wrftoCF — WRF-Chem Output to CF-Compliant NetCDF

NCL scripts that convert native WRF-Chem wrfout NetCDF files into CF-compliant and ACDD-compatible NetCDF files. Extends the original wrfout_to_cf script by Mark Seefeldt (University of Colorado) to include WRF-Chem chemical trace gas and aerosol variables.

Background

Native WRF and WRF-Chem wrfout files are difficult to use directly in many analysis and visualization tools because:

Variable names follow WRF-internal conventions rather than community standards.
Key variables such as wind components (U, V) are on the staggered WRF horizontal grid.
The vertical coordinate uses native WRF eta levels, not pressure levels or height.
Files contain many internal model-state variables not needed for most research applications.
NetCDF attributes are often incomplete or non-standard.

The CF (Climate and Forecast) metadata convention addresses these issues by defining standard variable attributes (standard_name, units, long_name, _FillValue, valid_range, etc.) and a time encoding convention, enabling interoperability with tools such as IDV, Panoply, VAPOR, and the MET verification suite.

What This Repository Adds

This repository is an extension of the original wrfout_to_cf script (v2.0.3, Mark Seefeldt, University of Colorado). The modifications made here are:

WRF-Chem chemical variables — trace gases and aerosol species produced by WRF-Chem are included as selectable output variables alongside the standard meteorological fields.
ACDD compatibility — global attributes following the Attribute Convention for Data Discovery (ACDD) are added to the output file, improving discoverability in data portals and catalogues.
Two operational variants — one script for routine operational post-processing (operacional) and one developed for the PAPILA project (papila).

Requirements

Component	Version	Notes
NCL	6.6.2 (recommended)	NCAR Command Language — download
WRF-NCL scripts	Bundled with NCL	Used internally for unstaggering grids, pressure interpolation, and WRF diagnostics

No compilation is required — NCL is an interpreted language. No additional libraries beyond a standard NCL installation are needed.

NCL v6.6.0+ users: A totype warning may appear for pressure-level output variables due to the deprecation of wrf_user_intrp3d. This is a cosmetic warning only and does not affect output correctness. See NCL End-of-Life Notice.

Repository Structure

wrftoCF/
├── wrfout_to_cf_operacional.ncl   # Operational post-processing variant
├── wrfout_to_cf_papila.ncl        # PAPILA project variant
└── README.md                      # This file

Scripts

`wrfout_to_cf_operacional.ncl`

General-purpose script for converting WRF-Chem output to CF-compliant NetCDF. Intended for routine operational post-processing of simulation output including both meteorological and chemical fields.

`wrfout_to_cf_papila.ncl`

Variant developed for the PAPILA (Prediction and Attribution of Present and Future Fluxes of Climate-Relevant Gases) project. Includes additional chemical species and ACDD global metadata tailored to that project's data management requirements.

Usage

Single file

ncl 'file_in="wrfout_d01_2020-01-01_00:00:00"' \
    'file_out="wrfpost_d01_2020-01-01_cf.nc"' \
    wrfout_to_cf_operacional.ncl

Alternatively, set file_in and file_out directly inside the script (near the top of the main program section) and call without arguments:

ncl wrfout_to_cf_operacional.ncl

Batch processing — multiple files

Option 1 — Process all wrfout_d* files in the current directory:

#!/bin/csh -f
foreach file_pre (`ls wrfout_d* | sed 's/\:00\:00//g'`)
  set file_in  = {$file_pre}:00:00
  set file_out = {$file_pre}-cf.nc
  ncl 'file_in="'{$file_in}'"' 'file_out="'{$file_out}'"' wrfout_to_cf_operacional.ncl
end

Option 2 — Loop over a year/month/day/domain matrix:

#!/bin/csh -f
set yyyy = ('2020' '2021')
set mm   = ('01' '02' '03' '04' '05' '06' '07' '08' '09' '10' '11' '12')
set hr   = ('00' '12')
set dom  = ('1' '2')

foreach y ($yyyy)
  foreach m ($mm)
    foreach d (01 02 03)    # adjust day range as needed
      foreach h ($hr)
        foreach n ($dom)
          set file_in  = wrfout_d0${n}_${y}-${m}-${d}_${h}:00:00
          set file_out = ${y}${m}${d}${h}-d0${n}-cf.nc
          ncl 'file_in="'{$file_in}'"' 'file_out="'{$file_out}'"' \
              wrfout_to_cf_operacional.ncl
        end
      end
    end
  end
end

Key Configuration Parameters

These parameters are set near the top of the NCL script. All subsetting index parameters accept (/0,9999/) to select the full available range.

Parameter	Example value	Description
`file_in`	`"wrfout_d01_2020-01-01_00:00:00"`	Path to the input `wrfout` NetCDF file
`file_out`	`"wrfpost_cf.nc"`	Path for the CF-compliant output file
`TimeUnits`	`"hours since 2001-01-01 00:00:00"`	Reference epoch for the CF time axis
`pressure`	`(/1000.,850.,700.,500.,300./)`	Target pressure levels for 3D pressure-level output (hPa)
`limTime`	`(/0,9999/)`	Time index range to subset from the input file
`limS_N`	`(/45,256/)`	South–North grid index range for spatial subsetting
`limW_E`	`(/41,151/)`	West–East grid index range for spatial subsetting
`limPres`	`(/0,4/)`	Pressure level index range for pressure-level output
`limEta`	`(/0,19/)`	Eta level index range for eta-level output
`limSoil`	`(/0,3/)`	Soil level index range
`outPtop`	`True` / `False`	Include the model top pressure variable (`P_TOP`)
`outDateTime`	`True` / `False`	Include a `yyyymmddhh` time field (not useful for sub-hourly output)
`outUTCDate`	`True` / `False`	Include `yr`, `mo`, `dy`, `hr`, `mn` individual time component fields

Selecting output variables

Variables are organised into named groups. To include a variable, both the group flag and the individual variable flag must be True. Setting a group flag to False excludes all variables in that group regardless of individual flags:

out2dMet        = True       ; enable the 2D surface meteorology group
out2dMet@T_2m   = True       ; include 2 m temperature
out2dMet@rh_2m  = True       ; include 2 m relative humidity
out2dMet@ws_10m = False      ; exclude 10 m wind speed

outEta          = False      ; disable entire 3D eta-level group (all variables excluded)

Output Variable Groups

2D Near-Surface Meteorology (`out2dMet`)

CF name	Long name	Standard name	Units
`SST`	Sea-Surface Temperature	`sea_surface_temperature`	K
`T_sfc`	Temperature at the Surface	`surface_temperature`	K
`p_sfc`	Pressure at the Surface	`surface_air_pressure`	hPa
`slp`	Sea-Level Pressure (WRF-NCL)	`air_pressure_at_sea_level`	hPa
`slp_b`	Sea-Level Pressure (lowest level)	`air_pressure_at_sea_level`	hPa
`T_2m`	Temperature at 2 m	`air_temperature`	°C
`Td_2m`	Dewpoint Temperature at 2 m	`dew_point_temperature`	°C
`rh_2m`	Relative Humidity at 2 m	`relative_humidity`	%
`u_10m_tr`	U-Component of Wind at 10 m (Earth)	`eastward_wind`	m s⁻¹
`v_10m_tr`	V-Component of Wind at 10 m (Earth)	`northward_wind`	m s⁻¹
`ws_10m`	Wind Speed at 10 m	`wind_speed`	m s⁻¹
`wd_10m`	Wind Direction at 10 m	`wind_from_direction`	degrees
`precip_g`	Accumulated Grid-Scale Precipitation	`large_scale_precipitation_amount`	mm
`precip_c`	Accumulated Cumulus Precipitation	`convective_precipitation_amount`	mm
`pblh`	PBL Height	`atmosphere_boundary_layer_thickness`	m
`rho`	Air Density at Lowest Model Level	`air_density`	kg m⁻³

3D Meteorology on Eta Levels (`outEta`)

CF name	Long name	Units
`p_e`	Pressure	hPa
`Z_e`	Geopotential Height	m
`T_e`	Temperature	K
`theta_e`	Potential Temperature	K
`r_v_e`	Water Vapor Mixing Ratio	kg kg⁻¹
`rh_e`	Relative Humidity	%
`u_tr_e`	U-Component of Wind (Earth)	m s⁻¹
`v_tr_e`	V-Component of Wind (Earth)	m s⁻¹
`ws_e`	Wind Speed	m s⁻¹
`w_e`	Vertical Wind Component	m s⁻¹
`r_cloud`	Cloud Water Mixing Ratio	kg kg⁻¹
`r_rain`	Rain Mixing Ratio	kg kg⁻¹
`r_ice`	Ice Mixing Ratio	kg kg⁻¹
`r_snow`	Snow Mixing Ratio	kg kg⁻¹
`r_graup`	Graupel Mixing Ratio	kg kg⁻¹
`pvo_e`	Potential Vorticity	PVU
`avo_e`	Absolute Vorticity	10⁻⁵ s⁻¹

3D Meteorology on Pressure Levels (`outPressure`)

Same variables as outEta but interpolated to the user-defined pressure levels set by the pressure parameter. Variable names use the suffix _p (e.g., T_p, ws_p, r_v_p).

Surface Energy Budget and Radiation (`out2dRadFlx`)

CF name	Long name	Units
`SW_d`	Downwelling Shortwave at Surface (instantaneous)	W m⁻²
`LW_d`	Downwelling Longwave at Surface (instantaneous)	W m⁻²
`SW_u`	Upwelling Shortwave at Surface (instantaneous)	W m⁻²
`LW_u`	Upwelling Longwave at Surface (instantaneous)	W m⁻²
`LW_u_toa`	Upwelling Longwave at TOA	W m⁻²
`SH`	Sensible Heat Flux at Surface (instantaneous)	W m⁻²
`LH`	Latent Heat Flux at Surface (instantaneous)	W m⁻²
`MH`	Moisture Heat Flux at Surface (instantaneous)	kg m⁻² s⁻¹
`LWP`	Liquid Water Path	kg m⁻²
`IWP`	Ice Water Path	kg m⁻²
`albedo`	Surface Albedo	—
`emiss_sfc`	Surface Emissivity	—
`u_star`	Friction Velocity (u*)	m s⁻¹

Accumulated counterparts (e.g., SW_d_acc, LH_acc) are also available in units of J m⁻².

Surface and Soil Variables (`out2dLandSoil` and `outSoil`)

Includes land mask, land use category, snow depth and water equivalent, snow density, sea ice fraction, soil temperature, soil moisture, soil liquid water, surface runoff, and sub-surface runoff. See the upstream variable reference for the full listing.

WRF-Chem Chemical Variables

This repository extends the original script to include chemical output from WRF-Chem. The exact set of available variables depends on the chemical mechanism configured for the WRF-Chem simulation (e.g., RADM2, RACM2, CBM-Z, MOZART, SAPRC). Typical additions include:

Category	Example variables
Trace gases	O₃, NO, NO₂, CO, SO₂, NH₃, HNO₃, individual VOC species
Particulate matter	PM2.5, PM10
Aerosol species	Sulfate, nitrate, ammonium, organic carbon (OC), elemental carbon (EC)
Photolysis rates	`J_NO2`, `J_O3D`
Optical properties	Aerosol optical depth (AOD)

Each chemical variable is written with the same CF standard attributes (standard_name, long_name, units, _FillValue) as the meteorological variables.

CF and ACDD Compliance

All output variables carry the following standard CF attributes where applicable:

Attribute	Description
`standard_name`	CF standard name (e.g., `air_temperature`)
`long_name`	Human-readable description
`units`	UDUNITS-compatible unit string
`_FillValue`	Fill/missing value
`missing_value`	Same as `_FillValue`
`valid_min` / `valid_max`	Physical plausibility range
`coordinates`	References the latitude/longitude coordinate variables

The CF time axis is encoded as:

time:units = "hours since YYYY-MM-DD HH:MM:SS" ;

where the reference epoch is controlled by the TimeUnits parameter.

In addition, these scripts write ACDD global attributes to the output file (e.g., title, summary, institution, source, history, geospatial_lat_min/max, time_coverage_start/end), improving discoverability in THREDDS catalogues and ERDDAP servers.

Validating the Output

CF and ACDD compliance of the output files can be verified with the IOOS Compliance Checker:

Online tool: https://compliance.ioos.us/index.html
Command-line installation:

pip install compliance-checker
compliance-checker --test cf:1.7 --test acdd output_cf.nc

NCL End-of-Life Notice

NCAR stopped active development of NCL at version 6.6.2, pivoting to Python-based tools. NCL 6.6.2 remains available and functional for the foreseeable future, and these scripts will continue to work with it. The upstream wrfout_to_cf v2.0.3 is expected to be the final NCL release of that project.

For new projects, Python alternatives worth considering:

Tool	Purpose
`wrf-python`	WRF diagnostic functions ported to Python
`xarray` + `cf_xarray`	CF-aware N-dimensional array manipulation
`geocat-comp`	NCAR's Python successor to NCL diagnostics
`netCDF4`	Low-level NetCDF I/O in Python

Attribution

This work is an extension of:

Seefeldt, M. W. wrfout_to_cf.ncl — NCL script to create CF-compliant NetCDF files from native WRF output. University of Colorado.
https://sundowner.colorado.edu/wrfout_to_cf/overview.html

Extended by José Agustín García Reynoso to include WRF-Chem chemical variables and ACDD global metadata attributes.

README last updated: March 2026

Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
.gitignore		.gitignore
README.md		README.md
wrfout_to_cf_operacional.ncl		wrfout_to_cf_operacional.ncl
wrfout_to_cf_papila.ncl		wrfout_to_cf_papila.ncl

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wrftoCF — WRF-Chem Output to CF-Compliant NetCDF

Table of Contents

Background

What This Repository Adds

Requirements

Repository Structure

Scripts

`wrfout_to_cf_operacional.ncl`

`wrfout_to_cf_papila.ncl`

Usage

Single file

Batch processing — multiple files

Key Configuration Parameters

Selecting output variables

Output Variable Groups

2D Near-Surface Meteorology (`out2dMet`)

3D Meteorology on Eta Levels (`outEta`)

3D Meteorology on Pressure Levels (`outPressure`)

Surface Energy Budget and Radiation (`out2dRadFlx`)

Surface and Soil Variables (`out2dLandSoil` and `outSoil`)

WRF-Chem Chemical Variables

CF and ACDD Compliance

Validating the Output

NCL End-of-Life Notice

Attribution

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Repository files navigation

wrftoCF — WRF-Chem Output to CF-Compliant NetCDF

Table of Contents

Background

What This Repository Adds

Requirements

Repository Structure

Scripts

wrfout_to_cf_operacional.ncl

wrfout_to_cf_papila.ncl

Usage

Single file

Batch processing — multiple files

Key Configuration Parameters

Selecting output variables

Output Variable Groups

2D Near-Surface Meteorology (out2dMet)

3D Meteorology on Eta Levels (outEta)

3D Meteorology on Pressure Levels (outPressure)

Surface Energy Budget and Radiation (out2dRadFlx)

Surface and Soil Variables (out2dLandSoil and outSoil)

WRF-Chem Chemical Variables

CF and ACDD Compliance

Validating the Output

NCL End-of-Life Notice

Attribution

About

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`wrfout_to_cf_operacional.ncl`

`wrfout_to_cf_papila.ncl`

2D Near-Surface Meteorology (`out2dMet`)

3D Meteorology on Eta Levels (`outEta`)

3D Meteorology on Pressure Levels (`outPressure`)

Surface Energy Budget and Radiation (`out2dRadFlx`)

Surface and Soil Variables (`out2dLandSoil` and `outSoil`)

Packages