View source for GEOS-FP implementation details

<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; ">'''NOTE: [[GEOS-FP]] is the current [http://gmao.gsfc.nasa.gov NASA/GMAO] operational met data product.  It is produced with a native resolution of 0.25&deg; (lon) x 0.3125&deg; (lat) x 72 hybrid vertical layers.  GEOS-FP replaced the older [[GEOS-5|GEOS-5.2.0]] operational data product in June 2013.<br><br>GEOS-FP was originally given the designation GEOS-5.7.1, which was later updated to GEOS-5.7.2.  Currently, GEOS-FP is being produced with version 5.11.0 of the GEOS Data Assimilation System (aka GEOS-DAS).  This means that the "5.7.x" nomenclature is no longer correct.  For this reason, we shall refer to this product as GEOS-FP from now on. (Bob Yantosca, 21 Aug 2013)'''</div>

On this page we list the necessary modifications to GEOS-Chem for compatibility with the [[GEOS-FP]] meteorological data.

== Overview ==

The [[GEOS-FP|GEOS-FP data product]] (aka GEOS5-FP) is the newest version of the operational meteorological data produced by NASA/GMAO.  Overall, the structure of GEOS-FP is very similar to MERRA.  Therefore, within GEOS-Chem we can (for the most part) treat GEOS-FP in the same way as we do for the [[MERRA|MERRA meteorology]].

=== Key similarities to MERRA === 

The following aspects of [[GEOS-FP]] are identical to the older [[GEOS-5|GEOS-5.2.0]] operational data product.

# The GEOS-FP vertical grid ([http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72 hybrid levels]) is identical to that of both MERRA and [[GEOS-5|GEOS-5.2.0]].
# By and large, the same data fields that were in the MERRA product are also contained in GEOS-FP:
#* GEOS-FP provides the same time-invariant fields (FRLAKE, FRLAND, FRLANDIC, FROCEAN, PHIS) as MERRA
#* The same correction that was applied to the [[List of MERRA met fields#SNOMAS|MERRA SNOMAS (snow mass) field]] has also been applied to the GEOS-FP SNOMAS field.
#* GEOS-FP contains the same precipitation fields (DQRCU, DQRLSAN, PFICU, PFILSAN, PFLCU, PFLLSAN, REEVAPCN, REEVAPLSAN) as MERRA.  This means that we can use the MERRA [[Wet deposition|wet deposition algorithms]] with the GEOS-FP data.
# The [[GEOS-FP#GEOS-FP_time_archiving|GEOS-FP time archiving]] is identical to that of MERRA ...
#* ... with one exception: GEOS-FP instantaneous data is archived every 3 hours, as opposed to 6 hours in MERRA.

--[[User:Bmy|Bob Y.]] 09:46, 21 August 2013 (EDT)

=== Key differences from MERRA ===

The following aspects of [[GEOS-FP]] differ from the MERRA operational data product:

# All GEOS-FP data are placed on a horizontal grid of 0.25&deg; x 0.3125&deg;.
#* MERRA data fields are placed on three different horizontal grids (0.5&deg; x 0.666&deg;, 1&deg; x 1.25&deg; and 1.25&deg; x 1.25&deg;).
# All GEOS-FP data are placed on the [http://acmg.seas.harvard.edu/geos/doc/man/appendix_3.html#GEOS-5_native 72-level hybrid grid]. 
#* Some MERRA fields were only available on a 42-level pressure grid (thus requiring interpolation).
# The following data GEOS-FP data fields differ from the corresponding MERRA fields:
#* RH is now a 3-hour time-averaged field, as opposed to a 6-hour instantaneous field in MERRA.
#* QV and T are now instantaneous 3-hour fields, as opposed to 3-hour time-averaged fields in MERRA.
#* The 3-D precipitation fields now make the (e.g. DQIDTMST, DQVDTMST, DQLDTMST, etc.) obsolete.  We no longer archive these.
# We have chosen to save the processed GEOS-FP data in netCDF format, as opposed to GEOS-Chem binary format.

--[[User:Bmy|Bob Y.]] 09:47, 21 August 2013 (EDT)

== Required coding changes in GEOS-Chem ==
 
'''''NOTE: This section is still under construction.  Not all tables have yet been updated.'''''

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 )

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 ===

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|Modifications made
|-
|Makefile_header.mk    
|
*Starting with [[GEOS-Chem v9-02 benchmark history#v9-02o|GEOS-Chem v9-02o]], we now use Makefile variables to set the various C-preprocessor switches.  In particular:
**<tt>MET=___</tt> selects the met field type( <tt>gcap, geos4, geos5, geosfp, merra</tt>)
**<tt>GRID=___</tt> selects the horizontal grid (<tt>4x5, 2x25, 05x0666, 025x03125</tt>)
**<tt>NEST=___</tt> specifies the nested-grid (<tt>CH, EU, NA, SE</tt>)
|}

--[[User:Bmy|Bob Y.]] 13:39, 7 November 2013 (EST)

=== Headers directory ===

The following modifications for [[GEOS-FP]] were made in the <tt>Headers/</tt> directory:

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|Modifications made
|-
|CMN_SIZE_mod.F     
|
*Added size parameters for GEOS-FP grids at 4&deg; x 5&deg; 2&deg; x 2.5&deg; and 0.25&deg; x 0.3125&deg; resolution
|-
|gigc_input_opt_mod.F90    
|
*This module was introduced to facilitate the [[Grid-Independent GEOS-Chem]] development.
*<tt>gigc_input_opt_mod.F90</tt> now collects the various logical switches, file paths, and related variables from <tt>logical_mod.F</tt>, <tt>directory_mod.F</tt>, <tt>unix_cmds_mod.F</tt>, and <tt>linoz_mod.F</tt>.
|-
|gigc_state_met_mod.F90    
|
*This module was introduced to facilitate the [[Grid-Independent GEOS-Chem]] development.
*<tt>gigc_state_met_mod.F90</tt> now holds all of the met field arrays that were formerly in <tt>GeosCore/dao_mod.F</tt>.  
*We now allocate all met field arrays in routine <tt>Init_GIGC_State_Met</tt>

|}

--[[User:Bmy|Bob Y.]] 13:52, 7 November 2013 (EST)

=== GeosUtil directory ===

The following modifications for GEOS-5.7.2 were made in the <tt>GeosUtil/</tt> directory:

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|Modifications made
|-
|bpch2_mod.F     
| 
In routine GET_MODELNAME: 
*Add <tt>GEOS5_47L</tt> and <tt>GEOSFP</tt> modelnames to the <tt>#if</tt> block
In routine GET_NAME_EXT: 
*Return grid name <tt>geos5</tt> for GEOS-FP fields
In routine GET_RES_EXT:
*Return resolution string <tt>025x03125</tt> for 0.25&deg; x 0.3125&deg; grids
|-
|grid_mod.F
|
In routine COMPUTE_GRID:
*Overwrite YMID at poles for 0.25&deg; x 0.3125&deg; grids (+/- 89.3975)
*Define YMID_R_W for 0.25&deg; x 0.3125&deg; nested grids
In routine INIT_GRID:
*Define IIIPAR=1152 and JJJPAR=721 for 0.25&deg; x 0.3125&deg; 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 <tt>DATE</tt> array for GEOS-FP the same way as is done for MERRA.
|-
|transfer_mod.F
|
In several routines:
*Changed code to <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|}

--[[User:Bmy|Bob Y.]] 13:55, 7 November 2013 (EST)

=== GeosCore directory ===

The following modifications for GEOS-5.7.2 were made in the <tt>GeosCore/</tt> directory:

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|Modifications made
|-
|calcrate.F
|Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|carbon_mod.F
|Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|cldice_HbrHOBr_mod.F
|Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|convection_mod.F
|
In routine DO_CONVECTION:
*Changed code to: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
*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: <tt>#elif defined( GEOS_4 ) || defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
In routine INTERP: 
*Add #if block for GEOS-FP
|-
|depo_mercury_mod.F
|
In routine ADD_Hg2_SNOWPACK
*Changed code to: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|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: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|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: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|gamap_mod.F
|
In routine INIT_TRACERINFO: 
*Changed code to: <tt>#elif defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|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: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|global_hno3_mod.F
|
In routine GET_GLOBAL_HNO3:
*Now use:<br><tt>#if defined( GEOS_3 ) || defined( GEOS_4 ) || defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|global_o3_mod.F
|
In routine GET_GLOBAL_O3
*Now use:: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|initialize.F
|
*Restructure USE statements for clarity
*Now also reset the counter for I3 timesteps by calling routine&nbsp;&nbsp;<tt>SET_CT_I3( RESET=.TRUE. )</tt>
|-
|input_mod.F
|
In routine READ_SIMULATION_MENU: 
*Read value for GEOS_FP_DIR from <tt>input.geos</tt> file and save into <tt>Input_Opt</tt>
*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: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
In routines SOILEMIS:
*Changed code to: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
*Extend #if statement for variable SOIL_EMIS_FAC to get the code to compile w/o error.<br>'''''(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 <tt>ANN_AVG_FLASHRATE</tt> 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 <tt>libNcUtils.a</tt> 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: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
*In the block that computes Hg0 exchange, changed code to: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|nei2005_anthro_mod.F
|
In routines EMISS_NEI2005_ANTHRO and EMISS_NEI_ANTHRO_05x0666:
*Changed code to: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|ocean_mercury_mod.F
|
Multiple instances:
*Now use: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|planeflight_mod.F
|
In routine PLANEFLIGHT
*Now use: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|strat_chem_mod.F90
|
Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|sulfate_mod.F
|
Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|tagged_ox_mod.F
|
Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|tpcore_bc_mod.F:
|
Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|tropopause_mod.F:
|
Multiple instances:
*Now use: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|vdiff_mod.F90
|
In routine VDIFFDR:
*Changed code to: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
|-
|wetscav_mod.F
|
In routines DO_WETDEP, DO_WASHOUT_ONLY
*Changed code to: <tt>#if defined( MERRA ) || defined( GEOS_FP )</tt>
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: <tt>#if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP )</tt>

|}

--[[User:Bmy|Bob Y.]] 14:23, 7 November 2013 (EST)

=== GeosApm directory ===

The following modifications for GEOS-5.7.2 were made in the <tt>GeosTomas/</tt> directory:

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|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
|}

--[[User:Bmy|Bob Y.]] 13:49, 9 February 2012 (EST)

=== NcdfUtil directory ===

We have added the <tt>NcdfUtil/</tt> 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 <tt>NETCDF=yes</tt> Makefile option.

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|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 <tt>make ncdfcheck</tt> 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
|}

--[[User:Bmy|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.

{| border=1 cellspacing=0 cellpadding=5 
|- bgcolor="#CCCCCC"
!width="175px"|File
!width="800px"|Description
|-
|StrTrim.pm
|Perl module used by the <tt>ncCode*</tt> 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 <tt>ncCode*</tt> scripts.  You can edit this.
|-
|definitions_cn.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#Constant_fields|GEOS-5.7.2 CN data]].
|-
|definitions_a1.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#A1 fields|GEOS-5.7.2 A1 data]].
|-
|definitions_a3cld.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#A3cld fields|GEOS-5.7.2 A3cld data]].
|-
|definitions_a3dyn.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#A3dyn fields|GEOS-5.7.2 A3dyn data]].
|-
|definitions_a3mstc.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#A3mstC fields|GEOS-5.7.2 A3mstC data]].
|-
|definitions_a3mste.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#A3mstE fields|GEOS-5.7.2 A3mstE data]].
|-
|definitions_i3.rc
|Customized version of <tt>nc_definitions.rc</tt> that will generate Fortran code for reading [[List of GEOS-5.7.2 met fields#I3 fields|GEOS-5.7.2 I3 data]].
|}

--[[User:Bmy|Bob Y.]] 10:34, 3 February 2012 (EST)

== Resolved issues ==

=== Fractional sea ice ===

In order to preserve some information about sea ice leads during the regridding process, we have binned the fractional sea ice coverage into deciles (0-10%, 10-20% ... 90-100% coverage) and saved those as separate fields in the GEOS-5.7.2 data archive for GEOS-Chem.  We have used 
[[List of MERRA met fields#Fractional sea ice|the same algorithm we developed for MERRA met fields]] to do the binning.

--[[User:Bmy|Bob Y.]] 16:12, 24 January 2012 (EST)

=== SNOMAS ===

The SNOMAS (snow depth) fields in both [[GEOS-5.7.2]] and [[MERRA]] differ from that in [[GEOS-5|GEOS-5.2.0]].  It appears that in GEOS-5.2.0 a default snow mass value was applied to grid boxes that had > 90% land ice coverage.  This was not done in MERRA or GEOS-5.7.2.  Bob Yantosca [[List of MERRA met fields#SNOMAS|had implemented an algorithm]] to adjust the MERRA SNOMAS field to be backwards-compatible with GEOS-5.2.0.  We have used this algorithm to adjust the GEOS-5.7.2 SNOMAS field accordingly.

--[[User:Bmy|Bob Y.]] 16:14, 24 January 2012 (EST)

=== Dust emissions ===

The dust emissions in GEOS-Chem rely on "tunable parameters" to scale the dust emissions to a specified total.  This is because the dust emissions are very highly dependent on the surface winds, and a small difference in winds (e.g. from GEOS-5 to GEOS-FP) can cause a huge difference in dust emission flux.

In routine <tt>DST_MBL</tt> (in <tt>dust_dead_mod.f</tt>), we have added the following code:

      !----------------------------------------------------------------
      ! Based on results from GEOS-FP 4x5 for 04/2012-04/2013
      !
      !   (GEOS-5 - GEOS-FP)/GEOS-5 * 100 is 23.56% in each size bin.
      !
      ! We need to scale to the parameter FLX_MSS_FDG_FCT to make the
      ! dust emissions consistent.  Consequently, to bring GEOS-FP 4x5
      ! dust emissions up to GEOS-5 levels, we need to MULTIPLY the
      ! FLX_MSS_FDG_FCT used for GEOS-5 by:
      !
      !             1 / (1. - 0.2356) = 1 / 0.7644 = 1.3082
      !
      !    -- R. Yantosca, M. Sulprizio, 07 Nov 2013
      !----------------------------------------------------------------
      REAL*8,  PARAMETER     :: FLX_MSS_FDG_FCT = 7.0d-4 * 1.3082d0

--[[User:Melissa Payer|Melissa Sulprizio]] 11:42, 7 November 2013 (EST)

=== Lightning ===

We now use OTD-LIS local redistribution files (provided by Lee Murray, dated 2013-11-07) from the <tt>lightning_NOx_201311/</tt> subdirectory.

--[[User:Bmy|Bob Y.]] 14:45, 7 November 2013 (EST)

=== Wet deposition and scavenging ===

Helen Amos, Bess Corbitt, and Qiaoqiao Wang had implemented an [http://acmg.seas.harvard.edu/geos/wiki_docs/deposition/v9-01-01_wetdep.pdf updated algorithm for wet scavenging] that takes advantage of the new precipitation fields from the MERRA data archive.  This was included in [[GEOS-Chem v9-01-01]] and higher versions.  

Because [[GEOS-5.7.2]] contains the same precipitation data fields as MERRA (i.e. DQRCU, DQRLSAN, PFICU, PFILSAN, PFLCU, PFLLSAN, REEVAPCN, REEVAPLSAN), we can use the new wet deposition algorithm with the GEOS-5.7.2 met data.

--[[User:Bmy|Bob Y.]] 16:16, 24 January 2012 (EST)

== Implementation history ==

=== Initial source code modifications for GEOS-FP ===

'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-01-03_benchmark_history#v9-01-03g|v9-01-03g]] and approved on 27 Feb 2012.'''''

<span style="color:#CC0000">'''NOTE: At the time of this update GEOS-FP has not been validated, so the <tt>#define GEOS_FP</tt> switch in define.h should not be used.'''</span>

The following modifications are slated to be incorporated into the 1-month benchmark [[GEOS-Chem v9-01-03 benchmark history#v9-01-03g|GEOS-Chem v9-01-03g]]:

#Modify the [[#Headers directory|Headers]], [[#GeosUtil directory|GeosUtil]], and [[#GeosCore directory|GeosCore]] directories for GEOS-FP
#Update the [[#GeosApm directory|GeosApm]] and [[#GeosTomas directory|GeosTomas]] directories, primarily to synchronize files with GeosCore
#Add [[#NcdfUtil directory|NcdfUtil directory]]
#Resolve several issues, including: [[#Fractional sea ice|Fractional sea ice]], [[#SNOMAS|SNOMAS]], [[#Wet deposition and scavenging|Wet deposition and scavenging]]

--[[User:Melissa Payer|Melissa Payer]] 17:29, 24 February 2012 (EST)

=== Bug fix for declaration of GEOS-5.7.2 PFICU, PFLCU, PFILSAN, PFLLSAN fields ===

'''''This update was tested in the 1-month benchmark simulation [[GEOS-Chem_v9-02_benchmark_history#v9-02g|v9-02g]] and approved on 24 Mar 2013.'''''

In module file <tt>GeosCore/gigc_state_met_mod.F90</tt>, it was discovered that the PFICU, PFLCU, PFILSAN, and PFLLSAN met fields for [[GEOS-FP]] were being allocated with the wrong vertical dimension.  In [[GEOS-FP]], these fields are placed on level edges and need to be allocated with <tt>LLPAR+1</tt> levels.  But in [[MERRA]], these fields are placed on level centers and need to be allocated with <tt>LLPAR</tt> levels.

We have introduced the following fix in routine <tt>Init_GIGC_State_Met</tt> of <tt>Headers/gigc_state_met_mod.F90</tt>:

     INTEGER :: LX
 
     ... 
 
 #elif defined( GEOS_FP ) || defined( MERRA )
 
     !=======================================================================
     ! GEOS_FP / MERRA met fields
     !=======================================================================
 #if defined( GEOS_57 )
     LX = LM + 1
 #elif defined( MERRA )
     LX = LM
 #endif
 
     ALLOCATE( State_Met%PFICU     ( IM, JM, LX   ), STAT=RC )
     IF ( RC /= GIGC_SUCCESS ) RETURN
     State_Met%PFICU    = 0d0
 
     ALLOCATE( State_Met%PFILSAN   ( IM, JM, LX   ), STAT=RC )
     IF ( RC /= GIGC_SUCCESS ) RETURN
     State_Met%PFILSAN  = 0d0
 
     ALLOCATE( State_Met%PFLCU     ( IM, JM, LX   ), STAT=RC )
     IF ( RC /= GIGC_SUCCESS ) RETURN
     State_Met%PFLCU    = 0d0
 
     ALLOCATE( State_Met%PFLLSAN   ( IM, JM, LX   ), STAT=RC )
     IF ( RC /= GIGC_SUCCESS ) RETURN
     State_Met%PFLLSAN  = 0d0

This will make sure that the fields will be declared properly for either GEOS-FP or MERRA.  (NOTE: <tt>LM</tt> is set to <tt>LLPAR</tt>, and thus <tt>LM+1</tt> = <tt>LLPAR+1</tt>.

--[[User:Bmy|Bob Y.]] 14:37, 7 November 2013 (EST)

=== Make sure State_Met%T is initialized properly for GEOS-FP simulations ===

For simulations with the [[GEOS-FP|GEOS-FP met fields]], temperature is an I3 (i.e. 3-hr instantaneous) met field.  We need to read temperature at times <tt>t</tt> and <tt>t+3hrs</tt>, and then interpolate linearly to the proper time.
    
At time <tt>t=0</tt> of a GEOS-FP simulation, the initial temperature is read from netCDF files into <tt>State_Met%TMPU1</tt>.  However, we must also save this into <tt>State_Met%T</tt>.  Otherwise, temperature will be not initialized properly until the first call to <tt>INTERP</tt>.  This can cause a floating-point error further upstream.  

We have added the following code to routine <tt>Geos57_Read_I3_1</tt> in <tt>GeosCore/geos57_read_mod.F90</tt>:

      ! For now, copy State_Met%TMPU1 to State_Met%T.  At the next met field 
      ! read, we will State_Met%T from the values of State_Met%TMPU1 and
      ! State_Met%TMPU2. (bmy, 9/6/13)
      State_Met%T = State_Met%TMPU1

This error condition was caught by the [[Debugging with the GEOS-Chem unit tester|GEOS-Chem unit tester]] when compiling with option <tt>FPE=yes</tt>.

--[[User:Bmy|Bob Y.]] 13:13, 12 September 2013 (EDT)