CosmoSim Blog

On request of one of our users, we now added a new column to each Rockstar catalogue: the forestId.
This id is used to indicate which merger trees (identified by their treeRootId) have “crossed” during their history, interchanging halos in between, i.e. halos can have a host or a descendant in another tree. Thus, in order to get the full merger information (the “forest”) with all possible halos involved, one needs to query for the common forestId.

Here’s an example:

SELECT treeRootId, forestId, rockstarId, scale, descId, pId, upId, Mvir, x, y, z 
FROM MDPL2.Rockstar 
WHERE forestId = 12568649357 
ORDER BY treeRootId, scale


This query retrieves all halos with the same forestId and sorts them by their treeRootId (the merger tree) and by time (scale). We have added database indizeson the forestId and treeRootId in order to make queries for these columns much faster, so the query above only takes a few seconds.

Plotting the resulting rows with TOPCAT (using SAMP, see Topcat and SAMP for general instructions how to do this) in a 3D coordinate system, we can get the image on the left.


This shows the 3D positions (x,y,z) of all the halos in the forest. There are two distinct merger trees, indicated by different markers and enclosed by the blue and green circles. The circle’s size represents roughly the mass of the halos at each timestep. Both merger trees (actually, it’s just one line here because we picked on of the smallest for this example) cross at some timestep, which is the reason why they were assigned the same forestId.

The image on the right side is another example, from MDR1.Rockstar: each dot represents a dark matter halo from the same forest, the different merger trees (halos with the same treeRootId) are marked with different colors.
The corresponding SQL query to get these halos is:

SELECT treeRootId, forestId, scale, Mvir, x, y, z 
FROM MDR1.Rockstar 
WHERE forestId = 789412595
ORDER BY treeRootId, scale

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We had some active developments for our UWS-client for Scripted database access.
One of the changes to make it more standard compliant was to add ‘/phase’ to the URI when starting a job with ‘phase=run’.
We adjusted our Daiquiri instance to answer these requests correctly now, but requests sent to the URI without ‘/phase’ will also still work to ensure backwards compatibility.

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The Rockstar catalogue for SMDPL is public now.
We’ve also added indexes for upId, the link to the top-most host halo, which accelerates subhalo-queries a lot. I.e. it’s now faster to retrieve all subhalos for a given host halo with a query like this:

SELECT rockstarId, x, y, z, Rvir, Mvir FROM SMDPL.Rockstar 
WHERE snapnum=116 AND upId=12067965493

This query retrieves all halos with the same upId and thus all halos with the same host halo. The chosen host halo in this case is the most massive halo at redshift 0, snapnum=116 for this simulation.
The index for upId was also added to MDPL2.Rockstar. For MDR1 this was not necessary, since that dataset is much smaller and queries in general faster.

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We have now Rockstar-catalogues available for two simulations: MDR1 and MDPL2. These catalogues contain dark matter halos along with their consistent merging tree information.
This can be used to track e.g. the mass accretion history of dark matter halos, the number of mergers in each time step and much more. They can also be used to add galaxies via semi-analytics later on. We may publish one or two of these semi-analytical-model-catalogues in the future.

For more background information on Rockstar, please visit our Rockstar documentation page and Rockstar table description and look into the given references.

Here’s an example query to get all progenitors of a selected halo which are more massive than 10^11 Msun/h.

SELECT p.x, p.y, p.z, p.Mvir, p.scale, p.rockstar_snapnum FROM MDPL2.Rockstar AS p, 
(SELECT depthFirstId, lastProg_depthFirstId FROM MDPL2.Rockstar WHERE rockstarId=12657871796) AS r 
WHERE p.depthFirstId BETWEEN r.depthFirstId AND r.lastProg_depthFirstId 
AND Mvir > 1.e11
ORDER BY p.snapnum

Plotted with Topcat, the spatial distribution of these progenitors looks like this:

Position of progenitors for a halo in 3D. The colors represent the scale factor, from early times (dark blue) until today (redshift 0, red).

Position of progenitors for a halo in 3D. The colors represent the scale factor, from early times (dark blue) until today (redshift 0, red).

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Thanks to one of our CosmoSim users we realized that there is a bug in UWS: whenever one sent queries on the user-table via UWS (scripted access), then the result returned was 0 rows. Always.
Luckily Jochen discovered the problem and fixed this bug! Queries including your own user tables should work now as expected.

If you happen to realize something strange going on that is not covered in this blog (see Known errors) or in the documentation, please send us a message via the Contact form. We need your feedback to improve this service!

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Getting the mass function of dark matter halos (and galaxies) is now easier than ever: we’ve added a “Mass function form” especially made to help you with this. You can find it at the Query interface on the left side, just below “SQL query”:

The new "Mass function query" form for calculating the mass functions for halos from different simulations and catalogues for different timesteps.

The new “Mass function query” form for calculating the mass functions for halos from different simulations and catalogues for different timesteps.

After selecting your desired simulation and (halo) catalogue, submit your query with the Submit button.
If your query times out (very likely for non-standard mass columns), then please select Long queue before submitting.

The form takes care of formulating the correct SQL query based on your selection. You can review the submitted query anytime in your job details.

You can check the available redshifts and snapshot numbers for each simulation and catalogue by querying the corresponding AvailHalos-table. The form already takes this into account by choosing the closest matching redshift from all available redshifts for the selected catalogue.

When your job is finished, you can see in the Results Table tab a table with the logarithmic mass at the center of your mass bin and the (logarithmic) number of halos for each bin. Want to have a quick plot of your results as well? Just use the Plot tab at the query interface or send your table to Topcat via SAMP. Sending multiple tables to Topcat will allow you to directly compare mass functions of different simulations and for different redshifts.

Mass functions for different simulations at redshift z = 0, extracted using the Mass function query form and plotted with Topcat

Mass functions for different simulations at redshift z = 0, extracted using the Mass function query form and plotted with Topcat

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Today I’ve renamed the density tables for MDR1 in the following way:
Dens512 => Dens512_z0
Dens1024 => Dens1024_z0.
This was done in order to have names matching the density tables for the Bolshoi simulation.
Now all density tables that end with _z0 were produced using the same algorithm by Jaime Forero Romero.
The density tables without this ending contain density information for more than one redshift and were produced by Anatoly Klypin, using a cloud-in-cell-smoothing on a 1024^3 grid, i.e. smoothing scale is one cell, ~ 244 kpc/h for Bolshoi. In order to produce densities on coarser grids for saving disk space and having shorter query time, the average density of adjacent grid cells was used.

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We updated now the web interface of CosmoSim to the latest Daiquiri version. There are only small differences, mainly restructuring the layout of the query interface, and fixing some minor bugs. The Query Form documentation is also already updated, so this should give you a good overview where to find what.

The main changes include:

  • New SQL query: At the Query interface, the ‘SQL query’ tab is now replaced by a link above the job list. If you browse your results and want to go back to enter a new query, click on this link or on the ‘Query’ link at the top menu of the page.
  • Job overview: The parameters given here are more structured now. The main parameters come first, followed by the Remove/Rename job links. The query plan comes last, since usually users won’t look into this anyway.
  • SAMP: The link for SAMP-connection has moved to a new SAMP-tab. Since we also made the switch from http to https, browser’s may have difficulties when executing the SAMP-script. Just follow the instructions given at the SAMP-tab of the query interface to confirm the security exception.
  • Examples, Database and Function browser: Links to open the database browser and list of examples are now placed on top, above the query form. We also added a function browser to see the available keywords and functions that you can use in your SQL query.

Query interface with the (9) Job Overview for a finished job. It shows the (10) executed query, (11) job parameters and timing, (12) buttons for renaming or deleting a job.
At the top one can also switch to the (8) Results Table tab, (13) SAMP tab for exchange of data, use the simple Plot feature or Download the result table. Also see the updated Query Form documentation

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Today we release two long awaited simulations: MultiDark Planck 2 (MDPL2) and the Small MultiDark Planck simulation (SMDPL).

MDPL2 is similar to MDPL in box size and particle resolution, but with a different random seed. We will add more data products for this simulation in the future. There are also more snapshots available, which makes this data set better suited for tracking the merging history of halos.

SMDPL has a smaller box size (400 Mpc/h side length), and comes with the same particle resolution (3840^3), which gives a very good mass resolution. Though its box size is larger than for the Bolshoi simulation, its mass resolution is still better by a factor of 1.4.

SMDPL image

Slice through the Small MultiDark Planck simulation (SMDPL) at redshift z = 0.51

Distribution of FOF halos from the MDPL2 simulation at z=0.

Distribution of FOF halos from a slice of the MDPL2 simulation at z=0. The size and color of regions indicates halo mass and projected density.

For both simulations we publish the usual FOF-catalogues. We are also working on making Rockstar-catalogues available. If you want to have a sneak preview into the Rockstar tables, please send a mail via the contact form and we will add you to our test users. This gives you access to the Rockstar data that is already there but not yet published for everyone.

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Last week we had out first teacher workshop with CosmoSim!
In the course of a teacher-training at Potsdam, Germany, called “100 Jahre Allgemeine Relativitätstheorie – Status und Ausblick” funded by the Heraeus foundation, we offered a hands-on session with CosmoSim. We guided the participants through querying density fields from the Bolshoi simulation for several time steps to show the process of evolving structure formation. It is also possible to overplot the positions of dark matter halos or extract the particle distribution of individual halos.
The tutorial is available here Tutorial, further material (including all the data files) is available here: Materials.
Since all the data is publicly available, even students and pupils can already get their hands on the latest data in cosmology!

For this workshop, we created special workshop-accounts, so that each participant can work on his/her own data set without having to register beforehand. If you want to have a set of > 10 accounts for your own workshop, please contact us and we’ll be happy to help.

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