Simulation examples

Arepo is a multi-purpose code that supports a number of different types of simulations. Here, we present some examples that in our opinion are particularly relevant. This list is by no means complete, and highly biased to the fields of interest of the authors. We encourage users that have other simulation setups to make them (or small test examples) available to us, in order to provide a more exhaustive list of examples in future code versions.

General Execution Structure of Examples

Examples can be run using the test.sh shell script (typing bash test.sh). The script itself, as the name suggests, is there to run a couple of verification simulations and report whether the simulation results agree with specifications. In particular, if this is the case, the script will delete the directory in which the example run in, which might not be desired when getting started with the code.

The general procedure to execute an example is (replace myexample by the desired one):

• create a run-directory, in which the simulation will be executed:

  mkdir -p ./run/examples/myexample
  

• copy the entire content of the example directory of interest to the run directory:

  cp -r ./examples/myexample/* ./run/examples/myexample/
  

• execute the create.py file, with the run directory as first argument:

  python ./run/examples/myexample/create.py \
  ./run/examples/myexample/
  

This creates initial conditions and possible other files required by the simulation.

• compile AREPO, using the provided Config.sh file:

  make CONFIG=./run/examples/myexample/Config.sh \
  BUILD_DIR=./run/examples/myexample/build \
  EXEC=./run/examples/myexample/Arepo
  

• change to run directory:

  cd ./run/examples/myexample/
  

• execute Arepo (here on 8 mpi ranks):

  mpiexec -np 8 ./Arepo param.txt
  

• change back to root directory:

  cd ../../../
  

• execute the check.py script to do analysis on the simulation output (again specifying the relative path to the run directory):

  python ./run/examples/myexample/check.py \
  ./run/examples/myexample/
  

Note that the only command that is crucial to be executed in a specific directory is the execution of Arepo itself, mpiexec -np 8 ./Arepo param.txt, because the parameter file contains relative paths to the initial conditions, other required files, and the output directory. All other commands can be executed from an arbitrary directory, as long as the relative path handed over is valid.

Cosmological Simulations

One of the main simulation types in Arepo are simulations on an expanding spacetime, where the coordinates are treated as comoving coordinates. This mode is actived whenever the parameter flag ComovingIntegrationOn is set to “1” in the parameter file. In this case, the code models an expanding spacetime described by the Friedmann equations.

The halo (FoF) and subhalo finder (subfind) are analysis tools mainly for these types of simulations.

Cosmological volumes

One of the standard types of cosmological simulations are cosmological volume simulations. These simulations have a uniform mass resolution and are set up by using cosmological perturbation theory, converted to small initial position and velocity perturbations in a periodic box with fixed comoving extent. These simulations can be done with gravity only, in which case the simulation particles are all of a single type (type > 0) and gravity is recommended to be calculated using a TreePM algorithm. This means that the compile time flags SELFGRAVITY and PMGRID are set. The example cosmo_box_gravity_only_3d is a very small representative of such a simulation.

In these cosmological simulations it is also possible to include gas. This can be done, for example, by reading in gravity only initial conditions and setting the compile-time option GENERATE_GAS_IN_ICS, which will split every input particle in a gas cell and a dark matter particle, with the mass ratio following the cosmic average mass and baryon fractions, Omega0 and OmegaBaryon, respectively, which are defined in the parameter file. Including gas in the simulation, it is also useful to use mesh regularization options as well as refinement and derefinement. On top of this, it is also possible to use prescriptions for radiative cooling and star formation using the respective compile-time flags COOLING and USE_SFR. The example cosmo_box_star_formation_3d is using such a setup.

Cosmological zoom simulations

A second class of cosmological simulations that have become popular in studies of galaxy and galaxy cluster formation are so-called zoom simulations, in which the Lagrangian region belonging to a single final object is sampled with significantly higher resolution than the rest of the cosmological volume. In this way, it is possible to accurately resolve the formation of an individual object, while still correctly modeling the large-scale environmental effects. These simulations can be run, as above, in gravity only mode or including gas physics. A gravity only example is given as cosmo_zoom_gravity_only_3d in the examples (note however that the ICs need to be created separately in this example, as they are slightly too large to include them into the main code repository). Technically, such a zoom simulation needs slightly different configuration in the particle-mesh algorithm. In particular, it is often useful to place a second particle-mesh layer which calculates forces only in the high-resolution region. This can be triggered by the compile-time flag PLACEHIGHRESREGION. In addition, the flag PM_ZOOM_OPTIMIZED will change the employed particle-mesh algorithm to one that is specifically optimized for this type of simulations.

Initial conditions generation

The creation of initial conditions for cosmological simulation is in general a complicated procedure, and not included in the Arepo code. However, we include in the examples the possibility to download and execute third-party initial condition generating software to illustrate the general procedure how to create them (MUSIC, Hahn & Abel 2011, MNRAS, 415, 2101 and N-GenIC, Springel et al. 2005, Nature, 435, 629) We note that these third party software packages generally have different library requirements than Arepo, and therefore might not work immediately on some machines. We also note that the initial conditions used in the examples are chosen for illustration purposes and to minimize computational effort to run them. They are generally not suited to be used directly in scientific work.

Newtonian space

Apart from comoving integration, Arepo can also handle an ordinary Newtonian spacetime by choosing the parameter option ComovingIntegrationOn 0. While cosmological simulations usually assume periodic boundary conditions, simulations in Newtonian space can also have reflective or inflow/outflow boundary conditions.

The first example of this class of simulations is an isolated, self-gravitating object, such as in isolated_galaxy_collisionless_3d. This particular case only contains collisionless particles, namely the dark matter and stellar component of a disk galaxy, and their gravitational interactions are calculated with a tree algorithm only, assuming non-periodic forces. The initial conditions of this problem are created with the GalIC code (Yurin & Springel 2014, MNRAS, 444, 62). The initial conditions generation can be triggered in the create.py script, however is a computationally expensive procedure. Therefore we also provide the initial conditions in the repository.

Another popular type of simulations in galactic astrophysics are mergers of galaxies. The example galaxy_merger_star_formation_3d shows such an example, which is similar to isolated_galaxy_collisionless_3d, however this particular case includes gas and two galaxies interacting. Arepo, as every grid code, requires a finite extent of the simulation box as well as positive density at every point. This is different from smoothed-particle-hydrodynamics simulations such as the ones performed with Gadget, where simply not placing gas particles in the initial conditions is an acceptable approach to treat low-density regions. The initial condition for galaxy_merger_sfr_3d are, for historic reasons, smoothed-particle-hydrodynamics initial conditions. To be able to use them in Arepo, the compile-time option ADDBACKGROUNDGRID was introduced. With this option enabled, the code does not perform a simulation, but converts the SPH gas particles into a hierarchical oct-tree structure of cells. Once this is done, the resulting output (using the specified box size) can be used for starting the actual simulation. Note that for this type of simulation, we do not provide the initial-condition generating code. Generally, using grid-code specific initial conditions is preferred over converting particle-based initial conditions, since the latter will always contain numerical noise which may degrade the quality of the simulation.

Simulations may also be completely hydrodynamical, with no gravitational forces involved. One such example is the setup of the Noh_3d problem. This example is an important test problem as it has an analytic solution, thus it is suitable for code verification. However, like for the more complex examples, we also here check against outcomes from previous code versions in order to ensure consistency.

Two-dimensional simulations

Two-dimensional simulations are often used as simplified examples which are significantly cheaper to run than their three-dimensional counterparts, and thus also very useful as test problems. Note that while the one-dimensional simulation code is in substantive parts detached from the rest, two-dimensional and three-dimensional simulations largely use the same routines. Thus these routines can be efficiently tested with 2d test problems.

One example of such a test is gresho_2d, a stationary vortex problem for which the pressure gradient balances the centrifugal forces. The same is true for the Yee vortex, yee_2d, which has the advantage of being smooth in the hydrodynamic properties and therefore is better suited to determine the convergence order of the code. Both these tests are sensitive to accurate hydrodynamical modelling and gradient estimates.

Other 2d test problems are noh_2d, a converging gas flow in 2d which introduces a strong shock and is a challenging problem for the Riemann solver, as well as current_sheet_2d, an MHD test probing numerical reconnection properties of the code.

One-dimensional simulations

Most of the one-dimensional simulations are test problems for particular solvers or numerical methods. Note that Arepo for the case of 1d problems is NOT MPI parallel, i.e. all the following examples can only be calculated using one MPI rank, i.e. in serial. Furthermore, refinement and derefinement is not supported in this case.

One of the most basic one-dimensional examples is a simple linear wave propagation test as in the example wave_1d. Such a test is well-suited to test the convergence order of a scheme. For such applications it is important to ensure that both input/output and calculation are done in double precision by using the compile-time flags INPUT_IN_DOUBLEPRECISION, OUTPUT_IN_DOUBLEPRECISION and DOUBLEPRECISION=1.

Another very important basic test is a 1d shocktube problem. Such a shocktube is calculated in the example shocktube_1d, where the time evolution can be compared to the exact solution. This tests both the Riemann solver as well as the gradient estimates and associated limiters. Similarly, mhd_shocktube_1d tests the time evolution of an MHD Riemann problem. Note that the verification in the latter case is only against a high-resolution simulation.

One example of a more complex one-dimensional test problem is the example interacting_blastwaves_1d. This is checked against a high-resolution solution calculated on a fixed grid.

One-dimensional simulations in spherical symmetry

An important set of simulations for stellar astrophysics are one dimensional simulations in spherical symmetry, such as given for example in polytrope_1d_spherical. Generally, Arepo is not optimized for such kind of simulations and can only run these in serial. However, this option has proven to be useful for quick test simulations as well as for calculating radial profiles which can then be used as initial conditions for three dimensional simulations. One of the key aspects for these simulations is the quality of the boundary conditions. In the spherically symmetric mode, Arepo uses a reflective inner boundary condition and an inflow/outflow boundary condition at the outer end.