Tracer Particles

Phoebus includes Lagrangian tracer particles. These are primarily for the purpose of post-processing simulation data for, e.g., nucleosynthesis. They are operator spit from the hydrodynamics and advected with a standard second order Runge-Kutta integrator. As Phoebus is a general relativistic code, we evolve tracer positions using a relativistic advection equation:

\[\frac{dx^i}{dt} = \frac{u^i}{u^0} = \alpha v^i - \beta^i\]

Tracers may be enabled by in the Phoebus input deck as follow:

<physics>
tracers = true

<tracers>
num_tracers = 1024

Similarly, tracers may be output by modifying an existing Parthenon output block, or creating a new one:

<parthenon/output1>
// ...
swarms = tracers
tracers_variables = rho, temperature, ye

file_type = hdf5
dt = // output cadence

Note that the position variables x, y, z are output for all swarms by default. See the Parthenon docs for more information.

Tracers must, however, be configured in the problem generator. In the generator, the tracers should be distributed through the domain, assigned positions and unique ids. An example from the advection pgen is shown below.

pmb->par_for(
    "ProblemGenerator::Advection::DistributeTracers", 0, max_active_index,
    KOKKOS_LAMBDA(const int n) {
      if (swarm_d.IsActive(n)) {
        auto rng_gen = rng_pool.get_state();

        // sample in ball
        Real r2 = 1.0 + rin * rin; // init > rin^2
        while (r2 > rin * rin) {
          x(n) = x_min + rng_gen.drand() * (x_max - x_min);
          y(n) = y_min + rng_gen.drand() * (y_max - y_min);
          z(n) = z_min + rng_gen.drand() * (z_max - z_min);
          r2 = x(n) * x(n) + y(n) * y(n) + z(n) * z(n);
        }
        id(n) = num_tracers_total * gid + n;

        bool on_current_mesh_block = true;
        swarm_d.GetNeighborBlockIndex(n, x(n), y(n), z(n), on_current_mesh_block);
        rng_pool.free_state(rng_gen);
      }
    });

In addition to position, tracers track a number of potentially useful quantities. These quantities include (bold quantities are 3-vectors with components _x, _y, _z)

Quantity	SwarmVar Name	Description
Density	rho	Primitive density
Temperature	temperature	Temperature
Ye	ye	Electron fraction (0 if ye is disabled)
Internal energy	energy	Primitive internal energy
Entropy	entropy	Entropy
Velocity	vel_x, …	Three velocity
Lorentz factor	lorentz	Relativistic Lorentz factor
Lapse	lapse	Relativistic lapse
Metric determinant	detgamma	Spatial metric determinant
Shift	shift_x, …	Relativistic shift
Mass	mass	Tracer mass
Total energy	bernoulli	Total energy Bernoulli quantity
Magnetic field	B_x, …	Primitive 3-magnetic field components (if mhd enabled)

To minimize unnecessary work, these quantities are only populated before output using phoebus::UserWorkBeforeOutput.

void UserWorkBeforeOutput(MeshBlock *pmb, ParameterInput *pin)

Describes work to be done prior to HDF5 output, such as populating tracer variables. This is connected to the appropriate Parthenon function.