Index: palm/trunk/SOURCE/CURRENT_MODIFICATIONS
===================================================================
--- palm/trunk/SOURCE/CURRENT_MODIFICATIONS	(revision 197)
+++ palm/trunk/SOURCE/CURRENT_MODIFICATIONS	(revision 198)
@@ -1,163 +1,13 @@
 New:
 ---
-The plant canopy model has been extended to the prognostic equation for   
-the potential temperature and the prognostic equation for the concentration 
-of a passive scalar, as proposed by Watanabe (2004) and Shaw and Schumann 
-(1992). (prognostic_equations, plant_canopy_model)  
 
-Within a job chain, the number of processors or the virtual processor grid
-is now allowed to be changed. This modifies the domain decomposition and
-requires that the PEs within a restart job have to know from which file(s) they
-have to read their restart data (up to now there is a one to one relation
-between the restart files and the PEs, i.e. processor 4 only reads data
-from file "_0004"). Informations about the subdomain index limits of all
-restart files are now written by PE0 (to file "_0000"). Also, all variables
-containing global values which do not depend on the subdomain are written
-to file "_0000" only. In a restart run, this file is opened by all PEs to
-read these global values and the informations about the subdomain index
-limits. Depending on these index limit information it is decided which
-restart file(s) has/have to be opened in order to read the complete data
-necessary for the current subdomain.
-
-The turbulence recycling method of Kataoka and Mizuno (2002) has been
-implemented. A pre-run with smaller model domain can be used to initialize
-the real run, in order to spare the CPU time needed to get the turbulence
-into a quasi-stationary state (see initializing_actions =
-'read_data_for_recycling').
-
-Particle advection adjusted for ocean runs.
-
-Multigrid levels are limited by subdomains if mg_switch_to_pe0_level = -1.
-
-User-defined spectra.
-
-Output of q*2 profile added.
-
-Argument -c introduced to most of the subjob calls, which allows the user to
-choose his own job catalog by setting job_catalog in the configuration file
-(default is ~/job_queue). Workaround for mpixec with -env option.
-Adjustments for lcxt4 (Bergen Center for Computational Science) (mrun, subjob)
-
-advec_particles, calc_spectra, check_open, check_parameters, data_output_spectra, header, init_particles, init_pegrid, init_3d_model, modules, netcdf, parin, particle_boundary_conds, plant_canopy_model, prognostic_equations, read_var_list, read_3d_binary, time_integration, user_interface, write_var_list, write_3d_binary
-
-New: inflow_turbulence
 
 
 Changed:
 -------
-Allow 100 spectra levels instead of 10 for consistency with 
-define_netcdf_header (calc_spectra, data_output_spectra, header, modules, 
-netcdf)
 
-Modification of the integrated version of the profile function for momentum 
-for unstable stratification; more consistent flux definitions. (wall_fluxes, 
-production_e)
-
-Strict grid matching along z is not needed for mg-solver. (check_parameters)
-
-Sharp lateral edges of the plant canopy introduced. Before smaller 
-values of the leaf area density than those applied in the prognostic 
-equation for the vertical velocity were used in the prognostic equations 
-for u and v at the boundaries of the plant_canopy. (init_3d_model)  
-
--cross_ts_* (read_var_list, write_var_list)
--dopr_time_count, old profil parameters (cross_..., dopr_crossindex,
- profile_***) removed (read_3d_binary, write_3d_binary)
-
-hom_sum moved, volume_flow_area, volume_flow_initial moved from ..._3d_binary
-to ..._var_list, hom_sum is now allocated in parin instead of init_3d_model
-
-npex, npey moved from inipar- to d3par-namelist (parin)
-
-myid_char14 removed. This was used since on IBM machines the process rank may
-be changed when the final communicator is defined, in order to save the
-preliminary processor-id for opening the binary output file for restarts
-(unit 14), because otherwise a mismatch occured when reading this file in a
-restart job. This mechanism is not needed any more since the subdomain
-informations are now contained in file _0000. (parin, check_open)
-
-Transpositions for the 2D domain decomposition have been optimized by using
-f_inv as an automatic array instead of providing the memory by a dummy argument.
-This spares one copy loop per transposition. Order of indices in the 3D loops
-in some of the transpose routines have been rearranged for better cache utilization.
-Both have been suggested by Roland Richter (SGI) as part of the
-HLRN-II benchmark process. (transpose)
-
-Workaround for getting information about the coupling mode. (palm)
-
-Format adjustments in order to allow CPU# > 999. (cpu_statistics)
-
-Provisional solution for run_control_1d output: add 'CALL check_open( 15 )'
-(init_1d_model)
-
-Subdomain data are read into temporary arrays pf_tmp/pf3d_tmp in order to
-avoid INTEL compiler warnings about (automatic) creation of temporary arrays
-(combine_plot_fields)
-
-Time coordinate t=0 stored on netcdf-file only if an output is required for
-this time for at least one of the profiles
-
-Spline timeseries splptx etc. removed, timeseries w'u', w'v', w'q' (k=0) added
-(flow_statistics)
-
-advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, calc_spectra, check_open, check_parameters, cpu_statistics, data_output_profiles, data_output_spectra, flow_statistics, header, init_1d_model, init_3d_model, modules, netcdf, palm, parin, poisfft, production_e, read_var_list, read_3d_binary, transpose, wall_fluxes, write_var_list, write_3d_binary
 
 
 Errors:
 ------
-Bugfix: exponent = 1.0 / ( ny + 1.0 ) in calc_spectra_x (calc_spectra)
 
-Bugfix: change definition of us_wall from 1D to 2D. Tests showed that this decreases 
-u* by some 10% and increases TKE and momentum fluxes by some 10% because friction 
-was underestimated and momentum fluxes were wrongly calculated due to the bug. 
-(prandtl_fluxes, wall_fluxes)
-
-Bugfix: calculation of horizontal fluxes at vertical walls (diffusion_s)
-
-Bugfix: zero assignments to tendency arrays in case of restarts (init_3d_model)
-
-Bugfix: wrong grid level used in multigrid solver, routine restrict (poismg)
-
-Bugfix: Construction of vertical profiles when 10 gradients have been 
-specified in the parameter list (ug, vg, pt, q, sa, lad). (check_parameters)
-
-Bugfix: Determination of the number of vertical levels for which spectra 
-shall be output - 100 replaced by 10. (netcdf)
-
-Bugfix: Lengths of those characters that are needed for the output of the 
-characteristic levels of potential temperature, the geostrophic wind, 
-scalar concentration, humidity and leaf area density to the header file 
-has been increased. (header) 
-
-Bugfix: add ')' in user_read_restart_data.
-
-The leaf area density is explicitly set to its surface value at k=0. (check_parameters)
-
-Introduce prefix_chr to ensure unique dvrp_file path.
-
-small bugfixes for user_interface sample code (comments):
-- initialize ustvst with 0.0 as it is now computed only until nxr and nyn
-- two ALLOCATE statements moved from user_read_restart_data back to user_init
-- remove 'READ (13) u2_av' statement in user_read_restart_data
-
-Bugfix: remove IF statement in plant_canopy_model_ij (plant_canopy_model)
-
-Bugfix: divide sums(k,8) (e) and sums(k,34) (e*) by ngp_2dh_s_inner(k,sr) 
-(like other scalars) (flow_statistics)
-
-Bugfix: dopr_time_count was written on the binary file, which caused that
-NetCDF files newly created by restart files (no append of existing files!)
-contained uneccessary time levels. (read_3d_binary, write_3d_binary)
-
-Bugfix: extra '*' removed in user_statistics sample code (user_interface)
-
-Bugfix: a stop command was missing in some cases of the parallel branch (local_stop)
-
-Bugfix in volume flow control for non-cyclic boundary conditions (pres)
-
-Bugfix: misplaced #endif directives (combine_plot_fields)
-
-data are collected from PE0 in an ordered sequence which seems to avoid hanging of processes on SGI-ICE (cpu_statistics)
-
-calc_spectra, check_parameters, cpu_statistics, diffusion_s, flow_statistics, init_dvrp, init_3d_model, local_stop, plant_canopy_model, poismg, prandtl_fluxes, pres, read_3d_binary, user_interface, wall_fluxes, write_3d_binary
-
