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| | --[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 22:13, 11 August 2015 (UTC) | | --[[User:Bmy|Bob Y.]] ([[User talk:Bmy|talk]]) 22:13, 11 August 2015 (UTC) |
| − |
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| − | === NcdfUtil directory ===
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| − |
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| − | 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.
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| − |
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| − | {| border=1 cellspacing=0 cellpadding=5
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| − | |- bgcolor="#CCCCCC"
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| − | !width="175px"|File
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| − | !width="800px"|Description
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| − | |-
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| − | |Makefile
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| − | |GNU Makefile used to build the NcdfUtil code.
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| − | |-
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| − | |TestNcdfUtil.F90
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| − | |Test program to verify that the netCDF libraries were built properly. (This is executed only when you issue a <tt>make ncdfcheck</tt> command.)
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| − | |-
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| − | |m_do_err_out.F90
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| − | |Routine to print out netCDF error messages.
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| − | |-
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| − | |m_netcdf_io_checks.F90
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| − | |Routines to check whether a netCDF file contains a specified variable or dimension.
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| − | |-
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| − | |m_netcdf_io_close.F90
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| − | |Routines to close a netCDF file.
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| − | |-
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| − | |m_netcdf_io_create.F90
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| − | |Routines used to open a netCDF file for output and to synchronize a netCDF file.
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| − | |-
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| − | |m_netcdf_io_define.F90
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| − | |Routines to define netCDF variables and attributes. Use this when writing data to a netCDF file.
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| − | |-
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| − | |m_netcdf_io_get_dimlen.F90
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| − | |Routines to return dimension information from a netCDF file.
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| − | |-
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| − | |m_netcdf_io_handle_err.F90
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| − | |Routines for netCDF I/O error handling.
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| − | |-
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| − | |m_netcdf_io_open.F90
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| − | |Routines for opening a netCDF file for reading or for writing.
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| − | |-
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| − | |m_netcdf_io_read.F90
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| − | |Routines for reading variables (of INTEGER, REAL*4, REAL*8, and CHARACTER types) from a netCDF file.
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| − | |-
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| − | |m_netcdf_io_readattr.F90
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| − | |Routines for reading global and variable attributes (of INTEGER, REAL*4, REAL*8, and CHARACTER types) from a netCDF file.
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| − | |-
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| − | |m_netcdf_io_write.F90
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| − | |Routines for writing data to a netCDF file
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| − | |}
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| − |
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| − | --[[User:Bmy|Bob Y.]] 10:34, 3 February 2012 (EST)
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| | | | |
| | === NcdfUtil/perl subdirectory === | | === NcdfUtil/perl subdirectory === |
Revision as of 15:04, 12 August 2015
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 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) 21:25, 11 August 2015 (UTC)
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
|
- 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) 21:26, 11 August 2015 (UTC)
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 MERRA2_47L and MERRA2 modelnames to the #if block
In routine GET_NAME_EXT:
- Return grid name merra2 for MERRA2 fields
In routine GET_NAME_EXT_2D:
- Now use #if defined( MERRA ) || defined( MERRA2 )
In routine GET_RES_EXT:
- Return resolution string <tt>05x0625 for 0.5° x 0.625° grids
|
| pressure_mod.F
|
In routines GET_PEDGE and GET_PEDGE_FULLGRID:
- Compute PEDGE for MERRA2 in the same way as for GEOS-5, MERRA, and GEOS-FP
In routine INIT_PRESSURE:
- Initialize Ap and Bp for MERRA2 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 MERRA2 the same way as is done for MERRA and GEOS-FP
|
| transfer_mod.F
|
In several routines:
- Changed code to #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
|
--Bob Y. (talk) 21:40, 11 August 2015 (UTC)
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 ) || 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 )
|
| 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 )
|
| 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 )
|
| 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 )
|
| 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).
|
| 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
|
| 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 )
|
| 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
|
In routine GET_REGIONAL_POX:
- Now use: #if defined( GEOS_5 ) || defined( MERRA ) || defined( GEOS_FP ) || defined( MERRA2 )
|
| tpcore_bc_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. (talk) 22:13, 11 August 2015 (UTC)
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)
