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--- palm/trunk/DOC/app/chapter_3.0.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_3.0.html	(revision 97)
@@ -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 3.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Marcus Oliver Letzel"> <meta name="CREATED" content="20040723;15213734"> <meta name="CHANGED" content="20041112;13170538"> <meta name="KEYWORDS" content="parallel LES model"> <style>
+<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 3.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Marcus Oliver Letzel"> <meta name="CREATED" content="20040723;15213734"> <meta name="CHANGED" content="20041112;13170538"> <meta name="KEYWORDS" content="parallel LES model"> <style>
 <!--
 @page { size: 21cm 29.7cm }
 -->
 </style></head>
-
 <body style="direction: ltr;" lang="en-US"><h2 style="font-style: normal; line-height: 100%;"><font size="4">3.0
 Execution of model runs</font></h2>
@@ -41,6 +39,6 @@
 changed by the user. Some of the most important parameters are not
 preset with default values and must be adjusted by the user in each
-case. Such a typical, minimum parameter set is described in <a href="chapter_4.4.html">chapter
-4.4</a>. For the subsequent analysis of model runs, graphical
+case. Such a typical, minimum parameter set is described in <a href="chapter_4.4.1.html">chapter
+4.4.1</a>. For the subsequent analysis of model runs, graphical
 visualization of model data is particularly important. <a href="chapter_4.5.html">Chapter
 4.5</a> describes, how such outputs are produced with the model. </p>
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--- palm/trunk/DOC/app/chapter_3.2.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_3.2.html	(revision 97)
@@ -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 3.2</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Marcus Oliver Letzel"> <meta name="CREATED" content="20040726;13164873"> <meta name="CHANGED" content="20050119;9245042"> <meta name="KEYWORDS" content="parallel LES model"> <style>
+<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 3.2</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Marcus Oliver Letzel"> <meta name="CREATED" content="20040726;13164873"> <meta name="CHANGED" content="20050119;9245042"> <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%;">3.2 Example of a minimum
 configuration
@@ -20,6 +18,6 @@
 here)
 and can be used, together with the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">parameter
-file</a> presented in <a href="chapter_4.4.html">chapter
-4.4</a>, for the execution of a simple model run. In chapter 4.4
+file</a> presented in <a href="chapter_4.4.1.html">chapter
+4.4.1</a>, for the execution of a simple model run. In chapter 4.4.1
 the
 complete <b>mrun</b> options which are necessary for the
@@ -85,6 +83,6 @@
 will
 interpret these colons as blanks (2 colons written one behind the
-other will be interpreted as a colon). Thus in the example above </font><tt><font face="Thorndale, serif">fopts
-has the value </font></tt>&ldquo;<font style="font-size: 10pt; font-family: monospace;" size="2"><i>-O3
+other will be interpreted as a colon). Thus in the example above</font> fopts
+has the value<tt><font face="Thorndale, serif"> </font></tt>&ldquo;<font style="font-size: 10pt; font-family: monospace;" size="2"><i>-O3
 -g
 -qrealsize=8 -Q -q64 -qmaxmem=-1 -qtune=pwr4 -qarch=pwr4 -qnosave
@@ -184,5 +182,5 @@
 explained in detail in the <b>mrun</b>
 description (<a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter6.3">chapter
-6.3</a>, in German) and are described here only as far as being
+6.3</a>, in German) and are described here only as far as
 necessary. A
 file connection statement usually consists of entries in 5 columns
Index: palm/trunk/DOC/app/chapter_3.4.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.4.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_3.4.html	(revision 97)
@@ -1,5 +1,5 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
 <html><head>
-<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>chapter_3.4</title> </head>
+<meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>chapter_3.4</title></head>
 <body><h3 style="line-height: 100%;"><font color="#000000">3.4 Input and
 output files</font></h3>
@@ -85,6 +85,6 @@
 is needed by the model in each case. Its content and structure is
 described in detail in</font> <a href="chapter_4.0.html">chapter
-4.0</a>. <a href="chapter_4.4.html">Chapter
-4.4</a> <font color="#000000">shows a simple
+4.0</a>. <a href="chapter_4.4.1.html">Chapter
+4.4.1</a> <font color="#000000">shows a simple
 example. </font> </p> </td> </tr> <tr valign="top"> <td style="text-align: center;" width="8%"> <p align="center">13</p> </td>
 <td width="12%"> <p><a name="BININ"></a>BININ/</p>
Index: palm/trunk/DOC/app/chapter_4.0.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.0.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.0.html	(revision 97)
@@ -131,6 +131,6 @@
 within routine <span style="font-family: monospace;">user_parin</span>
 in file <span style="font-family: monospace;">user_interface.f90</span>).
-<a href="chapter_4.4.html">Chapter
-4.4</a> shows a simple but complete example of the input file
+<a href="chapter_4.4.1.html">Chapter
+4.4.1</a> shows a simple but complete example of the input file
 PARIN.
 This example file can be used together with the configuration file
Index: palm/trunk/DOC/app/chapter_4.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.1.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.1.html	(revision 97)
@@ -208,5 +208,5 @@
 </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="pc_pt_t"></a><b>bc_pt_t</b></p>
 </td> <td style="vertical-align: top;">C * 20</td>
-<td style="vertical-align: top;"><span style="font-style: italic;">'initial gradient'</span></td>
+<td style="vertical-align: top;"><span style="font-style: italic;">'initial_ gradient'</span></td>
 <td style="vertical-align: top;"> <p style="font-style: normal;">Top boundary condition of the
 potential temperature.&nbsp; </p> <p>Allowed are the
@@ -299,5 +299,12 @@
 bc_s_t_val * dzu(nz+1)</p> </ul> <p style="font-style: normal;">(up to k=nz the prognostic
 equation for the scalar concentration is
-solved).</p> </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="bc_uv_b"></a><b>bc_uv_b</b></p>
+solved).</p> </td> </tr> <tr><td style="vertical-align: top;"><a name="bc_sa_t"></a><span style="font-weight: bold;">bc_sa_t</span></td><td style="vertical-align: top;">C * 20</td><td style="vertical-align: top;"><span style="font-style: italic;">'neumann'</span></td><td style="vertical-align: top;"><p style="font-style: normal;">Top boundary condition of the salinity.&nbsp; </p> <p>This parameter only comes into effect for ocean runs (see parameter <a href="#ocean">ocean</a>).</p><p style="font-style: normal;">Allowed are the
+values <span style="font-style: italic;">'dirichlet' </span>(sa(k=nz+1)
+does not change during the run) and <span style="font-style: italic;">'neumann'</span>
+(sa(k=nz+1)=sa(k=nz))<span style="font-style: italic;"></span>.&nbsp;<br><br>
+When a constant salinity flux is used at the top boundary (<a href="chapter_4.1.html#top_salinityflux">top_salinityflux</a>),
+<b>bc_sa_t</b> = <span style="font-style: italic;">'neumann'</span>
+must be used, because otherwise the resolved scale may contribute to
+the top flux so that a constant value cannot be guaranteed.</p></td></tr><tr> <td style="vertical-align: top;"> <p><a name="bc_uv_b"></a><b>bc_uv_b</b></p>
 </td> <td style="vertical-align: top;">C * 20</td>
 <td style="vertical-align: top;"><span style="font-style: italic;">'dirichlet'</span></td>
@@ -331,5 +338,8 @@
 Neumann condition yields the free-slip condition with u(k=nz+1) =
 u(k=nz) and v(k=nz+1) = v(k=nz) (up to k=nz the prognostic equations
-for the velocities are solved).</p> </td> </tr> <tr>
+for the velocities are solved).</p> </td> </tr> <tr><td style="vertical-align: top;"><a name="bottom_salinityflux"></a><span style="font-weight: bold;">bottom_salinityflux</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">0.0</span></td><td style="vertical-align: top;"><p>Kinematic salinity flux near the surface (in psu m/s).&nbsp;</p>This parameter only comes into effect for ocean runs (see parameter <a href="chapter_4.1.html#ocean">ocean</a>).<p>The
+respective salinity flux value is used
+as bottom (horizontally homogeneous) boundary condition for the salinity equation. This additionally requires that a Neumann
+condition must be used for the salinity, which is currently the only available condition.<br> </p> </td></tr><tr>
 <td style="vertical-align: top;"><span style="font-weight: bold;"><a name="building_height"></a>building_height</span></td>
 <td style="vertical-align: top;">R</td> <td style="vertical-align: top;"><span style="font-style: italic;">50.0</span></td> <td>Height
@@ -1111,5 +1121,11 @@
 be an integral multiple of
 the number of processors in x-direction (due to data transposition
-restrictions).</p> </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="omega"></a><b>omega</b></p>
+restrictions).</p> </td> </tr> <tr><td style="vertical-align: top;"><a name="ocean"></a><span style="font-weight: bold;">ocean</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;">Parameter to switch on&nbsp;ocean runs.<br><br>By default PALM is configured to simulate&nbsp;atmospheric flows. However, starting from version 3.3, <span style="font-weight: bold;">ocean</span> = <span style="font-style: italic;">.T.</span> allows&nbsp;simulation of ocean turbulent flows. Setting this switch has several effects:<br><br><ul><li>An additional prognostic equation for salinity is solved.</li><li>Potential temperature in buoyancy and stability-related terms is replaced by potential density.</li><li>Potential
+density is calculated from the equation of state for seawater after
+each timestep, using the algorithm proposed by Jackett et al. (2006, J.
+Atmos. Oceanic Technol., <span style="font-weight: bold;">23</span>, 1709-1728).<br>So far, only the initial hydrostatic pressure is entered into this equation.</li><li>z=0 (sea surface) is assumed at the model top (vertical grid index <span style="font-family: Courier New,Courier,monospace;">k=nzt</span> on the w-grid), with negative values of z indicating the depth.</li><li>Initial profiles are constructed (e.g. from <a href="#pt_vertical_gradient">pt_vertical_gradient</a> / <a href="#pt_vertical_gradient_level">pt_vertical_gradient_level</a>) starting from the sea surface, using surface values&nbsp;given by <a href="#pt_surface">pt_surface</a>, <a href="#sa_surface">sa_surface</a>, <a href="#ug_surface">ug_surface</a>, and <a href="#vg_surface">vg_surface</a>.</li><li>Zero salinity flux is used as default boundary condition at the bottom of the sea.</li><li>If switched on, random perturbations are by default imposed to the upper model domain from zu(nzt*2/3) to zu(nzt-3).</li></ul><br>Relevant parameters to be exclusively used for steering ocean runs are <a href="#bc_sa_t">bc_sa_t</a>, <a href="#bottom_salinityflux">bottom_salinityflux</a>, <a href="#sa_surface">sa_surface</a>, <a href="#sa_vertical_gradient">sa_vertical_gradient</a>, <a href="#sa_vertical_gradient_level">sa_vertical_gradient_level</a>, and <a href="#top_salinityflux">top_salinityflux</a>.<br><br>Section <a href="chapter_4.2.2.html">4.4.2</a> gives an example for appropriate settings of these and other parameters neccessary for ocean runs.<br><br><span style="font-weight: bold;">ocean</span> = <span style="font-style: italic;">.T.</span> does not allow settings of <a href="#timestep_scheme">timestep_scheme</a> = <span style="font-style: italic;">'leapfrog'</span> or <span style="font-style: italic;">'leapfrog+euler'</span> as well as <a href="#scalar_advec">scalar_advec</a> = <span style="font-style: italic;">'ups-scheme'</span>.<br><br><span style="font-weight: bold;">Current limitations:</span><br>Using
+a vertical grid stretching is not recommended since it would still
+stretch the grid towards the top boundary of the model (sea surface)
+instead of the bottom boundary.</td></tr><tr> <td style="vertical-align: top;"> <p><a name="omega"></a><b>omega</b></p>
 </td> <td style="vertical-align: top;">R</td>
 <td style="vertical-align: top;"><i>7.29212E-5</i></td>
@@ -1241,5 +1257,5 @@
 temperature to be used in all buoyancy terms (in K).<br><br>By
 default, the instantaneous horizontal average over the total model
-domain is used.</td></tr><tr> <td style="vertical-align: top;"> <p><a name="pt_surface"></a><b>pt_surface</b></p>
+domain is used.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>), always a reference temperature is used in the buoyancy terms with a default value of <span style="font-weight: bold;">pt_reference</span> = <a href="#pt_surface">pt_surface</a>.</td></tr><tr> <td style="vertical-align: top;"> <p><a name="pt_surface"></a><b>pt_surface</b></p>
 </td> <td style="vertical-align: top;">R</td>
 <td style="vertical-align: top;"><i>300.0</i></td>
@@ -1247,10 +1263,13 @@
 potential temperature (in K).&nbsp; </p> <p>This
 parameter assigns the value of the potential temperature
-pt at the surface (k=0)<b>.</b> Starting from this value,
+<span style="font-weight: bold;">pt</span> at the surface (k=0)<b>.</b> Starting from this value,
 the
 initial vertical temperature profile is constructed with <a href="#pt_vertical_gradient">pt_vertical_gradient</a>
 and <a href="#pt_vertical_gradient_level">pt_vertical_gradient_level
 </a>.
-This profile is also used for the 1d-model as a stationary profile.</p>
+This profile is also used for the 1d-model as a stationary profile.</p><p><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="#ocean">ocean</a>),
+this parameter gives the temperature value at the sea surface, which is
+at k=nzt. The profile is then constructed from the surface down to the
+bottom of the model.</p>
 </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="pt_surface_initial_change"></a><b>pt_surface_initial</b>
 <br> <b>_change</b></p> </td> <td style="vertical-align: top;">R</td> <td style="vertical-align: top;"><span style="font-style: italic;">0.0</span><br> </td>
@@ -1291,5 +1310,8 @@
 100 m and for z &gt; 1000.0 m up to the top boundary it is
 0.5 K / 100 m (it is assumed that the assigned height levels correspond
-with uv levels). </p> </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="pt_vertical_gradient_level"></a><b>pt_vertical_gradient</b>
+with uv levels).</p><p><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>),
+the profile is constructed like described above, but starting from the
+sea surface (k=nzt) down to the bottom boundary of the model. Height
+levels have then to be given as negative values, e.g. <span style="font-weight: bold;">pt_vertical_gradient_level</span> = <span style="font-style: italic;">-500.0</span>, <span style="font-style: italic;">-1000.0</span>.</p> </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="pt_vertical_gradient_level"></a><b>pt_vertical_gradient</b>
 <br> <b>_level</b></p> </td> <td style="vertical-align: top;">R (10)</td> <td style="vertical-align: top;"> <p><i>10 *</i>&nbsp;
 <span style="font-style: italic;">0.0</span><br>
@@ -1297,10 +1319,9 @@
 <p>Height level from which on the temperature gradient defined by
 <a href="#pt_vertical_gradient">pt_vertical_gradient</a>
-is effective (in m).&nbsp; </p> <p>The height levels
-are to be assigned in ascending order. The
+is effective (in m).&nbsp; </p> <p>The height levels have to be assigned in ascending order. The
 default values result in a neutral stratification regardless of the
 values of <a href="#pt_vertical_gradient">pt_vertical_gradient</a>
 (unless the top boundary of the model is higher than 100000.0 m).
-For the piecewise construction of temperature profiles see <a href="#pt_vertical_gradient">pt_vertical_gradient</a>.</p>
+For the piecewise construction of temperature profiles see <a href="#pt_vertical_gradient">pt_vertical_gradient</a>.</p><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs&nbsp;(see <a href="chapter_4.1.html#ocean">ocean</a>), the (negative) height levels have to be assigned in descending order.
 </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="q_surface"></a><b>q_surface</b></p>
 </td> <td style="vertical-align: top;">R</td>
@@ -1453,5 +1474,36 @@
 is switched
 on (see <a href="#prandtl_layer">prandtl_layer</a>).</p>
-</td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="scalar_advec"></a><b>scalar_advec</b></p>
+</td> </tr> <tr><td style="vertical-align: top;"><a name="sa_surface"></a><span style="font-weight: bold;">sa_surface</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">35.0</span></td><td style="vertical-align: top;"> <p>Surface salinity (in psu).&nbsp;</p>This parameter only comes into effect for ocean runs (see parameter <a href="chapter_4.1.html#ocean">ocean</a>).<p>This
+parameter assigns the value of the salinity <span style="font-weight: bold;">sa</span> at the sea surface (k=nzt)<b>.</b> Starting from this value,
+the
+initial vertical salinity profile is constructed from the surface down to the bottom of the model (k=0) by using&nbsp;<a href="chapter_4.1.html#sa_vertical_gradient">sa_vertical_gradient</a>
+and&nbsp;<a href="chapter_4.1.html#sa_vertical_gradient_level">sa_vertical_gradient_level
+</a>.</p></td></tr><tr><td style="vertical-align: top;"><a name="sa_vertical_gradient"></a><span style="font-weight: bold;">sa_vertical_gradient</span></td><td style="vertical-align: top;">R(10)</td><td style="vertical-align: top;"><span style="font-style: italic;">10 * 0.0</span></td><td style="vertical-align: top;"><p>Salinity gradient(s) of the initial salinity profile (in psu
+/ 100 m).&nbsp; </p> <p>This parameter only comes into effect for ocean runs (see parameter <a href="chapter_4.1.html#ocean">ocean</a>).</p><p>This salinity gradient
+holds starting from the height&nbsp;
+level defined by <a href="chapter_4.1.html#sa_vertical_gradient_level">sa_vertical_gradient_level</a>
+(precisely: for all uv levels k where zu(k) &lt;
+sa_vertical_gradient_level, sa_init(k) is set: sa_init(k) =
+sa_init(k+1) - dzu(k+1) * <b>sa_vertical_gradient</b>) down to the bottom boundary or down to the next height level defined
+by <a href="chapter_4.1.html#sa_vertical_gradient_level">sa_vertical_gradient_level</a>.
+A total of 10 different gradients for 11 height intervals (10 intervals
+if <a href="chapter_4.1.html#sa_vertical_gradient_level">sa_vertical_gradient_level</a>(1)
+= <i>0.0</i>) can be assigned. The surface salinity at k=nzt is
+assigned via <a href="chapter_4.1.html#sa_surface">sa_surface</a>.&nbsp;
+</p> <p>Example:&nbsp; </p> <ul><p><b>sa_vertical_gradient</b>
+= <i>1.0</i>, <i>0.5</i>,&nbsp; <br>
+<b>sa_vertical_gradient_level</b> = <i>-500.0</i>,
+-<i>1000.0</i>,</p></ul> <p>That
+defines the salinity to be constant down to z = -500.0 m with a salinity given by <a href="chapter_4.1.html#sa_surface">sa_surface</a>.
+For -500.0 m &lt; z &lt;= -1000.0 m the salinity gradient is
+1.0 psu /
+100 m and for z &lt; -1000.0 m down to the bottom boundary it is
+0.5 psu / 100 m (it is assumed that the assigned height levels correspond
+with uv levels).</p></td></tr><tr><td style="vertical-align: top;"><a name="sa_vertical_gradient_level"></a><span style="font-weight: bold;">sa_vertical_gradient_level</span></td><td style="vertical-align: top;">R(10)</td><td style="vertical-align: top;"><span style="font-style: italic;">10 * 0.0</span></td><td style="vertical-align: top;"><p>Height level from which on the salinity gradient defined by <a href="chapter_4.1.html#sa_vertical_gradient">sa_vertical_gradient</a>
+is effective (in m).&nbsp; </p> <p>This parameter only comes into effect for ocean runs (see parameter <a href="chapter_4.1.html#ocean">ocean</a>).</p><p>The height levels have to be assigned in descending order. The
+default values result in a constant salinity profile regardless of the
+values of <a href="chapter_4.1.html#sa_vertical_gradient">sa_vertical_gradient</a>
+(unless the bottom boundary of the model is lower than -100000.0 m).
+For the piecewise construction of salinity profiles see <a href="chapter_4.1.html#sa_vertical_gradient">sa_vertical_gradient</a>.</p></td></tr><tr> <td style="vertical-align: top;"> <p><a name="scalar_advec"></a><b>scalar_advec</b></p>
 </td> <td style="vertical-align: top;">C * 10</td>
 <td style="vertical-align: top;"><i>'pw-scheme'</i></td>
@@ -1835,5 +1887,19 @@
 Prandtl-layer is available at the top boundary so far.</p><p>See
 also <a href="#surface_heatflux">surface_heatflux</a>.</p>
-</td></tr><tr> <td style="vertical-align: top;">
+</td></tr><tr><td style="vertical-align: top;"><a name="top_salinityflux"></a><span style="font-weight: bold;">top_salinityflux</span></td><td style="vertical-align: top;">R</td><td style="vertical-align: top;"><span style="font-style: italic;">no prescribed<br>
+salinityflux</span></td><td style="vertical-align: top;"><p>Kinematic
+salinity flux at the top boundary, i.e. the sea surface (in psu m/s).&nbsp; </p>
+<p>This parameter only comes into effect for ocean runs (see parameter <a href="chapter_4.1.html#ocean">ocean</a>).</p><p>If a value is assigned to this parameter, the internal
+two-dimensional surface heat flux field <span style="font-family: monospace;">saswst</span> is
+initialized with the value of <span style="font-weight: bold;">top_salinityflux</span>&nbsp;as
+top (horizontally homogeneous) boundary condition for the salinity equation. This additionally requires that a Neumann
+condition must be used for the salinity (see <a href="chapter_4.1.html#bc_sa_t">bc_sa_t</a>),
+because otherwise the resolved scale may contribute to
+the top flux so that a constant value cannot be guaranteed.<span style="font-style: italic;"></span>&nbsp;</p>
+<p><span style="font-weight: bold;">Note:</span><br>The
+application of a salinity flux at the model top additionally requires the setting of
+initial parameter <a href="chapter_4.1.html#use_top_fluxes">use_top_fluxes</a>
+= .T..<span style="font-style: italic;"></span><span style="font-weight: bold;"></span> </p><p>See
+also <a href="chapter_4.1.html#bottom_salinityflux">bottom_salinityflux</a>.</p></td></tr><tr> <td style="vertical-align: top;">
 <p><a name="ug_surface"></a><span style="font-weight: bold;">ug_surface</span></p>
 </td> <td style="vertical-align: top;">R<br> </td>
@@ -1857,5 +1923,8 @@
 value, it is recommended to use a Galilei-transformation of the
 coordinate system, if possible (see <a href="#galilei_transformation">galilei_transformation</a>),
-in order to obtain larger time steps.<br> </td> </tr>
+in order to obtain larger time steps.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>),
+this parameter gives the velocity value at the sea surface, which is
+at k=nzt. The profile is then constructed from the surface down to the
+bottom of the model.<br> </td> </tr>
 <tr> <td style="vertical-align: top;"> <p><a name="ug_vertical_gradient"></a><span style="font-weight: bold;">ug_vertical_gradient</span></p>
 </td> <td style="vertical-align: top;">R(10)<br>
@@ -1872,5 +1941,8 @@
 total of 10 different gradients for 11 height intervals (10
 intervals&nbsp; if <a href="#ug_vertical_gradient_level">ug_vertical_gradient_level</a>(1)
-= 0.0) can be assigned. The surface geostrophic wind is assigned by <a href="#ug_surface">ug_surface</a>. <br> </td>
+= 0.0) can be assigned. The surface geostrophic wind is assigned by <a href="#ug_surface">ug_surface</a>.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>),
+the profile is constructed like described above, but starting from the
+sea surface (k=nzt) down to the bottom boundary of the model. Height
+levels have then to be given as negative values, e.g. <span style="font-weight: bold;">ug_vertical_gradient_level</span> = <span style="font-style: italic;">-500.0</span>, <span style="font-style: italic;">-1000.0</span>.<br> </td>
 </tr> <tr> <td style="vertical-align: top;">
 <p><a name="ug_vertical_gradient_level"></a><span style="font-weight: bold;">ug_vertical_gradient_level</span></p>
@@ -1880,8 +1952,7 @@
 gradient defined by <a href="#ug_vertical_gradient">ug_vertical_gradient</a>
 is effective (in m).<br> <br>
-The height levels are to be assigned in ascending order. For the
+The height levels have to be assigned in ascending order. For the
 piecewise construction of a profile of the u-component of the
-geostrophic wind component (ug) see <a href="#ug_vertical_gradient">ug_vertical_gradient</a>.<br>
-</td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="ups_limit_e"></a><b>ups_limit_e</b></p>
+geostrophic wind component (ug) see <a href="#ug_vertical_gradient">ug_vertical_gradient</a>.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs&nbsp;(see <a href="chapter_4.1.html#ocean">ocean</a>), the (negative) height levels have to be assigned in descending order.</td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="ups_limit_e"></a><b>ups_limit_e</b></p>
 </td> <td style="vertical-align: top;">R</td>
 <td style="vertical-align: top;"><i>0.0</i></td>
@@ -2063,5 +2134,8 @@
 if possible (see <a href="#galilei_transformation">galilei_transformation</a>),
 in order to obtain larger
-time steps.</td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="vg_vertical_gradient"></a><span style="font-weight: bold;">vg_vertical_gradient</span></p>
+time steps.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>),
+this parameter gives the velocity value at the sea surface, which is
+at k=nzt. The profile is then constructed from the surface down to the
+bottom of the model.</td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="vg_vertical_gradient"></a><span style="font-weight: bold;">vg_vertical_gradient</span></p>
 </td> <td style="vertical-align: top;">R(10)<br>
 </td> <td style="vertical-align: top;"><span style="font-style: italic;">10
@@ -2081,5 +2155,8 @@
 =
 0.0) can be assigned. The surface
-geostrophic wind is assigned by <a href="#vg_surface">vg_surface</a>.</td>
+geostrophic wind is assigned by <a href="#vg_surface">vg_surface</a>.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>),
+the profile is constructed like described above, but starting from the
+sea surface (k=nzt) down to the bottom boundary of the model. Height
+levels have then to be given as negative values, e.g. <span style="font-weight: bold;">vg_vertical_gradient_level</span> = <span style="font-style: italic;">-500.0</span>, <span style="font-style: italic;">-1000.0</span>.</td>
 </tr> <tr> <td style="vertical-align: top;">
 <p><a name="vg_vertical_gradient_level"></a><span style="font-weight: bold;">vg_vertical_gradient_level</span></p>
@@ -2089,7 +2166,7 @@
 gradient defined by <a href="#vg_vertical_gradient">vg_vertical_gradient</a>
 is effective (in m).<br> <br>
-The height levels are to be assigned in ascending order. For the
+The height levels have to be assigned in ascending order. For the
 piecewise construction of a profile of the v-component of the
-geostrophic wind component (vg) see <a href="#vg_vertical_gradient">vg_vertical_gradient</a>.</td>
+geostrophic wind component (vg) see <a href="#vg_vertical_gradient">vg_vertical_gradient</a>.<br><br><span style="font-weight: bold;">Attention:</span><br>In case of ocean runs&nbsp;(see <a href="chapter_4.1.html#ocean">ocean</a>), the (negative) height levels have to be assigned in descending order.</td>
 </tr> <tr> <td style="vertical-align: top;">
 <p><a name="wall_adjustment"></a><b>wall_adjustment</b></p>
Index: palm/trunk/DOC/app/chapter_4.2.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.2.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.2.html	(revision 97)
@@ -405,6 +405,8 @@
 = <span style="font-style: italic;">.TRUE.</span></td></tr><tr><td style="width: 106px; vertical-align: top;"><span style="font-style: italic;">qv</span></td><td style="width: 196px; vertical-align: top;">water vapor
 content (specific humidity)</td><td style="vertical-align: top;">kg/kg</td><td style="vertical-align: top;">requires <a href="chapter_4.1.html#cloud_physics">cloud_physics</a>
+= <span style="font-style: italic;">.TRUE.</span></td></tr><tr><td align="undefined" valign="undefined"><span style="font-style: italic;">rho</span></td><td align="undefined" valign="undefined">potential density</td><td align="undefined" valign="undefined">kg/m<sup>3</sup></td><td align="undefined" valign="undefined">requires&nbsp;<a href="chapter_4.1.html#ocean">ocean</a>
 = <span style="font-style: italic;">.TRUE.</span></td></tr><tr><td style="width: 106px; vertical-align: top;"><span style="font-style: italic;">s</span></td><td style="width: 196px; vertical-align: top;">concentration of
 the scalar</td><td style="vertical-align: top;">1/m<sup>3</sup></td><td style="vertical-align: top;">requires&nbsp;<a href="chapter_4.1.html#passive_scalar">passive_scalar</a>
+= <span style="font-style: italic;">.TRUE.</span></td></tr><tr><td align="undefined" valign="undefined"><span style="font-style: italic;">sa</span></td><td align="undefined" valign="undefined">salinity</td><td align="undefined" valign="undefined">psu</td><td align="undefined" valign="undefined">requires&nbsp;<a href="chapter_4.1.html#ocean">ocean</a>
 = <span style="font-style: italic;">.TRUE.</span></td></tr><tr><td style="width: 106px; vertical-align: top;"><span style="font-style: italic;">t*</span></td><td style="width: 196px; vertical-align: top;">(near surface)
 characteristic temperature</td><td style="vertical-align: top;">K</td><td style="vertical-align: top;">only horizontal cross section
@@ -663,7 +665,7 @@
 kg/kg).</td> </tr> <tr> <td style="vertical-align: top;"><font color="#ff6600"><i>ql</i></font></td>
 <td style="vertical-align: top;">Liquid water content
-(in kg/kg).</td> </tr> <tr> <td style="vertical-align: middle;"><font color="#ff6600">s</font></td>
+(in kg/kg).</td> </tr> <tr><td align="undefined" valign="undefined"><span style="font-style: italic; color: rgb(255, 102, 0);">rho</span></td><td align="undefined" valign="undefined">Potential density (in kg/m<sup>3</sup>).</td></tr><tr> <td style="vertical-align: middle; font-style: italic;"><font color="#ff6600">s</font></td>
 <td style="vertical-align: top;">Scalar concentration (in
-kg/m<sup>3</sup>).</td> </tr> <tr> <td style="vertical-align: middle;"><font color="#ff6600"><i>e</i></font></td>
+kg/m<sup>3</sup>).</td> </tr> <tr><td align="undefined" valign="undefined"><span style="font-style: italic; background-color: rgb(255, 255, 255); color: rgb(255, 102, 0);">sa</span></td><td align="undefined" valign="undefined">Salinity (in psu).</td></tr><tr> <td style="vertical-align: middle;"><font color="#ff6600"><i>e</i></font></td>
 <td style="vertical-align: top;">Turbulent kinetic energy
 (TKE, subgrid-scale) (in m<sup>2</sup>/s<sup>2</sup>).</td>
@@ -741,9 +743,10 @@
 </tr> <tr> <td style="vertical-align: middle;"><font color="#33ff33"><i>w*s*</i></font></td>
 <td style="vertical-align: top;">Resolved vertical scalar
-concentration flux (in kg/m<sup>3</sup>)</td> </tr>
+concentration flux (in kg/m<sup>3</sup> m/s).</td> </tr>
 <tr> <td style="vertical-align: middle;"><font color="#33ff33"><i>ws</i></font></td>
 <td style="vertical-align: top;">Total vertical scalar
 concentration flux (w"s" + w*s*) (in kg/m<sup>3 </sup>m/s).</td>
-</tr> <tr> <td style="vertical-align: top;"><font color="#33ff33"><i>w*e*</i></font></td>
+</tr> <tr><td align="undefined" valign="undefined"><span style="font-style: italic; color: rgb(51, 255, 51);">w"sa"</span></td><td align="undefined" valign="undefined">Subgrid-scale vertical
+salinity flux (in psu<sup> </sup>m/s).</td></tr><tr><td align="undefined" valign="undefined"><span style="font-style: italic; color: rgb(51, 255, 51);">w*sa*</span></td><td align="undefined" valign="undefined">Resolved vertical salinity flux (in psu m/s).</td></tr><tr><td align="undefined" valign="undefined"><span style="font-style: italic; color: rgb(51, 255, 51);">wsa</span></td><td align="undefined" valign="undefined">Total vertical salinity flux (w"sa" + w*sa*) (in psu<sup> </sup>m/s).</td></tr><tr> <td style="vertical-align: top;"><font color="#33ff33"><i>w*e*</i></font></td>
 <td style="vertical-align: top;">Vertical flux of
 perturbation energy (resolved)</td> </tr> <tr> <td style="vertical-align: top;"><font color="#ff6600"><i>u*2</i></font></td>
@@ -856,15 +859,15 @@
 </tr> <tr> <td style="vertical-align: top;"><p><a name="disturbance_level_b"></a><b>disturbance_level_b</b></p>
 </td> <td style="vertical-align: top;">R</td>
-<td style="vertical-align: top;"><i>zu(3)</i></td>
+<td style="vertical-align: top;"><i>zu(3) or<br>zu(nz*2/3)<br>see right</i></td>
 <td style="vertical-align: top;"> <p lang="en-GB"><font face="Thorndale, serif"><font size="3">Lower
 limit of the vertical range for which random perturbations are to be
 imposed on the horizontal wind field (</font></font>in <font face="Thorndale, serif"><font size="3">m).&nbsp;
 </font></font> </p> <p><span lang="en-GB"><font face="Thorndale, serif">This
-parameter must hold the condition zu<i>(3)</i> &lt;= <b>disturbance_level_b</b>
-&lt;= <i>zu(</i></font></span><i><a href="chapter_4.1.html#nz"><span lang="en-GB"><font face="Thorndale, serif">nz-1</font></span></a><span lang="en-GB"><font face="Thorndale, serif">)</font></span></i><span lang="en-GB"><font face="Thorndale, serif">.
+parameter must hold the condition zu(3) &lt;= <b>disturbance_level_b</b>
+&lt;= zu(</font></span><a href="chapter_4.1.html#nz"><span lang="en-GB"><font face="Thorndale, serif">nz-1</font></span></a><span lang="en-GB"><font face="Thorndale, serif">)</font></span><span lang="en-GB"><font face="Thorndale, serif">.
 Additionally, <b>disturbance_level_b</b>
 &lt;= </font></span><a href="#disturbance_level_t"><span lang="en-GB"><font face="Thorndale, serif">disturbance_level_t</font></span></a>
 <span lang="en-GB"><font face="Thorndale, serif">must
-also hold. <br> </font></span></p> <p><span lang="en-GB"><font face="Thorndale, serif">The
+also hold.</font></span></p><p><span lang="en-GB"><font face="Thorndale, serif">In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>) </font></span><span lang="en-GB"><span style="font-family: Thorndale,serif;">the default value is <span style="font-weight: bold;">disturbance_level_b</span> = <span style="font-style: italic;">(nz * 2) / 3</span>.</span></span><a href="chapter_4.1.html#nz"><span lang="en-GB"></span></a><span lang="en-GB"></span><span lang="en-GB"></span></p> <p><span lang="en-GB"><font face="Thorndale, serif">The
 parameter </font></span><a href="#create_disturbances"><span lang="en-GB"><font face="Thorndale, serif">create_disturbances</font></span></a><font face="Thorndale, serif"><span lang="en-GB">
 describes how to impose
@@ -872,5 +875,5 @@
 </font> </p> </td> </tr> <tr> <td style="vertical-align: top;"> <p><a name="disturbance_level_t"></a><b>disturbance_level_t</b></p>
 </td> <td style="vertical-align: top;">R</td>
-<td style="vertical-align: top;"><i>zu(nz/3)</i></td>
+<td style="vertical-align: top;"><i>zu(nz/3) or<br>zu(nzt-3)<br>see right</i></td>
 <td style="vertical-align: top;"> <p lang="en-GB"><font face="Thorndale, serif"><font size="3">Upper
 limit of the vertical range for which random perturbations are to be
@@ -882,5 +885,5 @@
 <span lang="en-GB"><font face="Thorndale, serif">&lt;=
 <b>disturbance_level_t</b>
-must also hold.<br> </font></span></p> <p><span lang="en-GB"><font face="Thorndale, serif">The
+must also hold.</font></span></p><span lang="en-GB"><font face="Thorndale, serif">In case of ocean runs (see <a href="chapter_4.1.html#ocean">ocean</a>) </font></span><span lang="en-GB"><span style="font-family: Thorndale,serif;">the default value is <span style="font-weight: bold;">disturbance_level_t</span> = <span style="font-style: italic;">nzt - 3</span>.</span></span><p><span lang="en-GB"><font face="Thorndale, serif">The
 parameter </font></span><a href="#create_disturbances"><span lang="en-GB"><font face="Thorndale, serif">create_disturbances</font></span></a><font face="Thorndale, serif"><span lang="en-GB">
 describes how to impose
Index: palm/trunk/DOC/app/chapter_4.4.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.4.1.html	(revision 97)
+++ palm/trunk/DOC/app/chapter_4.4.1.html	(revision 97)
@@ -0,0 +1,179 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head>
+<meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 4.4</title>
+<meta content="StarOffice 7 (Win32)" name="GENERATOR">
+<meta content="Siegfried Raasch" name="AUTHOR"> <meta content="20041013;13430732" name="CREATED"> <meta content="20041117;11162734" name="CHANGED"> <meta content="parallel LES model" name="KEYWORDS"> <style>
+<!--
+@page { size: 21cm 29.7cm }
+-->
+</style></head>
+<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">4.4.1 A minimum
+parameter set for the CBL</h3>
+
+<p style="line-height: 100%;">In this chapter a brief,
+simple and
+complete parameter set is described, which can be used to simulate a&nbsp;quasi-stationary,
+convective, atmospheric boundary layer with&nbsp; <font color="#000000">zero
+mean horizontal
+wind.</font> For evaluation purposes, cross sections and
+horizontally averaged vertical
+profiles of typical boundary layer variables
+are output at the end of the run. The run shall be carried out in
+batch mode on the IBM Regatta "hanni" of the HLRN.</p>
+<p style="line-height: 100%;">The parameter file necessary
+to carry
+out a run must be provided to the model as an input file under the
+local name <a href="chapter_3.4.html#PARIN">PARIN</a>
+and has the following contents:</p>
+<pre style="line-height: 100%;">&amp;inipar <a href="chapter_4.1.html#nx">nx</a> = <span style="font-style: italic;">39</span>, <a href="chapter_4.1.html#ny">ny</a> = <span style="font-style: italic;">39</span>, <a href="chapter_4.1.html#nz">nz</a> = <span style="font-style: italic;">40</span>,<br> <a href="chapter_4.1.html#dx">dx</a> = <span style="font-style: italic;">50.0</span>, <a href="chapter_4.1.html#dy">dy</a> = <span style="font-style: italic;">50.0</span>, <a href="chapter_4.1.html#dz">dz</a> = <span style="font-style: italic;">50.0</span>,<br> <a href="chapter_4.1.html#dz_stretch_level">dz_stretch_level</a> = <span style="font-style: italic;">1200.0</span>,<br> <a href="chapter_4.1.html#fft_method">fft_method</a> = <span style="font-style: italic;">'temperton-algorithm'</span>,<br> <a href="chapter_4.1.html#initializing_actions">initializing_actions</a> = <span style="font-style: italic;">'set_constant_profiles'</span>,<br> <a href="chapter_4.1.html#ug_surface">ug_surface</a> = <span style="font-style: italic;">0.0</span>, <a href="chapter_4.1.html#vg_surface">vg_surface</a> = <span style="font-style: italic;">0.0</span>,<br> <a href="chapter_4.1.html#pt_vertical_gradient">pt_vertical_gradient</a> = <span style="font-style: italic;">0.0</span>, <span style="font-style: italic;">1.0</span>,<br> <a href="chapter_4.1.html#pt_vertical_gradient_level">pt_vertical_gradient_level</a> = <span style="font-style: italic;">0.0</span>, <span style="font-style: italic;">800.0</span>,<br> <a href="chapter_4.1.html#surface_heatflux">surface_heatflux</a> = <span style="font-style: italic;">0.1</span>, <a href="chapter_4.1.html#bc_pt_b">bc_pt_b</a> = <span style="font-style: italic;">'neumann'</span>,/<br><br>&amp;d3par <a href="chapter_4.2.html#end_time">end_time</a> = <span style="font-style: italic;">3600.0</span>,<br> <a href="chapter_4.2.html#create_disturbances">create_disturbances</a> = <span style="font-style: italic;">.T.</span>,<br> <a href="chapter_4.2.html#dt_disturb">dt_disturb</a> = <span style="font-style: italic;">150.0</span>, <a href="chapter_4.2.html#disturbance_energy_limit">disturbance_energy_limit</a> = <span style="font-style: italic;">0.01</span>,<br> <a href="chapter_4.2.html#dt_run_control">dt_run_control</a> = <span style="font-style: italic;">0.0</span>,<br> <a href="chapter_4.2.html#data_output">data_output</a> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'w_xz'</span>, <span style="font-style: italic;">'w_xz_av'</span>, <span style="font-style: italic;">'pt_xy'</span>, <span style="font-style: italic;">'pt_xz'</span>,<br> <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> = <span style="font-style: italic;">900.0</span>,<br> <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> = <span style="font-style: italic;">1800.0</span>,<br> <a href="chapter_4.2.html#averaging_interval">averaging_interval</a> = <span style="font-style: italic;">900.0</span>,<br> <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a> = <span style="font-style: italic;">10.0</span>,<br> <a href="chapter_4.2.html#section_xy">section_xy</a> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>, <a href="chapter_4.2.html#section_xz">section_xz</a> = <span style="font-style: italic;">20</span>,<br> <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a> = <span style="font-style: italic;">.F.</span>,<br> <a href="chapter_4.2.html#dt_dopr">dt_dopr</a> = <span style="font-style: italic;">900.0</span>, <a href="chapter_4.2.html#averaging_interval_pr">averaging_interval_pr</a> = <span style="font-style: italic;">600.0</span>,<br> <a href="chapter_4.2.html#dt_averaging_input_pr">dt_averaging_input_pr</a> = <span style="font-style: italic;">10.0</span>,<br> <a href="chapter_4.2.html#data_output_pr">data_output_pr</a> = <span style="font-style: italic;">'#pt'</span>, <span style="font-style: italic;">'w&rdquo;pt&rdquo;'</span>, <span style="font-style: italic;">'w*pt*'</span>, <span style="font-style: italic;">'wpt'</span>, <span style="font-style: italic;">'w*2'</span>, <span style="font-style: italic;">'pt*2'</span>,<br> <a href="chapter_4.2.html#cross_profiles">cross_profiles</a> = <span style="font-style: italic;">' pt '</span>, <span style="font-style: italic;">' w"pt" w*pt* wpt '</span>, <span style="font-style: italic;">' w*2 '</span>, <span style="font-style: italic;">' pt*2 '</span>,<br> <a href="chapter_4.2.html#cross_xtext">cross_xtext</a> = <span style="font-style: italic;">'pot. temperature in K'</span>,<br> <span style="font-style: italic;">'heat flux in K ms&gt;-&gt;1'</span>,<br> <span style="font-style: italic;">'velocity variance in m&gt;2s&gt;-&gt;2'</span>,<br> <span style="font-style: italic;">'temperature variance in K&gt;2'</span>,<br> <a href="chapter_4.2.html#z_max_do1d">z_max_do1d</a> = <span style="font-style: italic;">1500.0</span>, /</pre>
+<p style="line-height: 100%;">The initialization
+parameters (<tt><font style="font-size: 10pt;" size="2">&amp;inipar</font></tt>)
+are located at the beginning of the file. For analysis of a
+convective boundary layer of approx. 1000 m thickness the horizontal
+size of the model domain should amount to at least 2 km x 2 km. In
+order to resolve the convective structures a grid spacing of <b>dx</b>
+=
+<b>dy</b> = <b>dz</b> = <i>50 m</i>
+is enough, since the typical
+diameter of convective plumes is more than 100 m. Thereby the
+upper array index in the two horizontal directions needs to be <b>nx</b>
+= <b>ny</b> = <i>39</i>. <font color="#000000">Since in
+each case the lower array index has the value 0, 40 grid points are
+used along both horizontal directions.</font> In the vertical
+direction
+the domain must be high enough to include the entrainment processes at
+the top of the boundary layer as well as the propagation of gravity
+waves, which were stimulated by
+the convection. However, in the stably stratified region the grid
+resolution has not necessarily to be as high as within the boundary
+layer. This can be obtained by a vertical stretching of the grid
+starting
+from 1200 m via <b>dz_stretch_level</b> = <i>1200.0
+m.</i> This saves
+grid points and computing time. <font color="#800000">T</font><font color="#000000">he
+upper boundary of the model is located at (see </font><a href="chapter_4.1.html#dz_stretch_factor"><font color="#000000">dz_stretch_factor</font></a><font color="#000000">)
+&hellip; m (computed by the model)</font>.</p><p style="line-height: 100%;">Fast Fourier transformations are
+calculated using the Temperton-algorithm, which -on the IBM Regatta- is
+faster than the default system-specific algorithm (from IBM essl
+library).</p><p style="line-height: 100%;">The
+initial profiles for
+wind and temperature can be assigned via <b>initializing_actions</b>
+= <span style="font-style: italic;">'set_constant_profiles'</span>.
+The wind speed, constant with
+height, amounts to <b>ug_surface</b> = <b>vg_surface</b>
+= <i>0.0 m/s</i>. In order
+to allow for a fast onset of convection, a neutral stratified layer up
+to z
+= 800 m capped by an inversion with dtheta/dz = 1K/100 m is given:
+<b>pt_vertical_gradient</b> = <i>0.0, 1.0</i>,
+<b>pt_vertical_gradient_level</b> = <i>0.0, 800.0.</i>
+The surface
+temperature, which by default amounts to 300 K, provides the fixed
+point for the temperature profile (see <a href="chapter_4.1.html#pt_surface">pt_surface</a>).
+Convection is driven by a given, near-surface sensible heat flux via <b>surface_heatflux</b>
+= <i>0.1 K m/s.</i> A given surface sensible heta flux
+requires the
+bottom boundary condition for potential temperature to be <b>bc_pt_b</b>
+=
+<span style="font-style: italic;">'neumann'</span> .
+Thus
+all initialization parameters are determined. These can not be
+changed during the run (also not for restart runs). </p>
+<p style="line-height: 100%;">Now the run parameters (<tt><font style="font-size: 10pt;" size="2">&amp;d3par</font></tt>)
+must be specified. To produce a quasi stationary boundary layer the
+simulated time should be at least one hour, i.e. <b>end_time</b>
+= <i>3600
+s.</i> To stimulate convection, the initially homogeneous (zero)
+wind
+field must be disturbed (<b>create_disturbances</b> = <i>.T.</i>).
+These perturbations should be repeated in a temporal interval of
+<b>dt_disturb</b> = <i>150.0 s</i> until the
+energy of the
+perturbations exceeds the value <b>disturbance_energy_limit</b>
+= 0.<i>01
+m<sup>2</sup>/s<sup>2</sup></i>. After
+each time step run time
+informations (e.g. size of the timestep, maximum velocities, etc.) are
+to be written to the local file <a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a>
+(<b>dt_run_control</b> = <i>0.0 s</i>).</p><p style="line-height: 100%;">Instantaneous cross section data
+of vertical velocity (<span style="font-style: italic;">w</span>)
+and potential temperature (<span style="font-style: italic;">pt</span>)
+are to be output for horizontal (<span style="font-style: italic;">xy</span>)
+and vertical (<span style="font-style: italic;">xz</span>)
+cross sections, and additionally, time averaged (<span style="font-style: italic;">av</span>) vertical cross
+section data are to be output for the vertical velocity: <span style="font-weight: bold;">data_output</span> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'w_xz'</span>, <span style="font-style: italic;">'w_xz_av'</span>, <span style="font-style: italic;">'pt_xy'</span>, <span style="font-style: italic;">'pt_xz'</span>. Output of
+instantaneous (time averaged) data is done after each 900 (1800)s: <span style="font-weight: bold;">dt_data_output</span> = <span style="font-style: italic;">900.0</span>, <span style="font-weight: bold;">dt_data_output_av</span> = <span style="font-style: italic;">1800.0</span>. The
+averaged data are time averaged over the last 900.0 s, where the
+temporal interval of data entering the average is 10 s: <span style="font-weight: bold;">averaging_interval</span> =
+<span style="font-style: italic;">900.0</span>, <span style="font-weight: bold;">dt_averaging_input</span> =
+<span style="font-style: italic;">10.0</span>.
+Horizontal cross sections are output for vertical levels with grid
+index k=2 and k=10, vertical cross sections are output for index j=20: <span style="font-weight: bold;">section_xy</span> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>, <span style="font-weight: bold;">section_xz</span> = <span style="font-style: italic;">20</span>. For runs on
+more than one processor, cross section data are collected and output on
+PE0: <span style="font-weight: bold;">data_output_2d_on_each_pe</span>
+= <span style="font-style: italic;">.F.</span>.</p><p style="line-height: 100%;">Output
+of vertical profiles is to be done after each 900 s. The profiles shall
+be temporally averaged<font color="#000000"> over the last
+<font color="#000000">600 </font>seconds, </font>whereby
+the temporal interval of the profiles entering the average has to be
+10 s: <b>dt_dopr</b> = <i>900.0 s</i>, <b>averaging_interval_pr</b>
+=
+<i>600.0 s</i>, <b>dt_averaging_input_pr</b> =
+<i>10.0 s.</i> The temperature
+profile including the initial temperature profile (therefore <span style="font-style: italic;">'#pt'</span>),
+the subgrid scale, resolved and total vertical sensible heat flux as
+well as the variances of the vertical velocity and the potential
+temperature are to be output:&nbsp; <b>data_output_pr</b>
+= <span style="font-style: italic;">'#pt'</span><i>,
+'w"pt&rdquo;',
+'w*pt*', 'wpt', 'w*2', 'pt*2'</i>.</p><p style="line-height: 100%;">If the data output format for
+graphic software <span style="font-weight: bold;">profil</span>
+is selected (see <a href="chapter_4.2.html#data_output_format">data_output_format</a>),
+the temperature
+profile and the individual variances are to be drawn into independent
+coordinate systems, and in contrast to this all heat flux profiles are
+to
+be
+drawn into the same system: <b>cross_profiles</b> = <span style="font-style: italic;">'pt'</span><i>,
+'w"pt"w*pt*wpt', 'w*2', 'pt*2'</i>. The legend of the x
+axes of these systems is set to <b>cross_xtext</b>= <i>'pot.
+temperature in K', 'heat flux in K ms&gt;-&gt;1', 'velocity
+variance
+in m&gt;2s&gt;-&gt;2', 'temperature variance in K&gt;2'</i>.
+The profiles are to be drawn up to a height level of <b>z_max_do1d</b>
+=
+<i>1500.0 m</i>. </p>
+<p style="line-height: 100%;">Before starting the mo<font color="#000000">del
+on the parallel computer, the number of processing elements must be
+specified.</font> Since relatively few grid points are used for
+this run, choosing of e.g. 8 PEs is sufficient. By default, a 1d domain
+decomposition along x is used on the IBM-Regatta, which means that a
+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>).
+</p><p style="line-height: 100%;">Provided that the
+parameters
+file described above are set within the file </p>
+<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/INPUT/example_p3d</font></pre></ul><p style="line-height: 100%;">and that the conditions
+mentioned in the
+first sections of <a href="chapter_3.2.html">chapter
+3.2</a> are met, the model run can be started with the command </p>
+<p style="line-height: 100%;"><font face="Cumberland, monospace"><font style="font-size: 10pt;" size="2">mrun
+-d example -h ibmh -K parallel -X 8 -T 8 -t 1800 -q cdev -r
+&ldquo;d3# xy# xz# pr#&rdquo;</font></font></p>
+<p style="line-height: 100%;">The output files will appear
+in the
+directories </p>
+<blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/MONITORING</font></tt><font style="font-size: 10pt;" size="2"><br> </font><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/OUTPUT
+,</font></tt></blockquote>
+<p style="line-height: 100%;">while the job protocol will
+appear in
+directory <font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">~/</font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">job_queue</font></font></tt>.
+<br>
+&nbsp; </p>
+<hr><p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.4.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik1" src="left.gif"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.4.2.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik3" src="right.gif"></font></a></font></font></p><p style="line-height: 100%;"><i>Last change:&nbsp;
+</i>$Id$
+<br>&nbsp; <br>
+&nbsp; </p>
+</body></html>
Index: palm/trunk/DOC/app/chapter_4.4.2.html
===================================================================
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+++ palm/trunk/DOC/app/chapter_4.4.2.html	(revision 97)
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html><head>
+<meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 4.4</title>
+<meta content="StarOffice 7 (Win32)" name="GENERATOR">
+<meta content="Siegfried Raasch" name="AUTHOR"> <meta content="20041013;13430732" name="CREATED"> <meta content="20041117;11162734" name="CHANGED"> <meta content="parallel LES model" name="KEYWORDS"> <style>
+<!--
+@page { size: 21cm 29.7cm }
+-->
+</style></head>
+<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">4.4.2 A&nbsp;parameter set for ocean runs</h3>
+<p style="line-height: 100%;">... to be completed ...</p><p style="line-height: 100%;">In this chapter a brief,
+simple and
+complete parameter set is described, which can be used to carry out a
+model run. The presented example is available via <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example
+file</a> and can be used (together with the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config">configuration
+file</a> described in <a href="chapter_3.2.html">chapter
+3.2)</a> for the execution of a simple model run. </p>
+<p style="line-height: 100%;">This run simulates a
+quasi-stationary,
+convective, atmospheric boundary layer with&nbsp; <font color="#000000">zero
+mean horizontal
+wind.</font> For evaluation purposes, cross sections and
+horizontally averaged vertical
+profiles of typical boundary layer variables
+are output at the end of the run. The run shall be carried out in
+batch mode on the IBM Regatta "hanni" of the HLRN.</p>
+<p style="line-height: 100%;">The parameter file necessary
+to carry
+out a run must be provided to the model as an input file under the
+local name <a href="chapter_3.4.html#PARIN">PARIN</a>
+and has the following contents:</p>
+<pre style="line-height: 100%;">&amp;inipar <a href="chapter_4.1.html#nx">nx</a> = <span style="font-style: italic;">39</span>, <a href="chapter_4.1.html#ny">ny</a> = <span style="font-style: italic;">39</span>, <a href="chapter_4.1.html#nz">nz</a> = <span style="font-style: italic;">40</span>,<br> <a href="chapter_4.1.html#dx">dx</a> = <span style="font-style: italic;">50.0</span>, <a href="chapter_4.1.html#dy">dy</a> = <span style="font-style: italic;">50.0</span>, <a href="chapter_4.1.html#dz">dz</a> = <span style="font-style: italic;">50.0</span>,<br> <a href="chapter_4.1.html#dz_stretch_level">dz_stretch_level</a> = <span style="font-style: italic;">1200.0</span>,<br> <a href="chapter_4.1.html#fft_method">fft_method</a> = <span style="font-style: italic;">'temperton-algorithm'</span>,<br> <a href="chapter_4.1.html#initializing_actions">initializing_actions</a> = <span style="font-style: italic;">'set_constant_profiles'</span>,<br> <a href="chapter_4.1.html#ug_surface">ug_surface</a> = <span style="font-style: italic;">0.0</span>, <a href="chapter_4.1.html#vg_surface">vg_surface</a> = <span style="font-style: italic;">0.0</span>,<br> <a href="chapter_4.1.html#pt_vertical_gradient">pt_vertical_gradient</a> = <span style="font-style: italic;">0.0</span>, <span style="font-style: italic;">1.0</span>,<br> <a href="chapter_4.1.html#pt_vertical_gradient_level">pt_vertical_gradient_level</a> = <span style="font-style: italic;">0.0</span>, <span style="font-style: italic;">800.0</span>,<br> <a href="chapter_4.1.html#surface_heatflux">surface_heatflux</a> = <span style="font-style: italic;">0.1</span>, <a href="chapter_4.1.html#bc_pt_b">bc_pt_b</a> = <span style="font-style: italic;">'neumann'</span>,/<br><br>&amp;d3par <a href="chapter_4.2.html#end_time">end_time</a> = <span style="font-style: italic;">3600.0</span>,<br> <a href="chapter_4.2.html#create_disturbances">create_disturbances</a> = <span style="font-style: italic;">.T.</span>,<br> <a href="chapter_4.2.html#dt_disturb">dt_disturb</a> = <span style="font-style: italic;">150.0</span>, <a href="chapter_4.2.html#disturbance_energy_limit">disturbance_energy_limit</a> = <span style="font-style: italic;">0.01</span>,<br> <a href="chapter_4.2.html#dt_run_control">dt_run_control</a> = <span style="font-style: italic;">0.0</span>,<br> <a href="chapter_4.2.html#data_output">data_output</a> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'w_xz'</span>, <span style="font-style: italic;">'w_xz_av'</span>, <span style="font-style: italic;">'pt_xy'</span>, <span style="font-style: italic;">'pt_xz'</span>,<br> <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> = <span style="font-style: italic;">900.0</span>,<br> <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> = <span style="font-style: italic;">1800.0</span>,<br> <a href="chapter_4.2.html#averaging_interval">averaging_interval</a> = <span style="font-style: italic;">900.0</span>,<br> <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a> = <span style="font-style: italic;">10.0</span>,<br> <a href="chapter_4.2.html#section_xy">section_xy</a> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>, <a href="chapter_4.2.html#section_xz">section_xz</a> = <span style="font-style: italic;">20</span>,<br> <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a> = <span style="font-style: italic;">.F.</span>,<br> <a href="chapter_4.2.html#dt_dopr">dt_dopr</a> = <span style="font-style: italic;">900.0</span>, <a href="chapter_4.2.html#averaging_interval_pr">averaging_interval_pr</a> = <span style="font-style: italic;">600.0</span>,<br> <a href="chapter_4.2.html#dt_averaging_input_pr">dt_averaging_input_pr</a> = <span style="font-style: italic;">10.0</span>,<br> <a href="chapter_4.2.html#data_output_pr">data_output_pr</a> = <span style="font-style: italic;">'#pt'</span>, <span style="font-style: italic;">'w&rdquo;pt&rdquo;'</span>, <span style="font-style: italic;">'w*pt*'</span>, <span style="font-style: italic;">'wpt'</span>, <span style="font-style: italic;">'w*2'</span>, <span style="font-style: italic;">'pt*2'</span>,<br> <a href="chapter_4.2.html#cross_profiles">cross_profiles</a> = <span style="font-style: italic;">' pt '</span>, <span style="font-style: italic;">' w"pt" w*pt* wpt '</span>, <span style="font-style: italic;">' w*2 '</span>, <span style="font-style: italic;">' pt*2 '</span>,<br> <a href="chapter_4.2.html#cross_xtext">cross_xtext</a> = <span style="font-style: italic;">'pot. temperature in K'</span>,<br> <span style="font-style: italic;">'heat flux in K ms&gt;-&gt;1'</span>,<br> <span style="font-style: italic;">'velocity variance in m&gt;2s&gt;-&gt;2'</span>,<br> <span style="font-style: italic;">'temperature variance in K&gt;2'</span>,<br> <a href="chapter_4.2.html#z_max_do1d">z_max_do1d</a> = <span style="font-style: italic;">1500.0</span>, /</pre><p style="line-height: 100%;"><br><br></p>
+<p style="line-height: 100%;">The initialization
+parameters (<tt><font style="font-size: 10pt;" size="2">&amp;inipar</font></tt>)
+are located at the beginning of the file. For analysis of a
+convective boundary layer of approx. 1000 m thickness the horizontal
+size of the model domain should amount to at least 2 km x 2 km. In
+order to resolve the convective structures a grid spacing of <b>dx</b>
+=
+<b>dy</b> = <b>dz</b> = <i>50 m</i>
+is enough, since the typical
+diameter of convective plumes is more than 100 m. Thereby the
+upper array index in the two horizontal directions needs to be <b>nx</b>
+= <b>ny</b> = <i>39</i>. <font color="#000000">Since in
+each case the lower array index has the value 0, 40 grid points are
+used along both horizontal directions.</font> In the vertical
+direction
+the domain must be high enough to include the entrainment processes at
+the top of the boundary layer as well as the propagation of gravity
+waves, which were stimulated by
+the convection. However, in the stably stratified region the grid
+resolution has not necessarily to be as high as within the boundary
+layer. This can be obtained by a vertical stretching of the grid
+starting
+from 1200 m via <b>dz_stretch_level</b> = <i>1200.0
+m.</i> This saves
+grid points and computing time. <font color="#800000">T</font><font color="#000000">he
+upper boundary of the model is located at (see </font><a href="chapter_4.1.html#dz_stretch_factor"><font color="#000000">dz_stretch_factor</font></a><font color="#000000">)
+&hellip; m (computed by the model)</font>.</p><p style="line-height: 100%;">Fast Fourier transformations are
+calculated using the Temperton-algorithm, which -on the IBM Regatta- is
+faster than the default system-specific algorithm (from IBM essl
+library).</p><p style="line-height: 100%;">The
+initial profiles for
+wind and temperature can be assigned via <b>initializing_actions</b>
+= <span style="font-style: italic;">'set_constant_profiles'</span>.
+The wind speed, constant with
+height, amounts to <b>ug_surface</b> = <b>vg_surface</b>
+= <i>0.0 m/s</i>. In order
+to allow for a fast onset of convection, a neutral stratified layer up
+to z
+= 800 m capped by an inversion with dtheta/dz = 1K/100 m is given:
+<b>pt_vertical_gradient</b> = <i>0.0, 1.0</i>,
+<b>pt_vertical_gradient_level</b> = <i>0.0, 800.0.</i>
+The surface
+temperature, which by default amounts to 300 K, provides the fixed
+point for the temperature profile (see <a href="chapter_4.1.html#pt_surface">pt_surface</a>).
+Convection is driven by a given, near-surface sensible heat flux via <b>surface_heatflux</b>
+= <i>0.1 K m/s.</i> A given surface sensible heta flux
+requires the
+bottom boundary condition for potential temperature to be <b>bc_pt_b</b>
+=
+<span style="font-style: italic;">'neumann'</span> .
+Thus
+all initialization parameters are determined. These can not be
+changed during the run (also not for restart runs). </p>
+<p style="line-height: 100%;">Now the run parameters (<tt><font style="font-size: 10pt;" size="2">&amp;d3par</font></tt>)
+must be specified. To produce a quasi stationary boundary layer the
+simulated time should be at least one hour, i.e. <b>end_time</b>
+= <i>3600
+s.</i> To stimulate convection, the initially homogeneous (zero)
+wind
+field must be disturbed (<b>create_disturbances</b> = <i>.T.</i>).
+These perturbations should be repeated in a temporal interval of
+<b>dt_disturb</b> = <i>150.0 s</i> until the
+energy of the
+perturbations exceeds the value <b>disturbance_energy_limit</b>
+= 0.<i>01
+m<sup>2</sup>/s<sup>2</sup></i>. After
+each time step run time
+informations (e.g. size of the timestep, maximum velocities, etc.) are
+to be written to the local file <a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a>
+(<b>dt_run_control</b> = <i>0.0 s</i>).</p><p style="line-height: 100%;">Instantaneous cross section data
+of vertical velocity (<span style="font-style: italic;">w</span>)
+and potential temperature (<span style="font-style: italic;">pt</span>)
+are to be output for horizontal (<span style="font-style: italic;">xy</span>)
+and vertical (<span style="font-style: italic;">xz</span>)
+cross sections, and additionally, time averaged (<span style="font-style: italic;">av</span>) vertical cross
+section data are to be output for the vertical velocity: <span style="font-weight: bold;">data_output</span> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'w_xz'</span>, <span style="font-style: italic;">'w_xz_av'</span>, <span style="font-style: italic;">'pt_xy'</span>, <span style="font-style: italic;">'pt_xz'</span>. Output of
+instantaneous (time averaged) data is done after each 900 (1800)s: <span style="font-weight: bold;">dt_data_output</span> = <span style="font-style: italic;">900.0</span>, <span style="font-weight: bold;">dt_data_output_av</span> = <span style="font-style: italic;">1800.0</span>. The
+averaged data are time averaged over the last 900.0 s, where the
+temporal interval of data entering the average is 10 s: <span style="font-weight: bold;">averaging_interval</span> =
+<span style="font-style: italic;">900.0</span>, <span style="font-weight: bold;">dt_averaging_input</span> =
+<span style="font-style: italic;">10.0</span>.
+Horizontal cross sections are output for vertical levels with grid
+index k=2 and k=10, vertical cross sections are output for index j=20: <span style="font-weight: bold;">section_xy</span> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>, <span style="font-weight: bold;">section_xz</span> = <span style="font-style: italic;">20</span>. For runs on
+more than one processor, cross section data are collected and output on
+PE0: <span style="font-weight: bold;">data_output_2d_on_each_pe</span>
+= <span style="font-style: italic;">.F.</span>.</p><p style="line-height: 100%;">Output
+of vertical profiles is to be done after each 900 s. The profiles shall
+be temporally averaged<font color="#000000"> over the last
+<font color="#000000">600 </font>seconds, </font>whereby
+the temporal interval of the profiles entering the average has to be
+10 s: <b>dt_dopr</b> = <i>900.0 s</i>, <b>averaging_interval_pr</b>
+=
+<i>600.0 s</i>, <b>dt_averaging_input_pr</b> =
+<i>10.0 s.</i> The temperature
+profile including the initial temperature profile (therefore <span style="font-style: italic;">'#pt'</span>),
+the subgrid scale, resolved and total vertical sensible heat flux as
+well as the variances of the vertical velocity and the potential
+temperature are to be output:&nbsp; <b>data_output_pr</b>
+= <span style="font-style: italic;">'#pt'</span><i>,
+'w"pt&rdquo;',
+'w*pt*', 'wpt', 'w*2', 'pt*2'</i>.</p><p style="line-height: 100%;">If the data output format for
+graphic software <span style="font-weight: bold;">profil</span>
+is selected (see <a href="chapter_4.2.html#data_output_format">data_output_format</a>),
+the temperature
+profile and the individual variances are to be drawn into independent
+coordinate systems, and in contrast to this all heat flux profiles are
+to
+be
+drawn into the same system: <b>cross_profiles</b> = <span style="font-style: italic;">'pt'</span><i>,
+'w"pt"w*pt*wpt', 'w*2', 'pt*2'</i>. The legend of the x
+axes of these systems is set to <b>cross_xtext</b>= <i>'pot.
+temperature in K', 'heat flux in K ms&gt;-&gt;1', 'velocity
+variance
+in m&gt;2s&gt;-&gt;2', 'temperature variance in K&gt;2'</i>.
+The profiles are to be drawn up to a height level of <b>z_max_do1d</b>
+=
+<i>1500.0 m</i>. </p>
+<p style="line-height: 100%;">Before starting the mo<font color="#000000">del
+on the parallel computer, the number of processing elements must be
+specified.</font> Since relatively few grid points are used for
+this run, choosing of e.g. 8 PEs is sufficient. By default, a 1d domain
+decomposition along x is used on the IBM-Regatta, which means that a
+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>).
+</p><p style="line-height: 100%;">Provided that the
+parameters
+file described above are set within the file </p>
+<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/INPUT/example_p3d</font></pre></ul><p style="line-height: 100%;">and that the conditions
+mentioned in the
+first sections of <a href="chapter_3.2.html">chapter
+3.2</a> are met, the model run can be started with the command </p>
+<p style="line-height: 100%;"><font face="Cumberland, monospace"><font style="font-size: 10pt;" size="2">mrun
+-d example -h ibmh -K parallel -X 8 -T 8 -t 1800 -q cdev -r
+&ldquo;d3# xy# xz# pr#&rdquo;</font></font></p>
+<p style="line-height: 100%;">The output files will appear
+in the
+directories </p>
+<blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/MONITORING</font></tt><font style="font-size: 10pt;" size="2"><br> </font><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/OUTPUT
+,</font></tt></blockquote>
+<p style="line-height: 100%;">while the job protocol will
+appear in
+directory <font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">~/</font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">job_queue</font></font></tt>.
+<br>
+&nbsp; </p>
+<hr><p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.4.1.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik1" src="left.gif"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.5.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik3" src="right.gif"></font></a></font></font></p><p style="line-height: 100%;"><i>Last change:&nbsp;
+</i>$Id$
+<br>&nbsp; <br>
+&nbsp; </p>
+</body></html>
Index: palm/trunk/DOC/app/chapter_4.4.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.4.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.4.html	(revision 97)
@@ -8,175 +8,20 @@
 -->
 </style></head>
-<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">4.4 Example of a minimum
-parameter set</h3>
-<p style="line-height: 100%;">In this chapter a brief,
-simple and
-complete parameter set is described, which can be used to carry out a
-model run. The presented example is available via <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example
-file</a> and can be used (together with the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config">configuration
-file</a> described in <a href="chapter_3.2.html">chapter
-3.2)</a> for the execution of a simple model run. </p>
-<p style="line-height: 100%;">This run simulates a
-quasi-stationary,
+<body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">4.4 Examples of
+parameter sets</h3>
+<p style="line-height: 100%;">This chapter gives examples of complete
+parameter sets for a variety of model runs. These parameter files can
+be found in the directory <span style="font-family: Courier New,Courier,monospace;">trunk/INSTALL</span> and can be used together with the <span style="font-weight: bold;">mrun</span> configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>) to carry out the respective model runs.</p><p style="line-height: 100%;">For
+a description of the basic parameter settings which are generally
+required, see chapter 4.4.1, which explains the settings for a simple
+run of a quasi-stationary,
 convective, atmospheric boundary layer with&nbsp; <font color="#000000">zero
 mean horizontal
-wind.</font> For evaluation purposes, cross sections and
-horizontally averaged vertical
-profiles of typical boundary layer variables
-are output at the end of the run. The run shall be carried out in
-batch mode on the IBM Regatta "hanni" of the HLRN.</p>
-<p style="line-height: 100%;">The parameter file necessary
-to carry
-out a run must be provided to the model as an input file under the
-local name <a href="chapter_3.4.html#PARIN">PARIN</a>
-and has the following contents:</p>
-<pre style="line-height: 100%;">&amp;inipar <a href="chapter_4.1.html#nx">nx</a> = <span style="font-style: italic;">39</span>, <a href="chapter_4.1.html#ny">ny</a> = <span style="font-style: italic;">39</span>, <a href="chapter_4.1.html#nz">nz</a> = <span style="font-style: italic;">40</span>,<br> <a href="chapter_4.1.html#dx">dx</a> = <span style="font-style: italic;">50.0</span>, <a href="chapter_4.1.html#dy">dy</a> = <span style="font-style: italic;">50.0</span>, <a href="chapter_4.1.html#dz">dz</a> = <span style="font-style: italic;">50.0</span>,<br> <a href="chapter_4.1.html#dz_stretch_level">dz_stretch_level</a> = <span style="font-style: italic;">1200.0</span>,<br> <a href="chapter_4.1.html#fft_method">fft_method</a> = <span style="font-style: italic;">'temperton-algorithm'</span>,<br> <a href="chapter_4.1.html#initializing_actions">initializing_actions</a> = <span style="font-style: italic;">'set_constant_profiles'</span>,<br> <a href="chapter_4.1.html#ug_surface">ug_surface</a> = <span style="font-style: italic;">0.0</span>, <a href="chapter_4.1.html#vg_surface">vg_surface</a> = <span style="font-style: italic;">0.0</span>,<br> <a href="chapter_4.1.html#pt_vertical_gradient">pt_vertical_gradient</a> = <span style="font-style: italic;">0.0</span>, <span style="font-style: italic;">1.0</span>,<br> <a href="chapter_4.1.html#pt_vertical_gradient_level">pt_vertical_gradient_level</a> = <span style="font-style: italic;">0.0</span>, <span style="font-style: italic;">800.0</span>,<br> <a href="chapter_4.1.html#surface_heatflux">surface_heatflux</a> = <span style="font-style: italic;">0.1</span>, <a href="chapter_4.1.html#bc_pt_b">bc_pt_b</a> = <span style="font-style: italic;">'neumann'</span>,/<br><br>&amp;d3par <a href="chapter_4.2.html#end_time">end_time</a> = <span style="font-style: italic;">3600.0</span>,<br> <a href="chapter_4.2.html#create_disturbances">create_disturbances</a> = <span style="font-style: italic;">.T.</span>,<br> <a href="chapter_4.2.html#dt_disturb">dt_disturb</a> = <span style="font-style: italic;">150.0</span>, <a href="chapter_4.2.html#disturbance_energy_limit">disturbance_energy_limit</a> = <span style="font-style: italic;">0.01</span>,<br> <a href="chapter_4.2.html#dt_run_control">dt_run_control</a> = <span style="font-style: italic;">0.0</span>,<br> <a href="chapter_4.2.html#data_output">data_output</a> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'w_xz'</span>, <span style="font-style: italic;">'w_xz_av'</span>, <span style="font-style: italic;">'pt_xy'</span>, <span style="font-style: italic;">'pt_xz'</span>,<br> <a href="chapter_4.2.html#dt_data_output">dt_data_output</a> = <span style="font-style: italic;">900.0</span>,<br> <a href="chapter_4.2.html#dt_data_output_av">dt_data_output_av</a> = <span style="font-style: italic;">1800.0</span>,<br> <a href="chapter_4.2.html#averaging_interval">averaging_interval</a> = <span style="font-style: italic;">900.0</span>,<br> <a href="chapter_4.2.html#dt_averaging_input">dt_averaging_input</a> = <span style="font-style: italic;">10.0</span>,<br> <a href="chapter_4.2.html#section_xy">section_xy</a> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>, <a href="chapter_4.2.html#section_xz">section_xz</a> = <span style="font-style: italic;">20</span>,<br> <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a> = <span style="font-style: italic;">.F.</span>,<br> <a href="chapter_4.2.html#dt_dopr">dt_dopr</a> = <span style="font-style: italic;">900.0</span>, <a href="chapter_4.2.html#averaging_interval_pr">averaging_interval_pr</a> = <span style="font-style: italic;">600.0</span>,<br> <a href="chapter_4.2.html#dt_averaging_input_pr">dt_averaging_input_pr</a> = <span style="font-style: italic;">10.0</span>,<br> <a href="chapter_4.2.html#data_output_pr">data_output_pr</a> = <span style="font-style: italic;">'#pt'</span>, <span style="font-style: italic;">'w&rdquo;pt&rdquo;'</span>, <span style="font-style: italic;">'w*pt*'</span>, <span style="font-style: italic;">'wpt'</span>, <span style="font-style: italic;">'w*2'</span>, <span style="font-style: italic;">'pt*2'</span>,<br> <a href="chapter_4.2.html#cross_profiles">cross_profiles</a> = <span style="font-style: italic;">' pt '</span>, <span style="font-style: italic;">' w"pt" w*pt* wpt '</span>, <span style="font-style: italic;">' w*2 '</span>, <span style="font-style: italic;">' pt*2 '</span>,<br> <a href="chapter_4.2.html#cross_xtext">cross_xtext</a> = <span style="font-style: italic;">'pot. temperature in K'</span>,<br> <span style="font-style: italic;">'heat flux in K ms&gt;-&gt;1'</span>,<br> <span style="font-style: italic;">'velocity variance in m&gt;2s&gt;-&gt;2'</span>,<br> <span style="font-style: italic;">'temperature variance in K&gt;2'</span>,<br> <a href="chapter_4.2.html#z_max_do1d">z_max_do1d</a> = <span style="font-style: italic;">1500.0</span>, /</pre><p style="line-height: 100%;"><br><br></p>
-<p style="line-height: 100%;">The initialization
-parameters (<tt><font style="font-size: 10pt;" size="2">&amp;inipar</font></tt>)
-are located at the beginning of the file. For analysis of a
-convective boundary layer of approx. 1000 m thickness the horizontal
-size of the model domain should amount to at least 2 km x 2 km. In
-order to resolve the convective structures a grid spacing of <b>dx</b>
-=
-<b>dy</b> = <b>dz</b> = <i>50 m</i>
-is enough, since the typical
-diameter of convective plumes is more than 100 m. Thereby the
-upper array index in the two horizontal directions needs to be <b>nx</b>
-= <b>ny</b> = <i>39</i>. <font color="#000000">Since in
-each case the lower array index has the value 0, 40 grid points are
-used along both horizontal directions.</font> In the vertical
-direction
-the domain must be high enough to include the entrainment processes at
-the top of the boundary layer as well as the propagation of gravity
-waves, which were stimulated by
-the convection. However, in the stably stratified region the grid
-resolution has not necessarily to be as high as within the boundary
-layer. This can be obtained by a vertical stretching of the grid
-starting
-from 1200 m via <b>dz_stretch_level</b> = <i>1200.0
-m.</i> This saves
-grid points and computing time. <font color="#800000">T</font><font color="#000000">he
-upper boundary of the model is located at (see </font><a href="chapter_4.1.html#dz_stretch_factor"><font color="#000000">dz_stretch_factor</font></a><font color="#000000">)
-&hellip; m (computed by the model)</font>.</p><p style="line-height: 100%;">Fast Fourier transformations are
-calculated using the Temperton-algorithm, which -on the IBM Regatta- is
-faster than the default system-specific algorithm (from IBM essl
-library).</p><p style="line-height: 100%;">The
-initial profiles for
-wind and temperature can be assigned via <b>initializing_actions</b>
-= <span style="font-style: italic;">'set_constant_profiles'</span>.
-The wind speed, constant with
-height, amounts to <b>ug_surface</b> = <b>vg_surface</b>
-= <i>0.0 m/s</i>. In order
-to allow for a fast onset of convection, a neutral stratified layer up
-to z
-= 800 m capped by an inversion with dtheta/dz = 1K/100 m is given:
-<b>pt_vertical_gradient</b> = <i>0.0, 1.0</i>,
-<b>pt_vertical_gradient_level</b> = <i>0.0, 800.0.</i>
-The surface
-temperature, which by default amounts to 300 K, provides the fixed
-point for the temperature profile (see <a href="chapter_4.1.html#pt_surface">pt_surface</a>).
-Convection is driven by a given, near-surface sensible heat flux via <b>surface_heatflux</b>
-= <i>0.1 K m/s.</i> A given surface sensible heta flux
-requires the
-bottom boundary condition for potential temperature to be <b>bc_pt_b</b>
-=
-<span style="font-style: italic;">'neumann'</span> .
-Thus
-all initialization parameters are determined. These can not be
-changed during the run (also not for restart runs). </p>
-<p style="line-height: 100%;">Now the run parameters (<tt><font style="font-size: 10pt;" size="2">&amp;d3par</font></tt>)
-must be specified. To produce a quasi stationary boundary layer the
-simulated time should be at least one hour, i.e. <b>end_time</b>
-= <i>3600
-s.</i> To stimulate convection, the initially homogeneous (zero)
-wind
-field must be disturbed (<b>create_disturbances</b> = <i>.T.</i>).
-These perturbations should be repeated in a temporal interval of
-<b>dt_disturb</b> = <i>150.0 s</i> until the
-energy of the
-perturbations exceeds the value <b>disturbance_energy_limit</b>
-= 0.<i>01
-m<sup>2</sup>/s<sup>2</sup></i>. After
-each time step run time
-informations (e.g. size of the timestep, maximum velocities, etc.) are
-to be written to the local file <a href="chapter_3.4.html#RUN_CONTROL">RUN_CONTROL</a>
-(<b>dt_run_control</b> = <i>0.0 s</i>).</p><p style="line-height: 100%;">Instantaneous cross section data
-of vertical velocity (<span style="font-style: italic;">w</span>)
-and potential temperature (<span style="font-style: italic;">pt</span>)
-are to be output for horizontal (<span style="font-style: italic;">xy</span>)
-and vertical (<span style="font-style: italic;">xz</span>)
-cross sections, and additionally, time averaged (<span style="font-style: italic;">av</span>) vertical cross
-section data are to be output for the vertical velocity: <span style="font-weight: bold;">data_output</span> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'w_xz'</span>, <span style="font-style: italic;">'w_xz_av'</span>, <span style="font-style: italic;">'pt_xy'</span>, <span style="font-style: italic;">'pt_xz'</span>. Output of
-instantaneous (time averaged) data is done after each 900 (1800)s: <span style="font-weight: bold;">dt_data_output</span> = <span style="font-style: italic;">900.0</span>, <span style="font-weight: bold;">dt_data_output_av</span> = <span style="font-style: italic;">1800.0</span>. The
-averaged data are time averaged over the last 900.0 s, where the
-temporal interval of data entering the average is 10 s: <span style="font-weight: bold;">averaging_interval</span> =
-<span style="font-style: italic;">900.0</span>, <span style="font-weight: bold;">dt_averaging_input</span> =
-<span style="font-style: italic;">10.0</span>.
-Horizontal cross sections are output for vertical levels with grid
-index k=2 and k=10, vertical cross sections are output for index j=20: <span style="font-weight: bold;">section_xy</span> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>, <span style="font-weight: bold;">section_xz</span> = <span style="font-style: italic;">20</span>. For runs on
-more than one processor, cross section data are collected and output on
-PE0: <span style="font-weight: bold;">data_output_2d_on_each_pe</span>
-= <span style="font-style: italic;">.F.</span>.</p><p style="line-height: 100%;">Output
-of vertical profiles is to be done after each 900 s. The profiles shall
-be temporally averaged<font color="#000000"> over the last
-<font color="#000000">600 </font>seconds, </font>whereby
-the temporal interval of the profiles entering the average has to be
-10 s: <b>dt_dopr</b> = <i>900.0 s</i>, <b>averaging_interval_pr</b>
-=
-<i>600.0 s</i>, <b>dt_averaging_input_pr</b> =
-<i>10.0 s.</i> The temperature
-profile including the initial temperature profile (therefore <span style="font-style: italic;">'#pt'</span>),
-the subgrid scale, resolved and total vertical sensible heat flux as
-well as the variances of the vertical velocity and the potential
-temperature are to be output:&nbsp; <b>data_output_pr</b>
-= <span style="font-style: italic;">'#pt'</span><i>,
-'w"pt&rdquo;',
-'w*pt*', 'wpt', 'w*2', 'pt*2'</i>.</p><p style="line-height: 100%;">If the data output format for
-graphic software <span style="font-weight: bold;">profil</span>
-is selected (see <a href="chapter_4.2.html#data_output_format">data_output_format</a>),
-the temperature
-profile and the individual variances are to be drawn into independent
-coordinate systems, and in contrast to this all heat flux profiles are
-to
-be
-drawn into the same system: <b>cross_profiles</b> = <span style="font-style: italic;">'pt'</span><i>,
-'w"pt"w*pt*wpt', 'w*2', 'pt*2'</i>. The legend of the x
-axes of these systems is set to <b>cross_xtext</b>= <i>'pot.
-temperature in K', 'heat flux in K ms&gt;-&gt;1', 'velocity
-variance
-in m&gt;2s&gt;-&gt;2', 'temperature variance in K&gt;2'</i>.
-The profiles are to be drawn up to a height level of <b>z_max_do1d</b>
-=
-<i>1500.0 m</i>. </p>
-<p style="line-height: 100%;">Before starting the mo<font color="#000000">del
-on the parallel computer, the number of processing elements must be
-specified.</font> Since relatively few grid points are used for
-this run, choosing of e.g. 8 PEs is sufficient. By default, a 1d domain
-decomposition along x is used on the IBM-Regatta, which means that a
-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>).
-</p><p style="line-height: 100%;">Provided that the
-parameters
-file described above are set within the file </p>
-<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/INPUT/example_p3d</font></pre></ul><p style="line-height: 100%;">and that the conditions
-mentioned in the
-first sections of <a href="chapter_3.2.html">chapter
-3.2</a> are met, the model run can be started with the command </p>
-<p style="line-height: 100%;"><font face="Cumberland, monospace"><font style="font-size: 10pt;" size="2">mrun
--d example -h ibmh -K parallel -X 8 -T 8 -t 1800 -q cdev -r
-&ldquo;d3# xy# xz# pr#&rdquo;</font></font></p>
-<p style="line-height: 100%;">The output files will appear
-in the
-directories </p>
-<blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/MONITORING</font></tt><font style="font-size: 10pt;" size="2"><br> </font><tt><font style="font-size: 10pt;" size="2">~/palm/current_version/JOBS/example/OUTPUT
-,</font></tt></blockquote>
-<p style="line-height: 100%;">while the job protocol will
-appear in
-directory <font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">~/</font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">job_queue</font></font></tt>.
-<br>
+wind.</font>
+All other examples only explain those settings which are specific for
+the respective runs (e.g. only the specific ocean parameters are
+described in the parameter set for simulating ocean convection).<br>
 &nbsp; </p>
-<hr><p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.3.html"><font color="#000080"><img name="Grafik1" src="left.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.5.html"><font color="#000080"><img name="Grafik3" src="right.gif" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;"><i>Last change:&nbsp;
+<hr><p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.3.html"><font color="#000080"><img name="Grafik1" src="left.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.4.1.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik3" src="right.gif"></font></a></font></font></p><p style="line-height: 100%;"><i>Last change:&nbsp;
 </i>$Id$
 <br>&nbsp; <br>
Index: palm/trunk/DOC/app/chapter_4.5.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.5.1.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.5.1.html	(revision 97)
@@ -163,6 +163,6 @@
 horizontal (xy) cross sections as example. The parameter settings
 described below are those of the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example
-parameter file</a> (see <a href="chapter_4.4.html">chapter
-4.4</a>) so this parameter file can be used to retrace the
+parameter file</a> (see <a href="chapter_4.4.1.html">chapter
+4.4.1</a>) so this parameter file can be used to retrace the
 following explanations.<br><br><ol><li>Output
 of xy cross
@@ -348,6 +348,6 @@
 NetCDF dataset described here contains data of instantaneous horizontal
 cross sections and has been created using the settings of the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example
-parameter file</a> (see <a href="chapter_4.4.html">chapter
-4.4</a>),
+parameter file</a> (see <a href="chapter_4.4.1.html">chapter
+4.4.1</a>),
 i.e. it contains section data of the w-velocity-component and of the
 potential temperature for vertical grid levels with index <span style="font-family: monospace;">k = 2</span> and <span style="font-family: monospace;">k = 10</span>,
Index: palm/trunk/DOC/app/chapter_4.5.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.5.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.5.html	(revision 97)
@@ -1,6 +1,5 @@
 <!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</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041015;12234229"> <meta name="CHANGED" content="20041022;13412723"> <meta name="KEYWORDS" content="parallel LES model"> <style>
+<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 4.5</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041015;12234229"> <meta name="CHANGED" content="20041022;13412723"> <meta name="KEYWORDS" content="parallel LES model"> <style>
 <!--
 @page { size: 21cm 29.7cm }
@@ -63,5 +62,5 @@
 </p>&nbsp;For most purposes it should be sufficient to read <a href="../app/chapter_4.5.1.html">chapter 4.5.1</a>
 which explains the PALM-NetCDF-output.<hr>
-<p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.4.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></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_4.5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p>
+<p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.4.2.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_4.5.1.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p>
 <p style="line-height: 100%;">&nbsp;<span style="font-style: italic;">Last
 change:</span> $Id$<br>
Index: palm/trunk/DOC/app/chapter_4.6.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.6.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_4.6.html	(revision 97)
@@ -123,5 +123,5 @@
 </td> <td style="vertical-align: middle;" width="5%">
 <p>I</p> </td> <td style="vertical-align: middle;" width="7%"> <p>C
-* 20</p> </td> <td style="vertical-align: middle;" width="16%"> <p><i>'neumann'</i></p>
+* 20</p> </td> <td style="vertical-align: middle;" width="16%"> <p><i>'initial_gradient'</i></p>
 </td> <td style="vertical-align: middle;" width="57%">
 <p>Top boundary condition of the
@@ -156,5 +156,5 @@
 <p>Top boundary condition of the
 scalar concentration. <br> </p> </td> </tr>
-<tr> <td style="vertical-align: middle;" width="15%">
+<tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#bc_sa_t"><span style="font-weight: bold;">bc_sa_t</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">C * 20</td><td align="undefined" valign="undefined"><span style="font-style: italic;">'neumann'</span></td><td align="undefined" valign="undefined">Top boundary condition of the salinity.&nbsp;</td></tr><tr> <td style="vertical-align: middle;" width="15%">
 <p><a href="chapter_4.1.html#bc_uv_b"><b>bc_uv_b</b></a></p>
 </td> <td style="vertical-align: middle;" width="5%">
@@ -171,5 +171,5 @@
 <p>Top boundary condition of the
 horizontal velocity components u and v.</p> </td> </tr>
-<tr> <td style="font-weight: bold;"><a href="chapter_4.1.html#building_height">building_height</a></td>
+<tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#bottom_salinityflux"><span style="font-weight: bold;">bottom_salinityflux</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;">0.0</span></td><td align="undefined" valign="undefined">Kinematic salinity flux near the surface (in psu m/s).</td></tr><tr> <td style="font-weight: bold;"><a href="chapter_4.1.html#building_height">building_height</a></td>
 <td>I</td> <td>R</td> <td style="font-style: italic;">50.0</td> <td>Height
 of a single building in m.</td> </tr> <tr> <td style="font-weight: bold;"><a href="chapter_4.1.html#building_length_x">building_length_x</a></td>
@@ -324,5 +324,5 @@
 <p>R</p> </td> <td style="vertical-align: middle;" width="7%"> <p>R</p>
 </td> <td style="vertical-align: middle;" width="16%">
-<p><i>zu(3)</i></p> </td> <td style="vertical-align: middle;" width="57%"> <p lang="en-GB"><font face="Thorndale, serif"><font size="3">Lower
+<p><i>zu(3) or zu(nz*2/3)</i></p> </td> <td style="vertical-align: middle;" width="57%"> <p lang="en-GB"><font face="Thorndale, serif"><font size="3">Lower
 limit of the vertical range for which random perturbations are to be
 imposed on the horizontal wind field (</font></font>in <font face="Thorndale, serif"><font size="3">m).&nbsp;
@@ -332,5 +332,5 @@
 <p>R</p> </td> <td style="vertical-align: middle;" width="7%"> <p>R</p>
 </td> <td style="vertical-align: middle;" width="16%">
-<p><i>zu(nz/3)</i></p> </td> <td style="vertical-align: middle;" width="57%"> <p lang="en-GB"><font face="Thorndale, serif"><font size="3">Upper
+<p><i>zu(nz/3) or zu(nzt-3)</i></p> </td> <td style="vertical-align: middle;" width="57%"> <p lang="en-GB"><font face="Thorndale, serif"><font size="3">Upper
 limit of the vertical range for which random perturbations are to be
 imposed on the horizontal wind field (</font></font>in <font face="Thorndale, serif"><font size="3">m). <br>
@@ -832,5 +832,5 @@
 <p><i>nz+1</i></p> </td> <td style="vertical-align: middle;" width="57%"> Limits
 the output of 3d volume data along the vertical direction (grid point
-index k).</td> </tr> <tr> <td style="vertical-align: middle;" width="15%"> <p><a href="chapter_4.1.html#omega"><b>omega</b></a></p>
+index k).</td> </tr> <tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#ocean"><span style="font-weight: bold;">ocean</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">Parameter to switch on&nbsp;ocean runs.</td></tr><tr> <td style="vertical-align: middle;" width="15%"> <p><a href="chapter_4.1.html#omega"><b>omega</b></a></p>
 </td> <td style="vertical-align: middle;" width="5%">
 <p>I</p> </td> <td style="vertical-align: middle;" width="7%"> <p>R</p>
@@ -1194,5 +1194,7 @@
 </td> <td style="vertical-align: middle;" width="16%">
 <p><i>0.1</i></p> </td> <td style="vertical-align: middle;" width="57%"> <p>Roughness
-length (in m). <br> </p> </td> </tr> <tr>
+length (in m). <br> </p> </td> </tr> <tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#sa_surface"><span style="font-weight: bold;">sa_surface</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;">35.0</span></td><td align="undefined" valign="undefined">Surface salinity (in psu).</td></tr><tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#sa_vertical_gradient"><span style="font-weight: bold;">sa_vertical_gradient</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">R(10)</td><td align="undefined" valign="undefined"><span style="font-style: italic;">10 * 0.0</span></td><td align="undefined" valign="undefined">Salinity gradient(s) of the initial salinity profile (in psu
+/ 100 m).</td></tr><tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#sa_vertical_gradient_level"><span style="font-weight: bold;">sa_vertical_gradient_level</span></a></td><td align="undefined" valign="undefined">I</td><td align="undefined" valign="undefined">R(10)</td><td align="undefined" valign="undefined"><span style="font-style: italic;">10 * 0.0</span></td><td align="undefined" valign="undefined">Height level from which on the salinity gradient defined by <a href="chapter_4.1.html#sa_vertical_gradient">sa_vertical_gradient</a>
+is effective (in m).</td></tr><tr>
 <td style="vertical-align: middle;" width="15%"> <p><a href="chapter_4.1.html#scalar_advec"><b>scalar_advec</b></a></p>
 </td> <td style="vertical-align: middle;" width="5%">
@@ -1369,5 +1371,6 @@
 <td>I</td> <td>C * 40</td> <td><span style="font-style: italic;">'flat'</span></td> <td>Topography
 mode.</td> </tr> <tr><td><a style="font-weight: bold;" href="chapter_4.1.html#top_heatflux">top_heatflux</a></td><td>I</td><td>R</td><td><span style="font-style: italic;">no prescribed heatflux</span></td><td>Kinematic
-sensible heat flux at the top surface (in K m/s).</td></tr><tr>
+sensible heat flux at the top surface (in K m/s).</td></tr><tr><td align="undefined" valign="undefined"><a href="chapter_4.1.html#top_salinityflux"><span style="font-weight: bold;">top_salinityflux</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;">no prescribed</span><br style="font-style: italic;"><span style="font-style: italic;">salinityflux</span></td><td align="undefined" valign="undefined">Kinematic
+salinity flux at the top boundary, i.e. the sea surface (in psu m/s).</td></tr><tr>
 <td style="vertical-align: middle;" width="15%"> <p><a href="chapter_4.1.html#ug_surface"><b>ug_surface</b></a></p>
 </td> <td style="vertical-align: middle;" width="5%">
Index: palm/trunk/DOC/app/chapter_5.0.html
===================================================================
--- palm/trunk/DOC/app/chapter_5.0.html	(revision 94)
+++ palm/trunk/DOC/app/chapter_5.0.html	(revision 97)
@@ -200,6 +200,6 @@
 as the </font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d"><font color="#000080">parameter
 file</font></a><font color="#000000">
-(described in </font><a href="chapter_4.4.html"><font color="#000080">chapter
-4.4</font></a>)<font color="#000000">. The
+(described in </font><a href="chapter_4.4.1.html"><font color="#000080">chapter
+4.4.1</font></a>)<font color="#000000">. The
 parameter file must be
 copied from the PALM working copy by<br>
Index: palm/trunk/DOC/app/index.html
===================================================================
--- palm/trunk/DOC/app/index.html	(revision 94)
+++ palm/trunk/DOC/app/index.html	(revision 97)
@@ -148,5 +148,5 @@
 <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;&nbsp; 3.2b<br>For date of last change see bottom line of each page. <o:p></o:p></span></p>
+version:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.<br>For date of last change see bottom line of each page. <o:p></o:p></span></p>
 <div style="text-align: center;" class="MsoNormal" align="center"><span style="font-family: Thorndale;">
 <hr align="center" size="2" width="100%"></span></div>
@@ -189,6 +189,5 @@
 </span><span style="font-family: Thorndale;"><a href="chapter_4.3.html"><span style="" lang="EN-GB">4.3</span></a></span><span style="font-family: Thorndale;" lang="EN-GB"> User-defined
 parameters <br>
-</span><span style="font-family: Thorndale;"><a href="chapter_4.4.html"><span style="" lang="EN-GB">4.4</span></a></span><span style="font-family: Thorndale;" lang="EN-GB"> Example of a
-minimum parameter set <br>
+</span><span style="font-family: Thorndale;"><a href="chapter_4.4.html"><span style="" lang="EN-GB">4.4</span></a></span><span style="font-family: Thorndale;" lang="EN-GB"> Examples of parameter sets</span></p><div style="margin-left: 120px;">&nbsp; <a href="chapter_4.4.1.html">4.4.1</a> A minimum parameter set for the CBL<br>&nbsp; <a href="chapter_4.4.2.html">4.4.2</a> A parameter set for ocean runs</div><p style="margin: 0cm 0cm 0.0001pt 72pt;"><span style="font-family: Thorndale;" lang="EN-GB">
 </span><span style="font-family: Thorndale;"><a href="chapter_4.5.html"><span style="" lang="EN-GB">4.5</span></a></span><span style="font-family: Thorndale;" lang="EN-GB"> Data analysis and
 visualization <o:p></o:p></span></p>
Index: palm/trunk/DOC/tec/technical_documentation.html
===================================================================
--- palm/trunk/DOC/tec/technical_documentation.html	(revision 94)
+++ palm/trunk/DOC/tec/technical_documentation.html	(revision 97)
@@ -12,5 +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;">3.2b</span></td> </tr>
+model version:</b></td> <td><span style="font-weight: bold;">3.3</span></td> </tr>
 <tr nosave=""> <td nosave=""><b>Last
 change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id$</b></td> </tr>
@@ -2311,5 +2311,16 @@
 replaced by multiplication of the inverse. For performance
 optimisation, this is done in the loop calculating the divergence
-instead of using a seperate loop.<br><br>Variables <span style="font-family: Courier New,Courier,monospace;">var_hom</span> and <span style="font-family: Courier New,Courier,monospace;">var_sum</span> are both renamed <span style="font-family: Courier New,Courier,monospace;">pr_palm</span>.</td><td style="vertical-align: top;">data_output_profiles, flow_statistics, init_3d_model, modules, parin, pres, read_var_list, run_control, time_integration</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: <span style="font-family: Courier New,Courier,monospace;">work_fft*_vec</span> removed from some PRIVATE-declarations (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>).<br><br>Bugfix: <span style="font-family: Courier New,Courier,monospace;">field_chr</span> renamed <span style="font-family: Courier New,Courier,monospace;">field_char</span> (<span style="font-family: Courier New,Courier,monospace;">user_interface</span>).<br><br>Bugfix: output of <span style="font-family: Courier New,Courier,monospace;">use_upstream_for_tke</span> (<span style="font-family: Courier New,Courier,monospace;">header</span>).</td><td style="vertical-align: top;">header, poisfft, user_interface</td></tr>
+instead of using a seperate loop.<br><br>Variables <span style="font-family: Courier New,Courier,monospace;">var_hom</span> and <span style="font-family: Courier New,Courier,monospace;">var_sum</span> are both renamed <span style="font-family: Courier New,Courier,monospace;">pr_palm</span>.</td><td style="vertical-align: top;">data_output_profiles, flow_statistics, init_3d_model, modules, parin, pres, read_var_list, run_control, time_integration</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: <span style="font-family: Courier New,Courier,monospace;">work_fft*_vec</span> removed from some PRIVATE-declarations (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>).<br><br>Bugfix: <span style="font-family: Courier New,Courier,monospace;">field_chr</span> renamed <span style="font-family: Courier New,Courier,monospace;">field_char</span> (<span style="font-family: Courier New,Courier,monospace;">user_interface</span>).<br><br>Bugfix: output of <span style="font-family: Courier New,Courier,monospace;">use_upstream_for_tke</span> (<span style="font-family: Courier New,Courier,monospace;">header</span>).</td><td style="vertical-align: top;">header, poisfft, user_interface</td></tr><tr><td style="vertical-align: top;">21/06/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.3</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">This version allows runs for the ocean. Ocean runs can be switched on with the ne inipar-parameter <span style="font-family: Courier New,Courier,monospace;">ocean</span>.<br><br>Setting this switch has several effects:<br><ul><li>An additional prognostic equation for salinity is solved.</li><li>Potential temperature in buoyancy and stability-related terms is replaced by potential density.</li><li>Potential
+density is calculated from the equation of state for seawater after
+each timestep, using the algorithm proposed by Jackett et al. (2006, J.
+Atmos. Oceanic Technol., <span style="font-weight: bold;">23</span>, 1709-1728).<br>So far, only the initial hydrostatic pressure is entered into this equation.</li><li>z=0 (sea surface) is assumed at the model top (vertical grid index <span style="font-family: Courier New,Courier,monospace;">k=nzt</span> on the w-grid), with negative values of z indicating the depth.</li><li>Initial profiles are constructed (e.g. from <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#pt_vertical_gradient">pt_vertical_gradient</a> / <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#pt_vertical_gradient_level">pt_vertical_gradient_level</a>) starting from the sea surface, using surface values&nbsp;given by <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#pt_surface">pt_surface</a>, <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#sa_surface">sa_surface</a>, <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#ug_surface">ug_surface</a>, and <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#vg_surface">vg_surface</a>.</li><li>Zero salinity flux is used as default boundary condition at the bottom of the sea.</li><li>If switched on, random perturbations are by default imposed to the upper model domain from zu(nzt*2/3) to zu(nzt-3).</li></ul>Relevant new inipar-parameters to be exclusively used for steering ocean runs are <span style="font-family: Courier New,Courier,monospace;">bc_sa_t</span>, <span style="font-family: Courier New,Courier,monospace;">bottom_salinityflux</span>, <span style="font-family: Courier New,Courier,monospace;">sa_surface</span>, <span style="font-family: Courier New,Courier,monospace;">sa_vertical_gradient</span>, <span style="font-family: Courier New,Courier,monospace;">sa_vertical_gradient_level</span>, and <span style="font-family: Courier New,Courier,monospace;">top_salinityflux</span>.<br><br>Salinity (<span style="font-family: Courier New,Courier,monospace;">sa</span>) and potential density (<span style="font-family: Courier New,Courier,monospace;">rho</span>) are included as new 2d/3d output quantities. Vertical profiles of salinity (<span style="font-family: Courier New,Courier,monospace;">sa</span>), salinity fluxes (<span style="font-family: Courier New,Courier,monospace;">w"sa"</span>, <span style="font-family: Courier New,Courier,monospace;">w*sa*</span>, <span style="font-family: Courier New,Courier,monospace;">wsa</span>), and potential density (<span style="font-family: Courier New,Courier,monospace;">rho</span>) can also be output.<span style="font-family: Courier New,Courier,monospace;"></span></td><td style="vertical-align: top;">advec_s_bc,
+average_3d_data, boundary_conds, buoyancy, check_parameters,
+data_output_2d, data_output_3d, diffusion_e, flow_statistics, header,
+init_grid, init_3d_model, modules, netcdf, parin, production_e,
+prognostic_equations, read_var_list, sum_up_3d_data, swap_timelevel,
+time_integration, user_interface, write_var_list, write_3d_binary<br><br><span style="font-weight: bold;">new:</span><br>eqn_state_seawater, init_ocean</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;">Inipar-parameter <span style="font-family: Courier New,Courier,monospace;">use_pt_reference</span> renamed <span style="font-family: Courier New,Courier,monospace;">use_reference.</span><br>Internal variable <span style="font-family: Courier New,Courier,monospace;">hydro_press</span> renamed <span style="font-family: Courier New,Courier,monospace;">hyp</span>, routine <span style="font-family: Courier New,Courier,monospace;">calc_mean_pt_profile</span> renamed <span style="font-family: Courier New,Courier,monospace;">calc_mean_profile</span>.<br><br>The format of the <span style="font-family: Courier New,Courier,monospace;">RUN_CONTROL</span> file has been adjusted for ocean runs.</td><td style="vertical-align: top;">advec_particles,
+buoyancy, calc_liquid_water_content, check_parameters, diffusion_e,
+diffusivities, header, init_cloud_physics, modules, production_e,
+prognostic_equations, run_control</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;"></td><td style="vertical-align: top;"></td></tr>
 </tbody>
 </table>&nbsp;<b><blink>Attention:</blink></b>
