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Update CMEPS; Add gocart userguide (was ufs-community#1182) (ufs-comm…
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…unity#1189)


* Update CMEPS submodule
* Add GOCART documentation

Co-authored-by: Li Pan <Li.Pan@noaa.gov>
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@DeniseWorthen @lipan-NOAA
DeniseWorthen and lipan-NOAA authored May 2, 2022
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2 changes: 1 addition & 1 deletion CMEPS-interface/CMEPS
Submodule CMEPS updated 27 files
+1 −1 cesm/driver/ensemble_driver.F90
+17 −9 cesm/driver/esm.F90
+0 −12 cesm/driver/esmApp.F90
+0 −0 cesm/nuopc_cap_share/esm_utils_mod.F90
+14 −3 cesm/nuopc_cap_share/nuopc_shr_methods.F90
+1 −0 cesm/nuopc_cap_share/seq_drydep_mod.F90
+3 −3 cesm/nuopc_cap_share/shr_ndep_mod.F90
+672 −0 cesm/nuopc_cap_share/shr_pio_mod.F90
+1 −1 cime_config/buildexe
+68 −95 cime_config/buildnml
+28 −9 cime_config/config_component.xml
+2 −0 cime_config/config_component_cesm.xml
+184 −27 cime_config/namelist_definition_drv.xml
+0 −207 cime_config/namelist_definition_modelio.xml
+32 −28 mediator/esmFldsExchange_cesm_mod.F90
+432 −213 mediator/esmFldsExchange_nems_mod.F90
+45 −12 mediator/fd_cesm.yaml
+19 −9 mediator/med.F90
+43 −4 mediator/med_diag_mod.F90
+50 −6 mediator/med_internalstate_mod.F90
+1 −0 mediator/med_io_mod.F90
+16 −46 mediator/med_map_mod.F90
+12 −0 mediator/med_phases_aofluxes_mod.F90
+1 −1 mediator/med_phases_post_lnd_mod.F90
+57 −0 mediator/med_phases_prep_atm_mod.F90
+89 −3 mediator/med_phases_prep_ocn_mod.F90
+2 −2 mediator/med_time_mod.F90
11 changes: 6 additions & 5 deletions doc/UsersGuide/source/CodeOverview.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -40,13 +40,13 @@ The ufs-weather-model repository supports the short- and medium-range UFS applic
- https://github.com/NOAA-EMC/CICE
* - NOAA/NCEP WAVEWATCH III Model (WW3)
- https://github.com/NOAA-EMC/WW3
* - The Goddard Chemistry Aerosol Radiation and Transport (GOCART)
- https://github.com/GEOS-ESM/GOCART
* - NUOPC Community Mediator for Earth Prediction Systems (CMEPS)
- https://github.com/NOAA-EMC/CMEPS
* - Community Data Models for Earth Prediction Systems (CDEPS)
- https://github.com/NOAA-EMC/CDEPS

.. TODO:: GOCART information in progress

In the table, the left column contains a description of each repository, and the right column shows the component repositories which are pointing to (or will point to) the authoritative repositories. The ufs-weather-model currently uses git submodule to manage the sub-components.

The umbrella repository for the UFS Weather Model is named ufs-weather-model. Under this repository reside a number of submodules that are nested in specific directories under the parent repository’s working directory. When the ufs-weather-model repository is cloned, the *.gitmodules* file creates the following directories:
Expand All @@ -68,6 +68,7 @@ The umbrella repository for the UFS Weather Model is named ufs-weather-model. U
├── CICE-interface
│ └── CICE https://github.com/NOAA-EMC/CICE
├── WW3 https://github.com/NOAA-EMC/WW3
├── GOCART https://github.com/GEOS-ESM/GOCART
├── CMEPS-interface
│ └── CMEPS https://github.com/NOAA-EMC/CMEPS
├── CDEPS-interface
Expand Down Expand Up @@ -118,6 +119,8 @@ When the ufs-weather-model is cloned, the basic directory structure will be simi
├── WW3
│ └── model --------- WW3 model
│ └── esmf --------- NUOPC WW3 cap
├── GOCART
│ └── ESMF --------- GOCART model
├── CDEPS-interface
│ └── CDEPS
│ ├── datm --------- CDEPS DATM
Expand All @@ -126,9 +129,7 @@ When the ufs-weather-model is cloned, the basic directory structure will be simi
├── tests -------- regression test infrastructure
│ └── parm
│ └── tests
│ └── fv3_conf
.. TODO:: GOCART information in progress
│ └── fv3_conf
The physics subdirectory in the *gfsphysics* directory is not used or supported
as part of this release (all physics is available through the :term:`CCPP` using
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240 changes: 219 additions & 21 deletions doc/UsersGuide/source/InputsOutputs.rst
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Expand Up @@ -738,41 +738,106 @@ 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_ControlFiles:

.. _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>`.
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.

.. _GOCART_GridICFiles:
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.

.. list-table:: *Input files containing grid information and initial conditions for global configurations*
:widths: 35 50 15
:header-rows: 1

* - 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. Ufs-utils in the global workflow that supports UFS models always provides a solution for this.

==========================
Model configuration files
Expand Down Expand Up @@ -1609,7 +1674,140 @@ 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*
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