PALM source code change log

Current revision:

r4901

Current fixed release: 4.0 (r1540)

The following table documents all changes to the PALM repository since 2013. Changes made during 2009-2012 can be found here. Older changes can be found ​here.

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.

Date	Author	svn Revision	Last Release	Type	Description
17/11/16	BM	r2071	4.0	B	Some minor bugfixes in USM (ls_forcing_mod.f90 urban_surface_mod.f90).
14/11/16	BM	r2069	4.0	C	Some style improvements for mrungui. Also, the xterm window should stay open for interactive jobs (mainwindow.cpp, about.ui, mainwindow.ui).
11/11/16	BM	r2065 r2067	4.0	N	Added the new tool "PALM job manager" (palm_jm), which allows to overview the existing jobs in the JOBS directory. It displays associated files in the INPUT and in the USER_CODE folders and allows to open these files for editing directly from the palm_jm interface. Moreover, palm_jm allows for creating new jobs based on a existent reference job. Moreover it allows to create a whole set of new jobs based on such a reference job (e.g. for parameter studies). (palm_jm, palm_jm.ui, palm_jm_create_set.ui). The job manager and watchdog can now be called from mrungui (mainwindow.cpp, mainwindow.ui).
10/11/16	SR	r2063	4.0	B	Bugfix: opening of PROGRESS file moved out of the NetCDF block. (check_open)
10/11/16	BM	r2061	4.0	B	Bugfix: return error messages in palm_wd when .wdd.config was not set up on remote host (palm_wdd).
10/11/16	BM	r2059	4.0	B	Bugfix: set minimum/maximum values for Rif in 1D model to the old values (-5 and 1, respectively) (init_1d_model.f90).
08/11/16	TG	r2053	4.0	N, B	New New outflow condition implemented in case of non-cyclic boundary condition. When using bc_lr='dirichlet/radiation' it is possible to use turubulent_outflow=.True.. This imposes an outflow boundary condition similar to the turbulence recycling method where instantaneous values of u, v, w, e, pt, s, and q are copied from a vertical plane inside the model domain to the outflow boundary. This prevents numerical errors which usually occur when negative velocities develop at the outflow boundary in combination with the radiation boundary condition. (outflow_turbulence,...) Bugfix Remove setting a default value for recycling_width as it does not work. The value is already needed in init_pegrid.f90 and so changing its value inside check_parameters does not have an effect. (check_parameters)
02/11/16	HK	r2044	4.0	B	Bugfix, added error codes for anelastic approximations. (check_parameters)
02/11/16	MS	r2042	4.0	B	Bugfix, read and write restart data for wall fluxes. (read_var_list, write_var_list) Bugfix, setting of constant_scalarflux. Additional checks for wall fluxes added. (check_parameters)
27/10/16	TG	r2041	4.0	C	Added missing svn-ID string from last check-in.
26/10/16	TG	r2040	4.0	C	Increased the number of possible statistic regions from 9 to 99 (netcdf_interface_mod.f90, check_parameters.f90); deleted open file 'PLOTTS_DATA' (check_open.f90).
26/10/16	HK	r2037	4.0	N, C	Implemented the anelastically approximated model equations. For a control description please see approximation.
24/10/16	MS	r2035	4.0	C	Remove check for npex and npey in nesting case. (parin)
21/10/16	TG	r2034	4.0	C	Updated .mrun.config blogs for HLRNIII: added compiler options -K trap=fp (abort if "floating point exception" occurs) and -hnoacc (ignore OpenACC pre-processor commands). Also unified module loads and IC commands throughout the .mrun.config files (.mrun.config.hlrnIII, .mrun.config.forwind_hlrnIII, .mrun.config.imuk_hlrnIII, .mrun.config.imuk_hlrnIII_rrtmg).
21/10/16	HK	r2031	4.0	C	Renamed variable rho to rho_ocean, rho_init to rho_ocean_init and rho_av to rho_ocean_av in all relevant source code files.
20/10/16	TG	r2030	4.0	B	Bugfix: checking for NCL version in NCL-scripts used by palmplot (cross_sections.ncl, profiles.ncl, spectra.ncl, timeseries.ncl).
18/10/16	MS	r2026	4.0	B,C	Bugfix, enable output of s*2. (check_parameters, flow_statistics) Change, calculation of domain_averaged perturbation energy. (flow_statistics) Some formatting adjustments. (data_output_profiles, flow_statistics)
12/10/16	FK	r2025	4.0	B,C,N	Bugfix Output of ssws* finally enabled. (check_parameters, sum_up_3d_data) Missing initialization of array lad_s added. (plant_canopy_model_mod) Deallocation of array plantt and reading of csf/csfsurf. (urban_surface_mod) Changes Increased DIMENSION of parameters data_output and data_output_user. (check_parameters) Optimization of MPI-RMA operations, re-naming/-declaration of some variables, splitting of arrays svf and svfsurf, use of new control parameter varnamelength, minor formatting and optimization (urban_surface_mod) New Added output variables usm_rad_ressw, usm_rad_reslw
07/10/16	MS	r2021	4.0	B	Bugfixes Restore flags for lateral nest boundaries in multigrid solver in case of mg_switch_to_pe0. (poismg_noopt, poismg_mod) Setting Neumann boundary conditions for topography arrays in case of non-cyclic boundary conditions at coarser grid levels. (init_grid)
30/09/16	AH	r2020	4.0	B	Bugfixes concerning the nesting mainly in the determination of the anterpolation index bounds. These errors were found when first time testing for grid-spacing ratio 3 (pmc_interface_mod.f90)
29/09/16	SR	r2017	4.0	B	Bugfix in case of # of output file connection statements in configuration file > 100. (interpret_config)
28/09/16	LV	r2015	4.0	B	Bugfix in wind turbine code. (wind_turbine_model_mod)
21/09/16	MS	r2013	4.0	B	Bugfix in format descriptor. (pmc_handle_communicator_mod)
19/09/16	FK	r2011	4.0	N, C	Change: Flag urban_surface is now defined in module control_parameters in order to avoid circular dependencies between modules during compilation. (average_3d_data, check_parameters, data_output_3d, init_3d_model, modules, netcdf_interface_mod, palm, prognostic_equations, radiation_model_mod, sum_up_3d_data, surface_layer_fluxes, swap_timelevel, time_integration, user_init_urban_surface) With this change, auxiliary SUBROUTINE get_usm_info is no longer needed and is removed. (radiation_model_mod, urban_surface_mod) Changed prefix for urban surface model output to "usm_" (average_3d_data, check_parameters, data_output_3d, netcdf_interface_mod, sum_up_3d_data) Renamed canopy_heat_flux to pc_heating_rate, since the original meaning/calculation of the quantity has changed, related to the urban surface model (USM) and similar future applications. In case of using the USM, heat sources within the plant canopy due to solar radiation are directly calculated as a heating rate (pc_heating_rate). This needs to be considered for the calculation of the pt-tendency in the plant canopy model (pcm_tendency), where the vertical divergences of the canopy heat flux were replaced by pc_heating_rate. In case of manual setting of the canopy heat flux, pc_heating_rate is calculated in pcm_init. (plant_canopy_model) Removed commented CALLs of global_min_max. (time_integration) urban_surface_mod: Major reformatting according to PALM coding standard (comments, blanks, alphabetical ordering, etc.), removed debug_prints. New: Introduced control parameter varnamelength to allow an easier change of the string length of various output-variable arrays, such as data_output (average_3d_data, check_parameters, data_output_3d, modules, netcdf_interface_mod, sum_up_3d_data) Added flag lsf_exception (inipar-Namelist parameter) to allow explicit enabling of large scale forcing together with buildings on flat terrain (check_parameters, modules, parin)
24/08/16	FK	r2007	4.0	N, C	Implementation of new urban surface model, which was coded by Jaroslav Resler, Pavel Krc and their team (CTU in Prague, ICS AS in Prague). New files: urban_surface_mod.f90, user_init_urban_surface.f90 Changes in existing files: average_3d_data.f90 data_output_3d.f90 check_parameters.f90 init_3d_model.f90 Makefile modules.f90 netcdf_interface_mod.f90 palm.f90 parin.f90 plant_canopy_model_mod.f90 prognostic_equations.f90 radiation_model_mod.f90 sum_up_3d_data.f90 surface_layer_fluxes_mod.f90 swap_timelevel.f90 time_integration.f90
24/08/16	MS	r2004	4.0	N	Humidity and passive scalar treated separately also in nesting mode (parin, pmc_interface_mod)
18/08/16	MS	r1996	4.0	B	Bugfix in calculation of turbulent fluxes in case the horizontal mean of vertical velocity is not zero. (advec_ws)
15/08/16	MS	r1994	4.0	B	Bugfix in definition of generic topography. (init_grid) Add missing check for proper setting of microphysics. (check_parameters)
12/08/16	MS	r1992	4.0	N, B	New New parameter top_scalarflux to prescribe scalar flux at model top. As a consequence of this, default of bc_s_t changed to 'initial_gradient', and new value 'neumann' can be prescribed if using top_scalarflux. (modules, init_3d_model, check_parameters, header, parin, read_restart_data, write_restart_data, boundary_conds) Bugfixes Close NetCDF file for flight data. (close_file) Declaration of look-up index as INTEGER. (surface_layer_mod) Averaging of passive scalar. (sum_up_3d_data) Initialization of surface and top salinity flux and top humidity flux. (init_3d_model) Initialization of profile data output in case of passive scalar. (check_parameters)
12/08/16	TG	r1991	4.0	B	Variable list was not written to time-series data which prevented these files to be extended in restart runs. (netcdf_interface_mod.f90)
10/08/16	TG	r1988	4.0	B,N	Bugfix: Check if output file can be opened in newly created directory (e.g. open binary output file in BINOUT). If not, call fortran_sleep and try again. (check_open.f90) New: Module for POSIX calls added. (posix_calls_from_fortran.f90)
01/08/16	MS	r1984	4.0	B	Bugfix: checking for bottom and top boundary condition for humidity and scalars. (check_parameters)
01/08/16	MS	r1982	4.0	B	Bugfix concering consistency check for topography. (init_grid)
29/07/16	MS	r1980	4.0	B	Bugfix concerning user-defined output. (data_output_2d, data_output_3d, data_output_mask, netcdf_interface_mod)
29/07/16	BM	r1977	4.0	B	Bugfix: initial values of pave_surface and water_surface were not set at model start (land_surface_model_mod.f90)
27/07/16	BM	r1976	4.0	B,C	Bugfix: restarts without land surface model crashed due to bug in previous revision (read_3d_binary.f90) Changes: Output of 2D and 3D radiation model data is now done in radiation_model_mod I/O of binary restart data for the radiation model is now done in radiation_model_mod. Grid definition for radiation quantities is now done in radiation_model_mod. The output of the radiation models has been harmonized and the calls to the radiation model was simplified to allow better modularization. (average_3d_data.f90, data_output_2d.f90, data_output_3d.f90, land_surface_model_mod.f90, netcdf_interface_mod.f90, palm.f90, radiation_model_mod.f90, read_3d_binary.f90, sum_up_3d_data.f90, write_3d_binary.f90)
26/07/16	TG	r1974	4.0	B	Bug: in case of non-extendable output files with using non-parallel I/O only PE0 was approaching an MPI_BARRIER call (check_open.f90)
26/07/16	BM	r1972	4.0	B, C	Bugfix: Units for land surface quantities were wrong/missing (etcdf_interface_mod.f90) Changes: Output of 2D and 3D land surface data is now done in land_surface_model_mod I/O of binary restart data for the land surface model is now done in land_surface_model_mod. Grid definition for land surface quantities is now done in land_surface_model_mod. (Makefile, average_3d_data.f90, check_parameters.f90, data_output_2d.f90, data_output_3d.f90, land_surface_model_mod.f90, netcdf_interface_mod.f90, palm.f90, read_3d_binary.f90, sum_up_3d_data.f90, user_init_land_surface.f90, write_3d_binary.f90)
18/07/16	MS	r1970	4.0	B	Bugfix, check for ibc_q_b and constant_waterflux in case of land-surface scheme. (check_parameters)
18/07/16	MS	r1968	4.0	C	PE-wise reading of topography, in order to get rid of scaling bottleneck due to global arrays nzb_local and nzb_tmp, which are (from now on) allocated locally. As a consequence, determination of single building and street canyon has changed, as well as the determination of wall-flags on different multigrid level. (init_grid, init_pegrid, exchange_horiz_2d, modules, user_init_grid)
18/07/16	BM	r1966	4.0	B	Bug in soil model corrected (calculation of m_total was not initialized with zero). (land_surface_model_mod.f90)
14/07/16	AH	r1965	4.0	B	Bug in vertical nesting mode corrected. (init_pegrid)
13/07/16	MS	r1962	4.0	B	Typo in error message removed. (check_parameters)
12/07/16	MS	r1960	4.0	N, B	New Humidity and passive scalar are treated separately, i.e. both can be applied simultaneously. (surface_layer_fluxes_mod, swap_timelevel, modules, advec_s_bc, user_spectra, init_3d_model, boundary_conds, plant_canopy_model_mod, data_output_spectra, netcdf_interface_mod, data_output_3d, prognostic_equations, read_var_list, spectra_mod, palm, flow_statistics, sum_up_3d_data, advec_ws, data_output_dvrp, init_1d_model, data_output_mask, time_integration, check_parameters, user_actions, inflow_turbulence, average_3d_data, header, parin, data_output_2d, virtual_flight_mod) Bugfix Labeling of space-time series concerning flight measurements. (virtual_flight_mod)
07/07/16	MS	r1959	4.0	N	Input and output files for flight measurements added. (.mrun.config.*)
07/07/16	MS	r1957	4.0	N	New module for virtual flight measurements (for further information, see flights). (check_open, header, data_output_flight, init_3d_model, Makefile, modules, netcdf_interface_mod, parin, read_var_list, time_integration, user_init_flight, user_flight, virtual_flight_mod, write_var_list)
01/07/16	AH	r1956	4.0	B	Bugfix, intializating_actions is set to 'set_constant_profiles' for all nest domains in order to make sure that diagnostic variables are properly initialized for nest domains. Prognostic variables are later initialized by interpolation from the parent domain. User may now leave intializating_actions undefined for nest domains.
21/06/16	MS	r1953	4.0	B	Bugfix, lad_s and lad must be public. (plant_canopy_model_mod)
20/06/16	MS	r1951	4.0	B	Bugfix in example initialization of user-defined canopy. (user_init_plant_canopy)
17/06/16	BM	r1949	4.0	B	Bugfixes for output of land surface model quantities and in the calculation of the soil evaporation in case of precipitation. (land_surface_model_mod.f09, sum_up_3d_data.f90)
15/06/16	MS	r1946	4.0	B	Bugfix dependency init_grid on advec_ws. (Makefile)
15/06/16	SR	r1944	4.0	N	Adjustments for using HLRN ssh-keys. If a specific keyfile shall be used, a line like %ssh_key id_rsa_hlrn lccrayh parallel has to be added to the configuration file. The files named id_rsa_hlrn and id_rsa_hlrn.pub are expected to be in folder $HOME/.ssh. (mbuild, mrun, subjob)
14/06/16	MS	r1942	4.0	N, C	New Topography filter implemented to fill holes resolved by only one grid point. (init_grid) Changed Initialization of flags for ws-scheme moved to advec_ws. (advec_ws, init_grid)
13/06/16	AH	r1939	4.0	B	Correction of dependency errors in Makefile that appeared in r1935. (Makefile)
13/06/16	MS	r1936	4.0	N	Deallocation of unused particle memory. (lpm, lpm_exchange_horiz, mod_particle_attributes, package_parin) Formatting adjustments. (lpm, lpm_advec)
13/06/16	AH	r1935	4.0	N, C	Introduction of the initial version of purely vertical nesting. Cleaning up of the pmc-code. Words server and client are systematically replaced by parent and child. Source-code files pmc_server_mod.f90 and pmc_client_mod.f90 are renamed as pmc_parent_mod.f90 and pmc_client_mod.f90. (pmc_child_mod, exchange_horiz, pmc_parent_mod, parin, init_pegrid, time_integration, palm, exchange_horiz_2d, boundary_conds.f90, pres, pmc_interface_mod, pmc_general_mod, pmc_mpi_wrapper_mod, pmc_handle_communicator_mod, Makefile)
10/06/16	MS	r1931	4.0	C	Rename subroutine poismg into poismg_noopt, as well as poismg_fast_mod into poismg_mod. (poismg_mod, poismg_noopt, Makefile) Rename multigrid into multigrid_noopt and multigrid_fast into multigrid, cpu-measures are renamed respectively. (check_parameters, cpulog_mod, header, init_grid, pres, poismg_mod, poismg_noopt).
09/06/16	MS	r1929	4.0	B, C	Bugfixes: Vertical logarithmic interpolation of particle speed above topography. (lpm_advec, lpm_init) Particle exchange between PEs. (lpm_exchange_horiz) Horizontal particle boundary conditions in serial mode. (lpm_exchange_horiz) Initial particle height and grid index in case of seed_follows_topography. (lpm_init) Particle random start positions, ensure that particles do not move more than one grid length. (lpm_init) Initial call of pres. (pres) Avoid segmentation fault in case one grid point is horizontally completely surrounded by topography. (surface_layer_fluxes_mod) Preprocessor directives for parallel and serial mode. (wind_turbine_model_mod) Check for use_upstream_for_tke. (check_parameters) Changes: Particle wall reflection rewritten. (lpm, lpm_boundary_conds) Stochastic equation for subgrid-scale particle speed is put into an extra subroutine. Moreover, near topography, memory and drift term in stochastic equation are disabled. (lpm_advec) Unused variables removed. (lpm_exchange_horiz)
07/06/16	AH	r1928	4.0	N, B	Error check for overlapping parallel nests added (pmc_interface.f90). Nesting synchronization is moved before CALL run_control, and exchange_horiz for pt after CALL pmci_datatrans is now only called if ( .NOT. neutral ) in time_integration.f90.
02/06/16	HK	r1924	4.0	B	Updated example_cbl_rc test case to reflect output changes made in r1918. (example_cbl_rc)
31/05/16	LB	r1922	4.0	B	Bugfix: array transposition checks are now restricted to cases if a fourier transform is used. Removed unused variable nnx_z. (init_pegrid)
30/05/16	MS	r1920	4.0	C	Avoid segmentation fault (see change in 1915) by different initialization of us instead of adding a very small number in the denominator. (init_3d_model, surface_layer_fluxes_mod)
27/05/16	SR	r1918	4.0	C, B	Changed: Ocean mode now uses initial density profile as reference in the buoyancy term. (check_parameters) Steering of pres modified. (init_3d_model, pres) Bugfixes: for calculating run control quantities: wrong divergence at timestep 0, wrong velocity extrema for timestep 1, wrong perturbation energy for timestep 0, time step length was lagged by one time step. (flow_statistics, init_3d_model, modules, pres, time_integration) In case of Neumann conditions for pressure both at bottom and top, mean vertical velocity is now also removed for the first time step. (pres)
27/05/16	BW	r1917	4.0	B	Removed misleading change comments (relicts from branch/forwind) in the file headers and added new change comment for the release of the wind turbine model in r1914 (Makefile, check_parameters, init_3d_model, package_parin, parin, prognostic_equations, time_integration, wind_turbine_model_mod).
27/05/16	MS	r1915	4.0	B	Avoid segmentation fault in case of most_method = 'circular' at first timstep. (surface_layer_fluxes_mod)
26/05/16	BW	r1914	4.0	N	Merged branch/forwind into trunk. Release of the preliminary version of the wind turbine model (WTM) (Makefile, check_parameters, init_3d_model, package_parin, parin, prognostic_equations, time_integration, wind_turbine_model_mod). The WTM calculates the effect of wind turbines on the flow field. The initial version contains only the advanced actuator disk with rotation method (ADM-R). The wind turbines include the tower effect, can be yawed and tilted. The wind turbine model includes controllers for rotational speed, pitch and yaw. Currently some specifications of the NREL 5 MW reference turbine are hardcoded whereas most input data comes from the external file WTM_DATA. Example case for the WTM created (trunk/EXAMPLES/wind_turbine)
26/05/16	SR	r1910	4.0	B	If topography is read from file, Neumann conditions are used for the nzb_local array (instead of cyclic conditions) in case that non-cyclic boundary conditions are switched on for the run. (init_grid)
25/05/16	MS	r1908	4.0	C	Calculate new divergence only at last Runge-Kutta step. (pres)
24/05/16	MS	r1906	4.0	C	Default value of mg_switch_to_pe0_level changed to -1, i.e. no gathering on PE0 at all. (modules)
11/05/16	MS	r1904	4.0	B	Bugfix: enable special_exchange_horiz only for finer grid levels. (poismg_fast_mod)
09/05/16	MS	r1902	4.0	C	Consider masking_method only for multigrid solver, not for multigrid_fast. (header, init_grid)
04/05/16	SR	r1900	4.0	C	Re-formatting of the remaining pmc routines to PALM style. File pmc_general.f90 has been renamed pmc_general_mod.f90. (Makefile, pmc_general_mod, pmc_handle_communicator_mod, pmc_interface_mod, pmc_mpi_wrapper_mod, pmc_server_mod)
03/05/16	MS	r1898	4.0	B, C	Bugfixes: bottom and top boundary condition for residual. (poismg_fast_mod) Changes: remove parts where topography via flags is considered. (poismg_fast_mod) Formatting adjustments; variable descriptions added in some declaration blocks. (poismg_fast_mod)
03/05/16	SR	r1896	4.0	C	Re-formatting to match PALM style. (pmc_client_mod)
27/04/16	SR	r1895	4.0	B	pt is not set as a data array in case that the temperature equation is switched off with neutral = .TRUE., and pt-inter- and anterpolations are omitted as well. (pmc_interface_mod)
22/04/16	FH	r1890	4.0	C	Some changes necessary for the consideration of aerosols in the LCM (lpm_init, lpm_droplet_condensation).
21/04/16	MS	r1888	4.0	B	Bugfix concerning logarithmic interpolation of particle speed (lpm_advec).
21/04/16	MS	r1886	4.0	B	Fixed bugs concerning advection flags near walls (init_grid). Additionally, variable descriptions were added in declaration block (init_grid).
21/04/16	FH	r1884	4.0	C	Conservation of mass is only checked if droplet collisions took place (lpm_droplet_collision).
20/04/16	AH	r1883	4.0	C	Precomputation of ijfc needed in pmci_anterp_tophat is added to pmci_init_anterp_tophat in pmc_interface_mod.f90. MPI_BCAST-calls to broadcast nesting_mode and nesting_datatransfer_mode are oved out from the DO i = 1, m_ncpl loop in pmc_handle_communicator_mod.f90. Files changed: pmc_interface_mod.f90 and pmc_handle_communicator_mod.f90.
20/04/16	FH	r1880	4.0	B	Bugfix: The index of the larger particle has to be chosen for interpolation of collection efficiencies and their turbulent enhancement factor (lpm_collision_kernels).
19/04/16	AH	r1878	4.0	C	New simpler synchronization for nested runs. Nesting related logc-arrays's index order changed for better cache utilisation. Removal of the zeroth element of the small array weight_pres as it is has become obsolent. Files changed: pmc_interface_mod.f90, time_integration.f90 and init_3dmodel.f90.
18/04/16	BM	r1873	4.0	C	Revised file naming convection introduced in r1850 (several "_mod.f90" files).
15/04/16	FH	r1871	4.0	N, C	A subroutine for initializing aerosol spectra has been added to lpm_init_mod. The dry aerosol radius is now explicitly considered in lpm_droplet_condensation. The aerosol spectrum is assumed to consist of up to 3 log-normal distributions, which can be steered by the parameters n1, n2, n3, s1, s2, s3, rm1, rm2, rm3. A probabilistic initialization can be chosen by setting the logical init_aerosol_probabilistic to true, otherwise the predefined aerosol spectrum is divided into logarithmically spaced bins and the weighting factor is calculated based on the number of aerosol within each bin. monodisperse_aerosols initializes a monodisperse aerosol spectrum with a dry radius of 0.1 micron. Necessary changes in package_parin, mod_particle_attributes, and Makefile.
14/04/16	FH	r1862	4.0	B	In case of vector machine optimized model runs, sums_ls_l should not be addressed if large_scale_forcing is false because sums_ls_l is not allocated (subsidence_mod).
13/04/16	FH	r1858 and r1860	4.0	C	Interpolation of collection kernel adjusted to more reasonable values. Reformatting of code. (lpm_collision_kernels_mod, lpm_droplet_collision)
13/04/16	BM	r1856	4.0	B	Bugfixes: PALM crashed when using radiation_scheme = 'clear-sky' due to missing allocation of rad_lw_out. (radiation_model_mod) The land surface model produced instabilities when prescribing water surfaces (radiation_model_mod)
11/04/16	BM	r1853	4.0	B	Bugfix: PALM crashed when using radiation_scheme = 'constant' in combination with the land surface model due to the fact that no outgoing longwave radiative flux was calculated at the surface, but required in the energy balance solver. (flow_statistics, time_integration, radiation_model_mod)
08/04/16	BM	r1850	4.0	B,C	Bugfixes: removed misplaced ":" in Makefile. (Makefile) Changes: Renamed several files according to the module naming convention. This implied adding the string "_mod" to those files.
08/04/16	FH	r1849	4.0	C	lpm_droplet_condensation: no interpolation of supersatuartion (lpm_droplet_condensation) mod_particle_attributes: several variables which only affect the LPM are moved from modules to mod_particle_attributes (mod_particle_attributes, modules). several changes for the modularization of microphysics (Makefile, data_output_2d, data_output_3d, diffusion_e., flow_statistics, header, init_3d_model, init_cloud_physics, land_surface_model_mod, microphysics, modules, parin, radiation_model_mod, read_3d_binary, read_var_list, sum_up_3d_data, time_integration, timestep, write_3d_binary, write_var_list)
08/04/16	SR	r1845	4.0	C	Array nzb_2d replaced by arrays nzb_s|u|v_inner. (init_3d_model, init_grid, interaction_droplets_ptq, microphysics, modules, pres) Kessler precipitation is stored on surface grid point (instead of nzb+1). (microphysics)
07/04/16	SR	r1833	4.0	C, B	Changed: Spectra routine spectrum renamed spectra_mod and further modularized. (Makefile, check_parameters, data_output_spectra, header, init_3d_model, init_pegrid, modules, netcdf_interface, package_parin, palm, parin, read_3d_binary, read_var_list, renamed: spectrum to spectra_mod, time_integration, user_parin, user_spectra, write_3d_binary, write_var_list) Bugfix: POINTER-attributes added, and long lines wrapped in coupler-routines to avoid gfortran error messages. (pmc_client, pmc_server)
07/04/16	FH	r1831	4.0	C	drizzle is renamed cloud_water_sedimentation, turbulence is renamed collision_turbulence (data_output_ptseries, diffusion_e, header, init_3d_model, microphysics, modules, package_parin, parin, read_var_list, time_integration, write_var_list). curvature_solution_effects is moved from inipar to particles_par (lpm_droplet_condensation, lpm_init, mod_particle_attributes, package_parin, parin).
07/04/16	BM	r1829	4.0	B	Output of user defined data required reset of the character variable unit. (check_parameters)
07/04/16	BM	r1826	4.0	B,C	Changed: Radiation model and plant canopy model were further modularized. This involved the reading of the NAMELIST &radiation_par/&canopy_par, check parameters, and header output. These actions are now treated in separate subroutines within the respective modules. The files radiation_model.f90 and plant_canopy_model.f90 were renamed to radiation_model_mod.f90 and plant_canopy_model_mod.f90, respectively. Some subroutines of both radiation and plant canopy model were renamed (abbreviation of plant canopy model is now "pcm"). (Makefile, check_parameters, header, init_3d_model, package_parin, parin, plant_canopy_model_mod, prognostic_equations, radiation_model_mod) Some cleanup in land surface model after modularization. (land_surface_model_mod) Added note on usage of document_change for MAS OS. (document_changes in r1826, mbuild by accident) Bugfixes: Fixed check if roughness_length is smaller than dz/2 (check_parameters)
07/04/16	TG	r1824	4.0	N	Check added if roughness_length is smaller than dz/2 (check_parameters)
07/04/16	FH	r1822	4.0	C, B	Changed: lpm_advec: turbulent velocity fluctuations can be used (set use_sgs_for_particles to true), terminal velocity is computed from a parameterization by Rogers et al. (1993) lpm_droplet_collision: a new collision algorithm is available (collision_algorithm='all_or_nothing', 'average_impact' turns on the original algorithm). Additional changes in mod_particle_attributes, package_parin. lpm_collision_kernel: the PALM kernel has been removed. Terminal velocities are also computed by the parameterization of Rogers et al. (1993) (analogously to lpm_advec). microphysics: Kessler bulk microphysics are not integrated in microphyics (i.e., calc_precipitation and impact_of_latent_heat are deleted). Microphysics can be steered via cloud_scheme with the following options: 'saturation_adjust' is a simple saturation adjustment scheme without precipitation, 'kessler' turns on the (one-moment) precipitation parametrization by Kessler (1996), 'seifert_beheng' the (two-moment) precipitation parameterization by Seifert and Beheng (2006). Additional changed in: advec_ws, boundary_conds, check_parameters, data_output_2d, data_output_3d, flow_statistics, header, init_3d_model, init_cloud_physics, init_masks, prognostic_equations, surface_layer_fluxes, swap_timelevel, time_integration, user_actions, write_3d_binary. several routines of the LPM (Lagrangian particle model): Tails are now removed [lpm, lpm_advec, lpm_boundary_conds.f90, lpm_calc_liquid_water_content, lpm_data_output_particles, lpm_exchange_horiz, lpm_extend_tail_array (deleted), lpm_extend_tails (deleted), lpm_init, lpm_init_sgs_tke, lpm_pack_arrays, lpm_read_restart_file, lpm_set_attributes, lpm_write_exchange_statistics, lpm_write_restart_file, data_output_dvrp]. lpm_release_set: Has been removed and directly integrated into lpm_init. Bugfixes: Calculation of the turbulent enhancement factor of collection efficiency is corrected (lpm_collision_kernels).
06/04/16	BM	r1817	4.0	C, B	Changed: The land surface model (lsm) was further modularized. This involved the reading of the NAMELIST &lsmpar, check parameters, and header output. These actions are now treated in separate subroutines within the lsm module. The file land_surface_model.f90 was renamed to land_surface_model_mod.f90. Some subroutines of the lsm were renamed. (Makefile, check_parameters, header, init_3d_model, land_surface_model_mod, package_parin, parin) Bugfixes: Copyright statement updated for most files. (r1818) Removal of the parameter file check completed in mbuild (mbuild).
06/04/16	SR	r1815	4.0	C, B	Changed: Comment change. (advec_s_bc) cpp-directives removed. (fft_xy, flow_tatistics, init_pegrid, modules, tridia_solver) Zero-settings for velocities inside topography re-activated (was deactivated in r1762). (init_3d_model) Bugfixes: Preprocessor directives included for the non-parallel case. (spectrum)
05/04/16 - 06/04/16	BM	r1810,r1813	4.0	C	The tool for moving comments from "Current revisions" to "Former revisions" now works on all subdirectories. Moreover, the copyright statement in the file headers is automatically updated (document_changes).
05/04/16	SR	r1808	4.0	C	Preprocessor directives using machine dependent flags (__lc, __ibm, etc.) mostly removed from the code. In particular: cpu measurements are done with standard FORTRAN routine on every machine. (cpulog, local_tremain_ini, local_tremain, combine_plot_fields) Routine local_flush replaced by FORTRAN statement. (Makefile, header, init_1d_model, init_coupling, message, palm, progress_bar, run_control, deleted: local_flush) Routine local_getenv replaced by standard FORTRAN routine. (Makefile, init_dvrp, deleted: local_getenv) MPI module used by default on all machines. (modules, pmc_client, pmc_general, pmc_handle_communicator, pmc_interface, pmc_mpi_wrapper, pmc_server, spectrum) Test output removed. (data_output_3d, read_3d_binary, read_var_list, time_integration, tridia_solver)
05/04/16	TG	r1806	4.0	B,C	Bugfixes: Added check for number of PE in y direction if recycling_yshift is used (inflow_turbulence, check_parameters) Changes: Added comments and removed redundancies in inflow_turbulence
05/04/16	BM	r1804	4.0	C	Changes: Parameter file check (for the NAMELIST files) was removed (mbuild, mrun, check_open, check_parameters, exchange_horiz, exchange_horoz_2d, init_grid, init_masks, init_pegrid, local_stop, modules, parin, poisfft, tridia_solver, user_statistics, mainwindow.cpp, mainwindow.ui). mrungui was updated to work with qt5 (main.cpp, mainwindow.cpp, mrungui.pro). notification about alpha version removed from document_changes tool (document_changes).
05/04/16	SR	r1801	4.0	B	Bugfix for r1797: zero setting of temperature within topography does not work and has been disabled. (pmc_interface)
05/04/16	TG	r1799	4.0	B	Bugfixes: Bugfixes for user defined timeseries and conserve_volume_flow (user_init, pres).
21/03/16	SR	r1797	4.0	N, C	New: Introduction of different data transfer modes in nested runs. (pmc_client, pmc_handle_communicator, pmc_interface. pmc_server, time_integration) Restart mechanism adjusted for nested runs. Parameter consistency checks between root and client model settings, e.g. end_time must have the same value for all models. (Makefile, check_for_restart, pmc_handle_communicator, pmc_interface) Changes: Further formatting cleanup. (pmc_interface)
18/03/16	SR	r1795	4.0	B	Setting of initial scalar profile in ocean runs. (check_parameters)
11/03/16	SR	r1791	4.0	N, C, B	New: Output of nesting informations of all domains. (Makefile, header) Changes: Debug-printouts commented out. Some variable-, keyword- and subroutine names renamed. Formatting cleanup. (pmc_client, pmc_handle_communicator, pmc_interface, pmc_server) Bugfixes: Filling up redundant ghost points introduced. As a result, call of routine pmci_update_new is not required any more. (pmc_interface, time_integration)
10/03/16	BM	r1788	4.0	B, C, N	Changes in land surface model: dewfall was removed and can no longer be switched off (land_surface_model, package_parin, header). Bugfixes in land surface model: Calculation of the skin heat conductivity is now based on temperature gradient between skin layer and soil layer instead of the atmospheric stability (Obukhov length) (land_surface_model). New: Simple Charnock-parameterization of water surfaces (lakes, ocean) as in the ECMWF model. The parameterization assumes that the sea surface temperature is constant in time (can be changed in user-interface). Roughness lengths for heat, moisture, and momentum then depend on the wind speed and are calculated as a function of the friction velocity (waves increase roughness). The parameterization required to introduce a separate roughness length for moisture (z0q (check_parameters, data_output_2d, init_3d_model, land_surface_model, modules, package_parin, radiation_model, read_3d_binary, sum_up_3d_data, surface_layer_fluxes, write_3d_binary). A new land surface and albedo type for paved surfaces was added to allow for prescribing e.g. asphalt concrete surfaces. The pavement depth, heat capacity and conductivity can be explicitly prescribed. Dry soil under the pavement is assumed. Moreover, evaporation of liquid water (due to precipitation) is considered from paved surfaces (land_surface_model, radiation_model, package_parin).
08/03/16	SR	r1786	4.0	C, B	Changes: The spectra-package has been modularized. Creating spectra-output does not require to set the cpp-switch __spectra any more. (Makefile, check_parameters, data_output_spectra, header, modules, package_parin, time_integration, Deleted: calc_spectra, New: spectrum) Change in client-server data transfer: server now gets data from client instead that client put's it to the server. (pmc_client, pmc_general, pmc_server) Bugfixes: id_var_time_sp made public. (netcdf_interface) nesting_mode is broadcast now. (pmc_handle_communicator)
06/03/16	SR	r1783	4.0	N, C, B	New: New d3par-parameter netcdf_deflate for compression of NetCDF4/HDF5 data. Changes: The PALM-NetCDF-routines have been modularized. Therefore, the old file netcdf.f90 has been renamed to netcdf_interface.f90, which now forms the new NetCDF-module. The variables from the old data module netcdf_control within modules.f90 have been moved to this new module. Recurring code sniplets for creating a dimension or variables in NetCDF are separated in subroutines, following a suggestion of Stefan Albensöder (see ​ticket#214). Attention: The required user interface version changed to r1783. (Makefile, check_open, check_parameters, close_file, data_output_2d, data_output_3d, data_output_mask, data_output_profiles, data_output_ptseries, data_output_spectra, data_output_tseries, flow_statistics, header, init_3d_model, init_masks, land_surface_model, lpm_data_output_particles, lpm_exchange_horiz, lpm_init, lpm_release_set, modules, palm, parin, radiation_model, read_var_list, time_integration, user_check_data_output_pr, user_init, user_parin, user_statistics, write_var_list, Deleted: netcdf, New: netcdf_interface) Further changes concerning the PMC: Calculation of nest top area simplified. Interpolation and anterpolation moved to seperate wrapper subroutines. (pmc_interface) Bugfixes: Wrong data-type in MPI_WIN_CREATE replaced. (pmc_client)
03/03/16	SR	r1781	4.0	C	Further changes concerning the PMC: _p 3d-arrays are set zero within buildings too, t.._m arrays and respective settings of them within buildings have been completely removed. (pmc_interface) Some pmc calls removed to the beginning (before timeloop). (time_integration) pmc initialization moved from time_integration to the main program. (palm, time_integration)
03/03/16	SR	r1779	4.0	C,B	Changes: Some changes within the PMC: Array management changed from linked list to sequential loop. (pmc_client, pmc_general, pmc_interface, pmc_server) Total number of PEs is given instead of npex/npey in the $nestpar-NAMELIST. Every model calculates its virtual PE grid in the standard way. (Makefile, init_pegrid, pmc_handle_communicator, pmc_interface) The coupling character string appended to files is extended to LEN=3 in order to allow using more than 10 coupled models. Therefore, filenames end now with _02, _03, etc. (check_open, init_grid, init_pegrid, modules) Setting of nest_domain and coupling_char moved from main program to pmci_init. (palm, pmc_interface) KIND=dp replaced by wp. (pmc_client, pmc_mpi_wrapper, pmc_server) dim_order removed from TYPE arraydef. (pmc_client, pmc_general, pmc_server) PMC_MPI_REAL removed. (pmc_general) Error messages removed or changed to PALM style. (pmc_server) MPI_DOUBLE_PRECISION replaced by MPI_REAL. (pmc_mpi_wrapper) Two unused elements removed from array define_coarse_grid_real. (pmc_interface) Some preliminary changes in mrun, checked in by mistake: ROPTS removed from execution commands. Warnings about missing optional files or user code changed to informative messages. (mrun) Bugfix: Internal procedure names in interaction_droplets_ptq shortened to avoid Intel compiler warnings about too long names. (interaction_droplets_ptq)
02/03/16	FH	r1776	4.0	B	Collection efficiencies have to be calculated for the larger droplet (lpm_collision_kernel).
29/02/16	SR	r1767	4.0	N	The pmc runs with PALM's pointer version now. (Makefile, pmc_general, pmc_interface, pmc_server, swap_timelevel)
28/02/16	SR	r1765	4.0	C, B	Several changes (mainly concerning code formatting and code internal structure) of the nested domain system. Changed: PMC_ACTIVE preprocessor flags have been completely removed, instead _parallel flags were added to the pmc_-routines because nesting requires MPI. MPI-datatype settings (REAL8) and kind-settings adjusted to PALM-style domain layout is read with new NAMELIST nestpar from standard file PARIN. New variable domain_layouts is used instead of m_couplers in the nestpar-NAMELIST output of (some) nesting informations to the RUN_CONTROL-header PALM error messages include the domain-id location messages added (which appear at the terminal or in the jobfile), they are only created from PE0 of the root domain nesting info (domain-id) has been added to the run-identifier string some error messages were made PALM conform (subroutine message is used) in case of a nested run, boundary conditions (nested or neumann) for bc_lr0}}, {{{bc_ns, bc_p_t, bc_uv_t, and bc_pt_t are explicitly set in subroutine parin and overwrite settings done by the user in the $inipar-NAMELIST (Makefile, check_parameters, header, init-pegrid, local_stop, message, modules, palm, parin, pmc_client, pmc_general, pmc_handle_communicator, pmc_interface, pmc_mpi_wrapper, pmc_server, time_integration) Bugfixes: Index bugfixes. (pmci_interp_tril_all) Nest synchronization after first call of timestep. (time_integration) Checks of bc_lr and bc_ns boundary conditions moved from check_parameters to parin. Checking them in check_parameters0}} is wrong, because they are already used in {{{init_pegrid and init_grid (which are called before check_parameters). (check_parameters, parin) Index bug for u_p at left outflow removed. (boundary_conds) Increase array-size of volume_flow_area_l and volume_flow_initial_l by 1. (init_3d_model)
25/02/16	AH	r1763	4.0	N	New: Implementation of the nested domain system. Still under finalization. More detailed description follows later. (Makefile, boundary_conds.f90, check_parameters.f90, exchange_horiz_2d.f90, init_3d_model.f90, init_grid.f90, init_pegrid.f90, modules.f90, palm.f90, parin.f90, poismg.f90, poismg_fast.f90, pres.f90, sor.f90, time_integration.f90, New: pmc_client.f90, pmc_general.f90, pmc_handle_communicator.f90, pmc_interface.f90, pmc_mpi_wrapper.f90, pmc_server.f90)
22/02/16	BM	r1759	4.0	B,C	New: flag parameter unscheduled_radiation_calls can be used to force additional radiation calls if required (e.g. to damp oscillations after switching radiation code on) (land_surface_model.f90, radiation_model.f90, package_parin.f90). Changes: allow for using a higher vertical resolution in nudging file than in LES model (nudging.f90). Added options menu for watchdog (wd.ui) Bugfixes: allocation of RRTMG arrays, initialisation of soil moisture (read_3d_binary.f90, land_surface_model.f90). Changes:
15/02/16	BM	r1751	4.0	B, C	Bugfixes in watchdog: Progress bar shows correct values, crashes when using more than 1 host. Changes in watchdog: Hosts can be switched on/off and update frequency can be set in GUI. Added security check for canceling jobs. (palm_wd, wdoptions.ui, .wd.condig.default, .wd.config.hlrnIII).
09/02/16	SR	r1749	4.0	B, C	Further OpenACC-adjustments for the surface layer parameterization, and one bugfix for the fft-routine. (fft_xy, surface_layer_fluxes)
08/02/16	SR	r1747	4.0	B, C	OpenACC-bugfixes and -adjustments for new surface layer parameterization. (flow_statistics, Makefile, palm, surface_layer_fluxes, swap_timelevel)
05/02/16	TG	r1745	4.0	B	Bugfixes for output via parallel NetCDF: warning if output interval is set to 0.0s; set output interval to fixed time step if a fixed time step is used (check_parameters) assure that PE0 deleted a non-extendible file before any other processor tries to reopen it (check_open) recalculating number of output time levels needed in files in case of restart runs (data_output_2d, data_output_3d, netcdf)
13/01/16	SR	r1743	4.0	B	Bugfix for calculation of nzb_s_outer and nzb_u_outer at north boundary of total domain. (init_grid)
13/01/16	SR	r1742	4.0	B	Bugfix for outflow Neumann boundary conditions at bottom and top. (boundary_conds)
13/01/16	SR	r1740	4.0	C	Unnecessary calculations of kmzm and kmzp removed from wall bounded parts of the code. (diffusion_u, diffusion_v)
18/12/15	SR	r1738	4.0	B	Bugfix for calculations in statistical regions which do not contain grid points in the lowest vertical levels. This was required in order to avoid ill defined data which caused NetCDF output to abort. The mean surface level height is considered now in the calculation of the characteristic vertical velocity. (calc_mean_profile, flow_statistics, init_3d_model, modules)
20/11/15	TG	r1729	4.0	B	Bugfix: when using large scale subsidence in combination with Rayleigh damping the initial profiles has to be shifted only once each time step (subsidence.f90).
20/11/15	HK	r1728	4.0	B	Bugfix: Cause of syntax warning gfortran preprocessor removed (mod_particle_attributes.f90).
17/11/15	FH	r1725	4.0	B	Bugfix: Processor-dependent seed for random function is generated before it is used (lpm_init.f90).
16/11/15	LB	r1723	4.0	C	Added a checkbox in mrungui to activate the cycling fill method (adds the string "cycfill" to mrun flag -r)
16/11/15	SR	r1721	4.0	B	Bugfixes: surface heatflux (shf) is reduced in areas covered with canopy only; canopy is set on top of topography. (plant_canopy_model)
11/11/15	SR	r1717	4.0	B	Bugfix of index error in outflow conditions for left boundary. (boundary_conds)
05/11/15	SR	r1711	4.0	B	Bugfix: loop moved into IF block to avoid usage of l without being defined. (diffusivities)
04/11/15	BM	r1709	4.0	B	Bugfixes: Calculation of Obukhov length and surface momentum fluxes corrected for runs with neutral = .TRUE. Calculation of Richardson number with low wind speeds fixed Restart runs with land surface model and RRTMG fixed Several bugfixes in land surface model Minor bugfix in RRTMG radiation interface Adjusted first time step of 1D model to avoid crashes with fine grid resolution (flow_statistics, init_1d_model, land_surface_model, radiation_model, read_3d_binary, surface_layer_fluxes, write_3d_binary)
02/11/15	BM	r1707	4.0	B	Bugfix: division by zero when initializing the Obukhov length from a 1D precursor run with neutral stratificaiton (init_3d_model).
02/11/15	BM	r1705	4.0	B	Bugfix: output of control parameters corrected (caused crash of restart runs). (write_var_list)
02/11/15	SR	r1703	4.0	B	Bugfix for output of single (*) xy-sections in case of parallel netcdf I/O. (data_output_2d)
02/11/15	BM	r1701	4.0	B	Bugfixes: Output of radiative heat fluxes corrected (check_parameters, data_output_2d) minor bugfix in calculation of sounding data for initialization of RRTMG (radiation_model) added possibility to use %login_init_cmd for lccrayh/lccrayb when compiling on remote host via subjob (subjob)
29/10/15	BM	r1699	4.0	B	Bugfix: binary version updated. (read_var_list)
28/10/15	SR	r1697	4.0	B	FORTRAN and OpenMP errors removed. (surface_layer_fluxes) Misplaced cpp-directive fixed. (land_surface_model) Small E- and F-FORMAT changes to avoid informative compiler messages about insufficient field width. This change affected the timestring format of the RUN_CONTROL file. (header, init_1d_model, print_1d, run_control, example_cbl_rc)
26/10/15	BM	r1695 r1693 r1691	4.0	B,C,N	The subroutine prandtl_fluxes.f90 has been replaced by surface_layer_fluxes.f90. In the course of the revision, new methods to calculate the Obukhov length and the surface fluxes have been introduced. Moreover, several modifications and bugfixes for the coupled atmosphere-land-surface-radiation were checked in (example_cbl_rc Makefile advec_s_bc.f90 average_3d_data.f90 check_parameters.f90 data_output_2d.f90 data_output_3d.f90 data_output_mask.f90 diffusion_s.f90 diffusion_u.f90 flow_statistics.f90 header.f90 init_1d_model.f90 init_3d_model.f90 init_cloud_physics.f90 init_grid.f90 land_surface_model.f90 lpm_advec.f90 lpm_exchange_horiz.f90 lpm_init.f90 microphysics.f90 modules.f90 netcdf.f90 package_parin.f90 parin.f90 prandtl_fluxes.f90 production_e.f90 prognostic_equations.f90 radiation_model.f90 read_3d_binary.f90 read_var_list.f90 sum_up_3d_data.f90 surface_layer_fluxes.f90 time_integration.f90 wall_fluxes.f90 write_3d_binary.f90 write_var_list.f90. Attention: The inipar parameter prandtl_layer has been replaced by the parameter constant_flux_layer. Moreover, the default calculation method of the surface fluxes within the constant flux layer has been changed! New: new module surface_layer_fluxes.f90 added (replaces {prandtl_fluxes.f90}). PALM now offers three methods to derive the surface fluxes that are steered via the inipar parameter most_method: the "old" method (most_method = 'circular', which is the fastest method, but inaccurate) a new method based on the evaluation of the Richardson number to derive the Obukhov length by using a Newton iteration algorithm (most_method = 'newton' accurate, but relatively slow) a new method (new default) based on the evaluation of the Richardson number to derive the Obukhov length using a lookup-table (most_method = 'lookup' accurate, faster than the Newton iteration method, but slightly slower than the old method). Please note that this method cannot be used when the surface roughness (in terms of roughness length) is not homogeneously distributed. Output of radiative heating rates added in case of RRTMG is used as radiation scheme. The radiation tendency for potential temperature is now directly calculated using the heating rates from RRTMG. new NAMELIST parameters: most_method, emissivity, constant_flux_layer, zeta_min, zeta_max Changed: in the course of the implementation of the new surface flux calculations, the following parameters have been changed: rif was removed rif_max and rif_min have been renamed to zeta_max and zeta_min (zeta = z_mo/L with z_mo being the height of the constant flux layer, and L being the Obukhov length limits for zeta_max and zeta_min have been changed to allow better representation of free convection and very stable conditions default values for dissipation_1d and mixing_length_1d were changed to 'detering' and {{{'blackadar'}, respectively. similarity functions for stable conditions has bee altered to allow for very stable conditions The output of the Obukhov length has been revised and is now evaluated as the horizontal average of the 2d field ol(j,i). Bugfix: Minor formatting corrections Calculation of trace gas profiles in RRTMG corrected Prognostic equations for skin temperature in land surface model corrected Calculation of the liquid water path was revised (output is now in kg/m² instead of m)
08/10/15	SR	r1685	4.0	B	Bugfix concerning vertical index calculation for particles in case of ocean runs. TKE is checked for negative values in lpm_advec (so far, only zero values were checked and adjusted to very small positive values). (lpm_advec.f90, lpm_exchange_horiz.f90, lpm_init.f90, lpm_pack_arrays.f90)
08/10/15	HK	r1684	4.0	C	All in-code documentation and description are made doxygen readable. File trunk/DOC/palm2doxygen.connfig has been added and can be used as the doxygen configuration file. (*.f90, palm2doxygen.config)
02/10/15	LB	r1677	4.0	B	Since the bugfix in r1629, the integer arrays wall_flags_0 and wall_flags_00 had to include the ghost points at the PE boundaries. In order to exchange ghost points of 3D integer arrays, the new subroutine exchange_horiz_int was added. (exchange_horiz.f90, init_grid.f90, init_pegrid.f90, modules.f90)
02/10/15	TG	r1675	4.0	B	Corrected a wrong calculation of topography grid levels. The topography height calculated in r1660 differed by one grid level compared to former versions. This is now corrected. (init_grid.f90, header.f90)
25/09/15	SR	r1671	4.0	B	Ghostpoint exchange for array diss in case that sgs velocities are used for particle advection. (time_integration.f90)
23/09/15	SR	r1668	4.0	C	Warning replaced by abort in case of failed user interface check. (palm.f90, user_parin.f90)
23/09/15	SR	r1666	4.0	N	Possible mismatch of current and required user interface revision is checked. (modules.f90, palm.f90, user_parin.f90)
23/09/15	HK	r1664	4.0	C	Update of the URL to the error message documentation to meet the new server structure (message.f90)
21/09/15	SR	r1661	4.0	C	Example run control file updated to current revision. (.../INSTALL/example_cbl_rc)
21/09/15	TG	r1660	4.0	B	Bugfix: Adjusted the definition of topography gird level in case grid stretching starts within the topography. (init_grid.f90, header.f90)
18/09/15	SR	r1658	4.0	B	Temporary reduction variables in the openacc branch are now initialized to zero. (flow_statistics)
17/09/15	SR	r1652	4.0	B, C	Bugfixes: Bugfix in calculation of energy production by turbulent transport of TKE (flow_statistics) Bugfix for terminal output of configuration settings (mbuild) Changed: output of login init commands (mbuild)
15/09/15	HK	r1649	4.0	C	Updated lectures and tutorials for PALM seminar in Hong Kong (exercise_cbl.tex, exercise_cumulus.tex, exercise_topography.tex, final_remarks.tex, fundamentals_of_les.tex, installation.tex, mrun_steering_parameters.tex, ncl.tex, numerics_bc.tex, program_control.tex, user_defined_code.tex).
02/09/15	FH	r1647	4.0	B	Bugfix: Wrong calculation of d_mean now fixed (microphysics.f90).
01/09/15	FH	r1645	4.0	C	Extended and updated version of tutorial: Exercise 3, user interface (exercise_interface.tex).
31/08/15	HK	r1640	4.0	B	Bugfix to match string length with declared LEN=13 in modules.f90.
31/08/15	FH	r1634	4.0	C	Extended and updated version of tutorial on Lagrangian particles (particle_model_cloud_physics.tex).
26/08/15	MS	r1629	4.0	B	Bugfix concerning wall_flags at left and south PE boundaries. (advec_ws)
21/07/15	RH	r1626	4.0	C	Bugfix to plot xy-cross sections in case variables contain only one level (like lwp*_xy, shf*_xy, ...) (cross_sections.ncl).
17/07/15	RH	r1620	4.0	C	Changed: Adjustments for DKRZ machine Mistral (lcbullhh) (.mrun.config.dkrz, mbuild, mrun, subjob).
13/07/15	BM	r1618	4.0	C	Changed: PALM watchdog is now steered via configuration files. palm_wd requires a file .wd.config in the palm working directory, whereas palm_wdd requires the file .wdd.config placed unter $HOME on each remote host to be monitored. Default configuration files have been added (palm_wd, palm_wdd, .wd.config.default, wd.config.hlrnIII, .wdd.config.default, .wdd.config.hlrnIII).
08/07/15	MS	r1615	4.0	N	Enable turbulent inflow for passive_scalar and humidity. (inflow_turbulence, init_3d_model, read_var_list)
08/07/15	BM	r1613	4.0	B,C	Bugfix: compilation of RRTMG as shared library incorporated faulty remove commands (intall_rrtmg). Removed nc2vdf from mbuild (mbuild). Changed: Added new watchdog context menu actions to view the parameter file and the run control file (palm_wd, palm_wdd, mainwindow.ui).
07/07/15	BM	r1611	4.0	N	Deleted: nc2vdf is outdated and no longer needed (batch_nc2vdf, nc2vdf, nc2vdf.config, nc2vdf.ncl). Old hlrn_watchdog is replaced by new palm watchdog (see below) (hrln_watchdog, hlrn_watchdog.kwinrule). New: A new palm watchdog for monitoring queuing systems on remote host added. The watchdog can be started either from mrungui? or by typing palm_wd into the shell. For more information see PALM watchdog (palm_wd, palm_wdd, mainwindow.cpp, mainwindow.h).
03/07/15	BM	r1609	4.0	B,C	Changed: random number for the temporary job directory on lccray is now set identical to the queuing number. (mrun). Bugfix: Compilation without __parallel failed due to missing pre-processor directives. (poismg_fast)
03/07/15	FK	r1608	4.0	B	Two parameters corrected in TUTORIAL file. (mrun_steering_parameters.tex)
29/06/15	BM	r1606	4.0	B	Bugfix: compilation without netCDF failed. (radiation_model, check_parameters)
11/06/15	SR	r1600	4.0	B	Bugfix: openMP threadprivate statement moved after variable declaration. (fft_xy)
29/05/15	SR	r1598	4.0	B	Bugfix for creating hostfile and determining the total number of MPI tasks if run in openmp-mode on one node. (mrun)
21/05/15	TG	r1596	4.0	B	Bugfix in masked data output. Read 'zu_3d' when trying to extend masked data (netcdf.f90).
08/05/15	BM	r1590	4.0	B	Bugfix: definition of character strings requires same length for all elements. This gives an error e.g. when compiling with gfortran (header.f90, land_surface_model.f90, radiation_model.f90).
04/05/15	BM	r1586	4.0	C	Changed: added parameter file check for albedo settings when using RRTMG. Added albedo class for snow surfaces (check_parameters.f90, radiation_model.f90).
30/04/15	BM	r1585	4.0	N	New: added support for the RRTMG radiation code, which is now delivered with PALM and can be linked to the default code either as static or shared library. (LIB/rrtmg/*, Makefile, average_3d_data.f90, check_parameters.f90, data_output_2d.f90, data_output_3d.f90, data_output_mask.f90, flow_statistics.f90, header.f90, init_3d_model.f90, land_surface_model.f90, netcdf.f90, package_parin.f90, prognostic_equations.f90, radiation_model.f90, read_3d_binary.f90, read_var_list.f90, sum_up_3d_data.f90, time_integration.f90, user_init_land_surface.f90, user_init_radiation.f90, write_3d_binary.f90, write_var_list.f90).
15/04/15	MS	r1583	4.0	B	Bugfix: particle advection within Prandtl-layer in case of Galilei transformation. (lpm_advec)
10/04/15	MS	r1580	4.0	B	Bugfix: setting flags for 5th order scheme near buildings. (init_grid) Bugfix: statistical evaluation of scalar fluxes in case of monotonic limiter. (advec_ws)
27/03/15	SR	r1575	4.0	N, C	New: Optimized version of the multigrid solver has been installed. Data along the k index (vertical direction) is sorted from alternate even and odd indices into two blocks of completely even and odd indices respectively, which allows vectorization on INTEL processors of loops in the red/black scheme. Additionally, topography flags are completely ignored (i.e. not used) in case of masking_method switched on. On fine grid levels only even or odd data are send for the lateral ghost point exchange. Speedup of the multigrid solver for medium sized cases (1024*1024*192 gridpoints) can be about 40%. ATTENTION: There are still small differences observed between the optimised and non-optimised version in case of topography with masking methid switched on. (calc_spectra, check_parameters, header, init_3d_model, init_grid, init_pegrid, modules, new: poismg_fast, pres, Makefile) New parameter seed_follows_topography implemented, which allows to set initial particle heights relative to a given topography. (header, lpm_init, mod_particle_attributes, package_parin) Changed: Queue adjustment for HLRN system. (subjob)
23/03/15	MS	r1573	4.0	B	Bugfix: check for advection schemes in case of non-cyclic boundary conditions. (check_parameters)
12/03/15	BM	r1571	4.0	B	Minor bugfixes in land surface model and radiation model (flow_statistics, land_surface_model, radiation_model).
12/03/15	SR	r1569	4.0	B	Bugfix for background communication. (exchange_horiz)
10/03/15	MS	r1567	4.0	B	Bugfixes in monotonic limiter. (advec_ws) Reverse changes for statistical evaluation of vertical fluxes for monotonic limiter. (flow_statistics)
09/03/15	MS	r1565	4.0	B	Refine if-clause for setting nbgp. (init_pegrid)
09/03/15	RH	r1563	4.0	B	REAL constants provided with KIND-attribute in call of intrinsic function like MAX and MIN (advec_ws.f90).
06/03/15	MK	r1561	4.0	N	New control parameter recycling_yshift, that allows for a y shift of the recycled inflow turbulence (header.f90, inflow_turbulence.f90, modules.f90, parin.f90, read_var_list.f90).
06/03/15	RH	r1559	4.0	B	Allow using NCL version 6.2.1 and higher. Backward compatibility is also ensured. (cross_sections.ncl, profiles.ncl, spectra.ncl, timeseries.ncl)
05/03/15	MS	r1557	4.0	N	Enable monotone advection for scalars using monotonic limiter. (advec_ws, check_parameters, flow_statistics, header, init_grid, init_pegrid, modules)
04/03/15	BM	r1555	4.0	C	Added output of aerodynamic resistance (r_a) and soil resistance (r_s) (timeseries, xy-section). Renumbering of LSM-related PA messages.
03/03/15	BM	r1553	4.0	C	Small adjustments in land surface model.
03/03/15	BM	r1551	4.0	B, C, N	Final version of the land surface model (LSM) released. The LSM comes with a simple clear-sky radiation model for the net radiation at the surface (for details see r1551) (Makefile, average_3d_data, check_open, check_parameters, data_output_2d, data_output_3d, flow_statistics, header, init_3d_model, land_surface_model, modules, netcdf, package_parin, prandtl_fluxes, radiation_model, read_3d_binary, read_var_list, sum_up_3d_data, swap_timelevel, time_integration, user_data_output_2d, user_data_output_3d, user_header, write_3d_binary, write_var_list, combine_plot_fields) For a description of the LSM, see Land surface model and &lsm_par. For a description of the clear-sky radiation model, see radiation model and &radiation_par.
30/01/15	MS	r1550	4.0	N	Enable interactive debug sessions with allinea debugger (mrun)
29/01/15	BW	r1548	4.0	C, N	adjustments for ForWind cluster lcflow (mbuild, mrun, subjob, .mrun.config.forwind_flow, .mrun.config.forwind_hlrnIII)
29/01/15	RH	r1546	4.0	C	Local host name for blizzard further specified (subjob).
28/01/15	FH	r1543	4.0	C	Small changes in exercise on bulk cloud physics (exercise_cumulus.tex).
28/01/15	FK	r1542	4.0	C	Updated some run examples, with corresponding steering parameters in INPUT file and RUN_CONTROL output (trunk/EXAMPLES/building, trunk/EXAMPLES/topo_file).
28/01/15	FK	r1541	4.0	C, N	Updated tutorial files, new figures added, old figures deleted (topography.tex, exercise_topography.tex).
28/01/15	SR	r1540	4.0	N	Release 4.0 created.
28/01/15	SR	r1539	4.0	C	Version update to 4.0 (palm)
27/01/15	FH	r1538	3.10	C	New figures for exercise on bulk cloud physics (exercise_cumulus.tex).
27/01/15	FH	r1537	3.10	C	Exercise on bulk cloud physics updated (exercise_cumulus.tex).
27/01/15	RH	r1534	3.10	C	Exercise on convection between plates and neutral boundary layer flow updated (exercise_cbl.tex, exercise_neutral.tex).
26/01/15	FH	r1533	3.10	C	Exercise on bulk cloud physics updated (exercise_cumulus.tex).
26/01/15	FH	r1532	3.10	C,N	Updated tutorials on NCL and the particle model (with cloud physics) (ncl.tex, particle_model_cloud_physics.tex). New exercise on bulk cloud physics (exercise_cumulus.tex).
26/01/15	MK	r1531	3.10	C	Several updates in the tutorial (basic_equations.tex, final_remarks.tex, non_cyclic_boundary_conditions.tex, parallelization.tex, perf_4.png, program_structure.tex, user_defined_code.tex).
22/01/15	FH	r1528	3.10	B	Bugfix: palmplot pr can now handle *pr.nc files consisting exclusively of user profiles (profiles.ncl).
22/01/15	MK	r1526	3.10	C	Several updates in the tutorial (fundamentals_of_les.tex, header_HANDOUT.tex, header_LECTURE.tex, header_WEB.tex, surface_bc.png, runs_with_mrun.tex, sgs_models.tex).
14/01/15	MK	r1524	3.10	B	Bugfix: dots_time_count is now incremented after the call of subroutine check_open. (data_output_tseries.f90) Typo corrected. (read_var_list.f90)
14/01/15	MK	r1522	3.10	N	Added queries for checking if the advection schemes for momentum and scalar quantities in a restart run are the same as the advection schemes used in the corresponding initial run. (read_var_list.f90)
08/01/15	FH	r1519	3.10	B	Bugfix: For the computation of collision efficiencies, it is necessary that the ratio of radii is smaller than one. Due to the new particle structure, this is not ensured by the order of particles (sorting of particles is not necessary for the new particle structure). (lpm_collision_kernels.f90)
07/01/15	FH	r1517	3.10	B	Bugfix: Bott-Chlond scheme is available again (Makefile, advec_s_bc, prognostic_equations)
02/01/15	LB	r1516	3.10	N	Added two new figures to the tutorial
02/01/15	LB	r1515	3.10	C	Several updates in the tutorial (atmosphere_ocean_coupling.tex, canopy_model.tex, cloud_physics.tex, debugging.tex, exercise_cbl.tex, exercise_interface.tex, exercise_neutral.tex, exercise_topography.tex, final_remarks.tex, mrun_data_analysis.tex, mrun_steering_parameters.tex, ncl.tex, non_cyclic_boundary_conditions.tex, numerics_bc.tex, ocean_version.tex, parallelization.tex, particle_model_cloud_physics.tex, program_control.tex, program_structure.tex, restarts_with_mrun.tex, runs_with_mrun.tex, topography.tex, user_defined_code.tex)
19/12/14	RH	r1514	3.10	B	Bugfix: provide REAL constants with _wp in call of MAX and MIN. (land_surface_model)
16/12/14	MS	r1512	3.10	B	Bugfix concerning spectra normalization. (calc_spectra)
16/12/14	RH	r1510	3.10	B	Bugfix: Prevent infinite loop in case of automatic restarts. (check_for_restart)
10/12/14	MS	r1508	3.10	B	Bugfix: Set horizontal velocity components to zero inside topography. (init_3d_model)
03/12/14	FK	r1502	3.10	B,C	Changed/Bugfix: Canopy module and parameters removed, since parameters are always read from canopy_par NAMELIST for initial and restart runs. (read_var_list, write_var_list) At the same time, this is a bugfix, since 1d-array lad in read_var_list was not allocated yet at the call of read_var_list. Bugfix: Added blanks in "cloud_top_radiation"-string to fill the string to a total of 30 characters. (write_var_list)
03/12/14	BM	r1500	3.10	B,C	Changes for the land surface model: Allow for dry runs with land surface model Added interception of rain fall by plants in the land surface model in case precipiation = .TRUE. (land_surface_model.f90) Bugfixes: Adjustments in Makefile for land surface and radiation models (Makefile) Calculation of aerodynamic resistance in land surface model (check_parameters.f90, land_surface_model.f90)
03/12/14	MS	r1498	3.10	N	Comments concerning statistical evaluation of vertical fluxes and variances added. (flow_statistics)
02/12/14	BM	r1496	3.10	N,C	A beta version of a land surface model (lsm) and a radiation model have been implemented. New: 1) Land surface model: Based on the TESSEL scheme used in the ECMWF IFS model (see ​IFS documentation, with modifications according to H-TESSEL. Implementation was realized similarily to the DALES code. The scheme consists of a solver to the energy balance of the skin layer and a four-layer soil model. Moreover, a liquid water reservoir allows the interception of water by plants. Activated by setting of &lsm_par Namelist. Required parameters for &lsm_par: veg_type = 0-19, soil_type = 0-5, soil_temperature (temperatures for each soil level), Several other optional parameters. A proper documentation will follow. Until then, the lsm should be used for testing purposes only. The implementation is still under construction. Open tasks: Proper calculation of the aerodynamic resistance (solved in r1500) Add support for binary I/O support (solved in r1551) Add support for lsm data output (solved in r1551) Add precipitation to liquid water reservoir (solved in r1571) Consider reaction of plants at wilting point and at atmospheric saturation Consider partial absorption of the net shortwave radiation by the skin layer Allow for water surfaces, check performance for bare soils 2) Radiation model: A simple radiation model for clear sky (no clouds) conditions Provides the net radiation for the energy balance solver of the lsm Activated by setting of &radiation_par Namelist. Required parameters for &radiation_par: lambda (longitude), albedo, day_init (day of the year at model start), time_utc_init (UTC time at model start, in seconds), dt_radiation (temporal interval for the call of the radiation model), latitude is given by the parameter phi in &inipar. Changed: The &inipar parameter radiation has been renamed to cloud_top_radiation as radiation is now used for the radiation model. (Makefile, check_parameters.f90, header.f90, init_3d_model.f90, land_surface_model.f90, modules.f90, package_parin.f90, parin.f90, prandtl_fluxes.f90, prognostic_equations.f90, radiation_model.f90, read_var_list.f90, swap_timelevel.f90, time_integration.f90, user_init_land_surface.f90, write_var_list.f90)
21/11/14	BM	r1494	3.10	B	Minor bugfixes in prandtl_fluxes.f90: Calculation of qs is now done directly after calculation of ts, Missing humidity term in the calculation of Rif added. These modifications will slightly alter simulations with humidity = .TRUE. Added support for topography for large-scale forcing (replaced k index 0-> nzb_s_inner, not tested). (prandtl_fluxes.f90)
12/11/14	FK	r1493	3.10	C	Update of tutorial presentation due to new code structure and steering of the plant canopy model. (canopy_model.tex) For details see r1484.
12/11/14	RH	r1492	3.10	B	bugfix: Correct setting of batch_job allowed for ibm-machines. This fixes a crash of batch jobs due to the output or progress_bar on IBM machines. (mrun)
30/10/14	SR	r1489	3.10	B	bugfix: sums_ls_l must not be used with large_scale_forcing switched off. (subsidence)
25/10/14	SR	r1487	3.10	C	bash compatibility adjustments: output formatting with printf instead of typeset -L/-R, print replaced by echo. (mbuild)
21/10/14	FK	r1484	3.10	N,C,B	Changes due to new code structure of the plant canopy model. All parts of the plant canopy model are now combined within module plant_canopy_model. New: Subroutine init_plant_canopy added to module plant_canopy_model_mod. (plant_canopy_model) Alternative method for lad-profile construction added, also, new parameters added. (header, package_parin, plant_canopy_model, read_var_list, write_var_list) plant_canopy_model-dependency added to several subroutines. (Makefile) New package/namelist canopy_par for canopy-related parameters added. (package_parin) Changed: Code structure of the plant canopy model changed, all canopy-model related code combined to module plant_canopy_model_mod. (check_parameters, init_3d_model, modules, timestep) Module plant_canopy_model_mod added in USE-lists of some subroutines. (check_parameters, header, init_3d_model, package_parin, read_var_list, user_init_plant_canopy, write_var_list) Canopy initialization moved to new subroutine init_plant_canopy. (check_parameters, init_3d_model, plant_canopy_model) Calculation of canopy timestep-criterion removed, instead, the canopy drag is now directly limited in the calculation of the canopy tendency terms. (plant_canopy_model, timestep) Some parameters renamed. (check_parameters, header, init_plant_canopy, plant_canopy_model, read_var_list, write_var_list) Unnecessary 3d-arrays removed. (init_plant_canopy, plant_canopy_model, user_init_plant_canopy) Parameter checks regarding canopy initialization added. (check_parameters) All canopy steering parameters moved from namelist inipar to canopy_par. (package_parin, parin) Some redundant MPI communication removed. (init_plant_canopy) Bugfixes: Missing KIND-attribute for REAL constant added. (check_parameters) DO-WHILE-loop for lad-profile output restricted. (header) Removed double-listing of use_upstream_for_tke in ONLY-list of module control_parameters. (prognostic_equations)
18/10/14	SR	r1482	3.10	N,C,B	New: Adjustments for using CUDA-aware OpenMPI. The local MPI rank is determined from environment variable OMPI_COMM_WORLD_LOCAL_RANK. (palm) Changed: Use 2d-decomposition, if accelerator boards are used. (poisfft) Bugfixes: cudafft workaround for data declaration of ar_tmp because of PGI 14.1 bug. (fft_xy) Information about calculated or predefined virtual processor topology adjusted. (header) Missing ngp_sums_ls added in accelerator version. (flow_statistics)
17/10/14	SR	r1480	3.10	N	Adjustments for 2nd stage of HLRNIII-system: new job-classes mpp1q, mpp1testq, mpp2q, mpp2testq. The Ivy-Bridge- (mpp1) or Haswell-nodes (mpp2) can be selected by including an additional line in the respective block of the .mrun.config-file, e.g.: %feature mpp2 lccrayb parallel (subjob)
24/09/14	BM	r1468	3.10	B,C,N	New: The user can now set two different flag files during the execution of batch jobs (DO_STOP_NOW and DO_RESTART_NOW). DO_STOP_NOW forces the model to terminate properly (this can include the preparation of binary output for restart runs!), whereas DO_RESTART_NOW forces the model to terminate and immediately submits a restart run. The flag files must be created in the temporary directory of the job (e.g. /tmp/user/jobid/). This can be achieved (here to terminate the run) by: touch DO_STOP_NOW A progress file (PROGRESS is now available in the temporary directory of the job. In contains the job name as well as the progress of the running job with respect to the next restart (first value), and to the end_time of the simulation. The file can be used for following the progress of the job and will later be used by a watchdog tool for PALM. Changed: PALM has been adjusted to allow (restart) runs with up to 6-digit processor cores (formely only 4-digit (< 9,999) cores were possible). Adjustments to use lcxe6 as a remote host (transfer of files). Identifier (character) string length for user-defined variables has been increased from 6-10 to 20. Bugfix: Transfer of data and initialization of automatic restart runs was not possible at IMUK due to problems with the shell environment. Typo removed in shell scripts (addres->address)
04/09/14	BW	r1466	3.10	N	Added new configuration file for ForWind jobs on HLRNIII. (.mrun.config.forwind_hlrnIII)
04/09/14	MS	r1462	3.10	B	Bugfix: set dirichlet boundary condition for passive_scalar at model domain top (boundary_conds)
29/08/14	RH	r1456	3.10	C	empty time records in volume, cross-section and masked data output prevented in case of non-parallel netcdf-output in restart runs (check_parameters)
22/08/14	RH	r1453	3.10	C	local hosts for ibmh (blizzard) added (subjob)
21/08/14	RH	r1451	3.10	B	ntnudge increased from 100 to 1000 to allow longer simulations (modules) prevent division by zero at first time-step when calculating large scale forcing statistics (flow_statistics) HLRN-III lccrayb queue adjusted (testq -> mpp1testq) (subjob)
07/08/14	BM	r1448	3.10	B,C	HLRN watchdog adapted for HLRN-III. Blanks removed from <> strings in all .mrun.config files (.mrun.config*, hlrn_watchdog)
02/08/14	ML	r1444	3.10	B	cpulog added to lpm_advec.o (Makefile)
24/07/14	SR	r1440	3.10	C, N	Some configuration files have been adjusted (mainly for compiler options). (.mrun.config.hlrnIII, .mrun.config.imuk, .mrun.config.imuknb, new: .mrun.config.imuk_hlrnIII)
22/07/14	RH	r1439	3.10	N	Mask output for nr, qc and qr added. (init_masks, data_output_mask)
22/07/14	SR	r1437	3.10	C	Contents of example run control file adjusted to current revision. (example_cbl_rc)
21/07/14	MK	r1436	3.10	B	Bugfix: Added missing parameter coupling_mode_remote to ONLY-attribute. (init_pegrid)
18/07/14	MK	r1434	3.10	N	Added new configuration file for the IMUK Linux notebooks. (.mrun.config.imuknb)
15/07/14	MS	r1432	3.10	C	Wavenumber-integrated spectra coincide with respective variance. (calc_spectra, modules, init_3d_model)
15/07/14	HK	r1430	3.10	N	Ensemble run capability added to the new parallel random number generator. By setting the initialization parameter ensemble_member_nr to an integer between 1 and 2000, palm will produce statistically independent members of a simulation. (check_parameters, header, init_3d_model, modules, parin)
07/07/14	BM	r1427	3.10	B	Bugfix in surface_coupler.f90​. Computation of latent heat of vaporization was set for 100° Celsius. (surface_coupler)
05/07/14	HK	r1426	3.10	B	Bugfix for the new parallel random number generator. Each processor is now generating random numbers only for the initial random perturbations in his own subdomain. Additionally some continuation line markers are moved to column 80. (check_parameters, disturb_field)
02/07/14	FK	r1422	3.10	C	Automatic restarts enabled for lccrayb and adjustment of path to compilervars.sh at IMUK (see automatic restarts). (mrun)
10/06/14	SR	r1420	3.10	C	-j1 option added to aprun command for lccrayf (CSC). (mrun)
06/06/14	JF	r1418	3.10	B	Bugfixes concerning grid stretching for the ocean and calculation of the salinity flux in routine surface_coupler (init_grid, surface_coupler)
04/06/14	MS	r1416	3.10	B	Bugfixes concerning new particles structure. (lpm, user_lpm_advec, user_lpm_init)
31/05/14	TG	r1414	3.10	B	Bugfix: First and last grid points as they appear in 3D volume data can now be included to masked data output. (init_masks)
26/05/14	MS	r1411	3.10	C	Initial horizontal velocity fields were not set to zero at the first vertical grid level in case of non-cyclic lateral boundary conditions. (init_3d_model)
23/05/14	MS	r1409	3.10	B	Bugfixes: Set inflow boundary conditions also if no humidity or passive_scalar is used. (boundary_conds) Set wall_flags_0 also at inflow and outflow boundary. (init_grid)
16/05/14	SR	r1406	3.10	B	openACC bugfix for PGI-compiler version 14.4: declare create statement moved behind array declaration. (poisfft, tridia_solver) Setting of initial horizontal velocities to zero at level k=1 only in case of no-slip boundary condition. (init_3d_model)
14/05/14	MK	r1404	3.10	B	Missing dependencies for progress_bar added. (Makefile)
09/05/14	SR	r1402	3.10	N	Output of location messages complemented. Output of progress bar to stdout added (does not appear in batch jobs). (Makefile, check_parameters, cpulog, init_pegrid, init_3d_model, message, palm, parin, time_integration, new: progress_bar) Preprocessor switch __intel_compiler added, -r8 compiler options removed. (.mrun.config.default, .mrun.config.imuk, .mrun.config.kiaps) Variable batch_job added to envpar-NAMELIST. (mrun, parin)
09/05/14	HK	r1400	3.10	N	A parallel random number generator has been added and can be selected by setting the parameter random_generator to 'random-parallel' . (Makefile, check_parameters, disturb_field, init_3d_model, read_3d_binary, write_3d_binary, new: random_generator_parallel) Note: The parallel random number generator is a preliminary feature and still buggy.
07/05/14	RH	r1398	3.10	C/B	Adjustments in case of nudging. u_init and v_init are set to the current nudging profiles. In Rayleigh-damping terms, u_init and v_init are used instead of ug and vg to homogenize the treatment in case of nudging. (boundary_conds, nudging, prognostic_equations) Bugfix: for KIND in CMPLX function (fft_xy)
06/05/14	SR	r1396	3.10	B	copyin clause replaced by update device statement in openACC-branch. (flow_statistics)
06/05/14	MK	r1394	3.10	B	KIND-attribute added to all INTEGER and REAL declaration statements. (combine_plot_fields)
06/05/14	SR	r1392	3.10	B	KIND attribute added to CMPLX functions. (fft_xy)
06/05/14	BM	r1391	3.10	B	Adjustments for compilation on lcxe6 (.mrun.config.lcxe6, mbuild)
05/05/14	LB	r1387	3.10	B	Bugfix: The output of large scale forcing tendencies (td_lsa_lpt|q, td_sub_lpt|q) has been corrected. The tendencies were calculated at the wrong (simulated) time. (flow_statistics.f90)
02/05/14	SR	r1384	3.10	N	Output of location messages to stdout (terminal or job protocol file) in order to allow for a better error detection. Preliminary. Will be further completed / modified in a later version. (check_parameters, init_pegrid, init_3d_model, message, parin, time_integration)
30/04/14	LB	r1383	3.10	C	Renamed variables which store large scale forcing tendencies: pt_lsa -> td_lsa_lpt, pt_subs -> td_sub_lpt, q_lsa -> td_lsa_q, q_subs -> td_sub_q, high|lowpt_lsa -> high|low_td_lsa_lpt, ... (flow_statistics.f90, ls_forcing.f90, modules.f90) Neumann boundary conditions were added to the profile data output of large scale advection, large scale subsidence and nudging terms at nzt+1. (flow_statistics.f90, nudging.f90, subsidence.f90) The weighting factor that is used in the summation of nudging and subsidence tendencies for profile data output was changed from weight_pres to weight_substep. (nudging.f90, subsidence.f90)
28/04/14	RH	r1381	3.10	C	Upper boundary conditions for pt and q in case of nudging adjusted. (boundary_conds, Makefile, nudging, prognostic_equations, subsidence, time_integration)
26/04/14	LB	r1377	3.10	B	Two typos corrected (header.f90)
25/04/14	SR	r1374	3.10	B	Several bugfixes for the case running PALM without pointers on NVidia-GPUs (switches -D__nopointer -D__openacc -D__cuda_fft are used): Missing variables added to ONLY lists in USE statements. (advec_s_bc, advec_s_pw, advec_s_up, advec_ws, buoyancy, diffusion_e, diffusion_s, fft_xy, flow_statistics, palm, prognostic_equations) Missing module kinds added. (cuda_fft_interfaces) Kind dpk renamed dp. (fft_xy) Missing dependency for check_open added. (Makefile) Variables removed from acc-present-list. (diffusion_e, diffusion_w, diffusivities, production_e, wall_fluxes) Syntax errors removed from openacc-branch. (flow_statistics) USE-statement for the nopointer-case added. (swap_timelevel)
24/04/14	SR	r1372	3.10	B	openMP-bugfix for fftw: some arrays defined as threadprivate. (fft_xy)
24/04/14	SR	r1369	3.10	N/C	New: Routine description added. (cpulog) Changed: Usage of module interfaces removed. (lpm_advec)
23/04/14	BW	r1368	3.10	B	Bugfix: module kinds must be used (package_parin)
22/04/14	LB	r1366	3.10	C/N	New: Large scale forcing for temperature and humidity enabled. If large_scale_forcing is set to .T., large scale advection tendencies and subsidence tendencies are read in from the external file LSF_DATA. The horizontal large scale advection tendencies are applied to the prognostic variables in the new subroutine ls_advec in the module ls_forcing. The new control parameter use_subsidence_tendencies determines how the large scale subsidence is computed. If it is set to .F. (default), the large scale subsidence velocity w_subs is used to advect the prognostic variables (subroutine subsidence). If it is set to .T., the subroutine subsidence is not called and the subsidence tendencies from LSF_DATA are applied to the prognostic variables in the new subroutine ls_advec. The usage of use_subsidence_tendencies requires large_scale_forcing = .T. as well as large_scale_subsidence = .T.. Note that because of these changes external files (LSF_DATA) that worked with previous revisions have to be modified. The profile data sets in LSF_DATA now must contain four new columns which provide large scale advection tendencies as well as subsidence tendencies. Standard output of profiles of large scale advection tendencies (td_lsa_lpt, td_lsa_q), large scale subsidence tendencies (td_sub_lpt, td_sub_q) and nudging tendencies (td_nud_lpt, td_nud_q, td_nud_u and td_nud_v) is now possible. A new section called 'Large scale forcing and nudging' has been added to the header. Changes: New module calc_mean_profile added (previously a subroutine in module buoyancy). Removed redundant calls of MPI_ALLREDUCE from nudging.f90. (buoyancy.f90, calc_mean_profile.f90, check_parameters.f90, flow_statistics.f90, header.f90, ls_forcing.f90, Makefile, modules.f90, nudging.f90, parin.f90, prognostic_equations.f90, subsidence.f90, time_integration.f90)
17/04/14	MK	r1364	3.10	B	cpulog added to lpm_pack_arrays.90 (Makefile)
16/04/14	FH	r1362	3.10	C/B	Two-moment cloud microphysics improved. As a new default, two-moment cloud microphysics are called just once before the time step (and not before every sub-time step). Not affecting the results substantial, these changes increases the computational feasibility of the two-moment cloud microphysics scheme. Note that the computation of microphysics before every sub-time step is still possible by setting the new parameter call_microphysics_at_all_substeps = .T.. A vector-type CPU optimized version of the two-moment cloud physics was added as well. Moreover, the individual subroutines of microphyiscs were reviewd to increase their computational performance. The computation of turbulent surface fluxes of rain water content (qr) and rain drop concentration (nr) were added (bugfix). The default of drizzle has been set to .T., since analysis showed that its computational needs are marginal. In prognostic_equations, w_subs is allocated only if it is not allocated before (bugfix). (advec_s_bc, advec_ws, boundary_conds, check_parameters, init_3d_model, init_cloud_physics, Makefile, microphysics, modules, parin, prandtl_fluxes, prognostic_equations)
11/04/14	FH	r1360	3.10	C/N/B	Integration of the new Lagrangian particle structure (4D-array insetad of 1d-array). Particle tails are currently not available. lpm_extend_particle_array.f90 and lpm_sort_arrays.f90 were deleted, since they are not necessary due to the new particle structure. mod_particle_attributes.f90 was added to PALM and contains all particle related variables (a former part of modules.f90). A bugfix in write_3d_binary.f90 was necessary to allow restart runs using particles. Several other files were changed (check_open.f90, check_parameters.f90, data_output_2d.f90, data_output_3d.f90, data_output_mask.f90, data_output_ptseries.f90, header.f90, init_3d_model.f90, lpm.f90, lpm_advec.f90, lpm_boundary_conds.f90, lpm_calc_liquid_water_content.f90, lpm_collision_kernels.f90, lpm_data_output_particles.f90, lpm_droplet_collision.f90, lpm_droplet_condensation.f90, lpm_exchange_horiz.f90, lpm_extend_particle_array.f90, lpm_extend_tail_array.f90, lpm_extend_tails.f90, lpm_init.f90, lpm_init_sgs_tke.f90, lpm_pack_arrays.f90, lpm_read_restart_file.f90, lpm_release_set.f90, lpm_set_attributes.f90, lpm_sort_arrays.f90, lpm_write_exchange_statistics.f90, lpm_write_restart_file.f90, Makefile, Makefile_check, mod_particle_attributes.f90, modules.f90, package_parin.f90, parin.f90, read_3d_binary.f90, sum_up_3d_data.f90, user_lpm_advec.f90, user_lpm_init.f90, user_lpm_set_attributes.f90, write_3d_binary.f90).
11/04/14	BW	r1358	3.10	C	Adjustments for lccrayh (automatic restarts on lccrayh outside of IMUK are now possible, mrun)
10/04/14	RH	r1356	3.10	C	Error message specified in case that the NUDGING_DATA has a maximum vertical height that is smaller than the vertical grid used in PALM. (nudging)
08/04/14	PALM team	r1354	3.10	B	Attention: About 74 PALM-FORTRAN-files in the SOURCE-directory are affected by these changes. All REAL constants are provided with KIND-attribute by using _wp due to consistency reasons.
04/04/14	BM	r1352	3.10	B	Re-adjustments for lcxe6 after software updates on hexagon (.mrun.config.lcxe6, subjob, mbuild).
27/03/14	SR	r1348	3.10	B	Some missed variables added to ONLY-list. (exchange_horiz, exchange_horiz_2d)
27/03/14	RH	r1347	3.10	B/C	Bugfix: REAL constants provided with KIND-attribute especially in call of intrinsic function like MAX, MIN, SIGN. (advec_bc, data_output_dvrp, inflow_turbulence, init_1d_model, init_advec, microphysics, lpm_collision_kernel, lpm_droplet_condensation) Changed: -qrealsize=8 removed, fftw include and library path added, debug options added (.mrun.config.ibmh)
26/03/14	FK	r1345	3.10	B	Bugfix: Added missing parameters bc_lr and bc_ns to ONLY-attribute. (exchange_horiz)
26/03/14	FK	r1343	3.10	B	Bugfix: REAL constants provided with KIND-attribute. (calc_spectra, fft_xy, pres, production_e, random_function, random_gauss, temperton_fft, time_integration, time_to_string, timestep, tridia_solver)
25/03/14	FK	r1341	3.10	B	Bugfix: REAL constants provided with KIND-attribute. (diffusion_e, diffusion_s, diffusion_u, diffusion_v, diffusion_w, diffusivities, init_3d_model, package_parin, plant_canopy_model, prandtl_fluxes)
25/03/14	RH	r1339	3.10	B	Bugfix: REAL constants provided with KIND-attribute. (prognostic_equations)
25/03/14	SR	r1337	3.10	C	Routine write_compressed removed. (Makefile, deleted: write_compressed)
25/03/14	RH	r1334	3.10	B	Bugfix: REAL constants provided with KIND-attribute. (init_cloud_physics, microphysics)
25/03/14	MS	r1332	3.10	B	Bugfix: call advec_ws or advec_pw for TKE only if NOT use_upstream_for_tke. (prognostic_equations)
24/03/14	MS	r1330	3.10	C	In case of SGS-particle velocity, advection of TKE is also allowed with dissipative 5th-order scheme. (check_parameters, prognostic_equations)
21/03/14	SR	r1327	3.10	C/B	Changed: -s real64 removed (.mrun.config.hlrnIII) -r8 removed (.mrun.config.imuk) deleted: .mrun.config.imuk_ice2_netcdf4 .mrun.config.imuk_hlrn REAL constants defined as wp-KIND. (modules) "baroclinicity" renamed "baroclinity", "ocean version" replaced by "ocean mode". (check_parameters) Code parts concerning old output formats "iso2d" and "avs" removed. netCDF is the only remaining output format. (check_open, check_parameters, close_file, data_output_mask, data_output_profiles, data_output_ptseries, data_output_spectra, data_output_tseries, data_output_2d, data_output_3d, header, lpm_data_output_part, lpm_exchange_horiz, lpm_init, lpm_release_set, modules, parin, deleted: write_compressed) Bugfixes: duplicate error message 56 removed. (check_parameters)
21/03/14	BM	r1326	3.10	N,B	New code: New script document:changes has been added, which allows the automatic move of comments from "Current revisions:" to "Former revisions" (document_changes). Bugfixes: Some old comments in "Current revisions:" have been moved to "Former revisions:" (buoyancy.f90, mrun, nc2vdf, nc2vdf.config, nc2vdf.ncl)
21/03/14	MS	r1324	3.10	B	Bugfixes in ONLY-attributes. (calc_spectra, data_output_spectra, header, init_masks, package_parin, surface_coupler, transpose, write_var_list)
20/03/14	PALM- team	r1322	3.10	C/B	Changes: REAL functions and a lot of REAL constants provided with KIND-attribute. (about 40 PALM-FORTRAN files) Bugfixes: Some missed ONLY-attributes added.
20/03/14	PALM- team	r1320	3.10	C	Attention: All PALM-FORTRAN-files in the SOURCE-directory are affected by these changes. ONLY-attribute added to USE-statements. KIND-parameters added to all INTEGER and REAL declaration statements. By default, all REALs are declared double precision (64bit) and INTEGERs single precision (32bit). kinds are defined in new module kinds, old module precision_kind has been removed. Revision history before 2012 removed. Comment fields (!:) to be used for variable explanations added to all variable declaration statements.
17/03/14	SR	r1318	3.10	C	Former files/routines cpu_log and cpu_statistics combined to one file/module cpulog, which also includes the former data module cpulog from the modules-file. (new: cpulog, removed: cpu_log, cpu_statistics, changed: about 50 routines)
17/03/14	RH	r1317	3.10	B	Bugfix: Allocation of w_subs. (init_3d_model)
14/03/14	MS	r1315	3.10	N	Vertical logarithmic interpolation of horizontal particle speed for particles between roughness height and first vertical grid level. (lpm_advec, lpm_init, modules)
14/03/14	JF	r1313	3.10	C	Text correction (header.f90)
14/03/14	RH	r1312	3.10	C	Bugfixes: forgotten dependency and #if clause not closed (data_output_2d, Makefile)
14/03/14	SR	r1310	3.10	C	Update of GPL copyright. (all files under GPL)
13/03/14	JF	r1308	3.10	C	Changed: Adjustments for parallel NetCDF output on Cray XC30 systems (lccrayh/lccrayb). Changes to increase the performance of the parallel netCDF output: Environmental variables, e.g. for disc striping, are set. (.mrun.config.hlrnIII) The time dimensions are set to limited instead of unlimited. (check_parameters, data_output_2d, data_output_3d, header, netcdf, modules, read_var_list, write_var_list) Output of axis data and update of time axis is done by PE0 only. (data_output_2d, data_output_3d, netcdf) Cross sections are first stored on a local array, collected by MPI_ALLREDUCE, and then output collectively. (data_output_2d, netcdf) The "no fill"-attribute is set for all variables using NF90_DEF_VAR_FILL. This prevents netCDF from initializing the complete file (writing zero-values) at the beginning, which turned out to be extremely time consuming. (netcdf) Attention: So far, parallel NetCDF output is only available for 2D- and 3D-data and not for masked data. If the user chooses netcdf_data_format = 5/6, parallel output is used for 2D- and 3D-data and for masked data netcdf_data_format is set internally to the value of 3/4, respectively (check_parameters, time_integration)
13/03/14	SR	r1306	3.10	N/C	New: module for declaring kind definitions added. (new: mod_kinds) Changed: openMP sections removed from FFT/ALLTOALL overlapping. (poisfft) Second argument removed from routine poisfft, because it was unused. (poisfft, pres)
12/03/14	SR	r1304	3.10	B/C	Bugfix: concerning openmp: work1 used in Temperton algorithm must be private. (fft_xy) single core MPI runs missed some settings of transpose indices. (init_pegrid) Changed: ulimit option changed from -Ss to -s. (mrun)
06/03/14	RH	r1301	3.10	C/B	Enable usage of large_scale_subsidence in combination with large_scale_forcing where the profile for the subsidence velocity w_subs can be prescribed. w_subs is now part of the standard profile output. (check_parameters, flow_statistics, header, init_3d_model, ls_forcing, parin)
04/03/14	SR	r1291	3.10	N	Release 3.10 created.
04/03/14	SR	r1289	3.10	C	Version update to 3.10. (palm) Script comments translated to English. fimm-, scirocco-, ibmy-, nech-, and sgi-specific code removed. (mbuild, mrun, subjob) Routine local_getenv removed. (interpret_config)
28/01/14	SR	r1279	3.9	N	tasks_per_node must not be an integral divisor of numprocs any more. This change was done in order to remove annoying restrictions concerning the number of processors, which appear on machines with larger nodes (e.g. containing 24 cores). Now, without this restriction, one of the nodes will be filled with less than the given number of tasks per node. A respective warning is given. (mrun, subjob)
21/01/14	JF	r1278	3.9	N	Temporary workaround for lccrayb/h, increasing the limit of open files per processor which is needed for combine_plot_fields. The system preferences is currently 1024 open files per processor (.mrun.config.hlrnIII).
15/01/14	RH	r1276	3.9	C	Usage of Dirichlet bottom boundary condition for scalars in conjunction with large scale forcing enabled (check_parameters, ls_forcing, prandtl_fluxes, time_integration)
09/01/14	RH	r1274	3.9	C	Adjustments for lccrayh (mbuild, mrun, subjob, .mrun.config.hlrnIII)
08/01/14	BW	r1272	3.9	C	Small adjustment for lcflow (mrun)
16/12/13	JF	r1270	3.9	C	Call of combine_plot_fields adjusted for lccrayb/lccrayh. aprun is used for calling combine_plot_fields on the CRAY-machine in Hannover and Berlin because otherwise the script is started on the Cray system managment (MOM) nodes were the stack size limit is too small for larger jobs.
12/12/13	RH	r1268	3.9	B	Bugfix: argument of calc_mean_profile corrected (nudging)
11/12/13	RH	r1266	3.9	C	Adjustment for lccrayb: use msub instead of qsub (subjob)
9/12/13	JF	r1264	3.9	B	Bugfix: Using number of nodes instead of number of processors for lccrayb (subjob)
9/12/13	JF	r1262	3.9	C	Further adjustments for lccrayb, change from qsub to msub command (subjob)
8/11/13	SR	r1257	3.9	N, C, B	New: openACC porting of timestep calculation. (modules, timestep, time_integration) Changed: openACC loop directives and vector clauses removed where they do not give performance improvements (concerning PGI compiler versions >= 13.6). (advec_ws, buoyancy, coriolis, diffusion_e, diffusion_s, diffusion_u, diffusion_v, diffusion_w, diffusivities, exchange_horiz, fft_xy, pres, production_e, transpose, tridia_solver, wall_fluxes) openACC loop independent clauses added. (boundary_conds, prandtl_fluxes, pres) openACC declare create statements moved after FORTRAN declaration statement. (diffusion_u, diffusion_v, diffusion_w, fft_xy, poisfft, production_e, tridia_solver) openACC end parallel replaced by end parallel loop. (flow_statistics, pres) openACC kernels do replaced by kernels loop. (prandtl_fluxes) output format for theta* changed to avoid output of * in the run-control file. Attention: Due to this modification, the format of the default run-control file has changed. (run_control, example_cbl_rc) Bugfix: Calculation of the advective timestep in case of vertically stretched grids has been corrected. Attention: Due to this modification, the contents of the default run-control output has changed. (timestep, example_cbl_rc)
7/11/13	JF	r1254	3.9	B	Bugfix: add ref_state to read_parts_of_var_list, otherwise ref_state is zero for initializing_actions = 'cyclic_fill' (read_var_list) Bugfix: q is set to qr in case that q is smaller than qr (calc_liquid_water_content)
7/11/13	RH	r1252	3.9	C	Bugfix: calculate dtm and dtp also in vector version (nudging)
6/11/13	RH	r1250	3.9	C	Remove call of user module and some reformatting (ls_forcing, nudging)
4/11/13	RH	r1248	3.9	C	NCL function getfilevarnames changed with NCL version 6.1.1 and higher. This required adaptation in the PALM NCL scripts. (cross_sections.ncl, profiles.ncl, spectra.ncl, timeseries.ncl)
1/11/13	RH	r1247	3.9	N	Enable usage of nudging also for accelerator version. (prognostic equations)
31/10/13	SR	r1244	3.9	B	Bugfix for index bounds in case of 3d-parallel output. (data_output_3d)
30/10/13	RH	r1243	3.9	N, C	New: It is now possible to use nudging and large_scale_forcing from an external file. To use these methods two additional files have to be provided in which information about nudging profiles (NUDGING_DATA) and large scale information (LSF_DATA) about the geostrophic wind components, large scale subsidence profiles and surface fluxes can be found. Note that the default PALM configuration files like .mrun.config.default are updated to contain entries for NUDGING_DATA and LSF_DATA. (boundary_conds, check_parameters, header, init_3d_model, ls_forcing, microphysics, modules, nudging, palm, parin, prognostic_equations, read_var_list, time_integration, write_var_list, Makefile, .mrun.config.default and its derivates) Changed: The subroutine calc_mean_profiles is generalized for a wider use in PALM (buoyancy.f90). It is now possible to output the geostrophic wind components ug and vg in profile data (check_parameters, flow_statistics).
14/10/13	FH	r1238	3.9	C	Configuration file for HLRN III changed (.mrun.config.hlrnIII).
27/09/13	SR	r1236	3.9	B	The number of spectra levels to be output is checked for 0. (check_parameters)
25/09/13	MK	r1235	3.9	N	Added new configuration file for the PALM seminar at CUHK (Chinese University of Hong Kong) (.mrun.config.cuhk)
25/09/13	FK	r1234	3.9	N	Update of some tutorial presentations. (installation.tex, palm_structure.tex, user_defined_code.tex)
23/09/13	FK	r1233	3.9	N	Update of tutorial presentation "PALM overview". (palm_overview.tex)
20/09/13	FK	r1232	3.9	C	Made some changes to create a more generic version of tutorial presentation "Debugging". (debugging.tex)
20/09/13	FK	r1231	3.9	N	Added new block (parallel trace) for debug version. (.mrun.config.default)
19/09/13	FK	r1228	3.9	B	Some typos have been removed in tutorial. (exercise_neutral.tex)
18/09/13	MF	r1227	3.9	N	Update of several tutorial presentations (exercise_neutral.tex, installation.tex, non_cyclic_boundary_conditions.tex, numerics_bc.tex,parallelization.tex, program_structure.tex, runs_with_mrun.tex, sgs_models.tex, topography.tex, user_defined_code.tex).
16/09/13	SR	r1224	3.9	N	First adjustments for HLRN-III system (lccrayb). (mrun, subjob, new: .mrun.config.hlrnIII) Dummy interface added to avoid compiler warnings. (cuda_fft_interfaces)
10/09/13	SR	r1221	3.9	N, C, B	New: openACC porting of reduction operations. An accelerator-version for flow_statistics with modified loop structure k,i,j has been implemented. It is activated with preprocessor flag -D__openacc. The extra accelerator version is required because so far, the openACC standard only allows reduction operations on simple scalars. Since 1D-vectors along k are used in flow_statistics, they had to be replaced by scalars and the k loop has now to be used as the outermost loop. Additional 3D-flag arrays have been introduced for replacing the 2D-index arrays nzb_s_inner and nzb_diff_s_inner in routines pres and flow_statistics. Respective "global-sum" loops are running from k = nzb. Within the loops, values for grid points below the surface (topography) are multiplied by zero, all others by one, using the flag array rflags_invers. This array is dimensioned (j,i,k) to allow for better cache usage in the loops of the accelerator version of flow_statistics. (flow_statistics, init_grid, init_3d_model, modules, palm, pres, time_integration) Changed: For PGI/openACC performance reasons (PGI compiler version 13.6, CUDA 5.0) the default compile options have been set to "-ta=nocache", which gives a speed-up of about 10-20%. For the same reason, the environment variable PGI_ACC_SYNCHRONOUS is set to 1 in the simple run script, which significantly improves the performance about 80%. (MAKE.inc.pgi.openacc, palm_simple_run) The type of flag array wall_flags_0, used in the Wicker-Skamarock scheme for advection of the vertical wind component, has been changed to 32bit INTEGER. An additional array wall_flags_00 has been introduced to hold flag bits 32-63. This is required because the former used KIND = SELECTED_INT_KIND(11) caused wrong results with openACC. (advec_ws, init_grid, modules, palm) Bugfix: Dummy argument tri in 1d-routines replaced by tri_for_1d because of name conflict with array tri in module arrays_3d. (tridia_solver)
30/08/13	RH	r1220	3.9	B	Usage of own branch for fftw enabled (fft_xy).
26/08/13	SR	r1216	3.9	N, C, B	New: Overlapping execution of fft and transpositions (MPI_ALLTOALL), steered with new parameter transpose_compute_overlap. Attention: real overlapping has not been activated so far, but better cache usage already gives performance improvements. Due to fftw (instead of Temperton, r1210), tridia-solver improvements (r1212) and the better cache usage, the fft-solver speeds up for about 20% (on a 1024x1024x512 grid). (fft_xy, header, modules, parin, poisfft, tridia_solver, Makefile_check) fftw implemented for 1D-decomposition. (fft_xy) Changed: Resorting of arrays moved to separate routines resort_for_... (calc_spectra, poisfft, transpose) Bugfix: Bugfix concerning Makefile_check. (mbuild)
21/08/13	FK	r1214	3.9	N	Added parameter check for simultaneous use of vertical grid stretching and particle advection (check_parameters).
15/08/13	SR	r1212	3.9	C	The tridiagonal solver has been moved to a separate module. The tridiagonal matrix coefficients of array tri are calculated only once at the beginning, which speeds up the solver by almost a factor of two. In connection with this change, the old hybrid Poisson-solver (which allowed parallel transposition/calculation in case of a 1d domain decomposition) has been removed. (Makefile, Makefile_check, check_parameters, header, modules, init_pegrid, init_3d_model, palm, poisfft, pres, new: tridia_solver, removed: poisfft_hybrid) Object file list replaced by a simple one line statement. (Makefile_check)
14/08/13	SR	r1210	3.9	N, C	New: fftw support added. Using fftw requires to set parameter fft_method = 'fftw' , to set the cpp-preprocessor '-D__fftw' in the %cpp_options-line of the configuration file, and to give the paths to the fftw include file and library by a %fftw_inc and %fftw_lib line, respectively. The fftw-routines are more than two times faster than the Temperton-fft. (check_parameters, fft_xy, mbuild, mrun) Changed: The object file list has been replaced by a simple one line statement. (Makefile)
13/08/13	SR	r1208	3.9	N	acc-update clauses added for array "ar", so that ffts other than cufft can also be used (although they are not ported and will give a poor performance). (poisfft)
18/07/13	BW	r1206	3.9	B	Bugfix: typo in preprocessor directive removed (netcdf)
15/07/13	FK	r1205	3.9	N,B	New: general requirement information has been added to tutorial for PALM installation at hlrn. (installation.tex) Bugfix: some typos have been removed in tutorial. (canopy_model.tex)
10/07/13	BW	r1202	3.9	C	Script adjustments for Forwind cluster (lcflow). (mrun, subjob, batch_scp, .mrun.config.forwind)
05/07/13	SR	r1199	3.9	N	Script adjustments for CSC Helsinki (lccrayf), Cray XC30 with SLURM batch system. (mrun, subjob, new: .mrun.config.csc_sisu) Executables for batch jobs can be created in advance (i.e. when mrun is called by the user), in order to avoid calling the compiler within the batch job. This feature is required for hosts which do not allow compiler calls on the batch nodes and which also do not allow ssh calls to the login nodes. The feature can be switched on by adding the line %create_executable_for_batch true in the configuration file. Attention: It only works if local host and remote host is identical, i.e. you have to call mrun on that host where the batch job should run (no remote batch jobs allowed).
04/07/13	FK	r1198	3.9	B	Bugfix: some typos have been removed in tutorial. (exercise_cbl.tex, exercise_neutral.tex)
01/07/13	RH	r1196	3.9	B	Bugfix: allocation of ref_state was moved from init_3d_model to parin and read_var_list (init_3d_model, parin, read_var_list)
25/06/13	RH	r1190	3.9	B	Enable automatic restarts of ibmh (mrun)
20/06/13	RH	r1188	3.9	B	Bugfix in modes 'min' and 'max': x and z component were interchanged (global_min_max)
18/06/13	SR	r1186	3.9	B	Bugfix: 0.0 replaced by zu(nzb) as the lowest default height level for masks, because a zero value does not work in case of ocean runs. (init_masks)
17/06/13	RH	r1184	3.9	C	Explicit use of classes cluster and express enabled for ibmh (mrun, subjob)
14/06/13	SR	r1179	3.9	N, C, B	New, Changed: Calculation and handling of reference state in buoyancy term revised. Initial profiles can be used as reference state in the buoyancy term. New parameter reference_state introduced. The default value is reference_state = 'initial_profile' . Previously, the instantaneous horizontally averaged profiles were used as the default reference state. This method can still be switched on using reference_state = 'horizontal_average' . (buoyancy, check_parameters, diffusion_e, diffusivities, flow_statistics, header, init_ocean, init_3d_model, modules, palm, parin, production_e, prognostic_equations, time_integration, write_var_list) Initial profile for rho added to array hom (id=77). (check_parameters) Attention: Model results from this version slightly differ from those of earlier versions due to the change in the default reference state. The example result file (see example_cbl_rc​). This version does not allow to read restart files created with earlier versions!
31/05/13	MG	r1174	3.9	B	Bugfix: Since r667 there was a bug in the definition of the initial profiles of pt, ug, vg, q and lad (in atmosphere). r667 sets the level zu(0) to 0 (in older revisons it was defined as dz(0)=-0.5 dz) and this change was not considered in the part which calculates the initial profiles from prescribed gradients. The bug had only an effect if a non-zero gradient was set between the first two grid levels and caused a small shift of the complete profile. (check_parameters)
30/05/13	SR	r1171	3.9	N, C, B	New: use_reference-case activated in accelerator version. (buoyancy, diffusion_e) New option -e for simple-run command, which defines the execution command to be used to run PALM. Compiler-option-set for pgi/openacc added. (palm_simple_run, new: MAKE.inc.pgi.openacc) Three parameter sets for openACC benchmarks added. (trunk/EXAMPLES/benchmark_acc) Changed: Split of prognostic_equations deactivated, for the time being. (time_integration) Bugfix: diss array is allocated with full size if accelerator boards are used. Allocation with dummy elements (e.g. (2,2,2)) still created error "call to cuCtxSetCurrent returned error 216: Other". (init_3d_model)
24/05/13	SR	r1166	3.9	C, B	Changed: Data type C_DOUBLE/COMPLEX reset to dpk. (cuda_fft_interfaces, fft_xy) Bugfix: PGI 13.4 / CUDA 5.0 require to give idata/odata arguments the DEVICE attribute. (cuda_fft_interfaces)
24/05/13	SR	r1165	3.9	C	Small changes in tutorial. (runs_with_mrun.tex)
21/05/13	JF	r1159	3.9	B	Bugfix: If radiation boundary conditions are used, the calculation method of the phase velocity is now set by the logical operator use_cmax. The case use_cmax = .T. was wrongly defined as Neumann boundary condition before. (boundary_conds, check_parameters, header, init_3d_model, init_pegrid, modules, parin, poismg).
10/05/13	SR	r1153	3.9	C	Code adjustments of accelerator version required by PGI 13.4 / CUDA 5.0. (buoyancy, cuda_fft_interfaces, fft_xy, init_3d_model, wall_fluxes)
18/04/13	SR	r1139	3.9	B	Bugfix for calculating the id of the PE carrying the recycling plane. (init_pegrid)
12/04/13	SR	r1128	3.9	N, C	New: Asynchronous transfer of ghost point data realized for acc-optimized version: prognostic_equations_acc is first called four times for those points required for the left-right and north-south exchange, respectively, and then for the remaining points. This feature is controlled with new inipar-parameter background_communication, which is not documented so far. (advec_ws, buoyancy, coriolis, diffusion_e, diffusion_s, diffusion_u, diffusion_v, diffusion_w, exchange_horiz, modules, parin, production_e, prognostic_equations, time_integration, wall_fluxes) Changed: Those parts requiring global communication moved from prognostic_equations to time_integration. (Makefile, prognostic_equations, time_integration).
11/04/13	FH	r1127	3.9	B	Bugfix: Legends (time, file) are plotted at the first plot of every page (profiles.ncl).
10/04/13	FH	r1126	3.9	B	Bugfix: Palmplot pr can be used with multiple files (file_1, ..., file_6). Palmplot pr changes var='cross_profiles' to var='all' if statistic regions are used. (profiles.ncl)
09/04/13	SR	r1124	3.9	B	Bugfix: variable memory is exported via typeset option -x, because otherwise an unknown side effect may lead to data loss while getopts is reading the script-option arguments. (mrun)
09/04/13	RH	r1122	3.9	B	Bugfix: change type of variable last_char from integer to character. (mrun)
05/04/13	SR	r1120	3.9	B	Calls of fft_x and fft_y replaced by fft_x_1d and fft_y_1d. (calc_spectra)
05/04/13	SR	r1119	3.9	B	Bugfix for setting -T option for subjob. (mrun)
27/03/13	MS	r1117	3.9	B	Bugfix in OpenMP parallelization. (pres)
26/03/13	FH	r1115	3.9	C, B	Changed: All changes are related to the two-moments cloud physics scheme. Calculation of microphysical tendencies is now based on sedimentation flux divergences to save computational resources (calc_liquid_water_content, microphysics, prognostic_equations, data_output_3d, data_output_2d, sum_up_3d_data, flow_statistics). The actual calculation of the microphysical tendencies is moved from prognostic_equations.f90 to microphysics.f90 (microphysics, prognostic_equations). Unused and unnecessary (from a physical point of view) variables are removed (modules, parin, init_3d_model, boundary_conds, read_3d_binary, read_var_list, write_3d_binary, write_var_list). It is now allowed to use the parameter drizzle without precipitation (check_parameters, advec_ws, prognostic_equations, calc_liquid_water_content, swap_timelevel, time_integration). Used parameters are written to the header (header). Some reformatting (microphysics). Bugfix: Wrong coefficient removed in the calculation of the evaporation of rain drops (microphysics).
10/03/13	SR	r1113	3.9	N, C, B	New: Further GPU-porting for vertical boundary conditions and several loops in pres. Most of cyclic boundary conditions now completely on device in single-core mode. (boundary_conds, exchange_horiz, modules, palm, pres, time_integration) Changed: Dummy argument "range" removed. (boundary_conds) Bugfix: Wrong index in loops of radiation boundary condition adjusted. (boundary_conds)
09/03/13	SR	r1111	3.9	N, C, B	New: GPU porting of pres, swap_timelevel. Further porting of poisfft (including the tridiagonal solver), which now runs completely on GPU without any host/device data transfer for serial and parallel runs (but parallel runs still require data transfer before and after the MPI transpositions). The tridiagonal routines have been split into external subroutines (instead using embedded routines with CONTAINS). There is no distinction between parallel/non-parallel runs in poisfft and tridia any more. The respective preprocessor directives have been removed. The tridia routines have been moved to the end of file poisfft.f90 because of a probable bug in the PGI compiler 12.5 (otherwise "invalid device function" is indicated during runtime). Resorting from/to array work have been changed in the transpose routines. work now has 4 dimensions instead of 1. Adjustments of openACC directives. Output of accelerator board information. (cuda_fft_interfaces, fft_xy, flow_statistics, header, init_3d_model, palm, poisfft, pres, prognostic_equations, swap_timelevel, time_integration, transpose, .mrun.config.imuk_gpu) Optimization of tridia routines: constant elements and coefficients of array tri are stored in separate arrays ddzuw and tric and only calculated once at beginning. Last dimension of tri has been reduced from 5 to 2. Routine poisfft_init is now called internally from poisfft. (Makefile, Makefile_check, init_pegrid, init_3d_model, modules, palm, poisfft, poisfft_hybrid) CPU-time per grid point and timestep is output to CPU_MEASURES file. (cpu_statistics, modules, time_integration) Changed: Array diss is allocated only if required. (init_3d_model) Pressure boundary condition "Neumann+inhomo" has been removed from the code. (check_parameters, header, poisfft, poisfft_hybrid, pres) Bugfixes: Missing dependency added for cuda_fft_interfaces. (Makefile) CUDA fft plans adjusted for domain decomposition (before they have always been defined for the total domain). (fft_xy)
05/03/13	SR	r1108	3.9	B	Bugfix for r1106. (header) Bugfix for coupled runs on lckyut/lckyuh. (mrun)
04/03/13	SR	r1106	3.9	N, B, C	New: Start with porting of FFT-solver for serial runs to GPU using CUDA FFT. It will be finished in some later revision. The porting required to rearrange preprocessor lines in the transpose routines, so that they can also be used in serial (non-parallel) mode. The transpositions are now also carried out in the serial mode, which makes it a little bit slower. Routines fftx, fftxp have been replaced by calls of fft_x. In turn, the old fft_x has been renamed fft_x_1d and is now used for the 1D-decomposition routines. (Makefile, Makefile_check, fft_xy, poisfft, poisfft_hybrid, transpose, new: cuda_fft_interfaces) --stdin argument has been added to mpiexec statement on lckyuh. Argument settings of -y and -Y output to header. (mrun) Changed: Module array_kind renamed precision_kind. (check_open, data_output_3d, fft_xy, modules, user_data_output_3d) Some format changes for coupled atmosphere-ocean runs. (header) Small changes in code formatting. (microphysics, prognostic_equations) Bugfixes: Default value (0) assigned to coupling_start_time. (modules) Initial time for preruns of coupled runs is output as -coupling_start_time. (data_output_profiles)
20/02/13	SR	r1103	3.9	B, C	Changed: mrun script running under ksh again, because of problems with reading from stdin, if the bash script is called from a Korn-shell environment. (mrun) subjob has also been made bash-compatible. (subjob) Further adjutments for lckyuh. (mrun, subjob, added: .mrun.config.hayaka) Bugfixes: Turbulent inflow must not require cyclic fill in restart runs. (check_parameters) tri, ar, and ar1 array arguments in tridia-routines (2d) are removed because they sometimes cause segmentation faults with the INTEL 12.1 compiler. (poisfft)
17/02/13	SR	r1101	3.9	C	mrun script now running under bash instead of ksh. This required small adjustments in output formatting (alignment is done with printf instead using strings defined with "typeset -L/-R"-command). print commands are replaced by echo. Small changes for reading from stdin. (mrun) Cross compilername on lckyuh compute nodes replaced by real compiler name. (mrun)
10/02/13	SR	r1099	3.9	N	Adjustments for Forwind cluster (lcflow). First, incomplete, adjustments for Kyushu University computing center (hayaka -lckyuh). Further small adjustments for lckyut (tatara). (batch_scp, mbuild, mrun, subjob, .mrun.config.forwind, .mrun.config.tatara)
03/02/13	SR	r1095	3.9	B	FORTRAN error in r1092 removed. (modules)
03/02/13	SR	r1094	3.9	N, C	New: ssh/scp port can be set explicitly in the configuration file using environment variable scp_port. (batch_scp, mrun, subjob) Changed: Unused variables removed from code. (interpret_config)
02/02/13	SR	r1092	3.9	C	Unused variables removed from several subroutines. (advec_s_bc, check_open, check_parameters, close_file, cpu_statistics, data_output_mask, data_output_profiles, data_output_tseries, diffusion_s, exchange_horiz_2d, fft_xy, header, inflow_turbulence, init_3d_model, init_grid, init_pegrid, local_tremain_ini, lpm_collision_kernels, lpm_droplet_collision, lpm_droplet_condensation, lpm_init, microphysics, modules, netcdf, palm, parin, poisfft, poismg, pres, prognostic_equations, random_function, read_var_list, surface_coupler, time_integration, timestep, transpose, write_compressed)
02/02/13	SR	r1090	3.9	N	Script adjustments for Kyushu-University computing center (lckyut). (batch_scp, mbuild, mrun, subjob)
04/01/13	BM	r1083	3.9	B	Bugfixes in the parameter file check (mrun, mbuild).