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Octopus
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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_canonicalized_xyz_file (dir, fname, space, latt, pos, atoms, box, 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. 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... | |
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.
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 781 of file io_function.F90.
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 816 of file io_function.F90.
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 864 of file io_function.F90.
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:
[in] | index | for use in writing animated files |
Definition at line 901 of file io_function.F90.
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for format specification see: http:
[in] | extra_atom | An extra atom, with ther symbol 'X' |
Definition at line 983 of file io_function.F90.
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Definition at line 1065 of file io_function.F90.
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Definition at line 1090 of file io_function.F90.
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 1198 of file io_function.F90.
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Reads a mesh function from a NetCDF file filename, and puts it into ff.
[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 1264 of file io_function.F90.
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Reads a mesh function from a obf file filename, and puts it into ff.
[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 1416 of file io_function.F90.
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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.
[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 1467 of file io_function.F90.
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[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 1618 of file io_function.F90.
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[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 1697 of file io_function.F90.
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:
Distinguishes between output formats that require a whole cube grid, and those that need a whole mesh.
[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 1784 of file io_function.F90.
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 | ||
) |
[in] | ff | (meshnp_global or meshnp_part_global) |
Definition at line 1902 of file io_function.F90.
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Definition at line 2275 of file io_function.F90.
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[in] | ff | (stnik) |
Definition at line 2593 of file io_function.F90.
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.
[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 2732 of file io_function.F90.
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[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 2880 of file io_function.F90.
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[in] | ff | (meshnp_global or meshnp_part_global) |
Definition at line 2973 of file io_function.F90.
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 3381 of file io_function.F90.
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Reads a mesh function from a NetCDF file filename, and puts it into ff.
[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 3447 of file io_function.F90.
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Reads a mesh function from a obf file filename, and puts it into ff.
[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 3623 of file io_function.F90.
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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.
[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 3674 of file io_function.F90.
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[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 3825 of file io_function.F90.
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[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 3904 of file io_function.F90.
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:
Distinguishes between output formats that require a whole cube grid, and those that need a whole mesh.
[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 3991 of file io_function.F90.
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 | ||
) |
[in] | ff | (meshnp_global or meshnp_part_global) |
Definition at line 4109 of file io_function.F90.
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Definition at line 4482 of file io_function.F90.
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[in] | ff | (stnik) |
Definition at line 4814 of file io_function.F90.
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.
[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 4953 of file io_function.F90.
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[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 5121 of file io_function.F90.
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[in] | ff | (meshnp_global or meshnp_part_global) |
Definition at line 5214 of file io_function.F90.
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doutput_kind => real variables; zoutput_kind => complex variables.
Definition at line 181 of file io_function.F90.
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Definition at line 181 of file io_function.F90.
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index to label mapping
Definition at line 186 of file io_function.F90.