Figure 5 shows the input and output files for JPROC. Like the rest of the CMAQ programs, there is a distinction between the options that are invoked at compilation versus those invoked at execution of the program. When compiling JPROC, the user specifies a chemical mechanism to determine the gas-phase chemistry for which to calculate photolysis rates. Setting the Mechanism variable in the JPROC compile script configures the program to use a specific set of mechanism include files to build an executable. JPROC executables are hard-wired to a specific mechanism configuration.
While JPROC does not require any configuration at execution, there are several required and optional input files that the user must provide to the program. For the selected photochemical mechanism, the user must provide a set of molecular absorption cross-section and quantum yield data files (CSQY) that are consistent with the photolysis reactions in the mechanism. CMAQ is distributed with a full set of CSQY files for the CB-IV and SAPRC-99 mechanism versions supported by the model. If new mechanisms are added to CMAQ, the user must produce the appropriate CSQY data files for the added mechanism. The user also has the option of using the default atmospheric profiles contained in the PROFILES input file or using total ozone mapping spectrometer data (TOMS) to replace the climatologically-derived ozone column data in the PROFILES file.
Table 5.9. JPROC input files
| File Name | Format | Description |
|---|---|---|
| ET | ASCII | Extraterrestrial radiation as a function of wavelength |
| PROFILES | ASCII | Seasonal vertical profiles of ozone concentrations, aerosol attenuation, temperature, air pressure and Dobson values |
| TOMS | ASCII | Total ozone column measurements from the Total Ozone Mapping Spectrometer instrument aboard the sun-synchronous polar orbiting Nimbus satellite |
| O2ABS | ASCII | Absorption cross-section and quantum yield data for molecular oxygen as a function of wavelength |
| O3ABS | ASCII | Absorption cross-section and quantum yield data for ozone as a function of wavelength |
| CSQY | directory path | Directory path containing absorption cross-section and quantum yield data for gas-phase photolysis reactions as a function of wavelength |
The configuration options listed here are set during compilation of the ICON executable. When these options are invoked they create a binary executable that is fixed to the specified configuration. To change these options it is necessary to recompile ICON and create a new executable.
-
Opt:[default: verbose]
Defines the action to be taken by the program M3BLD when extracting source code from CVS and compiling an executable.
- compile_all: force compile, even if all the object files are current
- clean_up: remove all source files upon successful compilation
- no_compile: do everything except compile
- no_link: do everything except link
- one_step: compile and link in one step
- parse_only: checks configuration file syntax
- show_only: shows requested commands but does not execute them
- verbose: shows requested commands as they are executed
-
MakeOpt:
Uncomment to build a Makefile to compile the executable
-
Mechanism:
Specifies the gas-phase, aerosol, and aqueous phase chemical mechanisms to create initial conditions. The choices for the Mechanism variable are the mechanism directory names under the $M3MODEL/include/release directory. Examples include:
- cb4_ae3_aq: CB-IV gas-phase mechanism, 3rd generation CMAQ aerosol mechanism, aqueous/cloud chemistry
- cb4_ae4_aq: CB-IV gas-phase mechanism, 4th generation CMAQ aerosol mechanism, aqueous/cloud chemistry
- saprc99_ae4_aq: SAPRC99 gas phase mechanism, 4th generation CMAQ aerosol mechanism, aqueous/cloud chemistry
- saprc99_ae3: SAPRC99 gas phase mechanism and 3rd generation CMAQ aerosol mechanism
Section 3.3 provides an overview of how to install and compile the CMAQ programs for the tutorial simulation. Follow the steps outlined in Section 3.3 to compile new versions of JPROC:
- If you have not already done so, build the CMAQ source code and compilation management program (M3BLD); this only needs to be done the first time you install CMAQ
- Install and compile the I/O API and netCDF libraries; if these are already available from a previous CMAQ compilation, configure the JPROC build script to use the available libraries
- Configure the JPROC build script for your application
- Invoke the build script to create an executable:
./bldit.jproc.pgf
The environment variables listed here are invoked during execution of the program and are set in the JPROC run script.
- EXEC: [default: JPROC_${CFG}]
Executable to use for the simulation
Table 5.10. JPROC output files
| File Name | Format | Description |
|---|---|---|
| JVfile (JTABLE_$Date} | ASCII | Daily clear-sky photolysis rates file |
The default location of the JPROC output files is the $M3DATA/jproc directory, controlled by the OUTDIR variable in the run script. The default naming convention for all JPROC output files uses the Date environment variable in the file name, which is aliased to the STDATE environment variable in the run script.