Design Spec for Control of MCell Initialization and Run-Time Output

  note:  "****" denotes output that could potentially flood the system
                for large models




A) Parse and Run-time errors

   True errors are always reported and are always fatal.



B) General Info and Warnings

  During Initialization:

  1) **** Molecule diffusion constant stats
     Output: molecule name, diffusion constant, l_r_bar, l_perp_bar, etc...
     3 output states:
       a) no stats output 
       b) brief summary
       c) full output
     Warnings:
       a) negative diffusion constant
          actions:
            i) correct and do nothing
            ii) correct and warn
            iii) treat as error
     
  2) **** Reaction probabilities
     Output: reaction def and transition probability
     3 output states:
       a) no output
       b) output on probability > p
       c) full output
     Warnings:
       a) warn on probability > p (default: p > 1)
          actions:
            i) do nothing
            ii) warn
            iii) treat as error

  3) Partitioning
     Output: partition locations
     2 output states:
       a) no output
       b) full output
     Warnings:
       a) partition spacing < 2*r_int
          actions:
            i) do nothing
            ii) warn
            iii) treat as error

  4) Box triangulation
     Output: box triangulation stats
     2 output states:
       a) no output
       b) full output
     Warnings: none

  5) Geometry initialization
     Output of warnings only
     Warnings:
       a) degenerate polygons found
          actions:
            i) correct and do nothing
            ii) correct and warn
            iii) treat as error

  6) Initialization progress
     Output:
       MCell version:date, current date, machine 
       reiteration of command line args
       progress report:
         Initializing...
         molecule defs
         reaction defs
         geometry defs
         viz output defs
         reaction output defs
       report starting time, iteration, and checkpoint sequence #
       running...
     2 output states:
       a) on
       b) off
  

  During Run-Time:

  1) **** Iteration reporting
     Output: iteration i of N, elapsed time.
     Output control:
       a) output frequency: 0 through Every iteration

  2) **** Release event reporting
     Output: time, molecule, number
     2 output states:
       a) on
       b) off

  3) **** Output file write notices
     Output: file name
     2 output states:
       a) on
       b) off
     Warnings:
       a) overwrite an existing file
          actions:
            i) overwrite and do nothing
            ii) overwrite and warn
            iii) treat as error

  4) Summary statement at end
     Output: run-time stats:
       random number usage
       RAM allocated
       diffusion steps performed
       polygon collision tests performed
       partition collision tests performed
       total actual collisions
       collision test efficiency
       CPU init time, exec time, total time, wallclock time
     2 output states:
       a) on
       b) off
     Warnings:
       a) Time step too long, missed reactions
          actions:
            i) do nothing
            ii) warn
            iii) treat as error
     


General warning control:

  1) set warning conditions
  2) disable/enable warnings
  3) continue/stop on warnings