Index: palm/trunk/DOC/app/chapter_3.4.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.4.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_3.4.html	(revision 197)
@@ -8,5 +8,4 @@
   
   <title>PALM chapter 3.4</title></head>
-
 <body>
 
@@ -2212,5 +2211,5 @@
 accuracy has to be
 indicated
-with the help of <a href="chapter_4.2.html#do3d_precision">do3d_precision</a>.
+with the help of <a href="chapter_4.2.html#do3d_comp_prec">do3d_comp_prec</a>.
 In favorable cases the file size can be reduced by
 a factor of up to 5. For the visualization of compressed data a special
Index: palm/trunk/DOC/app/chapter_3.8.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.8.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_3.8.html	(revision 197)
@@ -1,11 +1,10 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html>
-<head>
+<html><head>
 
   <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
-  <title>PALM chapter 3.8</title>
+  
 
 
-  <meta name="GENERATOR" content="StarOffice 7 (Win32)">
+  <title>PALM chapter 3.8</title><meta name="GENERATOR" content="StarOffice 7 (Win32)">
 
   <meta name="AUTHOR" content="Siegfried Raasch">
@@ -21,7 +20,5 @@
 @page { size: 21cm 29.7cm }
 -->
-  </style>
-</head>
-
+  </style></head>
 
 <body style="direction: ltr;" lang="en-US">
@@ -126,9 +123,8 @@
 <p style="line-height: 100%;"><br>
 
-<font color="#000080"><font color="#000080"><a href="chapter_3.7.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" src="left.gif" name="Grafik1"></font></a><a href="index.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.0.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p>
+<font color="#000080"><font color="#000080"><a href="chapter_3.7.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" src="left.gif" name="Grafik1"></font></a><a href="index.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_3.9.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" src="right.gif" name="Grafik3"></font></a></font></font></p>
 
 <p style="line-height: 100%;"><i>Last
 change:&nbsp;</i> $Id$</p>
 
-</body>
-</html>
+</body></html>
Index: palm/trunk/DOC/app/chapter_3.9.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.9.html	(revision 197)
+++ palm/trunk/DOC/app/chapter_3.9.html	(revision 197)
@@ -0,0 +1,52 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head>
+
+  <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252">
+  
+
+
+  <title>PALM chapter 3.9</title><meta name="GENERATOR" content="StarOffice 7 (Win32)">
+
+  <meta name="AUTHOR" content="Siegfried Raasch">
+
+  <meta name="CREATED" content="20040809;13460943">
+
+  <meta name="CHANGED" content="20041112;15085727">
+
+  <meta name="KEYWORDS" content="parallel LES model">
+
+  <style>
+<!--
+@page { size: 21cm 29.7cm }
+-->
+  </style></head>
+<body style="direction: ltr;" lang="en-US">
+
+<h3 style="line-height: 100%;">3.9 Setup for turbulent inflow</h3>
+
+<p style="line-height: 100%;">Starting from version 3.5
+PALM includes a so-called turbulence recycling method which allows a
+turbulent inflow with non-cyclic horizontal boundary conditions. The
+method follows the one described by Lund et al. (1998, J. Comp. Phys., <span style="font-weight: bold;">140</span>, 233-258), modified by Kataoka and Mizuno (2002, Wind and Structures, <span style="font-weight: bold;">5</span>, 379-392). The method is switched on by setting the initial parameter <a href="chapter_4.1.html#turbulent_inflow">turbulent_inflow</a> = <span style="font-style: italic;">.TRUE.</span>.</p><p style="line-height: 100%;">The turbulent signal A'(y,z) to be imposed at the left inflow boundary is taken from the simulation at a fixed distance x<sub>r</sub> from the inflow (given by parameter <a href="chapter_4.1.html#recycling_width">recycling_width</a>): A'(y,z) = A(x<sub>r</sub>,y,z) - <span style="font-weight: bold;">A(z)</span>, where <span style="font-weight: bold;">A(z)</span>
+is the horizontal average between the inflow boundary and the recycling
+plane. The turbulent quantity A'(y,z) is then added to a mean inflow
+profile a(z) which is the horizontal (and temporal) average as
+calculated from a precursor run. This is done after each timestep.</p><p style="line-height: 100%; font-weight: bold;">So far (09/16/08), a turbulent signal is imposed to all prognostic variables except humidity (passive scalar) and salinity!</p><p style="line-height: 100%;">In
+order to avoid a continous growth of the turbulent layer with time, the
+height up to which turbulence is recycled is limited by parameter <a href="chapter_4.1.html#inflow_damping_height">inflow_damping_height</a>. By default, this height is calculated and taken from the precursor run. </p>The following tries to give a short recipe about how to create a proper setup for using the turbulence recycling method:<br><br><ul><li>A
+precursor run with cyclic horizontal boundary conditions has to be
+carried out in order to create a (quasi-) stationary state. Since the
+horizontal average from this precursor run is used as the mean inflow
+profile for the main run, the wall-normal velocity component must point
+into the domain at every grid point and its magnitude should be large enough in order to guarantee an inflow even if a turbulence signal is added.</li><li>Since the main run requires &nbsp;...</li><li>The
+main run has to read the binary data from the precursor run .... &nbsp;
+&nbsp; set bc_lr = 'dirichlet/radiation' ... &nbsp;
+conserve_volume_flow = .TRUE. ? ....</li><li>The main run allows to use a larger domain along x and y than in the precursor run ...</li><li>Recycling width should be equal to the domain size of the precursor run (or larger?)</li></ul><pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">#</font><br><font style="font-size: 10pt;" size="2">RUN_CONTROL<span style="font-weight: bold;">_O</span></font><font style="font-size: 10pt;" size="2"> out:loc:tr d3<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/MONITORING <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">rc</font><br><font style="font-size: 10pt;" size="2">HEADER</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> out:loc:tr d3<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/MONITORING <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">header</font><br><font style="font-size: 10pt;" size="2">PLOT1D_PAR<span style="font-weight: bold;">_O</span></font><font style="font-size: 10pt;" size="2"> out:loc:tr pr<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/OUTPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">pr_par</font><br><font style="font-size: 10pt;" size="2">PLOT1D_DATA</font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">_O</span> out:loc:tr pr<span style="font-weight: bold;">o</span># ~/palm/current_version/JOBS/$fname/OUTPUT <span style="font-weight: bold;">_</span></font><font style="font-size: 10pt;" size="2"><span style="font-weight: bold;">o</span>_</font><font style="font-size: 10pt;" size="2">pr_in</font><br></pre><br><hr>
+<p style="line-height: 100%;"><br>
+
+<font color="#000080"><font color="#000080"><a href="chapter_3.8.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" src="left.gif" name="Grafik1"></font></a><a href="index.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.0.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" src="right.gif" name="Grafik3"></font></a></font></font></p>
+
+<p style="line-height: 100%;"><i>Last
+change:&nbsp;</i> $Id$</p>
+
+</body></html>
Index: palm/trunk/DOC/app/chapter_4.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.1.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_4.1.html	(revision 197)
@@ -5510,5 +5510,55 @@
 
 
-    <tr>
+    <tr><td style="vertical-align: top;"><p><a name="humidity"></a><b>humidity</b></p></td><td style="vertical-align: top;">L</td><td style="vertical-align: top;"><i>.F.</i></td><td style="vertical-align: top;"><p>Parameter to
+switch on the prognostic equation for specific
+humidity q.<br>
+
+
+
+
+
+
+ </p>
+
+
+
+
+
+
+ 
+      
+      
+      
+      
+      
+      
+      <p>The initial vertical
+profile of q can be set via parameters <a href="chapter_4.1.html#q_surface">q_surface</a>, <a href="chapter_4.1.html#q_vertical_gradient">q_vertical_gradient</a>
+and <a href="chapter_4.1.html#q_vertical_gradient_level">q_vertical_gradient_level</a>.&nbsp;
+Boundary conditions can be set via <a href="chapter_4.1.html#q_surface_initial_change">q_surface_initial_change</a>
+and <a href="chapter_4.1.html#surface_waterflux">surface_waterflux</a>.<br>
+
+
+
+
+
+
+
+      </p>
+
+
+
+
+
+
+
+If the condensation scheme is switched on (<a href="chapter_4.1.html#cloud_physics">cloud_physics</a>
+= .TRUE.), q becomes the total liquid water content (sum of specific
+humidity and liquid water content).</td></tr><tr><td style="vertical-align: top;"><span style="font-weight: bold;"><a name="inflow_damping_height"></a>inflow_damping_height</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">from precursor run</span></td><td style="vertical-align: top;">Height below which the turbulence signal is used for turbulence recycling (in m).<br><br>In case of a turbulent inflow (see <a href="chapter_4.1.html#turbulent_inflow">turbulent_inflow</a>),
+this parameter defines the vertical thickness of the turbulent layer up
+to which the turbulence extracted at the recycling plane (see <a href="chapter_4.1.html#recycling_width">recycling_width</a>)
+shall be imposed to the inflow. Above this level the turbulence signal
+is linearly damped to zero. The transition range within which the
+signal falls to zero is given by the parameter <a href="chapter_4.1.html#inflow_damping_width">inflow_damping_width</a>.<br><br>By default, this height is set as the height of the convective boundary layer as calculated from a precursor run. See <a href="chapter_3.9.html">chapter 3.9</a> about proper settings for getting this CBL height from a precursor run. </td></tr><tr><td style="vertical-align: top;"><span style="font-weight: bold;"><a name="inflow_damping_width"></a>inflow_damping_width</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">0.1 * <a href="chapter_4.1.html#inflow_damping_height">inflow_damping</a></span><a href="chapter_4.1.html#inflow_damping_height"><br style="font-style: italic;"><span style="font-style: italic;">_height</span></a></td><td style="vertical-align: top;">Transition range within which the turbulance signal is damped to zero (in m).<br><br>See <a href="chapter_4.1.html#inflow_damping_height">inflow_damping_height</a> for explanation.</td></tr><tr>
 
 
@@ -6022,33 +6072,29 @@
 must be switched of in the equation of motion&nbsp; for w (this
 requires the user to comment out the call of <span style="font-family: monospace;">buoyancy</span> in the
-source code of <span style="font-family: monospace;">prognostic_equations.f90</span>).</p>
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      </ul>
-
-
-
-
-
-
- 
-      
-      
-      
-      
-      
-      
-      <p style="font-style: normal;">Values may be
+source code of <span style="font-family: monospace;">prognostic_equations.f90</span>).</p></ul>
+
+
+
+
+
+
+ 
+      
+      
+      
+      
+      
+      
+      <p style="font-style: italic;">'read_data_for_recycling'</p><p style="font-style: normal; margin-left: 40px;">Here,
+3d-data from a precursor run are read by the initial (main) run. The
+precursor run is allowed to have a smaller domain along x and y
+compared with the main run. Also, different numbers of processors can
+be used for these two runs. Limitations are that the precursor run must
+use cyclic horizontal boundary conditions and that the subdomains of
+the main run must not be larger than the subdomains of the precursor
+run. If the total domain of the main run is larger than that of the precursor
+run, the domain is filled by cyclic repetition&nbsp;of the (cyclic)
+precursor data. This initialization method is recommended if a
+turbulent inflow is used (see <a href="chapter_4.1.html#turbulent_inflow">turbulent_inflow</a>). 3d-data must be made available to the run by activating an appropriate file connection statement for local file BININ. See <a href="chapter_3.9.html">chapter 3.9</a> for more details, where usage of a turbulent inflow is explained. </p><p style="font-style: normal;">Values may be
 combined, e.g. <b>initializing_actions</b> = <span style="font-style: italic;">'set_constant_profiles
 initialize_vortex'</span>, but the values of <span style="font-style: italic;">'set_constant_profiles'</span>,
@@ -6069,5 +6115,5 @@
       
       
-      <p style="font-style: italic;"> </p>
+      
 
 
@@ -6749,109 +6795,5 @@
 
 
- <tr>
-
-
-
-
-
-
- <td style="vertical-align: top;"> 
-      
-      
-      
-      
-      
-      
-      <p><a name="humidity"></a><b>humidity</b></p>
-
-
-
-
-
-
-
-      </td>
-
-
-
-
-
-
- <td style="vertical-align: top;">L</td>
-
-
-
-
-
-
-
-      <td style="vertical-align: top;"><i>.F.</i></td>
-
-
-
-
-
-
-
-      <td style="vertical-align: top;"> 
-      
-      
-      
-      
-      
-      
-      <p>Parameter to
-switch on the prognostic equation for specific
-humidity q.<br>
-
-
-
-
-
-
- </p>
-
-
-
-
-
-
- 
-      
-      
-      
-      
-      
-      
-      <p>The initial vertical
-profile of q can be set via parameters <a href="chapter_4.1.html#q_surface">q_surface</a>, <a href="chapter_4.1.html#q_vertical_gradient">q_vertical_gradient</a>
-and <a href="chapter_4.1.html#q_vertical_gradient_level">q_vertical_gradient_level</a>.&nbsp;
-Boundary conditions can be set via <a href="chapter_4.1.html#q_surface_initial_change">q_surface_initial_change</a>
-and <a href="chapter_4.1.html#surface_waterflux">surface_waterflux</a>.<br>
-
-
-
-
-
-
-
-      </p>
-
-
-
-
-
-
-
-If the condensation scheme is switched on (<a href="chapter_4.1.html#cloud_physics">cloud_physics</a>
-= .TRUE.), q becomes the total liquid water content (sum of specific
-humidity and liquid water content).</td>
-
-
-
-
-
-
- </tr>
+ 
 
 
@@ -7809,243 +7751,12 @@
 
 
-    <tr>
-
-
-
-
-
-
- <td style="vertical-align: top;"> 
-      
-      
-      
-      
-      
-      
-      <p><a name="npex"></a><b>npex</b></p>
-
-
-
-
-
-
- </td>
-
-
-
-
-
-
-
-      <td style="vertical-align: top;">I</td>
-
-
-
-
-
-
- <td style="vertical-align: top;"><br>
-
-
-
-
-
-
- </td>
-
-
-
-
-
-
- <td style="vertical-align: top;"> 
-      
-      
-      
-      
-      
-      
-      <p>Number of processors
-along x-direction of the virtual
-processor
-net.&nbsp; </p>
-
-
-
-
-
-
- 
-      
-      
-      
-      
-      
-      
-      <p>For parallel runs, the total
-number of processors to be used
-is given by
-the <span style="font-weight: bold;">mrun</span>
-option <a href="http://www.muk.uni-hannover.de/software/mrun_beschreibung.html#Opt-X">-X</a>.
-By default, depending on the type of the parallel computer, PALM
-generates a 1d processor
-net (domain decomposition along x, <span style="font-weight: bold;">npey</span>
-= <span style="font-style: italic;">1</span>) or a
-2d-net (this is
-favored on machines with fast communication network). In case of a
-2d-net, it is tried to make it more or less square-shaped. If, for
-example, 16 processors are assigned (-X 16), a 4 * 4 processor net is
-generated (<span style="font-weight: bold;">npex</span>
-= <span style="font-style: italic;">4</span>, <span style="font-weight: bold;">npey</span>
-= <span style="font-style: italic;">4</span>).
-This choice is optimal for square total domains (<a href="#nx">nx</a>
-= <a href="#ny">ny</a>),
-since then the number of ghost points at the lateral boundarys of
-the subdomains is minimal. If <span style="font-weight: bold;">nx</span>
-nd <span style="font-weight: bold;">ny</span>
-differ extremely, the
-processor net should be manually adjusted using adequate values for <span style="font-weight: bold;">npex</span> and <span style="font-weight: bold;">npey</span>.&nbsp; </p>
-
-
-
-
-
-
-
-      
-      
-      
-      
-      
-      
-      <p><b>Important:</b> The value of <span style="font-weight: bold;">npex</span> * <span style="font-weight: bold;">npey</span> must exactly
-correspond to the
-value assigned by the <span style="font-weight: bold;">mrun</span>-option
-      <tt>-X</tt>.
-Otherwise the model run will abort with a corresponding error
-message.&nbsp; <br>
-
-
-
-
-
-
-
-Additionally, the specification of <span style="font-weight: bold;">npex</span>
-and <span style="font-weight: bold;">npey</span>
-may of course
-override the default setting for the domain decomposition (1d or 2d)
-which may have a significant (negative) effect on the code performance.
-      </p>
-
-
-
-
-
-
- </td>
-
-
-
-
-
-
- </tr>
-
-
-
-
-
-
- <tr>
-
-
-
-
-
-
- <td style="vertical-align: top;"> 
-      
-      
-      
-      
-      
-      
-      <p><a name="npey"></a><b>npey</b></p>
-
-
-
-
-
-
-
-      </td>
-
-
-
-
-
-
- <td style="vertical-align: top;">I</td>
-
-
-
-
-
-
-
-      <td style="vertical-align: top;"><br>
-
-
-
-
-
-
- </td>
-
-
-
-
-
-
- <td style="vertical-align: top;"> 
-      
-      
-      
-      
-      
-      
-      <p>Number of processors
-along y-direction of the virtual
-processor
-net.&nbsp; </p>
-
-
-
-
-
-
- 
-      
-      
-      
-      
-      
-      
-      <p>For further information see <a href="#npex">npex</a>.</p>
-
-
-
-
-
-
- </td>
-
-
-
-
-
-
- </tr>
+    
+
+
+
+
+
+
+ 
 
 
@@ -11530,5 +11241,8 @@
 
 
- <tr>
+ <tr><td style="vertical-align: top;"><span style="font-weight: bold;"><a name="recycling_width"></a>recycling_width</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">0.1 * <a href="chapter_4.1.html#nx">nx</a> * <a href="chapter_4.1.html#dx">dx</a></span></td><td style="vertical-align: top;">Distance of the recycling plane from the inflow boundary (in m).<br><br>This
+parameter sets the horizontal extension (along the direction of the
+main flow) of the so-called recycling domain which is used to generate
+a turbulent inflow (see <a href="chapter_4.1.html#turbulent_inflow">turbulent_inflow</a>). <span style="font-weight: bold;">recycling_width</span> must be larger than the grid spacing (dx) and smaller than the length of the total domain (nx * dx).</td></tr><tr>
 
 
@@ -14376,7 +14090,7 @@
 = <a href="#scalar_advec">scalar_advec</a>
 = '<i>pw-scheme'</i>, <a href="chapter_4.2.html#psolver">psolver</a>
-= <i>'poisfft'</i> or '<i>poisfft_hybrid'</i>,
+/= <i>'sor</i><i>'</i>,
       <i>&nbsp;</i><a href="#alpha_surface">alpha_surface</a>
-= 0.0, <a href="#bc_lr">bc_lr</a> = <a href="#bc_ns">bc_ns</a> = <span style="font-style: italic;">'cyclic'</span>,&nbsp;<a style="" href="#galilei_transformation">galilei_transformation</a>
+= 0.0,<span style="font-style: italic;"></span>&nbsp;<a style="" href="#galilei_transformation">galilei_transformation</a>
 = <span style="font-style: italic;">.F.</span>,&nbsp;<a href="#cloud_physics">cloud_physics&nbsp;</a> = <span style="font-style: italic;">.F.</span>,&nbsp; <a href="#cloud_droplets">cloud_droplets</a> = <span style="font-style: italic;">.F.</span>,&nbsp;&nbsp;<a href="#humidity">humidity</a> = <span style="font-style: italic;">.F.</span>, and <a href="#prandtl_layer">prandtl_layer</a> = .T..<br>
 
@@ -14952,5 +14666,9 @@
 
 
-    <tr>
+    <tr><td style="vertical-align: top;"><a name="turbulent_inflow"></a><span style="font-weight: bold;">turbulent_inflow</span></td><td style="vertical-align: top;">L</td><td style="vertical-align: top;"><span style="font-style: italic;">.F.</span></td><td style="vertical-align: top;">Generates a turbulent inflow at side boundaries using a turbulence recycling method.<br><br>Turbulent inflow is realized using the turbulence recycling method from Lund et al. (1998, J. Comp. Phys., <span style="font-weight: bold;">140</span>, 233-258) modified by Kataoka and Mizuno (2002, Wind and Structures, <span style="font-weight: bold;">5</span>, 379-392).<br><br>A turbulent inflow requires Dirichlet conditions at the respective inflow boundary. <span style="font-weight: bold;">So far, a turbulent inflow is realized from the left (west) side only, i.e. </span><a style="font-weight: bold;" href="chapter_4.1.html#bc_lr">bc_lr</a><span style="font-weight: bold;">&nbsp;=</span><span style="font-style: italic; font-weight: bold;"> 'dirichlet/radiation'</span><span style="font-weight: bold;"> is required!</span><br><br>The initial (quasi-stationary) turbulence field should be generated by a precursor run and used by setting <a href="chapter_4.1.html#initializing_actions">initializing_actions</a> =<span style="font-style: italic;"> 'read_data_for_recycling'</span>.<br><br>The distance of the recycling plane from the inflow boundary can be set with parameter <a href="chapter_4.1.html#recycling_width">recycling_width</a>.
+The heigth above ground above which the turbulence signal is not used
+for recycling and the width of the layer within&nbsp;the magnitude of
+the turbulence signal is damped from 100% to 0% can be set with
+parameters <a href="chapter_4.1.html#inflow_damping_height">inflow_damping_height</a> and <a href="chapter_4.1.html#inflow_damping_width">inflow_damping_width</a>.<br><br>The detailed setup for a turbulent inflow is described in <a href="chapter_3.9.html">chapter 3.9</a>.</td></tr><tr>
 
 
Index: palm/trunk/DOC/app/chapter_4.2.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.2.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_4.2.html	(revision 197)
@@ -2575,5 +2575,5 @@
 
 
- <tr>
+ <tr><td align="undefined" valign="undefined"><span style="font-style: italic; color: rgb(255, 0, 0);">p</span></td><td align="undefined" valign="undefined">Perturbation pressure (in Pa)</td></tr><tr>
 
 
@@ -3717,5 +3717,5 @@
 assigned. This
 yields a loss of accuracy, but the file size is clearly reduced. The
-parameter <a href="chapter_4.2.html#do3d_precision">do3d_precision</a>
+parameter <a href="chapter_4.2.html#do3d_comp_prec">do3d_comp_prec</a>
 can be used to separately define the number of significant digits for
 each quantity.<br>
@@ -3747,5 +3747,5 @@
       
       
-      <p><a name="do3d_precision"></a><b>do3d_precision</b></p>
+      <p><a name="do3d_comp_prec"></a><b>do3d_comp_prec</b></p>
 
 
@@ -3817,5 +3817,5 @@
       
       
-      <p>The default assignment is <span style="font-weight: bold;">do3d_precision</span>
+      <p>The default assignment is <span style="font-weight: bold;">do3d_comp_prec</span>
 = <span style="font-style: italic;">'u2'</span>, <span style="font-style: italic;">'v2'</span>, <span style="font-style: italic;">'w2'</span>, <span style="font-style: italic;">'p5'</span>, <span style="font-style: italic;">'pt2'</span>.</p>
 
@@ -4817,9 +4817,6 @@
 
             <td style="vertical-align: top;">Subgrid-scale sensible
-heat flux near the surface (horizontal
-average)
-between z = 0 and z = z<sub>p</sub> = zu(1) (there it
-corresponds to
-the total heat flux) (in K m/s).</td>
+heat flux at k=0 (horizontal
+average), constant within Prandtl-layer (in K m/s).</td>
 
 
@@ -4856,5 +4853,8 @@
 
 
- <tr>
+ <tr><td align="undefined" valign="undefined"><span style="font-style: italic;">w"u"0</span></td><td align="undefined" valign="undefined">Subgrid-scale momentum flux (u-component) at k=0 (horizontal average), constant within Prandtl-layer (in m<sup>2</sup>/s<sup>2</sup>).</td></tr><tr><td align="undefined" valign="undefined"><span style="font-style: italic;">w"v"0</span></td><td align="undefined" valign="undefined">Subgrid-scale momentum flux (v-component) at k=0 (horizontal average), constant within Prandtl-layer (in m<sup>2</sup>/s<sup>2</sup>).</td></tr><tr><td align="undefined" valign="undefined"><span style="font-style: italic;">w"q"0</span></td><td align="undefined" valign="undefined">Subgrid-scale
+humidity flux at k=0 (horizontal average), constant within
+Prandtl-layer (in kg/kg m/s). Zero values are output if humidity is not
+used.</td></tr><tr>
 
 
@@ -4886,54 +4886,11 @@
 
 
- <tr>
-
-
-
-            <td style="vertical-align: top; font-style: italic;">splptx</td>
-
-
-
-            <td style="vertical-align: top;">Percentage of grid points
-using upstream scheme along x with
-upstream-spline advection switched on.</td>
-
-
- </tr>
-
-
- <tr>
-
-
-
-            <td style="vertical-align: top; font-style: italic;">splpty</td>
-
-
-
-            <td style="vertical-align: top;">Percentage of grid points
-using upstream scheme along y with
-upstream-spline
-advection switched on.</td>
-
-
- </tr>
-
-
- <tr>
-
-
- <td style="vertical-align: top; font-style: italic;">splptz</td>
-
-
-
-            <td style="vertical-align: top;">Percentage of grid points
-using upstream scheme along z with
-upstream-spline
-advection switched on.<br>
-
-
- </td>
-
-
- </tr>
+ 
+
+
+ 
+
+
+ 
 
 
@@ -5640,5 +5597,5 @@
 It is only possible to gather data from a level larger than the one
 determined automatically. A test run may be neccessary to determine
-this level.</td>
+this level.<br><br>Setting of <span style="font-weight: bold;">mg_switch_to_pe0_level</span> = <span style="font-style: italic;">-1</span> prevents that data are collected on PE0 at all, i.e. coarsening of grids is limited by the subdomains.</td>
 
 
@@ -5848,5 +5805,92 @@
 
 
- <tr>
+ <tr><td style="vertical-align: top;"><a href="npex"><span style="font-weight: bold;"></span></a><span style="font-weight: bold;"><a name="npex"></a>npex</span></td><td style="vertical-align: top;">I</td><td style="vertical-align: top;"></td><td style="vertical-align: top;"><p>Number of processors
+along x-direction of the virtual
+processor
+net.&nbsp; </p>
+
+
+
+
+
+
+ 
+      
+      
+      
+      
+      
+      
+      <p>For parallel runs, the total
+number of processors to be used
+is given by
+the <span style="font-weight: bold;">mrun</span>
+option <a href="http://www.muk.uni-hannover.de/software/mrun_beschreibung.html#Opt-X">-X</a>.
+By default, depending on the type of the parallel computer, PALM
+generates a 1d processor
+net (domain decomposition along x, <span style="font-weight: bold;">npey</span>
+= <span style="font-style: italic;">1</span>) or a
+2d-net (this is
+favored on machines with fast communication network and/or large number of processors (&gt;256)). In case of a
+2d-net, it is tried to make it more or less square-shaped. If, for
+example, 16 processors are assigned (-X 16), a 4 * 4 processor net is
+generated (<span style="font-weight: bold;">npex</span>
+= <span style="font-style: italic;">4</span>, <span style="font-weight: bold;">npey</span>
+= <span style="font-style: italic;">4</span>).
+This choice is optimal for square total domains (<a href="chapter_4.1.html#nx">nx</a>
+= <a href="chapter_4.1.html#ny">ny</a>),
+since then the number of ghost points at the lateral boundarys of
+the subdomains reaches a minimum. If <span style="font-weight: bold;">nx</span>
+and <span style="font-weight: bold;">ny</span>
+differ extremely, the
+processor net should be manually adjusted using adequate values for <span style="font-weight: bold;">npex</span> and <span style="font-weight: bold;">npey</span>.&nbsp; </p>
+
+
+
+
+
+
+
+      
+      
+      
+      
+      
+      
+      <p><b>Important:</b> The value of <span style="font-weight: bold;">npex</span> * <span style="font-weight: bold;">npey</span> must exactly match the
+value assigned by the <span style="font-weight: bold;">mrun</span>-option
+      <tt>-X</tt>.
+Otherwise the model run will abort with a corresponding error
+message.&nbsp; <br>
+
+
+
+
+
+
+
+Additionally, the specification of <span style="font-weight: bold;">npex</span>
+and <span style="font-weight: bold;">npey</span>
+may of course
+override the default setting for the domain decomposition (1d or 2d)
+which may have a significant (negative) effect on the code performance.
+      </p></td></tr><tr><td style="vertical-align: top;"><span style="font-weight: bold;"><a name="npey"></a>npey</span></td><td style="vertical-align: top;">I</td><td style="vertical-align: top;"></td><td style="vertical-align: top;"><p>Number of processors
+along y-direction of the virtual
+processor
+net.&nbsp; </p>
+
+
+
+
+
+
+ 
+      
+      
+      
+      
+      
+      
+      <p>For further information see <a href="chapter_4.2.html#npex">npex</a>.</p></td></tr><tr>
 
 
Index: palm/trunk/DOC/app/chapter_4.4.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.4.1.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_4.4.1.html	(revision 197)
@@ -151,6 +151,6 @@
 virtual processor topology (grid) of 8*1 (x*y) is used. (<span style="font-weight: bold;">Note:</span> the user may
 adjust this
-default domain decomposition with the help of the parameters <a href="chapter_4.1.html#npex">npex</a>
-and <a href="chapter_4.1.html#npey">npey</a>).
+default domain decomposition with the help of the parameters <a href="chapter_4.2.html#npex">npex</a>
+and <a href="chapter_4.2.html#npey">npey</a>).
 </p><p style="line-height: 100%;">Provided that the
 parameters
Index: palm/trunk/DOC/app/chapter_4.4.2.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.4.2.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_4.4.2.html	(revision 197)
@@ -155,6 +155,6 @@
 virtual processor topology (grid) of 8*1 (x*y) is used. (<span style="font-weight: bold;">Note:</span> the user may
 adjust this
-default domain decomposition with the help of the parameters <a href="chapter_4.1.html#npex">npex</a>
-and <a href="chapter_4.1.html#npey">npey</a>).
+default domain decomposition with the help of the parameters <a href="chapter_4.2.html#npex">npex</a>
+and <a href="chapter_4.2.html#npey">npey</a>).
 </p><p style="line-height: 100%;">Provided that the
 parameters
Index: palm/trunk/DOC/app/chapter_4.5.6.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.5.6.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_4.5.6.html	(revision 197)
@@ -1,11 +1,9 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
 <html><head>
-<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
-chapter 4.5.6</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041029;13171001"> <meta name="CHANGED" content="20041117;12013945"> <meta name="KEYWORDS" content="parallel LES model"> <style>
+<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 4.5.6</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041029;13171001"> <meta name="CHANGED" content="20041117;12013945"> <meta name="KEYWORDS" content="parallel LES model"> <style>
 <!--
 @page { size: 21cm 29.7cm }
 -->
 </style></head>
-
 <body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.6
 Plots of compressed
@@ -22,5 +20,5 @@
 = <i>.TRUE.</i> and by assigning the desired accuracy
 (number of
-significant digits) via <a href="chapter_4.2.html#do3d_precision">do3d_precision</a>.
+significant digits) via <a href="chapter_4.2.html#do3d_comp_prec">do3d_comp_prec</a>.
 A separate accuracy must be assigned for each individual quantity.
 Using uncompressed data, each grid point value is
Index: palm/trunk/DOC/app/chapter_4.6.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.6.html	(revision 189)
+++ palm/trunk/DOC/app/chapter_4.6.html	(revision 197)
@@ -3444,5 +3444,5 @@
 
 
- <td><a href="chapter_4.2.html#do3d_precision"><span style="font-weight: bold;">do3d_precision</span></a></td>
+ <td><a href="chapter_4.2.html#do3d_comp_prec"><span style="font-weight: bold;">do3d_comp_prec</span></a></td>
 
 
@@ -6408,5 +6408,5 @@
 
 
-    <tr>
+    <tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#inflow_damping_height"><span style="font-weight: bold;">inflow_damping_height</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">R</td><td align="undefined" valign="undefined"><span style="font-style: italic;">from precursor run</span></td><td align="undefined" valign="undefined">Height below which the turbulence signal is used for turbulence recycling (in m).</td></tr><tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#inflow_damping_width"><span style="font-weight: bold;">inflow_damping_width</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">R</td><td align="undefined" valign="undefined"><span style="font-style: italic;">0.1 * <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#inflow_damping_height">inflow_damping</a></span><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#inflow_damping_height"><span style="font-style: italic;">_height</span></a></td><td align="undefined" valign="undefined">Transition range within which the turbulance signal is damped to zero (in m).</td></tr><tr>
 
 
@@ -7704,5 +7704,5 @@
       
       
-      <p><a href="chapter_4.1.html#npex"><b>npex</b></a></p>
+      <p><a href="chapter_4.2.html#npex"><b>npex</b></a></p>
 
 
@@ -7717,5 +7717,5 @@
       
       
-      <p>I</p>
+      <p>R</p>
 
 
@@ -7781,5 +7781,5 @@
       
       
-      <p><a href="chapter_4.1.html#npey"><b>npey</b></a></p>
+      <p><a href="chapter_4.2.html#npey"><b>npey</b></a></p>
 
 
@@ -7794,5 +7794,5 @@
       
       
-      <p>I</p>
+      <p>R</p>
 
 
@@ -11650,5 +11650,5 @@
 
 
- <tr>
+ <tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#recycling_width"><span style="font-weight: bold;">recycling_width</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">R</td><td align="undefined" valign="undefined"><span style="font-style: italic;">0.1 * <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#nx">nx</a> * <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#dx">dx</a></span></td><td align="undefined" valign="undefined">Distance of the recycling plane from the inflow boundary (in m).<br></td></tr><tr>
 
 
@@ -13905,5 +13905,5 @@
 
 
-    <tr>
+    <tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#turbulent_inflow"><span style="font-weight: bold;">turbulent_inflow</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">L</td><td align="undefined" valign="undefined"><span style="font-style: italic;">.F.</span></td><td align="undefined" valign="undefined">Generates a turbulent inflow at side boundaries using a turbulence recycling method.</td></tr><tr>
 
 
Index: palm/trunk/DOC/app/index.html
===================================================================
--- palm/trunk/DOC/app/index.html	(revision 189)
+++ palm/trunk/DOC/app/index.html	(revision 197)
@@ -160,5 +160,4 @@
  <u3:LatentStyles DefLockedState="false" LatentStyleCount="156">  </u3:LatentStyles>
 </xml><![endif]--></head>
-
 <body style="" lang="DE" link="blue" vlink="blue">
 
@@ -177,5 +176,5 @@
 <p><span style="font-family: Thorndale;" lang="EN-GB">Current
 model
-version:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3.4a<br>
+version:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3.5<br>
 For date of last change see bottom line of each page. <o:p></o:p></span></p>
 
