View source for Overview of History diagnostics

'''''[[Guide to GEOS-Chem History diagnostics|Previous]] | [[Legend for History diagnostics|Next]] | [[Guide to GEOS-Chem History diagnostics]]'''''
#<span style="color:blue">'''Overview of History diagnostics'''</span>
#[[Legend for History diagnostics]]
#[[Collections for History diagnostics]]
#[[History collections for advection and mixing]]
#[[History collections for aerosols]]
#[[History collections for budgets]]
#[[History collections for chemistry and photolysis]]
#[[History collections for convection and wet deposition]]
#[[History collections for dry deposition]]
#[[History collections for mercury and POPs]]
#[[History collections for met fields and related quantities]]
#[[History collections for methane]]
#[[History collections for species concentrations]]
#[[History collections for TransportTracers]]
#[[Replicating the behavior of the prior timeseries diagnostics]]
#[[Adding new History diagnostics]]


== Overview ==

=== An introduction to netCDF diagnostics ===

[[GEOS-Chem 12#12.0,0|GEOS-Chem 12.0.0]] and later versions can save diagnostic output to netCDF format.  There are two types of netCDF diagnostic output files:

#[[Guide_to_HEMCO_emissions_diagnostics|Emissions diagnostics archived directly by HEMCO]]
#Non-emissions diagnostics computed by GEOS-Chem

The [[GEOS-Chem Support Team]] has developed a new netCDF diagnostic capability for GEOS-Chem "Classic" (point #2 above) that replicates how the existing netCDF diagnostics work in GCHP (aka "History"). A common input file named <tt>HISTORY.rc</tt> can be used for both GEOS-Chem "Classic" and GCHP.

Bob Yantosca has created [[Media:Netcdf_Diagnostics.pdf|an overview presentation about the new netCDF diagnostics for v11-02]].

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:40, 13 March 2019 (UTC)

=== Sample HISTORY.rc diagnostic input file ===

<span style="color:green">'''''NOTE: Horizontal and vertical subsetting (i.e. archiving regions that are smaller than the entire global grid) is available in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]] and later versions.  For details, see the SpeciesConcSubset collection in the sample HISTORY.rc file listed below.'''''</span>

Here is a sample <tt>HISTORY.rc</tt> file that is used to request netCDF diagnostic output from a GEOS-Chem “Classic” simulation.  

 #============================================================================ 
 # EXPID allows you to specify the beginning of the file path corresponding
 # to each diagnostic collection.  For example:
 #
 #   EXPID: ./GEOSChem 
 #      Will create netCDF files whose names begin "GEOSChem",
 #      in this run directory.
 #
 #   EXPID: ./OutputDir/GEOSChem
 #      Will create netCDF files whose names begin with "GEOSChem"
 #      in the OutputDir sub-folder of this run directory.
 #
 #============================================================================
 EXPID:  ./GEOSChem
 
 #==============================================================================
 # %%%%% COLLECTION NAME DECLARATIONS %%%%%
 #
 # To disable a collection, place a "#" character in front of its name
 #
 # NOTE: These are the "default" collections for GEOS-Chem.  
 # But you can create your own custom diagnostic collections as well.
 #==============================================================================
 COLLECTIONS: <span style="color:red">'SpeciesConc'</span>,
              <span style="color:darkcyan">'SpeciesConcSubset'</span>,
              <span style="color:blue">'ConcAfterChem'</span>,
 ::
 #==============================================================================
 # %%%%% THE SpeciesConc COLLECTION %%%%%
 #
 # GEOS-Chem species concentrations (default = advected species)
 #
 # Available for all simulations
 #==============================================================================
 <span style="color:red">SpeciesConc</span>.<span style="color:gray">template:           '%y4%m2%d2_%h2%n2z.nc4'</span>,
 <span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency:          00000000 060000</span>,
 <span style="color:red">SpeciesConc</span>.format:             'CFIO',
 <span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:           00000001 000000</span>,
 <span style="color:red">SpeciesConc</span>.<span style="color:brown">mode:               'instantaneous'</span>,
 <span style="color:red">SpeciesConc</span>.<span style="color:green">fields:             'SpeciesConc_?ADV?'</span>,  'GIGCchem',
 ::
 #==============================================================================
 # %%%%% THE SpeciesConcSubset COLLECTION %%%%%
 #
 # Same as the SpeciesConc collection, but will subset data in the horizontal
 # and vertical dimensions so that the netCDF diagnostic files will cover
 # a smaller region of the globe.  This can save disk space and memory.
 #
 # NOTE: This capability will be available in GEOS-Chem "Classic" 12.5.0
 # and later versions.
 #
 # Available for all simulations
 #==============================================================================
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:gray">template:     '%y4%m2%d2_%h2%n2z.nc4'</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:darkorange">frequency:    060000</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.format:       'CFIO',
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:purple">duration:     00000001 000000</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:brown">mode:         'instantaneous'</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:#CC0000">LON_RANGE:    -40.0 60.0</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:#CC0000">LAT_RANGE:    -10.0 50.0</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:#AAAA00">levels:       1 2 3 4 5</span>,
 <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:green">fields:       'SpeciesConc_?ADV?'</span>,  'GIGCchem',
 ::
 #==============================================================================
 # %%%%% THE ConcAfterChem COLLECTION %%%%%
 #
 # Concentrations of OH, HO2, O1D, O3P immediately after exiting the KPP solver
 # or OH after the CH4 specialty-simulation chemistry routine.
 #
 # OH:       Available for all full-chemistry simulations and CH4 specialty sim
 # HO2:      Available for all full-chemistry simulations
 # O1D, O3P: Availalbe for full-chemistry simulations using UCX mechanism
 #==============================================================================
 <span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template:         '%y4%m2%d2_%h2%n2z.nc4'</span>,
 <span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency:        00000100 000000</span>,
 <span style="color:blue">ConcAfterChem</span>.format:           'CFIO',
 <span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:         00000100 000000</span>,
 <span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode:             'time-averaged'</span>,
 <span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields:           'OHconcAfterChem'</span>,     'GIGCchem',
                                 <span style="color:green">'HO2concAfterChem'</span>,    'GIGCchem',
                                 <span style="color:green">'O1DconcAfterChem'</span>,    ‘GIGCchem’,
                                 <span style="color:green">'O3PconcAfterChem'</span>,    ‘GIGCchem’,
 ::


In this <tt>HISTORY.rc</tt> file, we are requesting three collections, or types of netCDF file output.  The table below explains in more detail parameters shown in the <tt>HISTORY.rc</tt> file above.

{| border=1 cellspacing=0 cellpadding=5 
|-valign="top" bgcolor="#CCCCCC"
!width="225px"|Attribute
!width="875px"|Explanation

|-valign="top"
!bgcolor="#CCFFFF" colspan="2"|The first collection: <tt>SpeciesConc</tt>

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span></tt>
|Name of the first collection in this <tt>HISTORY.rc</tt> file.  A collection is a series of files containing the same GEOS-Chem diagnostic quantities.

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:gray">template</span></tt> 
|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*The string <tt>%y4%m2%d2_%h2%n2z.nc4</tt> will print <tt>YYYYMMDD_hhmmz.nc4</tt> to the end of each netCDF filename
**<tt>YYYYMMDD</tt> is the date in year/month/day format
**<tt>hhmm</tt> is the time in hour:minutes format.
**<tt>z</tt> denotes "Zulu", which is an abbreviation for UTC time.
**<tt>.nc4</tt> denotes that the data file is in the netCDF-4 format.

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:darkorange">frequency</span></tt>
|Determines how often the diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> collection will be saved to a netCDF file. 
*This can be specified as either "<tt>hhmmss</tt>" or "<tt>YYYYMMDD hhmmss</tt>".
*In the above example, data belonging to the <tt><span style="color:red">SpeciesConc</span></tt> collection will be written to the file <span style="color:darkorange">every 6 hours</span>.  (Because <tt><span style="color:red">SpeciesConc</span></tt> is an <span style="color:brown">instantaneous</span> collection, no time-averaging will be performed.)

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.format</tt>
|For GCHP simulations only: indicates the I/O library that will be used.  This can be omitted for GEOS-Chem "Classic" simualations.

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:purple">duration</span></tt>
|Determines how often a new <tt><span style="color:red">SpeciesConc</span></tt> netCDF file will be created.  
*This can be specified as either <tt>hhmmss</tt> or <tt>YYYYMMDD hhmmss</tt>.
*In the above example, a new <tt><span style="color:red">SpeciesConc</span></tt> netCDF file will be created <span style="color:purple">every 24 hours</span>. 

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:brown">mode</span></tt>
|Determines the averaging method for the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*Possible values for <span style="color:brown"><tt>mode</tt></span> are either <span style="color:brown"><tt>'instantaneous'</tt></span> or <span style="color:brown"><tt>'time-averaged'</tt></span>.

In the example shown above:
*<tt><span style="color:red">SpeciesConc</span></tt> is defined as an <tt><span style="color:brown">'instantaneous'</span></tt> (aka "time-series") collection.  
*Diagnostic quantities belonging to <tt><span style="color:red">SpeciesConc</span></tt> will be written directly to disk without any temporal averaging, at the specified <tt><span style="color:darkorange">frequency</span></tt>.

|-valign="top"
|<tt><span style="color:red">SpeciesConc</span>.<span style="color:green">fields</span></tt>
|Lists the diagnostic quantities to be included in the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*In the above example, we are requesting to archive the <span style="color:green">concentrations of all advected species</span> to the <tt><span style="color:red">SpeciesConc</span></tt> collection.
*The text <tt>'GIGCchem'</tt> is only needed for GCHP simulations.  It is ignored for GEOS-Chem "Classic" simulations.  We keep the <tt>'GIGCchem'</tt> in the file in order <tt>HISTORY.rc</tt> files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.

See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.

NOTE: You may use wildcards to request a subset of all possible chemical species.  See the next section for more information about wildcards.

|-valign="top"
|<tt>::</tt>
|Signifies the end of the <tt><span style="color:red">SpeciesConc</span></tt> definition section. 
*"<tt>::</tt>" may be placed at any column in the file.

|-valign="top"
!bgcolor="#CCFFFF" colspan="2"|The second collection: <tt>SpeciesConcSubset</tt>

|-valign="top"
|<tt><span style="color:darkcyan">SpeciesConcSubset</span></tt>
|Name of the second collection in this <tt>HISTORY.rc</tt> file.

|-valign="top"
|<tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:gray">template</span></tt><br><tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:darkorange">frequency</span></tt><br><tt><span style="color:darkcyan">SpeciesConcSubset</span>.format</tt><br><tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:purple">duration</span></tt><br><tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:brown">mode</span></tt><br><tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:green">fields</span></tt><br><tt>::</tt>
|In the sample <tt>HISTORY.rc</tt> file above, these attributes of the <tt><span style="color:darkcyan">SpeciesConcSubset</span></tt> collection happen to be identical to those used by the <tt><span style="color:red">SpeciesConc</span></tt> collection (see above).  Therefore, we will omit re-describing these.

|-valign="top"
|<tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:#CC0000">LON_RANGE</span></tt><br>(OPTIONAL)
|Specifies a longitude range (<tt>lonMin lonMax</tt>). Only those grid boxes whose longitudes fall within this range will be archived to disk.
*In the above example, we have requested a subset region from -40 to 60 degrees longitude.
*If omitted, then all longitudes (-180..180) will be archived.
*New in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]].

|-valign="top"
|<tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:#CC0000">LAT_RANGE</span></tt><br>(OPTIONAL)
|Specifies a latitude range (<tt>latMin latMax</tt>). Only those grid boxes whose latitudes fall within this range will be archived to disk.
*In the above example, we have requested a subset region from 10 to 50 degrees latitude.
*If omitted, then all latitudes (-90..90) will be archived.
*New in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]].


|-valign="top"
|<tt><span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:#AAAA00">levels</span></tt><br>(OPTIONAL)
|Specifies the levels that you wish to be printed to disk.
*NOTE: In GEOS-Chem "Classic", all levels between the minimum and maximum level specified will be archived to disk.  This differs than the behavior in GCHP, which archives only the specified levels.
*In the above example, we are requesting output from levels 1-5.
*If omitted, then the entire vertical extent of the grid [(1 72) or (1 47), depending on simulation] will be archived.
*New in [[GEOS-Chem 12#12.6.0|GEOS-Chem 12.6.0]].

|-valign="top"
!bgcolor="#CCFFFF" colspan="2"|The thirdcollection: <tt>ConcAfterChem</tt>

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span></tt>
|Name of the third collection in this <tt>HISTORY.rc</tt> file.

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template</span></tt> 
|Determines the date and time format for each netCDF file name belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection.

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:magenta">frequency</span></tt>
|Determines the length of the period in which the diagnostic quantities belonging to <tt><span style="color:blue">ConcAfterChem</span></tt> collection will be temporally-averaged, before being saved to a netCDF file.
*This can be can be specified as either "<tt>hhmmss</tt>" or "<tt>YYYYMMDD hhmmss</tt>".
*In the above example, data belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection will be <span style="color:magenta">averaged into monthly mean output</span>.

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.format</tt>
|For GCHP simulations only: indicates the I/O library that will be used.  This can be omitted for GEOS-Chem "Classic" simualations.

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration</span></tt>
|Determines how often a new netCDF file belongng to the <tt><span style="color:blue">ConcAfterChem</span></tt> will be created.
*The <tt><span style="color:purple">duration</span></tt> attribute can be specified as either <tt>hhmmss</tt> or <tt>YYYYMMDD hhmmss</tt>.
*In the above example, a new <tt><span style="color:blue">ConcAfterChem</span></tt> netCDF file will be created <span style="color:purple">at the start of each new month</span>. 

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:darkcyan">mode</span></tt>
|Determines the averaging method for the <tt><span style="color:blue">ConcAfterChem</span></tt> collection
*In the above example, <tt><span style="color:blue">ConcAfterChem</span></tt> is defined as an <tt><span style="color:darkcyan">time-averaged</span></tt> collection.  
*Diagnostic quantities belonging to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection will be temporally-averaged for a period whose length is specified by the <tt><span style="color:magenta">frequency</span></tt> attribute before being written to a netCDF file.

|-valign="top"
|<tt><span style="color:blue">ConcAfterChem</span>.<span style="color:green">fields</span></tt>
|Lists the diagnostic quantities to be included in the <tt><span style="color:blue">ConcAfterChem</span></tt> collection.
*In the above example, we are requesting to archive to the <tt><span style="color:blue">ConcAfterChem</span></tt> collection the <span style="color:green">concentrations of OH, HO2, O1D, and O3P upon exiting the FlexChem/KPP solver</span>
*The text <tt>'GIGCchem'</tt> is only needed for GCHP simulations.  It is ignored for GEOS-Chem "Classic" simulations.  We keep the <tt>'GIGCchem'</tt> in the file in order <tt>HISTORY.rc</tt> files to be interchanged between GEOS-Chem "Classic" and GCHP simulations.

See the sections below for in-depth descriptions of all possible diagnostic quantities that can be archived to netCDF format.

NOTE: You may use wildcards to request a subset of all possible species.  See the next section for more information about wildcards.

|-valign="top"
|<tt>::</tt>
|Signifies the end of the <tt><span style="color:blue">ConcAfterChem</span></tt> definition section. 
*"<tt>::</tt>" may be placed at any column in the file.

|}

For more examples, please see [[Media:Netcdf_Diagnostics.pdf|Bob Yantosca’s netCDF diagnostics overview presentation]]. We will also add more documentation to the GEOS-Chem wiki in the coming weeks.

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 22:12, 8 February 2018 (UTC)

=== netCDF filename convention ===

The names of the netCDF files corresponding to each collection will adhere to this convention:

  EXPID.CollectionName.Template

Where <tt>EXPID</tt> can be specified at the very top of the <tt>HISTORY.rc</tt> file.  This parameter controls the filename prefix.  [[#Sample HISTORY.rc diagnostic input file|In the example from the previous section]], <tt>EXPID</tt> is set to <tt>./GEOSChem</tt>.  This means that all netCDF output files will be placed in the current run directory (specified by <tt>./</tt>) and will begin with <tt>GeosChem</tt>.  

If you wish to send the netCDF diagnostic output to a sub-folder of the run directory (say named <tt>OutputDir</tt>), then you can set e.g. <tt>EXPID: ./OutputDir/GeosChem</tt>.  (''NOTE: You can also omit the <tt>./</tt>, but we have included it to make it clear that the files will be placed in the same directory where the GEOS-Chem executable resides.'')

The <tt>CollectionName</tt> and <tt>Template</tt> settings are defined [[#Sample HISTORY.rc diagnostic input file|as shown in our example <tt>HISTORY.rc</tt> file from the previous section]], namely:

  <span style="color:red">SpeciesConc</span>.<span style="color:gray">template:           '%y4%m2%d2_%h2%n2z.nc4'</span>,
  <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:gray">template:     '%y4%m2%d2_%h2%n2z.nc4'</span>,
  <span style="color:blue">ConcAfterChem</span>.<span style="color:gray">template:         '%y4%m2%d2_%h2%n2z.nc4'</span>,

In the template tags:

* The notation <tt>%y4%m2%d5_%h2%n2</tt> specifies a in the format <tt>YYYYMMDD_hhmm</tt> into the netCDF filename.
* The lowercase <tt>z</tt>denotes UTC time (aka "Zulu time").
* The <tt>.nc4</tt> extension denotes that the file will be in netCDF-4 format.

Also recall that the <tt>duration</tt> tag of <tt>HISTORY.rc</tt> controls how often a new file will be written to disk, as we saw [[#Sample HISTORY.rc diagnostic input file|in our example from the previous section]]:

  <span style="color:red">SpeciesConc</span>.<span style="color:purple">duration:           00000001 000000</span>,     # Write a new file each day
  <span style="color:darkcyan">SpeciesConcSubset</span>.<span style="color:purple">duration:     00000001 000000</span>,     # Write a new file each day
  <span style="color:blue">ConcAfterChem</span>.<span style="color:purple">duration:         00000100 000000</span>,     # Write a new file each month

Therefore, based on all of these settings in our example <tt>HISTORY.rc</tt> file, GEOS-Chem will write the following netCDF files to disk in the current run directory:

 GEOSChem.SpeciesConc.20160101_0000z.nc4    GEOSChem.SpeciesConcSubset.20160101_0000z.nc4
 GEOSChem.SpeciesConc.20160102_0000z.nc4    GEOSChem.SpeciesConcSubset.20160102_0000z.nc4
 GEOSChem.SpeciesConc.20160103_0000z.nc4    GEOSChem.SpeciesConcSubset.20160102_0000z.nc4
 GEOSChem.SpeciesConc.20160104_0000z.nc4    GEOSChem.SpeciesConcSubset.20160104_0000z.nc4
 ... etc ...

and

 GEOSChem.ConcAfterChem.20160101_0000z.nc4
 GEOSChem.ConcAfterChem.20160201_0000z.nc4
 GEOSChem.ConcAfterChem.20160301_0000z.nc4
 GEOSChem.ConcAfterChem.20160401_0000z.nc4
 ... etc ...

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:24, 6 June 2019 (UTC)

=== Vertical coordinates in netCDF files ===

All netCDF files produced by GEOS-Chem (i.e. diagnostic files and restart files) adhere to the [[Preparing_data_files_for_use_with_HEMCO#The_COARDS_netCDF_standard|the COARDS netCDF convention]] for the lon, lat, and time dimensions.  

For the vertical dimension, we have chosen to use the following coordinate variables, emulating the file format of the NCAR Community Earth System Model (CESM):

 variables:
      double lev(lev) ;
          lev:long_name = "hybrid level at midpoints (1000*(A+B))" ;
          lev:units = "level" ;
          lev:positive = "down" ;\
          lev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
          lev:formula_terms = "a: hyam b: hybm p0: P0 ps: PS" ;
      double hyam(lev) ;
          hyam:long_name = "hybrid A coefficient at layer midpoints" ;
      double hybm(lev) ;
          hybm:long_name = "hybrid B coefficient at layer midpoints" ;
      double ilev(ilev) ;
          ilev:long_name = "hybrid level at interfaces (1000*(A+B))" ;
          ilev:units = "level" ;
          ilev:positive = "down" ;
          ilev:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
          ilev:formula_terms = "a: hyai b: hybi p0: P0 ps: PS" ;
      double hyai(ilev) ;
          hyai:long_name = "hybrid A coefficient at layer interfaces" ;
      double hybi(ilev) ;
          hybi:long_name = "hybrid B coefficient at layer interfaces" ;
      double P0 ;
          P0:long_name = "reference pressure" ;

The <tt>lev</tt> variable is used for data that is placed on the midpoints between vertical levels.  This is an "approximate" eta coordinate, which is close to 1 at the surface and close to zero at the atmosphere top.

  lev = 0.99250002413, 0.97749990013, 0.962499776, 0.947499955, 0.93250006, 
     0.91749991, 0.90249991, 0.88749996, 0.87249996, 0.85750006, 0.842500125, 
     0.82750016, 0.8100002, 0.78750002, 0.762499965, 0.737500105, 0.7125001, 
     0.6875001, 0.65625015, 0.6187502, 0.58125015, 0.5437501, 0.5062501, 
     0.4687501, 0.4312501, 0.3937501, 0.3562501, 0.31279158, 0.26647905, 
     0.2265135325, 0.192541016587707, 0.163661504087706, 0.139115, 0.11825, 
     0.10051436, 0.085439015, 0.07255786, 0.06149566, 0.05201591, 0.04390966, 
     0.03699271, 0.03108891, 0.02604911, 0.021761005, 0.01812435, 0.01505025, 
     0.01246015, 0.010284921, 0.008456392, 0.0069183215, 0.005631801, 
     0.004561686, 0.003676501, 0.002948321, 0.0023525905, 0.00186788, 
     0.00147565, 0.001159975, 0.00090728705, 0.0007059566, 0.0005462926, 
     0.0004204236, 0.0003217836, 0.00024493755, 0.000185422, 0.000139599, 
     0.00010452401, 7.7672515e-05, 5.679251e-05, 4.0142505e-05, 2.635e-05, 
     1.5e-05 ;

The <tt>lev</tt> variable may be used for quick plotting.  To compute the actual pressure at the midpoint of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file):

  Pmid = ( hyam(L) * PS(I,J) ) + hybm(L)

The <tt>ilev</tt> variable is used for data that is placed on vertical level edges or "interfaces" (hence the "i" in <tt>ilev</tt>).  This is also an "approximate" eta coordinate.

  ilev = 1, 0.98500004826, 0.969999752, 0.9549998, 0.94000011, 0.92500001, 
     0.90999981, 0.89500001, 0.87999991, 0.86500001, 0.85000011, 0.83500014, 
     0.82000018, 0.80000022, 0.77499982, 0.75000011, 0.7250001, 0.7000001, 
     0.6750001, 0.6375002, 0.6000002, 0.5625001, 0.5250001, 0.4875001, 
     0.4500001, 0.4125001, 0.3750001, 0.3375001, 0.28808306, 0.24487504, 
     0.208152025, 0.176930008175413, 0.150393, 0.127837, 0.108663, 0.09236572, 
     0.07851231, 0.06660341, 0.05638791, 0.04764391, 0.04017541, 0.03381001, 
     0.02836781, 0.02373041, 0.0197916, 0.0164571, 0.0136434, 0.0112769, 
     0.009292942, 0.007619842, 0.006216801, 0.005046801, 0.004076571, 
     0.003276431, 0.002620211, 0.00208497, 0.00165079, 0.00130051, 0.00101944, 
     0.0007951341, 0.0006167791, 0.0004758061, 0.0003650411, 0.0002785261, 
     0.000211349, 0.000159495, 0.000119703, 8.934502e-05, 6.600001e-05, 
     4.758501e-05, 3.27e-05, 2e-05, 1e-05 ;

To compute the actual pressure at the bottom and top edges of the grid box (I,J,L), you will need to supply your own 2-D surface pressure field (e.g. saved from another diagnostic file):

  Pbot = ( hyai(L  ) * PS(I,J) ) + hybi(L  )
  Ptop = ( hyai(L+1) * PS(I,J) ) + hybi(L+1)

'''''[[User:Sebastian D. Eastham|Seb Eastham]] wrote:'''''

<blockquote>Daniel Rothenberg has been in touch regarding how vertical co-ordinates are set up in CESM. It's mostly the same (as COARDS), with the exception that EVERY file which includes a vertical co-ordinate also includes both <tt>lev</tt> and <tt>ilev</tt> dimensions. In this case, <tt>lev</tt> is the cell mid-points, and <tt>ilev</tt> is cell edges ("i"nterfaces). Both <tt>lev</tt> and ilev are set up just as we discussed before, although CESM doesn't include the <tt>formula_terms</tt> attribute, which I think we should use. In this case <tt>formula_terms</tt> would be <tt>ap: hyai b: hybi p0: P0 ps: ps</tt> for the <tt>ilev</tt> dimension and <tt>ap: hyam b: hybm p0: P0 ps: ps</tt> for the <tt>lev</tt> dimension.

#For <tt>lev</tt> and <tt>ilev</tt>, they should be set to <tt>A/1000 + B</tt>, where <tt>P0</tt> = 1000.
#Both <tt>ilev</tt> and <tt>lev</tt> should be in all 3D files, even though only one of the two dimensions is used in a given file).
#I think we can leave <tt>PS</tt> out of the files. It will make them non-compliant but I think it's one of those "accepted" non-compliances. If it turns out to be a problem we can revisit it later, but for plotting the expectation is that it's up to the user to figure out where they're getting <tt>PS</tt> from, rather than automatically archiving it in every file.
</blockquote>

--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:27, 5 September 2018 (UTC)


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