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| 4 | <meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 4.5.1</title> |
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| 6 | <meta content="Siegfried Raasch" name="AUTHOR"> <meta content="20041022;12155949" name="CREATED"> <meta content="20041117;11232134" name="CHANGED"> <meta content="parallel LES model" name="KEYWORDS"> <style> |
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| 7 | <!-- |
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| 8 | @page { size: 21cm 29.7cm } |
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| 9 | --> |
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| 10 | </style></head><body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.1 |
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| 11 | NetCDF data output <span style="color: rgb(255, 0, 0);"></span></font></h4> |
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| 12 | <p style="line-height: 100%;">The standard data output of |
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| 13 | PALM is NetCDF (<span style="font-weight: bold;">Net</span>work |
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| 14 | <span style="font-weight: bold;">C</span>ommon <span style="font-weight: bold;">D</span>ata <span style="font-weight: bold;">F</span>orm) in 64-bit offset format. NetCDF is an |
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| 15 | interface to a library of data access functions for |
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| 16 | storing and retrieving data in the form of arrays. NetCDF is an |
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| 17 | abstraction that supports a view of data as a collection of |
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| 18 | self-describing, <span style="font-weight: bold;">portable</span> |
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| 19 | objects that can be accessed through a simple interface (protable means |
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| 20 | that NetCDF data files can be read on any machine regardless of where |
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| 21 | they |
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| 22 | have been created). Array values may be accessed directly, without |
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| 23 | knowing details of how the data are stored. Auxiliary information about |
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| 24 | the data, such as what units are used, may be stored with the data. |
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| 25 | Generic utilities and application programs can access NetCDF datasets |
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| 26 | (files) and transform, combine, analyze, or display specified fields of |
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| 27 | the data, e.g. the contents of a NetCDF dataset can be viewed using the |
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| 28 | command <span style="font-family: monospace;">ncdump</span> |
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| 29 | (see <a href="#ncdump">further below</a>). |
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| 30 | Many (public domain) graphic software has built in interfaces to read |
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| 31 | NetCDF datasets (e.g. <span style="font-weight: bold;">ferret</span> |
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| 32 | or <span style="font-weight: bold;">NCL</span>). |
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| 33 | The complete NetCDF documentation |
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| 34 | is available from the <a href="http://www.unidata.ucar.edu/packages/netcdf/docs.html">NetCDF |
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| 35 | homepage</a>. The NetCDF tutorial for FORTRAN90 can also be found |
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| 36 | on <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/manual/netcdf/netcdf-3_f90_tutorial.pdf">our |
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| 37 | web server</a>.</p><p style="line-height: 100%;">The |
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| 38 | general output format of PALM data is determined by the runtime-parameter <a href="chapter_4.2.html#data_output_format">data_output_format</a> |
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| 39 | (<span style="font-weight: bold;">data_output_format</span> |
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| 40 | = <span style="font-style: italic;">'netcdf'</span>, |
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| 41 | by default). For historical reasons, some alternative formats can be |
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| 42 | selected (see <a href="chapter_4.2.html#data_output_format">data_output_format</a>). |
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| 43 | The accuracy of the NetCDF output data can be set with parameter <a href="chapter_4.1.html#netcdf_precision">netcdf_precision</a>. |
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| 44 | By default, data have single (4 byte) precision. Runtime-parameter <a href="chapter_4.2.html#netcdf_data_format">netcdf_data_format</a> |
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| 45 | can be used to choose between the different NetCDF file formats |
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| 46 | (classic, 64-bit offset, NetCDF4/HDF5). The 64-bit offset format allows |
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| 47 | creating large files (file size only limited by the underlying file |
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| 48 | system), but each output variable (array) is still limited to 2GB. In |
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| 49 | NetCDF4 format, there is no limit for the size of variables, and it |
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| 50 | also allows parallel I/O into one output file. However, some (graphic) |
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| 51 | software still does not support NetCDF4 format.<br></p>PALM allows the output of |
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| 52 | various |
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| 53 | data (e.g. cross sections, vertical profiles, timeseries, etc.) into |
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| 54 | different files. The following table gives an overview about the |
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| 55 | different kind of NetCDF output data offered by PALM. Beside the local |
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| 56 | names of the files, the table also lists the minimum parameter settings |
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| 57 | which |
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| 58 | are necessary to switch on the output, as well as the parameters to be |
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| 59 | used to control the output.<br><br><table style="text-align: left; width: 750px; height: 226px;" border="1" cellpadding="2" cellspacing="2"><tbody><tr><td align="left" valign="top"><span style="font-weight: bold;">kind of data</span></td><td align="left" valign="top"><span style="font-weight: bold;">local filename</span></td><td align="left" valign="top"><span style="font-weight: bold;">parameter settings necessary to |
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| 60 | switch on output</span></td><td align="left" valign="top"><span style="font-weight: bold;">further |
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| 61 | parameters for output control</span></td></tr><tr><td align="left" valign="top">vertical profiles</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_PR_NETCDF">DATA_1D_PR_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_pr">data_output_pr</a>, |
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| 62 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 63 | (or <a href="chapter_4.2.html#dt_dopr">dt_dopr</a>)</td><td align="left" valign="top"><a href="chapter_4.2.html#averaging_interval">averaging_interval</a>, |
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| 64 | (or <a href="chapter_4.2.html#averaging_interval_pr">averaging_interval_pr</a>), |
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| 65 | <a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 66 | <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a>, |
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| 67 | <a href="chapter_4.2.html#dt_averaging_input_pr">dt_averaging_input_pr</a>, |
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| 68 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 69 | (or <a href="chapter_4.2.html#skip_time_dopr">skip_time_dopr</a>), |
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| 70 | <a href="chapter_4.1.html#statistic_regions">statistic_regions</a></td></tr><tr><td align="left" valign="top">timeseries</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_TS_NETCDF">DATA_1D_TS_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_dots">dt_dots</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 71 | <a href="chapter_4.1.html#statistic_regions">statistic_regions</a></td></tr><tr><td align="left" valign="top">spectra</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_SP_NETCDF">DATA_1D_SP_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#comp_spectra_level">comp_spectra_level</a>, |
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| 72 | <a href="chapter_4.2.html#data_output_sp">data_output_sp</a>, |
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| 73 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 74 | (or <a href="chapter_4.2.html#dt_dosp">dt_dosp</a>), |
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| 75 | <a href="chapter_4.2.html#spectra_direction">spectra_direction</a></td><td align="left" valign="top"><a href="chapter_4.2.html#averaging_interval">averaging_interval</a> (or |
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| 76 | <a href="chapter_4.2.html#averaging_interval_sp">averaging_interval_sp</a>), |
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| 77 | <a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 78 | <a href="chapter_4.2.html#dt_averaging_input_pr">dt_averaging_input_pr</a>, |
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| 79 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 80 | (or <a href="chapter_4.2.html#skip_time_dosp">skip_time_dosp)</a></td></tr><tr><td align="left" valign="top">2d cross section (xy)</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_2D_XY_NETCDF">DATA_2D_XY_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 81 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 82 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 83 | (or <a href="chapter_4.2.html#dt_do2d_xy">dt_do2d_xy</a>), |
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| 84 | <a href="chapter_4.2.html#section_xy">section_xy</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 85 | <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>, |
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| 86 | <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>, |
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| 87 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 88 | (or <a href="chapter_4.2.html#skip_time_do2d_xy">skip_time_do2d_xy</a>)</td></tr><tr><td align="left" valign="top">2d cross section (xy), |
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| 89 | time-averaged</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_2D_XY_AV_NETCDF">DATA_2D_XY_AV_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 90 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 91 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 92 | (or <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> or |
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| 93 | <a href="chapter_4.2.html#dt_do2d_xy">dt_do2d_xy</a>), |
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| 94 | <a href="chapter_4.2.html#section_xy">section_xy</a></td><td align="left" valign="top"><a href="chapter_4.2.html#averaging_interval">averaging_interval</a>, |
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| 95 | <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a>, |
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| 96 | <a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 97 | <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>, |
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| 98 | <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>, |
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| 99 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 100 | (or <a href="chapter_4.2.html#skip_time_data_output_av">skip_time_data_output_av</a>, |
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| 101 | or <a href="chapter_4.2.html#skip_time_do2d_xy">skip_time_do2d_xy</a>)</td></tr><tr><td align="left" valign="top">2d cross section (xz)</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_2D_XZ_NETCDF">DATA_2D_XZ_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 102 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 103 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 104 | (or <a href="chapter_4.2.html#dt_do2d_xz">dt_do2d_xz</a>), |
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| 105 | <a href="chapter_4.2.html#section_xz">section_xz</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 106 | <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>, |
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| 107 | <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>, |
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| 108 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 109 | (or <a href="chapter_4.2.html#skip_time_do2d_xz">skip_time_do2d_xz</a>)</td></tr><tr><td align="left" valign="top">2d cross section (xz), |
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| 110 | time-averaged</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_2D_XZ_AV_NETCDF">DATA_2D_XZ_AV_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 111 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 112 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 113 | (or <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> or |
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| 114 | <a href="chapter_4.2.html#dt_do2d_xz">dt_do2d_xz</a>), |
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| 115 | <a href="chapter_4.2.html#section_xz">section_xz</a></td><td align="left" valign="top"><a href="chapter_4.2.html#averaging_interval">averaging_interval</a>, |
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| 116 | <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a>, |
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| 117 | <a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 118 | <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>, |
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| 119 | <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>, |
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| 120 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 121 | (or <a href="chapter_4.2.html#skip_time_data_output_av">skip_time_data_output_av</a>, |
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| 122 | or <a href="chapter_4.2.html#skip_time_do2d_xz">skip_time_do2d_xz</a>)</td></tr><tr><td align="left" valign="top">2d cross section (yz)</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_2D_YZ_NETCDF">DATA_2D_YZ_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 123 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 124 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 125 | (or <a href="chapter_4.2.html#dt_do2d_yz">dt_do2d_yz</a>), |
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| 126 | <a href="chapter_4.2.html#section_yz">section_yz</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 127 | <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>, |
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| 128 | <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>, |
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| 129 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 130 | (or <a href="chapter_4.2.html#skip_time_do2d_yz">skip_time_do2d_yz</a>)</td></tr><tr><td align="left" valign="top">2d cross section (yz), |
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| 131 | time-averaged</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_2D_YZ_AV_NETCDF">DATA_2D_YZ_AV_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 132 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 133 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 134 | (or <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> or |
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| 135 | <a href="chapter_4.2.html#dt_do2d_yz">dt_do2d_yz</a>), |
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| 136 | <a href="chapter_4.2.html#section_yz">section_yz</a></td><td align="left" valign="top"><a href="chapter_4.2.html#averaging_interval">averaging_interval</a>, |
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| 137 | <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a>, |
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| 138 | <a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 139 | <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>, |
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| 140 | <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>, |
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| 141 | <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 142 | (or <a href="chapter_4.2.html#skip_time_data_output_av">skip_time_data_output_av</a>, |
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| 143 | or <a href="chapter_4.2.html#skip_time_do2d_yz">skip_time_do2d_yz</a>)</td></tr><tr><td align="left" valign="top">3d volume</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_3D_NETCDF">DATA_3D_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 144 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 145 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 146 | (or <a href="chapter_4.2.html#dt_do3d">dt_do3d</a>)</td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>, |
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| 147 | <a href="chapter_4.2.html#do3d_at_begin">do3d_at_begin</a>, |
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| 148 | <a href="chapter_4.2.html#nz_do3d">nz_do3d</a>, <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 149 | (or <a href="chapter_4.2.html#skip_time_do3d">skip_time_do3d</a>)</td></tr><tr><td align="left" valign="top">3d volume, time-averaged</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_3D_AV_NETCDF">DATA_3D_AV_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output">data_output</a> |
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| 150 | (or <a href="chapter_4.3.html#data_output_user">data_output_user</a>), |
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| 151 | <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 152 | (or <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> or |
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| 153 | <a href="chapter_4.2.html#dt_do3d">dt_do3d</a>)</td><td align="left" valign="top"><a href="chapter_4.2.html#averaging_interval">averaging_interval</a>, |
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| 154 | <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a>, |
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| 155 | <a href="chapter_4.2.html#data_output_format">data_output_format</a>, <a href="chapter_4.2.html#do3d_at_begin">do3d_at_begin</a>, |
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| 156 | <a href="chapter_4.2.html#nz_do3d">nz_do3d</a>, <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 157 | (or <a href="chapter_4.2.html#skip_time_data_output_av">skip_time_data_output_av</a>, |
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| 158 | or <a href="chapter_4.2.html#skip_time_do3d">skip_time_do3d</a>)</td></tr><tr><td align="undefined" valign="undefined">particle |
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| 159 | timeseries</td><td style="vertical-align: top;"><a href="chapter_3.4.html#DATA_1D_PTS_NETCDF">DATA_1D_PTS_NETCDF</a></td><td style="vertical-align: top;"><a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 160 | (or <a href="chapter_4.2.html#dt_dopts">dt_dopts</a>)</td><td align="undefined" valign="undefined"><br> |
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| 161 | </td></tr><tr><td align="left" valign="top">particle attributes</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_PRT_NETCDF">DATA_PRT_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_write_particle_data">dt_write_particle_data</a></td><td align="left" valign="top"><br> |
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| 162 | </td></tr></tbody></table><br><br><span style="font-weight: bold;">Creating, contents and |
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| 163 | post-processing of a PALM NetCDF file</span><br><br>This |
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| 164 | section describes, step-by-step, the creation, storage, and |
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| 165 | post-processing of PALM NetCDF datasets considering the output of 2d |
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| 166 | horizontal (xy) cross sections as example. The parameter settings |
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| 167 | described below are those of the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example |
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| 168 | parameter file</a> (see <a href="chapter_4.4.1.html">chapter |
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| 169 | 4.4.1</a>) so this parameter file can be used to retrace the |
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| 170 | following explanations.<br><br><ol><li>Output |
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| 171 | of xy cross |
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| 172 | sections requires to set at least three parameters: first, the temporal |
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| 173 | interval of the output time (run parameter <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
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| 174 | or <a href="chapter_4.2.html#dt_do2d_xy"><u>dt_do2d_xy)</u></a><span style="text-decoration: none;">, second<span style="text-decoration: none;"></span>, |
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| 175 | the names of the quantities for which cross section output is wanted</span><span style="text-decoration: none;"><span style="text-decoration: none;"> (<a href="chapter_4.2.html#data_output">data_output</a></span></span>), |
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| 176 | and third, the position (height level given as gridpoint index) of the |
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| 177 | cross sections (<a href="chapter_4.2.html#section_xy">section_xy</a>). |
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| 178 | The string <span style="font-style: italic;">'_xy'</span> |
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| 179 | must be appended to the name strings assigned to <span style="font-weight: bold;">data_output</span> in |
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| 180 | either case. Output times |
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| 181 | cannot be defined |
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| 182 | directly but only via the output time interval, starting from the |
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| 183 | beginning of the initial 3d run (t=0, but no cross sections are |
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| 184 | written at the time t=0; exceptions see <a href="chapter_4.2.html#do2d_at_begin">do2d_at_begin</a>). |
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| 185 | As an exception, the first output time can be set independently with |
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| 186 | parameter <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a> |
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| 187 | (or <a href="chapter_4.2.html#skip_time_do2d_xy">skip_time_do2d_xy</a>).<br><br><span style="font-weight: bold;">Very important:</span><br>If |
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| 188 | no values have been assigned to <b>data_output</b> , <span style="font-weight: bold;">dt_data_output</span> (or <span style="font-weight: bold;">dt_do2d_xy</span>), and <b>section_xy</b>, |
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| 189 | or |
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| 190 | if the values given for <span style="font-weight: bold;">dt_data_output</span> |
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| 191 | (or <b>dt_do2d_xy</b>) or <span style="font-weight: bold;">skip_time_data_output</span> |
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| 192 | (or <span style="font-weight: bold;">skip_time_do2d_xy</span>) |
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| 193 | are |
|---|
| 194 | larger than the simulated time (see <a href="chapter_4.1.html#end_time">end_time</a>), |
|---|
| 195 | <b>then there will be no output!<br><br></b>For |
|---|
| 196 | output of time-averaged data, the string <span style="font-style: italic;">'_av'</span> has to be |
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| 197 | additionally appended to the respective name string (see <a href="chapter_4.2.html#data_output">data_output</a>).<br><br><br></li><li> |
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| 198 | <p style="line-height: 100%;">Instantaneous data are |
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| 199 | output in NetCDF |
|---|
| 200 | format |
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| 201 | into the |
|---|
| 202 | local file <a href="chapter_3.4.html#DATA_2D_XY_NETCDF">DATA_2D_XY_NETCDF</a>. |
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| 203 | This file must be linked with a permanent file by |
|---|
| 204 | using a file connection statement in the <b>mrun</b> |
|---|
| 205 | configuration |
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| 206 | file (see e.g. <a href="chapter_3.2.html">chapter |
|---|
| 207 | 3.2</a>). At the end of the run the local file is copied to this |
|---|
| 208 | file. Such a statement can look like this:<br><br><span style="font-family: monospace;"> |
|---|
| 209 | DATA_2D_XY_NETCDF out:loc:tr xy# |
|---|
| 210 | ~/$fname/OUTPUT/$fname _xy nc .</span><br><br>If |
|---|
| 211 | the respective <b>mrun</b> call is |
|---|
| 212 | like<br><br><span style="font-family: monospace;"> |
|---|
| 213 | mrun -d test -r xy# ... </span><br style="font-family: monospace;"><br>then the local |
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| 214 | file <tt><font style="font-size: 10pt;" size="2">DATA_2D_XY_NETCDF</font></tt> |
|---|
| 215 | is copied to the permanent file <tt><font style="font-size: 10pt;" size="2">~/test/OUTPUT/test/test_xy.nc</font> |
|---|
| 216 | </tt>. However, the character string <span style="font-family: mon; font-style: italic;">'</span><tt style="font-style: italic;"><font style="font-size: 10pt;" size="2">xy#</font></tt><span style="font-style: italic;">'</span> activating the |
|---|
| 217 | file connection statement (see third column of the |
|---|
| 218 | statement) must be given in the <b>mrun</b> call as |
|---|
| 219 | argument of the |
|---|
| 220 | option -r (and/or -o)<b>.</b> <span style="text-decoration: none;">If |
|---|
| 221 | t</span>his is forgotten by mistake, the model outputs the data |
|---|
| 222 | to |
|---|
| 223 | the local file, but this is not copied to the permanent file and thus |
|---|
| 224 | the data are not available for the user after the run has finished.<br><br>The |
|---|
| 225 | last (6th) column of the file connection statement, which defines the |
|---|
| 226 | additional file suffix, should be the string <span style="font-style: italic;">'nc'</span>, because many |
|---|
| 227 | application programs expect NetCDF files to have the file extension <span style="font-style: italic;">'.nc'</span>. (This |
|---|
| 228 | additional suffix given in the 6th column is always put at the very end |
|---|
| 229 | of the filename, even |
|---|
| 230 | in case of cycle numbers.)<br><br>Time averaged data are |
|---|
| 231 | output into local file <a href="chapter_3.4.html#DATA_2D_XY_AV_NETCDF">DATA_2D_XY_AV_NETCDF</a> |
|---|
| 232 | which requires an additional file connection statement<br><br><span style="font-family: monospace;"> |
|---|
| 233 | DATA_2D_XY_AV_NETCDF out:loc:tr xy# |
|---|
| 234 | ~/$fname/OUTPUT/$fname _xy_av nc .</span><br></p></li><li>Using <a href="chapter_4.2.html#netcdf_data_format">netcdf_data_format</a> > <span style="font-style: italic;">2</span> or <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a> = <span style="font-style: italic;">.F.</span> generates a single NetCDF file containing data from all propcessors. However, with |
|---|
| 235 | parallel runs and choice of <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a> |
|---|
| 236 | = <i>.T.</i> |
|---|
| 237 | each PE outputs the data of its subdomain |
|---|
| 238 | not directly to the NetCDF file but to a separate file with the name |
|---|
| 239 | PLOT2D_XY_<processor-Id>, |
|---|
| 240 | where <processor-Id> is a four digit number (e.g. |
|---|
| 241 | PLOT2D_XY_0000). These files have FORTRAN binary format. After PALM has |
|---|
| 242 | finished, their content is merged into the final local destination file |
|---|
| 243 | DATA_2D_XY_NETCDF by the program <span style="font-family: monospace;">combine_plot_fields</span>. <span style="font-weight: bold;"></span>This is done by |
|---|
| 244 | adding the following output command to the configuration file:<br><br><span style="font-family: monospace;"> OC:[[$ |
|---|
| 245 | ( echo $localhost | cut -c1-3 ) = imbh ]] && |
|---|
| 246 | combine_plot_fields.x .</span><br><br>Using |
|---|
| 247 | this call, possibly existing |
|---|
| 248 | files of the other cross sections (xz, yz) and of 3d volume data are |
|---|
| 249 | also merged to their respective NetCDF files. The tool writes |
|---|
| 250 | informative messages about the actions accomplished into the job |
|---|
| 251 | protocol, even if no files were found (i.e. the output command |
|---|
| 252 | may remain in the configuration file, even if no appropriate files |
|---|
| 253 | are created during the simulation). <br><br><br></li><li><a name="ncdump"></a>The contents of a NetCDF dataset can |
|---|
| 254 | be simply analyzed with the tool <span style="font-family: monospace;">ncdump</span> |
|---|
| 255 | (which is part of the NetCDF software). It can be used to display the |
|---|
| 256 | dimension (coordinate) names and lengths; variable names, types, and |
|---|
| 257 | shapes; attribute names and values; and optionally,<br>the values |
|---|
| 258 | of |
|---|
| 259 | data for all variables or selected variables in a netCDF dataset. The |
|---|
| 260 | file content (without displaying the gridpoint data of the quantities) |
|---|
| 261 | can be displayed with the command<br><br><span style="font-family: monospace;"> ncdump |
|---|
| 262 | -c <filename> .</span><br><br>Usage |
|---|
| 263 | of the <span style="font-family: monospace;">ncdump</span> |
|---|
| 264 | command requires that the path to the NetCDF software is appropriately |
|---|
| 265 | set. On the IMUK-Linux-cluster this path is set by default, on the |
|---|
| 266 | HLRN-IBM-Regatta, the user has to execute the command<br><br><span style="font-family: monospace;"> module |
|---|
| 267 | load netcdf .</span><br><br>Please |
|---|
| 268 | refer to the system documentation or system administrator on |
|---|
| 269 | how |
|---|
| 270 | to setup the correct NetCDF path on the respective host.<br><br>An |
|---|
| 271 | example how to interpret the <span style="font-family: monospace;">ncdump</span>-output |
|---|
| 272 | will be given <a href="#NetCDF_example">further below</a>.<br><br></li><li>There |
|---|
| 273 | are several application programs which can be used for graphical |
|---|
| 274 | display of NetCDF datasets. One of the easiest ways to display the PALM |
|---|
| 275 | data is the <a style="font-family: monospace;" href="http://ferret.wrc.noaa.gov/Ferret/">ferret</a> |
|---|
| 276 | graphical user interface (GUI). On the IMUK-Linux-cluster, this can be |
|---|
| 277 | called by |
|---|
| 278 | executing the command<br><br><span style="font-family: monospace;"> ferret |
|---|
| 279 | -gui .</span><br><br><span style="font-family: monospace;">ferret</span> is also |
|---|
| 280 | available at <a href="http://www.hlrn.de/doc/ferret/index.html">HLRN</a>. |
|---|
| 281 | Another possible tool is <span style="font-family: monospace;">ncview</span>, |
|---|
| 282 | which is also available at HLRN (see the <a href="http://www.hlrn.de/doc/ncview/index.html">HLRN |
|---|
| 283 | documentation</a>). Beside these general tools, the PALM group |
|---|
| 284 | will develop a graphical interface based on <a href="http://www.ncl.ucar.edu/">NCL</a> |
|---|
| 285 | (NCAR Command Language). This interface will be specially |
|---|
| 286 | designed |
|---|
| 287 | to display the PALM Data. A detailed documentation will be linked here |
|---|
| 288 | as soon as available.<br><br><br></li><li><a name="netcdf_example_program"></a>One |
|---|
| 289 | of the most flexible general ways for postprocessing NetCDF data |
|---|
| 290 | is reading these data into a FORTRAN program. The <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/read_palm_netcdf_data.f90"><font color="#000080">example program</font></a> shows |
|---|
| 291 | how to read 2d or 3d NetCDF datasets created by PALM. Compiling this |
|---|
| 292 | program requires that the |
|---|
| 293 | NetCDF library is installed (if neccessary, please ask your system |
|---|
| 294 | administrator). Some compilation instructions are given in the header |
|---|
| 295 | of the |
|---|
| 296 | example program.<br><br><br></li><li>By |
|---|
| 297 | default, each PALM job creates its own NetCDF files. If permanent files |
|---|
| 298 | with respective filenames are already existing, then new files with |
|---|
| 299 | higher cycle numbers will be created. However, in case of a job chain, |
|---|
| 300 | it is possible to extend the NetCDF datasets created by the initial |
|---|
| 301 | run with data from the restart run(s). As a result, data of |
|---|
| 302 | all |
|---|
| 303 | output times of the complete job chain are contained in one file and |
|---|
| 304 | the number of data files to be handled by the user may be reduced |
|---|
| 305 | significantly.<br>To extend a NetCDF dataset (created by a |
|---|
| 306 | previous run |
|---|
| 307 | of a job chain) with data from the current run requires that this |
|---|
| 308 | dataset must be provided as an INPUT file. This may be difficult in |
|---|
| 309 | case that PALM is running on a remote host because typically the output |
|---|
| 310 | data files from the previous run have been already transferred by <span style="font-weight: bold;">mrun</span> to the local |
|---|
| 311 | workstation with a file connection statement like<br><br><span style="font-family: monospace;"> |
|---|
| 312 | DATA_2D_XY_NETCDF |
|---|
| 313 | out:loc:tr xy#:xyf |
|---|
| 314 | ~/palm/current_version/JOBS/$fname/OUTPUT |
|---|
| 315 | _xy nc</span><br><br>and thus |
|---|
| 316 | they are not available on the remote host any more. <br>A |
|---|
| 317 | workaround for solving this problem is to create an additional copy of |
|---|
| 318 | the output file on the remote machine by adding the file connection |
|---|
| 319 | statement<br><br><span style="font-family: monospace;"> |
|---|
| 320 | DATA_2D_XY_NETCDF out:loc xy#:xyf |
|---|
| 321 | ~/palm/current_version/JOBS/$fname/OUTPUT _xy nc</span><br><br>This |
|---|
| 322 | additional copy can then be accessed from a restart job as an input |
|---|
| 323 | file using the file connection statement<br><br><span style="font-family: monospace;"> |
|---|
| 324 | DATA_2D_XY_NETCDF in:locopt xyf |
|---|
| 325 | ~/palm/current_version/JOBS/$fname/OUTPUT _xy nc</span><br><br>Here |
|---|
| 326 | the file attribut <span style="font-family: monospace;">locopt</span> |
|---|
| 327 | (2nd column) guarantees that the job continues if a permanent file does |
|---|
| 328 | not exist (e.g. in case of an initial run). Otherwise, the job would be |
|---|
| 329 | aborted.<br>Although the dataset created by the last run of a job |
|---|
| 330 | chain |
|---|
| 331 | will contain data from all selected time levels of the complete job |
|---|
| 332 | chain, the main disadvantage of this workaround is that the datasets |
|---|
| 333 | created by the remaining jobs (with lower cycle numbers) still exist |
|---|
| 334 | and may consume large disc space. They have to be deleted "by hand" by |
|---|
| 335 | the user on the local machine as well as on the remote |
|---|
| 336 | machine because they only contain redundant data from the |
|---|
| 337 | earlier |
|---|
| 338 | time levels which are already contained in the dataset created |
|---|
| 339 | by |
|---|
| 340 | the last job of the job chain.<br><br><span style="font-weight: bold;">Note:</span><br>Extension |
|---|
| 341 | of PALM NetCDF datasets of 2d horizontal cross sections requires that |
|---|
| 342 | parameters <a href="chapter_4.2.html#data-output">data_output</a> |
|---|
| 343 | and <a href="chapter_4.2.html#section_xy">section_xy</a> |
|---|
| 344 | for the restart runs are set identical to the initial run. In case of a |
|---|
| 345 | value mismatch between initial and restart runs, a warning is issued in |
|---|
| 346 | the job protocol file and the dataset will contain only data from those |
|---|
| 347 | timelevels calculated within the restart run.<br>Similar |
|---|
| 348 | restrictions apply for all other PALM NetCDF datasets (i.e. profiles, |
|---|
| 349 | vertical cross sections, volume data, etc.).</li></ol><br> <br><span style="font-weight: bold;"><a name="NetCDF_example"></a>Example |
|---|
| 350 | of a PALM NetCDF dataset</span><br><br>The |
|---|
| 351 | NetCDF dataset described here contains data of instantaneous horizontal |
|---|
| 352 | cross sections and has been created using the settings of the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example |
|---|
| 353 | parameter file</a> (see <a href="chapter_4.4.1.html">chapter |
|---|
| 354 | 4.4.1</a>), |
|---|
| 355 | i.e. it contains section data of the w-velocity-component and of the |
|---|
| 356 | potential temperature for vertical grid levels with index <span style="font-family: monospace;">k = 2</span> and <span style="font-family: monospace;">k = 10</span>, |
|---|
| 357 | selected by the respective parameter settings <a href="chapter_4.2.html#data_output">data_output</a> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'pt_xy'</span>, and <a href="chapter_4.2.html#section_xy">section_xy</a> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>. Output has been |
|---|
| 358 | created after every 900 s (<a href="chapter_4.2.html#dt_data_output">dt_data_output</a> |
|---|
| 359 | = <span style="font-style: italic;">900.0</span>). |
|---|
| 360 | Because of <a href="chapter_4.2.html#end_time">end_time</a> |
|---|
| 361 | = <span style="font-style: italic;">3600.0</span>, |
|---|
| 362 | the file contains data of 4 time levels (t = 900, 1800, 2700, 3600 s).<br>Supposed |
|---|
| 363 | that the name of the NetCDF dataset is <span style="font-family: monospace;">example_xy.nc</span>, |
|---|
| 364 | an analysis of the file contents using the command<br><br><span style="font-family: monospace;"> ncdump |
|---|
| 365 | -c example_xy.nc</span><br><br>will create the |
|---|
| 366 | following output. The original ncdump output is displayed using <span style="font-family: monospace;">fixed spacing</span>, |
|---|
| 367 | additional explanations are given in <span style="font-style: italic; font-family: monospace;">italian</span>.<br><br><div style="margin-left: 40px;"><span style="font-family: monospace;">netcdf example_xy { |
|---|
| 368 | |
|---|
| 369 | <span style="font-style: italic;">! filename</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">dimensions: |
|---|
| 370 | |
|---|
| 371 | |
|---|
| 372 | <span style="font-style: italic;">! |
|---|
| 373 | 41 gridpoints along x and y, 4 timelevels</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 374 | time = UNLIMITED ; // (4 currently) <span style="font-style: italic;">! unlimited means |
|---|
| 375 | that additional time levels can be added (e.g. by</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 376 | |
|---|
| 377 | |
|---|
| 378 | |
|---|
| 379 | |
|---|
| 380 | <span style="font-style: italic;">! restart jobs)</span><br> |
|---|
| 381 | zu_xy = 2 ; |
|---|
| 382 | |
|---|
| 383 | <span style="font-style: italic;">! |
|---|
| 384 | vertical dimension (2, because two cross sections are selected);</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 385 | zw_xy = 2 ; |
|---|
| 386 | |
|---|
| 387 | <span style="font-style: italic;">! |
|---|
| 388 | there are two different vertical dimensions zu and zw because due</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 389 | zu1_xy = 1 ; |
|---|
| 390 | |
|---|
| 391 | <span style="font-style: italic;">! |
|---|
| 392 | to the staggered grid the z-levels of variables are those of the</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 393 | x = 41 ; |
|---|
| 394 | |
|---|
| 395 | <span style="font-style: italic;">! u- or the w-component of the |
|---|
| 396 | velocity</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 397 | y = 41 ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">variables: |
|---|
| 398 | |
|---|
| 399 | |
|---|
| 400 | <span style="font-style: italic;">! |
|---|
| 401 | precision, dimensions, and units of the variables</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 402 | double time(time) ; |
|---|
| 403 | <span style="font-style: italic;">! the variables containing the |
|---|
| 404 | time levels and grid point coordinates</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 405 | time:units = "seconds" ; |
|---|
| 406 | <span style="font-style: italic;">! have the same names as the |
|---|
| 407 | respective dimensions</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 408 | double zu_xy(zu_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 409 | zu_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 410 | double zw_xy(zw_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 411 | zw_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 412 | double zu1_xy(zu1_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 413 | zu1_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 414 | double ind_z_xy(zu_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 415 | ind_z_xy:units = "gridpoints" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 416 | double x(x) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 417 | x:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 418 | double y(y) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 419 | y:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 420 | float w_xy(time, zw_xy, y, x) ; |
|---|
| 421 | <span style="font-style: italic;">! array of the |
|---|
| 422 | vertical velocity; it has 4 dimensions: x and y,</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 423 | w_xy:long_name = "w_xy" ; |
|---|
| 424 | <span style="font-style: italic;">! because it is a horizontal |
|---|
| 425 | cross section, zw_xy, which defines</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 426 | w_xy:units = "m/s" ; |
|---|
| 427 | <span style="font-style: italic;">! the vertical levels of the |
|---|
| 428 | sections, and time, for the time levels</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 429 | float pt_xy(time, zu_xy, y, x) ; <span style="font-style: italic;">! array of the potential |
|---|
| 430 | temperature, which is defined on the u-grid</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 431 | pt_xy:long_name = "pt_xy" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 432 | pt_xy:units = "K" ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">// global attributes:</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 433 | :Conventions = "COARDS" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 434 | :title = "PALM |
|---|
| 435 | 3.0 run: |
|---|
| 436 | example.00 host: ibmh 13-04-06 15:12:43" ; |
|---|
| 437 | <span style="font-style: italic;">! PALM |
|---|
| 438 | run-identifier</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 439 | :VAR_LIST = ";w_xy;pt_xy;" ; |
|---|
| 440 | <span style="font-style: italic;">! |
|---|
| 441 | the list of output quantities contained in this dataset;</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
|---|
| 442 | |
|---|
| 443 | |
|---|
| 444 | |
|---|
| 445 | |
|---|
| 446 | <span style="font-style: italic;">! this global |
|---|
| 447 | attribute can be used by FORTRAN programs to identify</span><br> |
|---|
| 448 | |
|---|
| 449 | |
|---|
| 450 | |
|---|
| 451 | |
|---|
| 452 | <span style="font-style: italic;">! and read the |
|---|
| 453 | quantities contained in the file</span><br>data:</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;"> time = 905.3, |
|---|
| 454 | 1808.98, 2711.98, 3603.59 ; <span style="font-style: italic;">! |
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| 455 | values of the four time levels</span></span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;"> zu_xy = 75, 475 ; |
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| 456 | |
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| 457 | <span style="font-style: italic;">! heights of the two selected |
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| 458 | cross sections (u-grid)</span></span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;"> zw_xy = 100, 500 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;"> zu1_xy = 25 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;"> x = 0, 50, 100, |
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| 459 | 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, <span style="font-style: italic;">! x-coordinates of the gridpoints</span></span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
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| 460 | 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, |
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| 461 | 1350, </span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
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| 462 | 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, |
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| 463 | </span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
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| 464 | 2000 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;"> y = 0, 50, 100, |
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| 465 | 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, </span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
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| 466 | 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, |
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| 467 | 1350, </span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
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| 468 | 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, |
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| 469 | </span><br style="font-family: monospace;"><span style="font-family: monospace;"> |
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| 470 | 2000 ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">}</span><br></div><br>If |
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| 471 | the option <span style="font-family: monospace;">-c</span> |
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| 472 | is omitted in the <span style="font-family: monospace;">ncdump</span> |
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| 473 | call, then also the complete grid point data of all quantities are |
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| 474 | output to the terminal.<br><br>The <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/read_palm_netcdf_data.f90"><font color="#000080">example program</font></a><span style="font-weight: bold;"></span> shows how to read |
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| 475 | this 2d |
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| 476 | horizontal cross section dataset from a FORTRAN program (<a href="#netcdf_example_program">see above</a>).<br><hr> |
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| 477 | <p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.5.html"><font color="#000080"><img name="Grafik1" src="left.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.5.2.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik3" src="right.gif"></font></a></font></font></p><p style="line-height: 100%;"><span style="font-style: italic;">Last |
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| 478 | change:</span> $Id: chapter_4.5.1.html 493 2010-03-01 08:30:24Z hellstea $ </p> |
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| 479 | </body></html> |
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