= PALM Program control =
How to set up and run the model, how to process and interpret model output....

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'''PALM core'''\\\\
[wiki:doc/tec/gov     Governing equations ATMOSPHERE]\\
[wiki:doc/tec/ocean   Governing equations OCEAN]\\
[wiki:doc/tec/pres    Pressure solver]\\
[wiki:doc/tec/sgs     Turbulence closure]\\
[wiki:doc/tec/discret Discretization]\\
[wiki:doc/tec/bc      Boundary conditions]\\
[wiki:doc/tec/initialization Initialization]\\
{{{#!comment
[wiki:doc/tec/1dmodel 1D model for precursor runs]
}}}
      }}}
      {{{#!td style="border: none;vertical-align:top; width:20%"
'''Additional features'''\\\\
[wiki:doc/tec/coupled      Atmosphere-ocean coupling]\\
[wiki:doc/tec/microphysics Cloud microphysics]\\
[wiki:doc/tec/nesting      Grid nesting]\\
[wiki:doc/tec/lcm          Lagrangian cloud model (LCM)]\\
[wiki:doc/tec/lpm          Lagrangian particle model (LPM)]\\
[wiki:doc/tec/lsm          Land surface model (LSM)]\\
[wiki:doc/tec/lsf          Large-scale forcing]\\
[wiki:doc/tec/nudging      Nudging]\\
[wiki:doc/tec/canopy       Plant canopy model (PCM)]\\
[wiki:doc/tec/radiation    Radiation models]\\
[wiki:doc/tec/wtm          Wind turbine model (WTM)]\\
      }}}
      {{{#!td style="border: none;vertical-align:top; width:20%"
'''Technical aspects'''\\\\
[wiki:doc/tec/doxygen Code documentation with Doxygen]\\
[wiki:doc/tec/data Data handling]\\
[wiki:doc/tec/general General code structure]\\
[wiki:doc/ Machine-related information]\\
{{{#!comment
      * [wiki:doc/app/machine/kisti   IBM-Regatta (KISTI)]
      * [wiki:doc/app/machine/hlrnIII Cray-XC40 (HLRN)]
      * [wiki:doc/app/machine/kyushu_univ Kyushu University Computing Center]
}}}
[wiki:doc/tec/modeloperation Model operation]\\
[wiki:doc/tec/parallel Parallelization and optimization]\\
[wiki:doc/tec/particle Particle code structure]\\
[wiki:doc/tec/preproc Pre-processor directives]\\
[wiki:doc/tec/topography Topography implementation]\\
[wiki:doc/tec/user User-code implementation]\\

{{{#!comment
move somewhere else
      * [wiki:doc/tec/contributions Code contributions]
      * [wiki:doc/tec/naming_convention Rules of documentation and naming conventions]
}}}

      }}}
   }}}
}}}



== Model setup ==
* '''[wiki:doc/app/par Control parameters]'''
   * [wiki:doc/app/inipar     Initialization]
   * [wiki:doc/app/d3par      Runtime]
\\
   * Optional parameter packages
      * [wiki:doc/app/dvrpar     dvr graphics output]
      * [wiki:doc/app/parpar     Lagrangian particle model]
      * [wiki:doc/app/lsmpar     Land surface model]
      * [wiki:doc/app/nestpar    Nesting]
      * [wiki:doc/app/canpar     Plant canopy model]
      * [wiki:doc/app/radpar     Radiation model]
      * [wiki:doc/app/sppar      Spectra output]
      * [wiki:doc/app/flpar      Virtual flight model]
      * [wiki:doc/app/wind_turbine_par     Wind turbine model]
   * [wiki:doc/app/parlist    '''Alphabetical list of all parameters''']


== Model operation ==
* Launching a simulation (mrun, mrungui, example of minimum configuration file, Interactive mode and debugging)
* Monitoring a simulation (Monitoring batch jobs: PALM watchdog)
* Simulation chains (Initialization and restart runs)
\\
* Debugging

== User code ==
* [wiki:doc/app/userint/int     Available interfaces to PALM core]
* [wiki:doc/app/userint/comp    Compiling and linking of user code]
* [wiki:doc/app/userpar         User-defined control parameters (Definition of user-defined parameters)]
* [wiki:doc/app/userint/subd    User-defined domains (should be specified, no one can imagine what this means)]
* [wiki:doc/app/userint/output  User-defined data output]




= PALM Data I/O and visualization =
(to be resorted!!)
* '''[wiki:doc/app/iofiles Input/Output files]'''

* '''[wiki:doc/app/netcdf  netCDF data output]'''
   * [wiki:doc/app/ncgen Generation of a PALM netCDF file]
   * [wiki:doc/app/ncexample Example of a PALM netCDF data set]
   * [wiki:doc/app/maskedoutput Masked data output]
* '''[wiki:doc/app/ncl  Postprocessing with NCL]'''
   * [wiki:doc/app/nclparlist  List of parameters for PALM NCL scripts]
* [wiki:doc/app/idl Postprocessing with IDL]
* [wiki:doc/app/dvr Visualization with dvr]
* [wiki:doc/app/vapor Visualization with VAPOR]
* [wiki:doc/app/img2video Creating animations with img2video]
* [wiki:doc/app/img2stereo Creating stereo images with img2stereo]







= [wiki:doc/app/examples Simulation examples] =
!!!needs special care!!!
      * [wiki:doc/app/examples/cbl      Minimum set for simulating the CBL]
      * [wiki:doc/app/examples/topo     Topography]
      * [wiki:doc/app/examples/turbinf  Turbulent inflow]
      * [wiki:doc/app/examples/ocean    Ocean runs]
      * [wiki:doc/app/examples/coupled  Coupled atmosphere-ocean runs]
      * [wiki:doc/app/examples/lsf  Runs with large scale forcing and nudging]
      * [wiki:doc/app/examples/rrtmg  Run with land surface model and coupled to the RRTMG radiation model]




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[[TracNav(doc/toc|nocollapse)]]
}}}
= PALM Model Documentation =
----
==   Model description ==
===   Model formulation
...

=== Embedded models
...

=== Technical realization
...

----
==   User manual

===  [wiki:doc/app/jobsteering  Steering of interactive / batch runs]
      * [wiki:doc/app/jobcontrol     Job control with mrun]
      * [wiki:doc/app/mrungui        Using the GUI: mrungui]
      * [wiki:doc/app/palm_wd        Monitoring batch jobs: PALM watchdog]
      * [wiki:doc/app/configexample  Example of a minimum configuration file]
      * [wiki:doc/app/runs           Initialization and restart runs / Handling of large binary restart files]
      * [wiki:doc/app/intdbg         Interactive mode and debugging]
      * [wiki:doc/app/packages       Optional software packages]

===   Model steering
      * '''[wiki:doc/app/par Parameters]'''
         * [wiki:doc/app/inipar     Initialization]
         * [wiki:doc/app/d3par      Runtime]
         * [wiki:doc/app/nestpar    Nesting]
         * [wiki:doc/app/lsmpar     Land surface]
         * [wiki:doc/app/canpar     Plant canopy]
         * [wiki:doc/app/parpar     Particles]
         * [wiki:doc/app/radpar     Radiation]
         * [wiki:doc/app/sppar      Spectra]
         * [wiki:doc/app/stg_par    Synthetic Turbulence]
         * [wiki:doc/app/flpar      Virtual flights]
         * [wiki:doc/app/wind_turbine_par     Wind turbine model]
         * [wiki:doc/app/dvrpar     dvr graphics]
         * [wiki:doc/app/parlist    Alphabetical list of all parameters]
      * '''[wiki:doc/app/userint    User Interface]'''
         * [wiki:doc/app/userint/int     Interfaces]
         * [wiki:doc/app/userpar         Parameters for user interface]
         * [wiki:doc/app/userint/userpar         Definition of user-defined parameters]
         * [wiki:doc/app/userint/subd    User-defined domains]
         * [wiki:doc/app/userint/output  User-defined output quantities]
         * [wiki:doc/app/userint/comp    Compiling and linking]
      * '''[wiki:doc/app/iofiles Input/Output files]'''
         * [wiki:doc/app/iofiles/pids    Palm input data standard]

===   [wiki:doc/app/examples Steering examples for special setups]
      * [wiki:doc/app/examples/cbl      Minimum set for simulating the CBL]
      * [wiki:doc/app/examples/topo     Topography]
      * [wiki:doc/app/examples/turbinf  Turbulent inflow]
      * [wiki:doc/app/examples/ocean    Ocean runs]
      * [wiki:doc/app/examples/coupled  Coupled atmosphere-ocean runs]
      * [wiki:doc/app/examples/lsf  Runs with large scale forcing and nudging]
      * [wiki:doc/app/examples/rrtmg  Run with land surface model and coupled to the RRTMG radiation model]

===   Data handling/visualization
      * '''[wiki:doc/app/netcdf  netCDF data output]'''
         * [wiki:doc/app/ncgen Generation of a PALM netCDF file]
         * [wiki:doc/app/ncexample Example of a PALM netCDF data set]
         * [wiki:doc/app/maskedoutput Masked data output]
      * '''[wiki:doc/app/ncl  Postprocessing with NCL]'''
         * [wiki:doc/app/nclparlist  List of parameters for PALM NCL scripts]
      * [wiki:doc/app/idl Postprocessing with IDL]
      * [wiki:doc/app/dvr Visualization with dvr]
      * [wiki:doc/app/vapor Visualization with VAPOR]
      * [wiki:doc/app/img2video Creating animations with img2video]
      * [wiki:doc/app/img2stereo Creating stereo images with img2stereo]

===   [wiki:doc/app/errmsg  Error messages]
      * [wiki:doc/app/errmsg#PA0001 PALM standard code (PA****)]
      * [wiki:doc/app/errmsg#UI0001 User interface (UI****)]
      * [wiki:doc/app/errmsg#NC NetCDF (NC****)]
----

==   PALM code development
      * [wiki:doc/tec/releasenotes Release notes]
      * [wiki:doc/tec/changelog History of changes (2018-current)]
      * [wiki:doc/tec/changelog_2017 History of changes (2017)]
      * [wiki:doc/tec/changelog_2013-2016 History of changes (2013-2016)]
      * [wiki:doc/tec/changelog_2009-2012 History of changes (2009-2012)]
      * [wiki:doc/tec/developerrules Rules for developers]
      * [wiki:doc/tec/palm4udev PALM-4U development]
      * [wiki:doc/tec/eclipse Code development with eclipse]
      * [wiki:doc/tec/bugs Known bugs]
      * [wiki:doc/tec/testsuite Testsuite and Testserver]
      * [wiki:doc/tec/gpu OpenACC tests]

----

==   Machine related informations
...