Implementing advanced mode with -d flag to access

[jhmatthews]

As decided in telecon and discussed in #111 we want an advance dusers mode which one accesses with -d. Using -d turns modes.iadvanced to 1.

Currently this asks for a few options which are not asked for if you don't run with -d. These are:

write_atomicdata(0=no,1=yes)                        # near start after atomic data
adjust_grid(0=no,1=yes)                                  # near start after grid dimensions
Extra.diagnostics(0=no,1=yes)                        # very end

The variables for turning on modes are all in a global modes structure.

adjust_grid

allows one to turn adjust the scale lengths of the grid, asks for one or two options depending on type of grid used:

geo.xlog_scale
geo.zlog_scale

write_atomicdata(0=no,1=yes): write out a summary of atomic data, previously controlled with DEBUG

Extra.diagnostics(0=no,1=yes) - turns on extra diagnostics, and then looks for any of these options. Can give as many or as few as you want:

keep_ioncycle_windsaves
track_resonant_scatters
ispymode
save_cell_statistics
print_windrad_summary
print_dvds_info
save_extract_photons

more can be added here. One just has to add a variable to the modes structure and adjust the function get_extra_diagnostics().

there's an example parameter file with everything in examples/sv_detailedmode.pf

Use of Debug() is controlled by the verbosity -v flag.

1: Only print Log_parallel
2,3: Log_parallel, Logs and Errors
4: Log_parallel, Logs, Debug and Errors
5: Log_silent, Error_silent, Log_parallel, Logs, Debug and Errors

it's not perfect so I'm open to suggestions on future improvements, but we need to try using it first.

[jhmatthews]

@kslong Knox- I'm inclined to control the use of Debug() with the verbosity tag instead of using the same as the advanced options. What do you think?

[jhmatthews]

Merging this- @kslong @Higginbottom @smangham see comment above for how to use- I will update other docs in due course