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# Simulation examples
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AREPO is a multi-purpose code that supports a number of different types of
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Arepo is a multi-purpose code that supports a number of different types of
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simulations. Here, we present some examples that in our opinion are
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particularly relevant. This list is by no means complete, and highly biased
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to the fields of interest of the authors.
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We encourage users that have other simulation setups to make them (or small
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test examples) availlable to us, in order to provide a more exhaustive list of
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test examples) available to us, in order to provide a more exhaustive list of
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examples in future code versions.
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... | ... | @@ -65,29 +65,29 @@ specific directory is the execution of Arepo ``mpiexec -np 8 ./Arepo param.txt`` |
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because the parameter file contains relative paths of the initial
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conditions, other required files, and the output directory. All other
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commands can be executed from an arbitrary directory, as long as
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the relative path handed over is correct.
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the relative path handed over is valid.
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Cosmological Simulations
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========================
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One for the main simulation types in AREPO are simulations on an expanding
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One of the main simulation types in Arepo are simulations on an expanding
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spacetime, where the coordinates are treated as comoving coordinates.
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This mode is active whenever the parameter flag ``ComovingIntegrationOn`` is set
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to "1" in the parameter file. In this case the code models the expanding
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spacetime discribed by the Friedmann equations.
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spacetime described by the Friedmann equations.
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The halo (FoF) and subhalo finder (subfind) are analysis tools mainly for these
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types of simulatons.
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types of simulations.
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Cosmological volumes
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--------------------
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One of the standard types of cosmological simulations are
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cosmological volume simulations. These simulatons have a uniform mass
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cosmological volume simulations. These simulations have a uniform mass
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resolution and are set up using cosmological perturbation theory, converted
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to small initial position and velocity perturbations in a periodic box
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with fixed comoving extent. These simulatios can be done with gravity only,
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with fixed comoving extent. These simulations can be done with gravity only,
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in which case the simulation particles are all of a single type (type > 0) and
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gravity is recommended to be calculated using a TreePM
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algorithm. This means that the compile time flags ``SELFGRAVITY`` and ``PMGRID``
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... | ... | @@ -114,11 +114,11 @@ studies of galaxy and galaxy cluster formation are so-called zoom simulations, |
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in which the Lagrangian region belonging to a single final object is
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sampled with significantly higher resolution than the rest of the cosmological
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volume. This way, it is possible to accurately resolve the formation of an
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individual object, while still modelling the large-scale environmental
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individual object, while still modeling the large-scale environmental
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effects. These simulations are, as the above ones, possible to run in gravity
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only mode or including gas physics. A gravity only example is given as
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``cosmo_zoom_gravity_only_3d`` in the examples (note however that the ICs need to be created
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separately in this example, as they are slightly too large to inclue them
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separately in this example, as they are slightly too large to include them
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into the main code repository).
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Technically, such a zoom simulation needs slightly different configuration
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in the particle-mesh algorithm. In particular, it is useful to place a second
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... | ... | @@ -132,7 +132,7 @@ Initial conditions generation |
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-----------------------------
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The creation of initial conditions for cosmological simulation is in general
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a complicated procedure, and not included in the AREPO code. However, we included
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a complicated procedure, and not included in the Arepo code. However, we included
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in the examples the possibility to download and execute third-party initial condition
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generating software to illustrate the general procedure how to create them
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(MUSIC, Hahn&Abel 2011, MNRAS, 415, 2101 and N-GenIC,
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... | ... | @@ -140,7 +140,7 @@ Springel et al. 2005, Nature, 435, 629) |
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We note that these third party software packages generally
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have different library requirements than Arepo, and therefore might
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not work immediately on some machines. We also note that the
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initial conditions used in the examples are choosen for illustration
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initial conditions used in the examples are chosen for illustration
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purposes and to minimize computational effort to run them. They are
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generally not suited to be used directly in scientific work.
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... | ... | @@ -148,8 +148,8 @@ generally not suited to be used directly in scientific work. |
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Newtonian space
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===============
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Apart from comoving integration, AREPO can also handle ordinary Newtonian
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spacetime by coosing the parameter option ``ComovingIntegrationOn 0``.
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Apart from comoving integration, Arepo can also handle ordinary Newtonian
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spacetime by choosing the parameter option ``ComovingIntegrationOn 0``.
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While cosmological simulations usually assume periodic boundary conditions,
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simulations in Newtonian space can also have reflective or inflow/outflow
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boundary conditions.
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... | ... | @@ -159,11 +159,7 @@ object, such as in ``isolated_galaxy_collisionless_3d``. This particular case |
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only contains collisionless particles, namely the dark matter and stellar
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component of a disk galaxy, and their gravitational interactions
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are calculated with a tree algorithm only, assuming non-periodic forces.
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One specific compile-time flag recommended in these kind of simulations is
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``RANDOMIZE_DOMAINCENTER``. Without this flag it is possible that correlated
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force-errors cause an isolated galaxy to drift from the initial center of
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mass, which is prevented by de-correlating these errors by frequently choosing
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a new domain center. The initial conditions of this problem are created with
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The initial conditions of this problem are created with
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the GalIC code (Yurin&Springel 2014, MNRAS, 444, 62). The initial conditions
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generation can be triggered in the create.py script, however is a computationally
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expensive procedure. Therefore we also provide the initial conditions in the
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... | ... | @@ -172,15 +168,15 @@ repository. |
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Another popular type of simulations in galactic astrophysics are mergers of
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galaxies. The example ``galaxy_merger_star_formation_3d`` shows such an example,
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which is similar to ``isolated_galaxy_collisionless_3d``, however in this
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particular case includes gas and two galaxies interacting. AREPO, as every
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grid code, requires a finite extent of the simulation box as well as non-zero
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particular case includes gas and two galaxies interacting. Arepo, as every
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grid code, requires a finite extent of the simulation box as well as positive
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density at every point.
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This is different from Smoothed-Particle-Hydrodynamics simulations such as
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the ones performed with GADGET, where simply not placing gas particles in
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This is different from smoothed-particle-hydrodynamics simulations such as
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the ones performed with Gadget, where simply not placing gas particles in
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the initial condition is an acceptable solution to treat low-density regions.
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The initial condition for ``galaxy_merger_sfr_3d`` are, for historic reasons,
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Smoothed-Particle-Hydrodynamics initial conditions. To be able to use them
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in AREPO, the compile-time opiton ``ADDBACKGROUNDGRID`` was introduced.
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smoothed-particle-hydrodynamics initial conditions. To be able to use them
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in Arepo, the compile-time option ``ADDBACKGROUNDGRID`` was introduced.
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With this mode enabled, the code does not perform a simulation, but converts
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the SPH gas particles into a hierarchical oct-tree structure of cells.
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Once this is done, this output (using the recommended box size) can be used
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... | ... | @@ -215,7 +211,7 @@ convergence order of the code. Both these tests are sensitive to accurate |
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hydrodynamical modelling and gradient estimates.
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Other 2d test problems are ``noh_2d``, a converging gas flow in 2d which
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introduces a strong shock and is a challanging problem for the Riemann solver,
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introduces a strong shock and is a challenging problem for the Riemann solver,
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as well as ``current_sheet_2d``, an MHD test probing numerical reconnection
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properties of the code.
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... | ... | @@ -252,12 +248,12 @@ One-dimensional simulations in spherical symmetry |
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An important set of simulations for stellar astrophysics are one dimensional
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simulations in spherical symmetry, such as given for example in
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``polytrope_1d_spherical``. Generally, AREPO is not optimized for such kind of
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``polytrope_1d_spherical``. Generally, Arepo is not optimized for such kind of
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simulations and can only run these in serial. However, this option has proven
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to be useful for quick test simulations as well as for calculating radial
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profiles which are then used as initial conditions for three dimensional
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simulations. One of the key aspect for these simulation is the quality of the
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boundary conditions. In this spherically symmetric mode, AREPO uses a
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boundary conditions. In this spherically symmetric mode, Arepo uses a
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reflective inner boundary condition and an inflow/outflow boundary condition
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at the outer end.
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