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refactor CPLHIST mode and add DATM CPLHIST topo capability #1950

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Oct 13, 2017
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refactor CPLHIST mode and add DATM CPLHIST topo capability #1950

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ea7b212
changes to get datm cplhist mode working with a topo stream
Sep 25, 2017
367f381
more robust implementation of CPLHIST mode and refactor of format out…
Sep 28, 2017
bd6e114
updates to data model docs for cplhist mode
Sep 28, 2017
c458573
updates of data model documentation
Sep 29, 2017
84ea738
bug fixes
Oct 2, 2017
0526b1e
minor format fixes
Oct 4, 2017
b06b267
Minor documentation edits
billsacks Oct 11, 2017
bf2bb2b
Remove some log statements
billsacks Oct 11, 2017
7e054db
Make some documentation consistent
billsacks Oct 11, 2017
7dc983a
fix whitespace
billsacks Oct 11, 2017
ade2ccf
consistency changes for CPLHIST defaults and updated documentation
Oct 12, 2017
6e4d431
Minor documentation fix from Mariana
billsacks Oct 13, 2017
e879189
Improve documentation of CPLHIST_YR_ALIGN variables, from Keith Lindsay
billsacks Oct 13, 2017
d02a0a4
Add details on year_align
billsacks Oct 13, 2017
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89 changes: 45 additions & 44 deletions doc/source/data_models/data-atm.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -4,17 +4,17 @@ Data Atmosphere (DATM)
======================

DATM is normally used to provide observational forcing data (or forcing data produced by a previous run using active components) to drive prognostic components.
In the case of CESM, these would be: CLM (I compset), POP2 (C compset), and POP2/CICE (G compset).
In the case of CESM, these would be: CLM (I compset), POP2 (C compset), and POP2/CICE (G compset).
As a result, DATM variable settings are specific to the compset that will be targeted.
As examples, CORE2_NYF (CORE2 normal year forcing) is the DATM mode used in C and G compsets.
As examples, CORE2_NYF (CORE2 normal year forcing) is the DATM mode used in C and G compsets.
CLM_QIAN, CLMCRUNCEP, CLMGSWP3 and CLM1PT are DATM modes using observational data for forcing CLM in I compsets.

.. _datm-xml-vars:

------------------
xml variables
------------------
The following are ``$CASEROOT`` xml variables that CIME supports for DATM.
The following are ``$CASEROOT`` xml variables that CIME supports for DATM.
These variables are defined in ``$CIMEROOT/src/components/data_comps/datm/cime_config/config_component.xml``.
These variables will appear in ``env_run.xml`` and the resulting values are compset dependent.

Expand All @@ -24,42 +24,47 @@ These variables will appear in ``env_run.xml`` and the resulting values are comp
:header: "xml variable", "description"
:widths: 20, 80

"DATM_MODE", "Mode for atmospheric component"
"", "Valid values are: CORE2_NYF,CORE2_IAF,CLM_QIAN,CLM_QIAN_WISO,CLM1PT,CLMCRUNCEP,"
"", "CLMCRUNCEP_V5,CLMGSWP3,WW3,CPLHISTForcing"
"DATM_PRESAERO", "Prescribed aerosol forcing, if any"
"DATM_TOPO", "Surface topography"
"DATM_CO2_TSERIES", "CO2 time series type"
"DATM_CPLHIST_CASE", "Coupler history data mode case name"
"DATM_CPLHIST_DIR", "Coupler history data mode directory containing coupler history data"
"DATM_CPLHIST_YR_ALIGN", "Coupler history data model simulation year corresponding to data starting year"
"DATM_CPLHIST_YR_START", "Coupler history data model starting year to loop data over"
"DATM_CPLHIST_YR_END", "Coupler history data model ending year to loop data over"
"DATM_CLMNCEP_YR_ALIGN", "I compsets only - simulation year corresponding to data starting year"
"DATM_CPLHIST_YR_START", "I compsets only - data model starting year to loop data over"
"DATM_CPLHIST_YR_END", "I compsets only - data model ending year to loop data over"
"DATM_MODE", "Mode for atmospheric component"
"", "Valid values are: CORE2_NYF,CORE2_IAF,CLM_QIAN,CLM_QIAN_WISO,CLM1PT,CLMCRUNCEP,"
"", "CLMCRUNCEP_V5,CLMGSWP3,WW3,CPLHIST"

"DATM_PRESAERO", "Optional prescribed aerosol forcing"
"DATM_TOPO", "Optional Surface topography"
"DATM_CO2_TSERIES", "Optional CO2 time series type"

"DATM_CPLHIST_DOMAIN_FILE", "Coupler history forcing data mode - full pathname of model domain file "
"DATM_CPLHIST_CASE", "Coupler history forcing data mode - case name"
"DATM_CPLHIST_DIR", "Coupler history forcing data mode - directory containing coupler history data"
"DATM_CPLHIST_YR_ALIGN", "Coupler history forcing data mode - simulation year corresponding to DATM_CPLHIST_YR_START"
"DATM_CPLHIST_YR_START", "Coupler history forcing data mode - starting year to loop data over"
"DATM_CPLHIST_YR_END", "Coupler history forcing data mode - ending year to loop data over"

"DATM_CLMNCEP_YR_ALIGN", "I compsets only - simulation year corresponding to data starting year"
"DATM_CLMNCEP_YR_START", "I compsets only - data model starting year to loop data over"
"DATM_CLMNCEP_YR_END", "I compsets only - data model ending year to loop data over"

.. note:: If ``DATM_MODE`` is set to ``CPLHIST``, it is normally assumed that the model domain will be identical to **all** of the stream domains. To ensure this, the xml variables ``ATM_DOMAIN_PATH`` and ``ATM_DOMAIN_FILE`` are ignored and a valid setting **must be given** for ``DATM_CPLHIST_DOMAIN_FILE``. If ``DATM_CPLHIST_DOMAIN_FILE`` is set to ``null``, then the datm component domain information is read in from the first coupler history file in the target stream and it is assumed that the first coupler stream file that is pointed to contains the domain information for that stream. This is the default that should be used for this mode. Alternatively, ``DATM_CPLHIST_DOMAIN_FILE`` can be set to ``$ATM_DOMAIN_PATH/$ATM_DOMAIN_FILE`` in a non-default configuration.

.. _datm-datamodes:

--------------------
datamode values
--------------------

The xml variable ``DATM_MODE`` sets the streams that are associated with DATM and also sets the namelist variable ``datamode`` that specifies what additional operations need to be done by DATM on the streams before returning to the driver.
One of the variables in ``shr_strdata_nml`` is ``datamode``, whose value is a character string. Each data model has a unique set of ``datamode`` values that it supports.
The valid values for ``datamode`` are set in the file ``namelist_definition_datm.xml`` using the xml variable ``DATM_MODE`` in the ``config_component.xml`` file for DATM.
CIME will generate a value ``datamode`` that is compset dependent.
The xml variable ``DATM_MODE`` is used to set the streams that are associated with DATM and also to set the namelist variable ``datamode`` that specifies what additional operations need to be done by DATM on the streams before returning to the driver.
One of the variables in ``shr_strdata_nml`` is ``datamode``, whose value is a character string. Each data model has a unique set of ``datamode`` values that it supports.
The valid values for ``datamode`` are set in the file ``namelist_definition_datm.xml`` using the xml variable ``DATM_MODE`` in the ``config_component.xml`` file for DATM.
CIME will generate a value ``datamode`` that is compset dependent.

The following are the supported DATM datamode values and their relationship to the ``$DATM_MODE`` xml variable value.
The following are the supported DATM ``datamode`` values and their relationship to the ``$DATM_MODE`` xml variable value.

.. csv-table:: "Valid values for datamode namelist variable"
:header: "datamode variable", "description"
:widths: 20, 80

"NULL", "This mode turns off the data model as a provider of data to the coupler. The ``atm_present`` flag will be set to ``false`` and the coupler assumes no exchange of data to or from the data model."
"COPYALL", "The default science mode of the data model is the COPYALL mode. This mode will examine the fields found in all input data streams, if any input field names match the field names used internally, they are copied into the export array and passed directly to the coupler without any special user code. Any required fields not found on an input stream will be set to zero except for aerosol deposition fields which will be set to a special value. "
"CPLHIST","Uilize user-generated coupler history data to spin up prognostic component. Works exactly like COPYALL."
"CLMNCEP", "In conjunction with NCEP climatological atmosphere data, provides the atmosphere forcing favored by the Land Model Working Group when coupling an active land model with observed atmospheric forcing. This mode replicates code previously found in CLM (circa 2005), before the LMWG started using the CCSM flux coupler and data models to do active-land-only simulations."
"COPYALL", "The default science mode of the data model is the COPYALL mode. This mode will examine the fields found in all input data streams, if any input field names match the field names used internally, they are copied into the export array and passed directly to the coupler without any special user code. Any required fields not found on an input stream will be set to zero except for aerosol deposition fields which will be set to a special value. "
"CLMNCEP", "In conjunction with NCEP climatological atmosphere data, provides the atmosphere forcing favored by the Land Model Working Group when coupling an active land model with observed atmospheric forcing. This mode replicates code previously found in CLM (circa 2005), before the LMWG started using the CIME coupling infrastructure and data models to do active-land-only simulations."
"CORE2_NYF", "Coordinated Ocean-ice Reference Experiments (CORE) Version 2 Normal Year Forcing."
"CORE2_IAF", "In conjunction with with CORE Version 2 atmospheric forcing data, provides the atmosphere forcing favored by the Ocean Model Working Group when coupling an active ocean model with observed atmospheric forcing. This mode and associated data sets implement the CORE-IAF Version 2 forcing data, as developed by Large and Yeager (2008) at NCAR. Note that CORE2_NYF and CORE2_IAF work exactly the same way."

Expand Down Expand Up @@ -102,9 +107,9 @@ The following tabe describes the valid values of ``DATM_MODE``, and how it relat
"CLM1PT", "single point tower site atm input data"
"","streams: CLM1PT.$ATM_GRID"
"","datamode: CLMNCEP"
"CPLHISTForcing","user generated forcing data to spinup for I and G compsets"
"","streams: CPLHISTForcingForOcnIce.Solar,CPLHISTForcingForOcnIce.nonSolarFlux,"
"","CPLHISTForcingForOcnIce.State3hr,CPLHISTForcingForOcnIce.State1hr"
"CPLHIST","user generated forcing data from using coupler history files used to spinup relevant prognostic components (for CESM this is CLM, POP and CISM)"
"","streams: CPLHISTForcing.Solar,CPLHISTForcing.nonSolarFlux,"
"","CPLHISTForcing.State3hr,CPLHISTForcing.State1hr"
"","datamode: CPLHIST"
"WW3","WW3 wave watch data from a short period of hi WW3 wave watch data from a short period of hi temporal frequency COREv2 data"
"","streams: WW3"
Expand All @@ -114,7 +119,7 @@ The following tabe describes the valid values of ``DATM_MODE``, and how it relat
Namelists
--------------

The DATM namelist file is ``datm_in`` (or ``datm_in_NNN`` for multiple instances). DATM namelists can be separated into two groups: *stream-independent* namelist variables that are specific to the DATM model and *stream-specific* namelist variables whose names are common to all the data models.
The DATM namelist file is ``datm_in`` (or ``datm_in_NNN`` for multiple instances). DATM namelists can be separated into two groups: *stream-independent* namelist variables that are specific to the DATM model and *stream-specific* namelist variables whose names are common to all the data models.

Stream dependent input is in the namelist group ``"shr_strdata_nml`` which is discussed in :ref:`input streams <input-streams>` and is the same for all data models.

Expand All @@ -126,17 +131,17 @@ The stream-independent group is ``datm_nml`` and the DATM stream-independent nam
datm_nml vars description
===================== =============================================================================================
decomp decomposition strategy (1d, root)

1d => vector decomposition, root => run on master task
restfilm master restart filename
restfils stream restart filename
restfilm master restart filename
restfils stream restart filename
force_prognostic_true TRUE => force prognostic behavior
bias_correct if set, include bias correction streams in namelist
anomaly_forcing if set, includ anomaly forcing streams in namelist
factorfn filename containing correction factors for use in CORE2 modes (CORE2_IAF and CORE2_NYF)
presaero if true, prescribed aerosols are sent from datm
factorfn filename containing correction factors for use in CORE2 modes (CORE2_IAF and CORE2_NYF)
presaero if true, prescribed aerosols are sent from datm
iradsw frequency to update radiation in number of time steps (of hours if negative)
wiso_datm if true, turn on water isotopes
wiso_datm if true, turn on water isotopes
===================== =============================================================================================

.. _datm-mode-independent-streams:
Expand All @@ -145,23 +150,23 @@ wiso_datm if true, turn on water isotopes
Streams independent of DATM_MODE value
------------------------------------------

In general, each ``DATM_MODE`` xml variable is identified with a unique set of streams.
In general, each ``DATM_MODE`` xml variable is identified with a unique set of streams.
However, there are several streams in DATM that can accompany any ``DATM_MODE`` setting.
Currently, these are streams associated with prescribed aerosols, co2 time series, topography, anomoly forcing and bias correction.
These mode-independent streams are activated different, depending on the stream.

- ``prescribed aerosol stream:``
To add this stream, set ``$DATM_PRESAERO`` to a supported value other than ``none``.
To add this stream, set ``$DATM_PRESAERO`` to a supported value other than ``none``.

- ``co2 time series stream``:
To add this stream, set ``$DATM_CO2_TSERIES`` to a supported value other than ``none``.

- ``topo stream``:
To add this stream, set ``$DATM_TOPO`` to a supported value other than ``none``.

- ``anomaly forcing stream:``
To add this stream, you need to add any of the following keywword/value pair to the end of ``user_nl_datm``:
::
::

Anomaly.Forcing.Precip = <filename>
Anomaly.Forcing.Temperature = <filename>
Expand All @@ -174,7 +179,7 @@ These mode-independent streams are activated different, depending on the stream.

- ``bias_correct stream:``
To add this stream, you need to add any of the following keywword/value pair to the end of ``user_nl_datm``:
::
::

BC.QIAN.CMAP.Precip = <filename>
BC.QIAN.GPCP.Precip = <filename>
Expand Down Expand Up @@ -270,7 +275,3 @@ In general, the stream input file should translate the stream input variable nam
"snowl_HDO", "Faxa_snowl_HDO"
"shum_16O", "Sa_shum_16O"
"shum_18O", "Sa_shum_18O"




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