4. Model Input Files

March 19, 2025 · View on GitHub

4.1 Introduction

This chapter provides basic information on the format and content of CMAQ input files. It also provides information on using the pre-processing tools provided in the repository for preparing initial and boundary conditions and meteorology inputs. Links are provided for the emissions processing tools that are released through their own repository or website. A list of CMAQ input files can be found in Table 4-1. Some CMAQ input files are in ASCII format while the majority of them are in the Network Common Data Form (netCDF) format. CMAQ input and output files are self-describing netCDF-format files in which the file headers have all the dimensioning and descriptive information needed to define the resident data. Users should download the latest code for the NetCDF from the NetCDF website. Compilation and configuration information for the NetCDF is available through the Unidata website.

All CMAQ input and output files are conformed to I/O API netCDF file format. Please refer to the I/O API User's Manual for details.

Full input datasets for 2016 over two domains are publically available to download from the CMAS Data Warehouse. The input files are stored on Google Drive with metadata organized through Dataverse.

Domain	Simulation Dates	Dataverse DOI
Southeast US	July 1 - 14, 2016	https://doi.org/10.15139/S3/IQVABD
Conterminous U.S. (CONUS)	Jan 1 - Dec 31, 2016	https://doi.org/10.15139/S3/MHNUNE

4.2 CMAQ Pre-processors

Figure 2-1 shows the relationship between CMAQ pre-processors and the main CMAQ program, the CMAQ Chemistry Transport Model (CCTM). MCIP, ICON and BCON are included in the CMAQ repository and are used to create meteorological, initial conditions and boundary conditions inputs. SMOKE, FEST-C and Spatial Allocator Tools are external software packages used for creating emissions inputs for CMAQ. The following subsections provide more information on these tools and point the user to additional sources of documentation.

4.2.1 Meteorology-Chemistry Interface Processor (MCIP)

MCIP processes meteorological fields output by the WRF model into files that are compatible with the CCTM and SMOKE (an emissions processor that computes emissions inputs for CMAQ). The output files generated by MCIP are used by ICON and BCON and various other programs in CMAQ, so MCIP must be the first program run after installing the CMAQ source codes and initializing CMAQ environment variables. Configuration options for MCIP include the time periods over which to extract data from the meteorological model output files, horizontal grid definitions for output, and control for optional 3D output variables. MCIP can either process the full horizontal domain from WRF or a user-defined subset of that domain (that is, a "window"). Most of the fields that are simulated by WRF are not modified by MCIP for the CCTM or emissions model and are simply "passed through" to the output. Where needed, MCIP transforms data from the WRF projection and coordinate system to be consistent with that being used for CMAQ simulations.

Unlike many of the tools distributed with CMAQ, MCIP is compiled with a Makefile and then run with a run script. Instructions on how to compile and run MCIP are provided in the README.md file in the PREP/mcip folder.

4.2.2 Initial Conditions Processor (ICON)

ICON generates a gridded netCDF file of the chemical conditions for all grid cells in the modeling domain for the initial time of a simulation. It can generate these initial conditions from either an existing CCTM output file or one of four ASCII files of vertically resolved concentration profiles distributed with CMAQ. Running ICON requires that the user already generated MCIP files for their target modeling domain. For both input file options, ICON will interpolate the data to the horizontal and vertical structure of the target domain as defined in the MCIP files. The species in the ICON output file are identical to those in the input (either CCTM output or ASCII profile) file.

Using an existing CCTM output file to generate initial conditions is applicable when interpolating initial conditions from a coarse to a fine grid domain, as may occur when setting up nested simulations (simulations with finer-resolution grids that cover part of coarser-resolution grids). This is the preferred mode of specifying initial conditions since the spatial concentration patterns derived from the coarser-resolution simulation can be considered a first approximation of the concentration fields over the finer-resolution subdomain at the beginning of the simulation.

The four ASCII files of vertically resolved concentration profiles distributed with CMAQ represent annual average concentrations at a grid cell over the Pacific derived from a simulation with the hemispheric version of CMAQv5.3 beta2 for the year 2016. As such, these concentration profiles are reflective of conditions in a remote marine environment. The simulation was performed with the cb6r3m_ae7_kmtbr chemical mechanism and profiles for racm_ae6_aq, saprc07tc_ae6_aq, and saprc07tic_ae7i_aq were derived using the species mapping approach described in Step 3 of the CMAQ Tutorial on creating Initial and Boundary Conditions from Seasonal Average Hemispheric CMAQ Output. If one of these ASCII profile files is used to generate initial conditions, the resulting concentration fields will be uniform over the modeling domain and will not be a realistic representation of conditions over the modeling domain. As a result, simulations initialized with profile-derived rather than CCTM-derived concentration fields may require longer spin-up periods before conditions simulated within the domain no longer are influenced by these unrealistic initial concentration fields.

The configuration options for ICON include choosing whether the initial conditions are generated from an existing CCTM output file or from an ASCII profile, and defining the horizontal and vertical grids and time for which initial conditions are to be generated. Information on configuring ICON for the different kinds of input data, environment variables, input and output files, compiling and running ICON are provided in the README.md file in the PREP/icon folder.

4.2.3 Boundary Conditions Processor (BCON)

BCON generates a netCDF file of the chemical conditions along the lateral boundaries of the modeling domain. BCON will generate an output file with chemical concentrations for all grid cells along the modeling domain's horizontal boundaries. It can generate these boundary conditions from either an existing CCTM output file or one of four ASCII files of vertically resolved concentration profiles distributed with CMAQ. Running BCON requires that the user already generated MCIP files for their target modeling domain. For both input file options, BCON will interpolate the data to the horizontal and vertical structure of the target domain as defined in the MCIP files. The species in the BCON output file are identical to those in the input (either CCTM output or ASCII profile) file. Depending on user specified options and/or input datasets, the boundary conditions generated by BCON can be time varying, time independent, and either spatially uniform or variable across the model boundaries.

Using an existing CCTM output file to generate boundary conditions is applicable when setting up windowed simulations (simulations with the same resolution that cover only a part of the outer domain) or nested simulations (simulations with finer-resolution grids that cover part of coarser-resolution grids). This is the preferred mode of specifying boundary conditions since the spatial concentration patterns derived from the coarser-resolution simulation will be spatially varying along the boundaries of the finer-resolution domain. Boundary conditions generated from CCTM output files will be either time varying or time independent.

The four ASCII files of vertically resolved concentration profiles distributed with CMAQ represent annual average concentrations at a grid cell over the Pacific derived from a simulation with the hemispheric version of CMAQv5.3 beta2 for the year 2016. As such, these concentration profiles are reflective of conditions in a remote marine environment. The simulation was performed with the cb6r3m_ae7_kmtbr chemical mechanism and profiles for racm_ae6_aq, saprc07tc_ae6_aq, and saprc07tic_ae7i_aq were derived using the species mapping approach described in Step 3 of the CMAQ Tutorial on creating Initial and Boundary Conditions from Seasonal Average Hemispheric CMAQ Output. If one of these ASCII profile files is used to generate boundary conditions, the resulting concentration fields will be uniform along the boundaries of the modeling domain and will not vary in time. Therefore, they are not a realistic representation of conditions along the domain boundaries and should only be used in cases where boundary conditions are not expected to affect the interpretation of model results.

CMAQ can use boundary conditions derived from global chemistry models (GCMs). While BCON does not directly support processing of datasets from GCMs (other than the hemispheric version of CMAQ) in their native formats, users could develop their own custom codes to transform their GCM datasets into I/O API format, which would then allow these datasets to be input into BCON in the same way as an existing CCTM output file.

The configuration options for BCON include choosing whether the boundary conditions are generated from an existing CCTM output file or from an ASCII profile, and defining the horizontal and vertical grids and time period for which boundary conditions are to be generated. Information on configuring BCON for the different kinds of input data, environment variables, input and output files, compiling and running BCON are provided in the README.md file in the PREP/bcon folder.

4.2.4 External Software Programs for Preparing CMAQ Inputs

The SMOKE and FEST-C modeling systems and the Spatial Allocator tools are used to create CMAQ emissions and land surface inputs. These systems are maintained by EPA and CMAS developers and are hosted and supported by the CMAS Center. Links to documentation and software download for each system are provided below.

Emissions Processor (SMOKE) Sparse Matrix Operator Kerner Emissions (SMOKE) Modeling System is designed to create gridded, speciated, hourly emissions for input into CMAQ and other air quality models. SMOKE supports area, biogenic, mobile (both onroad and nonroad), and point source emissions processing for criteria, particulate, and toxic pollutants. For biogenic emissions modeling, SMOKE uses the Biogenic Emission Inventory System.

Fertilizer Emissions Processor (FEST-C) The Fertilizer Emission Scenario Tool for CMAQ (FEST-C) system is used to generate agricultural-land nitrogen and soil information for CMAQ bi-directional NH₃ modeling. FEST-C contains three main components: Java interface, Environmental Policy Integrated Climate (EPIC) model, and SA Raster Tools. The interface guides users through generating required land use and crop data and EPIC input files and simulating EPIC, and extracting EPIC output for CMAQ.

FEST-C is used to create the E2C_LU, E2C_SOIL, and E2C_CHEM files discussed later in this chapter.

Processing Spatial Data with the Spatial Allocator (SA) The Spatial Allocator is a set of tools that helps users manipulate and generate data files related to emissions and air quality modeling. The tools perform functions similar to Geographic Information Systems (GIS), but are provided to the modeling community free of charge. In addition, the tools are designed to support some of the unique aspects of the file formats used for CMAQ, SMOKE and WRF modeling.

SA is used to generate the surf zone and open ocean file that is a required input for utilizing marine emissions and chemistry in CMAQ. Some chemical mechanisms require the presence of additional variables in the ocean file which can be added by using a Python based tool. This file is discussed later in this chapter under the OCEAN_1: Sea spray mask section.

Python tool for adding DMS and CHLO in the OCEAN file An ocean mask file (OCEAN) containing OPEN (open ocean) and SURF (surf zone) is needed for sea spray emissions module in CMAQ. Some chemical mechanisms (e.g., CB6r5m_ae7_aq) in CMAQ include halogen and DMS chemistry which requires additional parameters in the OCEAN file: DMS (DMS concentrations in seawater) and CHLO (monthly climatological chl-a concentration from MODIS). A Python based tool has been developed for adding DMS and CHLO to the OCEAN file (PYTOOLS/dmschlo/CMAQ_DMS_ChlorA_Plot.ipynb). Not all chemical mechanisms need DMS and CHLO and some (CB6r5_ae7_aq) only need DMS.

Additional information on processing data for CMAQ inputs is provided in Appendix C.

4.3 CMAQ Input Files

Jump to Table of Input Files
Jump to CCTM Output Files in Chapter 7

CMAQ requires a basic set of input files: initial condition file, which is created by ICON process or previous day output; boundary condition file, which is created by BCON process; emission files; and meteorological data created by MCIP using WRF and terrain data. Additional input files may be required based on specific run time options. CMAQ output files include a basic set of files with aerosol and gas-phase species concentrations, wet and dry deposition estimates, and visibility metrics, and an auxiliary set of output files for diagnosing model performance and in-line-calculated emissions. Model outputs are discussed in Chapter 7.

Rather than forcing the user to deal with hard-coded file names or hard-coded unit numbers, the I/O API netCDF file format utilizes the concept of logical file names. The modelers can define the logical names as properties of a program, and then at run-time the logical names can be linked to the actual file name using environment variables. For programming purposes, the only limitations are that logical file names cannot contain blank spaces and must be at most 16 characters long. When a modeler runs a program that uses the I/O API format, environment variables must be used to set the values for the program’s logical file names. A complete list of CMAQ input is provided in Table 4-1.

This section describes each of the input files required by the various CMAQ programs. The section begins with a description of the grid definition file, GRIDDESC, which is used by several CMAQ programs, and then goes through a program-by-program listing of the CMAQ input file requirements. Table 4-1 lists the source, file type (e.g. ASCII, GRDDED3, BNDARY3, etc.), and temporal and spatial dimensions of each CMAQ input file. Typical time step is 1 hour; however a user can specify a finer one, e.g. 20 minutes. In addition, typical thickness of a boundary file is 1, i.e. NTHIK = 1 but it can be any positive integer.

Table 4-1. CMAQ input files. Note that when "Time-Dependence" is listed as "Hourly", it is shorthand for a time-varying file. It is recommended that CMAQ use a time increment that is no longer than one hour. However, CMAQ can be run with a Time Dependence that is shorter than hourly.

Environment Variable Name for File	File Type	Time-Dependence	Spatial Dimensions	Source	Required
General
GRIDDESC	ASCII	n/a	n/a	MCIP	required
gc_matrix_nml	ASCII	n/a	n/a	CMAQ repo	required
ae_matrix_nml	ASCII	n/a	n/a	CMAQ repo	required
nr_matrix_nml	ASCII	n/a	n/a	CMAQ repo	required
tr_matrix_nml	ASCII	n/a	n/a	CMAQ repo	required
MISC_CTRL_NML	ASCII	n/a	n/a	CMAQ repo	required
Initial Conditions Inputs
INIT_CONC_1	GRDDED3	Time-invariant	XYZ	ICON or CCTM	required
Boundary Conditions Inputs
BNDY_CONC_1	BNDARY3	Hourly	PERIM*Z	BCON	required
MCIP
GRID_CRO_2D	GRDDED3	Time-invariant	XY	MCIP	required
GRID_BDY_2D	BNDARY3	Time-invariant	PERIM*Z	MCIP	required
GRID_DOT_2D	GRDDED3	Time-invariant	(X+1)*(Y+1)	MCIP	required
MET_BDY_3D	BNDARY3	Hourly	PERIM*Z	MCIP	required
MET_CRO_2D	GRDDED3	Hourly	XY	MCIP	required
MET_CRO_3D	GRDDED3	Hourly	XYZ	MCIP	required
MET_DOT_3D	GRDDED3	Hourly	(X+1)*(Y+1)Z	MCIP	required
LUFRAC_CRO	GRDDED3	Time-invariant	XYL	MCIP	required
SOI_CRO	GRDDED3	Hourly	XYS	MCIP	optional (Contains soil moisture and soil temperature in layers. A two-layer representation of those fields is currently mirrored in MET_CRO_2D.)
MOSAIC_CRO	GRDDED3	Hourly	XYM	MCIP	optional (Contains surface fields in mosaic land use categories if Noah Mosaic LSM was run in WRF. Can work with STAGE deposition in CCTM.)
mcip.nc	netCDF	varies by field	varies by field	MCIP	required if IOFORM=2 (Currently not compatible with rest of CMAQ system.)
mcip_bdy.nc	netCDF	varies by field	varies by field	MCIP	required if IOFORM=2 (Currently not compatible with rest of CMAQ system.)
Emissions Inputs
DESID_CTRL_NML	ASCII	n/a	n/a	CMAQ repo	required
DESID_CHEM_CTRL_NML	ASCII	n/a	n/a	CMAQ repo	required
GR_EMIS_XXX*	GRDDED3	Hourly	XYZ	SMOKE	required
STK_GRPS_XXX	GRDDED3	Time-invariant	XY	SMOKE	required
STK_EMIS_XXX	GRDDED3	Hourly	XY	SMOKE	required
NLDN_STRIKES	GRDDED3	Hourly	XY	Must purchase data	optional for including NO from lightning
LTNGPARMS_FILE	GRDDED3	Time-invariant	XY	CMAS	required for including NO from lightning
Biogenic and Land Surface Inputs
OCEAN_1	GRDDED3	Time-invariant	XY	Spatial Allocator and a Python-based tool	required for running CMAQ with sea-spray aerosol, halogen or DMS chemistry
GSPRO	ASCII	Time-invariant	N/a	CMAQ repo	required for running CMAQ with online BEIS biogenics
BEIS_NORM_EMIS	GRDDED3	Time-invariant	XY	SMOKE	required for running CMAQ with online BEIS biogenics
MEGAN_CTS	GRDDED3	Time-invariant	XYZ	MEGAN preprocessor	required for running CMAQ with online MEGAN biogenics
MEGAN_LDF	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for running CMAQ with online MEGAN biogenics
MEGAN_EFS	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for running CMAQ with online MEGAN biogenics
MEGAN_LAI	GRDDED3	Time-invariant	XY	MEGAN preprocessor	optional for running CMAQ with online MEGAN biogenics
BDSNP_AFILE	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for BDSNP soil NO
BDSNP_NAFILE	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for BDSNP soil NO model
BDSNP_LFILE	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for BDSNP soil NO model
BDSNP_FFILE	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for BDSNP soil NO model
BDSNP_NFILE	GRDDED3	Time-invariant	XY	MEGAN preprocessor	required for BDSNP soil NO model
E2C_LU	GRDDED3	Time-invariant	XY	EPIC	required for running CMAQ with bidirectional NH3
E2C_SOIL	GRDDED3	Time-invariant	XY	EPIC	required for running CMAQ with bidirectional NH3
E2C_CHEM	GRDDED3	Daily	XY	EPIC	required for running CMAQ with bidirectional NH3
STAGE Deposition Option
STAGECTRL_NML	ASCII	n/a	n/a	CMAQ repo	required
Photolysis
OMI	ASCII	Daily	n/a	CMAQ repo or create_omi	required
OPTICS_DATA	ASCII	n/a	n/a	CMAQ repo	required
CSQY_DATA	ASCII	n/a	n/a	CMAQ repo	required

*XXX - three-digit variable indicating emission stream number. Gridded and Inline Point emissions are numbered independently.

4.3.1 Windowing Capability

Under the assumption that all inputs utilize the same projection and grid resolution, CMAQ allows users to provide a gridded input files which covers a different geographic extent but are a proper super set of the simulation domain. Proper super set means that the simulated domain must be at least one grid cell smaller at all sides than the gridded input (see Figure 4-3-1 below). This capability excludes the chemical boundary condition file (BCFILE) which must be created for the simulated domain using the BCON program. This capability applies to meteorological data files, however, METBDY3D won't be used, and the meteorological boundary information will be extracted from METCRO3D directly. For point source files, CMAQ already can discern if a particular point source is within the simulation domain or not as long as the files also use the same projection.

Figure 4-3-1

Figure 4-3-1. Appropriate Windowing Domain illustration

4.4 GRIDDESC and Species Namelist Files

GRIDDESC: Horizontal domain definition

Line	Column	Name	Type	Description	Options for Syntax:
1		File Type	String	String to delineate Gas Phase (GC), Aerosol (AE), Non-reactive (NR) and Tracer (TR) species namelist	{&GC_nml, &AE_nml, &NR_nml, &TR_nml}
3		Header ID	String	String to define data structure relating to namelist	{GC_SPECIES_DATA=, AE_SPECIES DATA= , NR_SPECIES_DATA= ,TR_SPECIES_DATA = }
5	1	SPECIES	String	CMAQ Species name, i.e. NO, HNO₃, PAR; dependent on chemical mechanism	-
	2	MOLWT	Integer	Species Molecular Weight	-
	3	IC	String	IC surrogate species name for the CMAQ Species	{'Species name', ' '}
	4	FAC	Integer	Scaling factor for the IC concentration	{Any real: default = -1 if IC is not specified}
	5	BC	String	BC surrogate species name for the CMAQ Species	{'Species name', ' '}
	6	FAC	Integer	Scaling factor for the BC concentration	{Any real: default = -1 if BC is not specified}
	7	DRYDEP SURR	String	Deposition velocity variable name for the CMAQ Species	{'Species name', ' '}
	8	FAC	Integer	Scaling factor for the deposition velocity	{Any real: default = -1 if SURR is not specified}
	9	WET-SCAV SURR	String	Wet Deposition Scavenging surrogate species	{'Species name', ' '}
	10	FAC	Integer	Scaling factor for Scavenging	{Any real: default = -1 if SURR is not specified}
	11	GC2AE SURR	String	Gas-to-aerosol transformation species	{'Species name', ' '}
	12	GC2AQ SURR	String	Gas-to-aqueous transformation species	{'Species name', ' '}
	13	TRNS	String	Transport Switch. NOTE: Instead of using one column labeled "TRNS" to turn/off both advection and diffusion for a pollutant, two separate columns labeled "ADV" and "DIFF" can be used to switch on/off advection and diffusion separately.	{YES/NO}
	14	DDEP	String	Dry deposition output file switch	{YES/NO}
	15	WDEP	Real	Wet deposition output file switch	{YES/NO}
	16	CONC	String	Concentration output file switch	{YES/NO}

Variable Name	Description	Units	Dimensions	File	Required
LAT	latitude	degrees, where Northern Hemisphere is positive	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	yes
LON	longitude	degrees, where Western Hemisphere is negative	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	yes
MSFX2	squared map-scale factor	m² m^-2	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	yes
HT	terrain elevation	m	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	yes
DLUSE	dominant land use	category	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	yes
LWMASK	land-water mask	1=land, 0=water	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	yes
PURB	urban percent of cell based on land coverage	percent	XY	GRIDCRO2D and GRIDBDY2D, or mcip.nc and mcip_bdy.nc	no, but refines vertical mixing in urban areas
LUFRAC	fraction of land use by category	1	XYL	LUFRACCRO or mcip.nc	yes
LATD	latitude	degrees, where Northern Hemisphere is positive (at cell corners)	XY	GRIDDOT2D or mcip.nc	no
LOND	longitude	degrees, where Western Hemisphere is negative (at cell corners)	XY	GRIDDOT2D or mcip.nc	no
MSFD2	squared map scale factor	m² m^-2 (at cell corners)	XY	GRIDDOT2D or mcip.nc	no
LATU	latitude	degrees, where Northern Hemisphere is positive (at cell west-east faces)	XY	GRIDDOT2D or mcip.nc	no
LONU	longitude	degrees, where Western Hemisphere is negative (at cell west-east faces)	XY	GRIDDOT2D or mcip.nc	no
MSFU2	squared map scale factor	m² m^-2 (at cell west-east faces)	XY	GRIDDOT2D or mcip.nc	yes
LATV	latitude	degrees, where Northern Hemisphere is positive (at cell south-north faces)	XY	GRIDDOT2D or mcip.nc	no
LONV	longitude	degrees, where Western Hemisphere is negative (at cell south-north faces)	XY	GRIDDOT2D or mcip.nc	no
MSFV2	squared map scale factor	m² m^-2 (at cell south-north faces)	XY	GRIDDOT2D or mcip.nc	yes
PRSFC	surface pressure	Pa	XYT	METCRO2D or mcip.nc	yes
USTAR	cell-averaged horizontal friction velocity	m s^-1	XYT	METCRO2D or mcip.nc	yes
WSTAR	convective velocity scale	m s^-1	XYT	METCRO2D or mcip.nc	yes
PBL	planetary boundary layer height	m	XYT	METCRO2D or mcip.nc	yes
ZRUF	surface roughness length	m	XYT	METCRO2D or mcip.nc	yes
MOLI	inverse Monin-Obukhov length	m^-1	XYT	METCRO2D or mcip.nc	yes
HFX	sensible heat flux	W m^-2	XYT	METCRO2D or mcip.nc	yes
LH	latent heat flux	W m^-2	XYT	METCRO2D or mcip.nc	yes
RADYNI	inverse aerodynamic resistance	m s^-1	XYT	METCRO2D or mcip.nc	yes
RSTOMI	inverse bulk stomatal resistance	m s^-1	XYT	METCRO2D or mcip.nc	yes
TEMPG	skin temperature at ground	K	XYT	METCRO2D or mcip.nc	yes
TEMP2	2-m temperature	K	XYT	METCRO2D or mcip.nc	yes
Q2	2-m water vapor mixing ratio	kg kg^-1	XYT	METCRO2D or mcip.nc	yes
WSPD10	10-m wind speed	m s^-1	XYT	METCRO2D or mcip.nc	yes
WDIR10	10-m wind direction	degrees	XYT	METCRO2D or mcip.nc	no
GLW	longwave radiation at ground	W m^-2	XYT	METCRO2D or mcip.nc	yes
GSW	solar radiation absorbed at ground	W m^-2	XYT	METCRO2D or mcip.nc	yes
RGRND	solar radiation reaching the surface	W m^-2	XYT	METCRO2D or mcip.nc	yes
RN	incremental (per output time step) nonconvective precipitation	cm	XYT	METCRO2D or mcip.nc	yes
RC	incremental (per output time step) convective precipitation	cm	XYT	METCRO2D or mcip.nc	yes
CFRAC	total column integrated cloud fraction	1	XYT	METCRO2D or mcip.nc	yes, if photolysis uses the table option in CCTM
CLDT	cloud layer top height	m	XYT	METCRO2D or mcip.nc	yes, if photolysis uses the table option in CCTM
CLDB	cloud layer bottom height	m	XYT	METCRO2D or mcip.nc	yes, if photolysis uses the table option in CCTM
WBAR	average liquid water content of cloud	g m^-3	XYT	METCRO2D or mcip.nc	yes, if photolysis uses the table option in CCTM
SNOCOV	snow cover	1=yes, 0=no	XYT	METCRO2D or mcip.nc	yes
VEG	vegetation coverage	1	XYT	METCRO2D or mcip.nc	yes
LAI	leaf-area index	m² m^-2	XYT	METCRO2D or mcip.nc	yes
WR	canopy moisture content	m	XYT	METCRO2D or mcip.nc	yes
SEAICE	sea ice	1	XYT	METCRO2D or mcip.nc	yes
SNOWH	snow height	m	XYT	METCRO2D or mcip.nc	yes
SOIM1	volumetric soil moisture in top cm	m³ m^-3	XYT	METCRO2D or mcip.nc	yes, but preferred to use from SOIM3D
SOIM2	volumetric soil moisture in top m	m³ m^-3	XYT	METCRO2D or mcip.nc	yes, but preferred to use from SOIM3D
SOIT1	soil temperature in top cm	K	XYT	METCRO2D or mcip.nc	yes, but preferred to use from SOIT3D
SOIT2	soil temperature in top m	K	XYT	METCRO2D or mcip.nc	yes, but preferred to use from SOIT3D
SLTYP	soil texture type	1	XYT	METCRO2D or mcip.nc	yes
WWLT_PX	soil wilting point from PX LSM	m³ m^-3	XYT	METCRO2D or mcip.nc	no, but used if available
WFC_PX	soil field capacity from PX LSM	m³ m^-3	XYT	METCRO2D or mcip.nc	no, but used if available
WSAT_PX	soil saturation from PX LSM	m³ m^-3	XYT	METCRO2D or mcip.nc	no, but used if available
CLAY_PX	clay from PX LSM	1	XYT	METCRO2D or mcip.nc	no, but used if available
CSAND_PX	coarse sand from PX LSM	1	XYT	METCRO2D or mcip.nc	no, but used if available
FMSAND_PX	fine-medium sand from PX LSM	1	XYT	METCRO2D or mcip.nc	no, but used if available
JACOBF	total Jacobian at layer face	m	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
JACOBM	total Jacobian at layer middle	m	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
DENSA_J	Jacobian-weighted total air density	kg m^-2	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
WHAT_JD	Jacobian- and density-weighted vertical contravariant velocity	kg m^-1 s^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
TA	air temperature	K	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
QV	water vapor mixing ratio	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
PRES	air pressure	Pa	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
DENS	air density	kg m^-3	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
WWIND	vertical velocity	m s^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
ZH	mid-layer height above ground	m	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
ZF	full layer height above ground	m	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
TKE	turbulent kinetic energy	J kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and met_bdy.nc	no
PV	potential vorticity	m² K kg^-1 s^-1 x 10^-6	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no, but required for PV scaling
WWIND	vertical velocity	m s^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no
CFRAC_3D	3D resolved cloud fraction	1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no, but used if available
QC	cloud water mixing ratio	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
QR	rain water mixing ratio	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	yes
QI	ice mixing ratio	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no, but used if available
QS	snow mixing ratio	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no, but used if available
QG	graupel mixing ratio	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no, but used if available
QC_CU	subgrid cloud water mixing ratio from KF	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no; only output if available from WRF; for future development
QI_CU	subgrid cloud ice mixing ratio from KF	kg kg^-1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no; only output if available from WRF; for future development
CLDFRA_DP	subgrid deep cloud fraction	1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no; only output if available from WRF; for future development
CLDFRA_SH	subgrid shallow cloud fraction	1	XYZT	METCRO3D and METBDY3D, or mcip.nc and mcip_bdy.nc	no; only output if available from WRF; for future development
UWIND	u-component of horizontal wind (cell corners)	m s^-1	XYZT	METDOT3D or mcip.nc	no
VWIND	v-component of horizontal wind (cell corners)	m s^-1	XYZT	METDOT3D or mcip.nc	no
UHAT_JD	contravariant-U x Jacobian x density	kg m^-1 s^-1 [cell faces; Arakawa-C grid]	XYZT	METDOT3D or mcip.nc	yes
VHAT_JD	contravariant-V x Jacobian x density	kg m^-1 s^-1 [cell faces; Arakawa-C grid]	XYZT	METDOT3D or mcip.nc	yes
UWINDC	u-component of horizontal wind (west-east cell faces)	m s^-1	XYZT	METDOT3D or mcip.nc	yes
VWINDC	v-component of horizontal wind (south-north cell faces)	m s^-1	XYZT	METDOT3D or mcip.nc	yes
SOIT3D	soil temperature	K	XYST	SOICRO or mcip.nc	yes
SOIM3D	soil moisture	kg kg^-1	XYST	SOICRO or mcip.nc	yes
LUFRAC2	fractional land use in mosaic categories	1	XYM	MOSAICCRO or mcip.nc	no, but can be used with STAGE deposition
MOSCAT	mosaic land use categories	1	XYM	MOSAICCRO or mcip.nc	no, but can be used with STAGE deposition
LAI_MOS	leaf area index (by mosaic categories)	m² m^-2	XYMT	MOSAICCRO or mcip.nc	no, but can be used with STAGE deposition
RAI_MOS	inverse of aerodynamic resistance (by mosaic categories)	m s^-1	XYMT	MOSAICCRO or mcip.nc	no, but can be used with STAGE deposition
RSI_MOS	inverse of stomatal resistance (by mosaic categories)	m s^-1	XYMT	MOSAICCRO or mcip.nc	no, but can be used with STAGE deposition
TSK_MOS	skin temperature (by mosaic categories)	K	XYMT	MOSCRO or mcip.nc	no, but can be used with STAGE deposition
ZNT_MOS	roughness length (by mosaic categories)	m	XYMT	MOSCRO or mcip.nc	no, but can be used with STAGE deposition

Variable Name	Description	Units	Required
SLOPE	linear equation parameter for estimating lightning flash count from hourly convective precipitation	unitless	yes
INTERCEPT	linear equation parameter for lightning flash count from hourly convective precipitation	km^-2*	yes
SLOPE_lg	logarithmic equation parameter for estimating lightning flash count from hourly convective precipitation	unitless	yes
INTERCEPT_lg	logarithmic equation parameter for estimating lightning flash count from hourly convective precipitation	km^-2*	yes
ICCG_SUM	Ratio of intercloud to cloud-to-ground flashes during the summer season	unitless	yes
ICCG_WIN	Ratio of intercloud to cloud-to-ground flashes during the winter season	unitless	yes
OCNMASK	Land/water mask to remove spurious flashes over the ocean	unitless	yes

Variable Name	Description	Units
Species Name	Deposited species name from the GR, NR, or TR namelists	unitless
rel_rx	Relative reactivity for resistance estimates for cuticular and soil surfaces	unitless
f0	Wesely (1989) mesophyll resistance parameter	unitless
Molar Vol	The LeBas molar volume of the trace gas	L mol^-1
Mass accommodation coef	The probability that a trace gas molecule is incorporated into a wet surface	unitless

Variable Name	Description	Units
Land Use Name	Name of the sub-grid land use	unitless
Land Use Tag	Name of the land use tag for aggrigating data₁	unitless
RSMIN	Minimum stomatal resistance of the land use₂	s m^-1
Z0	Momentum roughness lenght of the land use	m
Max VEG	Maximum vegetation coverage of the land use taken from the MODIS MCD12Q1 documentation	%
Min VEG	Minimum vegetation coverage of the land use taken from the MODIS MCD12Q1 documentation	%
Max VEG	Maximum single sided leaf area index of the vegetated fraction of the land use	ratio
Min VEG	Minimum single sided leaf area index of the vegetated fraction of the land use	ratio
Ground NH3 Gam	NH3 emissions potential of the non-vegetated surface, e.g. leaf litter, soil, etc.₃	mol NH3 (mol H)^-1
Veg NH3 Gam	NH3 emissions potential of the leaf mesophyll₃	mol NH3 (mol H)^-1
Soil Hg	Soil Hg content of the land use₄	micro mol Hg (g soil)^-1
Leaf Width	Aerodynamic leaf width	m
Alpha	Zhang et al. 2001 land use parameter for aerosol dry deposition	unitless
BAI	Building area index	ratio
Ahair	Leaf hair width	m
Fhair	Ratio of leaf covered in hair	ratio
Aleaf	Pleim et al. 2022 aerodynamic leaf width	m
LU Index	STAGE land use index for mapping	unitless

Variable Name	Description
Met_LU_Name	Name of the meteorological land use variable in LUFRAC_CRO (for documentation only)
Met_Index	Layer of the meteorological land use variable in LUFRAC_CRO
STAGE_LU_name	Name of the STAGE land use variable in the Land Use Name column of the STAGE_LU section of STAGECTRL_NML
STAGE_Index	Layer of the STAGE land use variable in the LU Index column of the STAGE_LU section of STAGECTRL_NML
Factor	Land use factor for the mapping. This must sum up to 1 for each unique element of the Met_Index
Description	Description of the meteorological model's land use (for documentation only)