== PALM source code change log ==

'''Current revision:'''  [[CRev]] [[BR]]
'''Current fixed release:''' 3.7a (r483)

The following table documents all changes to the PALM repository since 2009. Older changes can be found [http://www.muk.uni-hannover.de/~raasch/PALM_group/doc/tec/tec_doc_1998-2008.html here].

Please follow the [wiki:/doc/tec/developerrules rules for developers] when carrying out source code changes!

Entries in the fifth column specify the type of the change: change of existing code ('''C'''), new code ('''N''') or bugfix ('''B'''). More detailed information about the changes may sometimes be found in the header comment lines of the respectively changed routines. 

||='''Date'''  =||='''Author'''  =||='''svn\\Revision'''  =||='''Last\\Release'''  =||='''Type''' =||='''Description''' =||
|----------------
{{{#!td style="vertical-align:top;width: 50px"
05/10/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r580
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Renaming of {{{ws_vertical_gradient}}} to {{{subs_vertical_gradient}}}, {{{ws_vertical_gradient_level}}} to {{{subs_vertical_gradient_level}}} and {{{ws_vertical_gradient_level_ind}}} to {{{subs_vertical_gradient_level_i}}}
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
01/10/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
CH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r568
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
calculating {{{masks}}} expanded for user-defined quantities (check_parameters)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
30/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r566
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Formatting of NCL scripts adjusted (cross_sections.ncl, profiles.ncl, spectra.ncl, timeseries.ncl)\\
Re-sorting of items in {{{.ncl.config.default}}} and moving of xyc, xzc and yzc to cross_sections.ncl because they are no parameters any more. \\
star_f_1/end_f_1 are renamed to [[wiki:doc/app/nclparlist#start_f|start_f]]/[[wiki:doc/app/nclparlist#end_f|end_f]], placement of second legend in case of [[wiki:doc/app/nclparlist#over_pr|over]] = 1 changed, legend label strings are formatted with sprintf (profiles.ncl)\\
Explicit setting of minimum and maximum for x-axis (timeseries.ncl)\\
Error inquiry for parameter [[wiki:doc/app/nclparlist#height_level_sp|height_level]] extended, legend label strings are formatted with sprintf (spectra.ncl)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
Vector plot is now possible if [[wiki:doc/app/nclparlist#var|var]] is unequal to "all" (cross_sections.ncl)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
30/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
CH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r565
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
amount of defining masks changed from 20 to unlimited (check_open, check_parameters, close_file, data_output_mask, init_masks, modules, netcdf)

palm and netcdf message identifiers for masked output changed (check_open, check_parameters, close_file, data_output_mask, init_masks, netcdf)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
13/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r562
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N/B
}}}
{{{#!td style="vertical-align:top"
new: setting of {{{MPI_TYPE_DEPTH}}} for netCDF4/HDF5 with mpt-library (mrun)

bugfixes for wrong netCDF/3.6.3 module and r561 (mbuild, mrun)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
09/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
CH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r560
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix in calculation of {{{ngp_3d}}} for 64 bit. So far {{{ngp_3d}}} has not been 64 bit.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
07/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
CH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r557
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix for message string in if statement ({{{dz_stretch_level}}}) of subroutine {{{set_mask_locations}}}.

The change concerns the masked data output, which is still not documented.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
07/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r556
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Documentation for {{{surface_heatflux}}} in case of {{{prandtl_layer}}} = ''.F.'' improved.

bugfix for wrong netCDF/3.6.3 module on lcsgi (mbuild, mrun)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix in if statement (disturb_heatflux)

Bugfix: in 2201 statement: closing " was missing (interpret_config)

Bugfix: default setting of {{{nzb_local}}} for flat topography (init_grid)

Bugfix: wrong dimension used for {{{ts_value_l}}} (user_statistics)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
01/09/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
CH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r553
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
d3dpar-parameters for masked output {{{data_output_mask_*}}}, {{{data_output_mask_user_*}}}, {{{mask_*_x}}}, {{{mask_*_y}}}, {{{mask_*_z}}}, {{{mask_*_x_loop}}}, {{{mask_*_y_loop}}} and {{{mask_*_z_loop}}} have been replaced by corresponding (array-) parameters {{{data_output_masks}}}, {{{data_output_masks_user}}}, {{{mask_x}}}, {{{mask_y}}}, {{{mask_z}}}, {{{mask_x_loop}}}, {{{mask_y_loop}}}, and {{{mask_z_loop}}}.

inipar-parameter {{{masks}}} has been removed.

The changes concern the masked data output, which is still not documented.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
17/08/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
BM
}}}
{{{#!td style="vertical-align:top;width: 75px"
r544
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N/C/B
}}}
{{{#!td style="vertical-align:top"
new: {{{.mrun.config.lcxt4}}} for Cray-XT4 in !Bergen/Norway

changes: adjustments for lcxt4

bugfix: loading of user-defined modules (mbuild)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
15/06/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r540
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is done using the names hicegate0/bicegate0 instead of the IP addresses
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
21/04/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r532
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Large scale vertical motion (subsidence/ascent) can be added as additional source to the prognostic equation for humidity/passive scalar.
 
Character length for dopr_unit enlarged.

Adjustment of the NCL scripts to allow for output of png files. 
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix: unit of hyp changed to dbar (check_parameters)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
01/04/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r530
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix: treatment of special character * in NCL variables containing lists corrected
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
31/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r529
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
List of variable names have to be specified using blank separated lists and single quotes
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
30/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r526
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Adjustment of the NCL scripts and {{{palmplot}}} to allow for special characters in netCDF variable names.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
30/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r525
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix: "/" in netcdf profile variable names replaced by ":"
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
19/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r520
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
{{{#!td style="vertical-align:top"
netCDF4 support for particle data. Total number of particles is allowed to increase during the run, when {{{netcdf_data_format}}} > 2  is used.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Special characters like * and " are now allowed for netCDF variable names. Replacement of these characters has been removed (routine {{{clean_netcdf_varname}}} removed)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
18/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r516
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
{{{#!td style="vertical-align:top"
Simple installation method has been documented (see [wiki:doc/install]). Respective scripts and configuration files have been updated.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
opt=1 is forced for PGI-compiler in routine {{{buoyancy}}} by compiler-directive. Otherwise, program aborts with SIGFPE.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
16/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
RH
}}}
{{{#!td style="vertical-align:top;width: 75px"
r513
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
{{{#!td style="vertical-align:top"
NCL scripts can be run with the shell script {{{palmplot}}}.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
12/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r509
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
bugfix for r504: remode_md was given a wrong value
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
08/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r506
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
hack for better usage of '''mrun''' on Kyoto computing center machine (lckyoto)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
03/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r504
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
{{{combine_plot_fields}}} is now directly called within '''mrun''' and must not be given by an output command in the configuration file any more. Please remove the respective output command ({{{OC:combine_plot_fields.x}}}) from your configuration file!

Utility programs ({{{combine_plot_fields}}}, {{{interpret_config}}}) are created by '''mbuild''' separately for each block in the configuration file. Depending on option {{{-K}}}, '''mrun''' is using the utility programs for the respective block.

Utility programs are also compiled in parallel, depending on variable {{{%mopts}}} in the configuration file..

Default configuration files updated.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
02/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r496
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
Particle data for restart runs are only written if environment variable {{{write_binary}}} = ''.T.'', i.e. particle data are now handled in the same way as the other restart data. (palm)
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
01/03/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r494
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
{{{#!td style="vertical-align:top"
Output in netCDF4-format.

netCDF4 allows for parallel I/O. Also, variables are not limited in size any more (i.e. arrays can be larger than 2GB). The new d3par-parameter [wiki:/doc/app/d3par#netcdf_data_format netcdf_data_format] can be used to select among the different netCDF file formats (1: classic format, 2: 64-bit-offset format (this is now the default), 3: netCDF4/HDF5 format, 4: netCDF4 format with NF90_CLASSIC_MODEL bit set). Setting {{{netcdf_data_format}}} > 2 only affects 2d- and 3d-output, i.e. there is no parallel output for profiles, time series, spectra, and particles. Parallel output of particle data may be realized in the future.

In case of parallel output, all PEs write into one file, which means that postprocessing the data with {{{combine_plot_fields}}} (merging data from single files - one per PE - into one file) is not neccessary. In this case, flag files are automatically set, telling {{{combine_plot_fields}}} that nothing is to be done.

Using netCDF4 format requires a netCDF4/HDF5 library. Respective settings for {{{-I}}}, {{{-L}}}, and {{{-l}}} compiler/loader options for the SGI-ICE at HLRN can be found in the new example configuration file [source:palm/trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4 .mrun.config.imuk_ice2_netcdf4]

'''Attention:'''
So far, netCDF parallel I/O has only been tested a little. Further performance optimizations may be required, especially in case of large data sets (e.g. data chunking, or lustre file system settings with {{{lfs setstripe}}}). Please report bugs and performance problems immediately!

{{{combine_plot_fields}}} outputs cpu-time needed for file merging.

Modules to be loaded for compilation ('''mbuild''') or job execution ('''mrun''') can/should now be given in the configuration file ({{{.mrun.config}}}) using variable {{{%modules}}}. Example:
{{{
   %modules     ifort/11.0.069:netcdf       lcsgih parallel
}}}
This method replaces the (undocumented) {{{%mpilib}}}-variable.

'''WARNING:'''
All fixed settings of modules in the scripts '''mbuild''', '''mrun''', and '''subjob''' have been removed! Please set the {{{%modules}}} variable appropriately and remove the {{{%mpilib}}} variable in your configuration file.

Compilation time can be reduced be using parallel make. The number of allowed simultaneous compiler calls (threads) is set in the configuration file using variable {{{%mopt}}}, e.g.
{{{
   %mopts  -j:4   lcsgih parallel
}}}
allows a maximum of 4 routines to be compiled simultaneously (provided that the makefile does not show any dependencies between these routines).
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
d3par-parameters {{{netcdf_64bit}}} and {{{netcdf_64bit_3d}}}  have been removed. Use the new d3par-variable {{{netcdf_data_format}}} = 2 for choosing the netCDF 64bit-offset format (this is the default from now on). The offset-format can not be set independently for the 3d-output-data any more.

d3par-parameters {{{netcdf_format_mask}}}, {{{netcdf_format_mask_av}}}, and variables {{{nc_format_mask}}}, {{{format_parallel_io}}} removed. They are replaced by the new parameter {{{netcdf_data_format}}}. This change concerns the masked data output, which is still not documented.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
Bugfix in [source:palm/trunk/UTIL/Makefile Makefile]: forgot to compile for {{{interpret_config}}}.

Bugfix: timeseries data have to be collected by PE0 (user_statistics).
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
05/02/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r484
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
C
}}}
{{{#!td style="vertical-align:top"
{{{Actual revisions:}}} renamed {{{Current revisions:}}} in most of the source code file headers.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 50px"

}}}
{{{#!td style="vertical-align:top;width: 75px"

}}}
{{{#!td style="vertical-align:top"

}}}
{{{#!td style="vertical-align:top"
B
}}}
{{{#!td style="vertical-align:top"
{{{ngp_3d}}}, {{{ngp_3d_inner}}}  changed to 64 bit. Otherwise, on large grids > 2*10^9^ grid points some global statistics (e.g. total kinetic energy) have wrong values.
}}}
|----------------
{{{#!td style="vertical-align:top;width: 50px"
05/02/10
}}}
{{{#!td style="vertical-align:top;width: 50px"
SR
}}}
{{{#!td style="vertical-align:top;width: 75px"
r483
}}}
{{{#!td style="vertical-align:top"
3.7a
}}}
{{{#!td style="vertical-align:top"
N
}}}
{{{#!td style="vertical-align:top"
{{{compare_palm_logs}}} is additionally compiled with {{{mbuild -u}}}  . ([source:palm/trunk/UTIL/Makefile Makefile])

make options ({{{%mopts}}}) to be set by configuration file implemented. (mrun, mbuild)

{{{humidity}}} = ''.T.'' can be used for runs with topography. {{{wall_humidityflux}}} and
{{{wall_scalarflux}}} are the corresponding new inipar parameters.
(check_parameters, init_3d_model, parin)

Large scale vertical motion (subsidence/ascent) can be added as additional source to the prognostic equation for potential temperature. See new parameters {{{large_scale_subsidence}}}, {{{ws_vertical_gradient}}}, and {{{ws_vertical_gradient_level}}}. (check_parameters, header, Makefile, modules, parin, prognostic_equations, read_var_list, subsidence, write_var_list)

Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).

A simple method for installing and running palm (with limited features) has been added. (Makefile, new scripts palm_simple_install, palm_simple_run)

Masked data output has been implemented but it is not documented in the user manual so far. This feature can already use netCDF4 file format. (check_open, check_parameters, close_file, modules, netcdf, parin, time_integration, user_parin, new: data_output_mask, init_masks, user_data_output_mask)
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2d-decomposition is default for Cray-XT machines. (init_pegrid)

{{{var_ts}}} is replaced by {{{dots_max}}}. (modules, init_3d_model)

Every cloud droplet has now an own weighting factor and can be deleted due to collisions. Condensation and collision of cloud droplets are adjusted accordingly. (advec_particles)

Collision efficiency for large cloud droplets has changed according to table of Rogers and Yau. (collision_efficiency)
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Bugfix for generating serial jobs. (subjob)

Bugfix: index problem concerning gradient_level indices removed. (header)

Dimension of array stat in cascade change to prevent type problems with mpi2 libraries. (poisfft_hybrid)

Loop was split to make runs reproducible when using ifort compiler. (disturb_field)

Bugfix: exchange of ghost points for prho included. (time_integration)

Bugfix in calculation of time-averaged surface heatfluxes. (sum_up_3d_data)

Bugfix in calculation of precipitation_rate. (calc_precipitation)

Bugfix: initial data assignments to some dvrp arrays changed due to error messages from gfortran compiler. (modules)

Bugfix in calculation of cloud droplet velocity. (advec_particles)

Bugfix in transfer of particles at south/left edge. (advec_particles)

Bugfix in calculation of collision efficiency. (collision_efficiency)
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'''Most important changes:''' atmosphere-ocean coupling has been improved and steering of dvr-software is more user-friendly now. Beside that, the release contains a lot of optimizations, changes, and bugfixes which have accumulated over the last months.

The atmosphere-ocean coupling allows to use independent precursor runs in order to account for different spin-up times. The time when coupling has to be started is given by new inipar parameter {{{coupling_start_time}}}. The precursor ocean run has to be started using new '''mrun''' option "{{{-y}}}" in order to add the appendix "{{{_O}}}" to all output files. (check_for_restart, check_parameters, data_output_2d, data_output_3d, data_output_profiles, data_output_ptseries, data_output_spectra, data_output_tseries, header, init_coupling, modules, mrun, parin, read_var_list, surface_coupler, time_integration, write_var_list)

Clipping of dvrp output implemented. Default colourtable for particles implemented, particle attributes (color, dvrp_size) can be set with new parameters {{{particle_color}}}, {{{particle_dvrpsize}}}, {{{color_interval}}}, {{{dvrpsize_interval}}}. Slicer attributes (dvrp) are set with new routine {{{set_slicer_attributes_dvrp}}} and are controlled with existing parameter {{{slicer_range_limits}}}. (init_dvrp, data_output_dvrp, modules, set_slicer_attributes_dvrp,  user_data_output_dvrp)

Polygon reduction for topography and ground plate isosurface. Reduction level for buildings can be chosen with parameter {{{cluster_size}}}. (init_dvrp)

Variables {{{bc_lr}}} and {{{bc_ns}}}  in most subroutines replaced by {{{LOGICAL}}} variables {{{bc_lr_cyc}}} and
{{{bc_ns_cyc}}} for speed optimization. This gives a significant speedup of more than 10%. (check_parameters, diffusion_u, diffusion_v, diffusion_w, modules)

Scripts have been adapted for machine lck (Yonsei Univ.). (mrun, mbuild, subjob)

Additional timestep criterion in case of simulations with plant canopy. (timestep)

Check for illegal entries in {{{section_xy}}}|{{{xz}}}|{{{yz}}} that exceed {{{nz+1}}}|{{{ny+1}}}|{{{nx+1}}}. (check_parameters)

External pressure gradient can be used as driving force. (check_parameters, header, init_3d_model, modules, parin, prognostic_equations, read_var_list, write_var_list)

New topography case '' 'single_street_canyon' ''. (header, init_grid, modules, parin, read_var_list, user_check_parameters, user_header, user_init_grid, write_var_list)

Option to predefine a target bulk velocity for {{{conserve_volume_flow}}}. (check_parameters, header, init_3d_model, modules, parin, read_var_list, write_var_list)

Option for user defined 2D data output in xy cross sections at z=nzb+1. (data_output_2d, user_data_output_2d)

xy cross section output of surface heatfluxes (sensible and latent). (average_3d_data, check_parameters, data_output_2d, modules, read_3d_binary, sum_up_3d_data, write_3d_binary)
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Output of messages replaced by message handling routine. (advec_particles, advec_s_bc, buoyancy, calc_spectra, check_for_restart, check_open, coriolis, cpu_log, data_output_2d, data_output_3d, data_output_dvrp, data_output_profiles, data_output_spectra, fft_xy, flow_statistics, header,  init_1d_model, init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid, netcdf, parin, plant_canopy_model, poisfft_hybrid, poismg, read_3d_binary, read_var_list, surface_coupler, temperton_fft, timestep, user_actions, user_data_output_dvrp, user_dvrp_coltab, user_init_grid, user_init_plant_canopy, user_parin, user_read_restart_data, user_spectra)

Output of netCDF messages with aid of message handling routine. (check_open, close_file, data_output_2d, data_output_3d, data_output_profiles, data_output_ptseries, data_output_spectra,  data_output_tseries, netcdf)

{{{__lcmuk}}} changed to {{{__lc}}} to avoid problems with Intel compiler on sgi-ice. (poisfft)

For extended netCDF files, the updated title attribute includes an update of {{{time_average_text}}} where appropriate. (netcdf)

In case of restart runs without extension, initial profiles are not written to netCDF-file anymore. So far, time axis always started at t=0. (data_output_profiles, modules, read_var_list, write_var_list)

{{{initializing_actions}}}='' 'read_data_for_recycling' '' renamed to '' 'cyclic_fill' ''. A cyclic fill can now
be used independent of {{{turbulent_inflow}}}. (check_parameters, header, init_3d_model)

Two netCDF error numbers changed. (data_output_3d)

A link to the webspage appendix_a.html is printed for further information about possible reasons of the error that appeared. (message)

Temperature gradient criterion for estimating the boundary layer height replaced by the gradient criterion of Sullivan et al. (1998). (flow_statistics)

netCDF unit attribute in timeseries output in case of statistic regions added. (netcdf)

Maximum number of tails is calculated from maximum number of particles and {{{skip_particles_for_tail}}}. (init_particles)

Value of {{{vertical_particle_advection}}} is allowed to differ for each particle group. (advec_particles, header, modules)

First constant in array {{{den}}} also defined as type double. (eqn_state_seawater)

Parameter {{{dvrp_psize}}} moved from {{{particles_par}}} to {{{dvrp_graphics_par}}}. (package_parin)

{{{topography_grid_convention}}} moved from {{{userpar}}} to {{{inipar}}} (check_parameters, header, parin, read_var_list, user_check_parameters, user_header, user_init_grid, user_parin, write_var_list)

Default value of {{{grid_matching}}} changed to '' 'strict' ''. (modules)

Adjustments for runs on lcxt4 (necessary due to a software update on CRAY) and for coupled runs on ibmy. (mrun, subjob)
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Bugfix: Initial hydrostatic pressure profile in case of ocean runs is now calculated in 5 iteration steps. (init_ocean)

Bugfix: wrong sign in buoyancy production of ocean part in case of not using the reference density (only in 3D routine production_e). (production_e)

Bugfix: output of averaged 2d/3d quantities requires that an avaraging interval has been set, respective error message is included. (check_parameters)

Bugfix: Output on unit 14 only if requested by {{{write_binary}}}. (user_last_actions)

Bugfix to avoid zero division by {{{km_neutral}}}. (production_e)

Bugfix for extended netCDF files: In order to avoid 'data mode' errors if updated attributes are larger than their original size, {{{NF90_PUT_ATT}}} is called in '' 'define mode' '' enclosed by {{{NF90_REDEF}}} and {{{NF90_ENDDEF}}} calls. This implies a possible performance loss; an alternative strategy would be to ensure equal attribute size in a job chain. (netcdf)

Bugfix: correction of initial volume flow for non-flat topography. (init_3d_model)

Bugfix: zero initialization of arrays within buildings for '' 'cyclic_fill' ''. (init_3d_model)

Bugfix: {{{to_be_resorted => s_av}}} for time-averaged scalars. (data_output_2d, data_output_3d)

Bugfix: avoid that {{{ngp_2dh_s_inner}}} becomes zero. (init_3_model)

Typographical error: unit of {{{wpt}}} in {{{dots_unit}}}. (modules)

Bugfix: error in check, if particles moved further than one subdomain length. This check must not be applied for newly released particles. (advec_particles)

Bugfix: several tail counters are initialized, {{{particle_tail_coordinates}}} is only written to file if its third index is > 0, arrays for tails are allocated with a minimum size of 10 tails if there is no tail initially. (advec_particles, init_particles)

Bugfix: pressure included for profile output. (check_parameters)

Bugfix: Type of {{{count}}} and {{{count_rate}}} changed to default {{{INTEGER}}} on NEC machines. (cpu_log)

Bugfix: output of particle time series only if particle advection is switched on. (time_integration)

Bugfix: {{{qsws}}} was calculated in case of {{{constant heatflux}}} = ''.FALSE.''. (prandtl_fluxes)

Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0). (data_output_2d)

Typographical errors. (netcdf)

If the inversion height calculated by the prerun is zero, {{{inflow_damping_height}}} must be explicitly specified. (init_3d_model)

Small bugfix concerning 3d-64bit-netCDF output format. (header)

Bugfix: {{{dt_fixed}}} removed from the restart file, because otherwise, no change from a fixed to a variable timestep would be possible in restart runs. (read_var_list, write_var_list)

Bugfix: initial setting of {{{time_coupling}}} in coupled restart runs. (time_integration)
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This release contains further additions, changes, and bugfixes for the SGI-ICE system, as well as important changes like the splitting of the user-interface into single files, a complete revision of the pre-compiling mechanism allowing to use different make-depositories simultaneously, and a revision of the reading-mechanism from restart files, which has no more restrictions in case that the previous and current run have different domain/subdomain sizes. A new handling of all kind of output messages is introduced with this release and will be applied to all existing messages within the next releases.

'''New features are:'''

Restart runs on SGI-ICE are working. (mrun)
2d-decomposition is default on SGI-ICE systems. (init_pegrid)

Ocean-atmosphere coupling realized with MPI-1. '''mrun''' adjusted for this case ({{{-Y}}} option). Check that PALM is called with '''mrun'''-option "{{{-K parallel}}}" for coupling. Adjustments in '''mrun''', '''mbuild''', and '''subjob''' for lcxt4.

DVRP arguments changed to single precision, mode pathlines added.

User can add additional routines in files {{{user_additional_routines}}}.

User can check user parameters and deduce further quantities in {{{user_check_parameters}}}.
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User interface has been split into single files.

Type of variables count and count_rate changed to {{{INTEGER(8)}}} in order to avoid "out of range" problems, which result in measured negative time intervals. (cpu_log, local_tremain, local_tremain_ini)

Reading mechanism from restart files completely revised. The subdomain/total domain size is now allowed to vary arbitrarily between the current and previous run. (read_var_list, read_3d_binary, user_read_restart_data)

Precompilation mechanism ('''mbuild''') completely revised: the source-tarfile remains in the source directory (trunk/SOURCE). One depository per block (given in the config-file) is created. Always all files from the source directory are copied to the respective depository. No additional file checks are done any more ('''mrun''' version 2.1). The depository name used contains the conditions given by '''mrun'''-option "{{{-K}}}". (mbuild, mrun)

Output messages (including required stop of execution) can now be handled with the new subroutine message. All output messages will be replaced by this routine step by step within the next revisions.

Neumann boundary condition at k=nzb is explicitly set for better reading, although this has been already done in boundary_conds. (advec_s_bc)

Origin of the xy-coordinate system shifted from the center of the first grid cell (indices i=0, j=0) to the south-left corner of this cell. (netcdf) Topography definition according to new user parameter {{{topography_grid_convention}}}. (init_grid, modules, user_header, user_init_grid, user_parin)
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Bugfix: array {{{d}}} is reallocated in case that multigrid is used. (calc_spectra)

Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics, inflow_turbulence, timestep)

Size of {{{pf3d}}} adjusted to the required output size (1 gridpoint less, along all three dimensions), because output of a subset of the data ({{{pf3d(nxa:nxe...)}}}) in the {{{NF90_PUT_VAR}}} statement caused segmentation fault with the INTEL compiler. (combine_plot_fields)

Bugfix: error in {{{zu}}} index in case of {{{section_xy}}}=''-1''. (header)

Inconsistency removed: as the thermal stratification is not taken into account for the evaluation of the wall fluxes at vertical walls, the eddy viscosity km must not be used for the evaluation of the velocity gradients dudy, dwdy, dvdx and dwdx. (production_e)

Bugfix in calculating k index in case of oceans runs. (sort_particles)

Bugfix: no output of particle concentration and radius unless particles have been started. (data_output_2d)

Bugfix: reading of {{{spectrum_x}}}|{{{y}}} from restart files ignored if total numbers of grid points do not match. (read_3d_binary)

Bugfix: abort in case that absolute temperature is below zero. (init_cloud_physics)
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