Tangos Tutorial – Ramses+HOP

Initial set up

Make sure you have followed the initial set up instructions.

Next, download the raw simulation data required for this tutorial. Unpack the tar file either in your home folder or the folder that you pointed the TANGOS_SIMULATION_FOLDER environment variable to.

For most Linux or macOS systems, the following typed at your bash command line will download the required data and unpack it in the correct location:

cd $TANGOS_SIMULATION_FOLDER
curl https://zenodo.org/record/5155467/files/tutorial_ramses.tar.gz?download=1 | tar -xz

Import the simulation

At the unix command line type:

tangos add tutorial_ramses --min-particles 100 --no-renumber

The process should take about a minute on a standard modern computer, during which you’ll see a bunch of log messages scroll up the screen.

Let’s pick this command apart

• tangos is the command-line tool to administrate your tangos database
• add is a subcommand to add a new simulation
• tutorial identifies the simulation we’re adding
• --min-particles 100 imports only halos/groups with at least 100 particles.
• --no-renumber specifies that tangos should use the original HOP halo numbering, which starts from zero. Otherwise, tangos renumbers the halos starting from 1. This would have no impact on analyses since it is all handled internally, but it can be confusing if you are used to dealing with the raw catalogues, so we switch it off here.

Note that all tangos command-line tools provide help. For example tangos --help will show you all subcommands, and tangos add --help will tell you more about the possible options for adding a simulation.

At this point, the database knows about the existence of timesteps and their halos and groups in our simulation, but nothing about the properties of those halos or groups. We need to add more information before the database is useful.

If you want to speed up this process, it can be MPI parallelised since version 1.8.

Generate the merger trees

The merger trees are most simply generated using pynbody’s bridge function. To do this, type

tangos link --for tutorial_ramses

The construction of each merger tree should take a couple of minutes, and again you’ll see a log scroll up the screen while it happens.

If you want to speed up this process, it can be MPI parallelised.

Add the first property

Next, we will add some properties to the halos so that we can start to do some science. Because this is a zoom simulation, we only want to do science on the highest resolution regions. The first thing to calculate is therefore which halos fall in that region. From your shell type:

tangos write contamination_fraction --for tutorial_ramses

Here,

• tangos write is the main script for adding properties to a tangos database;
• contamination_fraction is the name of a built-in property which returns the fraction of dark matter particles which come from outside the high resolution region.

If you want to speed up this process, it can be MPI parallelised.

Once the command terminates, you can check that each halo now has a contamination_fraction associated with it, either in the web interface or from python, for example:

import tangos
tangos.get_halo("tutorial/output_00010/halo_1")['contamination_fraction'] # -> returns the appropriate fraction

Add some more interesting properties

Let’s finally do some science. We’ll add dark matter density profiles; from your shell type:

tangos write dm_density_profile --with-prerequisites --include-only="contamination_fraction<0.01"

If you want to speed up this process, it can be MPI parallelised.

Here,

• tangos write is the same script you called above to add properties to the database
• dm_density_profile is an array representing the dark matter density profile; to see all available properties you can call tangos list-possible-properties
• --with-prerequisites automatically includes any underlying properties that are required to perform the calculation. In this case, the dm_density_profile calculation actually needs to know an accurate center for the halo (known as shrink_center), so that calculation will be automatically performed and stored
• --include-only allows an arbitrary filter to be applied, specifying which halos the properties should be calculated for. In the present case, we use that to insist that only “high resolution” halos are included (specifically, those with a fraction of low-res particles smaller than 1%)

Explore what’s possible

Now that you have a minimal functioning tangos database, proceed to the data exploration tutorial.