Example: Create a carbon gases simulation run directory

The process of creating run directories for the GEOS-Chem specialty simulations is similar to that of the previous example. But the number of menus that you need to select from will likely be fewer than for the full-chemistry simulation. We’ll use the carbon gases simulation as an example.

Navigate to the GCClassic superproject folder and get a directory listing:
```
$ cd /path/to/your/GCClassic
$ ls -CF
AUTHORS.txt   CMakeLists.txt  CONTRIBUTING.md  LICENSE.txt  run@    src/        test@
CHANGELOG.md  CMakeScripts/   docs/            README.md    spack@  SUPPORT.md
```
As mentioned previously, run@ is a symbolic link. It actually points to the to the src/GEOS-Chem/run/GCClassic folder. This folder contains several scripts and template files for run directory creation.

Navigate to the run folder and get a directory listing:

$ cd run
$ ls -CF
archiveRun.sh*                  gitignore                   init_rd.sh*
createRunDir.sh*                HEMCO_Config.rc.templates/  README.md
geoschem_config.yml.templates/  HEMCO_Diagn.rc.templates/   runScriptSamples/
getRunInfo*                     HISTORY.rc.templates/       setupForRestarts.sh*

You can see several folders (highlighted in the directory display with /) and a few executable scripts (highlighted with *). The script we are interested in is createRunDir.sh.

Run the createRunDir.sh script.. Type:
```
$ ./createRunDir.sh
```

You will then be prompted to supply information about the run directory that you wish to create:

===========================================================
GEOS-CHEM RUN DIRECTORY CREATION
===========================================================

-----------------------------------------------------------
Choose simulation type:
-----------------------------------------------------------
   1. Full chemistry
   2. Aerosols only
   3. Carbon
   4. Hg
   5. POPs
   6. Tagged O3
   7. Trace metals
   8. TransportTracers
   9. CH4
  10. CO2
  11. Tagged CO
>>>

To select the GEOS-Chem carbon gases specialty simulation, type 3 followed by ENTER.

Tip

To exit, the run directory creation process, type Ctrl-C at any prompt.

You will be asked if you wish to set up a carbon simulation with all species (CH4, CO, CO2, OCS), or with just one of these species:

-----------------------------------------------------------
Do you wish to use a single advected species?
-----------------------------------------------------------
  1. Use all species
  2. Use CH4 only
  3. Use CO2 only
  4. Use CO only
  5. Use OCS only
>>>

Let’s pick the carbon simulation with all species. Type 1 followed by ENTER.

You will then be asked to specify the meteorology type for the simulation (GEOS-FP, MERRA-2), or GCAP 2.0):
```
-----------------------------------------------------------
Choose meteorology source:
-----------------------------------------------------------
  1. MERRA-2 (Recommended)
  2. GEOS-FP
  3. GEOS-IT
  4. GISS ModelE2.1 (GCAP 2.0)
>>>
```
To accept the recommended meteorology (MERRA-2), type 1 followed by ENTER.

Attention

The convection scheme used to generate archived GEOS-FP meteorology files changed from RAS to Grell-Freitas starting 01 June 2020 with impact on vertical transport. Discussion and analysis of the impact is available at https://github.com/geoschem/geos-chem/issues/1409.

To fix this issue, different GEOS-Chem convection schemes are called based on simulation start time. This ensures comparability in GEOS-Chem runs using GEOS-FP fields generated using the RAS convection scheme and fields generated using Grell-Freitas, but only if the simulation does not cross the 01 June 2020 boundary. We therefore recommend splitting up GEOS-FP runs in time such that a single simulation does not span this date. For example, configure one run to end on 01 June 2020 and then use its output restart to start another run on 01 June 2020.. Alternatively consider using MERRA2 which was entirely generated with RAS, or GEOS-IT which was entirely generated with Grell-Freitas. If you wish to use a GEOS-FP meteorology year different from your simulation year please create a GEOS-Chem GitHub issue for assistance to avoid accidentally using zero convective precipitation flux.

The next menu will prompt you for the horizontal resolution that you wish to use:

-----------------------------------------------------------
Choose horizontal resolution:
-----------------------------------------------------------
  1. 4.0  x 5.0
  2. 2.0  x 2.5
  3. 0.5  x 0.625
>>>

If you wish to set up a global simulation, type either 1 or 2 followed by ENTER.

If you wish to set up a nested-grid simulation, type 3 and hit ENTER. Then you will be followed by a nested-grid menu:

-----------------------------------------------------------
Choose horizontal grid domain:
-----------------------------------------------------------
  1. Global
  2. Asia
  3. Europe
  4. North America
  5. Custom
>>>

Type the number of your preferred option and then hit ENTER.

You will then be prompted for the vertical dimension of the grid.
```
-----------------------------------------------------------
Choose number of levels:
-----------------------------------------------------------
  1. 72 (native)
  2. 47 (reduced)
>>>
```
For most simulations, you will want to use 72 levels. Type 1 followed by ENTER.

For some memory-intensive simulations (such as nested-grid simulations), you can use 47 levels. Type 2 followed by ENTER.
You will then be prompted for the folder in which you wish to create the run directory.
```
-----------------------------------------------------------
Enter path where the run directory will be created:
-----------------------------------------------------------
>>>
```
You may enter an absolute path (e.g. $HOME/myusername/my-run-directories) followed by ENTER.

You may also enter a relative path (e.g. ~/my-run-directories) followed by ENTER). In this case you will see that the ./createRunDir.sh script will expand the path to an absolute path.

The next menu will prompt you for the run directory name.

-----------------------------------------------------------
Enter run directory name, or press return to use default:

NOTE: This will be a subfolder of the path you entered above.
-----------------------------------------------------------
>>>

You should use the default run directory name whenever possible. Type ENTER. The script will display the following output:

-- Using default directory name gc_4x5_merra2_carbon

or if you are creating a nested grid simulation:

-- Using default directory name gc_05x0625_merra2_carbon

and then

-- See rundir_vars.txt for summary of default run directory settings
-- This run directory has been set up to start on 20190101
-- A restart file for this date has been copied to the Restarts subdirectory
-- You may add more restart files using format GEOSChem.Restart.YYYYMMDD_HHmmz.nc4
-- Change simulation start and end dates in configuration file geoschem_config.yml
-- Default frequency and duration of diagnostics are set to monthly
-- Modify diagnostic settings in HISTORY.rc and HEMCO_Config.rc

The last menu will prompt you with:
```
-----------------------------------------------------------
Do you want to track run directory changes with git? (y/n)
-----------------------------------------------------------
>>>
```
Type y and then ENTER. Then you will be able to track changes that you make to GEOS-Chem configuration files with Git. This can be a lifesaver when debugging—you can revert to an earlier state and then start fresh.

You will then see output similar to this:
```
Initialized empty Git repository in /path/to/gc_4x5_merra2_carbon/.git/

Created /path/to/gc_4x5_merra2_carbon

>>>> REMINDER: You must compile with options: -DMECH=carbon <<<<
```
You can navigate to this directory and then start editing the GEOS-Chem configuration files.

Because the carbon simulation requires special compilation instructions, a reminder will be displayed with the proper command to use during the configuration step.

The procedure to set up run directories for other GEOS-Chem Classic simulations is similar to that shown above.