Index: palm/trunk/DOC/app/chapter_3.5.1.html
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--- palm/trunk/DOC/app/chapter_3.5.1.html	(revision 144)
+++ palm/trunk/DOC/app/chapter_3.5.1.html	(revision 212)
@@ -13,12 +13,13 @@
 the
 names and possible arguments of the subroutines involved as well as
-actions which can be accomplished in these subroutines. <br>
+actions which can be accomplished in these subroutines. The respective
+name of a source code files is the&nbsp;subroutine name followed by "<span style="font-family: Courier New,Courier,monospace;">.f90</span>". Exception: the file containing the module<span style="font-family: Courier New,Courier,monospace;"> user </span>has the name <span style="font-family: Courier New,Courier,monospace;">user_module.f90</span>.<br>
 &nbsp; </p>
 <table style="width: 100%;" border="1" cellpadding="2" cellspacing="4"> <col width="211"> <col width="117"> <col width="862"> <tbody> <tr><td width="211"> <p><font size="4"><b>Call
 location</b></font></p> </td> <td width="117"> <p><font size="4"><b>Subroutine
 name and
-argument</b></font></p> </td> <td style="width: 862px;"> <p><font size="4"><b>Possible
-actions</b></font></p> </td> </tr> <tr><td>---</td><td><span style="font-family: monospace;"><a name="user"></a>MODULE
-user</span></td><td>All
+argument(s)</b></font></p> </td> <td style="width: 862px;"> <p><font size="4"><b>Possible
+actions</b></font></p> </td> </tr> <tr><td style="vertical-align: top;">---</td><td style="vertical-align: top;"><span style="font-family: monospace;"><a name="user"></a>MODULE
+user</span></td><td style="vertical-align: top;">All
 user-defined variables which are used outside the respective local
 scopes of the user-defined subroutines have to be declared here.</td></tr><tr valign="top"> <td width="211"> <p>End
@@ -81,8 +82,11 @@
 within the category &ldquo;initialisation&rdquo;.</p><p>See
 also <tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a href="#user_init_3d_model">user_init_3d_model</a>.</font></font></tt></p>
-</td> </tr> <tr><td><tt><font style="font-size: 10pt;" size="2">DEFAULT</font></tt>
+</td> </tr> <tr><td style="vertical-align: top;">End of <span style="font-family: Courier New,Courier,monospace;">read_3d_binary.f90</span></td><td style="vertical-align: top;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_read_restart_data"></a>user_read_<br>restart_data( nxlc, nxlf,nxl_on_file, nxrc, nxrf, nxr_on_file, nync, nynf,nyn_on_file, nysc, nysf, nys_on_file, tmp_2d, tmp_3d )</font></font></tt></td><td style="vertical-align: top;">Reading of user-defined 2d- and 3d-arrays from the restart file.<br><br>In
+case of restart runs, user-defined quantities may have to be read from
+the restart file generated by the previous run. These quantities must
+have been output by the user in the previous run using routine <a href="#user_last_actions"><span style="font-family: Courier New,Courier,monospace;">user_last_actions</span></a>.<br><br>For usage, see example contained in <span style="font-family: Courier New,Courier,monospace;">read_3d_binary.f90</span> and <span style="font-family: Courier New,Courier,monospace;">user_last_actions.f90</span>.</td></tr><tr><td style="vertical-align: top;"><tt><font style="font-size: 10pt;" size="2">DEFAULT</font></tt>
 case of <tt><font style="font-size: 10pt;" size="2">SELECT
 CASE( TRIM(canopy_mode) ) </font></tt>command in the
-middle&nbsp;of <tt><font style="font-size: 10pt;" size="2">init_3d_model.f90</font></tt></td><td><a name="user_init_plant_canopy"></a><code>user_init_plant_canopy</code></td><td>User-defined initilisation of the plant canopy model.<br><br>Here, the user can define the two three-dimensional arrays <code>lad_s and cdc </code>that
+middle&nbsp;of <tt><font style="font-size: 10pt;" size="2">init_3d_model.f90</font></tt></td><td style="vertical-align: top;"><a name="user_init_plant_canopy"></a><code>user_init_plant_canopy</code></td><td style="vertical-align: top;">User-defined initilisation of the plant canopy model.<br><br>Here, the user can define the two three-dimensional arrays <code>lad_s and cdc </code>that
 stand for the leaf area density and the canopy drag coefficient. By
 this, the user can configure a&nbsp;plant canopy. This requires
@@ -206,5 +210,5 @@
 in the CASE
 structure of <tt><font style="font-size: 10pt;" size="2">user_actions_ij</font></tt>!</p> </td>
-</tr> <tr><td style="vertical-align: top;"><code>SUBROUTINE preprocess_spectra</code> in <code>calc_spectra.f90</code>, and <code>data_output_spectra.f90</code></td><td style="vertical-align: top;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_spectra"></a>user_spectra</font></font></tt></td><td style="vertical-align: top;"><p><a href="chapter_3.5.4.html#spectra">Spectra of user-defined
+</tr> <tr><td style="vertical-align: top;"><code>SUBROUTINE preprocess_spectra</code> in <code>calc_spectra.f90</code>, and <code>data_output_spectra.f90</code></td><td style="vertical-align: top;"><p><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_spectra"></a>user_spectra</font></font></tt></p></td><td style="vertical-align: top;"><p><a href="chapter_3.5.4.html#spectra">Spectra of user-defined
 quantities</a> can be computed here.</p>The
 routine contains some simple examples (as comment lines) in order to
@@ -224,5 +228,5 @@
 profiles
 are further processed (e.g. temporally averaged), like the standard profiles, in <tt><font style="font-size: 10pt;" size="2">flow_statistics</font></tt>.</p> </td>
-</tr> <tr><td style="vertical-align: top;">End
+</tr> <tr><td style="vertical-align: top;">Middle of <span style="font-family: Courier New,Courier,monospace;">advec_particles.f90</span>, after particle reflection from walls.</td><td style="vertical-align: top;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_advec_particles"></a>user_advec_<br>particles</font></font></tt></td><td style="vertical-align: top;">User-defined actions after the calculation of the new particle position.</td></tr><tr><td style="vertical-align: top;">End
 of <span style="font-family: monospace;">check_parameters.f90</span>
 where 2d/3d output quantities are checked</td><td style="vertical-align: top;"><span style="font-family: monospace;"><a name="user_check_data_output"></a>user_check_data_<br>output(
@@ -318,5 +322,5 @@
 creating user-defined output quantities.</td></tr><tr valign="top"> <td width="211"> <p>End
 of <tt><font style="font-size: 10pt;" size="2">palm.f90</font></tt></p>
-</td> <td width="117"> <p><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_last_action"></a>user_last_</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"> <br> </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">action</font></font></tt></p>
+</td> <td width="117"> <p><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_last_action"></a>user_last_</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"> <br> </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">actions</font></font></tt></p>
 </td> <td width="862"> <p>User-defined
 actions which are to be executed at the end
@@ -332,5 +336,5 @@
 within the category &ldquo;last actions&rdquo; (the time
 necessary for <tt><font style="font-size: 10pt;" size="2">close_files</font></tt> is included).</p>
-</td> </tr> </tbody></table><hr>
+</td> </tr><tr><td style="vertical-align: top;">Not called in the default PALM code</td><td style="vertical-align: top;"><p><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><a name="user_additional_routines"></a>user_additional_</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"> <br> </font></font><span style="font-family: Cumberland,monospace;">routines</span></p></td><td style="vertical-align: top;">This routine may contain additional routines defined by the user to be called from other user interface routines.</td></tr> </tbody></table><hr>
 <p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_3.5.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_3.5.2.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%;"><i>Last
 change: </i>$Id$</p>
