PALM source code change log

Current revision:

r4901

Current fixed release: 6.0 (r3477)

The following table documents all changes to the PALM repository since 2018.

Previous changes:

• Changes 2017
• Changes 2013-2016
• Changes 2009-2012.
• Changes ​1998-2008

Please follow the 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.

svn Revision	Date (YYYY/MM/DD)	Author	PALM version	Type	Description
r3484	2018/11/02	hellstea	6.0	C, B	SVN commit message: Nesting interpolation made mass-conservative (pmc_interface_mod, palm, time_integration)
r3483	2018/11/02	raasch	6.0	B, C	SVN commit message: bugfix: misplaced positions of cpp-directives for netCDF and MPI fixed; output format limited to a maximum line length of 80 (chem_emissions_mod, cpulog_mod, netcdf_data_input_mod, salsa_mod, surface_output_mod)
r3479	2018/11/01	gronemeier	6.0	B	SVN commit message: reworked check for output quantities; assign new palm-error numbers, set unit according to data standard (biometeorology_mod)
r3475	2018/10/30	kanani	5.0	N	SVN commit message: Add option for using MRT from RTM instead of simplified global value (biometeorology_mod)
r3474	2018/10/30	kanani	5.0	B, N	SVN commit message: Add netcdf input for uv exposure model (netcdf_data_input_mod, Makefile, .palm.iofiles), plus bugfixes (uv_exposure_model_mod)
r3473	2018/10/30	suehring	5.0	B	SVN commit message: Bugfix for previous commit (Makefile, init_3d_model, modules, netcdf_data_input_mod, parin, time_integration, salsa_mod, virtual_measurement_mod) Further, changes were documented.
r3472	2018/10/30	suehring	5.0	N	SVN commit message: module for virtual measurements added (in a preliminary state); new public routines to input NetCDF data directly from modules (.palm.iofiles, Makefile, init_3d_model, modules, netcdf_data_input_mod, parin, time_integration, virtual_measurement_mod)
r3469	2018/10/30	kanani	5.0	N	SVN commit message: Implement indoor climate and energy demand model (Makefile, indoor_model_mod, init_3d_model, modules, parin, time_integration) All changes are related to the implementation of the new indoor climate model, new CALLS, new namelist, etc.
r3467	2018/10/30	suehring	5.0	N	SVN commit message: Branch salsa @3446 re-integrated into trunk (EXAMPLE/test_salsa, .palm.iofiles, Makefile, advec_ws, average_3d_data, boundary_conds, check_parameters, chem_emissions_mod, data_output_2d, data_output_3d, data_output_mask, data_and_time_mod, header, init_3d_model, init_masks, modules, netcdf_data_input_mod, netcdf_interface_mod, parin, plant_canopy_model_mod, prognostic_equations, read_restart_data_mod, salsa_mod, salsa_util_mod, sum_up_3d_data, surface_mod, swap_timelevel, time_integration, write_restart_data_mod)
r3465	2018/10/30	kanani	5.0	N	SVN commit message: Replace crayh config file, add cray debug config file (+ .palm.config.crayb, + .palm.config.crayb_debug, - .palm.config.crayh)
r3464	2018/10/30	kanani	5.0	C, N	SVN commit message: from branch resler@3462: add MRT shaping function (radiation_model_mod), use basic constants (biometeorology_mod), adjust precision to wp (biometeorology_pt_mod) Perform missing document_changes on (netcdf_data_input_mod, netcdf_interface_mod)
r3459	2018/10/30	gronemeier	5.0	N, B	SVN commit message: add longitude and latitude to output files; update run_control files for tests (netcdf_data_input_mod, netcdf_interface_mod) New geographic latitude and longitude are output coordinate-reference-system variable (crs) from input file is considered Bugfix long_name attribute of UTM coordinates fixed updated run-controll files of test cases
r3458	2018/10/30	kanani	5.0	B, C, N	SVN commit message: Reintegrated fixes/changes from branch chemistry (Makefile, chem_emissions_mod, chem_modules, chemistry_model_mod, date_and_time_mod, flow_statistics, init_3d_model, netcdf_data_input_mod, palm, prognostic_equations, UTIL/chemistry/gasphase_preproc) Several bugfixes related to the chemistry code, as well as date_and_time_mod. Major new component is the deposition model as part of the chemistry_model_mod.
r3457	2018/10/30	raasch	5.0	C	SVN commit message: options -d -h in palmtest script renamed too (palmtest)
r3455	2018/10/30	raasch	5.0	C	SVN commit message: options -h and -d renamed -c and -r, respectively, job_queue renamed job_logfiles in sveral configuration files (palmbuild, palmrun, .palm.config.crayh, .palm.config.default, .palm.config.default.in, .palm.config.default_trace, .palm.config.idefix) Attention: palmrun and palmbuild options -h and -c have been changed to -c (configuration_identifier) and -r (run_identifier), respectively. Attention: In case you have a copy of .palm.iofiles in your working directory (palm/current_version), please edit this file and replace strings fname or jobname by run_identifier, or copy the current version of this file from current_version/trunk/SCRIPTS to your working directory.
r3454	2018/10/30	schwenkel	5.0	B	SVN commit message: Bugfix: Missing air_chemistry statement for profile check (check_parameters)
r3452	2018/10/30	schwenkel	5.0	B	SVN commit message: Bugfix for profiles output (bulk_cloud_model_mod, check_parameters, flow_statistics)
r3449	2018/10/29	suehring	5.0	C, N	SVN commit message: Branch resler -r 3439 re-integrated into current trunk: RTM 3.0, transpiration of plant canopy, output fixes in USM (basic_constants_and_equations_mod, chemistry_model_mod, plant_canopy_mod, radiation_model_mod, urban_surface_mod)
r3448	2018/10/29	kanani	5.0	C, N	SVN commit message: Implementation of human thermal indices (from branch biomet_p2 at r3444) (Makefile, average_3d_data, biometeorology_ipt_mod, biometeorology_mod, biometeorology_pet_mod, biometeorology_pt_mod, biometeorology_utci_mod, check_parameters, data_output_2d, data_output_3d, header, init_3d_model, modules, multi_agent_system, netcdf_interface_mod, parin, sum_up_3d_data, time_integration, uv_exposure_model_mod) All changes are related to the implementation of the new human thermal comfort feature. The main module is biometeorology_mod, and the other biometeorology... modules contain the calculation routines for the different thermal indices. This structure is preliminary, in the next step, these calculation routines will be combined into one module.
r3445	2018/10/29	schwenkel	5.0	B	SVN commit message: Minor bugfix and use of subroutine for supersaturation calculation in case of cache version (bulk_cloud_model_mod)
r3444	2018/10/29	schwenkel	5.0	B	SVN commit message: Bugfix in surface_wrd_local for cloud and rain water flux (surface_mod)
r3435	2018/10/26	gronemeier	5.0	B,C,N	SVN commit message: new: terrain-following masked output; bugfixes: increase vertical dimension of gamma_w_green_sat by 1, add checks for masked output for chemistry_model and radiation_model, reordered calls to xxx_define_netcdf_grid in masked output part (chemistry_model_mod.f90, data_output_mask.f90, init_masks.f90, modules.f90, netcdf_interface_mod.f90, parin.f90, radiation_model_mod.f90, urban_surface_mod.f90, user_data_output_mask.f90) Bugfixes In urban_surface_mod, variable surf_usm_h%gamma_w_green_sat needed to be allocated from nzb_wall to nzt_wall+1 In init_mask, added checks for chemistry model and radiation model In init_mask, reordered calls to xxx_define_netcdf_grid Changes In radiation_model_mod, use pointers for masked output New terrain-following output using masked output: with new namelist parameter mask_k_over_surface which is included in runtime_parameters, a terrain-following output can be selected. mask_k_over_surface specifies the height (in grid points) above the surface to be chosen for output. Several indices can be chosen. If a grid index is lies above the domain boundary, the value of the output variable at the top of the domain is output at that position.
r3430	2018/10/25	maronga	5.0	C	SVN commit message: added support for buildings with dynamic sgs model (turbulence_closure_mod)
r3421	2018/10/24	gronemeier and suehring	5.0	B, C, N	SVN commit message: new surface-data output; renamed output variables (pt to theta, rho_air to rho, rho_ocean to rho_sea_water) (data_output_mask, parin, check_parameters, netcdf_data_input_mod, check_open, average_3d_data, user_spectra, data_output_3d, Makefile, surface_output_mod, netcdf_interface_mod, spectra_mod, modules, ocean_mod, print_1d, sum_up_3d_data, data_output_dvrp, virtual_flight_mod, data_output_2d, init_masks, time_integration, data_output_spectra, init_3d_model) Bugfixes Moved output of rho_sea_water to ocean_mod.f90 Changes output variables were renamed: all output variables named pt are named theta now. This is also true if pt was part of the output name, e.g., wpt is now wtheta vpt renamed to thetav lpt renamed to thetal rho_ocean renamed to rho_sea_water rho_air renamed to rho u* renamed to us z_i_... renamed to zi_... New new module for output of unstructured surface data new output files for unstructured surface data SURFACE_DATA_BIN Please note, unstructured surface output can be used to visualize surface data via Paraview. In order to do this, however, a postprocessing tool is required in order to convert the output data into Paraview-readable files. This tool will follow soon.
r3418	2018/10/24	kanani	5.0	C, N	SVN commit message: Add green facades, update building data base, fix for thin walls in spinup (surface_mod, time_integration, time_integration_spinup, urban_surface_mod) Changes output variables usm_t_surf_* for bare building walll and roof tiles was renamed to usm_t_surf_wall_* (* = north/ south/ east/ west/ roof) calculation of short wave radiation inside window layers changed increased building database to provide parameters for all wall and window height levels (ground floor, above ground floor, roof level) window surface and layers temperatures are fixed during spinup to make larger time step dt_spinup possible New latent heat flux for green wall and roof tiles and output variables usm_qsws_*, usm_qsws_veg_*, usm_qsws_liq_* calculation of latent heat flax for green roof tiles according to soil water content output parameter usm_swc_* for soil water content of green substrate layers calculation of green roof substrate layers heat capacity and conductivity according to soil water content and soil parameters building database parameter green_type_roof to choose between intensiv and extensiv green roof type new boolean namelist parameter usm_wall_mod to decrease heat advection during spinup in the first two wall layers by factor 10 to increase the possible time step dt_spinup
r3417	2018/10/24	kanani	5.0	N	SVN commit message: add new test cases for palmtest (TESTS/cases/urban_environment, TESTS/cases/urban_environment_restart)
r3414	2018/10/24	raasch	5.0	B	SVN commit message: bugfix: envpar namelist adjusted to current PALM revision (palm_simple_run)
r3405	2018/10/23	raasch	5.0	B	SVN commit message: bugfix: BIND attribute added to derived type particle_type, bugfix: nx, ny are required in non-parallel case (data_output_3d, mod_particle_attributes)
r3404	2018/10/23	suehring	5.0	C	SVN commit message: Consider time-dependent geostrophic wind components in offline nesting (init_3d_model, nesting_offl_mod, netcdf_data_input_mod)
r3400	2018/10/23	sward	5.0	B	SVN commit message: Made agent_preprocessing fortran 2008 conform (agent_preprocessing) Made code Fortran 2008 conform: Changed 'X' in format statements to '1X' and replaced getcwd with GET_ENVIRONMENT_VARIABLE.
r3386	2018/10/19	gronemeier	5.0	C	SVN commit message: renamed tcm_prognostic to tcm_prognostic_equations (turbulence_closure_mod)
r3381	2018/10/19	raasch	5.0	N	SVN commit message: spin-up cooling for ocean surface implemented, see new parameter surface_cooling_spinup_time (ocean_mod)
r3378	2018/10/19	kanani	5.0	B,C	SVN commit message: merge fixes of radiation branch (r3362) to trunk (radiation_model_mod, time_integration, urban_surface_mod) Bugfix: nzut > nzpt in calculating maxboxes IF statement to call radiation_interaction Change: removed namelist parameters read/write_svf_on_init and read_dist_max_svf (not used anymore) check the requested output variables if they are correct minor formatting New: add unscheduled_radiation_calls switch to control force_radiation_call
r3376	2018/10/19	suehring	5.0	C, N	SVN commit message: Fix cpp directives and error messages (netcdf_data_input_mod, synthetic_turbulence_generator_mod)
r3373	2018/10/18	kanani	5.0	B	SVN commit message: Fix cpp directives and error messages (chem_emissions_mod, chemistry_model_mod)
r3372	2018/10/18	raasch	5.0	B	SVN commit message: bugfix: kind type of 2nd argument of mpi_win_allocate changed, misplaced __parallel directive (radiation_model_mod)
r3351	2018/10/15	suehring	5.0	B	SVN commit message: Do not overwrite values of albedo in radiation_init in case albedo has been already initialized in the urban-surface model via ASCII input (radiation_model_mod, surface_mod, urban_surface_mod)
r3349	2018/10/15	suehring	5.0	B	SVN commit message: Bugfix in initialization of soil properties from dynamic input file (land_surface_model_mod)
r3348	2018/10/15	suehring	5.0	B	SVN commit message: Fix for format descriptor (synthetic_turbulence_generator_mod)
r3347	2018/10/15	suehring	5.0	B, C, N	SVN commit message: Offline nesting revised and separated from large_scale_forcing_mod; Time-dependent synthetic turbulence generator; bugfixes in USM/LSM radiation model and init_pegrid (boundary_conds, check_parameters, header, init_3d_model, init_pegrid, land_surface_model_mod, large_scale_forcing_nudging_mod, Makefile, nesting_offl_mod, netcdf_data_input_mod, parin, pres, read_restart_data_mod, synthetic_turbulence_generator_mod, time_integration, urban_surface_mod) New: Time-dependent parametrization of Reynolds-stress in synthetic turbulence generator New module for the offline nesting, which was separated from large_scale_forcing_nudging_mod Changes: offline nesting modularized and revised Bugfixes Missing dependencies in Makefile Setting number of ghost layers in neutral case initialization of spectral albedos initialization of urban-surface model in case no static input file exist
r3346	2018/10/15	raasch	5.0	C	SVN commit message: job_id renamed run_id in configuration files, job_id is set for compatibility reasons with older versions of config files (palmrun, .palm.config.crayh, .palm.config.eddy_gfort, .palm.config.eddy_ifort, .palm.config.idefix)
r3337	2018/10/12	kanani	5.0	B,C,N	SVN commit message: reintegrate branch resler to trunk (Makefile, average_3d_data, biometeorology_mod, check_parameters, chem_emissions_mod, data_output_3d, modules, netcdf_data_input_mod, netcdf_interface_mod, palm, plant_canopy_model_mod, prognostic_equations, radiation_model_mod, sum_up_3d_data, time_integration_spinup, urban_surface_mod) All changes are somehow related to the advancement of the radiative transfer model (RTM), developed by Pavel Krc, Jaroslav Resler (ICS, Prague), summarized below: New RTM version 2.9: added calculation of the MRT inside the RTM module MRT fluxes are consequently used in the new biometeorology module for calculation of biological indices (MRT, PET) Fixes of v. 2.5 and SVN trunk: proper initialization of rad_net_l make arrays nsurfs and surfstart TARGET to prevent some MPI problems initialization of arrays used in MPI one-sided operation as 1-D arrays to prevent problems with some MPI/compiler combinations fix indexing of target displacement in subroutine request_itarget to consider nzub fix LAD dimmension range in PCB calculation check ierr in all MPI calls use proper per-gridbox sky and diffuse irradiance fix shading for reflected irradiance clear away the residuals of "atmospheric surfaces" implementation fix rounding bug in raytrace_2d introduced in SVN trunk New RTM version 2.5: (Pavel Krc, Jaroslav Resler, ICS, Prague) can use angular discretization for all SVF (i.e. reflected and emitted radiation in addition to direct and diffuse), allowing for much better scaling wih high resoltion and/or complex terrain Unite array grow factors Fix slightly shifted terrain height in raytrace_2d Use more efficient MPI_Win_allocate for reverse gridsurf index Fix random MPI RMA bugs on Intel compilers Fix approx. double plant canopy sink values for reflected radiation Fix mostly missing plant canopy sinks for direct radiation Fix discretization errors for plant canopy sink in diffuse radiation Fix rounding errors in raytrace_2d Further changes: NEW simple biometeorology model (will later be replaced by full version) CHANGE in USM output procedure, some formatting in chemistry code
r3322	2018/10/09	kanani	5.0	B,C	SVN commit message: Minor formatting, clean-up (.palm.iofiles, Makefile)
r3318	2018/10/08	sward	5.0	B	SVN commit message: Fixed faulty syntax in message string (chemistry_model_mod)
r3311	2018/10/05	raasch	5.0	N	SVN commit message: Stokes drift is regarded in timestep calculation, check if ocean mode is used for invalid combinations (ocean_mod, timestep)
r3303	2018/10/03	raasch	5.0	N, B	SVN commit message: salinity allowed to be switched off, bugfix for swapping in case of ocean mode (ocean_mod, swap_timelevel)
r3302	2018/10/03	raasch	5.0	N	SVN commit message: Craik-Leibovich force and wave breaking effects added to ocean mode, header output for ocean mode (advec_s_pw, advec_ws, check_parameters, header, init_3d_model, modules, ocean_mod, prognostic_equations, subsidence_mod)
r3300	2018/10/02	gronemeier	5.0	B	SVN commit message: bugfix: rename of variable (turbulence_closure_mod)
r3299	2018/10/02	gronemeier	5.0	B, C	SVN commit message: removed global array and call of function MAXLOC; updated include paths for IMUK config (turbulence_closure_mod, palm.config.imuk) Bugfix: The MAXLOC function used in function shortest_distance gives different results for different compiler configuration and was therefore replaced. Changes: The global array 'wall_flags_0_global' was removed. As a results, the limitation of the mixing length used in RANS mode only considers walls in a distance of 1 grid box in horizontal direction. In vertical direction, no changes are made. The example PALM configuration for the Linux cluster at IMUK was updated to contain the include paths for parallel NetCDF.
r3298	2018/10/02	kanani	5.0	B, C, N	SVN commit message: Merge chemistry branch at r3297 to trunk (Makefile, advec_ws, check_parameters, chem_emissions_mod, chem_gasphase_mod, chem_modules, chem_photolysis_mod, chemistry_model_mod, data_output_2d, data_output_mask, date_and_time_mod, flow_statistics, header, init_3d_model, modules, netcdf_data_input_mod, outflow_turbulence, palm, parin, prognostic_equations, read_restart_data_mod, surface_mod, time_integration) Most changes are related to the introduction of the chemistry emissions module (chem_emissions_mod), and to clean-up, formatting, commenting of the chemistry-related code.
r3294	2018/10/01	raasch	5.0	C	SVN commit message: modularization of the ocean code (Makefile, advec_ws, average_3d_data, boundary_conds, buoyancy, check_parameters, data_output_2d, data_output_3d, flow_statistics, header, init_3d_model, init_grid, init_masks, large_scale_forcing_nudging_mod, lpm_init, modules, netcdf_interface_mod, parin, plant_canopy_model_mod, prognostic_equations, read_restart_data_mod, subsidence_mod, sum_up_3d_data, surface_mod, swap_timelevel, time_integration, turbulence_closure_mod, write_restart_data_mod, new: ocean_mod, init_vertical_profiles, deleted: eqn_state_seawater, init_ocean) Modularization of the ocean option All code components which belong to PALM's ocean option are separated from the PALM model core and moved to the new module ocean_mod. Note that although this is a massive change in the code structure it does not lead to any changes in the physics and model outcomes. init_vertical_profiles has been split from file check_parameters.f90 to avoid circular module dependencies. Anyhow, there are still some dependencies remaining, which e.g. do not allow to move variables bottom_salinityflux, top_salinityflux, and constant_top_salinityflux to the new module. Ocean parameters now have to be given in new NAMELIST &ocean_parameters. Installation files (test_oceanml_p3d, test_oceanml_rc) have been adjusted.
r3291	2018/09/28	scharf	5.0	B	SVN commit message: corrected previous commit for 3D topography (sum_up_3d_data)
r3288	2018/09/28	suehring	5.0	B	SVN commit message: Bugfix in allocation of mean_inflow_profiles in case of restarts (init_3d_model, modules, read_restart_data_mod, synthetic_turbulence_generator_mod)
r3285	2018/09/27	scharf	5.0	B	SVN commit message: bugfix for shf_av and qsws_av output (sum_up_3d_data)
r3274	2018/09/24	knoop and schwenkel	5.0	N,C	SVN commit message: Modularization of all bulk cloud physics code components (changes in 59 source files) Modularization of bulk microphysics All code components which belong to the bulk cloud model (except of the prognostic equations) are seperated from the PALM model core and moved to the module bulk_cloud_model. Note that this massive change in the code structure does not lead to any changes in the physics and model outcomes. Introduction of basic_constants_and_equations_mod Moreover, a new module was introduced containig many (at the moment not all) constants and basic equantions such as the magnus formula or exener function. Renamed files microphysics_mod into bulk_cloud_model_mod Deleted files diagnostic_quantites_mod calc_liquid_water_content init_cloud_physics New files basic_constants_and_equations_mod
r3272	2018/09/24	suehring and M. Salim	5.0	C	SVN commit message: Merge with branch radition - improved representation of diffuse radiation (radiation_model_mod, LIB/rrtmg/rrtmg_sw_rad.nomcica.f90) (responsible M. Salim) Please note, if the PALM code is compiled with the pre-processor directive __rrtmg, an update and re-installation of the RRTMG model is required. Further, please note, the radiation_par parameter split_diffusion_radiation has been removed now.
r3271	2018/09/24	suehring	5.0	B	SVN commit message: Several critical bugfixes: initialization of surface temperature at water bodies; consider special case in initialization of vertical natural surface elements (land_surface_model_mod, surface_layer_fluxes_mod)
r3270	2018/09/24	raasch	5.0	B	SVN commit message: bugfix for r2502: wrong calculation of hyp(nzt) in second iterative step (init_ocean)
r3268	2018/09/21	sward	5.0	C	SVN commit message: Fix in pointer assignment in MAS and MAS-Examples updated (multi_agent_system_mod, EXAMPLES/agents)
r3261	2018/09/19	suehring	5.0	B	SVN commit message: Bugfix in raytrace_2d calls (radiation_model_mod)
r3259	2018/09/18	sward	5.0	B	SVN commit message: Updated agent preprocessing to avoid gfortran warnings (agent_preprocessing) Removed unused variables and fixed real-to-real comparisons.
r3258	2018/09/18	Giersch	5.0	C	SVN commit message: current revision number for user interface has been changed due to modifications in revision 3240 (user_parin, palm)
r3257	2018/09/17	suehring	5.0	C	SVN commit message: Further adjustment of checks for building_type and building_id (required as type and id can be modified by the topography filtering) (netcdf_data_input_mod)
r3256	2018/09/17	suehring	5.0	B	SVN commit message: Enable initialization of z0q for vegetation, pavement and water surfaces via namelist input (land_surface_model_mod)
r3255	2018/09/17	suehring	5.0	B	SVN commit message: Missing wall flags added (advec_w_up)
r3254	2018/09/17	suehring	5.0	C, N	SVN commit message: Additional checks for surface_fractions and building_id; Remove redundant subroutine argument in surface_mod (netcdf_data_input_mod, surface_mod)
r3253	2018/09/17	suehring	5.0	B	SVN commit message: Bugfix, missing deallocation of q_surface in case of restarts (surface_mod)
r3251	2018/09/14	raasch	5.0	C	SVN commit message: explicit kind settings (pmc_child_mode, pmc_parent_mode)
r3250	2018/09/14	sward	5.0	B	SVN commit message: Added an empty output string to STOP keywords to clean up job protocol (local_stop) When aborting with STOP keyword, some compilers had every PE print 'STOP' to the console/job protocol. This does not happen any longer after adding an empty string after the keyword (STOP ).
r3248	2018/09/14	sward	5.0	B	SVN commit message: Minor format changes (chemistry_model_mod, land_surface_model_mod, message, multi_agent_system_mod, package_parin, parin, plant_canopy_model_mod, radiation_model_mod, spectra_mod, synthetic_turbulence_generator_mod, urban_surface_mod, user_parin, uv_exposure_model_mod, virtual_flight_mod, wind_turbine_model_mod)
r3247	2018/09/14	sward	5.0	C	SVN commit message: parin_fail_message now also outputs the line number at which namelist reading failed (message)
r3246	2018/09/13	sward	5.0	C	SVN commit message: Added error handling for wrong input parameters (chemistry_model_mod, land_surface_model_mod, message, multi_agent_system_mod, package_parin, parin, plant_canopy_model_mod, radiation_model_mod, spectra_mod, synthetic_turbulence_generator_mod, urban_surface_mod, user_parin, uv_exposure_model_mod, virtual_flight_mod, wind_turbine_model_mod) Added routine parin_fail_message in message.f90. It is used to give the line in a specific namelist that caused an error during PARIN read.
r3241	2018/09/12	raasch	5.0	B	SVN commit message: various changes to avoid compiler warnings (mainly removal of unused variables) (affected files see below) Code has been revised with respect to warnings issued by gfortran options -Wall -Wextra. Following changes have been carried out: unused variables have been removed (advec_ws, boundary_conds, buoyancy, calc_liquid_water_content, calc_mean_profile, check_open, check_parameters, chem_photolysis_mod, chemistry_model_mod, close_file, coriolis, data_output_2d, data_output_3d, data_output_flight, data_output_mask, data_output_spectra, diffusion_u, diffusion_v, diffusion_w, disturb_heatflux, eqn_state_seawater, exchange_horiz, flow_statistics, header, init_3d_model, init_cloud_physics, init_grid, init_pegrid, land_surface_model_mod, large_scale_forcing_nudging_mod, lpm_advec, lpm_boundary_conds, lpm_calc_liquid_water_content, lpm_droplet_collision, lpm_droplet_condensation, lpm_init, lpm_init_sgs_tke, lpm_merging, lpm_pack_arrays, lpm_set_attributes, lpm_splitting, lpm_write_exchange_statistics, message, microphysics_mod, multi_agent_system_mod, netcdf_data_input_mod, netcdf_interface_mod, outflow_turbulence, package_parin, palm, plant_canopy_model_mod, pmc_child_mod, pmc_general_mod, pmc_interface_mod, pmc_parent_mod, pmc_particle_interface, poisfft_mod, poismg_mod, poismg_noopt_mod, radiation_model_mod, random_generator_parallel_mod, read_restart_data_mod, spectra_mod, sum_up_3d_data, surface_mod, swap_timelevel, synthetic_turbulence_generator_mod, temperton_fft_mod, time_integration, time_integration_spinup, timestep, transpose, tridia_solver_mod, turbulence_closure_mod, urban_surface_mod, uv_exposure_model_mod, vertical_nesting_mod, virtual_flight_mod, wind_turbine_model_mod) format statements removed (check_open, close_file, data_output_3d, data_output_profiles, data_output_tseries, print_1d, preprocessor switches added, mainly to hide omp_get_thread_num (fft_xy_mod, poisfft_mod, prognostic_equations) TYPE change to working precision (turbulence_closure)
r3240	2018/09/12	Giersch	5.0	B	SVN commit message: Bufgix for an error message in case of restarts and user-defined profiles (modules, parin, user_parin)
r3236	2018/09/10	raasch	5.0	C	SVN commit message: host identifier in header output renamed config. identifier, host_configuration renamed configuration_identifier, jobname renamed run_identifier, palmbuild: header output of PALM code revision, options -m, -s, and -S removed, palmrun: run_id renamed run_id_number, job_id renamed run_id, option -r renamed -i (palmbuild, palmrun, all configuration files, .palm.iofiles)
r3235	2018/09/07	sward	5.0	B, C	SVN commit message: Bugfix in MAS output, added related messages, reworked MAS cpu logging (Makefile, modules, multi_agent_system_mod, netcdf_interface_mod, palm) Agent output now has no unlimited dimensions by default. Messages regarding the size of the agent-number dimension were added. Reason: agent output was getting very slow with large number of agents.
r3234	2018/09/07	schwenkel	5.0	B	SVN commit message: The increase of dots_num in case of radiation or land surface model must be done before user_init is called (init_3d_model)
r3233	2018/09/07	schwenkel	5.0	C	SVN commit message: Adapted for the use of cloud_droplets (land_surface_mod, radiation_model_mod)
r3232	2018/09/07	raasch	5.0	C	SVN commit message: references to mrun replaced by palmrun, and updated (check_parameters, init_coupling, modules, palm, vertical_nesting_mod)
r3231	2018/09/06	schwenkel	5.0	B	SVN commit message: Bugfix for microphysic scheme = saturation_adjustment (diagnostic_quantities_mod)
r3230	2018/09/05	schwenkel	5.0	B	SVN commit message: Bugfix in radiation_constant_surf (radiation_model_mod)
r3229	2018/09/04	sward	5.0	B	SVN commit message: Bugfix: maximum time per log point now includes PE0 (cpulog_mod)
r3226	2018/08/31	suehring	5.0	B	SVN commit message: Bugfixes in calculation of sky-view and canopy-sink factors (radiation_model_mod)
r3225	2018/08/30	kanani	5.0	B	SVN commit message: Correct revision messages of last commit (header, progress_bar_mod)
r3224	2018/08/30	kanani	5.0	B, C	SVN commit message: Fix for progress bar, minor changes (header, progress_bar_mod)
r3222	2018/08/30	suehring	5.0	N, B	SVN commit message: Introduction of addtional surface variables indicating type and name of the surface elements; Bugfix in LSM (land_surface_model_mod, surface_mod, urban_surface_mod)
r3217	2018/08/29	suehring	5.0	B	SVN commit message: Revise calculation of index bounds for array index_list, prevent compiler (cray) to delete the loop at high optimization level. (pmc_interface_mod)
r3216	2018/08/29	sward	5.0	B	SVN commit message: Bugfix for gfortran: reordering of type definitions (agent_preprocessing) Also removed output of mesh and polygon size on disk due to incompatibility of STORAGE_SIZE with allocated arrays of derived data types.
r3210	2018/08/28	sward	5.0	B	SVN commit message: Minor bugfix in agent_preprocessing (agent_preprocessing, palmbuild) Changed intrinsic SIZEOF to STORAGE_SIZE. Executable of agent_preprocessing now remains in MAKE_DEPOSITORY after compilation on remote host.
r3209	2018/08/27	suehring	5.0	C, B, N	SVN commit message: Additional namelist parameter to switch on/off the nesting of chemical species; Enable the input of soil data from dynamic input files independent on atmosphere in order to initialize soil properties in nested child domains from dynamic input; Revise error message number for static/dynamic input; Revise and add checks for static/dynamic input; Bugfix, add netcdf4_parallel directive for collective read operation (chemistry_model_mod, land_surface_model_mod, netcdf_data_input_mod, pmc_interface_mod)
r3208	2018/08/27	sward	5.0	C	SVN commit message: Renamed nav_mesh to agent_preprocessing and added it to palmbuild (UTIL/nav_mesh/nav_mesh.f90 -> UTIL/agent_preprocessing/agent_preprocessing.f90, Makefile_utilities, palmbuild) Renamed nav_mesh to agent_preprocessing. Added build of this tool to palmbuild. The executable is moved to SCRIPTS and can be accessed from anywhere. agent_preprocessing has to be called from the INPUT folder of the current job directory.
r3207	2018/08/27	schwenkel	5.0	B	SVN commit message: Minor bugfix for sgs-velocities in case of cloud droplets (lpm_advec)
r3206	2018/08/24	raasch	5.0	N	SVN commit message: configuration file with debug options for Intel added (new: .palm.config.default_trace)
r3205	2018/08/24	raasch	5.0	C	SVN commit message: Intel compiler options revised in configuration files (.palm.config.default, .palm.config.idefix, .palm.config.imuk)
r3204	2018/08/23	raasch	5.0	B	SVN commit message: additional check for nz (parin)
r3203	2018/08/23	suehring	5.0	C	SVN commit message: Revise bulk parameter for emissivity at ground-floor level (urban_surface_model_mod)
r3202	2018/08/22	Giersch	5.0	C	SVN commit message: Unix-Shell in palmplot script has been changed from ksh to bash (palmplot)
r3201	2018/08/20	sward	5.0	B	SVN commit message: Missing pre-processor directive (multi_agent_system_mod) Added preprocessor directive to enable serial mode. Changed default of read_agents_from_restartfile to .FALSE. (restarts not yet implemented).
r3200	2018/08/17	suehring	5.0	B	SVN commit message: Missing pre-processor directive (init_grid)
r3199	2018/08/16	raasch	5.0	C	SVN commit message: module_commands and login_init_cmd in config files have been modified (.palm.config.crayh, .palm.config.default, .palm.config.default.in, .palm.config.eddy_gfort, .palm.config.eddy_ifort) Module commands moved from login_init_cmds to module_commands, to where they belong.
r3198	2018/08/15	sward	5.0	C, B	SVN commit message: Added MAS end time, used time_since_reference_point, corrected tolerance_dp in nav_mesh (modules.f90, multi_agent_system_mod.f90, nav_mesh.f90, netcdf_interface.f90, time_integration.f90) Check for MAS execution now uses time_since_reference_point instead of simulated_time. An end-time for execution of MAS was added (multi_agent_system_end). Start- and end-parameters had to be moved to modules.f90. Revised calculation of netCDF limited time-dimension using MAS start- and end-time. In nav_mesh.f90, fixed the initialization of tolerance_dp.
r3196	2018/08/13	maronga	5.0	C	SVN commit message: set maximum value for aerodynamic resistance over horiztonal surfaces (land_surface_model_mod.f90, urban_surface_model_mod.f90, mainwindow.ui)
r3193	2018/08/07	witha	5.0	C	SVN commit message: Updated config files for ForWind cluster EDDY (.palm.config.eddy_gfort, .palm.config.eddy_ifort)
r3187	2018/07/31	sward	5.0	B	SVN commit message: Reworked agent pathfinding and modified output (netcdf_interface_mod, multi_agent_system_mod) Changed agent output to be of type NF90_DOUBLE. Removed obstacle flags at model boundarys. They were relics from cyclic topography and obstructed agents from exiting the model domain. Reworked pathfinding. Split pathfinding up into two SUBROUTINES for clarity. Made pathfinding iterative, eliminating the possibility of navigation points being missed. This was occuring due to the fact that obstacle corners are used as nodes on the visibility graph but the navigation points for agents are shifted outward from those obstacle corners after pathfinding. This - in some cases - lead to parts of some agents' paths intersecting with buildings. Pathfinding is now run with each pair of successive intermittent targets of a path and more intermittent targets are added to the path, if necessary.
r3186	2018/07/30	suehring	5.0	B	SVN commit message: Mask topography while imposing inflow perturbations at the boundaries; do not impose perturbations at top boundary as well as ghost points; Remove print statement; Read zsoil dimension lenght only if soil variables are provided in dynamic driver (netcdf_data_input_mod, radiation_model_mod, synthetic_turbulence_generator_mod)
r3184	2018/07/27	suehring	5.0	B	SVN commit message: Bugfix in setting of passive scalar and chemistry top boundary condary condition in offline nesting mode (parin)
r3182	2018/07/27	suehring	5.0	B, C, N	SVN commit message: New Inifor features: grid stretching, improved command-interface, support start dates in different formats in both YYYYMMDD and YYYYMMDDHH, Ability to manually control input file prefixes (--radiation-prefix, --soil-preifx, --flow-prefix, --soilmoisture-prefix) for compatiblity with DWD forcast naming scheme; GNU-style short and long option; Prepared output of large-scale forcing profiles (no computation yet); Added preprocessor flag __netcdf4 to switch output format between netCDF 3 and 4; Updated netCDF variable names and attributes to comply with PIDS v1.9; Inifor bugfixes: Improved compatibility with older Intel Intel compilers by avoiding implicit array allocation; Added origin_lon/_lat values and correct reference time in dynamic driver global attributes; corresponding PALM changes: adjustments to revised Inifor; variables names in dynamic driver adjusted; enable geostrophic forcing also in offline nested mode; variable names in LES-LES and COSMO offline nesting changed; lateral boundary flags for nesting, in- and outflow conditions renamed (UTIL/inifor, advec_ws, boundary_conds, check_parameters, chemistry_model_mod, coriolis, exchange_horiz_2d, init_3d_model, init_grid, init_pegrid, large_scale_forcing_nudging_mod, modules, netcdf_data_input_mod, palm, parin, pmc_interface_mod, poismg_mod, poismg_noopt_mod, pres, prognostic_equations, read_restart_data_mod, sor, synthetic_turbulence_generator_mod, time_integration, turbulence_closure_mod) Inifor bugfixes (responsible Eckhard Kadasch, DWD) Improved compatibility with older Intel Intel compilers by avoiding implicit array allocation Added origin_lon/_lat values and correct reference time in dynamic driver global attributes Inifor changes Updated netCDF variable names and attributes to comply with PIDS v1.9 Inifor new code Introduced new PALM grid stretching Improved command-interface GNU-style short and long options Prepared output of large-scale forcing profiles (no computation yet) Added preprocessor flag for netcdf4 to switch output format between netCDF 3 and 4 PALM-related changes Inifor initialization and offline nesting in case of vertically stretched grids improved - no inter/extrapolation required any more synthetic turbulence generator works also in combination with stretched grids revise Inifor initialization Update netCDF variable names and attributes to comply with PIDS v1.9 variable names renamed in LES-LES and COSMO-offline nesting variable names renamed for lateral boundary flags for inflow/outflow or nesting conditions remove masking of geostrophic wind forcing in offline nesting case some unused variables in USE statements removed Replace simulated_time by time_since_reference_point in offline-nesting mode
r3178	2018/07/27	suehring	5.0	C	SVN commit message: Revise concept for calculation of radiative temperature (radiation_model_mod)
r3176	2018/07/26	suehring	5.0	B	SVN commit message: Major bugfix in calculation of ol and ts at building roofs; bugfix in restart data for surface elements; in 2D data output, mask latent heat flux at urban-type surfaces (data_output_2d, sum_up_3d_data, surface_mod, urban_surface_mod)
r3175	2018/07/26	suehring	5.0	B	SVN commit message: Bugfix for commit 3172 (radiation_model_mod)
r3174	2018/07/26	Giersch	5.0	B	SVN commit message: Bugfix in reading NAMELIST user_parameters, bugfix in wind turbine model related to the check of vertical stretching (user_parin, wind_turbine_model)
r3173	2018/07/26	suehring	5.0	B	SVN commit message: Further revision of 2D surface output for radiation and chemistry quantities; bugfix for commit 3170 (chemistry_model_mod, radiation_model_mod, sum_up_3d_data)
r3172	2018/07/26	suehring	5.0	B	SVN commit message: temporal work-around for calculation of effective radiative surface temperature; prevent positive solar radiation during nighttime (radiation_model_mod)
r3170	2018/07/25	suehring	5.0	B	SVN commit message: Bugfix in radiation forcing in case of RRTMG; further bugfix in output of surface variables in case of overhanging structures (radiation_model_mod, sum_up_3d_data)
r3168	2018/07/25	sward	5.0	B	SVN commit message: Updated NetCDF variable names (UTIL/nav_mesh/nav_mesh.f90) Updated NetCDF variable names to match PIDS (buildings_2d, buildings_3d, zt).
r3167	2018/07/24	suehring	5.0	B	SVN commit message: Bugfix, missing dependencies for multi-agent model (Makefile)
r3165	2018/07/24	sward	5.0	C	SVN commit message: Added agent ID output (multi_agent_system_mod.f90, netcdf_interface_mod.f90)
r3163	2018/07/23	witha	5.0	C	SVN commit message: Updated/added config files for ForWind cluster EDDY (.palm.config.eddy_gfort, .palm.config.eddy_ifort)
r3162	2018/07/23	Giersch	5.0	C	SVN commit message: Default value of dz_max has changed to a more uncommon value of 999. This value can not be a part of dz values when using new strechting procedure (modules.f90)
r3161	2018/07/23	maronga	5.0	C	SVN commit message: increased roughness lengths for asphalt (land_surface_model_mod.f90)
r3160	2018/07/20	sward	5.0	B	SVN commit message: Changed C_SIZEOF to STORAGE_SIZE (multi_agent_system_mod.f90)
r3159	2018/07/20	sward	5.0	C, N	SVN commit message: Added multi agent system (modules.f90, parin.f90, multi_agent_system_mod.f90, time_integration.f90, netcdf_interface_mod.f90, init_3d_model.f90, check_open.f90, trunk/UTIL/nav_mesh, trunk/EXAMPLES/agents) Multi agent system added. Model can be steered via &agents_par. Model is called from time_integration and executes multiple sub-timesteps until the model timestep is reached. NetCDF Output is written to OUTPUT folder. MAS needs a navigation file which is preprocessed by UTIL/nav_mesh/nav_mesh.f90. See the README file in that directory for explanation. Also see EXAMPLES/agents. Detailed documentation will follow.
r3157	2018/07/19	maronga	5.0	C	SVN commit message: added local free convection velocity scale in calculation of horizontal wind at first grid level (modules.f90, parin.f90, surface_layer_fluxes_mod.f90) New namelist parameter use_free_convection_scaling introduced that adds the local free convection velocity scale to the horizontal wind speed at first grid level. Might be useful for low wind simulations where u* tends to zero, leading to the breakdown of MOST (and the calculation of surface fluxes). This should effectively impose a physically based lower limit of u*.
r3152	2018/07/19	suehring	5.0	C	SVN commit message: Further adjustments for surface structure (land_surface_model_mod, surface_layer_fluxes_mod, surface_mod, urban_surface_mod)
r3151	2018/07/19	raasch	5.0	C	SVN commit message: output of PALM code revision number in palmrun header, some preprocessor define strings removed, small revisions in configuration files (palmrun, sum_up_3d_data.f90, urban_surface_mod.f90, .palm.config.default, .palm.config.default.in, .palm.config.eddy_gfort, .palm.config.imuk) Output of PALM code revision number in palmrun header. Additional listing of files to be compiled has been removed. (palmrun) Remaining preprocessor define strings __check and __chem have been removed. (sum_up_3d_data.f90, urban_surface_mod.f90) Small revisions in configuration files. (.palm.config.default, .palm.config.default.in, .palm.config.eddy_gfort, .palm.config.imuk)
r3146	2018/07/18	maronga	5.0	B	SVN commit message: major bugfix in calculation of Obukhov length and subsequent handling of surface information (land_surface_model_mod.f90, surface_mod.f90, surface_layer_fluxes_mod.f90)
r3145	2018/07/18	gronemeier	5.0	C	SVN commit message: Use MOST for km only in RANS mode (turbulence_closure_mod.f90)
r3143	2018/07/17	maronga	5.0	B	SVN commit message: modified calculation of surface resistance in land surface scheme (land_surface_model_mod.f90)
r3142	2018/07/17	suehring	5.0	B	SVN commit message: Bugfix in referencing buildings on orography top; minor bugfix for last LSM commit Further, accelerate building processing during initialization. (init_grid, land_surface_model_mod)
r3139	2018/07/17	Giersch	5.0	B	SVN commit message: Bugfix in calculation of alpha_attack and Bugfix for restarts in combination with grid stretching (init_grid, wind_turbine_model)
r3138	2018/07/17	maronga	5.0	B	SVN commit message: bugfix for sea surfaces with constant_roughness = .F. (land_surface_model_mod.f90)
r3137	2018/07/17	maronga	5.0	B	SVN commit message: minor bugfix in radiation model (radiation_model_mod.f90)
r3136	2018/07/16	suehring	5.0	B	SVN commit message: Limit roughness for heat and moisture in case it exceeds the model-assumed surface-layer height; Limit surface resistance to positive values. (land_surface_model_mod, urban_surface_mod)
r3135	2018/07/16	gronemeier	5.0	B	SVN commit message: Bugfix: add +1 to c_3 according to Sogachev et al. (2012) (model_1d_mod.f90)
r3133	2018/07/16	maronga	5.0	B	SVN commit message: bugfix for last commit (land_surface_model_mod.f90)
r3132	2018/07/16	raasch	5.0	B, C	SVN commit message: create consistent error messages in case of failed restarts, check existence of remote job catalog (palmrun)
r3130	2018/07/16	gronemeier	5.0	C	SVN commit message: calculate km according to MOST within the surface layer (surface_layer_fluxes_mod, turbulence_closure_mod) Caution: these changes will alter the simulation results if a constant flux layer is used!
r3127	2018/07/15	maronga	5.0	B, C	SVN commit message: bugfix for high vegetation surface temperatures (land_surface_model_mod.f90, radiation_model_mod.f90) Bugfix: Natural vegetation surfaces with dry soil cause high surface temperatures than may lead exceeding the limits of the Magnus formula, creating negative saturation water mixing ratios and leading to a model crash. This was fixed by limiting the surface temperature that enters the formula to 60°C. Change: Some pavement parameters have been updated (asphalt and concrete).
r3126	2018/07/13	gronemeier	5.0	B	SVN commit message: bugfix for pgi compiler: assign value of c_0 directly to variable instead of calculating it (model_1d_mod.f90)
r3123	2018/07/12	suehring	5.0	B	SVN commit message: Correct working precision for REAL and INTEGER numbers (pmc_particle_interface, radiation_model_mod, urban_surface_mod)
r3122	2018/07/11	maronga	5.0	B	SVN commit message: bugfix in radiation model that inhibited surface reflections (radiation_model_mod.f90)
r3121	2018/07/11	gronemeier	5.0	C	SVN commit message: consider wall function for Km within production_e_init (turbulence_closure_mod.f90) Changes will lead to differences in results compared to former revisions if a constant-flux layer is used.
r3120	2018/07/11	gronemeier	5.0	N	SVN commit message: implementation of dynamic sgs model See the documentation for details about the new dynamic SGS model. Code written by Hauke Wurps.
r3117	2018/07/11	maronga	5.0	B	SVN commit message: bugfixes in RRTMG interface (radiation_model_mod) In case of cloud_physics = .F., no humidity information was passed to RRTMG and led to low incoming longwave radiative fluxes Improvements for average_radiation with RRTMG The atmospheric humidity above the PALM domain is no longer considered dry. A standard humidity profile provided by RRTMG is used instead
r3116	2018/07/10	suehring	5.0	N	SVN commit message: Output of radiation terms at surface (radiation_model_mod)
r3115	2018/07/10	suehring	5.0	C	SVN commit message: Separate bridges as 3D building objects from normal surface-mounted buildings in terms of correct referencing onto the terrain (init_grid, urban_surface_mod)
r3107	2018/07/06	suehring	5.0	B	SVN commit message: Bugfix, missing index for dz (radiation_model_mod)
r3106	2018/07/06	suehring	5.0	C	SVN commit message: Slightly revise check for input of surface_fraction (netcdf_data_input_mod.f90)
r3103	2018/07/04	suehring	5.0	N	SVN commit message: Reference lowest terrain height to zero level; new check for negative terrain heights in static input file (init_grid, netcdf_data_input_mod.f90)
r3091	2018/06/28	suehring	5.0	B	SVN commit message: Limit aerodynamic resistance at vertial building walls; check for roughness not exceeding surface-layer height (land_surface_model, urban_surface_mod)
r3089	2018/06/27	suehring	5.0	B	SVN commit message: Revise call for message routine in case of local data inconsistencies (netcdf_data_input_mod.f90)
r3086	2018/06/25	gronemeier	5.0	B	SVN commit message: bugfix: set standard value for rans_const_sigma (turbulence_closure_mod.f90)
r3084	2018/06/19	gronemeier	5.0	B	SVN commit message: bugfix: limit increase of dt_3d only in case of RANS mode (timestep.f90)
r3083	2018/06/19	gronemeier	5.0	N,C,B	SVN commit message: merge with branch rans
r3069	2018/06/15	witha	5.0	B	SVN commit message: Initialization of some arrays changed (wind_turbine_model_mod)
r3068	2018/06/12	Giersch	5.0	C, N	SVN commit message: Warning message related to vertical grid stretching has been added, old example_cbl_rc file restored but with the new header, example_cbl_p3d changed to get the old run control output (example_cbl_p3d, example_cbl_rc, init_grid)
r3067	2018/06/12	suehring	5.0	C	SVN commit message: Remove write statements (lpm_boundary_conditions)
r3066	2018/06/12	Giersch	5.0	B, C	SVN commit message: Error messages related to the new vertical grid stretching revised, Bugfix in IF statement before error message (init_grid, radiation_model_mod, vertical_nesting_mod, wind_turbine_model_mod )
r3065	2018/06/12	Giersch	5.0	C, N	SVN commit message: New vertical stretching procedure has been introduced (example_cbl_rc, check_parameters, header, init_grid, init_masks, lpm_advec, lpm_exchange_horiz, lpm_init, lpm_set_attributes, modules, parin, plant_canopy_model_mod, pmc_interface_mod, radiation_model_mod, read_restart_data_mod, synthetic_turbulence_generator_mod, urban_surface_mod, user_init_grid, vertical_nesting_mod, virtual_flight_mod, wind_turbine_model_mod, write_restart_data_mod )
r3057	2018/06/05	raasch	5.0	B	SVN commit message: bugfix: check that nz is even in case that optimized multigrid is used (init_pegrid)
r3056	2018/06/04	Giersch	5.0	B	SVN commit message: Bugfix in case of restarts using cyclic fill (read_restart_data_mod)
r3055	2018/06/01	suehring	5.0	B	SVN commit message: Bugfix, initialization of surface elements also in case of restart runs and cyclic fill (surface_mod)
r3054	2018/06/01	gronemeier	5.0	B	SVN commit message: bugfix: force MPI abort if errors occur while reading bld heights from ASCII
r3053	2018/06/01	suehring	5.0	B	SVN commit message: Revise checks for relative surface fractions of vegetation, pavement and water surfaces
r3052	2018/05/31	raasch	5.0	C	SVN commit message: Do not open FORTRAN binary files in case of parallel netCDF I/O
r3051	2018/05/30	suehring	5.0	B, C	SVN commit message: Speed-up NetCDF input; Revise NetCDF-input routines and remove input via io-blocks; Temporarily revoke renaming of input variables in dynamic driver; More detailed error messages created; Bugfix in mapping 3D buildings; Bugfix in land-surface model at pavement surfaces; Bugfix in initialization with inifor
r3049	2018/05/29	Giersch	5.0	C	SVN commit message: Revision history corrected (see r3046)
r3048	2018/05/29	gronemeier	5.0	C	SVN commit message: add variable description (check_parameters.f90)
r3046	2018/05/29	Giersch	5.0	C	SVN commit message: Remaining error messages revised, comments extended (check_for_restart.f90, check_parameters.f90, cpulog_mod.f90, data_output_2d.f90, data_output_3d.f90, init_3d_model.f90, init_grid.f90, init_masks.f90, init_pegrid.f90, land_surface_model_mod.f90, large_scale_forcing_nudging_mod.f90, lpm_droplet_condensation.f90, lpm_exchange_horiz.f90, lpm_init.f90, lpm_read_restart_file.f90, model_1d_mod.f90, netcdf_data_input_mod.f90, netcdf_interface_mod.f90, package_parin.f90, parin.f90, plant_canopy_model_mod.f90, pmc_interface_mod.f90, pmc_parent_mod.f90, pmc_particle_interface.f90, radiation_model_mod.f90, read_restart_data_mod.f90, spectra_mod.f90, surface_coupler.f90, synthetic_turbulence_generator_mod.f90, temperton_fft_mod.f90, timestep.f90, urban_surface_mod.f90, user_data_output_dvrp.f90, user_parin.f90, user_spectra.f90, vertical_nesting_mod.f90, virtual_flight_mod.f90, wind_turbine_model_mod.f90)
r3045	2018/05/28	Giersch	5.0	C	SVN commit message: Code adjusted according to coding standards, renamed namelists, error messages revised until PA0347, output CASE 108 disabled (example_cbl_p3d, test_oceanml_p3d, check_for_restart.f90, check_open.f90, check_parameters.f90, chemistry_model_mod.f90, close_file.f90, cpulog_mod.f90, data_output_2d.f90, data_output_3d.f90, data_output_dvrp.f90, data_output_mask.f90, fft_xy_mod.f90, header.f90, init_3d_model.f90, init_grid.f90, init_masks.f90, init_pegrid.f90, land_surface_model_mod.f90, large_scale_forcing_nudging_mod.f90, lpm_droplet_condensation.f90, lpm_init.f90, lpm_read_restart_file.f90, model_1d_mod.f90, modules.f90, netcdf_data_input_mod.f90, netcdf_interface_mod.f90, parin.f90, plant_canopy_model_mod.f90, pmc_interface_mod.f90, radiation_model_mod.f90, read_restart_data_mod.f90, spectra_mod.f90, subsidence_mod.f90, surface_coupler.f90, surface_layer_fluxes_mod.f90, synthetic_turbulence_generator_mod.f90, temperton_fft_mod.f90, timestep.f90, turbulence_closure_mod.f90, urban_surface_mod.f90, vertical_nesting_mod.f90)
r3044	2018/05/25	gronemeier	5.0	N	SVN commit message: add missing variable descriptions (synthetic_turbulence_generator_mod)
r3043	2018/05/25	raasch	5.0	N, C	SVN commit message: check for setting of fast_io_catalog, update of default .palm.config.default (palmrun, .palm.config.default)
r3041	2018/05/25	gronemeier	5.0	C	SVN commit message: Add read of global attributes of static driver (netcdf_data_input_mod)
r3042 r3040	2018/05/25	schwenkel	5.0	C	SVN commit message: Changed the name specific humidity to mixing ratio (flow_statistics, init_3d_model, interactions_droplets_ptq, time_integration)
r3039	2018/05/24	schwenkel	5.0	B	SVN commit message: bugfix for lcm with grid stretching (lpm_calc_liquid_water_content, lpm_droplet_condensation, lpm_droplet_collision, lpm_init)
r3038	2018/05/24	gronemeier	5.0	C	SVN commit message: updated variable description (synthetic_turbulence_generator_mod)
r3037	2018/05/24	gronemeier	5.0	C	SVN commit message: renamed input dimension "depth" to "zsoil" (netcdf_data_input_mod)
r3036	2018/05/24	gronemeier	5.0	C	SVN commit message: renamed input variables according to UC2 data standard (netcdf_data_input_mod)
r3035	2018/05/24	schwenkel	5.0	N	SVN commit message: Add option to initialize warm air bubble close to surface (check_parameters. init_3d_model, init_pt_anomaly)
r3034	2018/05/24	raasch	5.0	B	SVN commit message: bugfix: check that initializing_actions has been set (check_parameters)
r3030	2018/05/23	raasch	5.0	C	SVN commit message: variable if renamed ivar (data_output_mask)
r3029	2018/05/23	raasch	5.0	B	SVN commit message: bugfix: close unit 151 instead of 90 (usm_surface_mod)
r3025	2018/05/22	raasch	5.0	C, B	SVN commit message: -T option not required for interactive runs (tasks per node = total number of cores is assumed as default, if option is not given), reformatting of a few messages, bugfix: destination output directory is created if attribute pe is set in .palm.iofiles (palmrun, .palm.iofiles)
r3022	2018/05/18	suehring	5.0	B	SVN commit message: Revise recent bugfix in nested runs at left and south boundary; bugfix in advection of u in case of OpenMP parallelization; bugfix in plant transpiration (advec_ws, plant_canopy_model_mod, pmc_interface_mod, prognostic_equations)
r3021	2018/05/16	maronga	5.0	B	SVN commit message: bugfixes for nested runs (pmc_interface_mod, prognostic_equations)
r3020	2018/05/14	hellstea	5.0	B	SVN commit message: Bugfix in pmci_define_loglaw_correction_parameters (pmc_interface_mod)
r3019	2018/05/13	maronga	5.0	B,C	SVN commit message: disabled suspicious MPI_BARRIER, speed-up of NetCDF input (message, netcdf_data_input_mod)
r3016	2018/05/09	Giersch	5.0	C	SVN commit message: Dollar sign added before Id; Revised structure of reading svf data according to PALM coding standard: svf_code_field/len and fsvf removed, error messages PA0493 and PA0494 added, allocation status of output arrays checked (pres, radiation_model_mod)
r3014	2018/05/09	maronga	5.0	B,C, N	SVN commit message: series of bugfixes (chemistry_model_mod.f90, data_output_2d.f90, data_output_3d.f90, gust_mod.f90, init_3d_model.f90, land_surface_model_mod.f90, modules.f90, plant_canopy_model_mod.f90, prognostic_equations.f90, radiation_model_mod.f90, time_integration.f90, turbulence_closure_mod.f90, urban_surface_mod.f90, user_data_output_2d.f90, uv_exposure_model_mod.f90) New: New variable pc_transpiration_rate was introduced (currently only a dummy) in anology to pc_heating_rate (plant canopy model) Changes: Deactivated automatic setting of a minumum raytracing distance (temporary solution). Bugfixes: 2d/3d data output with nz_do3d /= nzt+1 fixed for several code components Initialization of some variables added to avoid floating invalid during data output Pre-calculation of solar positions fixed for restart runs temperature tendency for plant canopy heating rate in case of land surface / urban surface model fixed Reduced memory required for storing plant canopy data in radiation model
r3012	2018/05/08	Giersch	5.0	N	SVN commit message: To avoid jumps while plotting w-profiles w level nzt+1 is set to w level nzt after velocity modifications through the pressure solver were carried out (This is only the case for nested domains, pres)
r3010	2018/05/07	Giersch	5.0	B	SVN commit message: The copying of spectra and time series output from temporary folder to the permanent destination has been activated through adding a star to the appropriate place in .palm.iofiles (.palm.iofiles)
r3004	2018/04/27	Giersch	5.0	B, C, N	SVN commit message: precipitation_rate removed, further allocation checks for data output of averaged quantities implemented, double CALL of flow_statistics at the beginning of time_integration removed, further minor bugfixes, comments added (average_3d_data, chemistry_model_mod, data_output_2d, data_output_3d, flow_statistics, gust_mod, init_3d_model, land_surface_model_mod, modules, netcdf_interface_mod, radiation_model_mod, read_restart_data_mod, sum_up_3d_data, time_integration, turbulence_closure_mod, user_3d_data_averaging, user_data_output_2d, user_data_output_3d, uv_exposure_model_mod, write_restart_data_mod) Bugfixes: Further allocation checks implemented concerning data output of averaged quantities. Restart does not crash in sum_up_3d_data anymore if an _av quantity is given in the restart run NAMELIST file (_p3dr) but not in the initial run NAMELIST file (_p3d) (average_3d_data, chemistry_model_mod, data_output_2d, data_output_3d, gust_mod, land_surface_model_mod, radiation_model_mod, sum_up_3d_data, turbulence_closure_mod, user_3d_data_averaging, user_data_output_2d, user_data_output_3d, uv_exposure_model_mod) CASE z0q* added for averaging (average_3d_data) Pointer to_be_resorted points to ql_vp_av and not ql_vp (data_output_2d) .NOT. found in if-query added to account for variables found in tcm (netcdf_interface_mod) Output of variable prr_av repaired (sum_up_3d_data) Changed: precipitation_rate removed (data_output_2d, init_3d_model, modules, read_restart_data_mod, sum_up_3d_data, write_restart_data_mod) First call of flow_statistics has been removed. It is already called in run_control itself (time_integration) New: Comments added (chemistry_model_mod, flow_statistics)
r3003	2018/04/23	Giersch	5.0	B	SVN commit message: Bugfix: W* and Z_I in the first line of the run control file of restarts correspond now to the values in the last run control output line of the previous run (flow_statistics, modules, read_restart_data_mod, write_restart_data_mod)
r3001	2018/04/20	suehring	5.0	B	SVN commit message: Bugfix, replace MERGE function by an if-condition in the anterpolation in order to avoid floating-point exceptions. (pmc_interface_mod)
r2997	2018/04/19	suehring	5.0	C	SVN commit message: Mask topography grid points in anterpolation. (pmc_interface_mod)
r2995	2018/04/19	Giersch	5.0	B, C	SVN commit message: Bugfixes related to spinup and radiation model (init_3d_model, parin, radiation_model_mod) Changed: CALL radiation_control during initialization is not necessary anymore because calculation of radiative fluxes at model start is done in radiation_init in any case (init_3d_model) Bugfixes: Time_since_reference_point must be calculated/initialized before the first call of functions related to the radiation model which occur in time_integration_spinup or time_integration (parin) In radiation_presimulate_solar_pos end_time has to be reduced by spinup_time because end_time in the model is the sum of end_time and the spinup_time specified in the p3d_file (radiation_model_mod) List of sky view factor related variables/fields that have to be written out or read in case of restarts has been extended by dsitrans, dsitransc, npcbl and ndsidir (radiation_model_mod)
r2990	2018/04/19	raasch	5.0	B	SVN commit message: bugfix: temporary SOURCES_FOR_RUN_CATALOG now created in base_directory and not in the working directory from where palmrun is called (palmrun)
r2984	2018/04/18	hellstea	5.0	B	SVN commit message: Bugfix in the log-law correction initialization and removal of the nest mass-conservation correction (pmc_interface_mod, time_integration)
r2983	2018/04/18	suehring	5.0	B	SVN commit message: Revise limitation of wall-adjacent velocity in spinup (time_integration_spinup)
r2980	2018/04/17	suehring	5.0	C	SVN commit message: Improvement for spinup checks concering consistency in nesting mode (check_parameters, parin)
r2977	2018/04/17	kanani	5.0	B, C, N	SVN commit message: Fixes for radiative transfer model (init_3d_model, palm, plant_canopy_model_mod, radiation_model_mod, surface_mod, time_integration, urban_surface_mod) Implement changes from branch radiation (r2948-2971) with minor modifications. Change: Improved default settings for radiative transfer calculations (shadows and surface reflections). Calculations activated by default (radiation_interactions = .TRUE.) only if vertical surfaces or trees are present. Flag average_radiation is set TRUE in this case, and it is no longer a namelist parameter. User can override this behavior by setting &radiation_parameters radiation_interactions_on = .F. (default value is TRUE). (init_3d_model, radiation_model_mod, surface_mod) Bugfixes: Deduct spinup_time from first RUN_CONTROL output time by using time_since_reference_point instead of simulated_time (palm) Edited read and write sky view factors and CSF routines to account for the sub-domains which may not contain any of them (radiation_model_mod) Replaced plant_canopy by npcbl to check tree existence to avoid weird allocation of related arrays (after domain decomposition some domains contain no trees although plant_canopy (global parameter) is still TRUE) (radiation_model_mod) Fixed bug in if statement for radiation_interactions (time_integration) New: Add plant canopy type to account for changes in LAD together with the ASCII input for 3D LAD distribution (plant_canopy_model_mod)
r2975	2018/04/16	suehring	5.0	N	SVN commit message: Give informative message in case initialization_actions has been changed in nested child domain. (parin)
r2974	2018/04/16	gronemeier	5.0	B	SVN commit message: Bugfix: check if dt_data_output_av is zero in case of parallel NetCDF output (check_parameters)
r2972	2018/04/16	witha	5.0	N	Added configuration file for ForWind cluster (.palm.config.eddy_gfort)
r2970	2018/04/13	suehring	5.0	B	SVN commit message: Bugfix in large-scale forcing (check_parameters, large_scale_forcing_nudging_mod, surface_mod)
r2969	2018/04/13	thiele	5.0	B	SVN commit message: Bugfix in Interpolation indices (lpm_advec) An error in the calculation of x and y in relation to the left or south u/v/w/... location led to wrong interpolations.
r2968	2018/04/13	suehring	5.0	B	SVN commit message: Bugfixes in initalization of land-surface model as well as timeseries data output in case of elevated model surfaces. (flow_statistics, init_grid, land_surface_model_mod, modules) In case of elevated model surfaces, i.e. the minimum orography height is higher than the first model grid level, mean horizontal profiles had zero values at first grid index (as this index lies within the topography). For correct initialization and data output, the minimum topography-top index is now calculated and used. Elevated surface levels may properly occur, e.g., in case of nested runs.
r2967	2018/04/13	raasch	5.0	B	SVN commit message: bugfix: missing parallel cpp-directives added (data_output_3d, header, lpm_init, lpm_write_exchange_statistics, parin, pmc_interface_mod, pmc_particle_interface, radiation_model_mod, synthetic_turbulence_generator_mod)
r2964	2018/04/12	Giersch	5.0	B, C	SVN commit message: Bugfix in the calculation of fixed number of output time levels for parallel netcdf output, error message related to reading sky view factors revised (check_open, check_parameters, modules, netcdf_interface_mod, radiation_model_mod)
r2963	2018/04/12	suehring	5.0	B, C	SVN commit message: Minor revision of static input file checks, bugfix in initialization of surface-fractions in LSM; minor bugfix in initialization of albedo at window-surfaces; for clearer access of albedo and emissivity introduce index for vegetation/wall, pavement/green-wall and water/window surfaces (data_output_2d, urban_surface_mod, land_surface_mod, netcdf_data_input_mod, radiation_model_mod, Makefile, sum_up_3d_data, surface_mod)
r2961	2018/04/12	suehring	5.0	C	SVN commit message: Synchronize location message between parent and child. Message will not be flushed before all models finished their task. (message)
r2958	2018/04/11	suehring	5.0	C	SVN commit message: Synchronize longitude and latitude between nested model domains (values are taken from the root model). (netcdf_data_input_mod)
r2957	2018/04/11	Giersch	5.0	N, C	SVN commit message: Sky view factors will always be read from file now in case of automatic restarts, corrected error message in case of writing sky view factors (palmrun, check_open)
r2956	2018/04/10	Giersch	5.0	B, C	SVN commit message: Bugfix of the allocation of spectrum_x and spectrum_y in case of restart runs, spectrum_x and spectrum_y are now treat as global restart data not local (read_restart_data_mod, write_restart_data_mod, spectra_mod)
r2955	2018/04/09	suehring	5.0	B, N	SVN commit message: Revise topography filter; extend checks for consistent setting of building ID and type; add cpu measures in netcdf-data input (init_grid, Makefile, netcdf_data_input_mod)
r2954	2018/04/09	schwenkel	5.0	B	SVN commit message: Bugfix for particle initialization in case of ocean (lpm_init)
r2953	2018/04/09	suehring	5.0	B	SVN commit message: Bugfix in checks for dynamic input file initialization data (netcdf_data_input_mod)
r2951	2018/04/06	kanani	5.0	N	SVN commit message: Add cpu measures for nesting initialization (palm, pmc_interface_mod)
r2947	2018/04/04	suehring	5.0	C	SVN commit message: Checks for dynamic input further revised (netcdf_data_input_mod)
r2946	2018/04/04	suehring	5.0	B	SVN commit message: Bugfix for revision 2945, perform checks only if dynamic input file is available; remove unused module load (netcdf_data_input_mod, synthetic_turbulence_generator_mod)
r2945	2018/04/04	suehring	5.0	B, C, N	SVN commit message: Bugfix in parallelization of synthetic turbulence generator; revision in control mimic of synthetic turbulence generator in case of RAN-LES nesting; checks for dynamic input file added; control mimic for topography input slightly revised. (netcdf_data_input_mod, synthetic_turbulence_generator_mod)
r2944	2018/04/03	suehring	5.0	B	SVN commit message: Fixed bad commit (radiation_model_mod)
r2943	2018/04/03	suehring	5.0	B	SVN commit message: Calculate exner function at all height levels in USM In order to avoid segmentation faults in case radiation-interactions are switched-off, calculate exner function at all height levels in USM . (urban_surface_model_mod, radiation_model_mod)
r2942	2018/04/03	suehring	5.0	B	SVN commit message: Bugfix in assigning surface element data after restart. (surface_mod)
r2941	2018/04/03	kanani	5.0	B, C	SVN commit message: Fixes for spinup and sky-view-factor (SVF) treatment (parin, radiation_model_mod, time_integration) Bugfix: Allocation of arrays in radiation_read_svf only if not yet allocated (radiation_model_mod) No spinup in case of restart run (parin) Change: Deduct spinup_time from RUN_CONTROL output of main 3d run, use time_since_reference_point instead of simulated_time (time_integration) Update of 2920 revision comment (radiation_model_mod) No read of nsurfl from SVF file since it is calculated in radiation_interaction_init (radiation_model_mod)
r2940	2018/04/03	suehring	5.0	B	SVN commit message: Bugfix in reading restart data of vertical surface elements (surface_mod) With revision -r 2894 reading restart data for surface elements does not work properly anymore, leading to segmentation faults or non-reproducible simulation results in case of natural- and/or urban-type surface elements. Please note, this problem is finally fixed in -r 2942.
r2939	2018/03/29	suehring	5.0	B	SVN commit message: Set lateral boundary conditions for divergence in multigrid solver (poismg_mod, poismg_noopt_mod)
r2938	2018/03/27	suehring	5.0	N, C	SVN commit message: Nesting in RANS-LES and RANS-RANS mode enabled; synthetic turbulence generator at all lateral boundaries in nesting or non-cyclic forcing mode; revised Inifor initialization in nesting mode (Makefile, boundary_conds, check_parameters, init_3d_model, init_pegrid, land_surface_model_mod, large_scale_forcing_nudging_mod, netcdf_data_input_mod, pmc_interface_mod, pmc_mpi_wrapper_mod, synthetic_turbulence_generator_mod, turbulence_closure_mod, time_integration) New RANS-RANS nesting and RANS-LES nesting synthetic turbulence generator at all lateral boundaries in case of RAN-LES nesting or nesting in COSMO model Changed For child domains, dynamic input is not required any more. Child is initialized by interpolation of parent data. Initialization of soil-related variables that are provided by Inifor are interpolated from parent to child
r2934	2018/03/26	suehring	5.0	N, C, B	SVN commit message: Synchronize parent and child model after initialization and spinup phase; Check for consistent setting of spinup times in parent and child model; remove obsolete masking of tendency arrays during initialization (Makefile, check_parameters, init_3d_model, time_integration, time_integration_spinup)
r2932	2018/03/26	maronga	5.0	C	SVN commit message: renamed all Fortran NAMELISTS (check_parameters, chemistry_model_mod, cpulog_mod, data_output_profiles, gust_mod, land_surface_model_mod, lpm_splitting, message, netcdf_interface_mod, package_parin, parin, plant_canopy_model_mod, pmc_handle_communicator_mod, radiation_model_mod, spectra_mod, urban_surface_mod, user_parin, uv_exposure_model_mod, virtual_flight_mod, wind_turbine_model_mod) All Fortran NAMELISTS have been renamed as follows (* indicates NAMELISTS where the deprecated names will still work until the next PALM release): inipar(*) --> initialization_parameters d3par(*) --> runtime_parameters chemistry_par --> chemistry_parameters gust_par --> gust_parameters lsm_par(*) --> land_surface_parameters spectra_par(*) --> spectra_parameters canopy_par(*) --> plant_canopy_parameters nestpar --> nesting_parameters radiation_par(*) --> radiation_parameters usm_par(*) --> urban_surface_parameters userpar(*) --> user_parameters uvexposure_par --> biometeorology_parameters flight_par(*) --> virtual_flight_parameters wind_turbine_par(*) --> wind_turbine_parameters
r2930	2018/03/23	suehring	5.0	C	SVN commit message: Remove default surfaces from radiation model and add check for this; revise checks for surface_fraction (netcdf_data_input_mod, radiation_model_mod)
r2927	2018/03/23	suehring	5.0	B	SVN commit message: Bugfix in setting boundary condition for topography index array in case of non-cyclic boundary conditions and Piascek-Williams advection scheme is used. (init_grid)
r2925	2018/03/23	suehring	5.0	N, C	SVN commit message: Check for further inconsistent settings of surface_fractions; error messages slightly rephrased and error numbers changed. (netcdf_data_input_mod)
r2921	2018/03/22	Giersch	5.0	B, N	SVN commit message: further inipar parameter has been added to restart data, bugfix in spinup mechanism Bugfix: Activation of spinup must be done after rrd_global is called (land_surface_model_mod, parin, urban_surface_mod) New: The parameters spinup_time, day_of_year_init and time_utc_init are also written/read now in case of restart runs (write_restart_data_mod, read_restart_data_mod, Makefile)
r2920	2018/03/22	kanani	5.0	B, C, N	SVN commit message: Optimize SVF calculation, clean-up, bugfixes Bugfix: Initialize pcbl array, plus further fixes (radiation_model_mod, urban_surface_mod) Change: Remove unused variables (urban_surface_mod) Correct comment for surface directions (surface_mod) Move radiation-related parameters to radiation model (plant_canopy_model_mod, radiation_model_mod) (radiation_model_mod) Removed virtual surfaces Separate processing of direct and diffuse solar radiation, new discretization by azimuth and elevation angles Diffuse radiation processed cumulatively using sky view factor Enabled limiting of number of view factors between real surfaces, thus greatly enhancing scalability New: Precalculation of apparent solar positions (init_3d_model, radiation_model_mod) New 2D raytracing process using whole vertical column at once (Optimized SVF calculation --> memory efficiency and much less RMA) and related code changes (radiation_model_mod)
r2918	2018/03/21	gronemeier	5.0	C	SVN commit message: moved initialization of mixing length to turbulence_closure_mod; consider walls in calculation of ml in rans-mode (check_parameters, init_grid, model_1d_mod, modules, turbulence_closure_mod)
r2906	2018/03/19	Giersch	5.0	C,B	SVN commit message: new procedure for reading/writing svf data, initialization of local variable ids (palm.iofiles, palmrun, check_open, init_3d_model, modules, parin, radiation_model_mod, urban_surface_mod)
r2903	2018/03/16	hellstea	5.0	B	SVN commit message: Nesting-related calls to pmci_ensure_nest_mass_conservation and pres after the nest initialization are removed as they may create unwanted initial perturbation in some cases (palm)
r2899	2018/03/15	hellstea	5.0	C	SVN commit message: Control logics improved to allow nesting also in cases with constant_flux_layer = .F. or constant_diffusion = .T. (pmc_interface_mod)
r2898	2018/03/15	suehring	5.0	C	SVN commit message: Check dimensions in static input files, further checks for building type. (netcdf_data_input_mod)
r2897	2018/03/15	suehring	5.0	C	SVN commit message: Relax restrictions for topography input via static input file, terrain and building heights, as well as building IDs can be input separately and are not mandatory any more. (init_grid, netcdf_data_input_mod)
r2895	2018/03/15	hellstea	5.0	C	SVN commit message: Change in the nest initialization (pmci_interp_tril_all). Bottom wall BC is no longer overwritten (pmc_interface_mod)
r2894	2018/03/15	Giersch	5.0	C,N	SVN commit message: Reading/Writing data in case of restart runs revised (Makefile, chemistry_model_mod, init_3d_model, land_surface_model_mod, modules, palm, parin, radiation_model_mod, read_3d_binary, read_restart_data_mod, read_var_list, sum_up_3d_data, surface_mod, synthetic_turbulence_generator_mod, urban_surface_mod, user_last_actions, user_module, user_read_restart_data, user_read_restart_data_mod, uv_exposure_model_mod, virtual_flight_mod, wind_turbine_model_mod, wrd_write_string, write_3d_binary, write_restart_data_mod, write_var_list) Changed: Structure of reading/writing restart data was changed to make it more clearly. Subroutine names with respect to reading/writing restart data has been renamed. Redundant skipping functions that skip module related global parameters have been removed. Arising mistakes that could occur during reading/writing new restart data have been prevented (e.g. the order of subroutine calls in case of reading/writing module related restart data does not matter). New: Strings and their respective lengths are written out (wrd_write_string) and read now in case of restart runs to get rid of prescribed character lengths. New module read_restart_data_mod contains modified content of read_3d_binary and read_var_list which have been deleted. New module write_restart_data_mod contains modified content of write_3d_binary and write_var_list which have been deleted. Introduction of modules that read/write user specific restart data (user_read_restart_data_mod, user_write_restart_data_mod) and deletion of the old user_read_restart_data file.
r2893	2018/03/14	suehring	5.0	C	SVN commit message: Revise informative message concerning filtered topography. (init_grid)
r2892	2018/03/14	suehring	5.0	B	SVN commit message: Bugfixes, missing coupling_char for child-domain ASCII file; uninitialized array in single_building setup (init_grid, plant_canopy_model_mod)
r2886	2018/03/14	thiele	5.0	B	SVN commit message: Bugfix in passive particle SGS Model (lpm_advec.f90) Sometimes the added SGS velocities would lead to a violation of the CFL criterion for single particles. For this a check was added after the calculation of SGS velocities.
r2884	2018/03/14	scharf	5.0	B	SVN commit message: Bugfix: corrected KIND of variable "parsize" for some MPI calls (pmc_particle_interface.f90)
r2883	2018/03/14	Giersch	5.0	C	SVN commit message: Format 325 of header output has been changed, dt_dopr_listing is not set to the default value zero anymore (check_parameters.f90, header.f90)
r2881	2018/03/13	maronga	5.0	B,C	SVN commit message: bugfix in land surface model and new option in spinup (land_surface_model_mod, modules, parin, time_integration_spinuo) Bugfix: Loop syntax led to wrong settings of hydraulic conductivity and capacity in water transport equation in soil model Changed: Added steering parameter calc_soil_moisture_during_spinup to switch on/off water transport equation in soil model during spinup. Default setting is .FALSE..
r2868	2018/03/09	hellstea	5.0	B	SVN commit message: Local conditional Neumann conditions for one-way coupling removed (pmc_interface_mod)
r2867	2018/03/09	suehring	5.0	B	SVN commit message: Revise mapping of 3D-buildings onto orography; further bugfix concering call of user_init (see commit -r 2865) Please see commit 2864, not 2865.
r2865	2018/03/08	kanani	5.0	N	SVN commit message: Add file connection for sky view factors (SVF) binaries (.palm.iofiles)
r2864	2018/03/08	suehring	5.0	B	SVN commit message: Bugfix, move call of user_init in front of initialization of grid-point arrays. (init_3d_model) (Usually, array 'rmask' used to set-up statistic regions is initialized in routine 'user_init'. To correctly set-up grid-point arrays used for horizontal averaging, it is necessary to call 'user_init' before doing this.)
r2853	2018/03/05	suehring	5.0	B	SVN commit message: Bugfix in init log-law correction. (pmc_interface_mod)
r2851	2018/03/05	maronga	5.0	B	SVN commit message: bugfix: calculation of output time levels for restart runs (parallel NetCDF). (check_parameters)
r2845	2018/03/01	raasch	5.0	B	SVN commit message: bugfix: set kinematic viscosity for sea water. (init_ocean)
r2841	2018/02/27	knoop	5.0	B	SVN commit message: Bugfix: wrong placement of include 'mpif.h' corrected. (lpm_write_exchange_statistics, pmc_child_mod, pmc_general_mod, pmc_handle_communicator_mod, pmc_interface_mod, pmc_mpi_wrapper_mod, pmc_parent_mod, pmc_particle_interface, spectra_mod, synthetic_turbulence_generator_mod)
r2839	2018/02/27	schwenkel	5.0	B	SVN commit message: Bugfix for Kessler microphysics. (diagnostic_quantities_mod)
r2837	2018/02/26	gronemeier	5.0	C	SVN commit message: palmplot: config file of ncl scripts can be chosen in shell command. With the command-line paramater file_config, an alternative NCL configuration file can be chosen to be loaded with the NCL scripts of palmplot.
r2836	2018/02/26	Giersch	5.0	B,C,N	SVN commit message: Bugfix in interpolation of lift and drag coefficients during initialization, default value of dt_dopr_listing is set to zero to allow header output. Bugfixes: Corrected interpolation of lift and drag coefficients on fine grid of radius segments and angles of attack. (wind_turbine_model_mod) Changes: Speed-up of the initialization of the wind turbine model through restricting radius specific calculations to the loop over the radius. (wind_turbine_model_mod) New: dt_dopr_listing is set to the default value zero to allow header output. (check_parameters)
r2834	2018/02/23	raasch	5.0	C	SVN commit message: fname renamed jobname. (palmbuild, palmrun, .palm.iofiles, .palm.config.*)
r2826	2018/02/21	hellstea	5.0	B	SVN commit message: Bugfix in setting the default boundary conditions for nest domains. (parin.f90)
r2825	2018/02/20	maronga	5.0	C	SVN commit message: adjustments in gui tools. (palm_gf, palm_jm, palm_wd, palm_wdd, palmrungui, palmrungui_files/mainwindow.ui)
r2818	2018/02/19	maronga	5.0	C	SVN commit message: improvements in spinup mechanism. (time_integration_spinup, read_var_list, write_var_list)
r2815	2018/02/19	kanani	5.0	B,N	SVN commit message: Enable restarts and vector optimization for chemistry model. (chemistry_model_mod, prognostic_equations)
r2813	2018/02/16	suehring	5.0	B	SVN commit message: Further bugfixes concering restart runs. (surface_mod)
r2812	2018/02/16	hellstea	5.0	B	SVN commit message: Bugfixes in computation of the interpolation loglaw-correction parameters. (pmc_interface_mod, surface_mod)
r2809	2018/02/15	schwenkel	5.0	B	SVN commit message: Bugfix for gfortran: Replace the function C_SIZEOF with STORAGE_SIZE. (lpm_exchange_horiz, pmc_child_mod, pmc_interface_mod, pmc_mpi_wrapper_mod, pmc_parent_mod, pmc_particle_interface, radiation_model_mod)
r2805	2018/02/14	suehring	5.0	B	SVN commit message: Bugfix in re-mapping surface-element data in case of restarts; bugfix in initialization of water-surface roughness; bugfix - uninitialized resistance at urban-type surfaces. (land_surface_model_mod, surface_mod, urban_surface_mod)
r2801	2018/02/14	thiele	5.0	N	SVN commit message: Introduce particle transfer in nested models. (pmc_general_mod, lpm_pack_arrays, lpm_init, lpm_exchange_horiz, pmc_child_mod, lpm_write_exchange_statistics, pmc_interface_mod, lpm_boundary_conds, time_integration, pmc_handle_communicator, lpm, pmc_particle_interface, palm, pmc_parent_mod)
r2799	2018/02/12	raasch	5.0	N	SVN commit message: parameters are allowed in output commands (OC:). (palmrun)
r2798	2018/02/09	suehring	5.0	C	SVN commit message: Bugfix initialization of %pt_surface array; Output of surface temperature also for default-type surfaces. (check_parameters, data_output_2d, land_surface_model, modules, sum_up_3d_data, write_3d_binary)
r2797	2018/02/08	suehring	5.0	C	SVN commit message: Output of ground-heat flux at natural- and urban-type surfaces in one output variable; enable restart data of _av variables that belong to both land- and urban-surface model. (average_3d_data, check_parameters, data_output_2d, land_surface_model, modules, read_3d_binary, sum_up_3d_data, urban_surface_mod, write_3d_binary)
r2796	2018/02/08	suehring	5.0	B	SVN commit message: Bugfix in 3D building initialization. (init_grid)
r2795	2018/02/07	hellstea	5.0	B	SVN commit message: Bugfix in nesting anterpolation relaxation functions. (pmc_interface_mod)
r2792	2018/02/07	Giersch	5.0	B	SVN commit message: Bugfix for restart runs if the wind turbine model is used. (wind_turbine_model_mod)
r2790	2018/02/06	suehring	5.0	B	SVN commit message: Bugfix in summation of surface sensible and latent heat flux. (sum_up_3d_data)
r2789	2018/02/06	raasch	5.0	B	SVN commit message: bugfix: exit if no queue has been given neither with option -q nor in the configuration file (palmrun)
r2787	2018/02/05	suehring	5.0	N	SVN commit message: Check if 3D building input is consistent to numeric grid. (netcdf_data_input_mod)
r2782	2018/02/02	maronga	5.0	B	SVN commit message: bugfix/adjusment in spinup mechanism (time_integration_spinup)
r2776	2018/01/31	Giersch	5.0	N,C	SVN commit message: Skipping of module related restart data changed + adapting synthetic turbulence generator to current restart procedure. New: _prerun flags for skipping module related parameters if restart data was outputted at the end of the precursor run. (modules, read_var_list, synthetic_turbulence_generator_mod, virtual_flight_mod, wind_turbine_model_mod) Changes: The variables synthetic_turbulence_generator and use_synthetic_turbulence_generator have been abbreviated to restrict the character length to 30. (check_parameters, header, init_3d_model, init_pegrid, modules, read_var_list, synthetic_turbulence_generator, time_integration, write_var_list)
r2773	2018/01/30	suehring	5.0	N,C,B	SVN commit message: Nesting for chemical species implemented; Bugfix passive scalar boundary condition after anterpolation; Timeseries output of surface temperature; Enable initialization of 3D topography (was commented out so far). Bugfixes: Passive scalar boundary condition after anterpolation. (flow_statistics) New: Nesting for chemical species. (chemistry_model_mod, Makefile, parin, pmc_interface_mod, time_integration) Timeseries output of surface temperature pt(0). (flow_statistics) Changes: Checks for correct initialization with Inifor in nesting mode moved. (check_parameters, netcdf_data_input_mod)
r2772	2018/01/29	suehring	5.0	C,B	SVN commit message: Enable initialization via inifor without running land-surface model; small bugfix in chemistry model string treatment. (chemistry_model_mod, netcdf_data_input_mod)
r2770	2018/01/25	kanani	5.0	B	SVN commit message: Correction of parameter check. (plant_canopy_model_mod)
r2769	2018/01/25	raasch	5.0	B	SVN commit message: bugfix for calculating number of required output time levels in case of output at the beginning of a restart run. (netcdf_interface_mod)
r2768	2018/01/24	kanani	5.0	B,C	SVN commit message: Added parameter check, reduced line length, some formatting. Bugfixes: Reduced line length to meet Fortran standard of max. 132 characters per line. (chemistry_model_mod) Changes: Added parameter check forpcm_heatrate, some formatting (plant_canopy_model)
r2766	2018/01/22	kanani	5.0	B,C	SVN commit message: Removal of __chem directive, plus minor changes. Bugfixes: Removed redundant commas in argument lists of some CALLs. (urban_surface_mod) Changes: Removed __chem preprocessor directive (average_3d_data, boundary_conds, check_parameters, chem_gasphase_mod, chem_modules, chem_photolysis_mod, chemistry_model_mod, data_output_3d, init_3d_model, netcdf_interface_mod, palm, parin, prognostic_equations, read_3d_binary, sum_up_3d_data, surface_layer_fluxes_mod, surface_mod, swap_timelevel, time_integration) Increased LEN of canopy_mode to 30. (plant_canopy_model)
r2765	2018/01/22	maronga	5.0	B,C	SVN commit message: major bugfix in calculation of aerodynamic resistance for vertical surface elements. Bugfixes: Major bugfix in application of Krayenhoff & Voogt parameterization of the aerodynamic resistance for vertical surfaces. (land_surface_model_mod.f90, urban_surface_mod.f90) Initial value of time_since_reference point was missing. (modules.f90) Changes: Renamed simulation_time_since_reference to time_to_be_simulated_from_reference_point. (check_parameters.f90)
r2764	2018/01/22	gronemeier	5.0	B	SVN commit message: Bugfix: remove duplicate SAVE statements. (turbulence_closure_mod)
r2762	2018/01/18	raasch	5.0	C	SVN commit message: file connection file is taken by default from trunk/SCRIPTS. (palmrun)
r2759	2018/01/17	suehring	5.0	B	SVN commit message: Major bugfix in horizontal diffusion of all scalar quantities at vertical surfaces; further bugfix: density is considered for vertical fluxes of passive scalar and salinity. (diffusion_s, surface_mod)
r2758	2018/01/17	suehring	5.0	B	SVN commit message: Bugfix, no initial masking of wind velocity at first prognostic grid level in case of land- or urban-surface spin-up.. (init_3d_model, time_integration_spinup)
r2756	2018/01/16	suehring	5.0	N	SVN commit message: Fill values for 3D data output of chemical species introduced. (chemistry_model_mod, data_output_3d)
r2753	2018/01/16	suehring	5.0	N	SVN commit message: Tile approach for spectral albedo implemented.. (flow_statistics, radiation_model_mod, surface_mod)
r2749	2018/01/15	raasch	5.0	B	SVN commit message: bugfix for BININ file connection statement. (.palm.iofiles)
r2747	2018/01/15	suehring	5.0	B	SVN commit message: Bugfix, topography is rounded to the nearest discrete grid level. (init_grid)
r2746	2018/01/15	suehring	5.0	C	SVN commit message: Read information from statitic driver for resolved vegetation independently from land- or urban-surface model. (check_parameters, data_output_3d, header, init_3d_model, modules, netcdf_data_input_mod, netcdf_interface_mod, plant_canopy_model_mod, prognostic_equations, radiation_model_mod, turbulence_closure_mod, urban_surface_mod)
r2743	2018/01/12	suehring	5.0	C	SVN commit message: In case of natural- and urban-type surfaces output surfaces fluxes in W/m2. (check_parameters, data_output_2d, sum_up_3d_data)
r2742	2018/01/12	suehring	5.0	N	SVN commit message: Output of surface temperature tsurf* at urban- and natural-type surfaces. (average_3d_data, check_parameters, data_output_2d, modules, sum_up_3d_data)
r2737	2018/01/11	kanani	5.0	C	SVN commit message: Removed unused variables t_surf_whole.... (urban_surface_mod)
r2735	2018/01/11	suehring	5.0	C	SVN commit message: Output of resistance also urban-type surfaces. (average_3d_data, check_parameters, data_output_2d, land_surface_model_mod, modules, sum_up_3d_data, surface_mod, urban_surface_mod)
r2732	2018/01/10	raasch	5.0	B	SVN commit message: bugfix: keyword Rev set for scrpts palmrun and palmbuild. (palmrun, palmbuild)
r2731	2018/01/09	suehring	5.0	C	SVN commit message: Enable vectorization by splitting the k-loop. (advec_ws)
r2729	2018/01/09	maronga	5.0	C	SVN commit message: input of deep soil temperature separated from prognostic soil temperature The lsmpar array soil_temperature must be of the same size as dz_soil and soil_moisture, which appears to be more intuitive to the user. The bottom boundary condition for the soil temperature is now a separate parameter called deep_soil_temperature. (land_surface_model_mod.f90, ex_lsm_clearksy_p3d) (land_surface_model_mod)
r2728	2018/01/09	maronga	5.0	C	SVN commit message: adjustments in spinup mechanism Set spatially homogeneous velocity fields during spinup periops. (time_integration_spinup.f90)
r2726	2018/01/08	kanani	5.0	B	SVN commit message: Exclude spinup time from progress bar (progress_bar_mod)
r2725	2018/01/05	kanani	5.0	B	SVN commit message: Exclude spinup time from progress bar Updated ex_lsm_clearsky_rc due to change of default value to average_radiation = .FALSE. in previous commit.
r2724	2018/01/05	maronga	5.0	C	SVN commit message: some changes in spinup mechanism and additional check in land surface model Further adjustments for spinup mechanism(time_integration_spinup.f90). Additional security check for soil_temperature to match the number of soil layers (land_surface_model_mod.f90). Set default value of average_radiation = .FALSE. (radiation_model_mod.f90)
r2723	2018/01/05	maronga	5.0	B	SVN commit message: bugfixes for spinup mechanism to work with lsm+usm+radiation Bugfixes for spinup mechanism to work with land surface model, urban surface model and radiation model (land_surface_model_mod.f90, radiation_model_mod.f90, time_integration_spinup.f90, urban_surface_mod.f90).
r2720	2018/01/02	kanani	5.0	C	SVN commit message: update of palm version Updated PALM version number. (palm) Corrected comment. (urban_surface_mod)
r2718	2018/01/02	maronga	5.0	C	SVN commit message: deleting of deprecated files; headers updated where needed