The SMOKE directory structure is the organization of UNIX directories and subdirectories (essentially the same as “folders” on Windows computers). These directories are defined and created using the SMOKE Assigns file. By “defined”, we mean that environment variables are set to the actual path name for each of the directories, and their relationships to one another are implicit in these definitions. As will be described in more detail in Chapter 4, How to Use SMOKE, you should create an Assigns file for each modeling case to organize your modeling runs. If created properly, the different Assigns files will cause the intermediate and output directories to be different for each case; this prevents overwriting files from one case with files from another. Some parts of the directory structure are shared by all modeling cases because they are usually the same (e.g., SMOKE support files), but the intermediate and output files are not assumed to be the same because they often differ between cases.
Before we can proceed with describing the scripts, we need to introduce the Assigns file. Detailed documentation on this file is provided in Section 4.2.2.2, “Assigns files”. For the purposes of the discussion here, we provide an example Assigns file to help clarify what it is. Because this file is quite lengthy, we have only included excerpts. In this subsection, the Assigns file is simply a set of setenv UNIX commands and calls to helper scripts.
The arrangement within the default Assigns file provided with SMOKE is:
Shell command (e.g., #!/bin/csh -fx for C shell)
Descriptive global comments
Settings for the naming roots
Settings for the episode dates and times
Settings for the directory structure and use of the set_dirs.scr helper script
Settings for SMOKE input and output files and calls to other helper scripts
The first settings section is used for naming roots. These settings allow users to set the inventory input and output identifiers,
the base-case scenario names, and the grid and chemical mechanism names (see Chapter 4, How to Use SMOKE for more details). The following lines provide the naming roots used in the default Assigns file provided with SMOKE, ASSIGNS.nctox.cmaq.cb4pm25_wtox.us12-nc. This file and the helper scripts can be found in the $ASSIGNS directory, which we will define in Section 3.2.2, “The basic SMOKE directories”.
# ## I/O Naming roots # setenv INVID nctox # Inventory input identifier setenv INVOP nctox # Base year inventory output name setenv INVEN nctox # Base year inventory name with version setenv ABASE nctox # Area base case output name setenv BBASE nctox # Biogenics base case output name setenv MBASE nctox # Mobile base case output name setenv PBASE nctox # Point base case output name setenv EBASE nctox # Output merged base case name setenv METSCEN 12km # Met scenario name setenv GRID us12-nc # Gridding root for naming setenv IOAPI_GRIDNAME_1 US12NC_66X52 # Grid selected from GRIDDESC file setenv IOAPI_ISPH 19 # Specifies spheroid type associated with grid setenv SPC cmaq.cb4p25_wtox # Speciation type
The next section of the file includes the settings for the episode:
## Mobile episode variables setenv EPI_STDATE 2001191 # Julian start date setenv EPI_STTIME 000000 # start time (HHMMSS) setenv EPI_RUNLEN 0480000 # run length (HHHMMSS) setenv EPI_NDAY 2 # number of full run days ## Per-period environment variables setenv G_STDATE 2001191 # Julian start date setenv G_STTIME 000000 # start time (HHMMSS) setenv G_TSTEP 10000 # time step (HHMMSS) setenv G_RUNLEN 250000 # run length (HHMMSS) setenv ESDATE 20010710 # Start date of emis time-based files/dirs setenv MSDATE 20010710 # Start date of met time-based files setenv NDAYS 1 # Duration in days of each emissions file setenv MDAYS 1 # Duration in days of met time-based files setenv YEAR 2001 # Base year for year-specific files
As described in Chapter 4, How to Use SMOKE, these settings control both the way SMOKE runs (e.g., SMOKE uses EPI_STDATE, the start date of the episode, to decide what day to start the simulation) and the way SMOKE names files (e.g., ESDATE is used to help name time-dependent files).
The next section of the Assigns file is used to set the user-defined input and output directory paths. It uses a helper script
called set_dirs.scr that applies the initial settings made by the Assigns file to set environment variables for the directories, as described
in Section 3.2.2, “The basic SMOKE directories”. The set_dirs.scr script also verifies that all of the directories are there and that the permissions of the directories are group readable
and writable.
## User-defined I/O directory settings setenv SMK_SUBSYS $SMK_HOME/subsys # SMOKE subsystem dir setenv SMKROOT $SMK_SUBSYS/smoke # System root dir setenv SMKDAT $SMK_HOME/data # Data root dir setenv ASSIGNS $SMKROOT/assigns # SMOKE assigns files <omitted section> ## Set dependent directory names # source $ASSIGNS/set_dirs.scr
Now that we have provided a little background on Assigns files, we will spend the rest of this chapter describing the SMOKE directory structure. We will return to discussion of the Assigns file and scripts in Chapter 4, How to Use SMOKE. It is important to understand the directory structure information in the rest of this chapter before moving on to Chapter 4, How to Use SMOKE.