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Doing a bit-for-bit restart with a new directory/machine/executable is called "branching" in CESM/ACME nomenclature. See the startup/branch/hybrid in CESM1.0 Documentation for a description. Note that one can also "clone" a case, which is like branching but preserves local modifications to the code base you're using (see how to clone in CESM1.x User's Guide). Since all good acme coders check all their changes into git before doing a run and because cloning is complicated, we shouldn't need to clone. This CESM documentation explains how to set up a branch run: branching in CESM2. Documentation. Unfortunately, branching functionality in ACME is broken for v1-alpha coupled runs because mpas uses different file names for restarts than previous versions of the code (and possibly other things). See github issue XXX. Here's how to continue a run without using branchingI didn't think the branch utility worked for ACME v1 coupled runs, so I wrote a description for how to branch manually below. It turns out the utility does work (at least using the run_acme.csh script for FC5AV1C-01 and A_WCYCL2000), so I include a description of using that simpler method as well.

Continuing a run using NCAR's "branch" utility and the run_acme.csh script:

1. Create a new case/build a new executable using the "run_acme.csh" style script that Peter Caldwell and Philip Cameron-Smith (Unlicensed) created for this:
   
   1. git clone https://github.com/ACME-Climate/SimulationScripts.git,
   2. cd SimulationScripts/serving_as_a_template/recommended,
   3. modify run_acme.template.csh as needed
      
      1. replace "template" in name with better descriptor,
      2. copy file to non-git directory (if desired)
      3. change stuff in file as needed. I can't say what you will want to change since each simulation is different, but at least think about:
         
         1. change run_name
         2. Change run length/restart freq/output freq. By default the code you just downloaded runs 5 days with daily atm output, then stops without writing any restart files.
   4. execute run_acme...csh and make sure it completes without errors
2. Modify your run_acme...csh script to do the following:
   1. change run_name to reflect the name you want to use for the continuation of the run.
   2. change model_start_type to "branch"
   3. change restart_files_dir to reflect the "run" directory containing the restart files you want to use to restart your run.
3. execute run_acme...csh again.

Continuing a run without using the "branch" utility:

1. Create a new case/build a new executable. I recommend using the "run_acme.csh" style script that Peter Caldwell and Philip Cameron-Smith (Unlicensed) created for this:
   
   1. git clone https://github.com/ACME-Climate/SimulationScripts.git,
   2. cd SimulationScripts/serving_as_a_template/recommended,
   3. modify run_acme.template.csh as needed
      
      1. replace "template" in name with better descriptor,
      2. copy file to non-git directory (if desired)
      3. change stuff in file as needed. I can't say what you will want to change since each simulation is different, but at least think about:
         
         1. change run_name
         2. in particular, change "submit_run" to false so you can set the code up for a restart before submitting it
         3. Change run length/restart freq/output freq. By default the code you just downloaded runs 5 days with daily atm output, then stops without writing any restart files.
   4. execute run_acme...csh and make sure it completes without errors
2. Copy restart files from previous run to ${run_root_dir}/run where ${run_root_dir} is the root directory where your run will occur (which will have subdirectories called run, case_scripts, build, etc)
   
   1. I wrote a script called cp_continue_run.sh to do this (based on input by Chris Golaz). It is also in the git repo from step 1b under subdirectory SimulationScripts/serving_as_a_template/recommended/. In cp_continue_run.sh:
      
      1. change TIME1 to the day you want to restart from
      2. change TIME2 to the month before the day you want to restart on
      3. set the CASE to the name of the case you want to use ***Note that for simplicity I'm assuming the name of the case you're branching from is the same as the case you want to continue from. We should generalize this in the future***
      4. INDIR is the absolute path to the restart files you want to copy
      5. OUTDIR is the absolute path to ${run_root_dir}/run.
   2. Execute cp_continue_run.sh and make sure the copied files exist in ${run_root_dir}/run as expected.
3. Change each of the rpointer files in ${run_root_dir}/run to reflect a consistent desired start date (if they don't already)
4. Change CONTINUE_RUN to TRUE in ${run_root_dir}/case_scripts/env_run.xml
5. Submit the run by typing "./$CASE.submit" (where $CASE is the name of your case) in subdirectory ${run_root_dir}/case_scripts/