PALM Source Code ChangeLog

Current revision:

r4901

Date	Author	svn Revision	Last Release	Type	Description
09/09/10	CH	r560	3.7a	B	Bugfix of calculating ngp_3d for 64 bit. So far ngp_3d has not been 64 bit.
07/09/10	CH	r557	3.7a	B	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.
07/09/10	SR	r556	3.7a	C	Documentation for surface_heatflux in case of prandtl_layer = .F. improved. bugfix for wrong netcdf/3.6.3 module on lcsgi (mbuild, mrun)
				B	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)
01/09/10	CH	r553	3.7a	C	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data_output_mask_user_*, mask_*_x, mask_*_y, mask_*_z, mask_*_x_loop, mask_*_y_loop and mask_*_z_loop have been replaced by corresponding (array-) parameters data_output_masks, data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop, mask_y_loop, and mask_z_loop.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.
17/08/10	BM	r544	3.7a	N/C/B	new: .mrun.config.lcxt4 for Cray-XT4 in Bergen/Norway changes: adjustments for lcxt4 bugfix: loading of user-defined modules (mbuild)
15/06/10	RH	r540	3.7a	C	ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is done using the names hicegate0/bicegate0 instead of the IP addresses
21/04/10	RH	r532	3.7a	C	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.
				B	Bugfix: unit of hyp changed to dbar (check_parameters)
01/04/10	RH	r530	3.7a	B	Bugfix: treatment of special character * in NCL variables containing lists corrected
31/03/10	RH	r529	3.7a	C	List of variable names have to be specified using blank separated lists and single quotes
30/03/10	RH	r526	3.7a	C	Adjustment of the NCL scripts and palmplot to allow for special characters in netCDF variable names.
30/03/10	SR	r525	3.7a	B	Bugfix: "/" in netcdf profile variable names replaced by ":"
19/03/10	SR	r520	3.7a	N	netCDF4 support for particle data. Total number of particles is allowed to increase during the run, when netcdf_data_format > 2 is used.
				C	Special characters like * and " are now allowed for netCDF variable names. Replacement of these characters has been removed (routine clean_netcdf_varname removed)
18/03/10	SR	r516	3.7a	N	Simple installation method has been documented (see doc/install). Respective scripts and configuration files have been updated.
				B	opt=1 is forced for PGI-compiler in routine buoyancy by compiler-directive. Otherwise, program aborts with SIGFPE.
16/03/10	RH	r513	3.7a	N	NCL scripts can be run with the shell script palmplot.
12/03/10	SR	r509	3.7a	B	bugfix for r504: remode_md was given a wrong value
08/03/10	SR	r506	3.7a	C	hack for better usage of mrun on Kyoto computing center machine (lckyoto)
03/03/10	SR	r504	3.7a	C	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.
02/03/10	SR	r496	3.7a	C	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)
01/03/10	SR	r494	3.7a	N	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 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 .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).
				C	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.
				B	Bugfix in Makefile​: forgot to compile for interpret_config. Bugfix: timeseries data have to be collected by PE0 (user_statistics).
05/02/10	SR	r484	3.7a	C	Actual revisions: renamed Current revisions: in most of the source code file headers.
				B	ngp_3d, ngp_3d_inner changed to 64 bit. Otherwise, on large grids > 2*109 grid points some global statistics (e.g. total kinetic energy) have wrong values.
05/02/10	SR	r483	3.7a	N	compare_palm_logs is additionally compiled with mbuild -u . (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)
				C	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)
				B	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)
23/09/09	SR	r392	3.7	N	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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