Particles¶

Particle containers¶

Particle structures and functions are defined in Source/Particles/. WarpX uses the Particle class from AMReX for single particles. An ensemble of particles (e.g., a plasma species, or laser particles) is stored as a WarpXParticleContainer (see description below) in a per-box (and even per-tile on CPU) basis.

class WarpXParticleContainer : public amrex::ParticleContainer<0, 0, PIdx::nattribs>

WarpXParticleContainer is the base polymorphic class from which all concrete particle container classes (that store a collection of particles) derive. Derived classes can be used for plasma particles, photon particles, or non-physical particles (e.g., for the laser antenna). It derives from amrex::ParticleContainer<0,0,PIdx::nattribs>, where the template arguments stand for the number of int and amrex::Real SoA and AoS data in amrex::Particle.

AoS amrex::Real: x, y, z (default), 0 additional (first template parameter)
AoS int: id, cpu (default), 0 additional (second template parameter)
SoA amrex::Real: PIdx::nattribs (third template parameter), see PIdx for the list.

WarpXParticleContainer contains the main functions for initialization, interaction with the grid (field gather and current deposition) and particle push.

Note: many functions are pure virtual (meaning they MUST be defined in derived classes, e.g., Evolve) or actual functions (e.g. CurrentDeposition).

Subclassed by LaserParticleContainer, PhysicalParticleContainer

Physical species are stored in PhysicalParticleContainer, that derives from WarpXParticleContainer. In particular, the main function to advance all particles in a physical species is PhysicalParticleContainer::Evolve (see below).

virtual void PhysicalParticleContainer::Evolve(int lev, const amrex::MultiFab &Ex, const amrex::MultiFab &Ey, const amrex::MultiFab &Ez, const amrex::MultiFab &Bx, const amrex::MultiFab &By, const amrex::MultiFab &Bz, amrex::MultiFab &jx, amrex::MultiFab &jy, amrex::MultiFab &jz, amrex::MultiFab *cjx, amrex::MultiFab *cjy, amrex::MultiFab *cjz, amrex::MultiFab *rho, amrex::MultiFab *crho, const amrex::MultiFab *cEx, const amrex::MultiFab *cEy, const amrex::MultiFab *cEz, const amrex::MultiFab *cBx, const amrex::MultiFab *cBy, const amrex::MultiFab *cBz, amrex::Real t, amrex::Real dt, DtType a_dt_type = DtType::Full, bool skip_deposition = false) override¶

Finally, all particle species (physical plasma species PhysicalParticleContainer, photon species PhotonParticleContainer or non-physical species LaserParticleContainer) are stored in MultiParticleContainer. The class WarpX holds one instance of MultiParticleContainer as a member variable, called WarpX::mypc (where mypc stands for “my particle containers”):

class MultiParticleContainer¶

The class MultiParticleContainer holds multiple instances of the polymorphic class WarpXParticleContainer, stored in its member variable “allcontainers”. The class WarpX typically has a single (pointer to an) instance of MultiParticleContainer.

MultiParticleContainer typically has two types of functions:

Functions that loop over all instances of WarpXParticleContainer in allcontainers and calls the corresponding function (for instance, MultiParticleContainer::Evolve loops over all particles containers and calls the corresponding WarpXParticleContainer::Evolve function).
Functions that specifically handle multiple species (for instance ReadParameters or mapSpeciesProduct).

Loop over particles¶

A typical loop over particles reads:

// pc is a std::unique_ptr<WarpXParticleContainer>
// Loop over MR levels
for (int lev = 0; lev <= finest_level; ++lev) {
    // Loop over particles, box by box
    for (WarpXParIter pti(*this, lev); pti.isValid(); ++pti) {
        // Do something on particles
        // [MY INNER LOOP]
    }
}

The innermost step [MY INNER LOOP] typically calls amrex::ParallelFor to perform operations on all particles in a portable way. For this reasons, the particle data needs to be converted in plain-old-data structures. The innermost loop in the code snippet above could look like:

// Get Array-Of-Struct particle data, also called data
// (x, y, z, id, cpu)
const auto& particles = pti.GetArrayOfStructs();
// Get Struct-Of-Array particle data, also called attribs
// (ux, uy, uz, w, Exp, Ey, Ez, Bx, By, Bz)
auto& attribs = pti.GetAttribs();
auto& Exp = attribs[PIdx::Ex];
// [...]
// Number of particles in this box
const long np = pti.numParticles();

Link fields and particles?¶

In WarpX, the loop over boxes through a MultiFab iterator MFIter and the loop over boxes through a ParticleContainer iterator WarpXParIter are consistent.

On a loop over boxes in a MultiFab (MFIter), it can be useful to access particle data on a GPU-friendly way. This can be done by:

// Index of grid (= box)
const int grid_id = mfi.index();
// Index of tile within the grid
const int tile_id = mfi.LocalTileIndex();
// Get GPU-friendly arrays of particle data
auto& ptile = GetParticles(lev)[std::make_pair(grid_id,tile_id)];
ParticleType* pp = particle_tile.GetArrayOfStructs()().data();
// Only need attribs (i.e., SoA data)
auto& soa = ptile.GetStructOfArrays();
// As an example, let's get the ux momentum
const ParticleReal * const AMREX_RESTRICT ux = soa.GetRealData(PIdx::ux).data();

On a loop over particles it can be useful to access the fields on the box we are looping over (typically when we use both field and particle data on the same box, for field gather or current deposition for instance). This is done for instance by adding this snippet in [MY INNER LOOP]:

// E is a reference to, say, WarpX::Efield_aux
// Get the Ex field on the grid
const FArrayBox& exfab = (*E[lev][0])[pti];
// Let's be generous and also get the underlying box (i.e., index info)
const Box& box = pti.validbox();

Main functions¶

Warning

doxygenfunction: Cannot find function “PhysicalParticleContainer::FieldGather” in doxygen xml output for project “WarpX” from directory: ../doxyxml/

virtual void PhysicalParticleContainer::PushPX(WarpXParIter &pti, amrex::FArrayBox const *exfab, amrex::FArrayBox const *eyfab, amrex::FArrayBox const *ezfab, amrex::FArrayBox const *bxfab, amrex::FArrayBox const *byfab, amrex::FArrayBox const *bzfab, const amrex::IntVect ngE, const int, const long offset, const long np_to_push, int lev, int gather_lev, amrex::Real dt, ScaleFields scaleFields, DtType a_dt_type = DtType::Full)¶

Warning

doxygenfunction: Unable to resolve function “WarpXParticleContainer::DepositCurrent” with arguments None in doxygen xml output for project “WarpX” from directory: ../doxyxml/. Potential matches:

- void DepositCurrent(WarpXParIter &pti, RealVector const &wp, RealVector const &uxp, RealVector const &uyp, RealVector const &uzp, int const *const ion_lev, amrex::MultiFab *const jx, amrex::MultiFab *const jy, amrex::MultiFab *const jz, long const offset, long const np_to_depose, int const thread_num, int const lev, int const depos_lev, amrex::Real const dt, amrex::Real const relative_time)
- void DepositCurrent(amrex::Vector<std::array<std::unique_ptr<amrex::MultiFab>, 3>> &J, const amrex::Real dt, const amrex::Real relative_t)

Note

The current deposition is used both by PhysicalParticleContainer and LaserParticleContainer, so it is in the parent class WarpXParticleContainer.

Buffers¶

To reduce numerical artifacts at the boundary of a mesh-refinement patch, WarpX has an option to use buffers: When particles evolve on the fine level, they gather from the coarse level (e.g., Efield_cax, a copy of the aux data from the level below) if they are located on the fine level but fewer than WarpX::n_field_gather_buffer cells away from the coarse-patch boundary. Similarly, when particles evolve on the fine level, they deposit on the coarse level (e.g., Efield_cp) if they are located on the fine level but fewer than WarpX::n_current_deposition_buffer cells away from the coarse-patch boundary.

WarpX::gather_buffer_masks and WarpX::current_buffer_masks contain masks indicating if a cell is in the interior of the fine-resolution patch or in the buffers. Then, particles depending on this mask in

void PhysicalParticleContainer::PartitionParticlesInBuffers(long &nfine_current, long &nfine_gather, long const np, WarpXParIter &pti, int const lev, amrex::iMultiFab const *current_masks, amrex::iMultiFab const *gather_masks, RealVector &uxp, RealVector &uyp, RealVector &uzp, RealVector &wp)¶

Note

Buffers are complex!

Runtime particle attributes¶

WarpX allows extra runtime attributes to be added to particle containers (through AddRealComp("attrname") or AddIntComp("attrname")). The attribute name can then be used to access the values of that attribute. For example, using a particle iterator, pti, to loop over the particles the command pti.GetAttribs(particle_comps["attrname"]).dataPtr(); will return the values of the "attrname" attribute.

Commonly used runtime attributes are described in the table below.

Attribute name	`int`/`real`	Description	Default value
`prev_x/y/z`	`real`	The coordinates of the particles at the previous timestep.

Note

Only use _ to separate components of vectors!