Data Types
interface	io_function_output_global_bz

interface	io_function_output_supercell

interface	io_function_output_vector

interface	io_function_output_vector_bz

Functions/Subroutines
subroutine, public	io_function_read_what_how_when (namespace, space, what, how, output_interval, what_tag_in, how_tag_in, output_interval_tag_in, ignore_error)

integer(int64) function, public	io_function_fill_how (where)
	Use this function to quickly plot functions for debugging purposes: call dio_function_output(io_function_fill_how("AxisX_and_PlaneX_and_DX"), &. More...

subroutine, public	write_standard_xyz_file (namespace, fname, pos, species, header)
	Write a standard xyz file with atom labels and positions (in Angstrom). More...

subroutine, public	write_canonicalized_xyz_file (dir, fname, space, latt, pos, atoms, box, namespace)
	Write canonicalized xyz file with atom labels and positions in Angstroms. More...

subroutine, public	write_xsf_geometry_file (dir, fname, space, latt, pos, atoms, mesh, namespace, total_forces)

subroutine, public	write_xsf_geometry (iunit, space, latt, pos, atoms, mesh, forces, index)
	for format specification see: http: More...

subroutine	write_xsf_geometry_supercell (iunit, space, latt, pos, atoms, mesh, centers, supercell, extra_atom)
	for format specification see: http: More...

subroutine	ncdf_error (func, status, filename, namespace, ierr)

subroutine	transpose3 (in, out)

subroutine, public	dio_function_input (filename, namespace, space, mesh, ff, ierr, map)
	Reads a mesh function from file filename, and puts it into ff. If the map argument is passed, the subroutine will reorder the values in the file according to it, missing values will be filled with zeros. (For the moment this is only implemented for the obf format.) More...

subroutine	dio_function_input_ncdf (filename, namespace, space, mesh, ff, ierr, map)
	Reads a mesh function from a NetCDF file filename, and puts it into ff. More...

subroutine	dio_function_input_obf (filename, namespace, space, mesh, ff, ierr, map)
	Reads a mesh function from a obf file filename, and puts it into ff. More...

subroutine	dio_function_input_csv (filename, namespace, space, mesh, ff, ierr)
	Reads a mesh function from a csv file filename, and puts it into ff. More...

subroutine	dio_function_output_vector (how, dir, fname, namespace, space, mesh, ff, unit, ierr, pos, atoms, grp, root)

subroutine	dio_function_output_vector_bz (how, dir, fname, namespace, space, kpt, kpoints, ff, unit, ierr, grp, root)

subroutine, public	dio_function_output (how, dir, fname, namespace, space, mesh, ff, unit, ierr, pos, atoms, grp, root)
	Top-level IO routine for functions defined on the mesh. More...

subroutine, public	dio_function_output_global (how, dir, fname, namespace, space, mesh, ff, unit, ierr)

subroutine	dio_cf_output_global (how, dir, fname, namespace, space, mesh, cube, cf, unit, ierr, pos, atoms)

subroutine	dio_function_output_global_bz (how, dir, fname, namespace, kpoints, ff, unit, ierr)

subroutine, public	dout_cf_netcdf (filename, ierr, cf, cube, space, spacing, transpose, unit, namespace)
	Writes a cube_function in netcdf format. More...

subroutine	dio_function_output_supercell (how, dir, fname, mesh, space, latt, ff, centers, supercell, unit, ierr, namespace, pos, atoms, grp, root, is_global, extra_atom)

subroutine	dio_function_output_global_supercell (how, dir, fname, mesh, space, latt, ff, centers, supercell, unit, ierr, namespace, pos, atoms, extra_atom)

subroutine, public	zio_function_input (filename, namespace, space, mesh, ff, ierr, map)
	Reads a mesh function from file filename, and puts it into ff. If the map argument is passed, the subroutine will reorder the values in the file according to it, missing values will be filled with zeros. (For the moment this is only implemented for the obf format.) More...

subroutine	zio_function_input_ncdf (filename, namespace, space, mesh, ff, ierr, map)
	Reads a mesh function from a NetCDF file filename, and puts it into ff. More...

subroutine	zio_function_input_obf (filename, namespace, space, mesh, ff, ierr, map)
	Reads a mesh function from a obf file filename, and puts it into ff. More...

subroutine	zio_function_input_csv (filename, namespace, space, mesh, ff, ierr)
	Reads a mesh function from a csv file filename, and puts it into ff. More...

subroutine	zio_function_output_vector (how, dir, fname, namespace, space, mesh, ff, unit, ierr, pos, atoms, grp, root)

subroutine	zio_function_output_vector_bz (how, dir, fname, namespace, space, kpt, kpoints, ff, unit, ierr, grp, root)

subroutine, public	zio_function_output (how, dir, fname, namespace, space, mesh, ff, unit, ierr, pos, atoms, grp, root)
	Top-level IO routine for functions defined on the mesh. More...

subroutine, public	zio_function_output_global (how, dir, fname, namespace, space, mesh, ff, unit, ierr)

subroutine	zio_cf_output_global (how, dir, fname, namespace, space, mesh, cube, cf, unit, ierr, pos, atoms)

subroutine	zio_function_output_global_bz (how, dir, fname, namespace, kpoints, ff, unit, ierr)

subroutine, public	zout_cf_netcdf (filename, ierr, cf, cube, space, spacing, transpose, unit, namespace)
	Writes a cube_function in netcdf format. More...

subroutine	zio_function_output_supercell (how, dir, fname, mesh, space, latt, ff, centers, supercell, unit, ierr, namespace, pos, atoms, grp, root, is_global, extra_atom)

subroutine	zio_function_output_global_supercell (how, dir, fname, mesh, space, latt, ff, centers, supercell, unit, ierr, namespace, pos, atoms, extra_atom)

Variables
integer, parameter, private	doutput_kind = 1
	doutput_kind => real variables; zoutput_kind => complex variables. More...

integer, parameter, private	zoutput_kind = -1

character(len=3), dimension(3), parameter	index2label = (/ 're ', 'im ', 'abs' /)
	index to label mapping More...

Function/Subroutine Documentation

◆ io_function_read_what_how_when()

subroutine, public io_function_oct_m::io_function_read_what_how_when	(	type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		logical, dimension(max_output_types), intent(inout)	what,
		integer(int64), dimension(0:max_output_types), intent(out)	how,
		integer, dimension(0:max_output_types), intent(out)	output_interval,
		character(len=*), intent(in), optional	what_tag_in,
		character(len=*), intent(in), optional	how_tag_in,
		character(len=*), intent(in), optional	output_interval_tag_in,
		logical, intent(in), optional	ignore_error
	)

Definition at line 211 of file io_function.F90.

◆ io_function_fill_how()

integer(int64) function, public io_function_oct_m::io_function_fill_how ( character(len=*), intent(in) where )

Use this function to quickly plot functions for debugging purposes: call dio_function_output(io_function_fill_how("AxisX_and_PlaneX_and_DX"), &.

Definition at line 796 of file io_function.F90.

◆ write_standard_xyz_file()

subroutine, public io_function_oct_m::write_standard_xyz_file	(	type(namespace_t), intent(in)	namespace,
		character(len=*), intent(in)	fname,
		real(real64), dimension(:,:), intent(in)	pos,
		character(len=*), dimension(:), intent(in)	species,
		character(len=*), intent(in), optional	header
	)

Write a standard xyz file with atom labels and positions (in Angstrom).

Periodic systems can be handled by passing the appropriate information in the header or directly calling write_canonicalized_xyz_file.

Parameters

[in]	fname	File name, prepended with the path
[in]	pos	Atomic positions
[in]	species	Atomic species labels
[in]	header	Optional header

Definition at line 830 of file io_function.F90.

◆ write_canonicalized_xyz_file()

subroutine, public io_function_oct_m::write_canonicalized_xyz_file	(	character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		real(real64), dimension(:,:), intent(in)	pos,
		type(atom_t), dimension(:), intent(in)	atoms,
		class(box_t), intent(in)	box,
		type(namespace_t), intent(in)	namespace
	)

Write canonicalized xyz file with atom labels and positions in Angstroms.

Includes information about simulation box and periodicity when applicable. This differs from a normal xyz file by including information about box shape and always using Angstroms.

Definition at line 876 of file io_function.F90.

◆ write_xsf_geometry_file()

subroutine, public io_function_oct_m::write_xsf_geometry_file	(	character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		real(real64), dimension(:,:), intent(in)	pos,
		type(atom_t), dimension(:), intent(in)	atoms,
		class(mesh_t), intent(in)	mesh,
		type(namespace_t), intent(in)	namespace,
		real(real64), dimension(:,:), intent(in), optional	total_forces
	)

Definition at line 913 of file io_function.F90.

◆ write_xsf_geometry()

subroutine, public io_function_oct_m::write_xsf_geometry	(	integer, intent(in)	iunit,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		real(real64), dimension(:,:), intent(in)	pos,
		type(atom_t), dimension(:), intent(in)	atoms,
		class(mesh_t), intent(in)	mesh,
		real(real64), dimension(:, :), intent(in), optional	forces,
		integer, intent(in), optional	index
	)

for format specification see: http:

Parameters

[in] index for use in writing animated files

Definition at line 950 of file io_function.F90.

◆ write_xsf_geometry_supercell()

subroutine io_function_oct_m::write_xsf_geometry_supercell	(	integer, intent(in)	iunit,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		real(real64), dimension(:,:), intent(in)	pos,
		type(atom_t), dimension(:), intent(in)	atoms,
		class(mesh_t), intent(in)	mesh,
		real(real64), dimension(:, :), intent(in)	centers,
		integer, dimension(:), intent(in)	supercell,
		real(real64), dimension(:), intent(in), optional	extra_atom
	)

private

for format specification see: http:

Parameters

[in] extra_atom An extra atom, with ther symbol 'X'

Definition at line 1032 of file io_function.F90.

◆ ncdf_error()

subroutine io_function_oct_m::ncdf_error	(	character(len=*), intent(in)	func,
		integer, intent(in)	status,
		character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		integer, intent(inout)	ierr
	)

private

Definition at line 1114 of file io_function.F90.

◆ transpose3()

subroutine io_function_oct_m::transpose3	(	real(real64), dimension(:, :, :), intent(in)	in,
		real(real64), dimension(:, :, :), intent(out)	out
	)

private

Definition at line 1139 of file io_function.F90.

◆ dio_function_input()

subroutine, public io_function_oct_m::dio_function_input	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr,
		integer(int64), dimension(:), intent(in), optional	map
	)

Reads a mesh function from file filename, and puts it into ff. If the map argument is passed, the subroutine will reorder the values in the file according to it, missing values will be filled with zeros. (For the moment this is only implemented for the obf format.)

On output, ierr signals how everything went: ierr > 0 => Error. The function ff was not read:
1 : illegal filename (must have ".obf" or ".ncdf" extension).
2 : file could not be successfully opened.
3 : file opened, but error reading.
4 : The number of points/mesh dimensions do not coincide.
5 : Format or NetCDF error (one or several warnings are written)
ierr = 0 => Success.
ierr < 0 => Success, but some kind of type conversion was necessary. The value of ierr is then:
-1 : function in file is real, sp.
-2 : function in file is complex, sp.
-3 : function in file is real, dp.
-4 : function in file is complex, dp.

Definition at line 1247 of file io_function.F90.

◆ dio_function_input_ncdf()

subroutine io_function_oct_m::dio_function_input_ncdf	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr,
		integer(int64), dimension(:), intent(in), optional	map
	)

private

Reads a mesh function from a NetCDF file filename, and puts it into ff.

Parameters

[in]	filename	Name of the file to read
[in]	space	Space definition
[in]	mesh	The mesh
[in,out]	ff	The function to read
[out]	ierr	Error code
[in]	map	Optional: Map to reorder the function

Definition at line 1313 of file io_function.F90.

◆ dio_function_input_obf()

subroutine io_function_oct_m::dio_function_input_obf	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr,
		integer(int64), dimension(:), intent(in), optional	map
	)

private

Reads a mesh function from a obf file filename, and puts it into ff.

Parameters

[in]	filename	Name of the file to read
[in]	space	Space definition
[in]	mesh	The mesh
[in,out]	ff	The function to read
[out]	ierr	Error code
[in]	map	Optional: Map to reorder the function

Definition at line 1465 of file io_function.F90.

◆ dio_function_input_csv()

subroutine io_function_oct_m::dio_function_input_csv	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr
	)

private

Reads a mesh function from a csv file filename, and puts it into ff.

Note that this function can only read real-valued CSV files. If the function is complex, the real part will be read and the imaginary part will be set to zero.

For parallel calculations, using domain decomposition, the whole function is read on all nodes, but only the part corresponding to the local domain is copied to ff.

Parameters

[in]	filename	Name of the file to read
[in]	space	Space definition
[in]	mesh	The mesh
[in,out]	ff	The function to read
[out]	ierr	Error code

Definition at line 1516 of file io_function.F90.

◆ dio_function_output_vector()

subroutine io_function_oct_m::dio_function_output_vector	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		class(mesh_t), intent(in)	mesh,
		real(real64), dimension(:, :), intent(in), target, contiguous	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root
	)

private

Parameters

[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data

Definition at line 1667 of file io_function.F90.

◆ dio_function_output_vector_bz()

subroutine io_function_oct_m::dio_function_output_vector_bz	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(distributed_t), intent(in)	kpt,
		type(kpoints_t), intent(in)	kpoints,
		real(real64), dimension(:, :), intent(in), target	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root
	)

private

Parameters

[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data

Definition at line 1746 of file io_function.F90.

◆ dio_function_output()

subroutine, public io_function_oct_m::dio_function_output	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		class(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(in), target, contiguous	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root
	)

Top-level IO routine for functions defined on the mesh.

Outputs functions defined on the mesh to several file and output formats:

DX
XCRYSDEN
CUBE
VTK
NETCDF

Distinguishes between output formats that require a whole cube grid, and those that need a whole mesh.

Parameters

[in]	how	Defines the output format in bitwise representation
[in]	dir	Output directory
[in]	fname	Output file, minus extension
[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data

Definition at line 1833 of file io_function.F90.

◆ dio_function_output_global()

subroutine, public io_function_oct_m::dio_function_output_global	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(in)	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr
	)

Parameters

[in] ff (meshnp_global or meshnp_part_global)

Definition at line 1951 of file io_function.F90.

◆ dio_cf_output_global()

subroutine io_function_oct_m::dio_cf_output_global	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		type(cube_t), intent(in)	cube,
		type(cube_function_t), intent(in)	cf,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms
	)

private

Definition at line 2324 of file io_function.F90.

◆ dio_function_output_global_bz()

subroutine io_function_oct_m::dio_function_output_global_bz	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		type(kpoints_t), intent(in)	kpoints,
		real(real64), dimension(:), intent(in)	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr
	)

private

Parameters

[in] ff (stnik)

Definition at line 2642 of file io_function.F90.

◆ dout_cf_netcdf()

subroutine, public io_function_oct_m::dout_cf_netcdf	(	character(len=*), intent(in)	filename,
		integer, intent(out)	ierr,
		type(cube_function_t), intent(in)	cf,
		type(cube_t), intent(in)	cube,
		class(space_t), intent(in)	space,
		real(real64), dimension(:), intent(in)	spacing,
		logical, intent(in)	transpose,
		type(unit_t), intent(in)	unit,
		type(namespace_t), intent(in)	namespace
	)

Writes a cube_function in netcdf format.

Parameters

[in]	filename	the file name
[out]	ierr	error message
[in]	cf	the cube_function to be written
[in]	cube	the underlying cube mesh
[in]	space	the spatial dimensions
[in]	spacing	the mesh spacing already converted to units_out
[in]	transpose	whether we want the function cf(x,y,z) to be saved as cf(z,y,x)
[in]	unit	unit of data in cf

Definition at line 2781 of file io_function.F90.

◆ dio_function_output_supercell()

subroutine io_function_oct_m::dio_function_output_supercell	(	integer(8), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		class(mesh_t), intent(in)	mesh,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		real(real64), dimension(:,:), intent(in), target, contiguous	ff,
		real(real64), dimension(:,:), intent(in)	centers,
		integer, dimension(:), intent(in)	supercell,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		type(namespace_t), intent(in)	namespace,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root,
		logical, intent(in), optional	is_global,
		real(real64), dimension(:), intent(in), optional	extra_atom
	)

private

Parameters

[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data
[in]	is_global	Input data is meshnp_global? And, thus, it has not be gathered

Definition at line 2929 of file io_function.F90.

◆ dio_function_output_global_supercell()

subroutine io_function_oct_m::dio_function_output_global_supercell	(	integer(8), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(mesh_t), intent(in)	mesh,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		real(real64), dimension(:,:), intent(in), contiguous	ff,
		real(real64), dimension(:,:), intent(in)	centers,
		integer, dimension(:), intent(in)	supercell,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		type(namespace_t), intent(in)	namespace,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		real(real64), dimension(:), intent(in), optional	extra_atom
	)

private

Parameters

[in] ff (meshnp_global or meshnp_part_global)

Definition at line 3022 of file io_function.F90.

◆ zio_function_input()

subroutine, public io_function_oct_m::zio_function_input	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr,
		integer(int64), dimension(:), intent(in), optional	map
	)

Reads a mesh function from file filename, and puts it into ff. If the map argument is passed, the subroutine will reorder the values in the file according to it, missing values will be filled with zeros. (For the moment this is only implemented for the obf format.)

On output, ierr signals how everything went: ierr > 0 => Error. The function ff was not read:
1 : illegal filename (must have ".obf" or ".ncdf" extension).
2 : file could not be successfully opened.
3 : file opened, but error reading.
4 : The number of points/mesh dimensions do not coincide.
5 : Format or NetCDF error (one or several warnings are written)
ierr = 0 => Success.
ierr < 0 => Success, but some kind of type conversion was necessary. The value of ierr is then:
-1 : function in file is real, sp.
-2 : function in file is complex, sp.
-3 : function in file is real, dp.
-4 : function in file is complex, dp.

Definition at line 3430 of file io_function.F90.

◆ zio_function_input_ncdf()

subroutine io_function_oct_m::zio_function_input_ncdf	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr,
		integer(int64), dimension(:), intent(in), optional	map
	)

private

Reads a mesh function from a NetCDF file filename, and puts it into ff.

Parameters

[in]	filename	Name of the file to read
[in]	space	Space definition
[in]	mesh	The mesh
[in,out]	ff	The function to read
[out]	ierr	Error code
[in]	map	Optional: Map to reorder the function

Definition at line 3496 of file io_function.F90.

◆ zio_function_input_obf()

subroutine io_function_oct_m::zio_function_input_obf	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr,
		integer(int64), dimension(:), intent(in), optional	map
	)

private

Reads a mesh function from a obf file filename, and puts it into ff.

Parameters

[in]	filename	Name of the file to read
[in]	space	Space definition
[in]	mesh	The mesh
[in,out]	ff	The function to read
[out]	ierr	Error code
[in]	map	Optional: Map to reorder the function

Definition at line 3672 of file io_function.F90.

◆ zio_function_input_csv()

subroutine io_function_oct_m::zio_function_input_csv	(	character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:), intent(inout)	ff,
		integer, intent(out)	ierr
	)

private

Reads a mesh function from a csv file filename, and puts it into ff.

Note that this function can only read real-valued CSV files. If the function is complex, the real part will be read and the imaginary part will be set to zero.

For parallel calculations, using domain decomposition, the whole function is read on all nodes, but only the part corresponding to the local domain is copied to ff.

Parameters

[in]	filename	Name of the file to read
[in]	space	Space definition
[in]	mesh	The mesh
[in,out]	ff	The function to read
[out]	ierr	Error code

Definition at line 3723 of file io_function.F90.

◆ zio_function_output_vector()

subroutine io_function_oct_m::zio_function_output_vector	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		class(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:, :), intent(in), target, contiguous	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root
	)

private

Parameters

[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data

Definition at line 3874 of file io_function.F90.

◆ zio_function_output_vector_bz()

subroutine io_function_oct_m::zio_function_output_vector_bz	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(distributed_t), intent(in)	kpt,
		type(kpoints_t), intent(in)	kpoints,
		complex(real64), dimension(:, :), intent(in), target	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root
	)

private

Parameters

[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data

Definition at line 3953 of file io_function.F90.

◆ zio_function_output()

subroutine, public io_function_oct_m::zio_function_output	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		class(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:), intent(in), target, contiguous	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root
	)

Top-level IO routine for functions defined on the mesh.

Outputs functions defined on the mesh to several file and output formats:

DX
XCRYSDEN
CUBE
VTK
NETCDF

Distinguishes between output formats that require a whole cube grid, and those that need a whole mesh.

Parameters

[in]	how	Defines the output format in bitwise representation
[in]	dir	Output directory
[in]	fname	Output file, minus extension
[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data

Definition at line 4040 of file io_function.F90.

◆ zio_function_output_global()

subroutine, public io_function_oct_m::zio_function_output_global	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		complex(real64), dimension(:), intent(in)	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr
	)

Parameters

[in] ff (meshnp_global or meshnp_part_global)

Definition at line 4158 of file io_function.F90.

◆ zio_cf_output_global()

subroutine io_function_oct_m::zio_cf_output_global	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		type(cube_t), intent(in)	cube,
		type(cube_function_t), intent(in)	cf,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms
	)

private

Definition at line 4531 of file io_function.F90.

◆ zio_function_output_global_bz()

subroutine io_function_oct_m::zio_function_output_global_bz	(	integer(int64), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(namespace_t), intent(in)	namespace,
		type(kpoints_t), intent(in)	kpoints,
		complex(real64), dimension(:), intent(in)	ff,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr
	)

private

Parameters

[in] ff (stnik)

Definition at line 4863 of file io_function.F90.

◆ zout_cf_netcdf()

subroutine, public io_function_oct_m::zout_cf_netcdf	(	character(len=*), intent(in)	filename,
		integer, intent(out)	ierr,
		type(cube_function_t), intent(in)	cf,
		type(cube_t), intent(in)	cube,
		class(space_t), intent(in)	space,
		real(real64), dimension(:), intent(in)	spacing,
		logical, intent(in)	transpose,
		type(unit_t), intent(in)	unit,
		type(namespace_t), intent(in)	namespace
	)

Writes a cube_function in netcdf format.

Parameters

[in]	filename	the file name
[out]	ierr	error message
[in]	cf	the cube_function to be written
[in]	cube	the underlying cube mesh
[in]	space	the spatial dimensions
[in]	spacing	the mesh spacing already converted to units_out
[in]	transpose	whether we want the function cf(x,y,z) to be saved as cf(z,y,x)
[in]	unit	unit of data in cf

Definition at line 5002 of file io_function.F90.

◆ zio_function_output_supercell()

subroutine io_function_oct_m::zio_function_output_supercell	(	integer(8), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		class(mesh_t), intent(in)	mesh,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		complex(real64), dimension(:,:), intent(in), target, contiguous	ff,
		real(real64), dimension(:,:), intent(in)	centers,
		integer, dimension(:), intent(in)	supercell,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		type(namespace_t), intent(in)	namespace,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		type(mpi_grp_t), intent(in), optional	grp,
		integer, intent(in), optional	root,
		logical, intent(in), optional	is_global,
		real(real64), dimension(:), intent(in), optional	extra_atom
	)

private

Parameters

[in]	grp	the group that shares the same data, must contain the domains group
[in]	root	which process is going to write the data
[in]	is_global	Input data is meshnp_global? And, thus, it has not be gathered

Definition at line 5170 of file io_function.F90.

◆ zio_function_output_global_supercell()

subroutine io_function_oct_m::zio_function_output_global_supercell	(	integer(8), intent(in)	how,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	fname,
		type(mesh_t), intent(in)	mesh,
		class(space_t), intent(in)	space,
		type(lattice_vectors_t), intent(in)	latt,
		complex(real64), dimension(:,:), intent(in), contiguous	ff,
		real(real64), dimension(:,:), intent(in)	centers,
		integer, dimension(:), intent(in)	supercell,
		type(unit_t), intent(in)	unit,
		integer, intent(out)	ierr,
		type(namespace_t), intent(in)	namespace,
		real(real64), dimension(:,:), intent(in), optional	pos,
		type(atom_t), dimension(:), intent(in), optional	atoms,
		real(real64), dimension(:), intent(in), optional	extra_atom
	)

private

Parameters

[in] ff (meshnp_global or meshnp_part_global)

Definition at line 5263 of file io_function.F90.

Variable Documentation

◆ doutput_kind

integer, parameter, private io_function_oct_m::doutput_kind = 1

private

doutput_kind => real variables; zoutput_kind => complex variables.

Definition at line 182 of file io_function.F90.

◆ zoutput_kind

integer, parameter, private io_function_oct_m::zoutput_kind = -1

private

Definition at line 182 of file io_function.F90.

◆ index2label

character(len=3), dimension(3), parameter io_function_oct_m::index2label = (/ 're ', 'im ', 'abs' /)

private

index to label mapping

Definition at line 187 of file io_function.F90.

Data Types

Functions/Subroutines

Variables

Function/Subroutine Documentation

◆ io_function_read_what_how_when()

◆ io_function_fill_how()

◆ write_standard_xyz_file()

◆ write_canonicalized_xyz_file()

◆ write_xsf_geometry_file()

◆ write_xsf_geometry()

◆ write_xsf_geometry_supercell()

◆ ncdf_error()

◆ transpose3()

◆ dio_function_input()

◆ dio_function_input_ncdf()

◆ dio_function_input_obf()

◆ dio_function_input_csv()

◆ dio_function_output_vector()

◆ dio_function_output_vector_bz()

◆ dio_function_output()

◆ dio_function_output_global()

◆ dio_cf_output_global()

◆ dio_function_output_global_bz()

◆ dout_cf_netcdf()

◆ dio_function_output_supercell()

◆ dio_function_output_global_supercell()

◆ zio_function_input()

◆ zio_function_input_ncdf()

◆ zio_function_input_obf()

◆ zio_function_input_csv()

◆ zio_function_output_vector()

◆ zio_function_output_vector_bz()

◆ zio_function_output()

◆ zio_function_output_global()

◆ zio_cf_output_global()

◆ zio_function_output_global_bz()

◆ zout_cf_netcdf()

◆ zio_function_output_supercell()

◆ zio_function_output_global_supercell()

Variable Documentation

◆ doutput_kind

◆ zoutput_kind

◆ index2label