source: palm/trunk/SOURCE/CURRENT_MODIFICATIONS @ 194

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.

User-defined spectra.

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)

advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, calc_spectra, check_open, check_parameters, cpu_statistics, data_output_spectra, 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)

calc_spectra, check_parameters, 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