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how to visualize the output binary files form SNaC

in addition to the binary files for visualization, SNaC generates a log file that contains information about the saved data; this information is then used to generate a single Xdmf metadata file for visualizing field data as a time series.

the steps are as follows:

  1. after the simulation has run, copy the contents of utils/visualize_fields/write_xdmf_all.py to the simulation data folder;
  2. run the file with python write_xdmf_all.py.
  3. load the generated Xdmf (*.xmf) file using paraview/visit or other visualization software.

example: how to visualize the default binary output

3D fields

when running the script write_xdmf_all.py we get the following prompts:

 $ python write_xdmf_all.py
 Name of the log file written by SNaC (excluding the block-specific suffix) [log_visu_3d]:
 Name to be appended to the grid files to prevent overwriting []:
 Block # 001 log files parsed and grid files generated.
 Block # 002 log files parsed and grid files generated.
 Block # 003 log files parsed and grid files generated.
 Name of the output file [viewfld_DNS.xmf]:
  • the first input is the name of the file that logged the saved data;
  • the second is a name to append to the grid files that are generated, which should change for different log files to prevent conflicts;
  • the last is the name of the visualization file.

by pressing enter after each prompt, the default values in the square brackets are assumed by the script; these correspond to the default steps required for visualizing 3D field data; the data can then be visualized with, e.g., $ paraview viewfld_DNS.xmf.

checkpoint files

a similar script also located in utils/visualize_fields/, named write_xdmf_restart.py, can be used to generate metadata that allows to visualize the field data contained in saved checkpoint files.

read binary data for post-processing

under utils/read_bindary_data are MATLAB and python scripts which may be used to load binary field data for post-processing; see tests/lid_driven_cavity/test.py for an example use of the python script.