Index: palm/trunk/DOC/tec/technical_documentation.html
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 <!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
 <html><head>
-<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> <meta content="Mozilla/4.73 [en] (X11; U; HP-UX B.10.20 9000/782) [Netscape]" name="GENERATOR"> <meta content="Siegfried Raasch" name="Author"> <meta content="parallel LES model" name="Keywords"><title>PALM technical/numerical
-documentation</title></head>
+<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> <meta content="Mozilla/4.73 [en] (X11; U; HP-UX B.10.20 9000/782) [Netscape]" name="GENERATOR"> <meta content="Siegfried Raasch" name="Author"> <meta content="parallel LES model" name="Keywords"><title>PALM technical/numerical documentation</title></head>
 <body><font size="+4">PALM&nbsp;&nbsp;
 </font>a
@@ -13,5 +12,5 @@
 <br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
 </tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current
-model version:</b></td> <td><span style="font-weight: bold;">3.1c</span></td> </tr>
+model version:</b></td> <td><span style="font-weight: bold;">3.2</span></td> </tr>
 <tr nosave=""> <td nosave=""><b>Last
 change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id$</b></td> </tr>
@@ -2254,21 +2253,50 @@
 modules, parin, production_e, prognostic_equations, read_var_list,
 read_3d_binary, swap_timelevel, write_var_list, write_3d_binary</td></tr><tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Prognostic equations for all
-scalars are now solved up to gridpoint <span style="font-family: monospace;">nzt</span> (formerly <span style="font-family: monospace;">nzt-1</span>).
+scalars are now solved up to gridpoint nzt (formerly nzt-1).
 Boundary conditions for scalars at top adjusted respectively (now
-applied only at <span style="font-family: monospace;">nzt+1</span>).<br><br>The
+applied only at nzt+1).<br><br>The
 default top boundary condition for temperature has been renamed to <span style="font-style: italic;">'initial_gradient'</span>.<br><br>Calls
-of <span style="font-family: monospace;">dvrp_output_local</span>,
+of dvrp_output_local,
 which were commented out for a long time, are now activated for all
 streams.</td><td style="vertical-align: top;">advec_s_pw,
 boundary_conds, calc_precipitation, check_parameters, diffusion_e,
 diffusion_s, impact_of_latent_heat, init_dvrp, init_pt_anomaly,
-modules, production_e, prognostic_equations, spline_z</td></tr><tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: 3d-array <span style="font-family: monospace;">p</span> is not a
-pointer any more.<br><br>Bugfix in <span style="font-family: monospace;">init_particles</span>:
-<span style="font-family: monospace;">MPI_REAL</span>
-argument in <span style="font-family: monospace;">MPI_ALLREDUCE</span>
-replaced by<br><span style="font-family: monospace;">MPI_INTEGER</span>
-(caused error on NEC only).<br><br>Bugfix:&nbsp; <span style="font-family: monospace;">ddzw</span> now
-dimensioned <span style="font-family: monospace;">1:nzt"+1".</span></td><td style="vertical-align: top;">diffusion_e, diffusion_s,
-diffusion_u, diffusion_v, diffusion_w, init_particles, modules</td></tr>
+modules, production_e, prognostic_equations, spline_z</td></tr><tr><td>&nbsp;</td><td>&nbsp;</td><td>&nbsp;</td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: 3d-array p is not a
+pointer any more.<br><br>Bugfix in init_particles:
+MPI_REAL
+argument in MPI_ALLREDUCE
+replaced by<br>MPI_INTEGER
+(caused error on NEC only).<br><br>Bugfix:&nbsp; ddzw now
+dimensioned 1:nzt"+1".</td><td style="vertical-align: top;">diffusion_e, diffusion_s,
+diffusion_u, diffusion_v, diffusion_w, init_particles, modules</td></tr><tr><td style="vertical-align: top;">29/03/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.2</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">The code, including scripts, utility programs and documentation is now under full control of <span style="font-family: Courier New,Courier,monospace;">subversion</span>. This revision includes a quite large number of new features, changes and bugfixes.<br>&nbsp;<br>Particle reflection from vertical walls implemented. The particle SGS model is also adjusted to these vertical walls.<br><br>Wall functions for vertical walls now include diabatic conditions. New subroutines <span style="font-family: Courier New,Courier,monospace;">wall_fluxes</span>, <span style="font-family: Courier New,Courier,monospace;">wall_fluxes_e</span>. New 4D-array <span style="font-family: Courier New,Courier,monospace;">rif_wall</span>.<br><br>Calculation/output of precipitation amount, precipitation rate and z0 (by setting "<span style="font-style: italic;">pra*</span>", "<span style="font-style: italic;">prr*</span>", "<span style="font-style: italic;">z0*</span>" with <span style="font-family: Courier New,Courier,monospace;">data_output</span>). The time interval on which the precipitation amount is defined is set by new d3par-parameter <span style="font-family: Courier New,Courier,monospace;">precipitation_amount_interval</span>.<br><br>New inipar-parameter <span style="font-family: Courier New,Courier,monospace;">loop_optimization</span> to control the loop optimization method.<br><br>New
+inipar-parameter <span style="font-family: Courier New,Courier,monospace;">pt_reference</span>. If given, this value is used as the
+reference that is used in the buoyancy terms (otherwise, the instantaneous
+horizontally averaged temperature is used).<br><br>New d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span>
+to switch on and especially to switch off 64bit offset&nbsp;for 3D
+files only (because still some pd-software is unable to handle 64bit
+offset).<br><br>New d3par-parameter <span style="font-family: Courier New,Courier,monospace;">dt_max</span> to set the maximum&nbsp;value allowed for the&nbsp;timestep. <br><br>New user interfaces <span style="font-family: Courier New,Courier,monospace;">user_advec_particles</span> and <span style="font-family: Courier New,Courier,monospace;">user_init_3d_model</span>. The new initializing action "<span style="font-style: italic;">by_user</span>" calls <span style="font-family: Courier New,Courier,monospace;">user_init_3d_model</span> and allows the initial setting of all 3d arrays under complete user control.<br><br>Samples added to the user interface which show how to add user-define time series quantities.<br><br>Topography height informations are stored on arrays <span style="font-family: Courier New,Courier,monospace;">zu_s_inner</span> and <span style="font-family: Courier New,Courier,monospace;">zw_w_inner</span> and output to the 2d/3d NetCDF files.<br><br>Unit 9 is generally opened for output of debug informations (file <span style="font-family: Courier New,Courier,monospace;">DEBUG_&lt;pe#&gt;</span>).</td><td style="vertical-align: top;">Makefile<br><br>advec_particles,
+average_3d_data, buoyancy, calc_precipitation, check_open,
+check_parameters, data_output_2d, diffusion_e, diffusion_u,
+diffusion_v, diffusion_w, diffusivities, header, impact_of_latent_heat,
+init_particles, init_3d_model, modules, netcdf, parin, production_e,
+read_var_list, read_3d_binary, sum_up_3d_data, user_interface,
+write_var_list, write_3d_binary<br><br><span style="font-weight: bold;">new:</span><br>wall_fluxes<br></td></tr><tr><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">General revision of non-cyclic horizontal boundary conditions:<br>Radiation boundary conditions are now used instead of Neumann conditions at the outflow (calculation needs velocity values for <span style="font-family: Courier New,Courier,monospace;">t-dt</span>, which are stored on new arrays <span style="font-family: Courier New,Courier,monospace;">u_m_l</span>, <span style="font-family: Courier New,Courier,monospace;">u_m_r</span>, etc.). The calculation of a mean outflow is not needed any more. Volume flow control is added for the outflow boundary (<span style="font-weight: bold;">currently only for the north boundary!!</span>). Additional gridpoints along x and y (<span style="font-family: Courier New,Courier,monospace;">uxrp</span>, <span style="font-family: Courier New,Courier,monospace;">vynp</span>) are not needed any more and removed from the code. Routine "<span style="font-family: Courier New,Courier,monospace;">boundary_conds</span>" now operates on timelevel <span style="font-family: Courier New,Courier,monospace;">t+dt</span> and is not split in two parts (<span style="font-style: italic;">main</span>, <span style="font-style: italic;">uvw_outflow</span>) any more. Neumann boundary conditions are used at inflow/outflow in case of non-cyclic boundary conditions <span style="font-weight: bold;">for all 2d-arrays</span> that are handled by <span style="font-family: Courier New,Courier,monospace;">exchange_horiz_2d</span>.<br><span style="font-weight: bold;">Attention:&nbsp;the
+non-cyclic boundary conditions of this revision still contain some bugs
+which will be removed within the next revisions!</span><br><br>The Bott-Chlond-scheme can now be used in the vectorization-optimized part (NEC, etc.). Equations are solved up to gridpoint <span style="font-family: Courier New,Courier,monospace;">nzt</span>.<br><br>The
+FFT-method for solving the Poisson-equation is now working with Neumann
+boundary conditions both at the bottom and the top. This requires
+adjustments of the tridiagonal coefficients and subtracting the
+horizontally averaged mean from the vertical velocity field.<br><br>Particles-package is now part of the default code ("<span style="font-family: Courier New,Courier,monospace;">-p particles</span>" is not needed as an <span style="font-weight: bold;">mrun</span>-option any more). New attribute <span style="font-family: Courier New,Courier,monospace;">age_m</span> in <span style="font-family: Courier New,Courier,monospace;">particle_type</span>.<br><br>Move call of <span style="font-family: Courier New,Courier,monospace;">user_actions</span>( '<span style="font-style: italic;">after_integration</span>' ) below the increments of times<br>and counters. <span style="font-family: Courier New,Courier,monospace;">user_actions</span> is now called for each statistic region and has as an argument the number of the respective region (<span style="font-family: Courier New,Courier,monospace;">sr</span>).<br><br>d3par-parameter <span style="font-family: Courier New,Courier,monospace;">data_output_ts</span> is removed. Timeseries output for <span style="font-weight: bold;">profil</span>-software removed. Timeseries are now switched on by setting <span style="font-family: Courier New,Courier,monospace;">dt_dots</span>. Timeseries data is collected in <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>.<br><br>Initial velocities at <span style="font-family: Courier New,Courier,monospace;">nzb+1</span>
+are regarded for volume flow control in case they have been set zero
+before (to avoid small timesteps); see new internal parameters <span style="font-family: Courier New,Courier,monospace;">u/v_nzb_p1_for_vfc</span>.<br><br><span style="font-family: Courier New,Courier,monospace;">q</span> is not allowed any more to become negative (<span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>).<br><br><span style="font-family: Courier New,Courier,monospace;">poisfft_init</span> is only called if the fft-solver is switched on (<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>).<br><br>d3par-parameter <span style="font-family: Courier New,Courier,monospace;">moisture</span> renamed to <span style="font-family: Courier New,Courier,monospace;">humidity</span>.<br><br>Subversion global revision number is read from <span style="font-weight: bold;">mrun</span> and added to the run description header and to the run control (<span style="font-family: Courier New,Courier,monospace;">_rc</span>) file.<br><br><span style="font-family: Courier New,Courier,monospace;">__vtk</span> directives removed from main program.<br><br>The uitility routine&nbsp;<span style="font-family: Courier New,Courier,monospace;">interpret_config</span> now reads PALM environment variables from <span style="font-family: Courier New,Courier,monospace;">NAMELIST</span> instead using the system call <span style="font-family: Courier New,Courier,monospace;">GETENV</span>.</td><td style="vertical-align: top;">advec_s_bc, advec_u_pw,
+advec_u_up, advec_v_pw, advec_v_up, asselin_filter, boundary_conds, check_parameters,
+coriolis, data_output_dvrp, data_output_ptseries, data_output_ts,
+data_output_2d, data_output_3d, diffusion_u, diffusion_v,
+disturb_field, exchange_horiz, exchange_horiz_2d, flow_statistics, header, init_grid,
+init_particles, init_pegrid, init_rankine, init_pt_anomaly,
+init_1d_model, init_3d_model, modules, palm, package_parin, parin,
+poisfft, poismg, prandtl_fluxes, pres, production_e,
+prognostic_equations, read_var_list, read_3d_binary, sor,
+swap_timelevel, time_integration, write_var_list, write_3d_binary</td></tr><tr><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">&nbsp;</td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: preset of tendencies <span style="font-family: Courier New,Courier,monospace;">te_em</span>, <span style="font-family: Courier New,Courier,monospace;">te_um</span>, and <span style="font-family: Courier New,Courier,monospace;">te_vm</span> (<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>).<br><br>Bugfix in sample for reading user defined data from restart file (<span style="font-family: Courier New,Courier,monospace;">user_init</span>).<br><br>Bugfix in setting diffusivities for cases with the outflow damping layer extending over more than one subdomain (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>).<br><br>Check for possible negative humidities in the initial humidity profile.<br><br>In <span style="font-family: Courier New,Courier,monospace;">Makefile</span>, default suffixes are removed from the suffix list to avoid calling of <span style="font-family: Courier New,Courier,monospace;">m2c</span> in cases of existing <span style="font-family: Courier New,Courier,monospace;">.mod</span> files (problem on Linux systems).</td><td style="vertical-align: top;">Makefile<br><br>check_parameters, init_1d_model, init_3d_model, user_interface</td></tr>
 </tbody>
 </table>&nbsp;<b><blink>Attention:</blink></b>
