Tracing Particles between Snapshots

The bridge module has tools for connecting different outputs which allows you to trace particles from one snapshot of the simulation to another. Normally, matching up particle IDs between different snapshots can be a pain, but bridge does all of this for you transparently. All that is needed is to initialize a Bridge object that links two snapshots together. Once connected, a bridge object called on a specific subset of particles in one snapshot will trace these particles back (or forward) to the second snapshot.

Basic usage

Load the data:

>>> f1 = pynbody.load(high_redshift_file)
>>> f2 = pynbody.load(low_redshift_file)

Load the halo catalogue:

>>> h_high_z = f1.halos()

Create the bridge object:

>>> b = pynbody.bridge.OrderBridge(f1, f2) # Or a different class, see "Which class to use" below

b is now an OrderBridge object that links the two outputs f1 and f2 together. Passing a SubSnap from one of the two linked snapshots to b will return a SubSnap with the same particles in the other snapshot. So, if we want to see where all the particles that were in halo 1 in the high-redshift snapshot (f1) end up at low redshift (f2), we can simply do:

>>> h1_at_low_z = b(h[1])

h1_at_low_z now contains the particles which were in h[1] in the high redshift output

Identifying halos between different outputs

You may wish to work out how a halo catalogue maps onto a halo catalogue for a different output. For this purpose a simple function, match_catalog, is provided. Extending the example above, this would be called as follows:

>>> cat = b.match_catalog()

cat is now a numpy index array such that f1.halos()[i] is (probably!) the major progenitor for f2.halos()[cat[i]].

Which class to use?

For files where the particle ordering is static, so that the particle with index i in the first snapshot also has index i in the second snapshot, use the Bridge class.

For files which can spawn new particles, and therefore have a monotonically increasing particle ordering array (e.g. “iord” in gasoline), use the OrderBridge class.

Snapshot formats where the particle ordering can change are not currently supported.