Today’s astrobite will be a sequel to a post I wrote a few months ago on using the smoothed particle hydrodynamics (SPH) code Gadget-2. In the first post, I went over how to install Gadget and showed how to run one of the test cases included in the Gadget distribution. Today, I’d like to show how to set up, run, and analyze a simple hydrodynamics test problem of your own.
Perhaps one of the oldest topics in astrophysics is the study of binary stars. In 1767, the British natural philosopher John Michell used an early form of statistical analysis to show that the number of closely separated pairs of stars in the night sky is far higher than what one might expect from a randomly distributed field of stars. How do these binary pairs form? Modern astrophysics offers several answers, and in today’s post, we will focus on one possible mechanism: the direct formation of a binary star pair by the collapse of a rotating isothermal sphere of gas.
We will approach this problem using a formulation first proposed by Alan Boss and Peter Bodenheimer in 1979 and later modified by Andreas Burkert and Peter Bodenheimer in 1993. The so-called standard isothermal test case models the gravitational collapse of a one solar mass, spherical, rigidly rotating molecular cloud with a small-amplitude m = 2 density perturbation.
If we wish to simulate the collapse, we first need to set up the initial conditions for the simulation. You can obtain initial conditions files from the following url: http://ngoldbaum.net/astrobites/SICtest.tgz. You can also generate your own initial conditions using the supplied codes. To summarize, the initial conditions are a cloud of radius , mass, , sound speed, angular velocity, . and a density profile of the form,
where φ is the angle in the azimuthal direction about the spin axis of the cloud and α is the amplitude of the perturbation, usually set to 10%. This density distribution creates two lobes of enhanced density that will eventually collapse and fragment into protostars.
Since SPH represents gas using tracer particles, we need to set up a spherical distribution of particles with these properties. The easiest way to do this is to randomly place particles within a spherical volume and then modulate the particle masses according to the m=2 density perturbation. A slightly more conceptually straightforward method would be to set up a regular grid of particles and then carve a sphere out of the grid. I’ve included an IDL program (setup_SIC.pro) that can generate initial conditions in a grid or with random positions.
Both of these choices have drawbacks. Placing particles on a regular grid imposes a preferred direction in space along the grid directions. This causes some grid artifacts to become apparent in the resulting evolution. Placing particles in random positions implies that the density field is dominated by shot noise and increases the amount of random noise in the resulting evolution. It turns out that the best choice is to use ‘glass-like‘ initial conditions that naturally have zero pressure and constant density. A particle glass can be obtained by starting with a regular grid or randomly sampled set of particles. An SPH code can then evolve the equations of hydrodynamics with an artificial frictional force applied to the particle accelerations. The friction damps out spurious pressure forces due to grid artifacts or shot noise and produces a particle glass after several dozen time steps.
Conveniently enough, Gadget can generate glass-like initial conditions out of the box, as described by Volker Springel here. I’ve included initial conditions for the standard isothermal collapse problem with four different choices of gas particle number, drawn from glass-like initial conditions. I’ve also included a code of mine that translates the output of the Gadget glassmaking mode, which will produce an equilibrium cubical box of particles, to the spherical, rotating initial conditions of the standard isothermal collapse problem.
If you would like to generate your own initial conditions files and don’t have IDL, you may have luck writing your own initial conditions generator in your language of choice. My code would be a good starting point, along with the c code for writing Gadget initial conditions included with the Gadget distribution.
Using one of the initial conditions files I’ve supplied, or using your own initial conditions file, you can now run your first hydrodynamics simulation! Since this simulation uses an isothermal equation of state, you will need to recompile Gadget, as by default Gadget assumes you will be using an adiabatic equation of state. All you need to do is to navigate to the directory where you have the Gadget source code stored and, using your favorite text editor, modify the makefile to turn on the ISOTHERM_EQS flag. You should also turn on the ADAPTIVE_GRAVSOFT_FORGAS option. Your makefile should look something like this:
#--------------------------------------- Basic operation mode of code
#OPT += -DPERIODIC
OPT += -DUNEQUALSOFTENINGS
#————————————— Things that are always recommended
OPT += -DPEANOHILBERT
OPT += -DWALLCLOCK
#————————————— TreePM Options
#OPT += -DPMGRID=128
#OPT += -DPLACEHIGHRESREGION=3
#OPT += -DENLARGEREGION=1.2
#OPT += -DASMTH=1.25
#OPT += -DRCUT=4.5
#————————————— Single/Double Precision
#OPT += -DDOUBLEPRECISION
#OPT += -DDOUBLEPRECISION_FFTW
#————————————— Time integration options
OPT += -DSYNCHRONIZATION
#OPT += -DFLEXSTEPS
#OPT += -DPSEUDOSYMMETRIC
#OPT += -DNOSTOP_WHEN_BELOW_MINTIMESTEP
#OPT += -DNOPMSTEPADJUSTMENT
#OPT += -DHAVE_HDF5
#OPT += -DOUTPUTPOTENTIAL
#OPT += -DOUTPUTACCELERATION
#OPT += -DOUTPUTCHANGEOFENTROPY
#OPT += -DOUTPUTTIMESTEP
#————————————— Things for special behaviour
#OPT += -DNOGRAVITY
#OPT += -DNOTREERND
#OPT += -DNOTYPEPREFIX_FFTW
#OPT += -DLONG_X=60
#OPT += -DLONG_Y=5
#OPT += -DLONG_Z=0.2
#OPT += -DTWODIMS
#OPT += -DSPH_BND_PARTICLES
#OPT += -DNOVISCOSITYLIMITER
#OPT += -DCOMPUTE_POTENTIAL_ENERGY
#OPT += -DLONGIDS
OPT += -DISOTHERM_EQS
OPT += -DADAPTIVE_GRAVSOFT_FORGAS
#OPT += -DSELECTIVE_NO_GRAVITY=2+4+8+16
#————————————— Testing and Debugging options
#OPT += -DFORCETEST=0.1
#————————————— Glass making
#OPT += -DMAKEGLASS=262144
Once you’ve modified the makefile, simply save it and then type ‘make’ in the same folder. This will produce a new Gadget2 executable. Next, you’ll need to unzip the .tar.gz file containing the initial conditions and parameter files. Put this in a different directory than the Gadget2 source code. Once that’s done, you should have a directory named ‘SICtest’. This should have four subdirectories, ’15’, ’17’, ’19’, and ’21’. Each of these subdirectories contains an initial conditions file and a parameter file for the standard isothermal collapse test at increasinly higher numerical resolution. The ’15’ folder contains initial conditions with 215 = 32,768 particles, the ’17’ folder contains initial conditions with 217 = 131,072 particles, and so on. Keep in mind that the time to complete a simulation scales with the number of particles. A simulation with 215 particles will finish much more quickly than a simulation with 221 = 2.1 million particles. On my laptop, the smallest simulation completes in about twenty minutes, while the largest simulation takes a good fraction of a day to finish. Also, keep in mind that Gadget will produce a number of snapshots of the simulation as the simulation proceeds. With very large numbers of particles, the snapshot files can grow to be quite large. For example, with 2 million particles, each snapshot is 88 megabytes. If you don’t have a lot of hard drive space on your computer, you may want to increase the ‘TimeBetSnapshot’ option in the paramater file. If you use the paramater file I’ve supplied, Gadget will produce about 520 snapshots.
Running the simulation is very easy. For example, to run the simulation with 32,768 files, simply place your Gadget2 executable in the SICtest folder, open a terminal and navigate to the ‘SICtest’ folder, and enter the following command
mpirun -np 2 ./Gadget2 15/SIC_015.param
This command assumes your computer has two processors. If your computer has a different number of processors, you should change the ‘-np 2’ to ‘-np x’ where x is the number of processors on your computer. If everything is working correctly, the simulation should proceed very quickly at first. I’ve scaled the time in the simulation to the free-fall time, so once the simulation time approaches 1.0, the gas will start to collapse very quickly, and the timestep will decrease accordingly. The code does this to avoid breaking the Courant condition.
Now that you’ve run your simulation, you will have a folder full of snapshot files that you probably want to take a look at! Luckily, there is a freely available SPH visualization suite: SPLASH. To install it, you will first need to install macports, and then use it to install pgplot. Once you’ve finished installing macports, simply type
sudo port -v selfupdate
sudo port -v install pgplot
This step will take quite a while, so don’t worry if it seems like the compilation process is taking a really long time. Next, you will need a copy of the gfortran compiler, which you can download from the mac high performance computing website. Simply download the gfortran binary file appropriate for your system (mine was gfortran-snwleo-intel-bin.tar.gz), and unzip it to /usr/ (or equivalent).
tar -xzvf gfortran-snwleo-intel-bin.tar.gz
export PATH=~/usr/local/bin:$PATH # This should also go in your .bash_profile
Now you need to download SPLASH, unzip the tarball, and then compile it.
tar -xzvf splash-1.14.1.tar.gz
export PGPLOT_LIB=/opt/local/lib # This should also go in your .bash_profile
export PGPLOT_DEV='/xw' # This should also go in your .bash_profile
sudo make install # This step is optional
Once SPLASH in compiled, you should end up with several splash executables. The one you will be using is the executable that can open gadget snapshot files, ‘gsplash’. You can use it to take a look at your simulation by typing something like
at the command line. This will work best if you place gsplash in your UNIX path somewhere (e.g. /usr/local/bin), which you can optionally do by typing ‘sudo make install’ when SPLASH finishes compiling. If everything is working correctly, SPLASH will write some output to the terminal and prompt you to make your first SPH visualization:
(_) _ _ _ _ (_)_
_ (_) ___ _ __ | | __ _ ___| |__ (_) _ (_)
_ (_) _ / __| '_ | |/ _` / __| '_ _ (_)
(_) _ (_) __ |_) | | (_| __ | | | _ (_) _
(_) _ |___/ .__/|_|__,_|___/_| |_| (_) _ (_)
(_) (_)|_| (_) (_) (_)(_) (_)(_) (_)(_)
( B | y ) ( D | a | n | i | e | l ) ( P | r | i | c | e )
( v1.14.0 [6th Dec ’10] Copyright (C) 2005-2010 )
* SPLASH comes with ABSOLUTELY NO WARRANTY.
This is free software; and you are welcome to redistribute it
under certain conditions (see LICENSE file for details). *
Comments, bugs, suggestions and queries to: firstname.lastname@example.org
Check for updates at: http://users.monash.edu.au/~dprice/splash
Please cite Price (2007), PASA, 24, 159-173 (arXiv:0709.0832) if you
use SPLASH for scientific work and if you plot something beautiful,
why not send me a copy for the gallery?
splash.defaults: file not found: using program settings
native byte order on this machine is LITTLE-endian
[byte order used to read data may be set by compiler flags/environment variables]
reading single dumpfile
———————– snap_000 ———————–
>> reading default Gadget format << time : 0.0000000000000000 z (redshift) : 0.00 (set GSPLASH_USE_Z=yes to use in legend) Npart (by type) : 32768 0 0 0 0 0 Mass (by type) : 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 N_gas : 32768 N_total : 32768 N data columns : 10 > allocating memory: parts = 32768 steps = 1 cols = 10
particle masses 32768
gas properties 32768
converting GADGET smoothing length on gas particles to usual SPH definition (x 0.5)
Simulations employ 64.4 neighbours,
corresponding to h = 1.24*(m/rho)^(1/3) in 3D
>> last step ntot = 32768
splash.units not found
setting plot limits: steps 1-> 1 cols 1-> 10
warning: vdz min = max = 0.00E+00
warning: u min = max = 1.27E-01
plot limits set
setting up integrated kernel table…
splash.limits not found
You may choose from a delectable sample of plots
1) x 6) vdz
2) y 7) particle mass
3) z 8 ) u
4) vdx 9) density
5) vdy 10) h
11) multiplot [ 4 ] m) set multiplot
d(ata) p(age) o(pts) l(imits) le(g)end h(elp)
r(ender) v(ector) x(sec/rotate) s,S(ave) q(uit)
Please enter your selection now (y axis or option):
There are two warnings, which are ok, they’re just letting you know that there are no motions in the z direction in the initial conditions and that the gas is all at the same temperature, an implicit consequence of using an isothermal equation of state. To make an image of the gas density distribution, simply type ‘2’, then ‘1’, then ‘9’, then hit return twice. You should end up with an image that looks something like this:
SPLASH can do a lot of really interesting things (see the user’s guide). You don’t have to just make column density maps of your simulations, you can map the gas pressure or temperature, overplot vectors to visualize the gas velocity, or tell it to write image files for each snapshot so that you can make a movie. Here are two example movies:
In the first, I’m showing a projection distribution of gas in the x-y plane as the cloud collapses. The colors vary proprotionally to the gas column density. In the second video I’m focusing on the center of the gas cloud so you can clearly see the binary star system that forms at the end of the simulation. The colors in this video vary proportionally to the logarithm of the gas column density to clearly show the large dynamic range in the simulation.
You may notice that there is an expanding bubble of gas towards the center of the cloud at the beginning of the simulation. This is actually an artifact of the somewhat artificial initial conditions. The gas expands because towards the center of the gas cloud, there are large density gradients because the density perturbation only depends on the azimuthal angle, and not on the radius. The density inhomogeneities quickly mix, leading to a pressure gradient in the x-y plane, which causes a sound wave to expand through the gas, until eventually the wave is stalled by the global collapse of the gas. Eventually, the entire cloud collapses into a double star system. There isn’t much point in following the simulation past this point, as we aren’t modeling the optically thick collapse of the gas. If we continue to simulate the collapse with an isothermal equation of state, eventually the gas will collapse into a filamentary, bar-like structure, the natural consequence of gravitational collapse in an isothermal fluid.