Changes between Version 84 and Version 85 of doc/app/iofiles

Timestamp:

Apr 24, 2014 1:39:53 PM (11 years ago)

Author:

raasch

Comment:

--

doc/app/iofiles

@@ -645 +645 @@
 }}}
 {{{#!td
-This file contains the data of the three-dimensional arrays (see [../d3par#data_output data_output]) written by the model in a format readable for the visualization software AVS. Beyond that AVS needs coordinate information, which are output into the local file [#PLOT3D_COOR PLOT3D_COOR], as well as the local files [#PLOT3D_FLD PLOT3D_FLD] and [#PLOT3D_FLD_COOR PLOT3D_FLD_COOR], which describe the structure of the files PLOT3D_DATA and PLOT3D_COOR in the so-called AVS-FLD-format. Due to the fact that AVS expects these information in only one (so-called FLD -) file, the content of the file PLOT3D_FLD_COOR must be appended to the file PLOT3D_FLD by the user after the end of the model run (e.g. with an appropriate OUTPUT - command in the '''mrun'''-configuration file: "{{{cat PLOT3D_FLD_COOR >> PLOT3D_FLD}}}"). \\\\
-With parallel runs each processing element writes the data of its subdomain to a separate file with the name PLOT3D_DATA_<Processor-Id>, where <Processor-Id> is a four digit number (e.g. PLOT3D_DATA_0000). These files are not suitable for AVS, but after the end of the model run they can be combined to one file readable for AVS with the help of the program {{{combine_plot_fields.x}}} (automatically activated by '''mrun'''). This tool expects the files of the individual processing elements under the names described above and outputs the combined file into a new file PLOT3D_DATA.
-The tool writes informative messages about the accomplished actions into the job protocol (e.g., even if no files were found). By the call of {{{combine_plot_fields.x}}} also possibly existing files with two-dimensional plot data (see e.g. [#PLOT2D_XY PLOT2D_XY]) are combined. \\\\   
-With parallel runs the output of data of large volume is also possible in compressed form. For this purpose the initialization parameter  [../d3par#do3d_compress do3d_compress] = ''.T.'' must be set and the desired output accuracy has to be indicated with the help of [../d3par#do3d_comp_prec do3d_comp_prec]. In favorable cases the file size can be reduced by a factor of up to 5. For the visualization of compressed data a special AVS module ({{{read_compressed_field}}}) and a further entry in the '''mrun'''-configuration file are needed. More details can be found in the postprocessing description of [../avs AVS].
-}}}
-|----------------
-{{{#!td style="vertical-align:top; width: 50px"
-31
-}}}
-{{{#!td style="vertical-align:top; width: 150px"
-[=#PLOT3D_COOR PLOT3D_COOR]
-}}}
-{{{#!td style="vertical-align:top; width: 50px"
-O
-}}}
-{{{#!td style="vertical-align:top; width: 100px"
-Binary
-}}}
-{{{#!td
-Coordinate information concerning the three-dimensional arrays (see [#PLOT3D_DATA PLOT3D_DATA]) needed by the visualization software AVS. \\\\  
-The file PLOT3D_COOR should be saved by the user into the same permanent directory as the file PLOT3D_DATA. \\\\
-For parallel runs PLOT3D_COOR is written by PE0 only.
-}}}
-|----------------
-{{{#!td style="vertical-align:top; width: 50px"
-32
-}}}
-{{{#!td style="vertical-align:top; width: 150px"
-[=#PLOT3D_FLD PLOT3D_FLD]
-}}}
-{{{#!td style="vertical-align:top; width: 50px"
-O
-}}}
-{{{#!td style="vertical-align:top; width: 100px"
-ASCII/ \\
-AVS-Fld
-}}}
-{{{#!td
-AVS-Fld-file describing the three-dimensional array data, saved by the model into the local file [#PLOT3D_DATA PLOT3D_DATA], needed by the visualization software AVS. \\\\
-This file describes the structure of the file PLOT3D_DATA (e.g. number of arrays, array dimensions, data type etc.). It uses the so-called AVS-Fld-format. It also contains the name of the file (inclusive cycle number, but without path) under which the local file PLOT3D_DATA is saved (this is the file name given in the file connection statement of the '''mrun'''–configuration) in the permanent directory of the user (possibly on remote computers). Under this name AVS expects the data which are to be visualized. If there is no file connection statement for PLOT3D_DATA indicated in the configuration file, that file (filename) is registered "unknown" in the file PLOT3D_FLD and the actual name must be inserted later by hand. The file PLOT3D_FLD should be saved by the user in the same permanent directory as PLOT3D_DATA, so that AVS can find the file PLOT3D_DATA without any problems. If the two files lie in different directories, then the path name of the file PLOT3D_DATA must be added. \\\\
-AVS-Fld-files are expected by AVS to have the suffix "{{{.fld}}}". Cycle numbers must not be attached behind this "{{{.fld}}}" suffix. This suffix is attached to the permanent file names (still after possible cycle numbers) by '''mrun''' if "{{{fld}}}" is indicated in the [wiki:column6 column6] of the file connection statement. \\\\
-Likewise, AVS expects information about the coordinate system underlying the arrays on this file. This information is output by the model into the local file [#PLOT3D_FLD_COOR PLOT3D_FLD_COOR], whose content the user has to append to the file PLOT3D_FLD after the end of the model run (e.g. with an appropriate OUTPUT-command in the '''mrun'''-configuration file: "cat PLOT3D_FLD_COOR >> PLOT3D_FLD"). \\\\
-For parallel runs, PLOT3D_FLD is produced by PE0 only. 
-}}}
-|----------------
-{{{#!td style="vertical-align:top; width: 50px"
-33
-}}}
-{{{#!td style="vertical-align:top; width: 150px"
-[=#PLOT3D_FLD_COOR PLOT3D_FLD_COOR]
-}}}
-{{{#!td style="vertical-align:top; width: 50px"
-O
-}}}
-{{{#!td style="vertical-align:top; width: 100px"
-ASCII/ \\
-AVS-Fld 
-}}}
-{{{#!td
-File for the description of the coordinate information output by the model into the local file [#PLOT3D_COOR PLOT3D_COOR], which is needed for the visualization of three-dimensional array data by visualization-software AVS. \\\\  
-This file describes the structure of the file PLOT3D_COOR (e.g. grid spacing, data type etc.) using the so-called AVS-Fld-format. It also contains the name of the file (inclusive cycle number, but without path) into which the local file PLOT3D_COOR (this is the file name described in the file connection statement of the '''mrun'''-configuration file) is output in the permanent directory of the user (possibly on remote computers). Under this name AVS expects the data which are to be visualized. If there is no file connection statement for PLOT3D_COOR indicated in the configuration file, that file is registered as "unknown" in the file PLOT3D_FLD_COOR and the actual name must be inserted later by hand. \\\\
-AVS expects the information contained in the file PLOT3D_FLD_COOR, as well as the remaining information about the three-dimensional arrays output by the model (see [#PLOT3D_FLD PLOT3D_FLD]) in one and the same file. This is satisfied by appending the file PLOT3D_FLD_COOR after the end of a run are to the file PLOT3D_FLD (e.g. with an appropriate OUTPUT-command in the '''mrun'''-configuration file: "cat PLOT3D_FLD_COOR >> PLOT3D_FLD"). \\\\
-For parallel runs, PLOT3D_FLD_COOR is written by PE0 only. 
+This file contains the data of the three-dimensional arrays (see [../d3par#data_output data_output]) in netCDF format. The specific netCDF format (e.g. classic, 64-bit offset, netcdf4, etc.) depends on the setting of d3par-parameter [../d3par#netcdf_data_format netcdf_data_format].\\\\
+With parallel runs and {{{netcdf_data_format}}} < ''5'', each processing element first writes the data of its subdomain in FORTRAN binary format to a separate file named PLOT3D_DATA_<Processor-Id>, where <Processor-Id> is a four digit number (e.g. PLOT3D_DATA_0000). After PALM has finished, contents of these files are collected by the helper routine {{{combine_plot_fields.x}}} (automatically executed by '''mrun'''). This tool expects the files of the individual processing elements under the names described above and outputs the combined data in netCDF format into the final file named PLOT3D_DATA. The tool writes informative messages about the accomplished actions into the job protocol (also if no files were found). Helper routine {{{combine_plot_fields.x}}} also collects files containing two-dimensional data (see e.g. [#PLOT2D_XY PLOT2D_XY]).\\\\
+With {{{netcdf_data_format}}} > ''4'' PALM directly writes the data of the subdomains into one single file using parallel I/O (MPI I/O), which makes a call of {{{combine_plot_fields.x}}} obsolete.
 }}}
 |----------------