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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_global (filename, namespace, space, mesh, ff, ierr, map) |
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_global (filename, namespace, space, mesh, ff, ierr, map) |
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 209 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 768 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 803 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 851 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 888 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 970 of file io_function.F90.
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Definition at line 1052 of file io_function.F90.
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Definition at line 1077 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 1185 of file io_function.F90.
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Definition at line 1230 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 1541 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 1620 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 1707 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 1825 of file io_function.F90.
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Definition at line 2198 of file io_function.F90.
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[in] | ff | (stnik) |
Definition at line 2516 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 2636 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 2784 of file io_function.F90.
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[in] | ff | (meshnp_global or meshnp_part_global) |
Definition at line 2877 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 3285 of file io_function.F90.
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Definition at line 3330 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 3665 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 3744 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 3831 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 3949 of file io_function.F90.
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Definition at line 4322 of file io_function.F90.
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[in] | ff | (stnik) |
Definition at line 4654 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 4774 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 4942 of file io_function.F90.
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[in] | ff | (meshnp_global or meshnp_part_global) |
Definition at line 5035 of file io_function.F90.
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doutput_kind => real variables; zoutput_kind => complex variables.
Definition at line 179 of file io_function.F90.
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Definition at line 179 of file io_function.F90.
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index to label mapping
Definition at line 184 of file io_function.F90.