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[Functions] source/IO/IO_init







  Perform IO initialization, which includes:
  getting the runtime parameters and if it is a restart
  calling IO_readCheckpoint.

  The IO unit uses a number of runtime parameters to determine
  if and when various types of output files need to be written.
  The IO unit writes checkpoint(restart) files, plotfiles for
  visualization, particle plotfiles, and .dat files which hold
  the diagnostic data like total energy, pressure, mass etc.

  To determine exactly which runtime parameters control these
  files, please check the Config file in IO/IOMain or the 
  setup_params file in the object directory.



   These are the runtime parameters used by the basic IO unit.
   Your specific implementation may have more runtime parameters.

   To see the default parameter values and all the runtime parameters
   specific to your simulation check the "setup_params" file in your
   object directory.
   You might have over written these values with the flash.par values
   for your specific run.  

   basenm [STRING]
        Base name for checkpoint files
    bytePack [BOOLEAN]
        compress plotfile data to bytes !!Only implemented with UG in hdf5 !!!
    checkpointFileIntervalStep [INTEGER]
        Checkpoint after this many steps
    checkpointFileIntervalTime [REAL]
        Checkpoint after this much time
    checkpointFileNumber [INTEGER]
        Initial checkpoint file number (used for restarts as well)
    memory_stat_freq [INTEGER]
        Specify the number of timesteps between memory statistic dumps to
    outputSplitNum [INTEGER]
        Split checkpoint, plotfiles, particle plots into this many files per
    output_directory [STRING]
        output dir for checkpoint file, can be absolute or relative path
    plotFileIntervalStep [INTEGER]
        Write a plotfile after this many steps
    plotFileIntervalTime [REAL]
        Write a plot after this much time
    plotFileNumber [INTEGER]
        Initial plot file number
    plot_var_1 [STRING]
        set what variables are to be stored in the plotfile. Up to 12 choices
        are allowed.  If plot_var_X is set to "none" then no variable will be
        saved. The parameter should have the same name as the variable
        corresponding to it. For exampe, if a variable is declared VARIABLE
        pres, to write that variable to a plotfile a parameter should be
        declared as PARAMETER plot_var_X STRING "pres"
    plot_var_10 [STRING]

    plot_var_11 [STRING]

    plot_var_12 [STRING]

    plot_var_2 [STRING]

    plot_var_3 [STRING]

    plot_var_4 [STRING]

    plot_var_5 [STRING]

    plot_var_6 [STRING]

    plot_var_7 [STRING]

    plot_var_8 [STRING]

    plot_var_9 [STRING]

    plot_grid_var_1 [STRING]
      scratch grid vars to be written to the checkpoint and plotfiles

    plot_grid_var_10 [STRING]

    plot_grid_var_11 [STRING]

    plot_grid_var_12 [STRING]

    plot_grid_var_2 [STRING]

    plot_grid_var_3 [STRING]

    plot_grid_var_4 [STRING]

    plot_grid_var_5 [STRING]

    plot_grid_var_6 [STRING]

    plot_grid_var_7 [STRING]

    plot_grid_var_8 [STRING]

    plot_grid_var_9 [STRING]

    prof_file [STRING]
        Don't think this is implemented yet in F3
    rolling_checkpoint [INTEGER]
        Checkpoint file number cycling span. Only the last rolling_checkpoint
        files are kept.
    stats_file [STRING]
        Name of the file integral quantities are written to (.dat file)
    wall_clock_checkpoint [REAL]
        Checkpoint after XX seconds (wallclock time) This is useful to ensure
        that the job outputs a restart file before a queue window closes.
    wr_integrals_freq [INTEGER]
        Number of timesteps between writing to flash.dat