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Feature/gocart userguide #1182

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Feature/gocart userguide #1182

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fe39bb0
adding GOCART inputs/outputs table in UFS user guide
lipan-NOAA Apr 15, 2022
b628977
correct grammar mistake
lipan-NOAA Apr 15, 2022
ca61292
Merge branch 'ufs-community:develop' into feature/gocart-userguide
lipan-NOAA Apr 21, 2022
98f5b03
The nems.configure for the coupled GOCART in S2SW application
lipan-NOAA Apr 21, 2022
dc1abdf
format changes for GOCART nems.configure
lipan-NOAA Apr 21, 2022
f6063ad
S2SW -> S2SAW
lipan-NOAA Apr 21, 2022
d557509
added GOCART related content to the CodeOverview.rst
lipan-NOAA Apr 26, 2022
3d458f0
change formats
lipan-NOAA Apr 26, 2022
88e090e
Merge branch 'ufs-community:develop' into feature/gocart-userguide
lipan-NOAA Apr 26, 2022
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240 changes: 218 additions & 22 deletions doc/UsersGuide/source/InputsOutputs.rst
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Expand Up @@ -738,41 +738,104 @@ GOCART
Static datasets (i.e., *fix files*)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. TODO:: GOCART information in progress
The static input files for GOCART configurations are listed and described in :numref:`Table %s <GOCART_ControlFiles>`.

The static input files for global configurations are listed and described in :numref:`Table %s <GOCART_FixFiles>`.
.. _GOCART_ControFiles:
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This is a typo (Control, not Contro).

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corrected it


.. _GOCART_FixFiles:
.. list-table:: *GOCART run control files*
:widths: 40 50
:header-rows: 1

.. list-table:: *Fix files containing climatological information*
* - Filename
- Description
* - AERO.rc
- Atmospheric Model Configuration Parameters
* - AERO_ExtData.rc
- Model Inputs related to aerosol emissions
* - AERO_HISTORY.rc
- Create History List for Output
* - AGCM.rc
- Atmospheric Model Configuration Parameters
* - CA2G_instance_CA.bc.rc
- Resource file for Black Carbon parameters
* - CA2G_instance_CA.br.rc
- Resource file for Brown Carbon parameters
* - CA2G_instance_CA.oc.rc
- Resource file for Organic Carbon parameters
* - CAP.rc
- Meteorological fields imported from atmospheric model (CAP_imports) & Prognostic Tracers Table (CAP_exports)
* - DU2G_instance_DU.rc
- Resource file for Dust parameters
* - GOCART2G_GridComp.rc
- The basic properties of the GOCART2G Grid Components
* - NI2G_instance_NI.rc
- Resource file for Nitrate parameters
* - SS2G_instance_SS.rc
- Resource file for Sea Salt parameters
* - SU2G_instance_SU.rc
- Resource file for Sulfur parameters

GOCART inputs defined in AERO_ExtData are listed and described in :numref:`Table %s <GOCART_InputFiles>`.

.. _GOCART_InputFiles:

.. list-table:: *GOCART inputs defined in AERO_ExtData.rc*
:widths: 40 50
:header-rows: 1

* - Filename
- Description
* -
-
* - ExtData/dust
- FENGSHA input files
* - ExtData/QFED
- QFED biomass burning emissions
* - ExtData/CEDS
- Anthropogenic emissions
* - ExtData/MERRA2
- DMS concentration
* - ExtData/PIESA/sfc
- Aviation emissions
* - ExtData/PIESA/L127
- H2O2, OH and NO3 mixing ratios
* - ExtData/MEGAN_OFFLINE_BVOC
- VOCs MEGAN biogenic emissions
* - ExtData/monochromatic
- aerosol monochromatic optics files
* - ExtData/optics
- aerosol radiation bands optic files for RRTMG
* - ExtData/volcanic
- SO2 volcanic pointwise sources

The static input files when using climatology (MERRA2) are listed and described in :numref:`Table %s <Climatology_InputFiles>`.

.. _Climatology_InputFiles:

.. list-table:: *Inputs when using climatology (MERRA2)*
:widths: 40 50
:header-rows: 1

* - Filename
- Description
* - merra2.aerclim.2003-2014.m$(month).nc
- MERRA2 aerosol climatology mixing ratio
* - Optics_BC.dat
- BC optical look-up table for MERAA2
* - Optics_DU.dat
- DUST optical look-up table for MERAA2
* - Optics_OC.dat
- OC optical look-up table for MERAA2
* - Optics_SS.dat
- Sea Salt optical look-up table for MERAA2
* - Optics_SU.dat
- Sulfate optical look-up table for MERAA2

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Grid description and initial condition files
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. TODO:: GOCART information in progress

The input files containing grid information and the initial conditions for global configurations are listed and described in :numref:`Table %s <GOCART_GridICFiles>`.

.. _GOCART_GridICFiles:

.. list-table:: *Input files containing grid information and initial conditions for global configurations*
:widths: 35 50 15
:header-rows: 1
Running GOCART in UFS does not require aerosol initial conditions, as aerosol models can always start from scratch (cold start), however, this approach does require more than two weeks of model spin-up to obtain reasonable aerosol simulation results. Therefore, the most popular method is to take previous aerosol simulation results. The result is not necessarily from the same model, it could be from a climatology result, such as MERAA2, or a different model but with the same aerosol species and bin/size distribution.
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I would suggest you break the first line into two sentences:

Running GOCART in UFS does not require aerosol initial conditions, as aerosol models can always start from scratch (cold start). However,.....

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changed it


* - Filename
- Description
- Date-dependent
* -
-
-
The aerosol initial input currently read by GOCART is the same format as the UFSAtm initial input data format of "gfs_data_tile[1-6].nc" in :numref:`Table %s <GridICFiles>`, so the aerosol initial conditions should be combined with the meteorological initial conditions as one initial input file. There are many tools available for this purpose. The global workflow that supports UFS models always provides a solution for this.
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Are you referring to ufs-utils here?

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yes, added it


==========================
Model configuration files
Expand Down Expand Up @@ -1609,7 +1672,140 @@ For more HAFS, HAFSW, and HAFS-ALL configurations please see the following nems.
- `HAFS ATM-OCN-WAV <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/nems.configure.hafs_atm_ocn_wav.IN>`_
- `HAFS ATM-DOCN <https://github.com/ufs-community/ufs-weather-model/blob/develop/tests/parm/nems.configure.hafs_atm_docn.IN>`_

.. TODO:: GOCART information in progress
For the coupled GOCART in S2SAW application, a sample *nems.configure* is shown below :

.. code-block:: console

# EARTH #
EARTH_component_list: MED ATM CHM OCN ICE WAV
EARTH_attributes::
Verbosity = 0
::

# MED #
MED_model: cmeps
MED_petlist_bounds: 0 287
::

# ATM #
ATM_model: fv3
ATM_petlist_bounds: 0 311
ATM_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
::

# CHM #
CHM_model: gocart
CHM_petlist_bounds: 0 287
CHM_attributes::
Verbosity = 0
::

# OCN #
OCN_model: mom6
OCN_petlist_bounds: 312 431
OCN_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ocn = mesh.mx025.nc
::

# ICE #
ICE_model: cice6
ICE_petlist_bounds: 432 479
ICE_attributes::
Verbosity = 0
DumpFields = false
ProfileMemory = false
OverwriteSlice = true
mesh_ice = mesh.mx025.nc
stop_n = 6
stop_option = nhours
stop_ymd = -999
::

# WAV #
WAV_model: ww3
WAV_petlist_bounds: 480 559
WAV_attributes::
Verbosity = 0
OverwriteSlice = false
::

# CMEPS warm run sequence
runSeq::
@1800
MED med_phases_prep_ocn_avg
MED -> OCN :remapMethod=redist
OCN -> WAV
WAV -> OCN :srcMaskValues=1
OCN
@300
MED med_phases_prep_atm
MED med_phases_prep_ice
MED -> ATM :remapMethod=redist
MED -> ICE :remapMethod=redist
WAV -> ATM :srcMaskValues=1
ATM -> WAV
ICE -> WAV
ATM phase1
ATM -> CHM
CHM
CHM -> ATM
ATM phase2
ICE
WAV
ATM -> MED :remapMethod=redist
MED med_phases_post_atm
ICE -> MED :remapMethod=redist
MED med_phases_post_ice
MED med_phases_prep_ocn_accum
@
OCN -> MED :remapMethod=redist
MED med_phases_post_ocn
MED med_phases_restart_write
@
::

# CMEPS variables

DRIVER_attributes::
::

MED_attributes::
ATM_model = fv3
ICE_model = cice6
OCN_model = mom6
history_n = 1
history_option = nhours
history_ymd = -999
coupling_mode = nems_frac
history_tile_atm = 384
::
ALLCOMP_attributes::
ScalarFieldCount = 2
ScalarFieldIdxGridNX = 1
ScalarFieldIdxGridNY = 2
ScalarFieldName = cpl_scalars
start_type = startup
restart_dir = RESTART/
case_name = ufs.cpld
restart_n = 6
restart_option = nhours
restart_ymd = -999
dbug_flag = 0
use_coldstart = false
use_mommesh = true
eps_imesh = 1.0e-1
stop_n = 6
stop_option = nhours
stop_ymd = -999
::

---------------------------------------
*The SDF (Suite Definition File) file*
Expand Down