Initial Conditions

To run anything more than examples from our suite, you will need to be able to produce your own initial conditions for SWIFT. We use the same initial conditions format as the popular GADGET-2 code, which uses HDF5 for its type 3 format. Note that we do not support the GADGET-2 types 1 and 2 formats.

One crucial difference is that whilst GADGET-2 can have initial conditions split over many files SWIFT only supports initial conditions in one single file. ICs split over multiple files cannot be read by SWIFT. See the “ICs split over multiple files” section below for possible solutions. In GADGET-2 having multiple files allows multiple ones to be read in parallel and is the only way the code can handle more than 2^31 particles. This limitation is not in place in SWIFT. A single file can contain any number of particles (well… up to 2^64…) and the file is read in parallel by HDF5 when running on more than one compute node.

The original GADGET-2 file format only contains 2 types of particles: gas particles and 5 sorts of collision-less particles that allow users to run with 5 separate particle masses and softenings. In SWIFT, we expand on this by using two of these types for stars and black holes.

As the original documentation for the GADGET-2 initial conditions format is quite sparse, we lay out here all of the necessary components. If you are generating your initial conditions from python, we recommend you use the h5py package. We provide a writing wrapper for this for our initial conditions in examples/KeplerianRing/write_gadget.py.

You can find out more about the HDF5 format on their webpages.

Structure of the File

There are several groups that contain ‘auxiliary’ information, such as Header. Particle data is placed in separate groups depending of the type of the particles. Some types are currently ignored by SWIFT but are kept in the file format for compatibility reasons.

HDF5 Group Name Physical Particle Type In code enum part_type
/PartType0/ Gas swift_type_gas
/PartType1/ Dark Matter swift_type_dark_matter
/PartType2/ Background Dark Matter swift_type_dark_matter_background
/PartType3/ Ignored  
/PartType4/ Stars swift_type_star
/PartType5/ Black Holes swift_type_black_hole

The last column in the table gives the enum value from part_type.h corresponding to a given entry in the files.

Note that the only particles that have hydrodynamical forces calculated between them are those in PartType0. The background dark matter particles are used for zoom-in simulations and can have different masses (and as a consequence softening length) within the /PartType2 arrays.

Necessary Components

There are several necessary components (in particular header information) in a SWIFT initial conditions file. Again, we recommend that you use the write_gadget script.

Particle Data

Now for the interesting part! You can include particle data groups for each individual particle type (e.g. /PartType0/) that have the following datasets:

  • Coordinates, an array of shape (N, 3) where N is the number of particles of that type, that are the cartesian co-ordinates of the particles. Co-ordinates must be within the box so, in the case of a cube within [0, L)^3 where L is the side-length of the simulation volume. In the case of cosmological simulations, these are the co-moving positions.
  • Velocities, an array of shape (N, 3) that is the cartesian velocities of the particles. When running cosmological simulations, these are the peculiar velocities. Note that this is different from GADGET which uses peculiar velocities divided by sqrt(a) (see below for a fix).
  • ParticleIDs, an array of length N that are unique identifying numbers for each particle. Note that these have to be unique to a particle, and cannot be the same even between particle types. The IDs must be >= 0. Negative IDs will be rejected by the code. Note, however, that if the parameters to remap the IDs upon startup is switched on (see Initial Conditions), the IDs can be omitted entirely from the ICs.
  • Masses, an array of length N that gives the masses of the particles.

For PartType0 (i.e. particles that interact through hydro-dynamics), you will need the following auxiliary items:

  • SmoothingLength, the smoothing lengths of the particles. These will be tidied up a bit, but it is best if you provide accurate numbers. In cosmological runs, these are the co-moving smoothing lengths.
  • InternalEnergy, an array of length N that gives the internal energies per unit mass of the particles. If the hydro-scheme used in the code is based on another thermodynamical quantity (entropy or total energy, etc.), the conversion will happen inside the code. In cosmological runs, this is the physical internal energy per unit mass. This has the dimension of velocity squared.

Note that for cosmological runs, all quantities have to be expressed in “h-free” dimensions. This means Mpc and not Mpc/h for instance. If the ICs have been generated for GADGET (where h-full values are expected), the parameter InitialConditions:cleanup_h_factors can be set to 1 in the Parameter Files to make SWIFT convert the quantities read in to h-free quantities. Switching this parameter on will also affect the box size read from the /Header/ group (see above).

Similarly, GADGET cosmological ICs have traditionally used velocities expressed as peculiar velocities divided by sqrt(a). This can be undone by switching on the parameter InitialConditions:cleanup_velocity_factors in the Parameter Files.

Optional Components

In the /Units/ HDF5 group, you cans specify what units your initial conditions are in. If this group is not present, the code assumes that you are using the same units for your initial conditions as in your Parameter Files (i.e. as the internal units system used by the code), but it is best to include them to be on the safe side. You will need:

  • Unit length in cgs (U_L)
  • Unit mass in cgs (U_M)
  • Unit time in cgs (U_t)
  • Unit current in cgs (U_I)
  • Unit temperature in cgs (U_T)

These are all floating point numbers. Note that we specify the time units and not the velocity units.

If the units specified in the initial conditions are different from the internal units (specified in the parameter file), SWIFT will perform a conversion of all the quantities when reading in the ICs. This includes a conversion of the box size read from the /Header/ group.

Summary

You should have an HDF5 file with the following structure:

Header/
  BoxSize=[x, y, z]
  Flag_Entropy_ICs=0
  NumPart_Total=[0, 1, 0, 0, 4, 5]
  NumPart_Total_HighWord=[0, 0, 0, 0, 0, 0]
Units/
  Unit current in cgs (U_I)=1.0
  Unit length in cgs (U_L)=1.0
  Unit mass in cgs (U_M)=1.0
  Unit temperature in cgs (U_T)=1.0
  Unit time in cgs (U_t)=1.0
PartType0/
  Coordinates=[[x, y, z]]
  Velocities=[[vx, vy, vz]]
  ParticleIDs=[...]
  Masses=[...]
  InternalEnergy=[...]
  SmoothingLength=[...]
PartType1/
  Coordinates=[[x, y, z]]
  Velocities=[[vx, vy, vz]]
  ParticleIDs=[...]
  Masses=[...]

ICs split over multiple files

A basic script tools/combine_ics.py is provided to merge basic GADGET-2 initial conditions split into multiple files into one single valid file. This script can handle simple HDF5 files (GADGET-2 type 3 ICs) that follow the format described above but split over multiple files.

The script can also convert ICs using a MassTable and create the corresponding particle fields. Note that additional fields present in ICs beyond the simple GADGET-2 specification will not be merged.

One additional option is to compress the fields in the files using HDF5’s gzip compression. This is very effective for the fields such as masses or particle IDs which are very similar. A checksum filter is also applied in all cases to help with data curation.

We caution that this script is very basic and should only be used with great caution.