MERRA-2 implementation details

Overview

MERRA-2 is the newest reanalysis meteorological data product from NASA/GMAO. It is created with the NASA/GMAO GEOS Data Assimilation System (aka GEOS-DAS), version 5.12.4. Overall, the structure of MERRA-2 is very similar to the GMAO "forward processing" data product, which we refer to as GEOS-FP. Therefore, within GEOS-Chem we can (for the most part) treat MERRA-2 in the same way as we do for the GEOS_FP.

For more information about MERRA-2, please see these resources:

• MERRA-2 page on the GEOS-Chem wiki
• List of MERRA-2 met fields used for GEOS-Chem
• Version history of GMAO reanalysis products

Comparing MERRA-2 to other GMAO met data products

The table below compares many features of MERRA-2 with other GMAO met data products:

Feature	MERRA-2	GEOS-FP	MERRA	GEOS-5
Native vertical grid	0.5° lat x 0.625° lon	0.25° lat x 0.3125° lon	0.5° lat x 0.667° lon (surface fields) 1° lat x 1.25° lon (most 3D fields) 1.25° x 1.25° lon (moist quantities)	0.5° lat x 0.667° lon
Native horizontal grid	72 hybrid levels	Same as MERRA-2	Same as MERRA-2	Same as MERRA-2
Time-invariant fields	FRLAKE FRLAND FRLANDIC(E) FROCEAN PHIS	Same as MERRA-2	Same as MERRA-2	Same as MERRA-2
Time archiving: surface fields	A1 (1-hr time averaged)	Same as MERRA-2	Same as MERRA-2	A3 (6-hr time average)
Time archiving: 3D fields	A3 (3-hr time averaged) I3 (3-hr instantaneous)	Same as MERRA-2 Same as MERRA-2	A3 (3-hr time average) I6 (6-hour instantaneous)	A6 (6-hr time average) and I6 (6-hr instantaneous)
Timestamps	See this wiki page	See this wiki page	See this wiki page	See this wiki page
Precipitation fields	DQRCU, DQRLSAN, PFICU, PFILSAN, PFLCU, PFLLSAN, REEVAPCN, REEVAPLSAN	Same as MERRA-2	Same as MERRA-2	DQIDTMST DQLDTMST DQVDTMST MOISTQ = DQIDTMST + DQLDTMST + DQVDTMST
Temperature	T [K] I3 (3-hr instantaneous)	Same as MERRA-2 Same as MERRA-2	Same as MERRA-2 A3 (6-hr time average)	Same as MERRA-2 A6 (6-hr time average)
Relative humidity	RH [1] A3 (3-hr time average)	Same as MERRA-2 Same as MERRA-2	Same as MERRA-2 I3 (6-hr instantaneous)	Same as MERRA-2 A6 (6-hr time-averaged)
Specific humidity	QV [kg kg-1] I3 (3-hr instantaneous)	Same as MERRA-2 Same as MERRA-2	Same as MERRA-2 A3 (3-hr time average)	Same as MERRA-2 A6 (6-hr time-averaged)
Vertical pressure velocity	OMEGA [Pa s-1] A3 (3-hr time average)	Same as MERRA-2 Same as MERRA-2	Same as MERRA-2 I6 (6-hr instantaneous)	Same as MERRA-2 A6 (6-hr time-averaged)
Ertel potential vorticity	PV [K m2 kg-1 s-1] A1 (1-hr time average)	Same as MERRA-2 Same as MERRA-2	Same as MERRA-2 I6 (6-hr instantaneous)	Same as MERRA-2 A6 (3-hr time-average)
Snow mass	SNOMAS [kg/m2] A1 (3-hr time average) Missing coverage at poles is now corrected, as per MERRA	Same as MERRA-2 Same as MERRA-2 Same as MERRA-2	Same as MERRA-2 Same as MERRA-2 Same as MERRA-2	SNOMAS [m] A3 (3-hr time average)
Sea level pressure	SLP [Pa] A1 (1-hr time average) Converted to hPa when read from disk	SLP [hPa] Same as MERRA-2	SLP [hPa] Same as MERRA-2	SLP [hPa] I6 (3-hr instantaneous)
Surface pressure	PS [Pa] I3 (3-hr instantaneous) Converted to hPa when read from disk	PS [hPa] I3 (3-hr instantaneous)	PS [hPa] I6 (6-hr instantaneous)	PS [hPa] I6 (3-hr instantaneous)
Tropopause pressure	TROPPT [Pa] A1 (1-hr time average) Converted to hPa when read from disk	TROPPT [hPa] Same as MERRA-2	TROPPT [hPa] Same as MERRA-2	TROPP [hPa] A3 (3-hr time average)
GEOS-Chem convection routine	DO_MERRA_CONVECTION (in convection_mod.F)	Same as MERRA-2	Same as MERRA-2	NFCLDMX (in convection_mod.F)
GEOS-Chem wet deposition routine	WETDEP_MERRA (wetscav_mod.F)	Same as MERRA-2	Same as MERRA-2	WETDEP (wetscav_mod.F)
GEOS-Chem transport routine	TPCORE_FVDAS (tpcore_fvdas_mod.F90)	Same as MERRA-2	Same as MERRA-2	Same as MERRA-2
File format read by GEOS-Chem	netCDF-4	netCDF-3	binary	binary

--Bob Y. (talk) 16:41, 17 August 2015 (UTC)

Timeline for integration into GEOS-Chem

Initial modifications

As of August 2015, we have we have modified GEOS-Chem (as described below) so that it can be driven by the new NASA/GMAO MERRA-2 reanalysis data product. These source code updates were validated with the 1-month benchmark simulation v11-01c and approved on 14 Sept 2015.

Currently, several of the GEOS-Chem specialty simulations are already compatible with MERRA-2. These include:

• CO2 simulation
• CH4 simulation
• Hg simulation (but some tuning factors for nested grids are still needed)
• POPs simulation
• Rn-Pb-Be simulation
• Tagged O3 simulation

--Bob Y. (talk) 14:54, 18 August 2015 (UTC)

UPDATE: GEOS-Chem v11-01 and newer versions can now be driven by the MERRA-2 reanalysis field data product.

Modifications for the nested grid simulations

There were several modifications needed to run nested grid simulations with MERRA-2. The source code updates for running MERRA-2 on the 0.5x0.625 nested NA and nested CH grids were included in v11-01e (approved 04 Jan 2016).

The nested CH grid for MERRA-2 is defined as 10S to 55N and 60E to 150E. It therefore includes China, Southeast Asia, Japan, and India. In order to make it transparent to users that this domain has been expanded, the nested CH grid has been renamed to the nested AS grid for MERRA-2. This update was included in v11-01h (approved 11 Oct 2016).

--Melissa Sulprizio (talk) 17:13, 14 December 2015 (UTC)

Modifications for the full-chemistry simulations

The various "full-chemistry simulations" (i.e. those using the benchmark, UCX, SOA, and tropchem chemistry mechanisms) use emissions (e.g. lightning, dust) that have scale factors that must be tuned specifically for each met field product. The GCST has computed the dust and lightning scale factors using MERRA-2 met fields for 2009–2014. These updates were included in v11-01f (approved 16 Apr 2016).

When the entire MERRA-2 coverage period (1980–present) has been processed, the lightning and dust scale factors for MERRA-2 will be adjusted as needed.

--Melissa Sulprizio (talk) 21:08, 5 February 2016 (UTC)

Required coding changes in GEOS-Chem

As noted in the section above, the similarities between MERRA-2 and GEOS-FP (especially of the vertical grids) means that in most cases we can just treat MERRA-2 in the same way as for GEOS-FP. In many areas of the code, the coding changes are straightforward and simply involve an extension of C-preprocessor statements such as:

#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )

to

#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )

In other areas of GEOS-Chem the changes are more involved. Below we provide a description of the areas of GEOS-Chem that were modified for MERRA-2:

Top-level directory

The following modifications for MERRA-2 were made in the root GEOS-Chem directory:

File	Modifications made
Makefile_header.mk	If MET=merra2 or MET=merra-2 (case-insensitive), then activate the MERRA2 C-preprocessor switch i.e. Add -DMERRA2 to the Makefile variable USER_DEFS. If GRID=05x0625 is added, then activate the GRID05x0625 C-preprocessor switch i.e. Add -DGRID05x0625 to the Makefile variable USER_DEFS.

--Bob Y. (talk) 18:28, 12 August 2015 (UTC)

Headers directory

The following modifications for MERRA-2 were made in the Headers/ directory:

File	Modifications made
CMN_SIZE_mod.F	Added size parameters for GEOS-FP grids at 4° x 5°, 2° x 2.5°, and 0.25° x 0.3125° resolution
gigc_input_opt_mod.F90	Add MERRA2_DIR to the OptInput derived type Set Input_Opt%MERRA2_DIR = './' in routine Init_GIGC_Input_Opt
gigc_state_met_mod.F90	Multiple instances: Now use: #if defined( GEOS_FP ) || defined( MERRA ) || defined( MERRA2 )

--Bob Y. (talk) 18:28, 12 August 2015 (UTC)

GeosUtil directory

The following modifications for MERRA-2 were made in the GeosUtil/ directory:

File	Modifications made
bpch2_mod.F	In routine GET_MODELNAME: Add MERRA2_47L and MERRA2 modelnames to the #if block In routine GET_NAME_EXT: Return grid name merra2 for MERRA-2 fields In routine GET_NAME_EXT_2D: Now use #if defined( MERRA ) || defined( MERRA2 ) In routine GET_RES_EXT: Return resolution string 05x0625 for 0.5° x 0.625° grids
pressure_mod.F	In routines GET_PEDGE and GET_PEDGE_FULLGRID: Compute PEDGE for MERRA-2 in the same way as for GEOS-5, MERRA, and GEOS-FP In routine INIT_PRESSURE: Initialize Ap and Bp for MERRA-2 in the same way as for GEOS-5, MERRA, and GEOS-FP
time_mod.F	In routine GET_A1_TIME: Compute the DATE array for MERRA-2 the same way as is done for MERRA and GEOS-FP
transfer_mod.F	In routine INIT_TRANSFER: Set L_COPY = 36 for MERRA-2 Changed code to #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In several routines: Changed code to #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )

--Bob Y. (talk) 20:33, 12 August 2015 (UTC)

GeosCore directory

The following modifications for MERRA-2 were made in the GeosCore/ directory:

File	Modifications made
calcrate.F	Multiple instances: Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
carbon_mod.F	Multiple instances: Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
cldice_HbrHOBr_mod.F	Multiple instances: Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
convection_mod.F	In routine DO_CONVECTION: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In routine DO_MERRA_CONVECTION: Changed code to #if defined( GEOS_FP ) || defined( MERRA2 ) where we set PFICU and PFLCU
dao_mod.F	In routine COPY_I6_FIELDS: Changed code to: #if defined( GEOS_FP ) || defined( MERRA2 ) In routine INTERP: Changed code to: #if defined( GEOS_FP ) || defined( MERRA2 )
depo_mercury_mod.F	In routine ADD_Hg2_SNOWPACK Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
dao_mod.F	In routine COPY_I6_FIELDS: Changed code to: #if defined( GEOS_FP ) || defined( MERRA2 ) In routine INTERP: Changed code to: #if defined( GEOS_FP ) || defined( MERRA2 )
diag3.F	Multiple instances: Changed code to: #if defined( GEOS_FP ) || defined( MERRA2 ), etc.
dust_dead_mod.F	In routine DST_MBL: For GEOS-FP, add a new value for parameter FLX_MSS_FDG_FCT. The scale factor ensures that we get the same dust totals (w/in roundoff error) as for GEOS-5.
fast_jx_mod.F	In routine FAST_JX: Do cloud overlapping for GEOS-FP in the same way as for GEOS-5 and MERRA. Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
gamap_mod.F	In routine INIT_TRACERINFO: Changed code to: #elif defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
global_ch4_mod.F	In routines WETLAND_EMIS and READ_COPROD: Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
input_mod.F	In routine READ_SIMULATION_MENU: Now read value for Input_Opt%MERRA2_DIR from input.geos Also set Input_Opt%RES_DIR accordingly for 0.5° x 0.625° nested grids Set LUNZIP=.FALSE. for MERRA-2 met In routine READ_CONVECTION_MENU: Change #if statement to allow non-local PBL mixing for MERRA-2 met data In routine VALIDATE_DIRECTORIES: Error check MERRA2_DIR for start & end date
land_mercury_mod.F	In routines LAND_MERCURY_FLUX: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In routines SOILEMIS: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) Extend #if statement for variable SOIL_EMIS_FAC to get the code to compile w/o error. Team Hg will need to supply an updated value later on.
main.F	In main.F: Changed code to if defined( GEOS_FP ) || defined( MERRA2 ) where we define N_DYN_STEPS Changed code to if defined( GEOS_FP ) || defined( MERRA2 ) where we define Input_Opt%USE_O3_FROM_MET In included routine READ_INITIAL_MET_FIELDS: Added calls to routines from merra2_read_mod.F90 In included routine READ_MET_FIELDS: Added calls to routines from merra2_read_mod.F90
mercury_mod.F	In routine CHEMMERCURY: Add placeholder K_RED_JNO2 parameter for the 0.5° x 0.625° nested grids. For now use the same value as for the 0.5° x 0.666° grid. Team Hg will need to supply an updated value later on. Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
merra2_read_mod.F90	Added this module w/ routines to read GEOS-FP met data (in netCDF format) Also added this modification to only open netCDF files once per day, to reduce time spent in file I/O.
ocean_mercury_mod.F	Multiple instances: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
planeflight_mod.F	In routine PLANEFLIGHT Now use: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
strat_chem_mod.F90	Multiple instances: Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In routine DO_SYNOZ: Add placeholder values for 0.5° x 0.625° grids
sulfate_mod.F	In routine CHEM_SO2: Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In routine INIT_SULFATE: Changed code to: #if !defined( GEOS_5 ) && !defined( MERRA ) && !defined( GEOS_FP ) && !defined( MERRA2 ) In routine SRCSFC30 (TOMAS-only): Added a placeholder value for TSCALE for the 0.5° x 0.625° grids
tagged_ox_mod.F	In routine GET_REGIONAL_POX: Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
tpcore_bc_mod.F:	Multiple instances: Added MERRA-2 values for I1_BC_CH, I2_BC_CH, J1_BC_CH, J2_BC_CH Added MERRA-2 values for I1_BC_EU, I2_BC_EU, J1_BC_EU, J2_BC_EU Added MERRA-2 values for I1_BC_NA, I2_BC_NA, J1_BC_NA, J2_BC_NA
vdiff_mod.F90	In routine VDIFFDR: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
wetscav_mod.F	In routine DO_WETDEP: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In routine DO_WASHOUT_ONLY:: Changed code to: #if defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 ) In routine MAKE_QQ: Changed code to: #defined( GEOS_FP ) || defined( MERRA2 ) In routine RAINOUT: Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )

--Bob Y. (talk) 18:29, 12 August 2015 (UTC)

HEMCO/Core directory

The following modifications for MERRA-2 were made in the HEMCO/Core directory:

File	Modifications made
hco_chartools_mod.F90	At the top of the module: Extend the #ifdef statement to add the parameter DEF_MET = 'merra2' Extend the #ifdef statement to add the parameter DEF_RES = '05x0625'
hco_interp_mod.F90	In routine MODLEV_INTERPOLATE: Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )

--Bob Y. (talk) 18:28, 12 August 2015 (UTC)

HEMCO/Extensions directory

The following modifications for MERRA-2 were made in the HEMCO/Extensions directory:

File	Modifications made
hcox_ch4wetland_mod.F90	In routine WETLAND_EMIS: Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
hcox_dustdead_mod.F	In routine HCOX_DUSTDEAD_GETTUN: Add values of FLX_MSS_FDG_FCT= -999 for the MERRA-2 2° x 2.5° and 4° x 5° grids. We will add the correct values once we can run simulations with at least a year of met data.
hcox_lightnox_mod.F	In routine GET_OTD_LIS_SCALE: Add placeholder values of ANN_AVG_FLASHRATE for the MERRA-2 0.5° x 0.625° grids. Add placeholder values of BETA for the MERRA-2 2° x 2.5° and 4° x 5° grids. We will add the correct values once we can run simulations with at least a year of met data.
hcox_megan_mod.F	In routine GET_GAMMA_SM: Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
hcox_tomas_dustdead_mod.F	In routine HCOX_TOMAS_DUSTDEAD_GETTUN: Add placeholder values of FLX_MSS_FDG_FCT = -999 for the MERRA-2 2° x 2.5° and 4° x 5° grids. We will add the correct values once we can run simulations with at least a year of met data.

--Bob Y. (talk) 18:53, 12 August 2015 (UTC)

Previous issues that are now resolved

Default timestep for MERRA-2 nested grid simulations

The original update was included in v11-02f (approved 17 May 2018). The final recommendation was included GEOS-Chem 12.0.0.

Bram Maasakkers wrote:

Melissa Sulprizio and I have been working on the methane simulation with MERRA-2 and the nested North America grid at 0.5x0.625. During our initial simulations, we found very high values in the stratosphere, originating at the edges of the domain and showing a checkerboard-like pattern in the domain. It appears this is caused by a violation of the CFL condition in the stratosphere due to strong stratospheric winds in MERRA-2. When the condition is violated at the boundaries, it leads to an out-of-bounds error but even preventing an out-of-bounds error there by capping the array index doesn’t prevent the high concentrations from originating. It seems that this previously occurred for the GEOS-5 simulation but it did not seem to compromise simulation results significantly. For our purposes of comparing total column measurements of GOSAT to model output, it is a larger problem. We found it also occurs in the full-chem simulation, I’m attaching a plot of column ozone here to illustrate, the high values are only present in the stratospheric layers.

I think that a variable timestep could be implemented to prevent this from happening. For now, we recommend using a 5/10 transport/chemistry timestep with MERRA-2 nested grid simulations instead of 10/20.

--Bob Yantosca (talk) 16:01, 17 May 2018 (UTC)

Ke Li wrote:

The default time steps for nested tropchem simulation using MERRA2 are 5 mins for transport and 10 mins for chemistry. It took me about 2 days to run 1 months of simulation at the cost of 24 cpu. Now I change time steps to 10 mins for transport and 20 mins for chemistry, and it costs 1.2 days to run 1 months of simulation at the cost of 24 cpu. The 5/20mins time step for a test simulation over Asia (Tropchem, MERRA-2, 24 CPUs) still costs about two days for one month of simulation. The cost time is estimated from that the test simulation has used 28.5 hours for 17.5 days of simulation, though it hasn’t finished.

Lin Zhang wrote:

I am fine to use 10/20 mins time step as default which does not seem to affect the tropospheric simulation of air pollutants. We used to run GEOS-5 at 0.5 degree resolution with 10/20 mins, and tropospheric simulations were working well.

We can also put a stop sign for CH4 and CO2 simulations to warn users changing time steps to 5/10 mins.

Yuxuan Wang wrote:

I agree with Lin and would also opt for a 10/20 mins time step as the default for full-chemistry nested-grid simulation. The reason is exactly as Daniel said. The nested-grid model users are predominantly using the full-chemistry option and concerns with tropospheric or surface concentration. The specialty nested-grid simulations, such as tagged CO, methane and CO2, used to require a separate development and model tuning, as least during the past before the HEMCO era. As a continuation of that ‘tradition’, the idea of putting a note or stop sign for the CH4 and CO2 nested-grid code should work well.

--Melissa Sulprizio (talk) 12:50, 30 July 2018 (UTC)

Unresolved issues

PBL height

Chris Holmes wrote:

I’ve documented many cases in which the reported PBLH in MERRA2 does not align with the mixing height that an observer would diagnose from the MERRA2 vertical profiles of potential temperature and humidity. In my group we are diagnosing our own PBL heights for use in GEOS-Chem.

--Melissa Sulprizio (talk) 20:25, 30 May 2017 (UTC)