SIMION 8.0 Issues/Bugs/Enhancements

Issue I130 [functional,resolved]
  Add batch mode operation.

  As of SIMION 8.0, various common operations (e.g. gem2pa, refine,
  fast adjust, and fly) can be invoked in batch mode, from the
  simion.exe command line or from Lua.  See Appendix M. Command Line
  Interface of the SIMION 8.0 manual for details.  For an application
  of batch mode, see the "geometry_optimization" example in SIMION 8.0.

  Originally requested by a number of users including dennisc:
  - example: optimize instruments with ~500,000 trajectories
    and measure energy/angle response.  Adjust voltages and lens
    distances (e.g. from GEM file).
  - would like an editable ASCII batch file, e.g. geometry fredine,
    potentials, fly.
  - What I would really like is to be able to run simion in batch mode 
    e.g. I would like to write a batch type file as follows:-
    SIMION LOAD_GEM "test.gem" SAVE_PA "test.PA#"
    SIMION REFINE "test.PA#" + various parameters interation limit,
       convergence objective
    If No Refine Error then
    SIMION FAST_ADJUST "Test.PA#", Potentail1, Potential2 etc
    SIMION LOAD_IOB "IOB_definition_file"
    (IOB definition to be as ASCII file that can be edited or created
     by the user or another program, e.g. may want to adjust instances
     or conditions for subsequent runs)
    SIMION LOAD_REC "definition_file"
    SIMION LOAD_TTAJ_FILE "test.ion"
    SIMION FLY record o/p to "Test.txt"  etc
    Run my own program to analyze the recorded data, then come up with
    new voltages or electrode positions etc,
    Repeat the process --dennisc
  - martin: > - Batch mode (very important)
    -> The SW we made uses two loops, an inner loop where only potentials are
    > adjusted and ions flown, and an outer loop where the geometry is
    > changed. All changes are done automatically by two simplex optimizers
    > which evaluate a carefully crafted objective function calculated from
    > the ion trajectories. gem and ion files are generated by the 
    > optimizers as needed. All results are logged and after a while
    - (a day or two) they are reviewed manually. After some changes to the 
    > parametrization of the problem or the initial values of the
    > parameters the optimization process is restarted.

  Added in 8.0.