
	   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 --- 
