Merge branch 'master' of https://github.com/teuben/nemo

docs/man_html/bibcode.html

@@ -12,7 +12,7 @@ <H1>NEMO BIBCODE Manual Reference  </H1>
 is located in NEMO.   For some codes that do not have a manual page,
 the source code file will be mentioned.
 <P>
-Created on: Sun Jun 23 10:11:06 AM EDT 2024 by teuben@pop-os(none)<P>
+Created on: Mon Jul  8 11:56:39 EDT 2024 by teuben@DL5420(none)<P>
 <!-- Created by ./make_bibcode.csh - do not edit -->
 <DIR COMPACT>
 <TABLE BORDER>

docs/man_html/index.html

@@ -16,5 +16,5 @@ <H1>Nemo Reference Manual</H1>
 <LI> <A HREF=bibcode.html>bibcode</A> pages.
 </UL>
 <hr>
-Automatically created by make_html on pop-os Sun Jun 23 10:11:06 AM EDT 2024 <P>
+Automatically created by make_html on DL5420 Mon Jul 8 11:56:39 EDT 2024 <P>
 </BODY></HTML>

docs/man_html/index5.html

@@ -7,91 +7,91 @@
 <CENTER>
 [<A HREF=index1.html>man1</A>,<A HREF=index3.html>man3</A>,<A HREF=index5.html>man5</A>,<A HREF=index6.html>man6</A>,<A HREF=index8.html>man8</A>,<A HREF=indexl.html>manl</A>,<A HREF=whatis.html>whatis</A>,.<A HREF=bibcode.html>bibcode</A>].</CENTER>
 <H1>Nemo Reference Manual(5)</H1>
-Created on pop-os: Sun Jun 23 10:11:06 AM EDT 2024 <P>
+Created on DL5420: Mon Jul  8 11:56:38 EDT 2024 <P>
 <CENTER>
 <TABLE BORDER>
 <tr>
-<td width=20%><a href=acceleration.5.html>acceleration</a></td>
-<td width=20%><a href=data.5.html>data</a></td>
+<td width=20%><a href=GalPot.5.html>GalPot</a></td>
+<td width=20%><a href=ccd.5.html>ccd</a></td>
+<td width=20%><a href=hugh.5.html>hugh</a></td>
+<td width=20%><a href=nemobench.5.html>nemobench</a></td>
+<td width=20%><a href=shells.5.html>shells</a></td>
+</tr>
+<tr>
+<td width=20%><a href=VOTable.5.html>VOTable</a></td>
+<td width=20%><a href=constants.5.html>constants</a></td>
 <td width=20%><a href=idf.5.html>idf</a></td>
 <td width=20%><a href=ntmpv.5.html>ntmpv</a></td>
 <td width=20%><a href=snap.5.html>snap</a></td>
 </tr>
 <tr>
-<td width=20%><a href=ads.5.html>ads</a></td>
-<td width=20%><a href=doc.5.html>doc</a></td>
+<td width=20%><a href=acceleration.5.html>acceleration</a></td>
+<td width=20%><a href=data.5.html>data</a></td>
 <td width=20%><a href=image.5.html>image</a></td>
 <td width=20%><a href=ommod.5.html>ommod</a></td>
 <td width=20%><a href=snapshot.5.html>snapshot</a></td>
 </tr>
 <tr>
-<td width=20%><a href=agui.5.html>agui</a></td>
-<td width=20%><a href=falcON.5.html>falcON</a></td>
+<td width=20%><a href=ads.5.html>ads</a></td>
+<td width=20%><a href=doc.5.html>doc</a></td>
 <td width=20%><a href=keywords.5.html>keywords</a></td>
 <td width=20%><a href=orbit.5.html>orbit</a></td>
 <td width=20%><a href=table.5.html>table</a></td>
 </tr>
 <tr>
-<td width=20%><a href=atlas.5.html>atlas</a></td>
-<td width=20%><a href=filestruct.5.html>filestruct</a></td>
+<td width=20%><a href=agui.5.html>agui</a></td>
+<td width=20%><a href=falcON.5.html>falcON</a></td>
 <td width=20%><a href=layout.5.html>layout</a></td>
 <td width=20%><a href=potential.5.html>potential</a></td>
 <td width=20%><a href=tipsy.5.html>tipsy</a></td>
 </tr>
 <tr>
-<td width=20%><a href=authors.5.html>authors</a></td>
-<td width=20%><a href=filter.5.html>filter</a></td>
+<td width=20%><a href=atlas.5.html>atlas</a></td>
+<td width=20%><a href=filestruct.5.html>filestruct</a></td>
 <td width=20%><a href=lut.5.html>lut</a></td>
 <td width=20%><a href=qac_stats.5.html>qac_stats</a></td>
 <td width=20%><a href=tldr.5.html>tldr</a></td>
 </tr>
 <tr>
-<td width=20%><a href=bench.5.html>bench</a></td>
-<td width=20%><a href=fits.5.html>fits</a></td>
+<td width=20%><a href=authors.5.html>authors</a></td>
+<td width=20%><a href=filter.5.html>filter</a></td>
 <td width=20%><a href=manipulator.5.html>manipulator</a></td>
 <td width=20%><a href=rotcur.5.html>rotcur</a></td>
 <td width=20%><a href=units.5.html>units</a></td>
 </tr>
 <tr>
-<td width=20%><a href=bodiesfunc.5.html>bodiesfunc</a></td>
-<td width=20%><a href=functions.5.html>functions</a></td>
+<td width=20%><a href=bench.5.html>bench</a></td>
+<td width=20%><a href=fits.5.html>fits</a></td>
 <td width=20%><a href=mass99.5.html>mass99</a></td>
 <td width=20%><a href=rotcurshape.5.html>rotcurshape</a></td>
-<td width=20%><a href=VOTable.5.html>VOTable</a></td>
+<td width=20%><a href=wcs.5.html>wcs</a></td>
 </tr>
 <tr>
-<td width=20%><a href=bodyfunc.5.html>bodyfunc</a></td>
-<td width=20%><a href=gadget.5.html>gadget</a></td>
+<td width=20%><a href=bodiesfunc.5.html>bodiesfunc</a></td>
+<td width=20%><a href=functions.5.html>functions</a></td>
 <td width=20%><a href=maxsizes.5.html>maxsizes</a></td>
 <td width=20%><a href=rv.5.html>rv</a></td>
-<td width=20%><a href=wcs.5.html>wcs</a></td>
+<td width=20%><a href=wcstools.5.html>wcstools</a></td>
 </tr>
 <tr>
-<td width=20%><a href=bodytrans.5.html>bodytrans</a></td>
-<td width=20%><a href=GalPot.5.html>GalPot</a></td>
+<td width=20%><a href=bodyfunc.5.html>bodyfunc</a></td>
+<td width=20%><a href=gadget.5.html>gadget</a></td>
 <td width=20%><a href=miller.5.html>miller</a></td>
 <td width=20%><a href=rvc.5.html>rvc</a></td>
-<td width=20%><a href=wcstools.5.html>wcstools</a></td>
+<td width=20%><a href=xvp.5.html>xvp</a></td>
 </tr>
 <tr>
-<td width=20%><a href=boom.5.html>boom</a></td>
+<td width=20%><a href=bodytrans.5.html>bodytrans</a></td>
 <td width=20%><a href=gsp.5.html>gsp</a></td>
 <td width=20%><a href=nbody4.5.html>nbody4</a></td>
 <td width=20%><a href=s2plot.5.html>s2plot</a></td>
-<td width=20%><a href=xvp.5.html>xvp</a></td>
+<td width=20%><a href=xyz.5.html>xyz</a></td>
 </tr>
 <tr>
-<td width=20%><a href=ccd.5.html>ccd</a></td>
+<td width=20%><a href=boom.5.html>boom</a></td>
 <td width=20%><a href=hi.5.html>hi</a></td>
 <td width=20%><a href=nbody6.5.html>nbody6</a></td>
 <td width=20%><a href=sdfits.5.html>sdfits</a></td>
-<td width=20%><a href=xyz.5.html>xyz</a></td>
-</tr>
-<tr>
-<td width=20%><a href=constants.5.html>constants</a></td>
-<td width=20%><a href=hugh.5.html>hugh</a></td>
-<td width=20%><a href=nemobench.5.html>nemobench</a></td>
-<td width=20%><a href=shells.5.html>shells</a></td>
 <td width=20%><a href=yapp.5.html>yapp</a></td>
 </tr>
 </TABLE>

docs/man_html/index6.html

@@ -7,7 +7,7 @@
 <CENTER>
 [<A HREF=index1.html>man1</A>,<A HREF=index3.html>man3</A>,<A HREF=index5.html>man5</A>,<A HREF=index6.html>man6</A>,<A HREF=index8.html>man8</A>,<A HREF=indexl.html>manl</A>,<A HREF=whatis.html>whatis</A>,.<A HREF=bibcode.html>bibcode</A>].</CENTER>
 <H1>Nemo Reference Manual(6)</H1>
-Created on pop-os: Sun Jun 23 10:11:06 AM EDT 2024 <P>
+Created on DL5420: Mon Jul  8 11:56:38 EDT 2024 <P>
 <CENTER>
 <TABLE BORDER>
 <tr>

docs/man_html/index8.html

@@ -7,7 +7,7 @@
 <CENTER>
 [<A HREF=index1.html>man1</A>,<A HREF=index3.html>man3</A>,<A HREF=index5.html>man5</A>,<A HREF=index6.html>man6</A>,<A HREF=index8.html>man8</A>,<A HREF=indexl.html>manl</A>,<A HREF=whatis.html>whatis</A>,.<A HREF=bibcode.html>bibcode</A>].</CENTER>
 <H1>Nemo Reference Manual(8)</H1>
-Created on pop-os: Sun Jun 23 10:11:06 AM EDT 2024 <P>
+Created on DL5420: Mon Jul  8 11:56:39 EDT 2024 <P>
 <CENTER>
 <TABLE BORDER>
 <tr>

docs/man_html/indexl.html

@@ -7,7 +7,7 @@
 <CENTER>
 [<A HREF=index1.html>man1</A>,<A HREF=index3.html>man3</A>,<A HREF=index5.html>man5</A>,<A HREF=index6.html>man6</A>,<A HREF=index8.html>man8</A>,<A HREF=indexl.html>manl</A>,<A HREF=whatis.html>whatis</A>,.<A HREF=bibcode.html>bibcode</A>].</CENTER>
 <H1>Nemo Reference Manual(l)</H1>
-Created on pop-os: Sun Jun 23 10:11:06 AM EDT 2024 <P>
+Created on DL5420: Mon Jul  8 11:56:39 EDT 2024 <P>
 <CENTER>
 <TABLE BORDER>
 <tr>

docs/man_html/nemovar.1.html

@@ -11,7 +11,7 @@
 
 <p> 
 <h2><a name='sect0' href='#toc0'>Name</a></h2>
-nemovar - get and set NEMO variables 
+nemovar - get and set NEMOVAR variables 
 <p> 
 <h2><a name='sect1' href='#toc1'>Synopsis</a></h2>
 <b>nemovar</b> [parameter=value]
@@ -179,6 +179,7 @@ <h2><a name='sect11' href='#toc11'>Author</a></h2>
 <h2><a name='sect12' href='#toc12'>History</a></h2>
 <br>
 <pre>7-mar-2024<tt> </tt>&nbsp;<tt> </tt>&nbsp;Created for NEMO2024<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
+24-jun-2024<tt> </tt>&nbsp;<tt> </tt>&nbsp;0.4:    write dummy if NEMOVAR does not exist<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT
 </pre><p>
 
 <hr><p>

docs/man_html/perorb.1.html

@@ -250,8 +250,10 @@ <h2><a name='sect6' href='#toc6'>See Also</a></h2>
 <a href='potlist.1.html'>potlist(1NEMO)</a>
 , <a href='orbint.1.html'>orbint(1NEMO)</a>
 , <a href='newton0.1.html'>newton0(1NEMO)</a>
+, <a href='henyey.1.html'>henyey(1NEMO)</a>
 , <a href='potential.5.html'>potential(5NEMO)</a>
- <br>
+
+<br>
 <pre>Particle Swarm Optimization (PSO): Skokos et al. - 2005MNRAS.359..251S
 </pre>
 <p> 

docs/man_html/reb2s.1.html

@@ -21,39 +21,43 @@ <h2><a name='sect2' href='#toc2'>Description</a></h2>
 <b>reb2s</b> converts a REBOUND SimulationArchive
 (RSA) to a NEMO <a href='snapshot.5.html'><i>snapshot(5NEMO)</i></a>
 . It currently converts all snapshots from
-the RSA, and only converts mass, position and velocity are converted, the
-accellerations are still ignored. <p>
-Using <b>verbose=t</b> a number of additional
-(integration) variables present in an RSA are shown. 
+the RSA, and only converts mass, position and velocity, the accellerations
+are still ignored. <p>
+Using <b>verbose=t</b> a number of additional (integration)
+variables present in an RSA are shown. 
 <p> 
 <h2><a name='sect3' href='#toc3'>Parameters</a></h2>
- The following
-parameters are recognized in order; they may be given in any order if the
-keyword is also given. Use <b>--help</b> to confirm this man page is up to date. 
-
+ The following parameters
+are recognized in order; they may be given in any order if the keyword
+is also given. Use <b>--help</b> to confirm this man page is up to date.  
 <dl>
 
 <dt><b>in=</b> </dt>
-<dd>input SimulationArchive. No default.  </dd>
+<dd>input
+SimulationArchive. <br>
+No default.  </dd>
 
 <dt><b>out=</b> </dt>
-<dd>optional output snapshot;
-If not specified, the input RSA is just scanned, and snapshot times are
-reported.  Default: only scan. </dd>
+<dd>optional output snapshot; If not specified, the input
+RSA is just scanned, and snapshot times are reported.   <br>
+Default: no output given, only scan the input. </dd>
 
 <dt><b>verbose=t|f</b> </dt>
-<dd>If verbose is set, additional information
-for each snapshot in the RSA is given (time, energy, angular momentum,
-center of mass, etc.).  [Default: <b>f</b>] 
+<dd>If verbose is
+set, additional information for each snapshot in the RSA is given (time,
+energy, angular momentum, center of mass, etc.). <br>
+[Default: <b>f</b>] 
 <p> </dd>
 </dl>
 
 <h2><a name='sect4' href='#toc4'>Caveat</a></h2>
-Since verbose output is on standard
-out, the following pipe will fail in unpredictable ways     reb2s p100.reb
-- verbose=t | tsf -<br>
+Since verbose output is on standard out, the following
+pipe will fail in unpredictable ways     reb2s p100.reb - verbose=t | tsf
+-<br>
   since now NEMO&rsquo;s snapshot as well as the verbose output are in the pipe.
+<p>
 
+<p> 
 <p> 
 <h2><a name='sect5' href='#toc5'>See Also</a></h2>
 <a href='s2reb.1.html'>s2reb(1NEMO)</a>

docs/man_html/reb_integrate.1.html

@@ -141,12 +141,14 @@ <h2><a name='sect6' href='#toc6'>See Also</a></h2>
 </pre>
 <p> 
 <h2><a name='sect7' href='#toc7'>Files</a></h2>
-NEMO/usr/hannorein/nemo/reb_integrate.c - source code 
+<br>
+<pre>NEMO/usr/hannorein/rebound - library source code
+NEMO/usr/hannorein/nemo/reb_integrate.c - source code
+NEMOLIB/librebound.so - linkable library 
+</pre>
 <p> 
 <h2><a name='sect8' href='#toc8'>Author</a></h2>
-Peter
-
-<p>Teuben 
+Peter Teuben 
 <p> 
 <h2><a name='sect9' href='#toc9'>History</a></h2>
 <br>

docs/man_html/reb_viewer.1.html

@@ -38,24 +38,24 @@ <h2><a name='sect3' href='#toc3'>Parameters</a></h2>
 <dl>
 
 <dt><b>in=</b> </dt>
-<dd>input SimulationArchive. No default.  </dd>
+<dd>input SimulationArchive. <br>
+No default.  </dd>
 
-<dt><b>server=</b><i>port</i>
-</dt>
-<dd>The port number used for the app. Default: 1234 
+<dt><b>server=</b><i>port</i> </dt>
+<dd>The port number used for the app. <br>
+Default: 1234 
 <p> </dd>
 </dl>
 
 <h2><a name='sect4' href='#toc4'>See Also</a></h2>
 <a href='s2reb.1.html'>s2reb(1NEMO)</a>
 , <a href='reb2s.1.html'>reb2s(1NEMO)</a>
+, <a href='reb_integrate.1.html'>reb_integrate(1NEMO)</a>
 ,
-<a href='reb_integrate.1.html'>reb_integrate(1NEMO)</a>
-, <a href='snapshot.5.html'>snapshot(5NEMO)</a>
+<a href='snapshot.5.html'>snapshot(5NEMO)</a>
 , <a href='rebound.8.html'>rebound(8NEMO)</a>
 , <a href='glnemo2.1.html'>glnemo2(1NEMO)</a>
-,
-<a href='snapplot.1.html'>snapplot(1NEMO)</a>
+, <a href='snapplot.1.html'>snapplot(1NEMO)</a>
  <br>
 <pre>https://rebound.readthedocs.io - REBOUND documentation
 </pre>

docs/man_html/rebound.8.html

@@ -37,19 +37,21 @@ <h2><a name='sect1' href='#toc1'>Description</a></h2>
 <p> 
 <h2><a name='sect2' href='#toc2'>Install</a></h2>
 
-<p> Before NEMO&rsquo;s rebound tools are installed, rebound needs to be
-installed within NEMO. A typical install can be: 
-<p>           cd $NEMO/usr/hannorein<br>
+<p> Before NEMO&rsquo;s rebound tools are installed, the rebound library
+needs to be installed within NEMO. A typical install can be: 
+<p>          
+cd $NEMO/usr/hannorein<br>
           make install<br>
           cd nemo<br>
           make install<br>
  <tt> </tt>&nbsp;<tt> </tt>&nbsp; <br>
-  The command <b>mknemo -a</b> can also be used to install, since the code lives
-in the NEMO/usr tree. 
+  The command <b>mknemo rebound</b> can also be used to install and/or update
+rebound. 
 <p> 
 <h2><a name='sect3' href='#toc3'>Files</a></h2>
 <br>
 <pre>NEMO/usr/hannorein/   -  top of rebound + tools source code
+NEMO/src/scripts/mknemo.d/rebound  - building via mknemo
 </pre>
 <p> 
 <h2><a name='sect4' href='#toc4'>Author</a></h2>
@@ -64,8 +66,10 @@ <h2><a name='sect6' href='#toc6'>See Also</a></h2>
 <a href='reb2s.1.html'>reb2s(1NEMO)</a>
 , <a href='reb_viewer.1.html'>reb_viewer(1NEMO)</a>
 , <a href='reb_integrate.1.html'>reb_integrate(1NEMO)</a>
-
-<p> 
+ <p>
+<a href='https://rebound.readthedocs.io'>https://rebound.readthedocs.io</a>
+
+
 <h2><a name='sect7' href='#toc7'>History</a></h2>
 <br>
 <pre>17-jan-2024<tt> </tt>&nbsp;<tt> </tt>&nbsp;Drafted<tt> </tt>&nbsp;<tt> </tt>&nbsp;<tt> </tt>&nbsp;<tt> </tt>&nbsp;PJT

docs/man_html/s2reb.1.html

@@ -28,31 +28,32 @@ <h2><a name='sect2' href='#toc2'>Description</a></h2>
 still ignored. <p>
 Note that following the REBOUND convention, data are appended
 to any pre-existing output filename (<b>out=</b>) that is specified, counter to
-the NEMO convention, which refuses to overwrite. 
+the NEMO convention, which refuses to overwrite existing files. 
 <p> 
 <h2><a name='sect3' href='#toc3'>Parameters</a></h2>
- The following
-parameters are recognized in order; they may be given in any order if the
-keyword is also given. Use <b>--help</b> to confirm this man page is up to date. 
 
+The following parameters are recognized in order; they may be given in
+any order if the keyword is also given. Use <b>--help</b> to confirm this man page
+is up to date.  
 <dl>
 
 <dt><b>in=</b> </dt>
-<dd>input NEMO snapshot. No default.  </dd>
+<dd>input NEMO snapshot. <br>
+No default.  </dd>
 
 <dt><b>out=</b> </dt>
-<dd>output SimulationArchive. No default.
-Note output will be appended to any existing RSA. 
+<dd>output SimulationArchive. Note output will be appended
+to any existing RSA. <br>
+No default. 
 <p> </dd>
 </dl>
 
 <h2><a name='sect4' href='#toc4'>Examples</a></h2>
-Here is an example
-of creating a NEMO snapshot, with 9 snapshots of 16 particles in a Plummer
-sphere configuration, from times 0 to 2.0 in steps of 0.25, and converting
-it to a REBOUND  SimulationArchive.  
-<p>   hackcode1 out=plum16.out nbody=16
-seed=16 fcells=2<br>
+Here is an example of creating a NEMO snapshot, with
+9 snapshots of 16 particles in a Plummer sphere configuration, from times
+0 to 2.0 in steps of 0.25, and converting it to a REBOUND  SimulationArchive.
+
+<p>   hackcode1 out=plum16.out nbody=16 seed=16 fcells=2<br>
    s2reb plum16.out plum16.bin debug=1<br>
 
 <p>  With <b>debug=1</b> you will also see the times and m, x, vx, ax of the first