Scripts and templates for automatically running M3D-C1

The fundamental python function is autoC1() which has the following call pattern

autoC1(task='all',machine='DIII-D')

Tasks proceed in the following order.
You can skip to a step by setting this keyword to the desired value.
Folder in which a given step occurs is given with parentheses.

• 'all' [DEFAULT]
  • Starts from the beginning with 'setup'
• 'setup'
  • Preprocess the g-, p-, and a-files into readable formats ('efit/')
  • Allows user to extend the profiles beyond the separatrix.
• 'efit'
  • Perform an igs=0 run to get the EFIT equilibrium ('uni_efit/')
• 'uni_equil'
  • Perform equilibrium calcalutions on a uniform mesh ('uni_equil/')
  • User can iterate on current.dat.out in this step to improvethe equilibrium match to the EFIT
  • Can launch IDL within this step to check the equilibrium match
• 'adapt'
  • Adapt the mesh to the equilibrium ('rw1_adapt/')
• 'calculation'

  • Perform linear calculations with adapted mesh

  • User will select from four options

    1. Calculate equilibrium ('rw1_equil/')
    2. Linear stability analysis ('n=<ntor>/eb1_1f_stab/')
            User selects desired toroidal mode number <ntor>
            Currently uses ExB rotation and single-fluid only
    3. Time-independent, linear response ('n=<ntor>/eb1_1f_<coil>/')
            User selects desired toroidal mode number <ntor>
            <coil> values are defined by the machine
            Currently uses ExB rotation and single-fluid only
    4. Open IDL to examine the results

Name of device to be modeled, so appropriate templates can be found.
Machines currently supported:

• 'DIII-D' [DEFAULT]
• 'NSTX-U'

1. Create a base directory to store the autoC1 scripts and templates.
2. Set the AUTOC1_HOME environmental variable to this base directory.
3. Make sure the M3DC1_ARCH enviornmental variable is set properly
   • On portalr6, M3DC1_ARCH = sunfire.r6
   • On saturn/iris, M3DC1_ARCH = saturn
4. cd to $AUTOC1_HOME
5. Download autoC1 from github
   • On portalr6, clone with SSH: 'git clone [email protected]:bclyons12/autoC1.git'
     • Cloning with SSH
     • Finding/generating your SSH key
   • On saturn/iris, clone with HTTPS: 'git clone https://github.com/bclyons12/autoC1.git'
6. Import the appropriate python module on your system. I use:
   • On portalr6, 'module load anaconda'
   • On saturn/iris, 'module load python'
7. Add $AUTOC1_HOME/python/ to your PYTHONPATH environmental variable

1. Create a new working directory for the current runs
2. Create a folder called 'efit/' within this working directory
3. Populate 'efit/' with the g-, p-, and a- files for this shot & time (format should be like g*.*)
4. From the base working directory, run 'python'
5. Within python, import the autoC1 function from the autoC1 module.
   For example: from autoC1 import autoC1
6. Run the autoC1 function (see above for keyword details)
7. The script should walk you through it's steps in a self-explanatory way.
   It will ask for user input when required, as well as prompt you to check certain things about the runs along the way.