source /home/nemo/nemo_startIf you don't really want it to be part of your default login, just make an alias to load it on demand instead.
% man mkplummer MKPLUMMER(1NEMO) MKPLUMMER(1NEMO) NAME mkplummer - generates a snapshot according to a truncated Plummer model SYNOPSIS mkplummer [parameters=values...] DESCRIPTION mkplummer constructs a Plummer model, with a spatial or mass cut-off, after which it performs a coordinate trans- ..(this also means you can use programs like 'gman' or 'tkman' to privide GUI based access to the manual pages. At last count we had well over 250 program man pages, and almost 1000 man pages (programs, library routines, data file info, etc.) in total.
In addition, each NEMO program has builtin help (after all, man pages are written separately from the program code and can be out of sync with the executable), which you can get via a system keyword help:
% mkplummer --help mkplummer out=??? nbody=??? mfrac=0.999 rfrac=22.8042468 seed=0 time=0.0 zerocm=t scale=-1 quiet=0 massname= massexpr=pow(m,p) masspars=p,0.0 massrange=1,1 headline= VERSION=2.6 % mkplummer help= mkplummer out=??? nbody=??? mfrac=0.999 rfrac=22.8042468 seed=0 time=0.0 zerocm=t scale=-1 quiet=0 massname= massexpr=pow(m,p) masspars=p,0.0 massrange=1,1 headline= VERSION=2.6 % mkplummer help=h out : Output file name [???] nbody : Number of particles [???] mfrac : Mass fraction used of Plummer distribution [0.999] rfrac : Radius fraction used of Plummer distribution NOTE: the above two values are chosen so that m( rfrac ) = mfrac [22.8042468] seed : Seed for the random number generator  time : Time at which snapshot is taken [0.0] zerocm : Centrate snapshot (t/f)? [t] scale : Model scale factor (-1=virial 1=natural) [-1] quiet : 0=noisy 1=somewhat quiet 2=more quiet  massname : If used Mass-function name (e.g. n(m))  massexpr : Mass function expression (e.g. pow(m,p)) [pow(m,p)] masspars : Mass function parameters (e.g. p,0.0) [p,0.0] massrange : Range for mass-spectrum (e.g. 1,2) [1,1] headline : Verbiage for output  VERSION : 19-oct-01 PJT [2.6] % mkplummer help=\? Help options are any combination of: a key=val (all) p,k key (parameter,key) d,v val (default,value) n >> add's a newline between above q >> quit's after above work done u >> show the usage string h >> show key and help strings t >> show as MIRIAD doc file z >> show as KHOROS pane file i >> show some internal variables o >> show the output key names ? >> this help (always quits) Numeric helplevels determine degree and type of assistence: They can be added to give combined functionality 1 keyword files used (prognam.def) 2 interactive prompting 4 menu interface using EDITOR environment variable 8 reserved 16 reserved VERSION_ID = 3.4b 1-aug-02 PJT NEMO VERSION = 3.0.14 INTERACT on NEMOINP on PUTPARAM on MACROREAD on HISTORY on INTERRUPT off MINMATCH on TCL off INDEXED on OUTKEYS on (testing) Precision: DOUBLEPRECAs you could perhaps see from the help system keyword, program keywords are used as command line parameters to pass information into the program. They are either fully specified by keyword=value, or by their position (order) on the command line. In the latter case the keyword= part can be ommited (you will often find the first two or three parameters to be the obvious ones that make writing command lines quick). For example, the follow three examples are identical:
% mkplummer p10 10 % mkplummer nbody=10 out=p10 % mkplummer - 10 > p10This last example shows a feature of the NEMO user interface that is often (ab)used, and that is using Unix pipes. When a filename is designated by a dash (-), it means it is at the sending or receiving end of a pipe, whichever is appropriate. Here is another example:
% mkplummer - 100 | snapscale - - rscale=1,1,0.1 | snapprint - x,y,z > p10.tabwhich takes a Plummer sphere of 100 particles, flattens it by scaling all Z-coordinates by 0.1, and writing out all X,Y,Z coordinates to an ASCII file.
% reduce99 input=isothermal_small.input tipsy=ywhich will convert all MASS99 files wih the name outfile.???? to ASCII tipsy files named ducky.????. Next the tipsy data will be converted to the NEMO snapshot format. Some information will be lost, since this program does not import pure gas properties in mixed-particle mode.
% tipsysnap ducky.0001 snap.0001 or % zcat ducky.0001.gz | tipsysnap - snap.0001Next we can do some simple plotting using NEMO's snapplot program: step3: plot the distribution, using the yapp= system keyword and the case where NEMO was compiled with PGPLOT (yapp means Yet Another Plotting Package and is just an interface to PGPLOT in this case).
% snapplot snap.0001 xrange=-32:32 yrange=-32:32 plot1 % snapplot snap.0001 xrange=-32:32 yrange=-32:32 yapp=/vps % snapplot snap.0001 xrange=-32:32 yrange=-32:32 yapp=snap.0001.gif/vgifAs you can see, the first galaxy was centered at the origin, the second one was offset a little bit. Probably in velocity too:
% snapplot snap.0001 xrange=-32:32 yrange=-4:4 yvar=vx plot2To visualize the 3D structure interactively, a crude program xyzview was written a long time ago, and it needs data in a simpler xyz format. So, before viewing, the snapshot is transformed into yet another format....:
% snapxyz snap.0001 xyz.0001 % xyzview xyz.0001 scale=32 plot3When the image comes up, you can use hold the '1', '2' or '3' keys, while moviing the mouse and resp. rotate, zoom or add velocity vectors to the image. Also note that as soon as you started interactive work, only a subset of the particles (nfast=2048 by default) is displayed. The ESC key will exit the window.
This is not a very interesting plot, as all three components are colored boring red. Luckily snapxyz can add colors to the particles, and like most NEMO programs, handles arbitrary expressions containing body variables. For example, color=1 is red, color=2 yellow, color=3 green we will paint the dark particles red, the gas particles yellow, and the star (i.e. disk) particles green.
% rm snap.001.xyz % snapxyz snap.0001 xyz.0001 color='i<4000?2:i<12000?1:3' % tsf xyz.0001 allline=t item=Color | more % xyzview xyz.0001 scale=32 nfast=20000 plot4surely a much more interesting view.
Make sure you specify "TEST_CASE = galaxy_disk" in the 'mass.input' file, and not an "INPUT_FILE". Set "MAX_STEPS = 1" so it simply creates, then ends.
Then, run "../create99". Once it stops, you should have a file 'data.0000' which contains your first galaxy. Move this to a new name (suggested, 'target.0000').
You want to make our second galaxy (which initially is pretty similar to our target galaxy) be of an appropriate mass. This can be 'the same mass', producing a collision of equal mass galaxies. Or, you can make it smaller, for a typical Cartwheel-like collision.
We also need to give to move Galaxy B away from our Galaxy A, and give it an initial velocity towards Galaxy A (so they will collide).
All of this is done in one pass with the "../scale99" routine. As this routine uses the 'mass.input' file, you need to comment out "TEST_CASE = galaxy_disk" and write in "INPUT_FILE = galaxyB.0000". [Future updates will manually ask for a file name, since otherwise this gets ridiculous trying to track these things.]
Now run "../scale99", and answer the questions as given below. For our coordinate scheme, the galaxies initially are created with the disk along the X-Y plane and scale heights along the Z axis.
In this recipe, we want to 'lift' Galaxy B up in 'Z' so that it will travel along the axis (roughly) of Galaxy A, impacting near the center of Galaxy A. We also want to give Galaxy B some non-perpendicular orientation to add variety.
From this, our Galaxy B becomes projectile galaxy B', saved as file 'data.0000'. Rename 'data.0000' to some better name, such as 'projectile.0000'. It is ready to hit the target. Now we need to add the target and the projectile into one file.
Now enter 2 for "Number of Input files to merge", and give (when promoted) their file names: target.0000 and projectile.0000. (This will bypass any input file names in the 'mass.input' file so no changes need to be done to that file here.)
This writes out 'data.0000', which you can now rename to 'collision.0000'. We now have a single data file for our collision! Run the "../reduce99" routine to create a set of projection files at 0,0 and 0,90 degrees to verify that the two galaxies are properly scaled and positioned.
Now run "../mass.input" and it will do your simulations. Your original 'collision.0000' file will remain untouched by this, so you can alter parameters and do multiple runs safely.