HEMCO extensions¶

Overview¶

Emission inventories sometimes include dynamic source types and nonlinear scale factors that have functional dependencies on local environmental variables such as wind speed or temperature, which are best calculated online during execution of the model. HEMCO includes a suite of additional modules (extensions) that perform online emission calculations for a variety of sources (see list below). Extensions are enabled in section Extension Switches of the HEMCO configuration file.

List of extensions¶

The full list of available extensions is given below. Extensions can be selected individually in the Extension Switches section of the The HEMCO configuration file, as can the species to be considered.

DustAlk¶

Species: DSTAL1, DSTAL2, DSTAL3, DSTAL4
Reference: Fairlie et al (check)

DustDead¶

Emissions of mineral dust from the DEAD dust mobilization model.

Species: DST1, DST2, DST3, DST4
Reference: Zender et al. [2003]

DustGinoux¶

Emissions of mineral dust from the P. Ginoux dust mobilization model.

Species: DST1, DST2, DST3, DST4
Reference: Ginoux et al. [2001]

Species: DST1, DST2, DST3, DST4

Reference: Ginoux et al. [2001]

GC_Rn-Pb-Be¶

Emissions of radionuclide species as used in the GEOS-Chem model.

Species: Rn222, Be7, Be7Strat, Be10, Be10Strat

ZHANG_Rn222¶

If ZHANG_Rn222 is on, then Rn222 emissions will be computed according to Zhang et al. [2021].

If ZHANG_Rn222 is off, then Rn222 emissions will be computed according to Jacob et al. [1997].

GFED¶

Biomass burning emissions from the GFED model.

Version: GFED3 and GFED4 are available.
Species: NO, CO, ALK4, ACET, MEK, ALD2, PRPE, C2H2, C2H4, C3H8, CH2O C2H6, SO2, NH3, BCPO, BCPI, OCPO, OCPI, POG1, POG2, MTPA, BENZ, TOLU, XYLE NAP, EOH, MOH, SOAP, and others
GFED_daily option: Applies a daily scale factor to emissions computed by GFED.
GFED_3hourly option: Applies a consistent diurnal profile for a given month (in 3-hr increments) to emissions computed by GFED. This is the default setting.
Reference: van der Werf et al. [2010]

Inorg_Iodine¶

Species: HOI, I2
Reference: TBD

LightNOx¶

Emissions of NOx from lightning.

Species: NO
Species: [Murray et al., 2012]

MEGAN¶

Biogenic VOC emissions.

Version: 2.1
Species: ISOP, ACET, PRPE, C2H4, ALD2, CO, OCPI, MONX, MTPA, MTPO, LIMO, SESQ
Reference: Guenther et al. [2012]

PARANOx¶

Plume model for ship emissions.

Species: NO, NO2, O3, HNO3
Reference: Vinken et al. [2011]

SeaFlux¶

Air-sea exchange.

Species: DMS, ACET, ALD2, MENO3, ETNO3, MOH
References: Johnson [2010], Nightingale et al. [2000]

SeaSalt¶

Sea salt aerosol emission.

Species: SALA, SALC, SALACL, SALCCL, SALAAL, SALCAL, BrSALA, BrSALC, MOPO, MOPI
References: Jaeglé et al. [2011], Gong [2003]

SoilNOx¶

Emissons of NOx from soils and fertilizers.

Species: NO
Reference: Hudman et al. [2012]

Volcano¶

Emissions of volcanic SO2 from AEROCOM.

Species: SO2
Reference:

TOMAS_Jeagle¶

Size-resolved sea salt emissions for TOMAS aerosol microphysics simulations.

Species: SS1, SS2, SS3, SS4, SS5, SS6, SS7, SS8, SS9, SS10, SS11, SS12, SS13, SS14, SS15, SS16, SS17, SS18, SS19, SS20, SS21, SS22, SS23, SS24, SS25, SS26, SS27, SS28, SS29, SS30, SS31, SS32, SS33, SS34, SS35, SS36, SS37, SS38, SS39, SS40
Reference: Jaeglé et al. [2011]

TOMAS_DustDead¶

Size-resolved dust emissions for TOMAS aerosol microphysics simulations.

Species: DUST1, DUST2, DUST3, DUST4, DUST5, DUST6, DUST7, DUST8, DUST9, DUST10, DUST11, DUST12, DUST13, DUST14, DUST15, DUST16, DUST17, DUST18, DUST19, DUST20, DUST21, DUST22, DUST23, DUST24, DUST25, DUST26, DUST27, DUST28, DUST29, DUST30, DUST31, DUST32, DUST33, DUST34, DUST35, DUST36, DUST37, DUST38, DUST39, DUST40
Reference: Zender et al. [2003]

Gridded data¶

HEMCO can host all environmentally independent data sets (e.g. source functions) used by the extensions. The environmental variables are either provided by the atmospheric model or directly read from file through the HEMCO configuration file. Entries in the HEMCO configuration file file are given priority over fields passed down from the atmospheric model, i.e. if the HEMCO configuration file contains an entry for a given environmental variable, this field will be used instead of the field provided by the atmospheric model. The field name provided in the HEMCO configuration file must exactly match the name of the HEMCO environmental parameter.

To use the NCEP reanalysis monthly surface wind fields (http:, , www.esrl.noaa.gov, psd, data, gridded, data.ncep.reanalysis.derived.surface.html) in all HEMCO extensions, add the following two lines to the Base Emissions section of the HEMCO configuration file:

* U10M /path/to/uwnd.mon.mean.nc uwnd 1948-2014/1-12/1/0 C xy m/s * - 1 1
* V10M /path/to/vwnd.mon.mean.nc vwnd 1948-2014/1-12/1/0 C xy m/s * - 1 1

This will use these wind fields for all emission calculations, even if the atmospheric model uses a different set of wind fields.

It is legal to assign scale factors (and masks) to the environmental variables read through the HEMCO configuration file. This is particularly attractive for sensitivity studies. For example, a scale factor of 1.1 can be assigned to the NCEP surface wind fields to study the sensitivity of emissions on a 10% increase in wind speed:

In the Base Emissions section:

* U10M /path/to/uwnd.mon.mean.nc uwnd 1948-2014/1-12/1/0 C xy m/s * 123 1 1
* V10M /path/to/vwnd.mon.mean.nc vwnd 1948-2014/1-12/1/0 C xy m/s * 123 1 1

In the Scale Factors section:

123 SURFWIND_SCALE 1.1 - - - xy 1 1

As for any other entry in the HEMCO configuration file, spatially uniform values can be set directly in the HEMCO configuration file. For example, a spatially uniform, but monthly varying surface albedo can be specified by adding the following entry to the Base Emissions section of the HEMCO configuration file:

* ALBD 0.7/0.65/0.6/0.5/0.5/0.4/0.45/0.5/0.55/0.6/0.6/0.7 - 2000/1-12/1/0 C xy 1 * - 1 1

Environmental fields used by HEMCO¶

The following fields can be passed from the atmospheric model to HEMCO for use by the various extensions:

AIR¶

Air mass.

Dim: xyz
Units: kg
Used by: GC_Rn-Pb-Be, PARANOx

AIRVOL¶

Air volume (i.e. volume of grid box).

Dim: xyz
Units: kg
Used by: PARANOx

ALBD¶

Surface albedo.

Dim: xy
Units: unitless
Used by: SoilNOx, SeaFlux

CLDFRC¶

Cloud fraction

Dim: xy
Units: unitless
Used by: MEGAN

CNV_MFC¶

Convective mass flux.

Dim: xyz
Units: kg/m2/s
Used by: LightNOx

FRAC_OF_PBL¶

Fraction of grid box within the planetary boundary layer (PBL).

Dim: xyz
Units: unitless
Used by: PARANOx, SeaFlux

FRCLND¶

Land fraction

Dim: xy
Units: unitless
Used by: GC_Rn-Pb-Be, SeaFlux

GWETROOT¶

Root soil moisture.

Dim: xy
Units: unitless
Used by: MEGAN

GWETTOP¶

Top soil moisture.

Dim: xy
Units: unitless
Used by: MEGAN

HNO3¶

HNO3 mass.

Dim: xyz
Units: kg
Used by: PARANOx

JO1D¶

Photolysis J-value for O1D.

Dim: xy
Units: 1/s
Used by: PARANOx

JNO2¶

Photolysis J-value for NO2.

Dim: xy
Units: 1/s
Used by: PARANOx

LAI¶

Leaf area index.

Dim: xy
Units: cm2 leaf/cm2 grid box
Used by: MEGAN

NO¶

NO mass.

Dim: xyz
Units: kg
Used by: PARANOx

NO2¶

NO2 mass.

Dim: xyz
Units: kg
Used by: PARANOx

O3¶

O3 mass.

Dim: xyz
Units: kg
Used by: PARANOx

PARDF¶

Diffuse photosynthetic active radiation

Dim: xy
Units: W/m2
Used by: MEGAN

PARDR¶

Direct photosynthetic active radiation

Dim: xy
Units: W/m2
Used by: MEGAN

RADSWG¶

Short-wave incident surface radiation

Dim: xy
Units: W/m2
Used by: SoilNOx

SNOWHGT¶

Snow height (mm of H2O equivalent).

Dim: xy
Units: kg H2O/m2
Used by: DustDead, TOMAS_DustDead

SPHU¶

Specific humidity

Dim: xyz
Units: kg H2O/kg air
Used by: DustDead, PARANOx, TOMAS_DustDead

SZAFACT¶

Cosine of the solar zenith angle.

Dim: xy
Units: unitless
Used by: MEGAN

TK¶

Temperature.

Dim: xyz
Units: K
Used by: DustDead, LightNOx, TOMAS_DustDead

TROPP¶

Tropopause pressure.

Dim: xy
Units: Pa
Used by: GC_Rn-Pb-Be, LightNOx

TSKIN¶

Surface skin temperature

Dim: xy
Units: K
Used by: SeaFlux, SeaSalt

U10M¶

E/W wind speed @ 10 meters above surface.

Dim: xy
Units: m/s
Used by: DustAlk, DustDead, DustGinoux, PARANOx, SeaFlux, SeaSalt, SoilNOx, TOMAS_DustDead, TOMAS_Jeagle

USTAR¶

Friction velocity.

Dim: xy
Units: m/s
Used by: DustDead, TOMAS_DustDead

V10M¶

N/S wind speed @ 10 meters above surface.

Dim: xy
Units: m/s
Used by: DustAlk, DustDead, DustGinoux, PARANOx, SeaFlux, SeaSalt, SoilNOx, TOMAS_DustDead, TOMAS_Jeagle

WLI¶

Water-land-ice flags (0 = water, 1 = land, 2 = ice).

Dim: xy
Units: unitless
Used by: Almost every extension

Z0¶

Roughness height.

Dim: xy
Units: m
Used by: DustDead, TOMAS_DustDead

Restart variables¶

Some extensions rely on restart variables, i.e. variables that are highly dependent on historical information such as previous-day leaf area index or soil NOx pulsing factor. During a simulation run, the extensions continuously archive all necessary information and update estart variables accordingly. The updated variables become automatically written into the HEMCO restart file (HEMCO_restart.YYYYMMDDhhmmss.nc) at the end of a simulation. The fields from this file can then be read through the HEMCO configuration file to resume the simulation at this date (“warm” restart). For example, the soil NOx restart variables can be made available to the soil NOx extension by adding the following lines to the Base Emissions section of the HEMCO configuration file.

PFACTOR         ./HEMCO_restart.$YYYY$MM$DD$HH00.nc  PFACTOR       $YYYY/$MM/$DD/$HH E xy  unitless NO - 1 1
DRYPERIOD       ./HEMCO_restart.$YYYY$MM$DD$HH00.nc  DRYPERIOD     $YYYY/$MM/$DD/$HH E xy  unitless NO - 1 1
GWET_PREV       ./HEMCO_restart.$YYYY$MM$DD$HH00.nc  GWET_PREV     $YYYY/$MM/$DD/$HH E xy  unitless NO - 1 1
DEP_RESERVOIR   ./HEMCO_restart.$YYYY$MM$DD$HH00.nc  DEP_RESERVOIR $YYYY/$MM/$DD/$HH E xy  unitless NO - 1 1

Many restart variables are very time and date-dependent. It is therefore recommended to set the time slice selection flag to E to ensure that only data is read that exactly matches the simulation start date (also see Base emissions. HEMCO will perform a “cold start” if no restart field can be found for a given simulation start date, e.g. default values will be used for those restart variables.

Built-in tools for scaling/masking¶

HEMCO has built-in tools to facilitate the application of both uniform and spatiotemporal scale factors to emissions calculated by the extensions. At this point, not all extensions take advantage of these tools yet. A list of extensions that support the built-in scaling tools are given below.

For extensions that support the built-in scaling tools, you can specify the uniform and/or spatiotemporal scale factors to be applied to the extension species of interest in section Extension switches the HEMCO configuration file.

For example, to uniformly scale GFED CO by a factor of 1.05 and GFED NO emissions by a factor of 1.2, add the following two lines to the HEMCO configuration file (highlighted in GREEN):

111    GFED              : on    CO/NO/ACET/ALK4
   --> GFED3             :       false
   --> GFED4             :       true
   --> GFED_daily        :       false
   --> GFED_3hourly      :       false
   --> Scaling_CO        :       1.05
   --> Scaling_NO        :       1.20

Similarly, a spatiotemporal field to be applied to the species of interest can be defined via setting ScaleField, e.g.

111     GFED              : on    CO/NO/ACET/ALK4
    --> GFED3             :       false
    --> GFED4             :       true
    --> GFED_daily        :       false
    --> GFED_3hourly      :       false
    --> Scaling_CO        :       1.05
    --> Scaling_NO        :       1.20
    --> ScaleField_NO     :       GFED_SCALEFIELD_NO

The corresponding scale field needs be defined in section Base emissions . A simple example would be a monthly varying scale factor for GFED NO emissions:

111 GFED_SCALEFIELD_NO   0.9/1.1/1.3/1.4/1.6/1.7/1.7/1.8/1.5/1.3/0.9/0.8 - 2000/1-12/1/0 C xy unitless * - 1 1

It is legal to apply scale factors and/or masks to the extension scale fields (in the same way as the ‘regular’ base emission fields). A more sophisticated example on how to scale soil NOx emissions is given in HEMCO examples.

Extensions supporting built-in scaling/masking¶

The following extensions currently support the built-in scaling/masking tools: SoilNOx, GFED, FINN.

Adding new HEMCO extensions¶

All HEMCO extensions are called through the extension interface routines in HEMCO/Extensions/hcox_driver_mod.F90: HCOX_INIT, HCOX_RUN, HCOX_FINAL. For every new extension, a corresponding subroutine call needs to be added to those three routines. You will quickly see that these calls only take a few arguments, most importantly the HEMCO state object HcoState and the extensions state object ExtState.

ExtState is defined in HEMCO/src/Extensions/hcox_state_mod.F90. It contains logical switches for each extension as well as pointers to any external data (such as met fields). For a new extension, you’ll have to add a new logical switch to the Ext_State object. If you need external data that is not yet included in ExtState, you will also have to add those (including the pointer associations in subroutine SET_EXTOPT_FIELDS in GeosCore/hco_interface_gc_mod.F90.

The initialization call (HCOX_XXX_INIT) should be used to initialize all extension variables and to read all settings from the HEMCO configuration file. There are a number of helper routines in HEMCO/src/Extensions/hco_extlist_mod.F90 to do this:

GetExtNr( ExtName ) returns the extension number for the given extension name. Will return –1 if extension is turned off!
GetExtOpt( ExtNr, Attribute, Value, RC ) can be used to read any additional extension options (logical switches, path and names of csv-tables, etc.). Note that value can be of various types (logical, character, double,…).
GetExtHcoID( HcoState, ExtNr, HcoIDs, SpcNames, nSpc, RC ) matches the extension species names (as defined in the configuration file) to the species defined in HEMCO state (i.e. to all available HEMCO species). A value of –1 is returned if the given species is not defined in HEMCO.

All ExtState variables used by this extension should be updated. This includes the logical switch and all external data needed by the extension. For example, if the extension needs temperature data, this pointer should be activated by setting ExtState%TK%DoUse = .TRUE.

The run call (HCOX_XXX_RUN) calculates the 2D fluxes and passes them to HcoState via subroutine HCO_EmisAdd( HcoState, Flux, HcoID, RC). External data is assessed through ExtState (e.g. ExtState%TX%Arr%Val(I,J,L)), and any data automatically read from netCDF files (through the HEMCO interface) can be obtained through EmisList_GetDataArr( am_I_Root, FieldName, Pointer, RC ) The body of the run routine is typically just the code of the original module.

It’s probably easiest to start from an existing extension (or the Custom extension template) and to add any modifications as is needed.