adding ts1 as an example

[K20shores]

Adds TS1 as an example

:: music_box -h                            
usage: music_box [-h] [-c CONFIG] [-e {CB5,Chapman,FlowTube,Analytical,TS1}] [-o OUTPUT] [-v] [--version] [--color-output] [--plot PLOT]

MusicBox simulation runner.

options:
  -h, --help            show this help message and exit
  -c CONFIG, --config CONFIG
                        Path to the configuration file. If --example is provided, this argument is ignored.
  -e {CB5,Chapman,FlowTube,Analytical,TS1}, --example {CB5,Chapman,FlowTube,Analytical,TS1}
                        Name of the example to use. Overrides --config.
                        Available examples:
                        CB5: Carbon bond 5
                        Chapman: The Chapman cycle with conditions over Boulder, Colorado
                        FlowTube: A fictitious flow tube experiment
                        Analytical: An example of an analytical solution to a simple chemical system
                        TS1: Many species involved in tropospheric-stratospheric chemistry
  -o OUTPUT, --output OUTPUT
                        Path to save the output file, including the file name. If not provided, result will be printed to the console.
  -v, --verbose         Increase logging verbosity. Use -v for info, -vv for debug.
  --version             show program's version number and exit
  --color-output        Enable color output for logs.
  --plot PLOT           Plot a comma-separated list of species if gnuplot is available (e.g., CONC.A,CONC.B).

Can be run with

music_box -e TS1

[carl-drews]

There was a comment/question from Rebecca Buchholz at the Demo yesterday; she was sitting next to me, and you may not have heard it. She asked about using initial_conditions.csv to set the initial species concentrations instead of my_config.json.

Initialization of concentrations involves a large number of floating-point numbers, and I believe that specification would be technically better in tabular form (CSV) instead of JSON. We have a JSON mechanism to include CSV file, rather than inserting many values into the JSON configuration. The CSV file would be better for our users to manage and review.

I know that we are retaining compatibility with the Fortran MusicBox. I recommend that we move forward soon with changes that will increase CSV usage through our product suite.

[K20shores]

There was a comment/question from Rebecca Buchholz at the Demo yesterday; she was sitting next to me, and you may not have heard it. She asked about using initial_conditions.csv to set the initial species concentrations instead of my_config.json.

Initialization of concentrations involves a large number of floating-point numbers, and I believe that specification would be technically better in tabular form (CSV) instead of JSON. We have a JSON mechanism to include CSV file, rather than inserting many values into the JSON configuration. The CSV file would be better for our users to manage and review.

I know that we are retaining compatibility with the Fortran MusicBox. I recommend that we move forward soon with changes that will increase CSV usage through our product suite.

@carl-drews That's completely fine with me. We have so few users now it's best we make as many changes as we want to the configuration. Please make this change