ADIOS2Writers.h File Reference

ADIOS2-based output writers. More...

#include "vtk_utils.h"
#include <adios2.h>
#include <algorithm>
#include <basix/mdspan.hpp>
#include <cassert>
#include <complex>
#include <concepts>
#include <dolfinx/common/IndexMap.h>
#include <dolfinx/fem/DofMap.h>
#include <dolfinx/fem/FiniteElement.h>
#include <dolfinx/fem/Function.h>
#include <dolfinx/mesh/Geometry.h>
#include <dolfinx/mesh/Mesh.h>
#include <filesystem>
#include <memory>
#include <mpi.h>
#include <stdexcept>
#include <string>
#include <type_traits>
#include <variant>
#include <vector>

Include dependency graph for ADIOS2Writers.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Classes
class	ADIOS2Writer
	Base class for ADIOS2-based writers. More...

Namespaces
namespace	dolfinx
	Top-level namespace.
namespace	dolfinx::fem
	Finite element method functionality.
namespace	dolfinx::io
	Support for file IO.

Functions
template<class T>
adios2::Attribute< T >	define_attribute (adios2::IO &io, std::string name, const T &value, std::string var_name="", std::string separator="/")
template<class T>
adios2::Variable< T >	define_variable (adios2::IO &io, std::string name, const adios2::Dims &shape=adios2::Dims(), const adios2::Dims &start=adios2::Dims(), const adios2::Dims &count=adios2::Dims())
template<std::floating_point T>
std::shared_ptr< const mesh::Mesh< T > >	extract_common_mesh (const typename adios2_writer::U< T > &u)
	Extract common mesh from list of Functions.
std::stringstream	create_vtk_schema (const std::vector< std::string > &point_data, const std::vector< std::string > &cell_data)
template<std::floating_point T>
std::tuple< std::vector< std::string >, std::vector< std::string > >	extract_function_names (const typename adios2_writer::U< T > &u)
	Extract name of functions and split into real and imaginary component.
template<typename T, std::floating_point X>
void	vtx_write_data (adios2::IO &io, adios2::Engine &engine, const fem::Function< T, X > &u)
template<std::floating_point T>
void	vtx_write_mesh (adios2::IO &io, adios2::Engine &engine, const mesh::Mesh< T > &mesh)
template<std::floating_point T>
std::pair< std::vector< std::int64_t >, std::vector< std::uint8_t > >	vtx_write_mesh_from_space (adios2::IO &io, adios2::Engine &engine, const fem::FunctionSpace< T > &V)
	Given a FunctionSpace, create a topology and geometry based on the function space dof coordinates. Writes the topology and geometry using ADIOS2 in VTX format.

Variables
constexpr std::array	field_ext = {"_real", "_imag"}

Detailed Description

ADIOS2-based output writers.

Function Documentation

create_vtk_schema()

std::stringstream create_vtk_schema	(	const std::vector< std::string > &	point_data,
		const std::vector< std::string > &	cell_data )

Create VTK xml scheme to be interpreted by the VTX reader https://adios2.readthedocs.io/en/latest/ecosystem/visualization.html#saving-the-vtk-xml-data-model

define_attribute()

template<class T>

adios2::Attribute< T > define_attribute	(	adios2::IO &	io,
		std::string	name,
		const T &	value,
		std::string	var_name = "",
		std::string	separator = "/" )

Safe definition of an attribute. First check if it has already been defined and return it. If not defined create new attribute.

define_variable()

template<class T>

adios2::Variable< T > define_variable	(	adios2::IO &	io,
		std::string	name,
		const adios2::Dims &	shape = adios2::Dims(),
		const adios2::Dims &	start = adios2::Dims(),
		const adios2::Dims &	count = adios2::Dims() )

Safe definition of a variable. First check if it has already been defined and return it. If not defined create new variable.

vtx_write_data()

template<typename T, std::floating_point X>

void vtx_write_data	(	adios2::IO &	io,
		adios2::Engine &	engine,
		const fem::Function< T, X > &	u )

Given a Function, write the coefficient to file using ADIOS2.

Note

Only supports (discontinuous) Lagrange functions.

For a complex function, the coefficient is split into a real and imaginary function.

Data is padded to be three dimensional if vector and 9 dimensional if tensor.

Parameters

[in]	io	ADIOS2 io object.
[in]	engine	ADIOS2 engine object.
[in]	u	Function to write.

vtx_write_mesh()

template<std::floating_point T>

void vtx_write_mesh	(	adios2::IO &	io,
		adios2::Engine &	engine,
		const mesh::Mesh< T > &	mesh )

Write mesh to file using VTX format

Parameters

[in]	io	The ADIOS2 io object
[in]	engine	The ADIOS2 engine object
[in]	mesh	The mesh

vtx_write_mesh_from_space()

template<std::floating_point T>

std::pair< std::vector< std::int64_t >, std::vector< std::uint8_t > > vtx_write_mesh_from_space	(	adios2::IO &	io,
		adios2::Engine &	engine,
		const fem::FunctionSpace< T > &	V )

Given a FunctionSpace, create a topology and geometry based on the function space dof coordinates. Writes the topology and geometry using ADIOS2 in VTX format.

Note

Only supports (discontinuous) Lagrange functions.

Parameters

[in]	io	The ADIOS2 io object
[in]	engine	The ADIOS2 engine object
[in]	V	The function space

Variable Documentation

field_ext

std::array field_ext = {"_real", "_imag"}

constexpr

String suffix for real and complex components of a vector-valued field