PALM source code change log 2017

The following table documents all changes to the PALM repository from 2017.

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
29/12/17	FK	r2717	5.0	B	Perform missing svn propset for "Id" keyword (palmrungui)
29/12/17	FK	r2716	5.0	B	Correction of "Former revisions" section in multiple files (in SCRIPTS, SOURCE, UTIL)
27/12/17	SR	r2714	5.0	B	nc suffix removed from input file connection statement for file/folder DATA_PRT_NETCDF. (.palm.iofiles) Variable cycle explicitly interpreted with 10 as the number base. (batch_scp)
20/12/17	FK	r2712	5.0	C	Formatting and clean-up. (vertical_nesting_mod)
20/12/17	MS	r2711	5.0	C	Subroutine renamed in order to avoid some double naming. (netcdf_data_input_mod)
19/12/17	MS	r2709	5.0	B	Bugfixes in CFL check and non-allocated array used in 1D decomposition. (lpm_exchange_horiz)
18/12/17	MS	r2706	5.0	B	Bugfixes in radiation model and restart runs in LSM case. (land_surface_model_mod, radiation_model_mod, surface_mod)
16/12/17	BM	r2704	5.0	N	Release 5.0 with PALM-4U components.
15/12/17	MS	r2701	4.0	B	Bugfix, missing initialization of surface attributes in case of inifor-initialization branch. (init_3d_model)
15/12/17	FK	r2699	4.0	B	Adaptation of output path for gasphase-chemistry code. (trunk/UTIL/chemistry/gasphase_preproc)
14/12/17	MS	r2698	4.0	B, N, C	New / Changed: (done by Philipp Thiele) Particle reflection at downward-facing walls Revision of particle interpolation at topography (lpm, lpm_advec, lpm_init, lpm_boundary_conds) Bugfixes: getting topography top indices (header, init_3d_model, init_grid, microphysics, plant_canopy_model_mod, pmc_interface_mod, radiation_model_mod, surface_mode, turbulence_closure_mod) definition of date constants (date_and_time_mod)
14/12/17	FK	r2697	4.0	B	Missing dependencies added. (Makefile)
14/12/17	FK	r2696	4.0	B, C, N	Major changes (see Release note)
13/12/17	SR	r2693	4.0	C	Replacement of variables given by {{<variable>}} in configuration file is now done in a more general way. Variable names are written in small letters. (palmrun, .palm.config.*)
12/12/17	SG	r2689	4.0	B	Bugfix in if query. (check_parameters)
12/12/17	SG	r2688	4.0	N, C	New: New error message PA0476. (check_parameters) Changed: Allocation and initialization of the latent heat flux (qsws) at the top of the ocean domain in case of coupled runs. Makes it possible to execute coupled runs without specifying humidity = .T. in the _o_p3d file. (surface_mod) Double if query removed. (surface_mod)
07/12/17	MS	r2674	4.0	B	Bugfix in output conversion of resolved-scale momentum fluxes in case of PW advection scheme. (flow_statistics)
06/12/17	SR	r2669	4.0	N, C, B	New: combine_plot_fields is now able to process data from child domains. (combine_plot_fields, pmc_interface_mod) Wildcard (*) allowed in .palm.iofiles as file activation string for output files. (palmrun, .palm.iofiles) Informative messages in case of missing optional input files shortened. (palmrun) Changed: Unit number for file containing turbulence generator data changed to 90. (synthetic_turbulence_generator) File attributes in .palm.iofiles restructured: loc attribute completely removed, (palmrun, .palm.iofiles) File name extension for masked data files is changed to _M## and is now appended at the end of the file name. File ids not used any more have been removed. (check_open) File extension for vertical nesting changed to _NV. (init_coupling) File extension for nested domains changed to _N##. (pmc_interface_mod) File name of turbine output changed to WTM_OUTPUT_DATA. File extension now includes the nest domain number. File extension changed to _T##. (wind_turbine_model_mod) CONTIGUOUS-attribut added to 3d pointer arrays. coupling_char extended to LEN=8. (modules) coupling_char removed. (plant_canopy_model) mrun-string replaced by palmrun. (check_parameters) Bugfix: Preprocessor directives added for MPI specific code. (synthetic_turbulence_generator) Variable cycle explicitly interpreted with 10 as the number base. (palmrun)
04/12/17	MS	r2663	4.0	B	Bugfix, wrong coarse-grid index in init_tkefactor used. (pmc_interface_mod)
27/11/17	SR	r2644	4.0	B	Further bugfix for r2636 (wrong datatype used for allocation). (read_3d_binary)
23/11/17	SR	r2638	4.0	B	Bugfix for cases where a constant top momentumflux is used. (diffusion_u, diffusion_v, surface_mod)
22/11/17	SR	r2636	4.0	B	Bugfix for reading data required for the parrallel random number generator. (read_3d_binary)
20/11/17	JS	r2632	4.0	B	Bugfix in write statement for revision 2629 (lpm_exchange_horiz)
20/11/17	PT/JS	r2629 r2628	4.0	C	Enabled particle advection with grid stretching. Furthermore, the CFL-criterion is checked for every particle at every time step. (check_parameters, lpm_init, lpm_pack_arrays, lpm_exchange_horiz) Also a few formation changes in lpm (lpm_advec).
16/11/17	MS	r2618	4.0	C, N	Reorder calls for initialization of surface quantities. (init_3d_model) Give example of user-defined initialization of surface quantities. (user_init_3d_model)
16/11/17	MS	r2617	4.0	B	Avoid that the mean reference state in buoyancy term become zero. (time_integration)
15/11/17	SR	r2610	4.0	N, B	New: Use of wildcards (*) in file connection statements enabled. (palmrun) Bugfix: usws was used by mistake in logarithmic interpolation of v-component for particles. (lpm_advec)
14/11/17	PT/JS	r2609	4.0	C	Integrated subroutine pack_and_sort into lpm_sort_in_subboxes. (lpm_pack_arrays)
13/11/17	JS	r2608	4.0	N,C	New Added diagnostic_quantities_mod which allows an unified calculation of magnus formula and saturation mixing ratio. The explicit calculation in the model parts is replaced by a function/subroutine call. Change The model now calculates the saturation mixing ratio instead of saturation specific humidity. So the factor 1 - R_d/R_v vanishes. This change can have a (significant!) impact of results considering liquid phase. The difference of saturation mixing ratio and saturation specific humidity is less than 1-3% (depending on temperature and moisture). However, relative changes in liquid water are greater and can intensified by interactions with dynamics.
09/11/17	PT/JS	r2606	4.0	C	Particle grid shift Changed particle box locations: center of particle box now coincides with scalar grid point of same index. Particle movement lpm_move_particle now moves inner particles that would leave the core to the respective boundary gridbox. Afterwards they get transferred by lpm_exchange_horiz. This allows particles to move more than one gridbox independent of domain composition. Renamed module and subroutines lpm_pack_arrays_mod -> lpm_pack_and_sort_mod lpm_pack_all_arrays -> lpm_sort_in_subboxes lpm_pack_arrays -> lpm_pack lpm_sort -> lpm_sort_timeloop_done (lpm_advec, lpm_boundary_conds, lpm_exchange_horiz, lpm_init, lpm_pack_arrays, lpm_read_restart_file, lpm)
09/11/17	SR	r2605	4.0	C	In case of remote jobs, input files with job or jobopt (new) attribute will not be sent with the job file any more, but copied into the SOURCES_FOR_RUN... folder on the remote host, before the job is submitted. After the job has been started on the remote host, these files will be moved (not copied!) from SOURCES_FOR_RUN... to PALM's local working directory. Using this method, the job file becomes very small and (even more important) also non-ASCII files can be send. (palmrun)
06/11/17	JS	r2604	4.0	B	bugfix for calculation of effective radius using morrison microphysics (radiation_model_mod).
03/11/17	AH	r2602	4.0	B	Index-limit related bug (occurred with vertical nesting_mode) fixed in pmci_interp_tril_t (pmc_interface_mod). Check for too high nest domain added in pmci_setup_parent (pmc_interface_mod). Some cleaning up made (pmc_interface_mod).
02/11/17	KS	r2601	4.0	B	Bugfix: added parameter emissivity to radiation_par
01/11/17	SR	r2600	4.0	C, N	Changed: Some further changes concerning the i/o grouping in r2599. (init_pegrid, parin, Makefile) New: Cycle numbers are now three digits wide. (batch_scp, palmrun)
01/11/17	AH	r2599	4.0	B	The i/o grouping was updated to work in nested runs (parin). A separate peer communicator (duplicate of MPI_COMM_WORLD) is introduced for MPI_INTERCOMM_CREATE (pmc_handle_communicator_mod). Some cleanup and commenting improvements made in pmc core (pmc_general_mod, pmc_handle_communicator_mod, pmc_mpi_wrapper_mod, pmc_parent_mod, pmc_child_mod).
26/10/17	AH	r2582	4.0	B	Resetting of e within buildings / topography in pmci_parent_datatrans removed as unnecessary since e is not anterpolated, and as incorrect since it overran the default Neumann condition (bc_e_b) (pmc_interface_mod).
24/10/17	SG	r2576	4.0	B,N	Bugfixes: Repaired procedure for reading and writing restart data. It was not working since r2563 (read_var_list, write_var_list). New code: Introduction of three functions for skipping module related parameters if skip_var_list is called (Makefile, read_var_list, synthetic_turbulence_generator_mod, virtual_flight_mod, wind_turbine_model_mod).
24/10/17	BM	r2575	4.0	B,C	Bugfixes: Calculation of albedos for shortwave and longwave radiation swapped in RRTMG (radiation_model_mod). Changes: Paved surface are now composed of several layers with different properties Namelist parameter pavement_depth replaced by pavement_depth_level Renamed: phi -> latitude, lambda -> longitude. The latter was moved to &inipar Namelist.
23/10/17	SG	r2574	4.0	B	Bugfix: corrected string length in write_var_list
20/10/17	KS	r2572	4.0	B	Bugfix: corrected string length in lsm_last_actions
20/10/17	SR	r2566	4.0	N, C	New: Adjustments for using grid engine batch systems. An execute command for combine_plot_fields can be explicitly set in the configuration file with variable execute_command_for_combine. (palmrun) Changed: Some informative messages have been switched off or reformatted. (palmbuild, palmrun)
19/10/17	SG	r2563 r2564	4.0	C,N	Changes: Adapted extent of the y-axis for plotting spectra with palmplot (spectra.ncl). Changed restart procedure to get rid of skipping functions for each module (Makefile, write_var_list, read_var_list, virtual_flight_mod). Position of functions calls for reading module related parameters changed from read_var_list to the end of _parin functions defined in each module. In that way, namelist parameters in the restart data overwrites the namelist parameters defined in the _p3d file of the specific restart run (synthetic_turbulence_generator_mod, read_var_list, parin.f90, virtual_flight_mod.f90). Parameter wind_turbine is now defined in module check_parameters (modules, prognostic_equations, time_integration, wind_turbine_model_mod). synthetic_turbulence_generator_mod.o was added to the list of write_var_list.o in the Makefile. New Code: Restart runs with the usage of the wind turbine model are possible now (write_var_list, wind_turbine_model_mod, Makefile).
18/10/17	SG	r2553	4.0	C,B	Bugfix of vertical loop in wtm_tendencies to account for different turbine heights, bugfix of the interpolation of the u-component concerning the vertical index and further small adjustments of the programming style.
18/10/17	SR	r2551	4.0	N	TEMPDIR added as replacement string to be used in batch directives. (palmrun)
16/10/17	LB	r2550	4.0	N,C	New: New inipar-parameter complex_terrain (check_parameters, modules, parin, header, init_3d_model) The cyclic fill method is modified in case of complex terrain to ensure robust initialization. (init_3d_model) Mean inflow profiles are adjusted according to height of inflow boundary. (init_3d_model) Changed: Lateral boundary conditions for topography set on all three ghost layers.(init_grid)
16/10/17	JS	r2548	4.0	B	Bugfix for r2547
16/10/17	JS	r2547	4.0	B,C	Bugfix Correction of if-statements for LCM usage and calculation of cloud droplet number concentration (radiation_model_mod). Changed: Extended by cloud_droplet option (land_surface_model, surface_layer_fluxes_mod, surface_mod)
11/10/17	BM	r2544	4.0	N,C	New: New module date_and_time_mod for calculating all quantities needed for datum-based actions (Makefile, date_and_time_mod) Changed: Date and time calculations moved from radiation model to new module (see above) (radiation_model_mod, header, parin, time_integration_spinup, urban_surface_model)
11/10/17	KS	r2532	4.0	B	Bugfix: corrected bounds of 3d output variables in LSM (see rev2512)
05/10/17	FK	r2523	4.0	B, N	Bugfix: Increased LEN for CHARACTER variable var_name, equal to the value in PALM (combine_plot_fields) New: Configuration file for running jobs locally (interactive or batch mode) on host idefix (.palm.config.idefix)
05/10/17	JS	r2522	4.0	B	Avoid dividing by zero in microphysics (microphysics_mod)
04/10/17	FK	r2515	4.0	B	The palmtest script now uses the default .palm.iofiles file (trunk/SCRIPTS) in order to avoid failing of tests due to user-modified settings in this file (palmtest)
04/10/17	MS	r2514	4.0	B	Remove tabs. (check_open, init_dvrp, init_pegrid, land_surface_model_mod, pmc_handle_communicator, urban_surface_model_mod, vertical_nesting_mod)
04/10/17	FK	r2513	4.0	B	Correction of dopr(_initial)_index values and units connected to passive-scalar output quantities. (check_parameters, init_3d_model)
04/10/17	SR	r2512	4.0	C	Upper bounds of cross section and 3d output changed from (nx+1,ny+1), (nx,ny). No output of redundant ghost layer data to NetCDF files any more. This way, stripe structures related to the domain decomposition which appeared in user-defined quantities and which were reported by users from time to time are avoided. A general exchange of ghost point data in routines data_output_... is not required any more. (check_open, data_output_2d, data_output_3d, land_surface_model_mod, netcdf_interface_mod, palm, plant_canopy_model_mod, radiation_model_mod, urban_surface_mod, user_data_output_2d, user_data_output_3d, user_parin, combine_plot_fields). Important: The user-interface required revision number has been updated to r2512. Old user-interfaces will need an update of routines data_output_2d and {{data_output_3d}}}. Furthermore, users should keep in mind that due to this change in case of cyclic boundary conditions the flow field features between grid points (nx,ny) and the cyclically adjacent points (0,0) will not be displayed in plots any more.
02/10/17	MS	r2508	4.0	B	Major bugfixes in SGS-TKE buoyancy production term. (production_e) Revised initialization of vertical gradient levels. (check_parameters, modules) Formatting adjustments. (surface_mod)
29/09/17	SR	r2507	4.0	B	Problem concerning determination of cycle numbers of NetCDF input files has been fixed. (palmrun)
29/09/17	SR	r2506	4.0	N,C	New: Option -V added to check for an existing SOURCES_FOR_RUN_... folder. (palmbuild, palmrun) Option -W added to allow for job dependencies. (palmrun) Changed: Host configuration (from option -h) is added to the SOURCES_FOR_RUN_... folder name. (palmbuild, palmrun)
27/09/17	BM	r2504	4.0	B,C	Bugfix: jobs were not loaded in PALM job manager (palm_jm). Changed: it now allowed to have water in the soil below paved surfaces (land_surface_model_mod) added several pavement types and reset their albedo type (land_surface_model_mod, radiation_model_mod).
26/09/17	TG	r2502	4.0	B	Bugfix: Use equation of state for seawater to calculate rho_ocean_init at nzt (init_ocean).
26/09/17	SR	r2501	4.0	C, B	Changed: Default value for number of cores (option -X) set to 1. (palmrun) Bugfix: Bugfix for mechanism which overwrites configuration file settings with values provided by palmrun options. (palmrun)
25/09/17	SR	r2500	4.0	B	Bugfix for r 2489. (palmbuild)
20/09/17	FK	r2499	4.0	B, C	B Some INPUT activation strings corrected, changed "f" to "r". (.palm.iofiles) C Description of palmrun option -h changed to "configuration identifier". (palmrun) Default value of fft_method changed to 'temperton-algorithm', since some system cannot handle 'system-specific'. (modules)
20/09/17	SR	r2489	4.0	N	Ask for compilation, if SOURCES_FOR_RUN_... exists. (palmbuild)
20/09/17	SR	r2487	4.0	B	Abort in case of compiling/linking errors in silent mode. (palmbuild)
20/09/17	BM	r2484	4.0	C	PALM logo added to job manager and palmrungui. Job manager adapted for change of standard USER_CODE directory. (palm_jm, palmrungui, mainwindow.ui, logo.png, palm_jm.ui)
19/09/17	SR, BM	r2480 r2479	4.0	N	New option -A to set a project account number for batch jobs. (palmrun, .palm.config.crayh, pamrungui.py, maindwindow.ui)
18/09/17	MS	r2478	4.0	B	Revised initialization of model-top fluxes. (surface_mod) Correct setting of flag controlling model-top fluxes. (init_grid) Bugfix concerning subgrid-TKE production in case no surface fluxes and no constant-flux layer is applied. (production_e)
18/09/17	BM	r2477	4.0	B,C	Bugfix and minor changes in palmrungui (palmrungui.py, maindwindo.ui).
18/09/17	BM	r2476	4.0	B	Bugfix in default settings for vegetation_type = 1 (bare soil). (land_surface_model_mod.f90).
11/09/17	TG	r2429	4.0	N	Minor changes to list of I/O files (.palm.iofiles).
08/09/17	SR	r2422	4.0	N	New scripts palmrun and palmbuild set to version number 1.0 (palmbuild, palmrun) Additional check for inconsistencies between d3par parameters restart_time and/or dt_restart and the file activation strings given with palmrun option -a. (check_parameters)
06/09/17	MS	r2418	4.0	B	Comment removed. (lpm)
06/09/17	MS	r2417	4.0	B	Major bugfix in modeling SGS particle speeds. In addition, particle time-stepping is optimized, only particles which has not been completed the LES timestep are accessed in particle advection loops. (lpm, lpm_advec, lpm_pack_arrays, user_lpm_advec).
06/09/17	BM	r2416	4.0	C	PALM watchdog adapted for used with palmrun (palm_wd, palm_wdd, .wdd.config.hrlnIII).
06/09/17	SG	r2414	4.0	C	Redundant preprocessor directives removed
06/09/17	BM	r2413	4.0	C	Adapted old tool mrungui for use with palmrun (in that course mrungui was renamed to palmrungui). (palmrungui.py, palmrungui, mainwindow.ui, about,ui, help.ui)
06/09/17	SG	r2410	4.0	C	Revised error message PA0462 and changed lclocal to lcmuk in testsuite
05/09/17	TG	r2408	4.0	C	Changed default value of mg_cycles from -1 to 4. (modules)
04/09/17	MS	r2397	4.0	B	Enable initialization of 3d model by user also in the child domain. (parin)
01/09/17	SR	r2380	4.0	N	Initial versions of new scripts tp compile and run PALM. (new: palmbuild, palmrun, Makefile_utilities)
31/08/17	MS	r2378	4.0	B	Bugfix in write restart data. (surface_mod)
29/08/17	JS	r2375	4.0	N,B,C	Improved aerosol initialization of bulk microphysics. Minor bugfixes for droplet sedimentation and some changes of USE and ONLY dependencies due to an exchange of variable from particle_attributes to modules. (check_parameters, lpm_droplet_collison, lpm_droplet_condensation, lpm_init, microphysics_mod, mod_particle_attributes, modules, package_parin, parin)
28/08/17	FK	r2374	4.0	N	Added todo list. (vertical_nesting_mod)
25/08/17	SW	r2372	4.0	N	Y-shift at periodic x-boundary. (init_pegrid, parin, modules, read/write_var_list)
24/08/17	FK	r2371	4.0	B	Dependency bugfix for vertical_nesting_mod. (local_stop, Makefile)
23/08/17	SR	r2370	4.0	B	Dependency bugfix for synthetic_turbulence_generator. (Makefile)
22/08/17	MS	r2369	4.0	B	No masking of topography, else prho becomes zero, causing divisions by zero. (eqn_state_seawater)
21/08/17	FK	r2365	4.0	N, B	New: Vertical grid nesting implemented as developed by Sadiq Huq from Karlsruhe Institute of Technology in Garmisch-Partenkirchen. (boundary_conds, check_parameters, combine_plot_fields, diffusivities, init_coupling, init_grid, init_pegrid, local_stop, mrun, parin, read_var_list, time_integration, timestep, vertical_nesting_mod (new file), write_var_list) Added hosts lckea and lckeam on KIT/IMK-IFU Garmisch clusters. (mrun, mbuild, subjob) Bugfix: Removed unnecessary dependency of surface_mod on init_pegrid. (Makefile)
21/08/17	AH	r2359	4.0	B	Minor indexing error corrected in pmci_init_loglaw_correction (pmc_interface_mod.f90).
17/08/17	JS	r2354	4.0	B	Minor bug fixes in land surface model (division of array with different dimension, set 'nzs' to correct value). Bugfix correlated to lsm_check_data_output_pr. If-statement for following checks is essential, otherwise units for lsm output are set to 'illegal' and palm will be aborted. (check_parameters, land_surface_model)
15/08/17	FK	r2351	4.0	C	Removed check for nopointer version. (pmc_interface_mod)
15/08/17	FK	r2350	4.0	B	Bugfixes and temporary workarounds for nopointer version. (init_3d_model, pmc_interface_mod, swap_timelevel, urban_surface_mod)
10/08/17	SG	r2349	4.0	N,C	Add parameter pitch_rate to namelist and revise/add error messages
10/08/17	FK	r2348	4.0	N	Check for simultaneous use of geostrophic wind and u_profile/v_profile, which can cause inconsistencies in the forcing. (check_parameters)
10/08/17	HK	r2347	4.0	N	Introduced a automatic testsuite that can be execute by typing testsuite. (SCRIPTS/testsuite)
09/08/17	MS	r2346	4.0	B	Determination of topography-top index corrected. (lpm_init)
09/08/17	SG	r2345	4.0	C	Remove error message PA0156 and the conserve_volume_flow_mode option inflow_profile
09/08/17	SR	r2344	4.0	B	Explicit setting of initial values for array domask, required due to a bug in the Cray compiler (appears only if option -eD is used). (init_masks)
08/08/17	SG	r2343	4.0	C	See revision 2341 but now with properly reordered revision description in changed file.
08/08/17	LB	r2342	4.0	B	Bugfix: Abort simulation if surface forcing data is not available until end of run (large_scale_forcing_nudging_mod.f90)
08/08/17	SG	r2341	4.0	C	Unit correction in Doxygen comments
07/08/17	TG	r2338	4.0	C	Modularized 1D model, renamed 'init_1d_model.f90' to 'model_1d_mod.f90' (Makefile, header.f90, model_1d_mod.f90, parin.f90, surface_mod.f90, check_parameters.f90, init_3d_model.f90, modules.f90, read_var_list.f90, write_var_list.f90)
07/08/17	TG	r2337	4.0	C,B	Changed calculation of mixing length (1D model); corrected calculation of virtual pot. temperature gradient (1D model); removed rounding of time step (1D model) (init_1d_model.f90, modules.f90)
04/08/17	FK	r2335	4.0	C	Update of module path (.mrun.config.idefix)
04/08/17	TG	r2334	4.0	B	Set model constant c_m to 0.4 within 1D model according to Detering and Etling (1985) (init_1d_model).
03/08/17	JS	r2330	4.0	B	Bugfix: Code also for gfortran compilable, function c_sizeof is not used (lpm_exchange_horiz, .mrun.config.gfortran, .mrun.config.cuhk, .mrun.config.forwind_eddy, .mrun.config.forwind_hlrnIII ).
03/08/17	HK	r2329	4.0	B	Major bugfix for topography usage with the anelastic approximation and the Boussinesq approximation while air density != 1 (advec_ws.f90, check_parameters.f90, init_3d_model.f90, production_e.f90). Bugfix: The divergence correction inside the Wicker-Skamarock advection scheme now correctly considers the air density The production of TKE is now based on kinematic rather that dynamic fluxes An index error prevented the correct output of density profiles fro rho_air and rho_air_zw Warning: Since r2252 PALM was not working correctly at all when used with topography!!! Since r2270 density profile output in PALM was not functioning correctly
03/08/17	BM	r2328	4.0	B,C	Various improvement of the land surface model (land_surface_model_mod.f90, radiation_model_mod.f90). Bugfix: setting of humidity = .T. now works with paved surfaces Changed: User input of soil layer is now done via NAMELIST parameter dz_soil (layer thickness) New skin layer concept realized Some default values in the lookup tables revised Emissivity and albedo type are now more flexible and can be set for each pixel Default surface_type is now 'vegetation'
01/08/17	TG	r2326	4.0	C	Updated variable descriptions (modules.f90)
26/07/17	SG	r2323	4.0	C	Change unit number of file WTM_DATA from 201 to 90 (wind_turbine_model_mod)
26/07/17	SG	r2322	4.0	B	Bugfix of error message and assign error numbers (wind_turbine_model_mod)
21/07/17	JS	r2321	4.0	B	Bugfix: Correct index in lookup table for Obukhov length. (surface_layer_fluxes)
21/07/17	MS	r2320	4.0	C	Large-scale forcing and nudging modularized. (boundary_conds, check_parameters, flow_statistics, header, init_3d_model, large_scale_forcing_nudging_mod, Makefile, modules, palm, prognostic_equations, read_var_list, time_integration)
20/07/17	MS	r2319	4.0	B	Remove print statement from last commit. (init_grid)
20/07/17	MS	r2318	4.0	C	In order to increase readability, get topography top index via function call. (init_grid, lpm_advec, lpm_boundary_conds, lpm_init, Makefile, mircrophysics, plant_canopy_model, pmc_interface_mod, radiation_model_mod, surface_mod, urban_surface_mod)
20/07/17	BM	r2316	4.0	C	The mrungui is now based on python instead of C/C++ (mrungui, mrungui.py, mbuild, about.ui, help.ui, mainwindow.ui).
14/07/17	FH	r2312	4.0	B, C	Various improvements of the LCM (check_parameters.f90, data_output_ptseries.f90, lpm_droplet_collision.f90, lpm_droplet_condensation.f90, lpm_init.f90, lpm_read_restart_file.f90, microphysics_mod.f90, mod_particle_attributes.f90, package_parin.f90): (i) SGS particle motions are now possible if 'curvature_solution_effects = .TRUE.'. (ii) Initialization of aerosol spectra has been improved (aero_type, aero_weight). (iii) New, more stable Rosenbrock method for the numerical integration of the diffusional growth equation. (iv) Gas-kinetic effects are now considered in the diffusional growth equation. (v) Collision and coalescence now considers redistribution of aerosol mass. (vi) Collision and coalescence does not underestimate collisions if the timestep is too long.
13/07/17	MS	r2311	4.0	N	Set bottom boundary conditions after nesting interpolation and anterpolation. (pmc_interface_mod, time_integration)
11/07/17	TG	r2310	4.0	B	Changed position of error calls for ENVPAR file and namelist (parin.f90).
10/07/17	TG	r2309	4.0	C, B, N	Updated version of palm_gf: location of temporary files for palm_gf is now configurable; sorting of results is implemented; several bugfixes and new additions in gui and calculation.
07/07/17	MS	r2307	4.0	B	Variable names corrected. (land_surface_model_mod).
06/07/17	FH	r2305	4.0	C	Improved calculation of particle IDs (lpm_init, lpm_exchange_horiz, lpm_read_restart_file, mod_particle_attributes).
04/07/17	MS	r2304	4.0	B	Bugfix, enable restarts for child domain. (parin)
04/07/17	SR	r2303	4.0	B	Default value for write_binary was missed. (mrun)
03/07/17	MS	r2302	4.0	B, C	Bugfixes in reading 3D topography from file. (init_grid) Change - reading of 3D topography using NetCDF data type NC_BYTE. (netcdf_interface_mod)
29/06/17	TG	r2301	4.0	B	Set length of variable name for masked output to global value. (init_masks)
29/06/17	SR	r2300	4.0	C	NEC related code partly removed. (advec_s_bc, disturb_field, fft_xy_mod, init_dvrp, temperton_fft_mod) host variable partly removed from the code. Host specific code completely removed. (check_open, check_parameters, close_file, fft_xy_mod, header, init_pegrid, poisfft_mod) Default values for variables host, loop_optimization, and termination_time_needed have been changed. (modules)
29/06/17	BM	r2299	4.0	C	Some minor modifications for the new spinup mechanism (header.f90, init_1d_model.f90, land_surface_model_mod.f90, radiation_model_mod.f90, surface_layer_fluxes_mod.f90, time_integration.f90, time_integration_spinup.f90). Air temperature is now estimated from incoming shortwave radiation Run control output added Soil moisture does not change during spinup Allow for performing lsm spinups followed by LES spinup.
29/06/17	SR	r2298	4.0	C	write_binary is of type LOGICAL now. (check_for_restart, land_surface_model_mod, modules, palm, radiation_model_mod, user_last_actions, mrun) User interface current revision updated. (user_parin) MPI2-atmosphere-ocean-coupling removed. (header, init_coupling, init_dvrp, init_pegrid, modules, palm, mrun) Obsolete variables removed. (check_open, modules, parin, mrun) Send/recieve in background related parts removed. (exchange_horiz, poismg_mod) Missing variable descriptions added. (modules) Comment change and reformatting. (pres)
28/06/17	KS	r2297	4.0	B	Bugfixes in time_integration_spinup.f90
28/06/17	BM	r2296	4.0	B, N	New: A new mechanism for performing model spinups without atmosphere (e.g. for land surface, urban surface, and radiation) is now available. It is steered via the inipar-Parameters spinup_time,spinup_pt_amplitude,spinup_pt_mean,dt_spinup,data_output_during_spinup. The mechanism currently imposes a sinusoidal atmospheric temperature with given parameters to allow soil and wall spinup before switching on the atmosphere code. Note that this is an initial version which still needs some minor modifications (e.g. better coupling to radiation input). (Makefile, land_surface_model_mod.f90, modules.f90, palm.f90, parin.f90, radiation_model_mod.f90, time_integration_spinup.f90, urban_surface_model_mod.f90). Bugfixes: Output of all radiative fluxes is now possible with radiation_scheme = 'constant' Bugfix in scaling of surface heat flux in urban surface model Bugfix in calculation of bare soil heat capacity in land surface model
27/06/17	SR	r2295	4.0	C, N	Script adjustments for using lcgeohu ( cirrus @ HUB ). Variable cpp_opts removed. (mrun, subjob)
22/06/17	MS	r2293	4.0	C	In anterpolation, exclude grid points which are used for interpolation. This avoids the accumulation of numerical errors leading to increased variances for shallow child domains. (pmc_interface_mod)
15/06/17	JS	r2292	4.0	N	Implementation of new microphysic scheme: cloud_scheme = 'morrison' includes two more prognostic equations for cloud drop concentration (nc) and cloud water content (qc). The process of activation is parameterized with a simple Twomey activion scheme or with considering solution and curvature effects (Khvorostyanov and Curry ,2006). The saturation adjustment scheme is replaced by the parameterization of condensation rates (Khairoutdinov and Kogan, 2000, Mon. Wea. Rev.,128). All other microphysical processes of Seifert and Beheng are used. Additionally, in those processes the reduction of cloud number concentration is considered. (advec_s_bc, advec_ws, average_3d_data, boundary_conds, calc_liquid_water_content, check_parameters, data_output_2d, data_output_3d, data_output_mask, flow_statistics, init_3d_model, init_masks, microphysics_mod, modules, netcdf_interface_mod, palm, parin, pmc_interface_mod, prognostic_eqautions, read_3d_binary, sum_up_3d_data, surface_layer_fluxes_mod, surface_mod, swap_timelevel, time_integration, wrtie_3d_binary)
15/06/17	MS	r2287	4.0	B	Bugfix in determination topography-top index. (urban_surface_mod)
15/06/17	SR	r2286	4.0	C	Test output of cycle numbers removed. (mrun)
15/06/17	MS	r2285	4.0	C	Consider multiple pure-vertical nest domains in overlap check. (pmc_interface_mod)
15/06/17	BW	r2284	4.0	C	Updated description of wind turbine example (example_wtm.txt)
14/06/17	MS	r2283	4.0	B	Bugfixes in initialization of log-law correction concerning new topography concept. (pmc_interface_mod)
13/06/17	JS	r2282	4.0	B	Bugfix for check of saturation moisture. (land_surface_model)
13/06/17	MS	r2281	4.0	C	Clean-up unnecessary index access to surface type. (surface_layer_fluxes_mod)
12/06/17	MS	r2280	4.0	B	Bugfix, set filepointer to the beginning of the file after namelist read. (pmc_handle_communicator)
12/06/17	JS	r2278	4.0	C	Added comments. (mod_particle_attributes, lpm_merging, lpm_splitting)
12/06/17	FK	r2277	4.0	C, N	Changed: Removed unused variables (close_file, data_output_2d, init_3d_model, modules, nudging_mod) New: Added doxygen comments for variables/parameters (modules)
09/06/17	SG	r2274	4.0	B	Error messages changed
09/06/17	SW	r2273	4.0	B	Error message changed
09/06/17	BW	r2272	4.0	N, C	Added configuration file for lceddy (.mrun.config.forwind_eddy) and removed the configuration file for lcflow Updated wind turbine example files
09/06/17	SW	r2271	4.0	B	Error messages and numbers changed
09/06/17	BM	r2270	4.0	B, C	Bugfixes: Time series output fixed (output of land surface / radiation quantities was faulty (flow_statistics.f90, init_3d_model.f90, netcdf_interface_mod.f90, radiaiton_model_mod.f90). Changed: Renamed "Prandtl layer" to "constant flux layer" (header.f90). Major changes in land surface model: Revised parameterization of heat conductivity between skin layer and soil (land_surface_model_mod.f90, surface_mod.f90) Scalar quantities are now defined at the center of the soil layers Renamed parameters to be in agreement with new PALM input data standard (veg_type --> vegetation_type, pave_type --> pavement_type, Addition, reduction, and renaming of look-up tables Revised and simplified land surface model initialization as required for new PALM input data standard Removed output of shf_eb (now directly out put in wpt0) and qsws_eb now directly out put in wq0) Removed ""_eb" strings throughout the model as no longer required Removed old Clapp & Hornberger parameterization
09/06/17	MS	r2269	4.0	N, B	Enable restarts with USM with different number of processors. (Makefile, read_3d_binary, urban_surface_mod) Bugfix in new surface structure in USM. (urban_surface_mod) Formatting adjustments and descriptions in surface_mod. (surface_mod)
09/06/17	SR	r2268	4.0	B	Calculating of cycle numbers for output files caused by r2262 fixed. (mrun)
09/06/17	TG	r2267	4.0	B	Several namelists were not read if "d3par" was not given in the namelist file. (parin)
09/06/17	SR	r2266	4.0	B, C	Bugfix: cpu-time per grid point is now calculated using ngp_3d in order to avoid INTEGER overflow. (cpulog_mod) Changed: nech related parts removed. (subjob)
08/06/17	JS	r2265	4.0	C	Unused variables removed. (lpm_init, lpm_read_restart_file, lpm_write_exchange_statistics, lpm_write_restart_file, mod_particle_attributes, netcdf_interface_mod, read_var_list, write_var_list)
08/06/17	JS	r2263	4.0	C,N	Implemented a splitting and merging algorithm for the Lagrangian cloud model. A detailed description can be found in the documentation. (lpm, lpm_init, lpm_merging, lpm_splitting, Makefile, mod_particle_attributes, package_parin)
08/06/17	SR	r2262	4.0	N, C, B	New: Unified cycle numbers for output files are used, i.e. mrun tries to give all output files the same cycle number. If that number (or a larger one) already exists for a specific file, the new cycle number of that file will be the largest existing number incremented by one. (palm, batch_scp, mrun) Paths and basenames of files are allowed to contain arbitrary numbers of dots ".". (batch_scp, mrun) Changed: Important: The feature "fl" in configuration files have to be replaced by "ln". It tells mrun that it should try to link that file/directory instead of copying. This feature should be given in case of very large files (e.g. the restart files). If the attribute "ln" is given, the permanent file has to reside in the same file system as mruns temporary working directory. If this isn't the case, mrun will try to copy the file. mrun does not create empty files/directories for restart files in the HOME-folder any more as it was done with feature "fl". Creation of file OUTPUT_FILE_CONNECTIONS removed. Archive feature completely removed from the script. nech related parts completely removed. (mrun) Bugfix: OpenMP statements from r2232 removed. (prognostic_equations)
08/06/17	TG	r2260	4.0	C	Update of .mrun.config files for new synthetic turbulence generator implemented since r2259.
08/06/17	TG	r2259	4.0	N	Implemented a synthetic turbulence generator. This generates turbulence at a non-cyclic inflow boundary using a method designed by Xie and Castro (2008) with modifications by Kim et al. (2013). The method can be switched on by setting using_synthetic_turbulence_generator = .T. within the new stg_par namelist.
08/06/17	MS	r2258	4.0	B	Bugfix, add pre-processor directives to enable non-parrallel mode. (header, pmc_interface_mod, timestep, urban_surface_mod)
07/06/17	BW	r2257	4.0	B, C	Bugfix: turb_cl_tab and turb_cd_tab were set to zero before being allocated (wind_turbine_model_mod) Change: adjustments for lceddy, removed lcflow-specific code (mbuild, mrun, subjob)
07/06/17	MS	r2256	4.0	B, C, N	Bugfix: remove ring-dependency. (Makefile) Change: change default value of zeta_min to -20. (modules) New: Enable heat/scalar/waterflux at downward-facing surfaces (modules, surface_mod)
07/06/17	HK	r2255	4.0	C	Implemented PALM specific error message handling for parallel random number generator. (random_generator_parallel_mod)
07/06/17	HK	r2252	4.0	C	Air density now depending on surface_pressure even in boussinesq mode and perturbation pressure now depending on flux_output_mode. (flow_statistics, init_3d_model)
06/06/17	SG	r2251	4.0	N	Doxygen comment added. (check_parameters)
06/06/17	SW	r2249	4.0	B	Changed error message. (check_parameters, land_surface_model_mod, radiation_model_mod)
06/06/17	SW	r2247	4.0	B	Changed error message. (land_surface_model_mod)
02/06/17	JS	r2245	4.0	B	Apply boundary conditions for y-direction. Otherwise the origin y-position of particles is also changed for boundary conditions of reflection and absorption. (lpm_exchange_horiz)
01/06/17	BM	r2242	4.0	C	Soil model was adjusted so that the number of soil layers are now freely adjustable via the NAMELIST. The default configuration was changes to a 8-layer setup in order to account for a faster response to turbulence. Note that the new configuration is made for temperature and moisture defined at the center of the soil layers. The current discretization as well as the skin layer still needs adaption. The land surface model thus should be used with care in the present form (land_surface_model_mod). The RRTMG interface was adjusted to allow for PALM runs without cloud physics and humidity. (radiation_model_mod)
01/06/17	AH	r2241	4.0	B	Minor indexing error in pmci_init_loglaw_correction is corrected (pmc_interface_mod)
01/06/17	MS	r2239	4.0	B	Bugfix xy-output of land-surface variables. (netcdf_interface_mod)
31/05/17	MS	r2238	4.0	B	Bugfixes in Makefile, and remove unnecessary module load. (init_pegrid, Makefile)
31/05/17	MS	r2237	4.0	B	Bugfix in writing restart data. (land_surface_model_mod) Bugfix in dependencies on new surface module. (Makefile)
31/05/17	MS	r2236	4.0	N	Add NetCDF input file for topography. (.mrun.config.*)
30/05/17	MS	r2232	4.0	N, C	New topography concept implemented: topography is now considered via flag arrays instead of 2D index arrays overhanging structures like bridges are now possible, i.e. the limitation of surface-mounted topography does not exist anymore new generic topography for tunnels added New surface-modeling concept implemented. surface elements are packed into one-dimensional arrays, belonging to derived data types each surface element comprises relevant data, e.g. modeled momentum and heatfluxes different surfaces are distinguished, i.e. urban-type, natural-type, and default-type surfaces; in addition, different surface facings are considered (upward-, downward-facing, northward-, southward, eastward- and westward-facing surfaces) land-surface model works now also with topography Enable input of topography data in NetCDF format OPENMP bugfix. (poismg_noopt) A documentation about the revised topography and surface-modelling concept can be found here.
30/05/17	AH	r2230	4.0	B	Minor indexing error in pmci_init_anterp_tophat that in certain case caused an overflow is corrected (pmc_interface_mod)
16/05/17	SR	r2225	4.0	C	Simple installation scripts now running under bash. (palm_simple_install, palm_simple_run)
15/05/17	MS	r2223	4.0	B	Add check for particle release at/above model top. (lpm_init)
10/05/17	FK	r2221	4.0	C	Update of .mrun.config.idefix due to change of software paths.
09/05/17	AH	r2220	4.0	B	Two near-wall correction-related array indexing bugs corrected in the interpolation routines (pmc_interface_mod.f90).
28/04/17	MS	r2215	4.0	B	Normalization of spectra output. (spectra_mod)
24/04/17	FK	r2214	4.0	B, C	Bugfix: Added exchange of ghost points in array pc_heating_rate needed for output of pcm_heatrate, and added onetime ghost point exchange of lad_s after initialization (plant_canopy_model_mod) Change: Formatting and clean-up of subroutine pcm_read_plant_canopy_3d, minor re-organization of canopy-heating initialization (plant_canopy_model_mod) Removal of output quantities usm_lad and usm_canopy_hr (urban_surface_mod)
19/04/17	FK	r2210	4.0	B, C, N	Bugfix: for division by zero (urban_surface_mod) Change: removed cpp switch __mpi3 (urban_surface_mod) some formatting in SUBROUTINE usm_find_boundary_face (urban_surface_mod) New: 3D plant canopy model output of leaf area density pcm_lad and plant canopy heat rate pcm_heatrate (check_parameters, data_output_3d, netcdf_interface_mod, plant_canopy_model_mod)
13/04/17	FK	r2202	4.0	N	New .mrun.config.idefix for MOSAIK workstation.
11/04/17	MS	r2200	4.0	C, B	Change: Remove monotonic adjustment for 5th-order advection scheme. (advec_ws, check_parameters, init_grid, init_pegrid, header, modules) Bugfixes: Fix bugs in reading restart data and 2D ghostpoint exchange. (radiation_model_mod)
24/03/17	SR	r2197	4.0	B	Do not allow odd values for nz at the coarsest grid level in case of optimized multigrid solver. This change may decrease the number of possible grid levels which may result in a slower convergence of the solver. Users should carefully choose nz in order to allow for as much levels as possible. Always the best choice would be a multiple of 2. (init_pegrid)
23/03/17	SR	r2194	4.0	B	In case of ocean runs, density is now used in single-value reference state instead of potential density. (init_ocean)
22/03/17	SR	r2192	4.0	B	Index bounds of arrays spectrum_x and spectrum_y revised. (spectra_mod) Misplaced and missing openMP directives from r2155. (prognostic_equations)
21/03/17	SR	r2189, r2190	4.0	B	String rho renamed rho_ocean for the cross section output. (data_output_2d, netcdf_interface_mod)
21/03/17	SR	r2187	4.0	C	Adjustment of compute node names for lckyuh. (subjob)
21/03/17	SR	r2185	4.0	B, C	Bugfix: localhost renamed local_host. (subjob) Change: Batch-environment on lckyu*-hosts is checked by environment variable PJM_ENVIRONMENT. (mrun)
17/03/17	JS	r2183	4.0	N	Added parameters for simplified particle initialization. An initial particle number concentration (number_concentration) for the LCM can be prescribed. Also the number of particles which are created in every grid box can be prescribed with the new parameter number_particles_per_gridbox . (lpm_init, mod_particle_attributes, package_parin)
17/03/17	AH	r2180	4.0	C	Recently added checks to ensure that pdims match the grid dimensions are removed as unnecessary in the automatic determination of pdims in init_pegrid.
17/03/17	AH	r2178	4.0	B	Index limits for perturbations are now set also in case of nested boundary conditions. (check_parameters) Setting perturbations at all times near inflow boundary is removed in case of nested boundaries. (time_integration) Calls for pmci_ensure_nest_mass_conservation and pres are added after the nest initialization. (palm) Checks to ensure that pdims match the grid dimensions are added in the automatic determination of pdims. (init_pegrid)
13/03/17	AH	r2176	4.0	B, N	Bugfixes: 3-D interpolation to create initial conditions for nests is now skipped in case of restart (palm). New: vertical cell-counts for anterpolation are now precomputed and stored in 1-D arrays kfc_w and kfc_s (pmc_interface_mod).
13/03/17	BM	r2174	4.0	B,N,C	Bugfixes: setting of kcb=0, excluding child corner point anterpolation. (pmc_interface_mod) New: nesting can now be used with cloud physics. (pmc_interface_mod, time_integration) Changed: default setting of most_method changed to 'newton' to avoid problems over non-homogeneous surfaces.
08/03/17	HK	r2172	4.0	B	Bugfix: Moved parallel random generator initialization into respective module and removed global array (dirturb_field, init_3d_model, random_generator_parallel_mod)
06/03/17	MS	r2169	4.0	B	Bugfix, move setting of topography_grid_convention to init_grid, else, in case of restarts generic topography may not set properly if no value is prescribed. (check_parameters, init_grid)
01/03/17	JS	r2164	4.0	B	Bugfix in radiation_check_data_output: missing case request for rad_lw_in, rad_lw_out, rad_sw_in, and rad_sw_out added and correct units for output variables added. (radiation_model_mod)
22/02/17	MS	r2157	4.0	B	Bugfix in read_restart_data in case radiation_scheme = 'clear_sky' or 'constant'. (radiation_model_mod)
21/02/17	FH	r2155	4.0	B	Bugfix: cloud microphysics are now also calculated on ghostpoints. (prognostic_equations, microphysics_mod)
17/02/17	LV	r2152	4.0	N, B	New Tip loss correction for the wind turbine parametrization (wind_turbine_model_mod) new control parameter tl_cor (Default=.FALSE.) Bugfix Bugfix in subroutine wtm_read_blade_tables (wind_turbine_model_mod)
09/02/17	KS	r2147	4.0	C, B	Changes improved label bar in palmplot (cross_sections.ncl) added gharbi and kuma to the list of known hosts (subjob) changed allocation of resources for lcbullhh (mrun) Bugfix Land surface parameters II corrected for veg_type 18 and 19 (land_surface_model_mod)
06/02/17	TG	r2141	4.0	C	Changed check for existing files in mrun at the beginning of a run. (mrun)
02/02/17	SR	r2134	4.0	N	Option -E added to msub commands on HLRN-III machines to allow output of more job information in the job protocol files. (subjob)
24/01/17	SR	r2130	4.0	B	In case of nested runs the stop condition in case of too small timesteps is communicated to all parent/child processes. (Makefile, timestep)
20/01/17	MS	r2128	4.0	B	Bugfix, setting of user-defined topography in case of ocean simulations. (init_grid)
20/01/17	SR	r2126	4.0	C	For ocean simulations, density in SGS-TKE-production is replaced by potential density. (production_e)
18/01/17	FH	r2122	4.0	C	A particle ID has been introduced. It is stored on the particle variables id1 and id2. (Creating two IDs is necessary due to the large number of potentially simulated particles.) For this purpose, the unused particles variables tailpoints and tail_id have been renamed. Moreover, the unused particle variable dvrp_psize has been renamed to user and can be used by the user. (lpm_data_output_particles, lpm_init, lpm_set_attributes, mod_particle_attributes) Additionally, the calculation of the equilibrium radius of aerosols has been improved (lpm_init). And the code has been reformatted (lpm_droplet_collision).
17/01/17	SR	r2118	4.0	C	All OpenACC directives and related parts removed from the code (trunk). See the new GPU-porting branch for the OpenACC-GPU version of PALM. (Makefile, advec_ws, boundary_conds, buoyancy, check_parameters, coriolis, cpulog_mod, diffusion_e, diffusion_s, diffusion_u, diffusion_v, diffusion_w, diffusivities, exchange_horiz, fft_xy_mod, flow_statistics, header, init_3d_model, modules, palm, parin, poisfft_mod, pres, production_e, prognostic_equations, surface_layer_fluxes_mod, swap_timelevel, time_integration, timestep, transpose, tridia_solver_mod, wall_fluxes, deleted: cuda_fft_interfaces_mod)
16/01/17	BM	r2116	4.0	N	Beta version of new tool palm_gf added. palm_gf allows to calculate all possible processor grids. A detailed description will follow.
12/01/17	FK	r2114	4.0	N	cpp switch __mpi3 added for MPI-3 standard code. (urban_surface_mod) This was necessary because some older compiler versions cannot handle MPI-3 operations, hence, respective parts of the code shall only be compiled if explicitly enabled by the cpp switch __mpi3. However, the urban surface model only works with these MPI-3 operations included.
09/01/17	FK	r2108	4.0	C	Preparation for doxygen comments. (modules)
06/01/17	HK	r2104	4.0	B	Bugfix: For approximation related flux input conversion (ls_forcing_mod)
05/01/17	MS	r2100	4.0	B	Bugfix: Prevent extremely large SGS-velocities by limiting TKE in stochastic terms. (lpm_advec) Copyright update. (all source-code files)