Index: palm/trunk/DOC/app/chapter_4.2.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.2.html	(revision 354)
+++ palm/trunk/DOC/app/chapter_4.2.html	(revision 493)
@@ -1,5 +1,6 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
+<html><head>
+
+
 
 
@@ -11,18 +12,5 @@
   
   
-  <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">
-
-
-
-
-  
-  
-  
-  
-  <title>PALM chapter 4.2</title>
-</head>
-
-
-<body>
+  <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"><title>PALM chapter 4.2</title></head><body>
 
 
@@ -1733,5 +1721,5 @@
       
       <p>Umlauts
-are possible (write &ldquo; in front of, similar to TeX), as
+are possible (write &#8220; in front of, similar to TeX), as
 well as super- and subscripts (use "&gt;" or "&lt;" in front of
 each
@@ -2007,5 +1995,6 @@
 
 
-            <td></td>
+            <td><br>
+</td>
 
 
@@ -2071,5 +2060,6 @@
 
 
-            <td style="vertical-align: top;"></td>
+            <td style="vertical-align: top;"><br>
+</td>
 
 
@@ -2237,5 +2227,6 @@
 
 
-            <td style="vertical-align: top;"></td>
+            <td style="vertical-align: top;"><br>
+</td>
 
 
@@ -2391,5 +2382,6 @@
 
 
-            <td style="vertical-align: top;"></td>
+            <td style="vertical-align: top;"><br>
+</td>
 
 
@@ -2610,5 +2602,6 @@
 
 
-            <td style="vertical-align: top;"></td>
+            <td style="vertical-align: top;"><br>
+</td>
 
 
@@ -2673,5 +2666,6 @@
 
 
-            <td style="vertical-align: top;"></td>
+            <td style="vertical-align: top;"><br>
+</td>
 
 
@@ -2735,5 +2729,6 @@
 
 
-            <td style="vertical-align: top;"></td>
+            <td style="vertical-align: top;"><br>
+</td>
 
 
@@ -2765,5 +2760,6 @@
 
 
-            <td></td>
+            <td><br>
+</td>
 
 
@@ -3109,6 +3105,6 @@
 the file
 PLOT3D_FLD (by suitable OUTPUT command in the <span style="font-weight: bold;">mrun</span>
-configuration file: &ldquo;<span style="font-family: monospace;">cat
-PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</span>&rdquo;)
+configuration file: &#8220;<span style="font-family: monospace;">cat
+PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</span>&#8221;)
 after PALM has
 finished.&nbsp;To reduce the amount of data, output to this file
@@ -3147,6 +3143,6 @@
 respective files with suffix _GLOBAL (by
 suitable OUTPUT commands in the <span style="font-weight: bold;">mrun</span>
-configuration file, e.g.: &ldquo;<span style="font-family: monospace;">cat
-PLOT2D_XY_LOCAL &gt;&gt; PLOT2D_XY_GLOBAL</span>&rdquo;)
+configuration file, e.g.: &#8220;<span style="font-family: monospace;">cat
+PLOT2D_XY_LOCAL &gt;&gt; PLOT2D_XY_GLOBAL</span>&#8221;)
 after PALM has
 finished. Cross sections can be directly plotted with <span style="font-weight: bold;">iso2d</span> using the
@@ -3228,5 +3224,5 @@
 default, all data (profiles, time
 series, spectra, particle data, cross sections, volume data) are output
-in NetCDF format (see chapter <a href="chapter_4.5.1.html">4.5.1</a>).
+in NetCDF 64bit-offset format (see chapter <a href="chapter_4.5.1.html">4.5.1</a>).
 Exception: restart data (local files <a href="chapter_3.4.html#BININ">BININ</a>, <a href="chapter_3.4.html#BINOUT">BINOUT</a>, <a href="chapter_3.4.html#PARTICLE_RESTART_DATA_IN">PARTICLE_RESTART_DATA_IN</a>,
       <a href="chapter_3.4.html#PARTICLE_RESTART_DATA_OUT">PARTICLE_RESTART_DATA_OUT</a>)
@@ -3242,18 +3238,10 @@
 
 The
-numerical precision of the NetCDF output is determined with parameter <a href="#chapter_4.1.html#netcdf_precision">netcdf_precision</a>.<br>
-
-
-
-
-      <br>
-
-
-
-
-The
-maximum file size for NetCDF files is 2 GByte by default. Use the
-parameter <a href="#netcdf_64bit">netcdf_64bit</a>
-if larger files have to be created.<br>
+numerical precision of the NetCDF output is determined with parameter <a href="chapter_4.1.html#netcdf_precision">netcdf_precision</a>.<br>
+
+
+
+
+      <br>Other NetCDF formats (classic, NetCDF4/HDF5) can be selected with parameter <a href="#netcdf_data_format">netcdf_data_format</a>.<br>
 
 
@@ -8428,159 +8416,55 @@
 
  <tr>
-
-
-
-
- <td style="vertical-align: top;"><a name="netcdf_64bit"></a><span style="font-weight: bold;">netcdf_64bit</span><br>
-
-
-
-
-
+      <td style="vertical-align: top;"><span style="font-weight: bold;"><a name="netcdf_data_format"></a>netcdf_data_format</span><br>
       </td>
-
-
-
-
- <td style="vertical-align: top;">L<br>
-
-
-
-
- </td>
-
-
-
-
-
-      <td style="vertical-align: top;"><span style="font-style: italic;">.F.</span><br>
-
-
-
-
- </td>
-
-
-
-
-
-      <td style="vertical-align: top;">All NetCDF files - except those containing 3d
-volume data - will have 64
-bit offset format if&nbsp;<span style="font-weight: bold;">netcdf_64bit</span>
-= .TRUE..<br>
-
-
-
-
+      <td style="vertical-align: top;">I<br>
+      </td>
+      <td style="vertical-align: top;"><span style="font-style: italic;">2</span><br>
+      </td>
+      <td style="vertical-align: top;">Data format for NetCDF files.<br>
       <br>
-
-
-
-
-By
-default, the maximum file size of the NetCDF files opened by PALM is 2
-GByte. Using <span style="font-weight: bold;">netcdf_64bit</span> = .TRUE. allows file sizes larger than 2
-GByte.<br>
-
-
-
-
+This variable defines the format of the NetCDF files. Following values are allowed:<br>
       <br>
-
-
-
-
-The 64 bit offset format for those NetCDF files containing 3d volume data (<span style="font-family: Courier New,Courier,monospace;">DATA_3D_NETCDF</span>,
-      <span style="font-family: Courier New,Courier,monospace;">DATA_3D_AV_NETCDF</span>)
-is controlled independently by the switch <a href="#netcdf_64bit_3d">netcdf_64bit_3d</a>.<br>
-
-
-
-
+      <table style="text-align: left; width: 100%;" border="0" cellpadding="2" cellspacing="2">
+        <tbody>
+          <tr>
+            <td style="vertical-align: top;"><span style="font-style: italic;">1</span><br>
+            </td>
+            <td style="vertical-align: top;">NetCDF classic format (filesize limited to 2GB)<br>
+            </td>
+          </tr>
+          <tr>
+            <td style="vertical-align: top;"><span style="font-style: italic;">2</span><br>
+            </td>
+            <td style="vertical-align: top;">NetCDF 64-bit-offset format (large file support, but single variable still limited to 2GB)<br>
+            </td>
+          </tr>
+          <tr>
+            <td style="vertical-align: top;"><span style="font-style: italic;">3</span><br>
+            </td>
+            <td style="vertical-align: top;">NetCDF-4 (HDF5) format (files can be as large as file system supports; unlimited variable size; allows parallel I/O)<br>
+            </td>
+          </tr>
+          <tr>
+            <td style="vertical-align: top;"><span style="font-style: italic;">4</span><br>
+            </td>
+            <td style="vertical-align: top;">NetCDF-4 format, but with NF90_CLASSIC_MODEL bit set (some new features of NetCDF4 are not available)<br>
+            </td>
+          </tr>
+        </tbody>
+      </table>
       <br>
-
-
-
-
-      <span style="font-weight: bold;">Warning:</span><br>
-
-
-
-
-Some
-(PD or commercial) software may not support the 64 bit offset format.<br>
-
-
-
-
-
+      <span style="font-weight: bold;">Important:</span><br>
+Setting <span style="font-weight: bold;">netcdf_data_format </span>&gt; <span style="font-style: italic;">2 </span>requires a NetCDF4 library (set <span style="font-family: Courier New,Courier,monospace;">-I</span>, <span style="font-family: Courier New,Courier,monospace;">-L</span>, and<span style="font-family: Courier New,Courier,monospace;"> -l </span>options for compiling and linking appropriately in configuration file). Also, preprocessor switch <span style="font-family: Courier New,Courier,monospace;">__netcdf4 </span>has to be set (see line starting with <span style="font-family: Courier New,Courier,monospace;">%cpp_opts </span>in the configuration file).<br>
+      <br>
+Files with NetCDF4 format cannot be read with NetCDF3 libraries.<br>
       </td>
-
-
-
-
- </tr>
-
-
-
-
-    <tr>
-
-
-
-
-      <td style="vertical-align: top;"><a name="netcdf_64bit_3d"></a><span style="font-weight: bold;">netcdf_64bit_3d</span></td>
-
-
-
-
-      <td style="vertical-align: top;">L</td>
-
-
-
-
-      <td style="vertical-align: top;">.T.</td>
-
-
-
-
-      <td style="vertical-align: top;">NetCDF files containing 3d
-volume data will have 64 bit offset format if&nbsp;<span style="font-weight: bold;">netcdf_64bit_3d</span>
-= .TRUE..<br>
-
-      <br>
-
-
-
-
-By
-default, the maximum file size of the NetCDF files opened by PALM is 2
-GByte. Using <span style="font-weight: bold;">netcdf_64bit_3d</span> = .TRUE. allows file sizes larger than 2
-GByte.<br>
-
-      <br>
-
-
-
-
-The 64 bit offset format for all other NetCDF files (<span style="font-style: italic;">not</span> containing 3d volume data) is controlled independently by the switch <a href="chapter_4.2.html#netcdf_64bit">netcdf_64bit</a>.<br>
-
-      <br>
-
-
-
-
-      <span style="font-weight: bold;">Warning:</span><br>
-
-
-
-
-Some
-(PD or commercial) software may not support the 64 bit offset format.</td>
-
-
-
-
     </tr>
+
+
+
+
+
+    
 
 
@@ -8741,5 +8625,6 @@
       <td style="vertical-align: top;">I</td>
 
-      <td style="vertical-align: top;"></td>
+      <td style="vertical-align: top;"><br>
+</td>
 
       <td style="vertical-align: top;">
@@ -8837,5 +8722,6 @@
       <td style="vertical-align: top;">I</td>
 
-      <td style="vertical-align: top;"></td>
+      <td style="vertical-align: top;"><br>
+</td>
 
       <td style="vertical-align: top;">
@@ -11938,5 +11824,5 @@
 user-interface (subroutine</span></font> <span style="font-family: monospace;">user_init_particles</span>)<span lang="en-GB"><font face="Thorndale, serif">.
 Particles can pull a
-&ldquo;tail&rdquo; behind themselves to improve their
+&#8220;tail&#8221; behind themselves to improve their
 visualization.
 This is steered via the parameter&nbsp;<a href="chapter_4.2.html#use_particle_tails">use_particle_tails</a>.</font></span><a href="chapter_4.2.html#maximum_number_of_tailpoints"><span lang="en-GB"></span></a></p>
@@ -11996,5 +11882,5 @@
 
 
-      <td style="vertical-align: top;"><i>&acute;reflect&acute;</i></td>
+      <td style="vertical-align: top;"><i>ŽreflectŽ</i></td>
 
 
@@ -12021,5 +11907,5 @@
 default, particles are reflected at the bottom boundary.
 Alternatively, a particle absorption can set by <b>bc_par_b</b>
-= <i>&acute;absorb&acute;</i>.</p>
+= <i>ŽabsorbŽ</i>.</p>
 
 
@@ -12064,5 +11950,5 @@
 
 
-      <td style="vertical-align: top;"><i>&acute;cyclic&acute;</i></td>
+      <td style="vertical-align: top;"><i>ŽcyclicŽ</i></td>
 
 
@@ -12090,6 +11976,6 @@
 are used along x.
 Alternatively, reflection (<b>bc_par_lr</b>
-= <i>&acute;reflect&acute;</i>) or absorption (<b>bc_par_lr</b>
-= <i>&acute;absorb&acute;</i>)
+= <i>ŽreflectŽ</i>) or absorption (<b>bc_par_lr</b>
+= <i>ŽabsorbŽ</i>)
 can be set. <br>
 
@@ -12152,5 +12038,5 @@
 
 
-      <td style="vertical-align: top;"><i>&acute;cyclic&acute;</i></td>
+      <td style="vertical-align: top;"><i>ŽcyclicŽ</i></td>
 
 
@@ -12178,6 +12064,6 @@
 are used along y.
 Alternatively, reflection (<b>bc_par_ns</b>
-= <i>&acute;reflect&acute;</i>) or absorption (<b>bc_par_ns</b>
-= <i>&acute;absorb&acute;</i>)
+= <i>ŽreflectŽ</i>) or absorption (<b>bc_par_ns</b>
+= <i>ŽabsorbŽ</i>)
 can be set.<br>
 
@@ -12230,5 +12116,5 @@
 
 
-      <td style="vertical-align: top;"><i>&acute;absorb&acute;</i></td>
+      <td style="vertical-align: top;"><i>ŽabsorbŽ</i></td>
 
 
@@ -12255,5 +12141,5 @@
 particles are absorbed at the top boundary.
 Alternatively, a reflection condition can be set by <b>bc_par_t</b>
-= <i>&acute;reflect&acute;</i>.</p>
+= <i>ŽreflectŽ</i>.</p>
 
 
@@ -14324,5 +14210,5 @@
 
  <td style="vertical-align: top;">Rear
-(&ldquo;north&rdquo;) edge of a
+(&#8220;north&#8221;) edge of a
 particle source (in m). </td>
 
@@ -14424,5 +14310,5 @@
 
  <td style="vertical-align: top;">Front
-(&ldquo;south&rdquo;) edge of a
+(&#8220;south&#8221;) edge of a
 particle source (in m). </td>
 
@@ -14614,5 +14500,5 @@
       
       
-      <p><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"><font color="#000000">Initial position of the</font></span>
+      <p><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"><font color="#000000">Initial position of the</font></span>
 particles is
 varied randomly within certain limits.&nbsp; </p>
@@ -16290,5 +16176,5 @@
 (cross sections), and <span style="font-style: italic;">'particles'</span>.
 Within the strings the hash characters ("##") have to be replaced by two
-digits 01&le;##&le;99. Up to 10 objects
+digits 01&#8804;##&#8804;99. Up to 10 objects
 can be assigned at the same time, e.g.:&nbsp; </p>
 
@@ -17353,5 +17239,5 @@
 subsequent columns. </font>The order
 of the data in the file follows the order used in the assignment for <b>data_output_sp</b>
-(<b>data_output_sp</b> = <span style="font-style: italic;">'u'</span>, <span style="font-style: italic;">'v'</span>,&hellip;
+(<b>data_output_sp</b> = <span style="font-style: italic;">'u'</span>, <span style="font-style: italic;">'v'</span>,&#8230;
 means that the file starts with the spectra of the u-component,
 followed by the v-component spectra, etc.). Additional to the files
@@ -17748,4 +17634,4 @@
 
 
-</body>
-</html>
+
+</body></html>
