10. Model diagnostics and output

While it is possible to run a POP ocean simulation without generating any output at all, most users desire a means of looking at the results of their simulation. POP offers several types of model output with choices governed by several types of model input. The following sections describe all of the options currently available.

11. Output formats

POP supports both netCDF and binary output formats. The format for a particular type of file is chosen at run time through namelist input for each of the output types. Restart files are always written in full double-precision (64-bit) format. By default, other output is written in single precision (32-bit) format.

The advantages and disadvantages of using netCDF and binary output formats are discussed in the following sections.

POP2 supports a compile-time option to create double-precison time-averaged (“tavg”) history files, which are often useful for debugging purposes and in the evaluation of successful ports to new machines.

To invoke the double-precision tavg option, compile POP2 must be compiled with the -DTAVG_R8 option.

11.1. netCDF

The netCDF output format provides a self-describing output file which is portable across machines. It is also recognized by many graphics and post-processing utilities. These are important and very useful features and are the reasons a netCDF option has been included in POP. However, there are two disadvantages to using this format.

The most serious disadvantage with netCDF format is that netCDF does not currently permit parallel I/O; all netCDF operations are funneled through a single processor. For high resolution simulations, this can present a serious performance bottleneck as the model attempts to pass several Gbytes through a single processor. If netCDF output is desired and is proving to be too slow, the user should switch to binary format and convert the binary files off-line to netCDF.

Currently, the data portion of a netCDF file utilizes IEEE binary format. For portability, if a machine does not use IEEE format for its native binary format, netCDF will be performing a conversion (hidden to the user) to this format. In such a case, loss of precision during this conversion will occur and exact restart can not be guaranteed. To avoid this, binary format should typically be chosen for all restart files.

POP2 supports parallel netCDF I/O through the use of its PIO library.

11.2. binary

The binary format option creates files in local machine binary format. These files are written as Fortran direct-access files so there are no record headers or footers and the file can be read by other applications as a pure binary stream. Typically, each record in the file contains a horizontal slice of a particular field (so the record length is the size of a horizontal slice of the global data). On parallel machines, fast parallel I/O is achieved by reading/writing each of these slices from a different processor with the number of processors reading/writing data specified in the Input/Output section.

Unlike netCDF, these binary files contain no information about themselves (not self-describing) and no information about the fields in the files. To remedy this, each binary file written by POP is accompanied by a ‘header file’ with the same name as the binary file and an additional suffix ‘.hdr’. This header file is an ASCII file which contains all the information you would find in a netCDF file, including file attributes, fields in the file and attributes of those fields. As part of the field attributes, the starting record of the field in the binary file is included. Such a header file provides some of the capability of a self-describing data format and also provides information for easy conversion to netCDF (or other self-describing format).

Because binary formats differ across machines, binary files are not typically portable across machines. To achieve portability, the user is encouraged to convert the binary files to a more portable data format like netCDF.

12. File-naming conventions

All output file names have the form: root-filename.runid.time-indicator.output-format. Here root-filename is a name defined by the user through namelist input for each file type, `runid <node33.html#sec:op-timemanager>`__ is a character identifier for the run sequence, time-indicator depends on the output frequency chosen and output-format is either ‘nc’ for netCDF files or ‘bin’ for binary files.If the output file is written at a frequency of nday, nmonth or nyear, the time-indicator is typically the date in yyyymmdd (where yyyy, mm and dd can be optionally separated by a character defined in the time manager namelist). If the output file is written every nstep steps, the time-indicator is the step number.

A convention has been developed for naming POP output files in which the root filenames for restart, time-averaged history, snapshot history, and moviefiles are simply the one-letter names ‘d’, ‘t’, ‘h’, ‘m’ respectively. These are the default values in the namelists for each of these options, but the user is not required to follow this convention. Come up with your own convention. We don’t mind. Really. Have fun with it. The only requirement is that the root-filename must be distinct for each type of output file. Because ‘.’ is used to delimit runid in file names and ‘/’ is reserved as a separator in Unix path names, neither should be used within runid.

The CIME scripts automatically generate POP2 output filenames that conform with the naming conventions, which, when written in the syntax of the LANL conventions, can be described as: $CASE.pop.root-filename.time-indicator.output-format

$CASE is the CIME “case name” assigned to a given CIME run.

root-filename values are chosen to be the same as LANL values whenever possible; unfortunately, the convention is in direct conflict with two of the LANL settings. root-filename is ‘h’ (history) for time-averaged history files created by the tavg.F90 module, and ‘s’ (snapshot) for history files created by the history.F90 module. For diagnostics output files, root-filename is a two-character string beginning with the first character ‘d’, with the second character intended to indicate the type of diagnostics output file.

The full POP2 convention for root-filename is:

  • *’dd’*   diag_outfile
  • *’dt’*   diag_transport_outfile
  • *’dv’*   diag_velocity_outfile
  • *’h’*     tavg_outfile
  • *’m’*   movie_outfile
  • *’r’*     restart_outfile
  • *’s’*     history_outfile

The time-indicator takes various forms, depending on the contents of the output file.

The full convention for time-indicator is as follows, and is automatically generated by the POP2 code, depending on the frequency of the file:

  • *’yyyy-mm-dd-sssss’*   ‘nhour’, ‘nsecond’, or ‘nstep’ frequency
  • *’yyyy-mm-dd’*             daily frequency
  • *’yyyy-mm’*                   monthly frequency
  • *’yyyy’*                           annual frequency

13. Model diagnostics

The progress of a POP simulation is recorded in a ‘log file’ that is either written to standard output (stdout) or redirected to an optional log file. A new log file is created each time the model is started. Values of the model version number, release date, date and time of the run, input namelist parameters, and initial or restart conditions are documented at the beginning of each log file. After the introductory information, the log file will contain output from model timers and all the scalar diagnostics.

There are three types of scalar diagnostics available. Global diagnostics compute a variety of globally-averaged values of tracers, kinetic energy and several tendencies for checking balances. CFL diagnostics compute the Courant numbers for advection and diffusion terms. Transport diagnostics compute mass, heat and salt transports through various regions defined in an input file.

These diagnostics are chosen by setting the frequency freq_opt at which each diagnostic is computed. If diagnostics are chosen, the diagnostics are written both to the log file (or stdout) and to a separate diagnostics output file. Monitoring this output as the model runs is a useful way of making sure the model is behaving reasonably. For example, the Courant numbers reported in the CFL diagnostics should remain small and various tendencies reported in the global diagnostics should remain balanced.

In addition to printing these diagnostics to a log file, the diagnostics are printed to other output files in a format more suitable for various graphics programs. The output files are ASCII files with each line containing tday (decimal time in days for the entire simulation), the value of the diagnostic and a name for the diagnostic. The name of these output files can be changed using the variables diag_outfile, diag_transport_outfile.

Model diagnotics are controlled by the diagnostics_nml namelist.

Tracer budget diagnostics are controlled by the budget_diagnostics_nml namelist.

13.1. Transport diagnostics

Computing transport diagnostics requires an input file describing the requested transports. A sample transport input file is provided with the LANL distribution. The transport input file must contain the number of transport regions in the first record. Each following record must contain 6 integers imin, imax, jmin, jmax, kmin, kmax which are global array indices which define the transport region. Note that the region must be a plane so that one of the horizontal dimensions must be fixed.Following these integers must be a 5-character string that specifies ‘zonal’ or ‘merid’ transport. Note that this descriptor defines the orientation of the section and not the direction of the velocity normal to it. A ‘zonal’ section implies the transport across that section uses the meridional velocity (velocity perpendicular to the section). The last item in each record is a name for the transport region (e.g. ‘Drake Passage’).

Table: Table: Transport descriptions

imin imax jmin jmax kmin kmax section label
64 64 1 128 1 20 merid sample meridional section
1 192 64 64 1 10 zonal sample zonal section

POP2 is capable of computing transport diagnostics, such as meridional overturning circulation, northward termperature and salt transports, and zonal averages on an auxilary latitudinal grid.

The transports_nml namelist controls the creation of these diagnostics.

The auxilary latitudinal grid choices have the following definitions:

  • ‘southern’ assumes that the model grid is regular lat-lon in the Southern Hemisphere only and uses it identically in the Southern Hemisphere. it is flipped across the Equator and padded at northern high latitudes if necessary.
  • ‘full’ assumes that the entire model grid is regular lat-lon. simply copies this grid into the axilary grid arrays.
  • ‘user’ allows the user to specify an equally-spaced grid, starting at lat_aux_begin and ending at lat_aux_end. the grid dimension/resolution is specified with n_lat_aux_grid. lat_aux_begin and lat_aux_end specify the egde coordinates in degrees north.

The following are the resolution-specific transport contents files for POP2. CIME scripts automatically use the appropriate resolution-specific transport contents file based upon the resolution specified in the create_newcase command.

To customize a transport contents file for your own research, copy the appropriate resolution-specific contents file from your CESM distribution into your $CASE/SourceMods/src.pop2 directory, modify it to suit your needs, and then run your case.


 297  297   24   47    1   60 merid  Drake Passage
  65   76  103  103    1   60 zonal  Mozambique Channel
 198  202  333  333    1   60 zonal  Bering Strait
 242  248  372  372    1   60 zonal  Northwest Passage
 131  131  164  167    1   60 merid  Indonesian Throughflow I
 138  161  156  156    1   60 zonal  Indonesian Throughflow II
 284  284  264  270    1   60 merid  Florida Strait
 289  292  258  258    1   60 zonal  Windward Passage I
 292  292  257  258    1   60 merid  Windward Passage II
  32   32  290  295    1   60 merid  Gibraltar
 234  234  373  380    1   60 merid  Nares Strait


  93   93   10   17    1   60 merid  Drake Passage
  61   64   84   84    1   60 zonal  Bering Strait
  45   45   32   38    1   60 merid  Indonesian Throughflow
  89   89   71   73    1   60 merid  Florida Strait


 436  436  287  521    1   42 merid  ACC-Drake
 292  292 1418 1443    1   42 merid  Florida Strait
 230  256 1403 1403    1   42 zonal  Yucatan Passage (Zonal)
 256  256 1404 1406    1   42 merid  Yucatan Passage (Merid)
 332  357 1369 1369    1   42 zonal  Jamaica Channel
 350  367 1385 1385    1   42 zonal  Windward Passage
 414  428 1369 1369    1   42 zonal  Mona Passage
 442  470 1366 1366    1   42 zonal  Anegada+Virgin Passage
 470  482 1356 1356    1   42 zonal  Antigua (Zonal)
 469  469 1357 1357    1   42 merid  Antigua (Merid)
 483  483 1348 1356    1   42 merid  Guadeloupe Passage
 486  486 1340 1347    1   42 merid  Dominica Passage
 487  487 1332 1337    1   42 merid  Martinique Passage (Merid)
 488  489 1331 1331    1   42 zonal  Martinique Passage (Zonal)
 491  491 1324 1329    1   42 merid  St Lucia Channel
 489  489 1317 1322    1   42 merid  St Vincent Passage
 484  484 1305 1316    1   42 merid  Grenadines (Merid)
 485  488 1316 1316    1   42 zonal  Grenadines (Zonal)
 484  484 1290 1304    1   42 merid  Trinidad
 470  470 1290 1366    1   42 merid  Antilles Inflow
 300  313 1458 1458    1   42 zonal  Grand Bahama
 320  320 1442 1460    1   42 merid  NW Providence Channel
 324  324 1409 1427    1   42 merid  Old Bahama Channel
 368  368 1385 1397    1   42 merid  Great Inagua
 452  452 1368 1524    1   42 merid  St Thomas-Bermuda
 452  452 1524 1669    1   42 merid  Bermuda-Yarmouth
2929 2947 1979 1979    1   42 zonal  Bering Strait
3141 3141 2239 2284    1   42 merid  Amundsen Gulf
3032 3072 2328 2328    1   42 zonal  MClure Strait
3104 3111 2361 2361    1   42 zonal  Prince of Wales Strait
3021 3030 2368 2368    1   42 zonal  Fitzwilliam Strait
3000 3000 2369 2385    1   42 merid  Ballantyne Strait
2983 2993 2386 2386    1   42 zonal  Wilkins Strait
 623  623 2377 2398    1   42 merid  Gustaf Adolf Strait
 608  608 2382 2400    1   42 merid  Hazen Strait (Merid)
 605  608 2381 2381    1   42 zonal  Hazen Strait (Zonal)
 603  623 2377 2377    1   42 zonal  MacLean Strait
 638  662 2362 2362    1   42 zonal  Peary Channel
 665  665 2348 2358    1   42 merid  Axel Heiber Island
 630  630 2348 2354    1   42 merid  Hassel Sound
 616  621 2332 2332    1   42 zonal  Hendricksen Strait
 599  613 2320 2320    1   42 zonal  Belcher Channel
 619  634 2320 2320    1   42 zonal  Norweigan Bay
 584  584 2323 2337    1   42 merid  Penny Strait
 578  590 2370 2370    1   42 zonal  Desbarats Strait
 559  559 2363 2375    1   42 merid  Byam Martin Channel
 540  540 2368 2375    1   42 merid  Byam Channel
 542  542 2339 2361    1   42 merid  Austin Channel
 550  550 2316 2324    1   42 merid  McDougall Sound
 595  598 2294 2294    1   42 zonal  Cardigan Strait
 554  554 2287 2298    1   42 merid  Wellington Channel
 619  619 2240 2248    1   42 merid  Glacier Strait
 609  617 2238 2238    1   42 zonal  Lady Ann Strait
 582  582 2202 2231    1   42 merid  Lancaster Sound
 576  576 2171 2181    1   42 merid  Pond Inlet
 539  539 2253 2268    1   42 merid  Prince Regent Inlet
 538  555 2275 2275    1   42 zonal  Barrow Strait
 518  518 2299 2311    1   42 merid  Peel Sound
 516  546 2326 2326    1   42 zonal  East Viscount Melville
 501  501 2338 2363    1   42 merid  McClintock Channel
 501  537 2375 2375    1   42 zonal  West Viscount Melville
 366  375 2351 2351    1   42 zonal  Dolphin and Union Strait
 385  385 2295 2307    1   42 merid  Victoria Strait
 386  386 2283 2289    1   42 merid  James Ross Strait
 687  687 2248 2258    1   42 merid  Robeson Channel
 583  656 2010 2010    1   42 zonal  Davis Strait
 522  522 1920 1951    1   42 merid  Hudson Bay
 867  867 1941 2003    1   42 merid  Denmark Strait
 911 1107 1907 1907    1   42 zonal  Iceland-Norway
 921 1022 2215 2215    1   42 zonal  Fram Strait
1097 1388 2211 2211    1   42 zonal  Barents Sea
2241 2241  958 1096    1   42 merid  Indonesian Throughflow
1380 1380  810  833    1   42 merid  Agulhas
1477 1540 1005 1005    1   42 zonal  Mozambique Channel
2125 2135 1196 1196    1   42 zonal  Malacca Strait
2144 2195 1171 1171    1   42 zonal  Karimata Strait
2158 2158 1121 1124    1   42 merid  Sunda Strait
2225 2225 1111 1150    1   42 merid  Java Sea
2255 2261 1095 1095    1   42 zonal  Lombok Strait
2292 2295 1096 1096    1   42 zonal  Sape Strait
2292 2292 1088 1095    1   42 merid  Sumba Passage
2298 2298 1096 1126    1   42 merid  Flores Sea
2275 2297 1175 1175    1   42 zonal  Makassar Strait
2350 2350 1092 1100    1   42 merid  Ombai Strait
2351 2351 1100 1103    1   42 merid  Unknown Strait (Merid)
2352 2359 1103 1103    1   42 zonal  Unknown Strait (Zonal)
2275 2297 1175 1175    1   42 zonal  Makassar Strait
2364 2364 1097 1103    1   42 merid  Wetar Strait
2373 2410 1098 1098    1   42 zonal  Banda-Timor Seas (Zonal)
2410 2410 1099 1100    1   42 merid  Banda-Timor Seas (Merid)
2411 2478 1101 1101    1   42 zonal  Arafura Sea
2419 2428 1111 1111    1   42 zonal  Tanimbar (Zonal)
2428 2428 1112 1124    1   42 merid  Tanimbar (Merid)
2428 2428 1127 1145    1   42 merid  Kai
2408 2428 1145 1145    1   42 zonal  Ceram Sea
2403 2403 1152 1162    1   42 merid  Misool
2404 2404 1165 1180    1   42 merid  Dampier Strait
2380 2404 1180 1180    1   42 zonal  Halmahera Sea
2381 2398 1166 1166    1   42 zonal  Ceram Sea (Zonal)
2398 2398 1162 1166    1   42 merid  Ceram Sea (Merid)
2376 2376 1170 1175    1   42 zonal  Obi Strait
2363 2375 1164 1164    1   42 zonal  Mangole (Zonal)
2375 2375 1165 1166    1   42 merid  Mangole (Merid)
2361 2361 1151 1158    1   42 merid  Sanana
2371 2380 1150 1150    1   42 zonal  Buru
2317 2344 1164 1164    1   42 zonal  Banggai
2352 2376 1197 1197    1   42 zonal  Molucca Sea
2352 2352 1198 1218    1   42 merid  Southeast Celebes Sea (Merid)
2353 2356 1218 1218    1   42 zonal  Southeast Celebes Sea (Zonal)
2356 2356 1218 1241    1   42 merid  Northeast Celebes Sea
2368 2380 1203 1203    1   42 zonal  Talaud (Zonal)
2367 2367 1203 1223    1   42 merid  Talaud (Merid)
2362 2368 1227 1227    1   42 zonal  Mindanao (Zonal)
2361 2361 1227 1247    1   42 merid  Mindanao (Merid)
2293 2293 1236 1247    1   42 merid  Sulu Archipelago (Merid)
2294 2320 1247 1247    1   42 zonal  Sulu Archipelago (Zonal)
2273 2273 1249 1266    1   42 merid  Balabac Strait
2296 2296 1296 1301    1   42 merid  Linapacan Strait (Merid)
2297 2300 1301 1301    1   42 zonal  Linapacan Strait (Zonal)
2300 2311 1306 1306    1   42 zonal  Mindoro Strait
2313 2320 1302 1302    1   42 zonal  Tablas Strait (Zonal)
2312 2312 1303 1306    1   42 merid  Tablas Strait (Merid)
2332 2332 1268 1274    1   42 merid  Bohol Sea
2183 2299 1345 1345    1   42 zonal  South China Sea
2525 2525 1074 1090    1   42 merid  Torres Strait
2309 2309 1372 1408    1   42 merid  Luzon Strait
2302 2302 1426 1463    1   42 merid  Taiwan Strait
2318 2338 1434 1434    1   42 zonal  Ryuku1
2339 2354 1434 1434    1   42 zonal  Ryuku2 (Zonal)
2354 2354 1435 1438    1   42 merid  Ryuku2 (Merid)
2354 2354 1435 1454    1   42 merid  Ryuku3 (Merid)
2355 2378 1454 1454    1   42 zonal  Ryuku3 (Zonal)
2383 2383 1461 1476    1   42 merid  Ryuku4 (Merid)
2384 2393 1476 1476    1   42 zonal  Ryuku4 (Zonal)
2397 2405 1479 1479    1   42 zonal  Tokara Strait (Zonal)
2405 2405 1480 1499    1   42 merid  Tokara Strait (Merid)
2407 2407 1500 1509    1   42 merid  Ohsumi Strait
2396 2396 1532 1546    1   42 merid  Southern Korea Strait
2396 2396 1547 1557    1   42 merid  Northern Korea Strait
2508 2508 1618 1622    1   42 merid  Tsugaru Strait
2527 2527 1667 1675    1   42 merid  La Perouse Strait

14. Model output files

In this section, we often refer to ‘model dates’ and ‘model times’ as corresponding to actual dates and times in the real world. This is only true if the model initial time was set appropriately and only has true meaning if the model is forced by actual observed forcing fields with proper dates associated with them. Otherwise, ‘model time’ simply refers to the model’s internal calendar.

14.1. Time-averaged history files

The time-averaged history-file (“tavg”) module provides:

  • support for the creation of multiple, simultaneous output streams generated during a single model run
  • “timeseries files,” which are output files containing multiple time levels per file.
  • an “offset” date specification, which allows finer control over the tavg_freq and tavg_freq_opt options described below.
  • the option for a “one-time header,” in which all time-invariant information is written into the first tavg file of each stream, at the beginning of each run segment, and then omitted from all subsequent files in that stream for the remainder of the run segment.
  • support for double-precision tavg output files

POP2 supports the creation of a maximum of four concurrent tavg output streams, with a hard limit of nine streams possible if the tavg module is appropriately modified. Options for each of the streams is set individually, using array syntax in the namelist.

The first character of each line in the tavg_contents file is either a comment character or an integer in the interval [1,4]. The next two characters must be blank; the remaining characters on the line spell out the short name of a requested variable.

If the leading character is a comment character – either the pound sign (#) or the exclamation point (!) – then the entire line is treated as a comment. If the leading character on the line is an integer, it identifies the number of the output stream in which the requested field will appear. Each requested tavg output field may be assigned to only one stream; assigning the same field to more than one stream will result in the model ignoring it and all subsequent requests. Similarly, duplicate requests of the same field within the same stream will be eliminated. In all cases, a summary of field and stream assignments is printed in the output log file, which allows the user to confirm which fields will be written to which stream.

Output filenames for the each stream are determined from within the tavg module, incorporating the stream number into the output filename in all but the first stream. This seemingly inconsistent treatment of tavg output filenames was chosen based on the requirement for backwards-compatability in filenames. For example, a one-stream case would generate tavg output files of the form $CASE.pop.h.*; an N-stream case would generate tavg output files of the form $CASE.pop.h.*, $CASE.pop.h2.*, ..., $CASE.pop.hN.*

Most of the tavg namelist variables are now arrays of length (max_avail_tavg_streams), which allows the user to set controls for each tavg history-file stream on a stream-by-stream basis.

In the table below, any array element that is undefined in the POP namelist file is set to the default value identified in curly braces.

The tavg_nml namelist controls how time average files are created.

Table: Table: Current available tavg fields

Name Units Description
SHF W/m:sup:`2` Surface Heat Flux
SFWF mm/day Surface Freshwater Flux (p-e)
SSH cm Sea Surface Height
SSH2 cm:sup:`2` SSH2
H3 unitless (Δ:sub:`x`(SSH)):sup:`2` + (Δ:sub:`y`(SSH)):sup:`2`
TAUX dyne/cm:sup:`2` Zonal windstress
TAUY dyne/cm:sup:`2` Meridional windstress
UVEL cm/s Zonal Velocity
VVEL cm/s Meridional Velocity
KE cm:sup:`2`/s:sup:`2` Horizontal Kinetic Energy (U:sup:2 + V2)/2
TEMP :sup:`o`C Potential Temperature
SALT g/g Salinity
TEMP2 :sup:`o`C:sup:`2` Temperature2
SALT2 (g/g):sup:`2` Salt2
UET :sup:`o`C/s East Flux of Heat
VNT :sup:`o`C/s North Flux of Heat
WTT :sup:`o`C/s Top Flux of Heat
UES g/g/s East Flux of Salt
VNS g/g/s North Flux of Salt
WTS g/g/s Top Flux of Salt
UEU cm/s:sup:`2` East Flux of Zonal Momentum
VNU cm/s:sup:`2` North Flux of Zonal Momentum
UEV cm/s:sup:`2` East Flux of Meridional Momentum
VNV cm/s:sup:`2` North Flux of Meridional Momentum
PV 1/s Potential Vorticity
Q g/cm:sup:`4` z-derivative of potential density
PD g/cm:sup:`3` Potential density referenced to surface
UDP erg Pressure work
PEC g/cm:sup:`3` Potential energy release due to convection
NCNV adjustments/s Convective adjustments per second
WTU cm/s:sup:`2` Top flux of Zonal Momentum
WTV cm/s:sup:`2` Top flux of Meridional Momentum
ST :sup:`o`Cg/g Temperature*Salinity
RHO g/cm:sup:`3` In-situ density

Table: Additional available tavg fields Name Units Description

“QFLUX”, “Watts/m:sup:`2`”, “Internal Ocean Heat Flux Due to Ice Formation; heat of fusion > 0 or ice-melting potential < 0”,

“BSF”, “Sv”, “Barotropic Stream Function”,

“TFW_T”, “Watts/m:sup:`2`”, “T flux due to freshwater flux”,

“TFW_S”, “kg/m:sup:`2`/s”, “S flux due to freshwater flux (kg of salt/m^2/s)”,

“RESID_T”, “Watts/m:sup:`2`”, “Free-Surface Residual Flux (T)”,

“RESID_S”, “kg/m:sup:`2`/s”, “Free-Surface Residual Flux (S)”,

“QSW_HTP”, “Watts/m:sup:`2`”, “Solar Short-Wave Heat Flux in top layer”,

“QSW_HBL”, “Watts/m:sup:`2`”, “Solar Short-Wave Heat Flux in boundary layer”,

“SHF_QSW”, “Watts/m:sup:`2`”, “Solar Short-Wave Heat Flux”,

“PREC_F”, “kg/m:sup:`2`/s”, “Precipitation Flux from Coupler (rain+snow)”,

“SNOW_F”, “kg/m:sup:`2`/s”, “Snow Flux from Coupler”,

“EVAP_F”, “kg/m:sup:`2`/s”, “Evaporation Flux from Coupler”,

“MELT_F”, “kg/m:sup:`2`/s”, “Melt Flux from Coupler”,

“ROFF_F”, “kg/m:sup:`2`/s”, “Runoff Flux from Coupler”,

“IOFF_F”, “kg/m:sup:`2`/s”, “Ice Flux from Coupler due to Land-Model Snow Capping”,

“SALT_F”, “kg/m:sup:`2`/s”, “Salt Flux from Coupler (kg of salt/m^2/s)”,

“SENH_F”, “kg/m:sup:`2`/s”, “Sensible Heat Flux from Coupler”,

“LWUP_F”, “Watts/m:sup:`2`”, “Longwave Heat Flux (up) from Coupler”,

“LWDN_F”, “Watts/m:sup:`2`”, “Longwave Heat Flux (down) from Coupler”,

“MELTH_F”, “Watts/m:sup:`2`”, “Melt Heat Flux from Coupler”,

“IFRAC”, “unitless fraction”, “Ice Fraction from Coupler”,

“HMXL and HMXL_2”, “cm”, “Mixed-Layer Depth”,

“XMXL and XMXL_2”, “cm”, “Maximum Mixed-Layer Depth”,

“TMXL”, “cm”, “Minimum Mixed-Layer Depth”,

“HBLT”, “cm”, “Boundary-Layer Depth”,

“XBLT”, “cm”, “Maximum Boundary-Layer Depth”,

“TBLT”, “cm”, “Minimum Boundary-Layer Depth”,

“FW”, “cm/s”, “Freshwater Flux”,

“ADVT”, “cm/:sup:`o`C/s”, “Vertically-Integrated T Advection Tendency”,

“ADVS”, “cm g/km/s”, “Vertically-Integrated S Advection Tendency”,

“dTEMP_POS_2D”, “:sup:`o`C”, “max positive column temperature timestep diff”,

“dTEMP_NEG_2D”, “:sup:`o`C”, “max negative column temperature timestep diff”,

“KAPPA_ISOP”, “cm:sup:`2`/s”, “Isopycnal diffusion coefficient”,

“KAPPA_THIC”, “cm:sup:`2`/s”, “Thickness diffusion coefficient”,

“HOR_DIFF”, “cm:sup:`2`/s”, “Horizontal diffusion coefficient”,

“DIA_DEPTH”, “cm”, “Depth of the Diabatic Region at the Surface”,

“TLT”, “cm”, “Transition Layer Thickness”,

“INT_DEPTH”, “cm”, “Depth at which the Interior Region Starts”,

“UISOP”, “cm/s”, “Bolus Velocity in grid-x direction (diagnostic)”,

“VISOP”, “cm/s”, “Bolus Velocity in grid-y direction (diagnostic)”,

“WISOP”, “cm/s”, “Vertical Bolus Velocity (diagnostic)”,

“ADVT_ISOP”, “cm/:sup:`o`C/s”, “Vertically-Integrated T Eddy-Induced Advection Tendency (diagnostic)”,

“ADVS_ISOP”, “cm g/km/s”, “Vertically-Integrated S Eddy-Induced Advection Tendency (diagnostic)”,

“VNT_ISOP”, “:sup:`o`C/s”, “Heat Flux Tendency in grid-y Dir due to Eddy-Induced Vel (diagnostic)”,

“VNS_ISOP”, “g/km/s”, “Salt Flux Tendency in grid-y Dir due to Eddy-Induced Vel (diagnostic)”,

“KVMIX”, “cm:sup:`2`/s”, “Vertical diabatic diffusivity due to background or Tidal Mixing + background”,

“KVMIX_M”, “cm:sup:`2`/s”, “Vertical viscosity due to background or Tidal Mixing + background”,

“TPOWER”, “erg/s”, “Energy Used by Vertical Mixing”,

“VVC_BCK”, “cm:sup:`2`/s”, “Vertical viscosity due to background”,

“USUBM”, “cm/s”, “Submeso velocity in grid-x direction (diagnostic)”,

“VSUBM”, “cm/s”, “Submeso velocity in grid-y direction (diagnostic)”,

“WSUBM”, “cm/s”, “Vertical submeso velocity (diagnostic)”,

“ADVT_SUBM”, “cm/:sup:`o`C/s”, “Vertically-Integrated T submeso Advection Tendency (diagnostic)”,

“ADVS_SUBM”, “cm g/km/s”, “Vertically-Integrated S submeso Advection Tendency (diagnostic)”,

“VNT_SUBM”, “:sup:`o`C/s”, “Heat Flux Tendency in grid-y Dir due to submeso Vel (diagnostic)”,

“VNS_SUBM”, “:sup:`o`C/s”, “Salt Flux Tendency in grid-y Dir due to submeso Vel (diagnostic)”,

“HLS_SUBM”, “cm”, “Horizontal length scale used in submeso”,

“VDC_T”, “cm:sup:`2`/s”, “total diabatic vertical TEMP diffusivity”,

“VDC_S”, “cm:sup:`2`/s”, “total diabatic vertical SALT diffusivity”,

“UVEL2”, “cm:sup:`2`/s:sup:`2`”, “Velocity in grid-x direction”,

“VVEL2”, “cm:sup:`2`/s:sup:`2`”, “Velocity in grid-y direction”,

“WVEL2”, “cm:sup:`2`/s:sup:`2`”, “Vertical Velocity2”,

“RHO_VINT”, “g/cm:sup:`2`”, “Vertical Integral of In-Situ Density”,

“SFWF_WRST”, “kg/m:sup:`2`/s”, “Virtual Salt Flux due to weak restoring”,

“TAUX2”, “dyne:sup:`2`/cm:sup:`4`”, “Windstress2 in grid-x direction”,

“TAUY2”, “dyne:sup:`2`/cm:sup:`4`”, “Windstress2 in grid-y direction”,

“SSH2”, “cm:sup:`2`”, “SSH2”,

“VVC”, “cm:sup:`2`/s”, “total vertical momentum viscosity”,

“VDC_BCK”, “cm:sup:`2`/s”, “Vertical diabatic diffusivity due to background”,

Note that we append “_2” to a variable name in order to write that variable to two tavg output files; this convention can be extended to more than two streams in a similar fashion.

To customize tavg output in your run:

  • > create_newcase -case $CASE ... per the instructions
  • > cd $CASE
  • > cd $CASE/SourceMods/src.pop2
  • > cp $CCSMROOT/models/ocn/pop2/input_templates/$RES_tavg_contents .
  • > edit $RES_tavg_contents – comment out, activate, or change streams according the the instructions above.

then continue with the CIME $CASE configure, build, and run procedure.

14.2. Snapshot history files

If sufficient memory is not available for run-time accumulation of time-averaged history files or if the user simply needs an instantaneous view of the ocean state, snapshot history files can be written at regular intervals. The interval must be short enough that whatever time-averaging interval may be desired in the future, there will be three or more samples (snapshots) per averaging-interval. For monthly averages, snapshots should be collected at intervals of 10 days or less. Only one time-level of the prognostic variables and selected diagnostic variables needs to be saved, since second-moments and correlations can be computed later from these snapshot files, at the cost of retrieving a potentially large number of snapshot files. To choose which fields are written to the history files, a history contents file must be supplied with a list of fields desired. A sample file is included which contains all the currently available fields; the user may edit this file to select the desired fields. If a field is not currently included in the list of available fields, the user must modify the source code to make that field available (see the Reference Manual).

Table: History file namelist &history_nml Generation of snapshot history files history_freq_opt [‘never’],’nstep’, ‘nyear’, ‘nmonth’, ‘nday’, ‘nhour’, ‘nsecond’ units of time for history_freq history_freq [100000] number of units between output of snapshot history files history_outfile [‘unknown’] root filename with path of history file output (suffixes will be added) history_fmt [‘bin’],’nc’ format for history files (binary or netCDF) history_contents [‘history_contents’] input file containing names of fields requested to be output /

Table: Currently available history fields Name Units Description SHGT cm surface height UBTROP cm/s barotropic ‘zonal’ velocity VBTROP cm/s barotropic ‘meridional’ velocity UVEL cm/s ‘zonal’ velocity VVEL cm/s ‘meridional’ velocity TEMP ° C potential temperature SALT g/g (msu) salinity SUF cm2/s:sup:2 surface velocity flux in U direction SVF cm2/s:sup:2 surface velocity flux in V direction SHF W/m2 surface heat flux SFWF m/year surface fresh water flux SOLAR W/m2 solar short wave flux at surface

14.3. Movie files

One of the most exciting aspects of ocean simulation is the opportunity to visualize and animate the evolution of the model variables in time and space. Making movies that progress smoothly requires either output of model variables frequently enough to avoid jerkiness or temporal interpolation of model variables to similarly frequent intervals. Experience has shown that a snapshot every three days (see movie_freq) gives satisfactory results. Any variable can be output, but to reduce archiving cost and retrieval time, movie files typically contain only a few two-dimensional arrays, such as sea-surface temperature, salinity and height, and a few sub-surface variables. The choice of fields is made through an input movie contents file containing the names (one per line) of the fields requested. A sample file is included with a list of available fields; the user may modify this list to choose the desired fields. If a field does not appear in the list of available fields, the user may add fields by modifying the source code as described in the Reference Manual.

Table: Movie file namelist &movie_nml generation of snapshot movie files movie_freq_opt [‘never’], ‘nstep’, ‘nyear’,’nmonth’,’nday’, ‘nhour’,’nsecond’ units of time for movie_freq movie_freq [100000] number of units between output of movie files movie_outfile [‘unknown’] root filename with path of movie file output (suffixes will be added) movie_fmt [‘bin’],’nc’ format for movie file output (binary or netCDF) movie_contents [‘sample_movie_contents’] input file containing names of fields requested for movie output /

Table: Currently available movie fields Name Units Description SHGT cm surface height UTRANS cm:sup:`2`/s vertically integrated ‘zonal’ transport VTRANS cm:sup:`2`/s vertically integrated ‘meridional’ transport TEMP1_2 :sup:`°`C potential temperature averaged over levels 1,2 SALT1_2 g/g (msu) salinity averaged over levels 1,2 TEMP6 :sup:`°`C potential temperature at level 6 SALT6 g/g (msu) salinity at level 6 VORT 1/s relative vorticity at surface

POP2 does not support for current meters, drifters, or hydrographic sections.