From a36ffb8bde7dbf0330fb1a2e4d10b1827123e9bb Mon Sep 17 00:00:00 2001 From: Adiv Paradise Date: Thu, 10 Dec 2020 00:50:53 -0500 Subject: [PATCH] Added burn7 postprocessor documentation --- docs/index.rst | 9 +- docs/postprocessor.rst | 262 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 269 insertions(+), 2 deletions(-) create mode 100644 docs/postprocessor.rst diff --git a/docs/index.rst b/docs/index.rst index 87502da..1382c0d 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,15 +19,20 @@ __ tut_ * :ref:`genindex` * `Tutorial`__ +* `Postprocessor`__ * :ref:`search` -Package Contents -================ +.. _post: postprocessor.html +__ post_ + +Contents +======== .. toctree:: :maxdepth: 3 tutorial.rst + postprocessor.rst source/exoplasim .. :caption: Contents: diff --git a/docs/postprocessor.rst b/docs/postprocessor.rst new file mode 100644 index 0000000..d834497 --- /dev/null +++ b/docs/postprocessor.rst @@ -0,0 +1,262 @@ +--------------------------- +Burn7 Postprocessor Options +--------------------------- + +Building and Compiling +---------------------- + +To build ``burn7`` for the very first time, in the exoplasim/postprocessor folder, run::: + + ./build_init.sh + +**You must have a netCDF C++ library already available, which contains netcdf.h.** A +patched NetCDF library will be built with the features burn7 needs, and it will need +your netcdf.h. + +To recompile the postprocessor without rebuilding the patched NetCDF library, in the +exoplasim/postprocessor folder, run::: + + ./compile.sh + +Manual Usage +------------ + +To postprocess raw ExoPlaSim output into NetCDF files, you will need to provide ``burn7`` +with a namelist, direct its standard output to a log file, specify the raw output file, +and specify an output file (which does not need to exist yet)::: + + ./burn7.x -nburnout [raw_output_file] [output_file] + +If instead of ``-n`` you use ``-g``, ``.srv`` SERVICE files will be written, and a GraDS +control file will be create--e.g. if ``output_file`` is ``mymodel``, the output will be +``mymodel.srv`` and ``mymodel.ctl``. If you wish to use NetCDF output (the default), +you will need to give ``mymodel.nc`` as ``output_file`` instead of simply ``mymodel``.` + +The namelist file can take the following parameters: + +Parameters +########## + code : list of integers + A comma-separated list of integers, corresponding to the output codes listed in the table below. + vtype : {S, P} + Whether output vertical structure should be by sigma level (as is native for PlaSim), or converted to pressure levels. Strongly recommend keeping this to S, for sigma levels. + htype : {S, F, Z, G} + Whether horizontal representation should be as spherical harmonics (S), Fourier coefficients (F), zonal averagez (Z), or Gauss-spaced latitude-longitude grid (G). Strongly recommend keeping this to G, unless you know what you're doing. + mean : {0, 1, 2, 3} + What kind of averaging to do. 3 is the default, and 0 is no time averaging. 1 is monthly means, and 2 is monthly standard deviations. 3 is a combination of both. Mean!=0 can only be used with htype=G. + netcdf : {0, 1} + If 1, write NetCDF output file; if 0, write ``.srv`` SERVICE output. + mars : {0, 1} (optional) + If 1, use Mars defaults for computing derived variables. + gravity : float (optional) + Surface gravity in m/s\ :sup:`2`. Defaults to Earth gravity. + radius : float (optional) + Planet radius in meters. Defaults to Earth's radius. + +Postprocessor Variable Codes +---------------------------- + ++----------+-------+----------------------------------------+---------------------------+---------------+ +| Variable | Code | Description | Units | Notes | ++==========+=======+========================================+===========================+===============+ +| mld | 110 | mixed layer depth | m | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| sg | 129 | surface geopotential | m\ :sup:`2` s\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| ta | 130 | air temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| ua | 131 | eastward wind | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| va | 132 | northward wind | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| hus | 133 | specific humidity | kg/kg | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| ps | 134 | surface air pressure | hPa | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| wap | 135 | vertical air velocity | Pa s-1 | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| wa | 137 | upward wind | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| zeta | 138 | atm relative vorticity | s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| ts | 139 | surface temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| mrso | 140 | lwe of soil moisture content | m | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| snd | 141 | surface snow thickness | m | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| prl | 142 | lwe of large scale precipitation | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| prc | 143 | convective precipitation rate | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| prsn | 144 | lwe of snowfall amount | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| bld | 145 | dissipation in boundary layer | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| hfss | 146 | surface sensible heat flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| hfls | 147 | surface latent heat flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| stf | 148 | streamfunction | m\ :sup:`2` s\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| psi | 149 | velocity potential | m\ :sup:`2` s\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| psl | 151 | air pressure at sea level | hPa | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| pl | 152 | log surface pressure | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| d | 155 | divergence of wind | s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| zg | 156 | geopotential height | m | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| hur | 157 | relative humidity | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tps | 158 | tendency of surface air pressure | Pa s-1 | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| u3 | 159 | u* | m\ :sup:`3` s\ :sup:`-3` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| mrro | 160 | surface runoff | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| clw | 161 | liquid water content | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| cl | 162 | cloud area fraction in layer | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tcc | 163 | total cloud cover | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| clt | 164 | cloud area fraction | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| uas | 165 | eastward wind 10m | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| vas | 166 | northward wind 10m | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tas | 167 | air temperature 2m | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| td2m | 168 | dew point temperature 2m | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tsa | 169 | surface temperature accumulated | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tsod | 170 | deep soil temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dsw | 171 | deep soil wetness | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| lsm | 172 | land binary mask | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| z0 | 173 | surface roughness length | m | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| alb | 174 | surface albedo | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| as | 175 | surface albedo | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| rss | 176 | surface net shortwave flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| rls | 177 | surface net longwave flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| rst | 178 | toa net shortwave flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| rlut | 179 | toa net longwave flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tauu | 180 | surface eastward stress | Pa | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tauv | 181 | surface northward stress | Pa | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| evap | 182 | lwe of water evaporation | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tso | 183 | climate deep soil temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| wsoi | 184 | climate deep soil wetness | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| vegc | 199 | vegetation cover | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| rsut | 203 | toa outgoing shortwave flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| ssru | 204 | surface solar radiation upward | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| stru | 205 | surface thermal radiation upward | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tso2 | 207 | soil temperature level 2 | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tso3 | 208 | soil temperature level 3 | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tso4 | 209 | soil temperature level 4 | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| sic | 210 | sea ice cover | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| sit | 211 | sea ice thickness | m | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| vegf | 212 | forest cover | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| snm | 218 | snow melt | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| sndc | 221 | snow depth change | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| prw | 230 | atmosphere water vapor content | kg m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| glac | 232 | glacier cover | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| tsn | 238 | snow temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| spd | 259 | wind speed | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| pr | 260 | total precipitation | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| ntr | 261 | net top radiation | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| nbr | 262 | net bottom radiation | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| hfns | 263 | surface downward heat flux | W m\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| wfn | 264 | net water flux | m s\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| lwth | 266 | local weathering | W earth | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| grnz | 267 | ground geopotential | m\ :sup:`2` s\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| icez | 301 | glacier geopotential | m\ :sup:`2` s\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| netz | 302 | net geopotential | m\ :sup:`2` s\ :sup:`-2` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dpdx | 273 | d(ps)/dx | Pa m\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dpdy | 274 | d(ps)/dy | Pa m\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| hlpr | 277 | half level pressure | Pa | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| flpr | 278 | full level pressure | Pa | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| czen | 318 | cosine solar zenith angle | nondimensional | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| wthpr | 319 | weatherable precipitation | mm day\ :sup:`-1` | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| mint | 320 | minimum temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| maxt | 321 | maximum temperature | K | | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| cape | 322 | convective available potential energy | J kg\ :sup:`-1` | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| lnb | 323 | level of neutral buoyancy | hPa | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| sdef | 324 | troposphere entropy deficit | nondimensional | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| absz | 325 | sigma-0.85 abs vorticity | s\ :sup:`-1` | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| umax | 326 | maximum potential intensity | m s\ :sup:`-1` | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| vent | 327 | ventilation index | nondimensional | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| vrumax | 328 | ventilation-reduced maximum wind | m s\ :sup:`-1` | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| gpi | 329 | genesis potential index | nondimensional | Storm Clim. | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dfu | 404 | shortwave up | W m\ :sup:`-2` | Snapshot Only | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dfd | 405 | shortwave down | W m\ :sup:`-2` | Snapshot Only | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dftu | 406 | longwave up | W m\ :sup:`-2` | Snapshot Only | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dftd | 407 | longwave down | W m\ :sup:`-2` | Snapshot Only | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dtdt | 408 | radiative heating rate | K s\ :sup:`-1` | Snapshot Only | ++----------+-------+----------------------------------------+---------------------------+---------------+ +| dfdz | 409 | flux convergence | W m\ :sup:`-3` | Snapshot Only | ++----------+-------+----------------------------------------+---------------------------+---------------+ + \ No newline at end of file