Changes between Version 239 and Version 240 of doc/app/runtime_parameters

Timestamp:

Mar 20, 2014 6:01:10 PM (11 years ago)

Author:

raasch

Comment:

--

doc/app/runtime_parameters

@@ -135 +135 @@
 By default, with parallel runs, processors output only data of their respective subdomains into seperate local files (file names are constructed by appending the four digit processor ID, e.g. <filename>_0000, <filename>_0001, etc.). After PALM has finished, the contents of these individual files are sampled into one final file using the program {{{combine_plot_fields.x}}} (automatically activated by '''mrun''').\\\\
 Alternatively, PALM is able to collect all grid points of a cross section on PE0 before output is done. In this case only one  output file ([[../iofiles#DATA_2D_XY_NETCDF|DATA_2D_XY_NETCDF]], etc.) is created and {{{combine_plot_fields.x}}} does not have to be called. In case of very large numbers of horizontal gridpoints, sufficient memory is required on PE0.  This method can be used by assigning [#data_output_2d_on_each_pe data_output_2d_on_each_pe] = ''.F.''.\\\\
-3d volume data output is always handled seperately by each processor so that {{{combine_plot_fields.x}}} has to be called anyway after PALM has been finished.\\\\
-'''Old formats:'''\\\\
-Beside the netCDF format, 2d cross section data and 3d volume data can also be output, for historical reasons, in a different (binary) format using parameter [#data_output_format data_output_format].\\\\
-By assigning '''data_output_format''' = '' 'avs' '', the 3d volume data is output to the local file [[../iofiles#PLOT3D_DATA|PLOT3D_DATA]]. Output is in FORTRAN binary format readable by the plot software '''AVS'''.  The order of data on the file follows the order used in the assignment for '''data_output''' (e.g. '''data_output''' = '' 'p', 'v',...'' means that the file starts with the pressure data, followed by the v-component of the velocity, etc.). Both instantaneous and time averaged data are written on this file! Additional to this file, PALM creates a second binary file (local name [[../iofiles#PLOT3D_COOR|PLOT3D_COOR]]) with coordinate information needed by '''AVS'''. As third and fourth file two ASCII files are created (AVS-FLD-format, local name [[../iofiles#PLOT3D_FLD|PLOT3D_FLD]] and [[../iofiles#PLOT3D_FLD_COOR|PLOT3D_FLD_COOR]]), which describe the contents of the data file and/or coordinate file and are used by '''AVS'''. However, '''AVS''' expects the content description in one file. This needs the local file PLOT3D_FLD_COOR to be appended to the file PLOT3D_FLD (by suitable OUTPUT command in the '''mrun''' configuration file: {{{“cat PLOT3D_FLD_COOR >> PLOT3D_FLD”}}}) after PALM has finished. To reduce the amount of data, output to this file can be done in compressed form (see [#do3d_compress do3d_compress]). Further details about plotting 3d volume data with '''AVS''' can be found in [../avs Postprocessing with AVS].\\\\
-'''Important:'''\\
-There is no guarantee that avs-output will be available in future PALM versions (later than 3.0). 
-}}}
-|----------------
-{{{#!td style="vertical-align:top"
-[=#data_output_format '''data_output_format''']
-}}}
-{{{#!td style="vertical-align:top"
-C * 10 (10)
-}}}
-{{{#!td style="vertical-align:top"
-'netcdf'
-}}}
-{{{#!td
-Format of output data.\\\\
-By default, all data (profiles, time series, spectra, particle data, cross sections, volume data) are output in netCDF 64bit-offset format (see [../netcdf netCDF data output]). Exception: restart data (local files [[../iofiles#BININ|BININ]], [[../iofiles#BINOUT|BINOUT]], [[../iofiles#PARTICLE_RESTART_DATA_IN|PARTICLE_RESTART_DATA_IN]], [[../iofiles#PARTICLE_RESTART_DATA_OUT|PARTICLE_RESTART_DATA_OUT]]) are always output in FORTRAN binary format.\\\\
-The numerical precision of the netCDF output is determined with parameter [#netcdf_precision netcdf_precision].\\\\
-Other netCDF formats (classic, netCDF4/HDF5) can be selected with parameter [#netcdf_data_format netcdf_data_format].\\\\
-For historical reasons, other data formats are still available. Beside 'netcdf', data_output_format may be assigned the following values:
-||'' 'avs' '' ||output of 3d volume data in FORTRAN binary format to be read by the graphic software '''AVS''' (see chapter [../avs Postprocessing with AVS])||
-Multiple values can be assigned to '''data_output_format''', i.e. if the user wants to have both the "old" data format as well as cross section data in netCDF format, then '''data_output_format''' = '' 'avs', 'netcdf' '' has to be assigned.\\\\
-'''Warning:''' There is no guarantee that the "old" formats will be available in future PALM versions (beyond 3.0)!
+3d volume data output is always handled seperately by each processor so that {{{combine_plot_fields.x}}} has to be called anyway after PALM has been finished. 
 }}}
 |----------------
@@ -349 +324 @@
 |----------------
 {{{#!td style="vertical-align:top"
-[=#do3d_compress '''do3d_compress''']
-}}}
-{{{#!td style="vertical-align:top"
-L
-}}}
-{{{#!td style="vertical-align:top"
-.F.
-}}}
-{{{#!td
-Output of data for 3d plots in compressed form.\\\\
-This parameter only applies for [#data_output_format data_output_format] = '' 'avs'.''\\\\
-Output of 3d volume data may need huge amounts of disc storage (up to several Terabytes ore more). Data compression can serve to reduce this requirement. PALM is able to output 3d data in compressed form using 32-bit integers, if '''do3d_compress''' = ''.T.'' is assigned. This yields a loss of accuracy, but the file size is clearly reduced. The parameter [#do3d_comp_prec do3d_comp_prec] can be used to separately define the number of significant digits for each quantity.\\\\
-So far compressed data output is only possible for Cray-T3E machines. Additional information for handling compressed data is given in [../avs Postprocessing with AVS].
-}}}
-|----------------
-{{{#!td style="vertical-align:top"
-[=#do3d_comp_prec '''do3d_comp_prec''']
-}}}
-{{{#!td style="vertical-align:top"
-C * 7 (100)
-}}}
-{{{#!td style="vertical-align:top"
-see right
-}}}
-{{{#!td
-Significant digits in case of compressed data output.\\\\
-This parameter only applies for [#data_output_format data_output_format] = '' 'avs'. ''\\\\
-In case that data compression is used for output of 3d data (see [#do3d_compress do3d_compress]), this parameter determines the number of significant digits which are to be output.\\\\
-Fewer digits clearly reduce the amount of data. Assignments have to be given separately for each individual quantity via a character string of the form '' '<quantity name><number of significant digits>','' e.g. '' 'pt2'.'' Only those quantities listed in [#data_output data_output] are admitted. Up to 9 significant digits are allowed (but large values are not very reasonable because they do not effect a significant compression).\\\\
-The default assignment is '''do3d_comp_prec''' = '' 'u2', 'v2', 'w2', 'p5', 'pt2'. ''
-}}}
-|----------------
-{{{#!td style="vertical-align:top"
 [=#dt_averaging_input '''dt_averaging_input''']
 }}}
@@ -866 +808 @@
 {{{#!td
 Defines the accuracy of the netCDF output.\\\\
-By default, all netCDF output data (see [#data_output_format data_output_format]) have single precision  (4 byte) accuracy. Double precision (8 byte) can be choosen alternatively.\\
+By default, all netCDF output data have single precision  (4 byte) accuracy. Double precision (8 byte) can be choosen alternatively.\\
 Accuracy for the different output data (cross sections, 3d-volume data, spectra, etc.) can be set independently.\\
 '' '<out>_NF90_REAL4' '' (single precision) or '' '<out>_NF90_REAL8' '' (double precision) are the two principally allowed values for netcdf_precision, where the string '' '<out>' '' can be chosen out of the following list:\\
@@ -951 +893 @@
 {{{#!td
 Position of cross section(s) for output of 2d horizontal cross sections (grid point index k).\\\\
-If output of horizontal cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_xy''' the corresponding vertical grid point index/indices k of the requested cross section(s). The exact location (height level) of the cross section depends on the variable for which the output is made: zu(k) for scalars and horizontal velocities, zw(k) for the vertical velocity. Information about the exact location of the cross section is contained in the netCDF output file (if the default netCDF output is switched on; see [#data_output_format data_output_format]).\\\\
+If output of horizontal cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_xy''' the corresponding vertical grid point index/indices k of the requested cross section(s). The exact location (height level) of the cross section depends on the variable for which the output is made: zu(k) for scalars and horizontal velocities, zw(k) for the vertical velocity. Information about the exact location of the cross section is contained in the netCDF output file.\\\\
 Assigning '''section_xy''' = ''-1'' creates the output of horizontal cross sections averaged along z. In the netCDF output file these (averaged) cross sections are given the z-coordinate -1.0.\\\\
 Assignments to '''section_xy''' does not effect the output of horizontal cross sections of variable u* and theta* and the liquid water path lwp*. For these quantities always only one cross section (for z=zu(1)) is output.
@@ -967 +909 @@
 {{{#!td
 Position of cross section(s) for output of 2d (xz) vertical cross sections (grid point index j).\\\\
-If output of vertical xz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_xz''' the corresponding horizontal grid point index/indices j of the requested cross section(s). The exact position (in y-direction) of the cross section is given by j*[[../inipar#dy|dy]] or (j-0.5)*[[../inipar#dy|dy]], depending on which grid the output quantity is defined. However, in the netCDF output file (if the default netCDF output is switched on; see [#data_output_format data_output_format]) no distinction is made between the quantities and j*'''dy''' is used for all positions.\\\\
+If output of vertical xz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_xz''' the corresponding horizontal grid point index/indices j of the requested cross section(s). The exact position (in y-direction) of the cross section is given by j*[[../inipar#dy|dy]] or (j-0.5)*[[../inipar#dy|dy]], depending on which grid the output quantity is defined. However, in the netCDF output file no distinction is made between the quantities and j*'''dy''' is used for all positions.\\\\
 Assigning '''section_xz''' = ''-1'' creates the output of vertical cross sections averaged along y. In the netCDF output file these (averaged) cross sections are given the y-coordinate -1.0.
 }}}
@@ -982 +924 @@
 {{{#!td
 Position of cross section(s) for output of 2d (yz) vertical cross sections (grid point index i).\\\\
-If output of vertical yz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_yz''' the corresponding horizontal grid point index/indices i of the requested cross section(s). The exact position (in x-direction) of the cross section is given by i*[[../inipar#dx|dx]] or (i-0.5)*[[../inipar#dx|dx]], depending on which grid the output quantity is defined. However, in the netCDF output file (if the default netCDF output is switched on; see [#data_output_format data_output_format]) no distinction is made between the quantities and i*'''dx''' is used for all positions.\\\\
+If output of vertical yz cross sections is selected (see [#data_output data_output]), this parameter can be used to define the position(s) of the cross section(s). Up to 100 positions of cross sections can be selected by assigning '''section_yz''' the corresponding horizontal grid point index/indices i of the requested cross section(s). The exact position (in x-direction) of the cross section is given by i*[[../inipar#dx|dx]] or (i-0.5)*[[../inipar#dx|dx]], depending on which grid the output quantity is defined. However, in the netCDF output file no distinction is made between the quantities and i*'''dx''' is used for all positions.\\\\
 Assigning '''section_yz''' = -1 creates the output of vertical cross sections averaged along x. In the netCDF output file these (averaged) cross sections are given the x-coordinate -1.0.
 }}}
@@ -1142 +1084 @@
 '''Note:'''\\
 On the IBM computers of the HLRN the time used by the job '''before''' the start of PALM have also to be accounted for (e.g. for compilation and copying of input files).
-}}}
-|----------------
-{{{#!td style="vertical-align:top"
-[=#use_prior_plot1d_parameters '''use_prior_plot1d_parameters''']
-}}}
-{{{#!td style="vertical-align:top"
-L
-}}}
-{{{#!td style="vertical-align:top"
-.F.
-}}}
-{{{#!td
-'''Currently this parameter cannot be used.'''\\\\
-Additional plot of vertical profile data with '''profil''' from preceding runs of the job chain.\\\\
-This parameter only applies for [#data_output_format data_output_format] = '' 'profil'.''\\\\
-By default, plots of horizontally averaged vertical profiles (see [#data_output_pr data_output_pr]) only contain profiles of data produced by the model run. If profiles of prior times (i.e. data of preceding jobs of a job chain) shall be plotted additionally (e.g. for comparison purposes), '''use_prior_plot1d_parameters''' = ''.T.'' must be set.\\\\
-}}}
-|----------------
-{{{#!td style="vertical-align:top"
-[=#z_max_do2d '''z_max_do2d''']
-}}}
-{{{#!td style="vertical-align:top"
-R
-}}}
-{{{#!td style="vertical-align:top"
-zu(nz)
-}}}
-{{{#!td
-'''Currently this parameter cannot be used.'''\\\\
-Height level up to which 2d cross sections are to be plotted with '''iso2d''' (in m).\\\\
-This parameter only applies for [#data_output_format data_output_format] = '' 'iso2d'.''\\\\
-It affects plots of  2d vertical cross sections ([#data_output data_output]) when plotted with '''iso2d'''. By default, vertical sections are plotted up to the top boundary. In contrast, with '''z_max_do2d''' the visualization within the plot can be limited to a certain height level (0 <= z <= '''z_max_do2d'''). Nevertheless, '''all''' grid points of the complete cross section are still output to the local files PLOT2D_XZ or PLOT2D_YZ. The level up to which the section is visualized can later be changed by manually editing the file PLOT2D_XZ_GLOBAL or PLOT2D_YZ_GLOBAL (the respective '''iso2d'''-parameter is '''yright''').
 }}}
 \\\\