GEOS-FP implementation details: Difference between revisions

From Geos-chem
Jump to navigation Jump to search
 
(9 intermediate revisions by 2 users not shown)
Line 8: Line 8:
== Overview ==
== 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]] and [[MERRA2]] met data products..  Therefore, within GEOS-Chem we can (for the most part) treat GEOS-FP in the same way as we do for the MERRA and MERRA2.
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]] and [[MERRA-2]] met data products..  Therefore, within GEOS-Chem we can (for the most part) treat GEOS-FP in the same way as we do for the MERRA and MERRA-2.


The table below compares many features of GEOS-FP with other met field products.
The table below compares many features of GEOS-FP with other met field products.
Line 15: Line 15:
|-bgcolor="#CCCCCC"
|-bgcolor="#CCCCCC"
!width="250px"|Feature
!width="250px"|Feature
!width="200px"|[[MERRA2]]
!width="200px"|[[MERRA-2]]
!bgcolor="#CCFFFF" width="200px"|[[GEOS-FP]]
!bgcolor="#CCFFFF" width="200px"|[[GEOS-FP]]
!width="200px"|[[MERRA]]
!width="200px"|[[MERRA]]
Line 91: Line 91:
|Timestamps
|Timestamps
|
|
*[[MERRA2#MERRA2_time_archiving|See this wiki page]]
*[[MERRA-2#MERRA-2_time_archiving|See this wiki page]]
|bgcolor="#CCFFFF"|
|bgcolor="#CCFFFF"|
*[[GEOS-FP#GEOS-FP_time_archiving|See this wiki page]]
*[[GEOS-FP#GEOS-FP_time_archiving|See this wiki page]]
Line 140: Line 140:
*A3 (3-hr time average)
*A3 (3-hr time average)
|
|
*Same as MERRA2
*Same as MERRA-2
*I3 (6-hr instantaneous)
*I3 (6-hr instantaneous)
|
|
*Same as MERRA2
*Same as MERRA-2
*A6 (6-hr time-averaged)
*A6 (6-hr time-averaged)


Line 202: Line 202:
*[[List_of_MERRA_met_fields#SNOMAS|Missing coverage at poles is now corrected, as per MERRA]]
*[[List_of_MERRA_met_fields#SNOMAS|Missing coverage at poles is now corrected, as per MERRA]]
|
|
*Same as MERRA2
*Same as MERRA-2
*Same as MERRA2
*Same as MERRA-2
*Same as MERRA2
*Same as MERRA-2
|
|
*SNOMAS [m]
*SNOMAS [m]
Line 819: Line 819:
=== Initial source code modifications for GEOS-FP ===
=== 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:green">'''''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>


#Modify the [[#Headers directory|Headers]], [[#GeosUtil directory|GeosUtil]], and [[#GeosCore directory|GeosCore]] directories for GEOS-FP
#Modify the [[#Headers directory|Headers]], [[#GeosUtil directory|GeosUtil]], and [[#GeosCore directory|GeosCore]] directories for GEOS-FP
Line 830: Line 830:
=== Bug fix for declaration of GEOS-5.7.2 PFICU, PFLCU, PFILSAN, PFLLSAN fields ===
=== 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.'''''
<span style="color:green">'''''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.'''''</span>


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.
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.
Line 877: Line 877:
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.   
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>:
We have added the following code to routine <tt>Geos57_Read_I3_1</tt> in <tt>GeosCore/geosfp_read_mod.F90</tt>:


       ! For now, copy State_Met%TMPU1 to State_Met%T.  At the next met field  
       ! For now, copy State_Met%TMPU1 to State_Met%T.  At the next met field  
Line 890: Line 890:
=== Modifications to reduce the number of times netCDF files are opened ===
=== Modifications to reduce the number of times netCDF files are opened ===


<span style="color:red">'''''NOTE: The following only applies to simulations done with GEOS-Chem "Classic".  The HPC-enabled version of GEOS-Chem (akak "GEOS-Chem HP" uses the ESMF and MAPL libraries for file I/O.'''''</span>
<span style="color:green">'''''This update was validated in the 1-month benchmark simulation [[GEOS-Chem v11-01 benchmark history#v11-01e|v11-01e]] (approved 04 Jan 2016).'''''</span>
 
<span style="color:green">'''''NOTE: The following only applies to simulations done with GEOS-Chem "Classic".  The HPC-enabled version of GEOS-Chem (aka "GEOS-Chem HP" uses the ESMF and MAPL libraries for file I/O.'''''</span>


In [[GEOS-Chem v11-01#v11-01e|GEOS-Chem v11-01e]], we have taken steps to reduce the number of times each GEOS-FP or MERRA-2 netCDF file is opened.  This should reduce  
In [[GEOS-Chem v11-01#v11-01e|GEOS-Chem v11-01e]], we have taken steps to reduce the number of times each GEOS-FP or MERRA-2 netCDF file is opened.  This should reduce  


:1.  We added several new global module variables for the netCDF file ID's to the top of <tt>GeosCore/geosfp_read_mod.F90 and <tt>GeosCore/merra2_read_mod.F90</tt>:
:1.  We added several new global module variables for the netCDF file ID's to the top of <tt>GeosCore/geosfp_read_mod.F90</tt> and <tt>GeosCore/merra2_read_mod.F90</tt>:
   
   
       ! netCDF file ID's
       ! netCDF file ID's
Line 915: Line 917:
         . . .
         . . .
    
    
         <span style="color:green">'''! NOTE: Moved this code up front'''</span>
         <span style="color:green">'''NOTE: Moved this code up front'''</span>
         ! Find the proper time-slice to read from disk
         ! Find the proper time-slice to read from disk
         time_index = ( HHMMSS / 10000 ) + 1
         time_index = ( HHMMSS / 10000 ) + 1
Line 928: Line 930:
         . . .         
         . . .         
   
   
         <span style="color:green">'''!NOTE: Put this code in an IF block:'''</span>
         <span style="color:green">'''NOTE: Put this code in an IF block:'''</span>
         IF ( time_index == 1 .or. first ) THEN  
         IF ( time_index == 1 .or. first ) THEN  
           . . .  
           . . .  

Latest revision as of 14:15, 15 May 2017

NOTE: GEOS-FP is the current NASA/GMAO operational met data product. It is produced with a native resolution of 0.25° (lon) x 0.3125° (lat) x 72 hybrid vertical layers. GEOS-FP replaced the older GEOS-5.2.0 operational data product in June 2013.

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.


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

Overview

The 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 and MERRA-2 met data products.. Therefore, within GEOS-Chem we can (for the most part) treat GEOS-FP in the same way as we do for the MERRA and MERRA-2.

The table below compares many features of GEOS-FP with other met field 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
  • Same as GEOS-FP
  • 72 hybrid levels
  • Same as GEOS-FP
  • Same as GEOS-FP
Time-invariant fields
  • Same as GEOS-FP
  • FRLAKE
  • FRLAND
  • FRLANDIC(E)
  • FROCEAN
  • PHIS
  • Same as GEOS-FP
  • Same as GEOS-FP
Time archiving: surface fields
  • Same as GEOS-FP
  • A1 (1-hr time averaged)
  • Same as GEOS-FP
  • A3 (6-hr time average)
Time archiving: 3D fields
  • Same as GEOS-FP
  • Same as GEOS-FP
  • A3 (3-hr time averaged)
  • I3 (3-hr instantaneous)
  • A3 (3-hr time average)
  • I6 (6-hour instantaneous)
  • A6 (6-hr time average) and
  • I6 (6-hr instantaneous)
Timestamps
Precipitation fields
  • Same as GEOS-FP
  • DQRCU, DQRLSAN,
  • PFICU, PFILSAN,
  • PFLCU, PFLLSAN,
  • REEVAPCN, REEVAPLSAN
  • Same as GEOS-FP
  • DQIDTMST
  • DQLDTMST
  • DQVDTMST
  • MOISTQ = DQIDTMST + DQLDTMST + DQVDTMST
Temperature
  • Same as GEOS-FP
  • Same as GEOS-FP
  • T [K]
  • I3 (3-hr instantaneous)
  • Same as GEOS-FP
  • A3 (6-hr time average)
  • Same as GEOS-FP
  • A6 (6-hr time average)
Relative humidity
  • Same as GEOS-FP
  • Same as GEOS-FP
  • RH [1]
  • A3 (3-hr time average)
  • Same as MERRA-2
  • I3 (6-hr instantaneous)
  • Same as MERRA-2
  • A6 (6-hr time-averaged)
Specific humidity
  • Same as GEOS-FP
  • Same as GEOS-FP
  • QV [kg kg-1]
  • I3 (3-hr instantaneous)
  • Same as GEOS-FP
  • A3 (3-hr time average)
  • Same as GEOS-FP
  • A6 (6-hr time-averaged)
Vertical pressure velocity
  • Same as GEOS-FP
  • Same as GEOS_FP
  • OMEGA [Pa s-1]
  • A3 (3-hr time average)
  • Same as GEOS-FP
  • I6 (6-hr instantaneous)
  • Same as GEOS-FP
  • A6 (6-hr time-averaged)
Ertel potential vorticity
  • Same as GEOS-FP
  • Same as GEOS-FP
  • PV [K m2 kg-1 s-1]
  • A1 (1-hr time average)
  • Same as GEOS-FP
  • I6 (6-hr instantaneous)
  • TROPP (hPa)
  • A6 (3-hr time-average)
Snow mass
  • Same as GEOS-FP
  • Same as GEOS-FP
  • Same as GEOS-FP
  • Same as MERRA-2
  • Same as MERRA-2
  • Same as MERRA-2
  • SNOMAS [m]
  • A3 (3-hr time average)
Sea level pressure
  • SLP [Pa]
  • Same as GEOS-FP)
  • Converted to hPa when read from disk
  • SLP [hPa]
  • A1 (1-hr time average)
  • Same as GEOS-FP
  • Same as GEOS-FP
  • Same as GEOS-FP
  • I6 (3-hr instantaneous)


Surface pressure
  • PS [Pa]
  • Same as GEOS-FP
  • PS [hPa]
  • I3 (3-hr instantaneous)
  • Same as GEOS-FP
  • I6 (6-hr instantaneous)
  • Same as GEOS-FP
  • I6 (3-hr instantaneous)
Tropopause pressure
  • TROPPT [Pa]
  • Same as GEOS-FP
  • TROPPT [hPa]
  • A1 (1-hr time average)
  • Same as GEOS-FP
  • Same as GEOS-FP
  • TROPP [hPa]
  • A3 (3-hr time average)
GEOS-Chem convection routine
  • Same as GEOS-FP
  • DO_MERRA_CONVECTION
    (in convection_mod.F)
  • Same as GEOS-FP
  • NFCLDMX
    (in convection_mod.F)
GEOS-Chem wet deposition routine
  • Same as GEOS-FP
  • WETDEP_MERRA
    (wetscav_mod.F)
  • Same as GEOS-FP
  • WETDEP
    (wetscav_mod.F)
GEOS-Chem transport routine
  • Same as GEOS-FP
  • TPCORE_FVDAS
    (tpcore_fvdas_mod.F90)
  • Same as GEOS-FP
  • Same as GEOS-FP
File format read by GEOS-Chem
  • netCDF-4
  • netCDF-3
  • binary
  • binary

--Bob Y. (talk) 17:48, 17 August 2015 (UTC)

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 )

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
  • Starting with GEOS-Chem v9-02o, we now use Makefile variables to set the various C-preprocessor switches. In particular:
    • MET=___ selects the met field type( gcap, geos4, geos5, geosfp, merra)
    • GRID=___ selects the horizontal grid (4x5, 2x25, 05x0666, 025x03125)
    • NEST=___ specifies the nested-grid (CH, EU, NA, SE)

--Bob Y. 13:39, 7 November 2013 (EST)

Headers directory

The following modifications for GEOS-FP 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)

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-FP data archive for GEOS-Chem. We have used the same algorithm we developed for MERRA met fields to do the binning.

--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-5.2.0. 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 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.

--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 DST_MBL (in dust_dead_mod.f), 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

--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 lightning_NOx_201311/ subdirectory.

--Bob Y. 14:45, 7 November 2013 (EST)

Wet deposition and scavenging

Helen Amos, Bess Corbitt, and Qiaoqiao Wang had implemented an 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.

--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 v9-01-03g and approved on 27 Feb 2012.

  1. Modify the Headers, GeosUtil, and GeosCore directories for GEOS-FP
  2. Update the GeosApm and GeosTomas directories, primarily to synchronize files with GeosCore
  3. Add NcdfUtil directory
  4. Resolve several issues, including: Fractional sea ice, SNOMAS, Wet deposition and scavenging

--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 v9-02g and approved on 24 Mar 2013.

In module file GeosCore/gigc_state_met_mod.F90, 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 LLPAR+1 levels. But in MERRA, these fields are placed on level centers and need to be allocated with LLPAR levels.

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

    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: LM is set to LLPAR, and thus LM+1 = LLPAR+1.

--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 met fields, temperature is an I3 (i.e. 3-hr instantaneous) met field. We need to read temperature at times t and t+3hrs, and then interpolate linearly to the proper time.

At time t=0 of a GEOS-FP simulation, the initial temperature is read from netCDF files into State_Met%TMPU1. However, we must also save this into State_Met%T. Otherwise, temperature will be not initialized properly until the first call to INTERP. This can cause a floating-point error further upstream.

We have added the following code to routine Geos57_Read_I3_1 in GeosCore/geosfp_read_mod.F90: 

     ! 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 GEOS-Chem unit tester when compiling with option FPE=yes.

--Bob Y. 13:13, 12 September 2013 (EDT)

Modifications to reduce the number of times netCDF files are opened

This update was validated in the 1-month benchmark simulation v11-01e (approved 04 Jan 2016).

NOTE: The following only applies to simulations done with GEOS-Chem "Classic". The HPC-enabled version of GEOS-Chem (aka "GEOS-Chem HP" uses the ESMF and MAPL libraries for file I/O.

In GEOS-Chem v11-01e, we have taken steps to reduce the number of times each GEOS-FP or MERRA-2 netCDF file is opened. This should reduce

1. We added several new global module variables for the netCDF file ID's to the top of GeosCore/geosfp_read_mod.F90 and GeosCore/merra2_read_mod.F90:
     ! netCDF file ID's
     INTEGER :: fA1     = -1
     INTEGER :: fA3cld  = -1
     INTEGER :: fA3dyn  = -1
     INTEGER :: fA3mstC = -1
     INTEGER :: fA3mstE = -1
     INTEGER :: fI3_1   = -1
     INTEGER :: fI3_2   = -1
2 In both GeosCore/geosfp_read_mod.F90 and GeosCore/merra2_read_mod.F90, reorganized routines that read netCDF data files from disk according to the following template:
     SUBROUTINE GeosFp_Read_A1( YYYYMMDD, HHMMSS, Input_Opt, State_Met )
       . . . 

       NOTE: added this line:
       LOGICAL, SAVE      :: first    = .TRUE.  ! First time reading data?
                
       . . .
 
       NOTE: Moved this code up front
       ! Find the proper time-slice to read from disk
       time_index = ( HHMMSS / 10000 ) + 1

       ! Stop w/ error if the time index is invalid
       IF ( time_index < 1 .or. time_index > 24 ) THEN
          WRITE( 6, 100 ) time_index
    100   FORMAT( 'Time_index value ', i5, ' must be in the range 1 to 24!' )
          CALL Error_Stop( errMsg, caller )
       ENDIF
 
       . . .        

       NOTE: Put this code in an IF block:
       IF ( time_index == 1 .or. first ) THEN 
          . . . 
   
          ! Open netCDF file
          CALL NcOp_Rd( fA1, TRIM( nc_file ) )
       
          ! Read the dimensions from the netCDF file
          CALL NcGet_DimLen( fA1, 'lon',   X )
          CALL NcGet_DimLen( fA1, 'lat',   Y )
          CALL NcGet_DimLen( fA1, 'time',  T )

          ! Make sure the dimensions of the file are valid
          CALL Check_Dimensions( lon=X,            lat=Y,        time=T,  &
                                 time_expected=24, caller=caller         )

          NOTE: added this line:
          ! Reset first-time flag
          first = .FALSE.
       ENDIF

       . . .

       NOTE: Use one of the module variables for the netCDF file ID.
       ! Read ALBEDO
       v_name = "ALBEDO"
       CALL NcRd( Q, fA1, TRIM(v_name), st3d, ct3d )
       State_Met%ALBD = Q

       . . . read other met fields from disk . . .

       NOTE: Close the file on the last timestep
       ! If it's the last time slice, then close the netCDF file
       ! and set the file ID to -1 to indicate that it's closed.
       IF ( time_index == 24 ) THEN
          CALL NcCl( fA1 )
          fA1 = -1
       ENDIF
and we do the same for all of the other file-reading routines in the both modules.
3. We added subroutine Cleanup_GeosFp_Read to the end of GeosCore/geosfp_read_mod.F90. This subroutine will be called from the CLEANUP routine at the end of a simulation to close any netCDF files that may still be open. This can happen if a simulation ends in the middle of a day.
     SUBROUTINE Cleanup_GeosFp_Read()
       . . .
       !=======================================================================
       ! Close any netCDF file ID's that are still open
       !=======================================================================
       IF ( fA1 > 0 ) THEN
          CALL NcCl( fA1 )
          WRITE( 6, 100 ) 'A1    '
       ENDIF

       IF ( fA3cld > 0 ) THEN
          CALL NcCl( fA3cld  )
          WRITE( 6, 100 ) 'A3cld '
       ENDIF

       IF ( fA3dyn > 0 ) THEN
          CALL NcCl( fA3dyn  )
          WRITE( 6, 100 ) 'A3dyn '
       ENDIF
 
       IF ( fA3mstC > 0 ) THEN
          CALL NcCl( fA3mstC )
          WRITE( 6, 100 ) 'A3mstC'
       ENDIF
   
       IF ( fA3mstE > 0 ) THEN
          CALL NcCl( fA3mstE )
          WRITE( 6, 100 ) 'A3mstE'
       ENDIF

       IF ( fI3_1 > 0 ) THEN
          CALL NcCl( fI3_1   )
          WRITE( 6, 100 ) 'I3_1  '
       ENDIF

       IF ( fI3_2 > 0 ) THEN
          CALL NcCl( fI3_2   )
          WRITE( 6, 100 ) 'I3_2  '
       ENDIF

       ! Format strings
   100 FORMAT( '     - Closing the GEOS-FP ', a6, ' file at end of simulation' )

     END SUBROUTINE Cleanup_GeosFp_Read
We also added the corresponding subroutine Cleanup_Merra2_Read to GeosCore/merra2_read_mod.F90.
4. We modified GeosCore/cleanup.F to call the Cleanup_GeosFp_Read and Cleanup_Merra2_Read routines:
     USE GEOSFP_READ_MOD,         ONLY : CLEANUP_GEOSFP_READ
     USE MERRA2_READ_MOD,         ONLY : CLEANUP_MERRA2_READ
     . . .
          ! Close GEOS-FP or MERRA2 met field files that may still be open
   #if defined( GEOS_FP )
         CALL Cleanup_GeosFp_Read()
   #elif defined( MERRA2 )
         CALL Cleanup_Merra2_Read()
   #endif
5. We added geosfp_read_mod.o and merra2_read_mod.o to the dependencies listing in GeosCore/Makefile:
   cleanup.o                   : cleanup.F                                      \
                                 aerosol_mod.o                                  \
                                 . . .
                                 geosfp_read_mod.o       merra2_read_mod.o      \
                                 . . .

--Bob Yantosca (talk) 22:41, 4 December 2015 (UTC)

Retrieved from "https://wiki.seas.harvard.edu/geos-chem/index.php?title=GEOS-FP_implementation_details&oldid=32654"