MERRA-2 implementation details

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Required coding changes in GEOS-Chem

As noted in the section above, the similarities between MERRA and GEOS-FP (especially of the vertical grids) means that in most cases we can just treat MERRA in the same way as for GEOS-5. 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 )

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:

Top-level directory

File Modifications made
Makefile_header.mk
  • If MET=merra2 or MET=merra-2 (case-insensitive), then the MERRA2 C-preprocessor switch will be activated (i.e. -DMERRA2< will be added to the Makefile variable USER_DEFS).

--Bob Y. (talk) 20:33, 11 August 2015 (UTC)

Headers directory

The following modifications for MERRA2 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
  • This module was introduced to facilitate the Grid-Independent GEOS-Chem development.
  • gigc_input_opt_mod.F90 now collects the various logical switches, file paths, and related variables from logical_mod.F, directory_mod.F, unix_cmds_mod.F, and linoz_mod.F.
gigc_state_met_mod.F90
  • This module was introduced to facilitate the Grid-Independent GEOS-Chem development.
  • gigc_state_met_mod.F90 now holds all of the met field arrays that were formerly in GeosCore/dao_mod.F.
  • We now allocate all met field arrays in routine Init_GIGC_State_Met

--Bob Y. 13:52, 7 November 2013 (EST)

GeosUtil directory

The following modifications for GEOS-FP were made in the GeosUtil/ directory:

File Modifications made
bpch2_mod.F

In routine GET_MODELNAME:

  • Add GEOS5_47L and GEOSFP modelnames to the #if block

In routine GET_NAME_EXT:

  • Return grid name geos5 for GEOS-FP fields

In routine GET_RES_EXT:

  • Return resolution string 025x03125 for 0.25° x 0.3125° grids
grid_mod.F

In routine COMPUTE_GRID:

  • Overwrite YMID at poles for 0.25° x 0.3125° grids (+/- 89.3975)
  • Define YMID_R_W for 0.25° x 0.3125° nested grids

In routine INIT_GRID:

  • Define IIIPAR=1152 and JJJPAR=721 for 0.25° x 0.3125° global grid
pressure_mod.F

In routines GET_PEDGE and GET_PEDGE_FULLGRID:

  • Compute PEDGE for GEOS-FP in the same way as for GEOS-5 and MERRA

In routine INIT_PRESSURE:

  • Initialize Ap and Bp for GEOS-FP in the same way as for GEOS-5 and MERRA
time_mod.F

In routine GET_A1_TIME:

  • Compute the DATE array for GEOS-FP the same way as is done for MERRA.
transfer_mod.F

In several routines:

  • Changed code to #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )

--Bob Y. 13:55, 7 November 2013 (EST)

GeosCore directory

The following modifications for GEOS-FP were made in the GeosCore/ directory:

File Modifications made
calcrate.F Multiple instances:
  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
carbon_mod.F Multiple instances:
  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
cldice_HbrHOBr_mod.F Multiple instances:
  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
convection_mod.F

In routine DO_CONVECTION:

  • Changed code to: #if defined( MERRA ) || defined( GEOS_FP )
  • For GEOS-FP, PFICU and PFLCU fields are defined on level edges. Pass the top edge value at each level (stored in local arrays T_PFICU and T_PFLCU) to DO_MERRA_CONVECTION.
  • Add T_PFICU and T_PFLCU arrays to the PRIVATE statement of the OpenMP loop.
dao_mod.F

In routine COPY_I6_FIELDS:

  • Renamed this routine to COPY_I3_I6_FIELDS
  • Added #if block for GEOS-FP met

In routines IS_ICE, IS_LAND, IS_NEAR, IS_WATER:

  • Now use: #elif defined( GEOS_4 ) || defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )

In routine INTERP:

  • Add #if block for GEOS-FP
depo_mercury_mod.F

In routine ADD_Hg2_SNOWPACK

  • Changed code to: #if defined( MERRA ) || defined( GEOS_FP )
diag3.F
  • Add SCALE_I3 counter for instantaneous met fields
  • Modify ND66 diagnostic to divide by proper # of A3 increments (i.e. every 3 hours)
    • With the exception of T, SPHU, which are I3 fields
  • Modify ND67 diagnostic to divide by proper # of A1 increments (i.e. every hour)
    • With the exception of CLDTOPS, which is an A3 field
dust_mod.F

In routine SRC_DUST_DEAD:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
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_j.F
  • 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 )
gamap_mod.F

In routine INIT_TRACERINFO:

  • Changed code to: #elif defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
geosfp_read_mod.F90
  • Added this module w/ routines to read GEOS-FP met data (in netCDF format)
global_ch4_mod.F

In routines WETLAND_EMIS and READ_COPROD:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
global_hno3_mod.F

In routine GET_GLOBAL_HNO3:

  • Now use:
    #if defined( GEOS_3 ) || defined( GEOS_4 ) || defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
global_o3_mod.F

In routine GET_GLOBAL_O3

  • Now use:: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
initialize.F
  • Restructure USE statements for clarity
  • Now also reset the counter for I3 timesteps by calling routine  SET_CT_I3( RESET=.TRUE. )
input_mod.F

In routine READ_SIMULATION_MENU:

  • Read value for GEOS_FP_DIR from input.geos file and save into Input_Opt
  • Set LUNZIP=.FALSE. for GEOS-FP met

In routine READ_CONVECTION_MENU:

  • Change #if statement to allow non-local PBL mixing for GEOS-FP met data

In routine READ_EMISSIONS_MENU:

  • Turn off LMEGANMONO when LMEGAN is turned off

In routine VALIDATE_DIRECTORIES:

  • Error check GEOS_FP_DIR for start & end date
land_mercury_mod.F

In routines LAND_MERCURY_FLUX:

  • Changed code to: #if defined( MERRA ) || defined( GEOS_FP )

In routines SOILEMIS:

  • Changed code to: #if defined( MERRA ) || defined( GEOS_FP )
  • Extend #if statement for variable SOIL_EMIS_FAC to get the code to compile w/o error.
    (NOTE: Team Hg: you will have to submit a proper value for this later.
lightning_nox_mod.F

In routine LIGHTNING:

  • Eliminate the shallow-cloud inhibititon trap for GEOS-FP, as we already do for GEOS-5 and MERRA

In routine GET_OTD_LIS_SCALE:

  • Now use updated values for ANN_AVG_FLASHRATE computed by Lee Murray (2013-11-07).
Makefile
  • Added dependencies for new routines
  • Added the following targets
    • libnc: Compiles the code in the NcdfUtil directory and creates the libNcUtils.a library
    • ncdfcheck: Compiles a program that will test the integrity of the netCDF library installation.
main.F
  • Rewrote USE statements for clarity
  • Added calls to routines from geosfp_read_mod.F
  • Split off the code that reads met fields into internal subroutines READ_INITIAL_MET_FIELDS and READ_MET_FIELDS, for clarity.
  • Renamed NN to NNN to avoid name confusion
megan_mod.F

At top of module

  • For MERRA and GEOS-FP met: define DAY_DIM parameter = 24 for hourly temperature data
  • For all other met data: define DAY_DIM parameter = 8 for 3-hourly temperature data

In routine INIT_MEGAN:

  • For MERRA and GEOS-FP met: define G4AHEAD = 003000
  • Now call GEOS57_READ_A1 (from geosfp_read_mod.F90) to read surface temperature data
mercury_mod.F

In routine CHEM_Hg0_Hg2:

  • In the block that computes LWC, changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
  • In the block that computes Hg0 exchange, changed code to: #if defined( MERRA ) || defined( GEOS_FP )
nei2005_anthro_mod.F

In routines EMISS_NEI2005_ANTHRO and EMISS_NEI_ANTHRO_05x0666:

  • Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
ocean_mercury_mod.F

Multiple instances:

  • Now use: #if defined( MERRA ) || defined( GEOS_FP )
planeflight_mod.F

In routine PLANEFLIGHT

  • Now use: #if defined( MERRA ) || defined( GEOS_FP )
strat_chem_mod.F90

Multiple instances:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
sulfate_mod.F

Multiple instances:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
tagged_ox_mod.F

Multiple instances:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
tpcore_bc_mod.F:

Multiple instances:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
tropopause_mod.F:

Multiple instances:

  • Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )
vdiff_mod.F90

In routine VDIFFDR:

  • Changed code to: #if defined( MERRA ) || defined( GEOS_FP )
wetscav_mod.F

In routines DO_WETDEP, DO_WASHOUT_ONLY

  • Changed code to: #if defined( MERRA ) || defined( GEOS_FP )

In routine MAKE_QQ:

  • Add #if block for GEOS-FP met
  • Refer to PFILSAN(I,J,L+1) and PFLLSAN(I,J,L+1), since these fields are defined on level edges

In routine RAINOUT:

  • Changed code to: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )

--Bob Y. 14:23, 7 November 2013 (EST)

GeosApm directory

The following modifications for GEOS-FP were made in the GeosTomas/ directory:

File Modifications made
Makefile
  • Added dependencies for geos57_read_mod.F
  • Removed references to obsolete GEIA biogenic emissions
carbon_mod.F
  • Synchronized with GeosCore/carbon_mod.F
dao_mod.F
  • Synchronized with GeosCore/dao_mod.F
dust_mod.F
  • Synchronized with GeosCore/dust_mod.F
dust_dead_mod.F
  • Synchronized with GeosCore/dust_dead_mod.F
main.F
  • Synchronized with GeosCore/main.F
sulfate_mod.F
  • Synchronized with GeosCore/sulfate_mod.F
wetscav_mod.F
  • Synchronized with GeosCore/wetscav_mod.F
  • NOTE: Needs validation by APM team

--Bob Y. 13:49, 9 February 2012 (EST)

NcdfUtil directory

We have added the NcdfUtil/ directory, which contains routines for netCDF file I/O. These routines are based on the NcdfUtilities package by Bob Yantosca. These are built when you compile GEOS-Chem with the NETCDF=yes Makefile option.

File Description
Makefile GNU Makefile used to build the NcdfUtil code.
TestNcdfUtil.F90 Test program to verify that the netCDF libraries were built properly. (This is executed only when you issue a make ncdfcheck command.)
m_do_err_out.F90 Routine to print out netCDF error messages.
m_netcdf_io_checks.F90 Routines to check whether a netCDF file contains a specified variable or dimension.
m_netcdf_io_close.F90 Routines to close a netCDF file.
m_netcdf_io_create.F90 Routines used to open a netCDF file for output and to synchronize a netCDF file.
m_netcdf_io_define.F90 Routines to define netCDF variables and attributes. Use this when writing data to a netCDF file.
m_netcdf_io_get_dimlen.F90 Routines to return dimension information from a netCDF file.
m_netcdf_io_handle_err.F90 Routines for netCDF I/O error handling.
m_netcdf_io_open.F90 Routines for opening a netCDF file for reading or for writing.
m_netcdf_io_read.F90 Routines for reading variables (of INTEGER, REAL*4, REAL*8, and CHARACTER types) from a netCDF file.
m_netcdf_io_readattr.F90 Routines for reading global and variable attributes (of INTEGER, REAL*4, REAL*8, and CHARACTER types) from a netCDF file.
m_netcdf_io_write.F90 Routines for writing data to a netCDF file

--Bob Y. 10:34, 3 February 2012 (EST)

NcdfUtil/perl subdirectory

In this directory, we have added scripts for automatically generating Fortran code with the proper calls from the NcdfUtilities package. We anticipate that this will be a convenience for GEOS-Chem users, as it will relieve some of the drudgery of writing these calls by hand.

File Description
StrTrim.pm Perl module used by the ncCode* scripts. Contains routines for stripping withe space from strings.
ncCodeDef Perl script that generates Fortran code to open a netCDF file and define the various dimensions, variables, and attributes.
ncCodeWrite Perl script that will generate Fortran code to write data to a netCDF file.
ncCodeRead Perl script that will generate Fortran code to read data from a netCDF file.
nc_definitions.rc Generic input file used by the ncCode* scripts. You can edit this.
definitions_cn.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP CN data.
definitions_a1.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP A1 data.
definitions_a3cld.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP A3cld data.
definitions_a3dyn.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP A3dyn data.
definitions_a3mstc.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP A3mstC data.
definitions_a3mste.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP A3mstE data.
definitions_i3.rc Customized version of nc_definitions.rc that will generate Fortran code for reading GEOS-FP I3 data.

--Bob Y. 15:49, 12 May 2014 (EDT)

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