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Simulation of ram-pressure stripping using Gadget2

A galaxy move in the “wind-tunnel” of hot gas (galaxy cluster environment).

Stripped-mass as function of time

Stripped-mass as function of time

Plot density vs internal energy (temperature) of gas particle in wind tunnel (red) and in galaxy (blue).


For next project we can use GalIC to generate initial condition and also use Gizmo instead of Gadget2 to do simulation.


COMAC Workshop 2016 (+ working group 3)
– Dr. Dominik Steinhauser
– Chalawan HPC at NARIT


Cosmological simulation using Gadget2

Today, I’m going to talk about how to basic on cosmological simulation using Gadget2. Before you are running a simulation using Gadget2, you have to make sure that your system can be categorise as a collisionless system. In the case of dark matter in our universe (for cosmological simulation), it is the mother of collisionless system!

Let’s do the cosmological simulation!

    • Zero’th step: install Gadget2 dependencies (e.g. GSL, FFTW, OpenMPI/Mpich, HDF5, etc.), MUSIC (MUlti-Scale-Initial-Conditions) (for initial condition), Gadgetviewer (to plot the snapshot), and Rockstar (Halo finder).(you can skip this step if you can ask your cluster administrator to install it for you.. :v)

    • First step: compile Gadget2
      Change Makefile, for this cosmological simulation you have to make sure that the boundary of your simulation box is periodic.

      #--------------------------------------- Basic operation mode of code
      OPT   +=  -DPERIODIC
      #--------------------------------------- Things that are always recommended
      OPT   +=  -DWALLCLOCK
      #--------------------------------------- TreePM Options
      OPT   +=  -DPMGRID=128
      #OPT   +=  -DENLARGEREGION=1.2
      #OPT   +=  -DASMTH=1.25
      #OPT   +=  -DRCUT=4.5
      #--------------------------------------- Single/Double Precision
      #--------------------------------------- Time integration options
      #OPT   +=  -DFLEXSTEPS

      Just type:


      in Gadget2 directory. If success, you will have executable called Gadget2, copy this file to your working directory.

    • Second step: make initial condition.
      You can use MUSIC to make initial condition for cosmological simulation. Example of music.conf given here is for simulation withboxsize: 60 * 60 * 60 Mpc/h
      number of particles: 128 * 128 * 128
      starting at redshift z: 50
      cosmological parameters: Planck (2015)Run MUSIC with:

      MUSIC music.conf

      and you will get your IC file “ics_60_gadget_128.dat”.

    • Third step: edit Gadget2 parameter file (e.g. cosmo.param) and run your simulation.The most important parameter to set is the IC file, ouputdir, cosmology parameter, ComovingIntegrationOn, and softening. In case you want to make “movie” from snapshot, you can use list ouput file (don’t forget to set OutputListOn = 1), and fill the OutputListFilename with the file that has list of “scale factor” which Gadget2 will create snapshot. For good movie we have to make a list of scale factor with stepsize is set to be equidistant in time (prepare it using astropy for example).Run Gadget2 in your working directory
      mpirun -n 4 ./Gadget2 ./cosmo.param

      If you run this simulation in a cluster computer you can set the “jobscript.sh” and qsub your jobscript.

    • Fourth step: plot the snapshot or make movie, you can use gadgetviewer.

    • Fifth step: Do analysis, e.g. make halo mass function.You can use rockstar to find (dark matter) halo in your simulation (snapshot file). Set the input file for rockstar rockstar.cfgRun rockstar:
      rockstar -c rockstar.cfg &

      Enter 2x and then:

      rockstar -c ./output/auto-rockstar.cfg

      you will get the output file which contain the list of darkmatter halo found in your snapshot.

      You can plot the result and compare with other result (or model)


COMAC Workshop 2016 (+ working group 3)
– Dr. Dominik Steinhauser
– Chalawan HPC at NARIT