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Government Agency Original Software Designation: GSC-15354-1 ! Government Agency Original Software Title: GEOS-5 GCM Modeling Software ! User Registration Requested. Please Visit http://opensource.gsfc.nasa.gov ! Government Agency Point of Contact for Original Software: ! Dale Hithon, SRA Assistant, (301) 286-2691 ! ! +-======-+ How to Create GEOS-5 GOCART/StratChem Restarts Arlindo da Silva NASA/GSFC, GMAO, Code 610.1 Arlindo.daSilva@nasa.gov Last Update: Tue Jan 27 12:18:57 EST 2009 Contents -------- I. Manipulating GEOS-5 Chem Restarts with lats4d EXAMPLE 1: Create a ctl for an existing GOCART restart EXAMPLE 2: Create a subset of a GOCART restart EXAMPLE 3: Create a GOCART restart with a different horizontal resolution EXAMPLE 4: Create a GOCART restart with additional variables EXAMPLE 5: Dump statistics from a binary restart file EXAMPLE 6: Change vertical resolution II. Generating GEOS-5 Restarts from GEOS-4 Chem Bundle files I. Manipulating GEOS-5 Chem Restarts with lats4d --------------------------------------------- While the binary GEOS-5 restarts do not come with any describing metadata, a GrADS control file (ctl) can be created using the ctl_crst.x utility: ctl_crst.x Chem_Registry.rc [rs_filename [res] ] where *Chem_Registry.rc* is the Chem Registry used in the run that produced the binary restart file *rs_fielname*. The optional parameter *res* specify the the resolution of the run, e.g., b72, c72, ..., where "72" is the number opf levels the the first letter is the horizontal resolution: b - 2x2.5 deg c - 1x1.25 deg d - 0.5 x 2/3 deg e - 0.25 x 1/3 deg etc. The default is res = 'd72'. When the binary restart file name is omitted, only the lats4d sample line is written (see below). If you are not familiar with Lats4D, before proceeding you may want to read this: http://opengrads.org/wiki/index.php?title=Lats4D EXAMPLE 1: Create a ctl for an existing GOCART restart ...................................................... % set g5home = /discover/nobackup/dao_ops/intermediate/d520_fp % ctl_crst.x $g5home/run/Chem_Registry.rc \ $g5home/recycle/d520_fp.gocart_internal_rst.20080814_03z.bin \ > old.ctl Here are the (abbreviated) contents of old.ctl: --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- DSET /discover/nobackup/dao_ops/intermediate/d520_fp/recycle/d520_fp.gocart_internal_rst.20080814_03z.bin TITLE Chem Restart File UNDEF 1.0E20 XDEF 540 LINEAR -180 0.666667 YDEF 361 LINEAR -90 0.500000 ZDEF 72 LINEAR 1 1 TDEF 1 LINEAR 05feb1960 6hr VARS 32 CO 0 72 Global carbon monoxide ... OCphilicbbnb 0 72 Hydrophilic Organic Carbon (Non-Boreal Biomass Burning, Particulate Matter) ENDVARS --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- You can open this file directly in GrADS and verify that it can correctly read the restart. When the binary restart file name is omitted, a sample *lats4d* command line is written. This is useful for creating variable subsets with lats4d; see the next example. EXAMPLE 2: Create a subset of a GOCART restart .............................................. Suppose you want to create a shorter GOCART restart with fewer variables from and existing restart. In this case run *ctl_crst.x* using the *Chem_Registry.rc* that contains the desired subset list of variables, e.g., % ctl_crst ./Chem_Registry.rc which produces lats4d.sh -i old.ctl -o new -format sequential -v -vars co co2 du001 du002 du003 du004 du005 ss001 ss002 ss003 ss004 ss005 dms so2 so4 msa bcphobic bcphilic ocphobic ocphilic If *old.ctl* was produced as in EXAMPLE 1 then you just run the command above (the output file name was changed from new to new2): % lats4d.sh -i old.ctl -o new2 -format sequential -v\ -vars CO CO2 \ du001 du002 du003 du004 du005 \ ss001 ss002 ss003 ss004 ss005 \ dms so2 so4 msa \ bcphobic bcphilic ocphobic ocphilic which will produce the new (Fortran sequential) binary file *new2.bin*. You can examine the contents of this file by first creating a ctl for it: % ctl_crst.x ./Chem_Registry.rc new2.bin > new2.ctl EXAMPLE 3: Create a GOCART restart with a different horizontal resolution ......................................................................... Suppose you want to create a shorter GOCART restart with fewer variables from and existing restart and also with a different horizontal resolution. In this case run *ctl_crst.x* using the *Chem_Registry.rc* that contains the desired list of variables, e.g., % ctl_crst ./Chem_Registry.rc which produces lats4d.sh -i old.ctl -o new -format sequential -v -vars CO CO2 du001 du002 du003 du004 du005 ss001 ss002 ss003 ss004 ss005 DMS SO2 SO4 MSA BCphobic BCphilic OCphobic OCphilic You can use the following Lats4D options to produce the output file at a different resolution: -geos0.25 1/4 by 1/3 degrees -geos0.5 1/2 by 2/3 degrees -geos1x125 1 by 1 1/4 degrees -geos1x1 1 x 1 degree (GEOS-3) -geos4x5 4 x 5 degrees -geos2x25 2 x 2 1/2 degrees All the GEOS grids are global, [90S,90N], [180W,180E). For each of these options there are variants "a" for box- averaging and "s" for bessel interpolation. The default is linear interpolation. For example, use -geos4x5 for linear interpolation, -geos4x5a for box-averaging and -geos4x5s for bessel interpolation. If *old.ctl* was produced as in EXAMPLE 1 then you just add the interpolation option, e.g., % lats4d.sh -i old.ctl -o new3 -format sequential -v\ -geos2x25 -vars CO CO2 \ du001 du002 du003 du004 du005 \ ss001 ss002 ss003 ss004 ss005 \ DMS SO2 SO4 MSA \ BCphobic BCphilic OCphobic OCphilic which will produce the new (Fortran sequential) binary file *new3.bin*. You can examine the contents of this file by first creating a ctl for it: % ctl_crst.x ./Chem_Registry.rc new3.bin > new3.ctl IMPORTANT: It has been reported that lats4d may run out of memory and give segmentation fault in re() when regriding to 1/4 x 1/3 degree resolutions. One solution has been to use lats4d with a x86_64 build of GrADS and have plenty of memory. EXAMPLE 4: Create a GOCART restart with additional variables ............................................................ If you have a modified *Chem_Registry.rc* file which puts additional variables into the GOCART restart, then you may want to convert an existing GOCART into one which is consistent with the new *Chem_Registry.rc* by adding zeros as placeholders for the new variables. Let's start with the new2.bin file from Example 2 above. Suppose the modified *Chem_Registry.rc* adds five variables, COBBAE, COBBNA, COBBLA, COBBAF, COBBGL, after the CO variable, and two new variables, CFC12S and CFC12T, after the MSA variable. Use the following procedures to convert new2.bin. First create three subsets of new2.bin based on the locations for the new variables. % lats4d.sh -i new2.ctl -vars co -o subfile1 -format sequential % lats4d.sh -i new2.ctl -vars co2 du001 du002 du003 du004 du005 \ ss001 ss002 ss003 ss004 ss005 dms so2 so4 msa \ -o subfile2 -format sequential % lats4d.sh -i new2.ctl -vars bcphobic bcphilic ocphobic ocphilic \ -o subfile3 -format sequential The outputs from these commands are subfile1.bin, subfile2.bin, and subfile3.bin. Now create a record of zeros to use as a placeholder for the new variables. Note that it is not important which old variable is used in this command since all the values are multiplied by zero. % lats4d.sh -i new2.ctl -vars co -o zeros -func '0*@' -format sequential The output from this command is zeros.bin. Finally, use the *cat* command to create the new GOCART: % cat zeros.bin zeros.bin > zeros2.bin % cat zeros.bin zeros.bin zeros.bin zeros.bin zeros.bin > zeros5.bin % cat subfile1.bin zeros5.bin subfile2.bin zeros2.bin subfile3.bin > new4.bin You can create a ctl file for new4.bin using the modified *Chem_Registry.rc* mentioned at the beginning of this example: % ctl_crst.x ./Chem_Registry.rc new4.bin > new4.ctl To check that the old variables from new2.bin were transferred correctly, it is a good idea to dump and compare the statistics from both new2.bin and new4.bin (see EXAMPLE 5). EXAMPLE 5: Dump statistics from a binary restart file ..................................................... Use lats4d.sh and the ctl file (e.g. new.ctl) to dump statistics from a binary file. % lats4d.sh -i new.ctl -format stats EXAMPLE 6: Change vertical resolution ..................................... Lats4D cannot really change the vertical resolution. Your best option is to use the GFIO_remap.x utility in this case. This utility however, can only handle COARDS compliant files in either NetCDF-3, HDF-4 or even NetCDF-4/HDF-5 (provided it has been compiled with the correct library.) The first step is to use Lats4D to create a COARDS compliante file. For the case in the previous example, simply omit the "-format sequential" option: % lats4d.sh -i old.ctl -o new72 -v \ -geos2x25 -vars CO CO2 \ du001 du002 du003 du004 du005 \ ss001 ss002 ss003 ss004 ss005 \ DMS SO2 SO4 MSA \ BCphobic BCphilic OCphobic OCphilic This will create file "new72.nc". Next, use GFIO_remap.x to change the number of vertical layers: % setenv G5BIN $HOME/GEOSgcm/Linux/bin % $G5BIN/GFIO_remap.x -nlev 91 -o new91.nc new72.nc Finally, use lats4d again to convert this file to binary % lats4d.sh -i new91.nc -o new91 -format sequential -v \ -geos2x25 -vars CO CO2 \ du001 du002 du003 du004 du005 \ ss001 ss002 ss003 ss004 ss005 \ DMS SO2 SO4 MSA \ BCphobic BCphilic OCphobic OCphilic You could also have used GFIO_remap.x for the horizontal interpolation; type GFIO_remap.x without arguments for a list of command line options. II. Generating GEOS-5 Restarts from GEOS-4 Chem Bundles --------------------------------------------------- These notes explain how to produce GOCART/StratChem Internal Restart files for GEOS-5, based on GEOS Chem Bundle files (either c_rst or chem.eta files). 1) Required utilities: - GFIO_remap.x (provided in GMAO_Shared/GMAO_hermes) Purpose: used to convert the GEOS-4 fields to the necessaty GEOS-5 vertical/horizontal resolution - Chem_BundleToG5rs.x (provided in GMAO_Shared/Chem_Base) Purpose: used to convert the GEOS-4 Chem Bundle (a HDF-4 file) to the GEOS-5 (GrADS) binary format. At this point the Chem Bundle should be exactly at the same resolution as required by GEOS-5 (including 72 levels), although the input file could have more variables than necesary. The longitudinal swap (from [0,360) to [-180,180) is performed by this utility. 2) Required "resource" files: Prepare the resource file "Chem_Registry.rc" in a way consistent with the way it will be used in GEOS-5. Pay particular attention to the number of bins (nbins_?? resources), as GEOS-4 may have been run with 8 CO tracers but you only need 1 global CO tracer, for example. You should activate only those variables to be included in the GEOS-5 binary restart file (excluding "pchem"/GMI which do not have GEOS-4 heritage.) Notice that, - if producing "gocart_internal_restart", set to "yes" all tracers from doing_CO through doing_OC, inclusive. All other tracers should be set to "no". - if producing "stratchem_internal_restart", set to "yes" tracers doing_SC and doing_XX, all others to "no". 3) Notes about dates The GEOS-5 binary restarts to not include dates, therefore you are free to use restarts from any data you choose. It is recommended that you at least match the day/month/time as to provide restarts that are climatologically realistic. 4) Which GEOS-4 experiments to use Because usually GEOS-5 will run with CO2, you need to use runs that had CO, CO2 and aerosols. For example, the First Look systems used for CRAVE; the AVE_Houston/INTEX-B did not include CO2. As of this writing, the CRAVE files can be found at NCCS in the following directory: /output/dao_ops/GEOS-4_CRAVE/a_flk_04C/rs Spin-up runs can be found here: /output/dasilva/a_flk_04C/rs Always take a look in the contents of the file to make sure the fields are spun up. For example, in GrADS do this ga-> d ave((du001+du002+du003+du004+du005)*delp,z=1,z=55) to make sure you have a well established dust plume. 3) Example 1: creating a 2x2.5 GEOS-5 "gocart_internal_restart" from a GEOS-4 chem restart file for 21 December 1992. a) Locate a GEOS-4 chem restart for this date. In this case we have a_flk_04C.rst.chem.20051221_18z.bin available from /output/dasilva/a_flk_04C/rs/Y2005/M12 (don't be fooled by the .bin extension - this is a HDF-4 file!) b) Use the "SAMPLE FILE 1" below for Chem_Registry.rc (or modify current Chem_Registry.rc file if there were structural changes. c) Copy files to a scratch location: % setenv CRAVE /output/dasilva/a_flk_04C % cp $CRAVE/rs/Y2005/M12/a_flk_04C.rst.chem.20051221_18z.bin $TMPDIR % (place Chem_Registry.rc in $TMPDIR as well) d) Remap to 2x2.5 horizontal/72 layer resolution in 2 steps: % setenv G5BIN $HOME/GEOSgcm/Linux/bin % $G5BIN/GFIO_remap.x -res b -o b55.hdf a_flk_04C.rst.chem.20051221_18z.bin % $G5BIN/GFIO_remap.x -nlev 72 -o b72.hdf b55.hdf Hint: Typer GFIO_remap.x without arguments for a list of command line options. e) Convert to remaped GEOS-4 file to GEOS-5 binary format: % $G5BIN/Chem_BundleToG5rs.x b72.hdf gocart_internal_restart 20051221 180000 The last 2 parameters are the date/time of the INPUT GEOS-4 file; the GEOS-5 output file will have no date inside. That is it! The gocart_internal_restart is ready for use in a GEOS-5 2x2.5 run. 3) EXAMPLE 2: creating a 0.5x2/3 degree GEOS-5 "gocart_internal_restart" from a GEOS-4 chem restart file for 21 December 1992. a) through c) same as in EXAMPLE 1 d) Remap to 0.5x2/3 horizontal/72 layer resolution in 2 steps: % $G5BIN/GFIO_remap.x -res d -o d55.hdf a_flk_04C.rst.chem.20051221_18z.bin % $G5BIN/GFIO_remap.x -nlev 72 -o d72.hdf d55.hdf e) Convert to remaped GEOS-4 file to GEOS-5 binary format: % $G5BIN/Chem_BundleToG5rs.x d72.hdf gocart_internal_restart 20051221 180000 ............................................................................ ------------------------------- SAMPLE FILE 1: Chem_Registry.rc ------------------------------- --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- # # Chemistry Registry Resource File # # !REVISION HISTORY: # # 27May2005 da Silva Added variable tables for SU/BC/OC. # 19dec2005 da Silva Changed volume mixing ratio units to mol/mol # 10Feb2006 Hayashi Added analysis update frequency # 27Jul2006 da Silva No more analysis frequencies; added GMI/PChem (GEOS-5) # #----------------------------------------------------------------------- # Whether to include the constituent in the simulation # ---------------------------------------------------- doing_H2O: no # water vapor (must always ON for fvGCM) doing_O3: no # ozone (must be always ON for fvGCM in DAS mode) doing_CO: yes # carbon monoxide doing_CO2: yes # carbon dioxide doing_DU: yes # mineral dust doing_SS: yes # sea salt doing_SU: yes # sulfates doing_BC: yes # black carbon doing_OC: yes # organic carbon doing_SC: no # stratospheric chemistry doing_AC: no # auto chem doing_XX: no # generic tracer doing_PC: no # parameterized chemistry (GEOS-5) doing_GMI: no # GMI chemistry (GEOS-5) # You can select the number of bins (e.g., particle size) # for each of the constituents. Note nbins>1 may not be # supported by some constituents # ---------------------------------------------------- nbins_H2O: 1 # water vapor nbins_O3: 3 # ozone nbins_CO: 1 # carbon monoxide nbins_CO2: 1 # carbon dioxide nbins_DU: 5 # mineral dust nbins_SS: 5 # sea salt nbins_SU: 4 # sulfates nbins_BC: 2 # black carbon nbins_OC: 2 # organic carbon nbins_SC: 34 # stratospheric chemistry nbins_AC: 35 # auto chem nbins_XX: 18 # generic tracer nbins_PC: 1 # parameterized chemistry (GEOS-5) nbins_GMI: 1 # GMI chemistry (GEOS-5) # Units for each constituent # -------------------------- units_H2O: kg/kg # water vapor units_O3: kg/kg # ozone units_CO: kg/kg # carbon monoxide units_CO2: kg/kg # carbon dioxide units_DU: kg/kg # mineral dust units_SS: kg/kg # sea salt units_SU: kg/kg # sulfates units_BC: kg/kg # black carbon units_OC: kg/kg # organic carbon units_SC: kg/kg # stratospheric chemistry units_AC: kg/kg # auto chem units_XX: kg/kg # generic tracer units_PC: kg/kg # parameterized chemistry (GEOS-5) units_GMI: kg/kg # GMI chemistry (GEOS-5) # Variable names to override defaults. Optional. Name and Units must # be 1 token. Long names can be more than one token. # -------------------------------------------------------------------- variable_table_O3:: # Name Units Long Name # ----- ------ -------------------------------- O3PARAM mol/mol Parameterized ozone OXSTRAT mol/mol Stratospheric odd oxygen OXTROP mol/mol Tropospheric ozone :: variable_table_CO:: # Name Units Long Name # ----- ------ -------------------------------- CO mol/mol Global carbon monoxide CONOAMAN mol/mol North American anthropogenic CO COCEAMAN mol/mol Central American anthropogenic CO COWHBB mol/mol Western Hemisphere biomass burning CO COASIAAN mol/mol Asian anthropogenic CO COASNBB mol/mol Northern Asia biomass burning CO COASSBB mol/mol Southern Asia biomass burning CO COFDAN mol/mol Mexico City anthropogenic CO :: variable_table_CO2:: # Name Units Long Name # ----- ------ -------------------------------- CO2 mol/mol Carbon Dioxide CO2nam mol/mol North American Carbon Dioxide CO2sam mol/mol South American Carbon Dioxide CO2afr mol/mol African :: variable_table_SU:: # Name Units Long Name # ----- ------ -------------------------------- DMS kg/kg Dimethylsulphide SO2 kg/kg Sulphur dioxide SO4 kg/kg Sulphate aerosol MSA kg/kg Methanesulphonic acid :: variable_table_BC:: # Name Units Long Name # ----- ------ -------------------------------- BCphobic kg/kg Hydrophobic Black Carbon BCphilic kg/kg Hydrophilic Black Carbon :: variable_table_OC:: # Name Units Long Name # ----- ------ -------------------------------- OCphobic kg/kg Hydrophobic Organic Carbon (Particulate Matter) OCphilic kg/kg Hydrophilic Organic Carbon (Particulate Matter) :: variable_table_SC:: # Name Units Long Name # ----- ------ -------------------------------- OXSTRAT mol/mol Stratospheric odd oxygen NOX mol/mol Odd nitrogen HNO3 mol/mol Nitric acid N2O5 mol/mol Dinitrogen pentoxide HO2NO2 mol/mol Peroxynitric acid CLONO2 mol/mol Chlorine nitrate CLX mol/mol Odd chlorine HCL mol/mol Hydrochloric acid HOCL mol/mol Hypochlorous acid H2O2 mol/mol Hydrogen peroxide BRX mol/mol Odd bromine N2O mol/mol Nitrous oxide CL2 mol/mol Molecular chlorine OCLO mol/mol Chlorine dioxide BRCL mol/mol Bromine chloride HBR mol/mol Hydrogen bromide BRONO2 mol/mol Bromine nitrate CH4 mol/mol Methane HOBR mol/mol Hypobromous acid CH3OOH mol/mol Methyl hydroperoxide CO mol/mol Carbon monoxide HNO3COND mol/mol Condensed nitric acid H2OCOND mol/mol Condensed water vapor in chemistry F11 mol/mol CFC-11 (CCl3F) F12 mol/mol CFC-12 (CCl2F2) F113 mol/mol CFC-113 (CCl2FCClF2) HCFC mol/mol HCFC CCL4 mol/mol Carbon tetrachloride CH3CCL3 mol/mol Methyl chloroform CH3CL mol/mol Methyl chloride CH3BR mol/mol Methyl bromide H1301 mol/mol Halon 1301 (CBrF3) H12_24 mol/mol Halon 12_24 Q4AGE mol/mol SSG for computing age-of-air :: variable_table_AC:: # Name Units Long Name # ----- ------ -------------------------------- OXSTRAT mol/mol Stratospheric odd oxygen NOX mol/mol Odd nitrogen HNO3 mol/mol Nitric acid N2O5 mol/mol Dinitrogen pentoxide HO2NO2 mol/mol Peroxynitric acid CLONO2 mol/mol Chlorine nitrate CLX mol/mol Odd chlorine HCL mol/mol Hydrochloric acid HOCL mol/mol Hypochlorous acid H2O2 mol/mol Hydrogen peroxide BRX mol/mol Odd bromine N2O mol/mol Nitrous oxide CL2 mol/mol Molecular chlorine OCLO mol/mol Chlorine dioxide BRCL mol/mol Bromine chloride HBR mol/mol Hydrogen bromide BRONO2 mol/mol Bromine nitrate CH4 mol/mol Methane HOBR mol/mol Hypobromous acid CH3OOH mol/mol Methyl hydroperoxide CO mol/mol Carbon monoxide HNO3COND mol/mol Condensed nitric acid H2OCOND mol/mol Condensed water vapor in chemistry F11 mol/mol CFC-11 (CCl3F) F12 mol/mol CFC-12 (CCl2F2) F113 mol/mol CFC-113 (CCl2FCClF2) HCFC mol/mol HCFC CCL4 mol/mol Carbon tetrachloride CH3CCL3 mol/mol Methyl chloroform CH3CL mol/mol Methyl chloride CH3BR mol/mol Methyl bromide H1301 mol/mol Halon 1301 (CBrF3) H12_24 mol/mol Halon 12_24 :: variable_table_XX:: # Name Units Long Name # ----- ------ -------------------------------- O3CHEM mol/mol Ozone from chemistry O3P mol/mol Atomic oxygen in the ground state O1D mol/mol Atomic oxygen in the first excited state N mol/mol Atomic nitrogen NO mol/mol Nitric oxide NO2 mol/mol Nitrogen dioxide NO3 mol/mol Nitrogen trioxide HATOMIC mol/mol Atomic hydrogen OH mol/mol Hydroxyl radical HO2 mol/mol Hydroperoxyl radical CL mol/mol Atomic chlorine CLO mol/mol Chlorine monoxide BRO mol/mol Bromine monoxide BR mol/mol Atomic bromine CL2O2 mol/mol Dichlorine peroxide CH2O mol/mol Formaldehyde CH3O2 mol/mol Methyl peroxide RO3OX none Ozone-to-odd oxygen ratio :: #........................................................................ # ------------------- # Not Implemented Yet # ------------------- # Whether to advect the constituent # --------------------------------- advect_H2O: yes # water vapor advect_O3: yes # ozone advect_CO: yes # carbon monoxide advect_CO2: yes # carbon dioxide advect_DU: yes # mineral dust advect_SS: yes # sea salt advect_SU: yes # sulfates advect_BC: yes # black carbon advect_OC: yes # organic carbon advect_SC: yes # stratospheric chemistry advect_AC: yes # stratospheric chemistry advect_XX: no # generic tracer advect_PC: yes # parameterized chemistry (GEOS-5) advect_GMI: yes # GMI chemistry (GEOS-5) # Whether to diffuse the constituent # ---------------------------------- diffuse_H2O: yes # water vapor diffuse_O3: yes # ozone diffuse_XX: yes # generic tracer diffuse_CO: yes # carbon monoxide diffuse_CO2: yes # carbon dioxide diffuse_DU: yes # mineral dust diffuse_SS: yes # sea salt diffuse_SU: yes # sulfates diffuse_BC: yes # black carbon diffuse_OC: yes # organic carbon diffuse_SC: yes # stratospheric chemistry diffuse_XX: yes # generic tracer diffuse_PC: yes # parameterized chemistry (GEOS-5) diffuse_GMI: yes # GMI chemistry (GEOS-5) --- cut --- --- cut --- --- cut --- --- cut --- --- cut --- --- cut ---