D box.
MeshBlock	cartesian_3d_block (uint32_t nx, uint32_t ny, uint32_t nz, rtype Lx, rtype Ly, rtype Lz, MeshType kind, uint64_t first_cell, uint64_t end_cell, uint64_t first_node, uint64_t end_node, const Stretching &stretching)
	A generated 3D box (see Mesh::init_cart_3d): the cells [first_cell, end_cell) and nodes [first_node, end_node) in the global numbering of the whole box, and the boundary faces of those cells.
bool	is_hdf5_mesh (const std::string &filename)
	Whether a mesh file name denotes an HDF5 mesh file (.h5 or .hdf5).
MeshBlock	read_mesh_block (const toml::value &input)
	This rank's block of the mesh described by the [mesh] table (collective): an HDF5 mesh file (.h5), a Gmsh file, or a generated mesh. Generated meshes number cells and nodes exactly as Mesh::init. A Gmsh file is read whole by every rank, so large meshes should be converted to HDF5 first.
bool	have_hdf5 ()
	Whether this build reads and writes HDF5 mesh files.
bool	have_parallel_hdf5 ()
	Whether several ranks can write one HDF5 mesh file together.
void	write_mesh_h5 (const std::string &, const MeshBlock &)
	Write the mesh whose blocks the ranks hold, in rank order, to an HDF5 mesh file (collective; several ranks need parallel HDF5).
MeshBlock	read_mesh_h5 (const std::string &filename, bool)
	Read this rank's block of an HDF5 mesh file (collective): cells, nodes and boundary faces split evenly in global order. With whole, this rank reads the whole file on its own (not collective).

Detailed Description

Mesh blocks: generated meshes, HDF5 mesh files.

Author

Matthew Bonanni (mbona.nosp@m.nni0.nosp@m.01@gm.nosp@m.ail..nosp@m.com)

Version

0.4

Date

2026-10-02

Copyright

Copyright (c) 2026 Matthew Bonanni

Function Documentation

cartesian_2d_block()

MeshBlock cartesian_2d_block	(	uint32_t	nx,
		uint32_t	ny,
		rtype	Lx,
		rtype	Ly,
		MeshType	kind,
		int	r,
		int	p,
		const Stretching &	stretching
	)

Part r of p of a generated 2D mesh (cartesian, cartesian_tri or wedge): near-equal blocks of its cells and nodes, numbered as Mesh::init_cart, init_cart_tri and init_wedge number them, and the boundary faces of those cells.

cartesian_3d_block()

MeshBlock cartesian_3d_block	(	uint32_t	nx,
		uint32_t	ny,
		uint32_t	nz,
		rtype	Lx,
		rtype	Ly,
		rtype	Lz,
		MeshType	kind,
		uint64_t	first_cell,
		uint64_t	end_cell,
		uint64_t	first_node,
		uint64_t	end_node,
		const Stretching &	stretching
	)

A generated 3D box (see Mesh::init_cart_3d): the cells [first_cell, end_cell) and nodes [first_node, end_node) in the global numbering of the whole box, and the boundary faces of those cells.

cartesian_3d_size()

std::array< uint64_t, 2 > cartesian_3d_size	(	uint32_t	nx,
		uint32_t	ny,
		uint32_t	nz,
		MeshType	kind
	)

Total cell and node counts of a generated 3D box.

have_hdf5()

bool have_hdf5

(

)

Whether this build reads and writes HDF5 mesh files.

have_parallel_hdf5()

bool have_parallel_hdf5

(

)

Whether several ranks can write one HDF5 mesh file together.

is_hdf5_mesh()

bool is_hdf5_mesh

(

const std::string &

filename

)

Whether a mesh file name denotes an HDF5 mesh file (.h5 or .hdf5).

mesh_stretching()

Stretching mesh_stretching

(

const toml::value &

input

)

[mesh] stretching: the tanh factor of each direction, 0 (uniform) if not given.

read_mesh_block()

MeshBlock read_mesh_block

(

const toml::value &

input

)

This rank's block of the mesh described by the [mesh] table (collective): an HDF5 mesh file (.h5), a Gmsh file, or a generated mesh. Generated meshes number cells and nodes exactly as Mesh::init. A Gmsh file is read whole by every rank, so large meshes should be converted to HDF5 first.

read_mesh_h5()

MeshBlock read_mesh_h5	(	const std::string &	filename,
		bool	whole
	)

Read this rank's block of an HDF5 mesh file (collective): cells, nodes and boundary faces split evenly in global order. With whole, this rank reads the whole file on its own (not collective).

stretched_coordinate()

rtype stretched_coordinate	(	uint32_t	i,
		uint32_t	n,
		rtype	L,
		rtype	beta
	)

Node i of n along a side of length L of a generated mesh, clustered toward both ends by the tanh stretching factor beta > 0: L / 2 (1 + tanh(beta (2 i / n - 1)) / tanh(beta)).

wedge_node()

std::array< rtype, 2 > wedge_node	(	rtype	x,
		rtype	y,
		rtype	Ly
	)

Node (x, y) of the supersonic wedge mesh, moved from the box node (x, y).

write_mesh_h5()

void write_mesh_h5	(	const std::string &	filename,
		const MeshBlock &	block
	)

Write the mesh whose blocks the ranks hold, in rank order, to an HDF5 mesh file (collective; several ranks need parallel HDF5).