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

README.md

@@ -116,12 +116,34 @@ use of Unix pipes, with a dash denoting the piped file:
          ccdgen out=- object=gauss spar=1,20 size=128 | ccdplot - 
          mkorbit - 0 1 0  0.4 0 0 potname=plummer | orbint - - nsteps=1000 dt=0.05 | orbplot - 
 
+or graphically
+
+```mermaid
+   graph LR;
+   A[tabgen]-->B[tabplot]
+
+   C[mkplummer]-->D[snapplot]
+
+   E[ccdgen]-->F[ccdplot]
+   
+   G[mkorbit]-->H[orbint]
+   H-->I[orbplot]
+```
+
 There are more examples of scripts and figures in
 https://teuben.github.io/nemo/examples/ 
 and an example ipython notebook is shown here
 https://github.com/teuben/nemo/blob/master/nemo_start_example.ipynb
 for something completely different.
 
+A reproducable example is given in this notebook. To run this from the command line
+and print the phase space coordinates of the first particle, use this:
+
+      mkplummer - 10 seed=123| snapprint -  | head -1
+      ### nemo Debug Info: x y z vx vy vz 
+      -0.609486 -0.221687 -0.450963 -0.0766784 -0.209397 0.396561 
+
+
 ## Documentation and Help
 
 There are several additional entry points if you are starting out with NEMO:

docs/source/clustertools.rst

@@ -1,5 +1,16 @@
-ClusterTools (*)
-----------------
+ClusterTools
+------------
 
 
-This python package can also read NEMO (gyrfalcON) files. More on this later.
+This python package can also read NEMO (gyrfalcON) files. Installation can be done
+as follows:
+
+.. code-block::
+
+      cd $NEMO/local
+      git clone https://github.com/webbjj/clustertools
+      pip install -e clustertools
+
+
+For a few packages, we have a few existing examples in the ``$NEMO/usr`` tree
+(e.g. amuse, martini, unsio and uns_projects)

docs/source/codes.rst

@@ -1,7 +1,7 @@
 .. _codes:
 
-Related Codes (*)
-=================
+Related Codes
+=============
 
 Here we summarize some codes used in stellar dynamics that are similar to NEMO.
 We only list codes that are (publically) available. SPH/hydro codes are currently

docs/source/examples.rst

@@ -163,14 +163,14 @@ As an example consider:
 .. code-block::
 
     12% snapplot in=r001.dat xvar=r yvar="x*vy-y*vx" xrange=0:10 yrange=-2:2 \
-                 "visib=-0.2<z&&z<0.2&&i%2==0"
+                 "visib=-0.2<z&z<0.2&i%2==0"
 
     
-plots the angular momentum of the particles along the z axis,
+plots the angular momentum of the particles along the :math:`z` axis,
 :math:`J_z = x.v_y - y.v_x` ,
 against their radius, :math:`r`, but only for the even numbered particles,
 (``i%2==0``) within
-a distance of ``0.2`` of the X-Y plane (:math:`-0.2<z && z<0.2`).
+a distance of ``0.2`` of the X-Y plane (:math:`-0.2<z \& z<0.2`).
 Again note that some of the expressions are within quotes, to prevent
 the shell of giving them a special meaning. 
 
@@ -180,23 +180,23 @@ dynamically loaded into the program for
 execution.
 The expressions must contain legal C expressions and depending
 on their nature must return a value in the context of the
-program. {\it E.g.} {\tt xvar} and {\tt yvar} must return a 
-real value, whereas {\tt visib} must return a boolean (false/true or
+program. {\it E.g.} ``xvar`` and ``yvar`` must return a 
+real value, whereas ``visib`` must return a boolean (false/true or
 0/non-0) value. This should be explained in the manual page of the
 corresponding programs.
 
 In the context of snapshots, the expression can contain 
 basic body variables which
 are understood to the *bodytrans(3NEMO)* routine.
 The real
-variables {\tt x, y, z, vx, vy, vz} are the cartesian phase-space
-coordinates, {\tt t} the time,
-{\tt m} the mass, {\tt phi} the potential,
-{\tt ax,ay,az} the cartesian acceleration and {\tt aux} 
+variables ``x, y, z, vx, vy, vz`` are the cartesian phase-space
+coordinates, ``t`` the time,
+``m`` the mass, ``phi`` the potential,
+``ax,ay,az`` the cartesian acceleration and ``aux``
 some auxiliary information.
 The integer variables are
-{\tt i}, the index of the particle in the snapshot (0 being the
-first one in the usual C tradition) and {\tt key}, another
+``i``, the index of the particle in the snapshot (0 being the
+first one in the usual C tradition) and ``key``, another
 spare slot.
 
 
@@ -210,7 +210,7 @@ body variables listed above can be used in an expression.
 When you need a complex expression that has be used over and
 over again, it is handy to be able to store these expression under
 an alias for later retrieval. 
-With the program {\tt bodytrans}
+With the program ``bodytrans``
 it is possible to save such compiled expressions object files under
 a new name. 
 
@@ -490,12 +490,6 @@ code snippet:
     B% tcppipe A | tsf -
 
 
-Images
-------
-
-.. todo:: examples/Images
-
-
 Tables
 ------
 

docs/source/filestr.rst

@@ -1,7 +1,7 @@
 .. _filestr:
 
-Filestructure (*)
-=================
+Filestructure
+=============
 
 .. note::
    NEMO stores its persistent data in binary files, which under most circumstances
@@ -288,6 +288,7 @@ A very peculiar data file format encountered in NEMO is that of the
 function descriptors. They present themselves to the user through
 one or more keywords, and in reality point to a compiled
 piece of code that will get loaded by NEMO (using *loadobj(3NEMO)*).
+They normally live in ``$NEMOOBJ``.
 We currently have 4 of these in NEMO:
 
 

docs/source/graphics.rst

@@ -1,7 +1,7 @@
 .. _graphics:
 
-Graphics and Image Display (*)
-==============================
+Graphics and Image Display
+==========================
 
 .. note::
    Most NEMO graphics programs select their graphics output with

docs/source/iface.rst

@@ -1,7 +1,7 @@
 .. _iface:
 
-User Interface (*)
-==================
+User Interface
+==============
 
 .. note::
    The NEMO command line user interface is a series of *keyword=value* pairs, where
@@ -333,15 +333,18 @@ of investment the programmability of higher level scripts can give you
 a very powerful programming environment.
 
 
-tkrun
-~~~~~
+tkrun, qtrun
+~~~~~~~~~~~~
 
 The ``tkrun`` program can take directives strategically placed in the
 comment fields of a shell script, and provide a dynamical GUI frontend to
 the command line parameters. Since the GUI is built up automatically,
 the number of keyword should be limited to a dozen or so, as vertical
 space is limited in most desktop managers.
 
+The ``qtrun`` program is an updated version using python and the Qt library.
+
+
 Interrupt to the REVIEW section 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -615,7 +618,7 @@ yapp_pgplot
 ~~~~~~~~~~~
 
 The YAPP interface to the common PGPLOT library is the most used
-interface, and allow one to select from a variety of graphics output
+interface, and allows one to select from a variety of graphics output
 devices without having to recompile the program.
 
 A graphics device in PGPLOT

docs/source/install.rst

@@ -23,11 +23,11 @@ or
    
    curl -LO https://teuben.github.io/nemo/install_nemo.sh
 
-after which
+after which installation can be done with something like
 
 .. code-block:: bash
    
-   bash install_nemo.sh  nemo=$HOME/opt/nemo yapp=pgplot bench5=1 python=1
+   bash install_nemo.sh nemo=$HOME/opt/nemo yapp=pgplot bench5=1 python=1
    source  $HOME/opt/nemo/nemo_start.sh
 
 where the arguments to the
@@ -47,9 +47,9 @@ A more manual install, bypassing this script, can be:
    source nemo_start.sh
 
 
-On a Mac with their new
+On a Mac with 
 `SIP protection <https://macpaw.com/how-to/disable-enable-system-integrity-protection>`_,
-the ``--disable-shared`` flag may need to be added
+enabled, the ``--disable-shared`` flag may need to be added.
 
 .. code-block:: bash
 
@@ -136,8 +136,7 @@ With so many useful python packages around, and so many different methods
 (anaconda, conda, venv etc.), we will not recommend a method, as this will
 likely depend on your own situation. The installation examples below
 should give you enough information how to adapt it for your python
-installation.  It goes without saying (it 2021 here) we only support
-python3.
+installation.  
 
 However, if you install python from within NEMO, there will be a
 ``$NEMO/anaconda3`` directory, that gets automatically activated once

docs/source/refs.rst

@@ -3,9 +3,9 @@
 References
 ==========
 
-Here are some references.
 We also keep a list of
-`codes with papers in NEMO <https://teuben.github.io/nemo/man_html/bibcode.html>`_.
+`codes with papers  <https://teuben.github.io/nemo/man_html/bibcode.html>`_
+in NEMO. These are maintained based on ``@ads`` tags in the manual pages.
 
 
 *A Hierarchical O(N log N) Force-Calculation* -

docs/source/starlab.rst

@@ -21,13 +21,11 @@ distribution. If installed within NEMO, this should be in
 $NEMO/local/starlab/EXAMPLES.
 
 
-For details on a specific tool, type
+For details on a specific program, type
 
 .. code-block::
 
-        tool-name --help
-
-   
+        program --help
 
 
 - Create a linked list of 100 equal-mass nodes of unit total mass

docs/source/using.rst

@@ -43,10 +43,11 @@ write permission in the ``$NEMO`` directory tree:
 
    mknemo -u tsf
    mknemo -h
-   man mknemo		
-
-and an updated version should now be available (check the value of the ``VERSION=``
-value in the output of ``--help``).
+   man mknemo
+   tsf --help
+		
+and an updated version should now be available. Check the value of the ``VERSION=``
+value in the output of ``--help`` of the recompiled program.
 
 Writing NEMO program programs is covered in :ref:`progr`, or see
 also :ref:`install`.

man/man1/pvtrace.1

@@ -1,9 +1,12 @@
 .TH PVTRACE 1NEMO "9 June 2009"
-.SH NAME
+
+.SH "NAME"
 pvtrace \- PV diagram envelope tracing 
-.SH SYNOPSIS
+
+.SH "SYNOPSIS"
 \fBpvtrace\fP in=image [parameter=value] 
-.SH DESCRIPTION
+
+.SH "DESCRIPTION"
 \fBpvtrace\fP tries to recover the rotation curve from a single 
 position-velocity (PV) diagram, by tracing the outer edges of
 the signal that, after correction for a velocity dispersion
@@ -45,7 +48,8 @@ the ISM, instrumental resolution and beam smearing.
 .PP
 WAMET = WArped Modified Envelope-Tracing method
 
-.SH PARAMETERS
+.SH "PARAMETERS"
+.so man1/parameters
 .TP 20
 \fBin=\fP
 Input image file - must be an PV \fIimage(5NEMO)\fP with position
@@ -105,7 +109,8 @@ Output file in case input file was a cube and output is now a map, not a table.
 \fBmode=\fP
 Which of the output modes (see OUTPUT below) will be used for the output map.
 [Default: 2]
-.SH OUTPUT
+
+.SH "OUTPUT"
 Output of the program will be an ASCII table, with various derived velocities
 as function of position along the P axis in the PV-diagram. The following
 columns are returned (see also \fBmode=\fP above):
@@ -121,13 +126,15 @@ columns are returned (see also \fBmode=\fP above):
 7	half gaussian fit
 8	half gaussian fit, with for MET correction
 .fi
-.SH CAVEATS
+
+.SH "CAVEATS"
 Position axis must be carefully created such that the galaxy center is at P=0,
 whereas for velocity it can be corrected with VSYS=. This is easy for theoretical
 data, but cumbersome for real data.
 .PP
 The MET mode is still not very robust, clipping helps.
-.SH SEE ALSO
+
+.SH "SEE ALSO"
 rotcur(1NEMO), runvelfitss07(1NEMO), ccdvel(1NEMO), snapgrid(1NEMO), ccdmom(1NEMO), ccdsub(1NEMO)
 .PP
 .nf
@@ -137,15 +144,19 @@ Sofue et al 1997 PASJ 49, 17
 Sofue et al 523, 136 
 Sofue et al (1997AJ....114.2428S)
 Gentile et al. (2004MNRAS.351..903G) - MET/WAMET method
+Aso & Sai - Spectral Line Analysis/Modeling (SLAM) - https://arxiv.org/abs/2311.07988
 .fi
-.SH FILES
+
+.SH "FILES"
 .nf
 .ta +2i
 src/image/rotcur	sources
 .fi
-.SH AUTHOR
+
+.SH "AUTHOR"
 Peter Teuben
-.SH UPDATE HISTORY
+
+.SH "HISTORY"
 .nf
 .ta +1.0i +4.0i
 5-May-01	V1.0 Created	PJT

man/man5/yapp.5

@@ -1,4 +1,4 @@
-.TH YAPP 5NEMO "24 December 2019"
+.TH YAPP 5NEMO "23 November 2023"
 
 .SH "NAME"
 yapp \- Yet Another Plotting Package
@@ -120,6 +120,9 @@ PGPLOT_FOREGROUND	n/a	1 is the foreground color ("white" for /xs)
 PGPLOT_GIF_WIDTH	850	pixels for /gif (interchange for /vgif)
 PGPLOT_GIF_HEIGHT	680	pixels for /gif (i.e. 85 dpi)
 
+PGPLOT_PNG_WIDTH	680	pixels for /png
+PGPLOT_PNG_HEIGHT	680	pixels for /png
+
 PGPLOT_PPM_WIDTH	850	pixels for /ppm (interchange for /vppm)
 PGPLOT_PPM_HEIGHT	680	pixels for /ppm (i.e. 85 dpi)
 
@@ -178,7 +181,7 @@ NEMO/src/kernel/yapp	various yapp_* implementations
 Peter Teuben
 
 .SH "SEE ALSO"
-catps(1NEMO), catpgps(1NEMO), yapp(3NEMO)
+catps(1NEMO), catpgps(1NEMO), yapp(1NEMO), yapp(3NEMO)
 
 .SH "UPDATE HISTORY"
 .nf