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):

Attention

We are still evaluating GEOS-Chem with the new NASA GEOS-IT meterorology product. Please select one of the other meteorology options for the time being.
```
-----------------------------------------------------------
Choose meteorology source:
-----------------------------------------------------------
  1. MERRA-2 (Recommended)
  2. GEOS-FP
  3. GEOS-IT (Beta release)
  4. GISS ModelE2.1 (GCAP 2.0)
>>>
```
To accept the recommended meteorology (MERRA-2), type 1 followed by ENTER.

Important

The convection scheme used for GEOS-FP met generation changed from RAS to Grell-Freitas with impact on GEOS-FP meteorology files starting June 1, 2020. For this reason we recommend using MERRA-2 instead of GEOS-FP if running a simulation across June 1, 2020 to avoid unexpected discontinuities. Additional information about the impact of the convection change is at geoschem/geos-chem#1409.

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.