Changes between Version 178 and Version 179 of doc/app/runtime_parameters

Timestamp:

Sep 16, 2010 3:33:54 PM (15 years ago)

Author:

weinreis

Comment:

--

doc/app/runtime_parameters

@@ -119 +119 @@
 {{{#!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 chapter [[4.5.1]]). 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.\\\\
+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 [[4.5.5]])||
+||'' '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)!
@@ -140 +140 @@
 Quantities for which masked data are to be output.\\\\
 Up to 20 different masks can be defined (see [../maskedoutput Masked data output]). For each mask (up to 100) different instantaneous or temporally averaged quantities can be output. The masks are steered with the parameters [#mask_x mask_x], [#mask_y mask_y], [#mask_z mask_z], [#mask_x_loop mask_x_loop], [#mask_y_loop mask_y_loop] and [#mask_z_loop mask_z_loop]. It is possible to scale the masked data with a specified length for each direction (see [#mask_scale_x mask_scale_x], [#mask_scale_y mask_scale_y] and [#mask_scale_z mask_scale_z]).\\\\
-By default, masked data are output to local files [[../iofiles#DATA_MASK_01_NETCDF|DATA_MASK_01_NETCDF]], [[../iofiles#DATA_MASK_02_NETCDF|DATA_MASK_02_NETCDF]], ... and [[../iofiles#DATA_MASK_20_NETCDF|DATA_MASK_20_NETCDF]]. If the user has switched on the output of temporally averaged data, these are written seperately to local files [[../iofiles#DATA_MASK_01_AV_NETCDF|DATA_MASK_01_AV_NETCDF]], [[../iofiles#DATA_MASK_02_AV_NETCDF|DATA_MASK_02_AV_NETCDF]], ... and [[../iofiles#DATA_MASK_20_AV_NETCDF|DATA_MASK_20_AV_NETCDF]]. The file's format is netCDF. Further details about processing netCDF data are given in chapter [[4.5.1]].\\\\
+By default, masked data are output to local files [[../iofiles#DATA_MASK_01_NETCDF|DATA_MASK_01_NETCDF]], [[../iofiles#DATA_MASK_02_NETCDF|DATA_MASK_02_NETCDF]], ... and [[../iofiles#DATA_MASK_20_NETCDF|DATA_MASK_20_NETCDF]]. If the user has switched on the output of temporally averaged data, these are written seperately to local files [[../iofiles#DATA_MASK_01_AV_NETCDF|DATA_MASK_01_AV_NETCDF]], [[../iofiles#DATA_MASK_02_AV_NETCDF|DATA_MASK_02_AV_NETCDF]], ... and [[../iofiles#DATA_MASK_20_AV_NETCDF|DATA_MASK_20_AV_NETCDF]]. The file's format is netCDF. Further details about processing netCDF data are given in [../netcdf netCDF data output].\\\\
 The following quantities are available for output by default:\\\\
 ||='''Quantity name''' =||='''Meaning''' =||='''Unit''' =||='''Remarks''' =||
@@ -189 +189 @@
 {{{#!td
 Quantities for which vertical profiles (horizontally averaged) are to be output.\\\\
-By default vertical profile data is output to the local file [[../iofiles#DATA_1D_PR_NETCDF|DATA_1D_PR_NETCDF]]. The file's format is netCDF. Further details about processing netCDF data are given in chapter [[4.5.1]].\\\\
+By default vertical profile data is output to the local file [[../iofiles#DATA_1D_PR_NETCDF|DATA_1D_PR_NETCDF]]. The file's format is netCDF. Further details about processing netCDF data are given in chapter [../netcdf netCDF data output].\\\\
 For horizontally averaged vertical profiles always '''all''' vertical grid points (0 <= k <= [[../inipar#nz|nz]]+1) are output to file. Vertical profile data refers to the total domain but profiles for subdomains can also be output (see [#statistic_regions statistic_regions]).\\\\
 The temporal interval of the output times of profiles is assigned via the parameter [#dt_dopr dt_dopr].\\\\
@@ -316 +316 @@
 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 chapter [[4.5.6]].
+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].
 }}}
 |----------------
@@ -481 +481 @@
 }}}
 (which minimizes the number of calls of routine {{{flow_statistics}}}).\\\\
-By default time series data is output to the local file [[../iofiles#DATA_1D_TS_NETCDF|DATA_1D_TS_NETCDF]]. Because of the default settings of '''dt_dots''', it will generally be created for each model run. The file's format is netCDF.  Further details about processing netCDF data are given in chapter [[4.5.1]].\\\\
+By default time series data is output to the local file [[../iofiles#DATA_1D_TS_NETCDF|DATA_1D_TS_NETCDF]]. Because of the default settings of '''dt_dots''', it will generally be created for each model run. The file's format is netCDF.  Further details about processing netCDF data are given in chapter [../netcdf netCDF data output.\\\\
 The file contains the following timeseries quantities (the first column gives the name of the quantities as used in the netCDF file):\\\\
 ||='''Quantity name''' =||='''Meaning''' =||='''Unit''' =||
@@ -1051 +1051 @@
 {{{#!td
 CPU time needed for terminal actions at the end of a run in batch mode (in s).\\\\
-If the environment variable '''write_binary''' is set ''.T.'' (see [[chapter 3.3]]), PALM checks the remaining CPU time of the job after each timestep. Time integration must not consume the CPU time completely, since several actions still have to be carried out after time integration has finished (e.g. writing of binary data for the restart run, carrying out output commands, copying of local files to their permanent destinations, etc.) which also takes some time. The maximum possible time needed for these activities plus a reserve is to be given with the parameter '''termination_time_needed'''. Among other things, it depends on the number of grid points used. If its value is selected too small, then the respective job will be prematurely aborted by the queuing system, which may result in a data loss and will possibly interrupt the job chain.\\\\
+If the environment variable '''write_binary''' is set ''.T.'' (see [../runs Initialization and restart runs]), PALM checks the remaining CPU time of the job after each timestep. Time integration must not consume the CPU time completely, since several actions still have to be carried out after time integration has finished (e.g. writing of binary data for the restart run, carrying out output commands, copying of local files to their permanent destinations, etc.) which also takes some time. The maximum possible time needed for these activities plus a reserve is to be given with the parameter '''termination_time_needed'''. Among other things, it depends on the number of grid points used. If its value is selected too small, then the respective job will be prematurely aborted by the queuing system, which may result in a data loss and will possibly interrupt the job chain.\\\\
 An abort happens in any way, if the environment variable '''write_binary''' is not set to ''true'' and if moreover the job has been assigned an insufficient CPU time by '''mrun''' option {{{-t}}}.\\\\
 '''Note:'''\\