Documentation for CESM2 release

This issue documents things needed for the cism-in-cesm documentation for the cesm2 release.

• Rewrite chapter 1 (introduction) - Gunter (with help from Bill L, Bill S)

• Chapter 2 (quick start) - Bill S

  • Rewrite overview
  • For the most part, point to CESM quick start and/or cime documentation
  • Keep modifying namelist settings, rewrite as needed
  • Keep modifying source code... talk about modifying in-source vs. SourceMods, and the two different places for SourceMods to go
  • Point out specific things useful for LIWG
    • One-way vs. two-way coupling

• New chapter on developing and modifying CISM

  • Add a section on directory structure (taken from current chapter 4) - Bill S
  • Move the "simulating the Greenland ice sheet" section from the current chapter 4 to there - Gunter

• Add a section on grids (rewritten from the section in the current chapter 4) - Bill S (with help from others)

  • Point to wiki page on new CISM grid. Update 2018-05-31: Maybe move that wiki page into the user's guide... in that case, maybe make grids its own chapter.
  • Note need for glacier region to be consistent in CLM: need to have virtual columns and melt_replaced_by_ice in the CISM domain

• Chapter 3 (TG compsets) - Bill S

• Chapter 4 (the dynamic ice sheet model) - Gunter

  • May cut the description of the dynamic ice sheet model (4.1) entirely, just pointing to the full CISM documentation
  • However, we want to keep the "coupling to CLM" section, but move this to a separate chapter (see below)
  • Also keep description of different directories, but move to quick start guide (Bill S)
  • Keep some description of time steps - Gunter

• Chapter 5 (ice sheets in the community land model, and coupling) - Bill L with help from Bill S

  • Rework what's there, and/or point to CLM documentation
  • Include remapping between CISM and CLM - Bill L
  • Add other fields sent from CISM - Bill S / Bill L

• Chapter 6 (FAQ) - cut this for now; can add things back in later as needed (note that they'll need documentation for the new code)

  • But see below: move some of this into a new chapter on output

• New chapter on controlling output from cism and clm

  • Add a section on input/output (rewritten from the section in the current chapter 4) - Bill S
  • Move the old 6.7 and 6.8 here

• Chapter 7 (acknowledgements) - Bill L

• Chapter 8 (references) - Gunter and Bill L

Other things we want to mention somewhere:

• Need to set restart=0 when doing a hybrid run where you have changed cisminputfile to point to a restart file from a standalone case, or a case with different physics (Laura Muntjewerf's issue August, 2018)