Initial conditions¶

There are a couple main ways in which initial conditions can be set in Nyx: using an ASCII particle file, using binary particle file(s), using a uniform particle setup, using a random particle setup, using a binary mesh file setup, or using an analytic setup. As said in the Units section of the documentation, the units are: Mpc, M\(_\odot\), and km/s, and particle velocities should be peculiar proper velocities.

Start from an ASCII file¶

To enable this option, set:

nyx.particle_init_type = AsciiFile
nyx.ascii_particle_file = *particle_file*

Here particle_file is the user-specified name of the file. The first line in this file is (long) assumed to contain the number of particles. Each line after that contains

x y z mass vx vy vz

Start from a binary file¶

To enable this option, set:

nyx.particle_init_type = BinaryFile
nyx.binary_particle_file = *particle_file*

With binary file, the header should have 3 numbers: (long) NP, which is the total number of particles in the file followed by the (int) DM=3 (number of dimensions), and (int) NX=4 (number of “extra” fields). Following this small header, 7 float numbers should be listed for each particle as before: x y z mass vx vy vz.

The main difference between the ASCII and binary format thus amounts to a different header. Here is an example C++ code which writes a Nyx-readable binary file:

fwrite(&npart, sizeof(long), 1, outFile);
fwrite(&DM, sizeof(int), 1, outFile);
fwrite(&NX, sizeof(int), 1, outFile);
for(i=0; i<Npart; i++) {
   fwrite(&x[i], sizeof(float), 1, outFile);
   fwrite(&y[i], sizeof(float), 1, outFile);
   fwrite(&z[i], sizeof(float), 1, outFile);
   fwrite(&mass[i], sizeof(float), 1, outFile);
   fwrite(&vx[i], sizeof(float), 1, outFile);
   fwrite(&vy[i], sizeof(float), 1, outFile);
   fwrite(&vz[i], sizeof(float), 1, outFile);
}

Start from a binary “meta” file¶

This option allows you to read particles from a series of files rather than just a single file. This is very convenient for large simulations. To enable this option, set:

nyx.particle_init_type = BinaryMetaFile
nyx.binary_particle_file =*particle file*

In this case the particle_file you specify is an ASCII file specifying a list of file names with full paths. Each of the files in this list is assumed to be binary and is read sequentially (individual files are read in parallel) in the order listed.

Since individual files are read sequentially, more particles should be read before redistributing across MPI ranks. This is set by optimizing the maximum number of readers and increasing the number of particles per read:

amr.nreaders
amr.nparts_per_read

Start from a plotfile or checkpoint¶

To enable this option, set:

nyx.particle_init_type = Restart
nyx.restart_particle_file = *plot_file*

In this case the plot_file should contain particles in directory DM. Testing of this functionality is mainly for the current default Version_Two_Dot_Zero_single.

Reading SPH particles¶

The above initialization from a single particle specie assumes that baryons trace dark matter. Baryon density and velocity is set by CIC-mapping particles onto the Eulerian grid. Alternatively, one can initialize the baryonic gas from the SPH particles. To enable this option, you must set:

nyx.do_santa_barbara = 1
nyx.init_with_sph_particles =1

The SPH-type particles can then be read in by setting where sph_particle_file is the user-specified name of the file containing the SPH particles. The type of sph_particle_file must be the same (Ascii, Binary or BinaryMeta) as the dark matter particle file as specified by The SPH particles will be discarded by the code once the grid data has been initialized.

Initial conditions for testing purposes¶

The following are used for code testing purposes and will not result in a meaningful cosmological simulation.

Random placement¶

To enable this option, set:

nyx.particle_init_type = Random

There are then a number of parameters to set, for example:

nyx.particle_initrandom_count = 100000
nyx.particle_initrandom_mass_total = 100000
nyx.particle_initrandom_iseed = 15
nyx.fix_random_seed = 0

Random placement (1 particle per grid cell)¶

To enable this option, set:

nyx.particle_init_type = RandomPerCell

Then only set the mass per particle:

nyx.particle_initrandom_mass = 1

Note to increase the number of cells and keep the problem domain size and total mass fixed, the mass per particle must decrease proportionally. An alternative is to set the total mass of all particles in the simulation. This will cause Nyx to scale the mass per particle to fit the number of cells. The following will all have the same total mass:

nyx.particle_initrandom_mass = 1
amr.n_cell = 64 64 64

nyx.particle_initrandom_mass = 1
nyx.particle_initrandom_mass_total = 262144
amr.n_cell = 64 64 64

nyx.particle_initrandom_mass = -1
nyx.particle_initrandom_mass_total = 262144
amr.n_cell = 64 64 64

nyx.particle_initrandom_mass = 0.125
amr.n_cell = 128 128 128

nyx.particle_initrandom_mass = 0.125
nyx.particle_initrandom_mass_total = 262144
amr.n_cell = 128 128 128

nyx.particle_initrandom_mass = -1
nyx.particle_initrandom_mass_total = 262144
amr.n_cell = 128 128 128

Uniform placement¶

To enable this option, set:

nyx.particle_init_type = OnePerCell

There are then a number of parameters to set, for example:

nyx.particle_inituniform_mass = 1
nyx.particle_inituniform_vx = -1
nyx.particle_inituniform_vy = 1
nyx.particle_inituniform_vz = 1

Initial Multifab-based setup¶

To enable this option, set:

nyx.particle_init_type = Cosmological
nyx.do_readinics = 1

Then set the directory name of the MultiFab to restart the state variables from:

nyx.readin_ics_fname = "mf"

Initial Analytic Problem Setup¶

To enable this option, set:

nyx.do_santa_barbara = 0
nyx.init_sb_vels = 0

For different executable directories, the Prob.cpp setup can be further customised with prob. input flags. For the HydroTests directory, prob.prob_type=0 corresponds to Sod, StrongShockTube and DoubleRarefaction type tests, and prob.prob_type!=0 corresponds to the Sedov type tests.