create xdmf¶

The page defines the application programing interface specification for the xdmf operation.

The command line interface for the xdmf catagory of operations is:

usage: flashkit create xdmf BASENAME [--low INT] [--high INT] [--skip INT] [<opt>...] [<flg>...]
Create an xdmf file associated with flash simulation HDF5 output.

arguments:  
BASENAME     STRING  Basename for flash simulation, will be guessed if not provided
                     (e.g., INS_LidDr_Cavity for files INS_LidDr_Cavity_hdf5_plt_cnt_xxxx)

options:
-b, --low    INT     Begining number for timeseries hdf5 files; defaults to 0.
-e, --high   INT     Ending number for timeseries hdf5 files; defaults to 0.
-s, --skip   INT     Number of files to skip for timeseries hdf5 files; defaults to 1.
-f, --files  LIST    List of file numbers (e.g., <1,3,5,7,9>) for timeseries.
-p, --path   PATH    Path to timeseries hdf5 simulation output files; defaults to cwd.
-d, --dest   PATH    Path to xdmf (contains relative paths to sim data); defaults to cwd.
-o, --out    FILE    Output XDMF file name follower; defaults to a footer ''.
-c, --plot   STRING  Plot/Checkpoint file(s) name follower; defaults to '_hdf5_plt_cnt_'.
-g, --grid   STRING  Grid file(s) name follower; defaults to '_hdf5_grd_'.
-q, --force  STRING  Plot/Checkpoint file(s) substring to ignore; defaults to 'forced'.

flags:
-A, --auto           Force behavior to attempt guessing BASENAME and [--files LIST].
-B, --find           Force behavior to attempt guessing [--files LIST].
-I, --ignore         Ignore configuration file provided arguments, options, and flags.
-O, --options        Show the available options (i.e., defaults and config file format) and exit.
-h, --help           Show this message and exit.

note:  If neither BASENAME nor either of [-b/-e/-s] or -f is specified,
       the --path will be searched for FLASH simulation files and all
       such files identified will be used in sorted order.

Please consult the discussion on command line syntax for help in formating the above options (e.g., LIST or PATH).

The python interface for the xdmf operation is accessed with the following code:

from flashkit import flash
...
flash.create.xdmf(options=value, flag=True, ...)

The python interface specification for xdmf is as follows:

xdmf(**arguments: Any) → None¶

Python application interface for creating xdmf from command line or python code.

This method creates a metadata file (i.e., xdmf format) associated with a desired set of HDF5 binary simulation data suitable for using in supporting visualization software (e.g., Paraview). The arguments povide flexibility in creating this metadata file that covers most usecases (e.g., time-series 3d data).

Keyword Arguments

basename (str) – Basename for flash simulation, will be guessed if not provided (e.g., INS_LidDr_Cavity for files INS_LidDr_Cavity_hdf5_plt_cnt_xxxx)
low (int) – Begining number for timeseries hdf5 files.
high (int) – Ending number for timeseries hdf5 files.
skip (int) – Number of files to skip for timeseries hdf5 files.
files (list) – List of file numbers (e.g., <1,3,5,7,9>) for timeseries.
path (str) – Path to timeseries hdf5 simulation output files.
dest (str) – Path to xdmf (contains relative paths to sim data).
out (str) – Output XDMF file name follower.
plot (str) – Plot/Checkpoint file(s) name follower.
grid (str) – Grid file(s) name follower.
force (str) – Plot/Checkpoint file(s) substring to ignore.
auto (bool) – Force behavior to attempt guessing BASENAME and [–files LIST].
find (bool) – Force behavior to attempt guessing [–files LIST].
ignore (bool) – Ignore configuration file provided arguments, options, and flags.

Note

If neither BASENAME nor either of [LOW/HIGH/SKIP] or -f is specified, the PATH will be searched for flash simulation files and all such files identified will be used in sorted order.

The complete specification of library defaults values (as shown above) and mappings is as follows:

The following library defaults are provided for flashkit create xdmf:

Options          Default Values
-------          --------------
high             0
low              0
skip             1
grid             _hdf5_grd_
force            forced
plot             _hdf5_plt_cnt_
out              --
dest             --
path             --


The following outlines the general section options, which can be mapped
in the configuration file, that are provided for flashkit create xdmf:

Options          flash.toml Sections and Options
-------          -------------------------------
grid             [general.files]
                 grid = ...

force            [general.files]
                 forced = ...

plot             [general.files]
                 plot = ...

out              [general.files]
                 output = ...

dest             [general.paths]
                 working = ...

path             [general.paths]
                 working = ...

Please consult the tutorial discussion on configuration file formating for help in specifying the above options in a flash.toml file and what mapping general options are, as well as the full specification on FlashKit library options.