path: root/Docs/source/running_cpp/parameters.rst

.. _running-cpp-parameters:

Input parameters
================

.. warning::

   This section is currently in development.


Overall simulation parameters
-----------------------------

* ``authors`` (`string`: e.g. ``"Jane Doe <jane@example.com>, Jimmy Joe <jimmy@example.com>"``)
    Authors of an input file / simulation setup.
    When provided, this information is added as metadata to (openPMD) output files.

* ``max_step`` (`integer`)
    The number of PIC cycles to perform.

* ``warpx.gamma_boost`` (`float`)
    The Lorentz factor of the boosted frame in which the simulation is run.
    (The corresponding Lorentz transformation is assumed to be along ``warpx.boost_direction``.)

    When using this parameter, some of the input parameters are automatically
    converted to the boosted frame. (See the corresponding documentation of each
    input parameters.)

    .. note::

        For now, only the laser parameters will be converted.

* ``warpx.boost_direction`` (string: ``x``, ``y`` or ``z``)
    The direction of the Lorentz-transform for boosted-frame simulations
    (The direction ``y`` cannot be used in 2D simulations.)

* ``warpx.zmax_plasma_to_compute_max_step`` (`float`) optional
    Can be useful when running in a boosted frame. If specified, automatically
    calculates the number of iterations required in the boosted frame for the
    lower `z` end of the simulation domain to reach
    ``warpx.zmax_plasma_to_compute_max_step`` (typically the plasma end,
    given in the lab frame). The value of ``max_step`` is overwritten, and
    printed to standard output. Currently only works if the Lorentz boost and
    the moving window are along the z direction.

* ``warpx.verbose`` (`0` or `1`)
    Controls how much information is printed to the terminal, when running WarpX.

* ``warpx.random_seed`` (`string` or `int` > 0) optional
    If provided ``warpx.random_seed = random``, the random seed will be determined
    using `std::random_device` and `std::clock()`,
    thus every simulation run produces different random numbers.
    If provided ``warpx.random_seed = n``, and it is required that `n > 0`,
    the random seed for each MPI rank is `(mpi_rank+1) * n`,
    where `mpi_rank` starts from 0.
    `n = 1` and ``warpx.random_seed = default``
    produce the default random seed.
    Note that when GPU threading is used,
    one should not expect to obtain the same random numbers,
    even if a fixed ``warpx.random_seed`` is provided.

* ``warpx.do_electrostatic`` (`0` or `1`; default is `0`)
    Run WarpX in electrostatic mode. Instead of updating the fields
    at each iteration with the full Maxwell equations, the fields are
    instead recomputed at each iteration from the (relativistic) Poisson
    equation. There is no limitation on the timestep in this case, but
    electromagnetic effects (e.g. propagation of radiation, lasers, etc.)
    are not captured.

Setting up the field mesh
-------------------------

* ``amr.n_cell`` (`2 integers in 2D`, `3 integers in 3D`)
    The number of grid points along each direction (on the **coarsest level**)

* ``amr.max_level`` (`integer`)
    When using mesh refinement, the number of refinement levels that will be used.

    Use 0 in order to disable mesh refinement.

* ``geometry.is_periodic`` (`2 integers in 2D`, `3 integers in 3D`)
    Whether the boundary conditions are periodic, in each direction.

    For each direction, use 1 for periodic conditions, 0 otherwise.

* ``geometry.coord_sys`` (`integer`) optional (default `0`)
    Coordinate system used by the simulation. 0 for Cartesian, 1 for cylindrical.

* ``geometry.prob_lo`` and ``geometry.prob_hi`` (`2 floats in 2D`, `3 integers in 3D`; in meters)
    The extent of the full simulation box. This box is rectangular, and thus its
    extent is given here by the coordinates of the lower corner (``geometry.prob_lo``) and
    upper corner (``geometry.prob_hi``). The first axis of the coordinates is x (or r with cylindrical)
    and the last is z.

* ``warpx.fine_tag_lo`` and ``warpx.fine_tag_hi`` (`2 floats in 2D`, `3 integers in 3D`; in meters) optional
    **When using static mesh refinement with 1 level**, the extent of the refined patch.
    This patch is rectangular, and thus its extent is given here by the coordinates
    of the lower corner (``warpx.fine_tag_lo``) and upper corner (``warpx.fine_tag_hi``).

* ``warpx.n_current_deposition_buffer`` (`integer`)
    When using mesh refinement: the particles that are located inside
    a refinement patch, but within ``n_current_deposition_buffer`` cells of
    the edge of this patch, will deposit their charge and current to the
    lower refinement level, instead of depositing to the refinement patch
    itself. See the section :doc:`../../theory/amr` for more details.
    If this variable is not explicitly set in the input script,
    ``n_current_deposition_buffer`` is automatically set so as to be large
    enough to hold the particle shape, on the fine grid

* ``warpx.n_field_gather_buffer`` (`integer`; 0 by default)
    When using mesh refinement: the particles that are located inside
    a refinement patch, but within ``n_field_gather_buffer`` cells of
    the edge of this patch, will gather the fields from the lower refinement
    level, instead of gathering the fields from the refinement patch itself.
    This avoids some of the spurious effects that can occur inside the
    refinement patch, close to its edge. See the section
    :doc:`../../theory/amr` for more details. If this variable is not
    explicitly set in the input script, ``n_field_gather_buffer`` is
    automatically set so that it is one cell larger than
    ``n_current_deposition_buffer``, on the fine grid.

* ``particles.deposit_on_main_grid`` (`list of strings`)
    When using mesh refinement: the particle species whose name are included
    in the list will deposit their charge/current directly on the main grid
    (i.e. the coarsest level), even if they are inside a refinement patch.

* ``particles.gather_from_main_grid`` (`list of strings`)
    When using mesh refinement: the particle species whose name are included
    in the list will gather their fields from the main grid
    (i.e. the coarsest level), even if they are inside a refinement patch.

* ``warpx.n_rz_azimuthal_modes`` (`integer`; 1 by default)
    When using the RZ version, this is the number of azimuthal modes.

Distribution across MPI ranks and parallelization
-------------------------------------------------


* ``amr.max_grid_size`` (`integer`) optional (default `128`)
    Maximum allowable size of each **subdomain**
    (expressed in number of grid points, in each direction).
    Each subdomain has its own ghost cells, and can be handled by a
    different MPI rank ; several OpenMP threads can work simultaneously on the
    same subdomain.

    If ``max_grid_size`` is such that the total number of subdomains is
    **larger** that the number of MPI ranks used, than some MPI ranks
    will handle several subdomains, thereby providing additional flexibility
    for **load balancing**.

    When using mesh refinement, this number applies to the subdomains
    of the coarsest level, but also to any of the finer level.

* ``warpx.load_balance_int`` (`integer`) optional (default `-1`)
    How often WarpX should try to redistribute the work across MPI ranks,
    in order to have better load balancing (expressed in number of PIC cycles
    inbetween two consecutive attempts at redistributing the work).
    Use 0 to disable load_balancing.

    When performing load balancing, WarpX measures the wall time for
    computational parts of the PIC cycle. It then uses this data to decide
    how to redistribute the subdomains across MPI ranks. (Each subdomain
    is unchanged, but its owner is changed in order to have better performance.)
    This relies on each MPI rank handling several (in fact many) subdomains
    (see ``max_grid_size``).

* ``warpx.load_balance_with_sfc`` (`0` or `1`) optional (default `0`)
    If this is `1`: use a Space-Filling Curve (SFC) algorithm in order to
    perform load-balancing of the simulation.
    If this is `0`: the Knapsack algorithm is used instead.

* ``warpx.load_balance_efficiency_ratio_threshold`` (`float`) optional (default `1.1`)
    Controls whether to adopt a proposed distribution mapping computed during a load balance.
    If the the ratio of the proposed to current distribution mapping *efficiency* (i.e.,
    average cost per MPI process; efficiency is a number in the range [0, 1]) is greater
    than the threshold value, the proposed distribution mapping is adopted.  The suggested
    range of values is ``warpx.load_balance_efficiency_ratio_threshold >= 1``, which ensures
    that the new distribution mapping is adopted only if doing so would improve the load
    balance efficiency. The higher the threshold value, the more conservative is the criterion
    for adoption of a proposed distribution; for example, with
    ``warpx.load_balance_efficiency_ratio_threshold = 1``, the proposed distribution is
    adopted *any* time the proposed distribution improves load balancing; if instead
    ``warpx.load_balance_efficiency_ratio_threshold = 2``, the proposed distribution is
    adopted only if doing so would yield a 100% to the load balance efficiency (with this
    threshold value, if the  current efficiency is ``0.45``, the new distribution would only be
    adopted if the proposed efficiency were greater than ``0.9``).

* ``algo.load_balance_costs_update`` (`Heuristic` or `Timers`) optional (default `Timers`)
    If this is `Heuristic`: load balance costs are updated according to a measure of
    particles and cells assigned to each box of the domain.  The cost :math:`c` is
    computed as

    .. math::

            c = n_{\text{particle}} \cdot w_{\text{particle}} + n_{\text{cell}} \cdot w_{\text{cell}},

    where
    :math:`n_{\text{particle}}` is the number of particles on the box,
    :math:`w_{\text{particle}}` is the particle cost weight factor (controlled by ``algo.costs_heuristic_particles_wt``),
    :math:`n_{\text{cell}}` is the number of cells on the box, and
    :math:`w_{\text{cell}}` is the cell cost weight factor (controlled by ``algo.costs_heuristic_cells_wt``).

    If this is `Timers`: costs are updated according to in-code timers.

* ``algo.costs_heuristic_particles_wt`` (`float`) optional
    Particle weight factor used in `Heuristic` strategy for costs update; if running on GPU,
    the particle weight is set to a value determined from single-GPU tests on Summit,
    depending on the choice of solver (FDTD or PSATD) and order of the particle shape.
    If running on CPU, the default value is `0.9`.

* ``algo.costs_heuristic_cells_wt`` (`float`) optional
    Cell weight factor used in `Heuristic` strategy for costs update; if running on GPU,
    the cell weight is set to a value determined from single-GPU tests on Summit,
    depending on the choice of solver (FDTD or PSATD) and order of the particle shape.
    If running on CPU, the default value is `0.1`.

* ``warpx.do_dynamic_scheduling`` (`0` or `1`) optional (default `1`)
    Whether to activate OpenMP dynamic scheduling.

* ``warpx.safe_guard_cells`` (`0` or `1`) optional (default `0`)
    For developers: run in safe mode, exchanging more guard cells, and more often in the PIC loop (for debugging).

Math parser and user-defined constants
--------------------------------------

WarpX provides a math parser that reads expressions in the input file.
It can be used to define the plasma density profile, the plasma momentum
distribution or the laser field (see below `Particle initialization` and
`Laser initialization`).

The parser reads python-style expressions between double quotes, for instance
``"a0*x**2 * (1-y*1.e2) * (x>0)"`` is a valid expression where ``a0`` is a
user-defined constant and ``x`` and ``y`` are variables. The names are case sensitive. The factor
``(x>0)`` is `1` where `x>0` and `0` where `x<=0`. It allows the user to
define functions by intervals. User-defined constants can be used in parsed
functions only (i.e., ``density_function(x,y,z)`` and ``field_function(X,Y,t)``,
see below). User-defined constants can contain only letter, numbers and character _.
The name of each constant has to begin with a letter. The following names are used
by WarpX, and cannot be used as user-defined constants: `x`, `y`, `z`, `X`, `Y`, `t`.
For example, parameters ``a0`` and ``z_plateau`` can be specified with:

* ``my_constants.a0 = 3.0``
* ``my_constants.z_plateau = 150.e-6``

Particle initialization
-----------------------

* ``particles.nspecies`` (`int`)
    The number of species that will be used in the simulation.

* ``particles.species_names`` (`strings`, separated by spaces)
    The name of each species. This is then used in the rest of the input deck ;
    in this documentation we use `<species_name>` as a placeholder.

* ``particles.use_fdtd_nci_corr`` (`0` or `1`) optional (default `0`)
    Whether to activate the FDTD Numerical Cherenkov Instability corrector.

* ``particles.rigid_injected_species`` (`strings`, separated by spaces)
    List of species injected using the rigid injection method. The rigid injection
    method is useful when injecting a relativistic particle beam, in boosted-frame
    simulation ; see the section :doc:`../../theory/input_output` for more details.
    For species injected using this method, particles are translated along the `+z`
    axis with constant velocity as long as their ``z`` coordinate verifies
    ``z<zinject_plane``. When ``z>zinject_plane``,
    particles are pushed in a standard way, using the specified pusher.
    (see the parameter ``<species_name>.zinject_plane`` below)

* ``<species_name>.species_type`` (`string`) optional (default `unspecified`)
    Type of physical species, ``"electron"``, ``"positron"``, ``"photon"``, ``"hydrogen"``.
    Either this or both ``mass`` and ``charge`` have to be specified.

* ``<species_name>.charge`` (`float`) optional (default `NaN`)
    The charge of one `physical` particle of this species.
    If ``species_type`` is specified, the charge will be set to the physical value and ``charge`` is optional.
    When ``<species>.do_field_ionization = 1``, the physical particle charge is equal to ``ionization_initial_level * charge``, so latter parameter should be equal to q_e (which is defined in WarpX as the elementary charge in coulombs).

* ``<species_name>.mass`` (`float`) optional (default `NaN`)
    The mass of one `physical` particle of this species.
    If ``species_type`` is specified, the mass will be set to the physical value and ``mass`` is optional.

* ``<species_name>.injection_style`` (`string`)
    Determines how the particles will be injected in the simulation.
    The options are:

    * ``NUniformPerCell``: injection with a fixed number of evenly-spaced particles per cell.
      This requires the additional parameter ``<species_name>.num_particles_per_cell_each_dim``.

    * ``NRandomPerCell``: injection with a fixed number of randomly-distributed particles per cell.
      This requires the additional parameter ``<species_name>.num_particles_per_cell``.

    * ``SingleParticle``: Inject a single macroparticle.
      This requires the additional parameters:
      ``<species_name>.single_particle_pos`` (`3 doubles`, particle 3D position [meter])
      ``<species_name>.single_particle_vel`` (`3 doubles`, particle 3D normalized momentum, i.e. :math:`\gamma \beta`)
      ``<species_name>.single_particle_weight`` ( `double`, macroparticle weight, i.e. number of physical particles it represents)

    * ``gaussian_beam``: Inject particle beam with gaussian distribution in
      space in all directions. This requires additional parameters:
      ``<species_name>.q_tot`` (beam charge),
      ``<species_name>.npart`` (number of particles in the beam),
      ``<species_name>.x/y/z_m`` (average position in `x/y/z`),
      ``<species_name>.x/y/z_rms`` (standard deviation in `x/y/z`),
      ``<species_name>.x/y/z_rms`` (standard deviation in `x/y/z`),
      ``<species_name>.x/y/z_cut`` (optional, particles with ``abs(x-x_m) > x_cut*x_rms`` are not injected, same for y and z. ``<species_name>.q_tot`` is the charge of the un-cut beam, so that cutting the distribution is likely to result in a lower total charge),
      and optional argument ``<species_name>.do_symmetrize`` (whether to
      symmetrize the beam in the x and y directions).

    * ``external_file``: inject macroparticles with properties (charge, mass, position, and momentum) according to data in external file.
      It requires the additional arguments ``<species_name>.injection_file`` and ``<species_name>.q_tot``, which are the string corresponding to the openPMD file name and the beam charge.
      When using this style, it is not necessary to add other ``<species_name>.(...)`` paramters, because they will be read directly from the file.

* ``<species_name>.num_particles_per_cell_each_dim`` (`3 integers in 3D and RZ, 2 integers in 2D`)
    With the NUniformPerCell injection style, this specifies the number of particles along each axis
    within a cell. Note that for RZ, the three axis are radius, theta, and z and that the recommended
    number of particles per theta is at least two times the number of azimuthal modes requested.
    (It is recommended to do a convergence scan of the number of particles per theta)

* ``<species_name>.do_continuous_injection`` (`0` or `1`)
    Whether to inject particles during the simulation, and not only at
    initialization. This can be required with a moving window and/or when
    running in a boosted frame.

* ``<species_name>.initialize_self_fields`` (`0` or `1`)
    Whether to calculate the space-charge fields associated with this species
    at the beginning of the simulation.

* ``<species_name>.self_fields_required_precision`` (`float`, default: 1.e-11)
    The relative precision with which the initial space-charge fields should
    be calculated. More specifically, the initial space-charge fields are
    computed with an iterative Multi-Level Multi-Grid (MLMG) solver.
    For highly-relativistic beams, this solver can fail to reach the default
    precision within a reasonable time ; in that case, users can set a
    relaxed precision requirement through ``self_fields_required_precision``.

* ``<species_name>.profile`` (`string`)
    Density profile for this species. The options are:

    * ``constant``: Constant density profile within the box, or between ``<species_name>.xmin``
      and ``<species_name>.xmax`` (and same in all directions). This requires additional
      parameter ``<species_name>.density``. i.e., the plasma density in :math:`m^{-3}`.

    * ``parse_density_function``: the density is given by a function in the input file.
      It requires additional argument ``<species_name>.density_function(x,y,z)``, which is a
      mathematical expression for the density of the species, e.g.
      ``electrons.density_function(x,y,z) = "n0+n0*x**2*1.e12"`` where ``n0`` is a
      user-defined constant, see above. WARNING: where ``density_function(x,y,z)`` is close to zero, particles will still be injected between ``xmin`` and ``xmax`` etc., with a null weight. This is undesirable because it results in useless computing. To avoid this, see option ``density_min`` below.

* ``<species_name>.density_min`` (`float`) optional (default `0.`)
    Minimum plasma density. No particle is injected where the density is below
    this value.

* ``<species_name>.density_max`` (`float`) optional (default `infinity`)
    Maximum plasma density. The density at each point is the minimum between
    the value given in the profile, and `density_max`.

* ``<species_name>.radially_weighted`` (`bool`) optional (default `true`)
    Whether particle's weight is varied with their radius. This only applies to cylindrical geometry.
    The only valid value is true.

    * ``predefined``: use one of WarpX predefined plasma profiles. It requires additional
      arguments ``<species_name>.predefined_profile_name`` and
      ``<species_name>.predefined_profile_params`` (see below).

* ``<species_name>.momentum_distribution_type`` (`string`)
    Distribution of the normalized momentum (`u=p/mc`) for this species. The options are:

    * ``constant``: constant momentum profile. This requires additional parameters
      ``<species_name>.ux``, ``<species_name>.uy`` and ``<species_name>.uz``, the normalized
      momenta in the x, y and z direction respectively.

    * ``gaussian``: gaussian momentum distribution in all 3 directions. This requires
      additional arguments for the average momenta along each direction
      ``<species_name>.ux_m``, ``<species_name>.uy_m`` and ``<species_name>.uz_m`` as
      well as standard deviations along each direction ``<species_name>.ux_th``,
      ``<species_name>.uy_th`` and ``<species_name>.uz_th``.

    * ``maxwell_boltzmann``: Maxwell-Boltzmann distribution that takes a dimensionless
      temperature parameter ``<species_name>.theta`` as an input, where theta is kb*T/(m*c^2),
      kb is the Boltzmann constant, c is the speed of light, and m is the mass of the species.
      It also includes the optional parameter ``<species_name>.beta`` where beta is equal to v/c.
      The plasma will be initialized to move at drift velocity beta*c in the
      ``<species_name>.drift_vel_dir = (+/-) 'x', 'y', 'z'`` direction. Please leave no whitespace
      between the sign and the character on input. A direction without a sign will be treated as
      positive. The MB distribution is initialized in the drifting frame by sampling three Gaussian
      distributions in each dimension using, the Box Mueller method, and then the distribution is
      transformed to the simulation frame using the flipping method. The flipping method can be
      found in Zenitani 2015 section III. B. (Phys. Plasmas 22, 042116).

      Note that though the particles may move at relativistic speeds in the simulation frame,
      they are not relativistic in the drift frame. This is as opposed to the Maxwell Juttner
      setting, which initializes particles with relativistic momentums in their drifting frame.

    * ``maxwell_juttner``: Maxwell-Juttner distribution for high temperature plasma. This mode
      requires a dimensionless temperature parameter ``<species_name>.theta``, where theta is equal
      to kb*T/(m*c^2), where kb is the Boltzmann constant, and m is the mass of the species. It also
      includes the optional parameter ``<species_name>.beta`` where beta is equal to v/c. The plasma
      will be initialized to move at velocity beta*c in the
      ``<species_name>.drift_vel_dir = (+/-) 'x', 'y', 'z'`` direction. Please leave no whitespace
      between the sign and the character on input. A direction without a sign will be treated as
      positive. The MJ distribution will be initialized in the moving frame using the Sobol method,
      and then the distribution will be transformed to the simulation frame using the flipping method.
      Both the Sobol and the flipping method can be found in Zenitani 2015 (Phys. Plasmas 22, 042116).

      Please take notice that particles initialized with this setting can be relativistic in two ways.
      In the simulation frame, they can drift with a relativistic speed beta. Then, in the drifting
      frame they are still moving with relativistic speeds due to high temperature. This is as opposed
      to the Maxwell Boltzmann setting, which initializes non-relativistic plasma in their relativistic
      drifting frame.

    * ``radial_expansion``: momentum depends on the radial coordinate linearly. This
      requires additional parameter ``u_over_r`` which is the slope.

    * ``parse_momentum_function``: the momentum is given by a function in the input
      file. It requires additional arguments ``<species_name>.momentum_function_ux(x,y,z)``,
      ``<species_name>.momentum_function_uy(x,y,z)`` and ``<species_name>.momentum_function_uz(x,y,z)``,
      which gives the distribution of each component of the momentum as a function of space.

* ``<species_name>.zinject_plane`` (`float`)
    Only read if  ``<species_name>`` is in ``particles.rigid_injected_species``.
    Injection plane when using the rigid injection method.
    See ``particles.rigid_injected_species`` above.

* ``<species_name>.rigid_advance`` (`bool`)
    Only read if ``<species_name>`` is in ``particles.rigid_injected_species``.

    * If ``false``, each particle is advanced with its
      own velocity ``vz`` until it reaches ``zinject_plane``.

    * If ``true``, each particle is advanced with the average speed of the species
      ``vzbar`` until it reaches ``zinject_plane``.

* ``species_name.predefined_profile_name`` (`string`)
    Only read of ``<species_name>.electrons.profile`` is `predefined`.

    * If ``parabolic_channel``, the plasma profile is a parabolic profile with
      cosine-like ramps at the beginning and the end of the profile.
      The density is given by

      .. math::

          n = n_0 n(x,y) n(z)

      with

      .. math::

          n(x,y) = 1 + 4\frac{x^2+y^2}{k_p^2 R_c^4}

      where :math:`k_p` is the plasma wavenumber associated with density :math:`n_0`.
      Here, :math:`n(z)` is a cosine-like up-ramp from :math:`0` to :math:`L_{ramp,up}`,
      constant to :math:`1` from :math:`L_{ramp,up}` to :math:`L_{ramp,up} + L_{plateau}`
      and a cosine-like down-ramp from :math:`L_{ramp,up} + L_{plateau}` to
      :math:`L_{ramp,up} + L_{plateau}+L_{ramp,down}`. All parameters are given
      in ``predefined_profile_params``.

* ``<species_name>.predefined_profile_params`` (list of `float`)
    Parameters for the predefined profiles.

    * If ``species_name.predefined_profile_name`` is ``parabolic_channel``,
      ``predefined_profile_params`` contains a space-separated list of the
      following parameters, in this order: :math:`L_{ramp,up}` :math:`L_{plateau}`
      :math:`L_{ramp,down}` :math:`R_c` :math:`n_0`

* ``<species_name>.do_backward_propagation`` (`bool`)
    Inject a backward-propagating beam to reduce the effect of charge-separation
    fields when running in the boosted frame. See examples.

* ``<species_name>.do_splitting`` (`bool`) optional (default `0`)
    Split particles of the species when crossing the boundary from a lower
    resolution domain to a higher resolution domain.

* ``<species_name>.split_type`` (`int`) optional (default `0`)
    Splitting technique. When `0`, particles are split along the simulation
    axes (4 particles in 2D, 6 particles in 3D). When `1`, particles are split
    along the diagonals (4 particles in 2D, 8 particles in 3D).

* ``<species_name>.do_not_deposit`` (`0` or `1` optional; default `0`)
    If `1` is given, both charge deposition and current deposition will
    not be done, thus that species does not contribute to the fields.

* ``<species_name>.do_not_gather`` (`0` or `1` optional; default `0`)
    If `1` is given, field gather from grids will not be done,
    thus that species will not be affected by the field on grids.

* ``<species_name>.do_not_push`` (`0` or `1` optional; default `0`)
    If `1` is given, this species will not be pushed
    by any pusher during the simulation.

* ``<species>.plot_species`` (`0` or `1` optional; default `1`)
    Whether to plot particle quantities for this species.

* ``<species>.plot_vars`` (list of `strings` separated by spaces, optional)
    List of particle quantities to write to `plotfiles`. By defaults, all
    quantities are written to file. Choices are

    * ``w`` for the particle weight,
    * ``ux`` ``uy`` ``uz`` for the particle momentum,
    * ``Ex`` ``Ey`` ``Ez`` for the electric field on particles,
    * ``Bx`` ``By`` ``Bz`` for the magnetic field on particles.

    The particle positions are always included. Use
    ``<species>.plot_vars = none`` to plot no particle data, except
    particle position.

* ``<species>.do_back_transformed_diagnostics`` (`0` or `1` optional, default `1`)
    Only used when ``warpx.do_back_transformed_diagnostics=1``. When running in a
    boosted frame, whether or not to plot back-transformed diagnostics for
    this species.

* ``warpx.serialize_ics`` (`0 or 1`)
    Whether or not to use OpenMP threading for particle initialization.

* ``<species>.do_field_ionization`` (`0` or `1`) optional (default `0`)
    Do field ionization for this species (using the ADK theory). Currently,
    this is slow on GPU.

* ``<species>.physical_element`` (`string`)
    Only read if `do_field_ionization = 1`. Symbol of chemical element for
    this species. Example: for Helium, use ``physical_element = He``.

* ``<species>.ionization_product_species`` (`string`)
    Only read if `do_field_ionization = 1`. Name of species in which ionized
    electrons are stored. This species must be created as a regular species
    in the input file (in particular, it must be in `particles.species_names`).

* ``<species>.ionization_initial_level`` (`int`) optional (default `0`)
    Only read if `do_field_ionization = 1`. Initial ionization level of the
    species (must be smaller than the atomic number of chemical element given
    in `physical_element`).

* ``<species>.do_classical_radiation_reaction`` (`int`) optional (default `0`)
    Enables Radiation Reaction (or Radiation Friction) for the species. Species
    must be either electrons or positrons. Boris pusher must be used for the
    simulation

* ``<species>.do_qed`` (`int`) optional (default `0`)
    If `<species>.do_qed = 0` all the QED effects are disabled for this species.
    If `<species>.do_qed = 1` QED effects can be enabled for this species (see below).
    **Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**

* ``<species>.do_qed_quantum_sync`` (`int`) optional (default `0`)
    It only works if `<species>.do_qed = 1`. Enables Quantum synchrotron emission for this species.
    Quantum synchrotron lookup table should be either generated or loaded from disk to enable
    this process (see "Lookup tables for QED modules" section below).
    `<species>` must be either an electron or a positron species.
    **Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**

* ``<species>.do_qed_breit_wheeler`` (`int`) optional (default `0`)
    It only works if `<species>.do_qed = 1`. Enables non-linear Breit-Wheeler process for this species.
    Breit-Wheeler lookup table should be either generated or loaded from disk to enable
    this process (see "Lookup tables for QED modules" section below).
    `<species>` must be a photon species.
    **Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**

* ``<species>.qed_quantum_sync_phot_product_species`` (`string`)
    If an electron or a positron species has the Quantum synchrotron process, a photon product species must be specified
    (the name of an existing photon species must be provided)
    **Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**

* ``<species>.qed_breit_wheeler_ele_product_species`` (`string`)
    If a photon species has the Breit-Wheeler process, an electron product species must be specified
    (the name of an existing electron species must be provided)
    **Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**

* ``<species>.qed_breit_wheeler_pos_product_species`` (`string`)
    If a photon species has the Breit-Wheeler process, a positron product species must be specified
    (the name of an existing positron species must be provided).
    **Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**


Laser initialization
--------------------

* ``lasers.nlasers`` (`int`) optional (default `0`)
    Number of lasers pulses.

* ``lasers.names`` (list of `string`. Must contain ``lasers.nlasers`` elements)
    Name of each laser. This is then used in the rest of the input deck ;
    in this documentation we use `<laser_name>` as a placeholder. The parameters below
    must be provided for each laser pulse.

* ```<laser_name>`.position`` (`3 floats in 3D and 2D` ; in meters)
    The coordinates of one of the point of the antenna that will emit the laser.
    The plane of the antenna is entirely defined by ``<laser_name>.position``
    and ``<laser_name>.direction``.

    ```<laser_name>`.position`` also corresponds to the origin of the coordinates system
    for the laser tranverse profile. For instance, for a Gaussian laser profile,
    the peak of intensity will be at the position given by ``<laser_name>.position``.
    This variable can thus be used to shift the position of the laser pulse
    transversally.

    .. note::
        In 2D, ```<laser_name>`.position`` is still given by 3 numbers,
        but the second number is ignored.

    When running a **boosted-frame simulation**, provide the value of
    ``<laser_name>.position`` in the laboratory frame, and use ``warpx.gamma_boost``
    to automatically perform the conversion to the boosted frame. Note that,
    in this case, the laser antenna will be moving, in the boosted frame.

* ``<laser_name>.polarization`` (`3 floats in 3D and 2D`)
    The coordinates of a vector that points in the direction of polarization of
    the laser. The norm of this vector is unimportant, only its direction matters.

    .. note::
        Even in 2D, all the 3 components of this vectors are important (i.e.
        the polarization can be orthogonal to the plane of the simulation).

*  ``<laser_name>.direction`` (`3 floats in 3D`)
    The coordinates of a vector that points in the propagation direction of
    the laser. The norm of this vector is unimportant, only its direction matters.

    The plane of the antenna that will emit the laser is orthogonal to this vector.

    .. warning::

        When running **boosted-frame simulations**, ``<laser_name>.direction`` should
        be parallel to ``warpx.boost_direction``, for now.

* ``<laser_name>.e_max`` (`float` ; in V/m)
    Peak amplitude of the laser field.

    For a laser with a wavelength :math:`\lambda = 0.8\,\mu m`, the peak amplitude
    is related to :math:`a_0` by:

    .. math::

        E_{max} = a_0 \frac{2 \pi m_e c}{e\lambda} = a_0 \times (4.0 \cdot 10^{12} \;V.m^{-1})

    When running a **boosted-frame simulation**, provide the value of ``<laser_name>.e_max``
    in the laboratory frame, and use ``warpx.gamma_boost`` to automatically
    perform the conversion to the boosted frame.

* ``<laser_name>.wavelength`` (`float`; in meters)
    The wavelength of the laser in vacuum.

    When running a **boosted-frame simulation**, provide the value of
    ``<laser_name>.wavelength`` in the laboratory frame, and use ``warpx.gamma_boost``
    to automatically perform the conversion to the boosted frame.

* ``<laser_name>.profile`` (`string`)
    The spatio-temporal shape of the laser. The options that are currently
    implemented are:

    - ``"Gaussian"``: The transverse and longitudinal profiles are Gaussian.
    - ``"Harris"``: The transverse profile is Gaussian, but the longitudinal profile
      is given by the Harris function (see ``<laser_name>.profile_duration`` for more details)
    - ``"parse_field_function"``: the laser electric field is given by a function in the
      input file. It requires additional argument ``<laser_name>.field_function(X,Y,t)``, which
      is a mathematical expression , e.g.
      ``<laser_name>.field_function(X,Y,t) = "a0*X**2 * (X>0) * cos(omega0*t)"`` where
      ``a0`` and ``omega0`` are a user-defined constant, see above. The profile passed
      here is the full profile, not only the laser envelope. ``t`` is time and ``X``
      and ``Y`` are coordinates orthogonal to ``<laser_name>.direction`` (not necessarily the
      x and y coordinates of the simulation). All parameters above are required, but
      none of the parameters below are used when ``<laser_name>.parse_field_function=1``. Even
      though ``<laser_name>.wavelength`` and ``<laser_name>.e_max`` should be included in the laser
      function, they still have to be specified as they are used for numerical purposes.
    - ``"from_txye_file"``: the electric field of the laser is read from an external binary file
      whose format is explained below. It requires to provide the name of the binary file
      setting the additional parameter ``<laser_name>.txye_file_name`` (string). It accepts an
      optional parameter ``<laser_name>.time_chunk_size`` (int). This allows to read only
      time_chunk_size timesteps from the binary file. New timesteps are read as soon as they are needed.
      The default value is automatically set to the number of timesteps contained in the binary file
      (i.e. only one read is performed at the beginning of the simulation).
      The external binary file should provide E(x,y,t) on a rectangular (but non necessarily uniform)
      grid. The code performs a bi-linear (in 2D) or tri-linear (in 3D) interpolation to set the field
      values. x,y,t are meant to be in S.I. units, while the field value is meant to be multiplied by
      ``<laser_name>.e_max`` (i.e. in most cases the maximum of abs(E(x,y,t)) should be 1,
      so that the maximum field intensity can be set straightforwardly with ``<laser_name>.e_max``).
      The binary file has to respect the following format:

        * flag to indicate if the grid is uniform or not (1 byte, 0 means non-uniform, !=0 means uniform)

        * np, number of timesteps (uint32_t, must be >=2)

        * nx, number of points along x (uint32_t, must be >=2)

        * ny, number of points along y (uint32_t, must be 1 for 2D simulations and >=2 for 3D simulations)

        * timesteps (double[2] if grid is uniform, double[np] otherwise)

        * x_coords (double[2] if grid is uniform, double[nx] otherwise)

        * y_coords (double[1] if 2D, double[2] if 3D & uniform grid, double[ny] if 3D & non uniform grid)

        * field_data (double[nt * nx * ny], with nt being the slowest coordinate).

      A file at this format can be generated from Python, see an example at ``Examples/Modules/laser_injection_from_file``


*  ``<laser_name>.profile_t_peak`` (`float`; in seconds)
    The time at which the laser reaches its peak intensity, at the position
    given by ``<laser_name>.position`` (only used for the ``"gaussian"`` profile)

    When running a **boosted-frame simulation**, provide the value of
    ``<laser_name>.profile_t_peak`` in the laboratory frame, and use ``warpx.gamma_boost``
    to automatically perform the conversion to the boosted frame.

*  ``<laser_name>.profile_duration`` (`float` ; in seconds)

    The duration of the laser, defined as :math:`\tau` below:

    - For the ``"gaussian"`` profile:

    .. math::

        E(\boldsymbol{x},t) \propto \exp\left( -\frac{(t-t_{peak})^2}{\tau^2} \right)

    - For the ``"harris"`` profile:

    .. math::

        E(\boldsymbol{x},t) \propto \frac{1}{32}\left[10 - 15 \cos\left(\frac{2\pi t}{\tau}\right) + 6 \cos\left(\frac{4\pi t}{\tau}\right) - \cos\left(\frac{6\pi t}{\tau}\right) \right]\Theta(\tau - t)

    When running a **boosted-frame simulation**, provide the value of
    ``<laser_name>.profile_duration`` in the laboratory frame, and use ``warpx.gamma_boost``
    to automatically perform the conversion to the boosted frame.

* ``<laser_name>.profile_waist`` (`float` ; in meters)
    The waist of the transverse Gaussian laser profile, defined as :math:`w_0` :

    .. math::

        E(\boldsymbol{x},t) \propto \exp\left( -\frac{\boldsymbol{x}_\perp^2}{w_0^2} \right)

* ``<laser_name>.profile_focal_distance`` (`float`; in meters)
    The distance from ``laser_position`` to the focal plane.
    (where the distance is defined along the direction given by ``<laser_name>.direction``.)

    Use a negative number for a defocussing laser instead of a focussing laser.

    When running a **boosted-frame simulation**, provide the value of
    ``<laser_name>.profile_focal_distance`` in the laboratory frame, and use ``warpx.gamma_boost``
    to automatically perform the conversion to the boosted frame.

* ``<laser_name>.stc_direction`` (`3 floats`) optional (default `1. 0. 0.`)
    Direction of laser spatio-temporal couplings.
    See definition in Akturk et al., Opt Express, vol 12, no 19 (2014).

* ``<laser_name>.zeta`` (`float`; in meters.seconds) optional (default `0.`)
    Spatial chirp at focus in direction ``<laser_name>.stc_direction``. See definition in
    Akturk et al., Opt Express, vol 12, no 19 (2014).

* ``<laser_name>.beta`` (`float`; in seconds) optional (default `0.`)
    Angular dispersion (or angular chirp) at focus in direction ``<laser_name>.stc_direction``.
    See definition in Akturk et al., Opt Express, vol 12, no 19 (2014).

* ``<laser_name>.phi2`` (`float`; in seconds**2) optional (default `0.`)
    Temporal chirp at focus.
    See definition in Akturk et al., Opt Express, vol 12, no 19 (2014).

* ``<laser_name>.do_continuous_injection`` (`0` or `1`) optional (default `0`).
    Whether or not to use continuous injection.
    If the antenna starts outside of the simulation domain but enters it
    at some point (due to moving window or moving antenna in the boosted
    frame), use this so that the laser antenna is injected when it reaches
    the box boundary. If running in a boosted frame, this requires the
    boost direction, moving window direction and laser propagation direction
    to be along `z`. If not running in a boosted frame, this requires the
    moving window and laser propagation directions to be the same (`x`, `y`
    or `z`)

* ``<laser_name>.min_particles_per_mode`` (`int`) optional (default `4`)
    When using the RZ version, this specifies the minimum number of particles
    per angular mode. The laser particles are loaded into radial spokes, with
    the number of spokes given by min_particles_per_mode*(warpx.n_rz_azimuthal_modes-1).

* ``warpx.num_mirrors`` (`int`) optional (default `0`)
    Users can input perfect mirror condition inside the simulation domain.
    The number of mirrors is given by ``warpx.num_mirrors``. The mirrors are
    orthogonal to the `z` direction. The following parameters are required
    when ``warpx.num_mirrors`` is >0.

* ``warpx.mirror_z`` (list of `float`) required if ``warpx.num_mirrors>0``
    ``z`` location of the front of the mirrors.

* ``warpx.mirror_z_width`` (list of `float`) required if ``warpx.num_mirrors>0``
    ``z`` width of the mirrors.

* ``warpx.mirror_z_npoints`` (list of `int`) required if ``warpx.num_mirrors>0``
    In the boosted frame, depending on `gamma_boost`, ``warpx.mirror_z_width``
    can be smaller than the cell size, so that the mirror would not work. This
    parameter is the minimum number of points for the mirror. If
    ``mirror_z_width < dz/cell_size``, the upper bound of the mirror is increased
    so that it contains at least ``mirror_z_npoints``.

* ``warpx.B_ext_grid_init_style`` (string) optional (default is "default")
    This parameter determines the type of initialization for the external
    magnetic field. The "default" style initializes the
    external magnetic field (Bx,By,Bz) to (0.0, 0.0, 0.0).
    The string can be set to "constant" if a constant magnetic field is
    required to be set at initialization. If set to "constant", then an
    additional parameter, namely, ``warpx.B_external_grid`` must be specified.
    If set to ``parse_B_ext_grid_function``, then a mathematical expression can
    be used to initialize the external magnetic field on the grid. It
    requires additional parameters in the input file, namely,
    ``warpx.Bx_external_grid_function(x,y,z)``,
    ``warpx.By_external_grid_function(x,y,z)``,
    ``warpx.Bz_external_grid_function(x,y,z)`` to initialize the external
    magnetic field for each of the three components on the grid.
    Constants required in the expression can be set using ``my_constants``.
    For example, if ``warpx.Bx_external_grid_function(x,y,z)=Bo*x + delta*(y + z)``
    then the constants `Bo` and `delta` required in the above equation
    can be set using ``my_constants.Bo=`` and ``my_constants.delta=`` in the
    input file. For a two-dimensional simulation, it is assumed that the first dimension     is `x` and the second dimension in `z`, and the value of `y` is set to zero.
    Note that the current implementation of the parser for external B-field
    does not work with RZ and the code will abort with an error message.

* ``warpx.E_ext_grid_init_style`` (string) optional (default is "default")
    This parameter determines the type of initialization for the external
    electric field. The "default" style initializes the
    external electric field (Ex,Ey,Ez) to (0.0, 0.0, 0.0).
    The string can be set to "constant" if a constant electric field is
    required to be set at initialization. If set to "constant", then an
    additional parameter, namely, ``warpx.E_external_grid`` must be specified
    in the input file.
    If set to ``parse_E_ext_grid_function``, then a mathematical expression can
    be used to initialize the external magnetic field on the grid. It
    required additional parameters in the input file, namely,
    ``warpx.Ex_external_grid_function(x,y,z)``,
    ``warpx.Ey_external_grid_function(x,y,z)``,
    ``warpx.Ez_external_grid_function(x,y,z)`` to initialize the external
    electric field for each of the three components on the grid.
    Constants required in the expression can be set using ``my_constants``.
    For example, if ``warpx.Ex_external_grid_function(x,y,z)=Eo*x + delta*(y + z)``
    then the constants `Bo` and `delta` required in the above equation
    can be set using ``my_constants.Eo=`` and ``my_constants.delta=`` in the
    input file. For a two-dimensional simulation, it is assumed that the first
    dimension is `x` and the second dimension in `z`,
    and the value of `y` is set to zero.
    Note that the current implementation of the parser for external E-field
    does not work with RZ and the code will abort with an error message.

* ``warpx.E_external_grid`` & ``warpx.B_external_grid`` (list of `int`)
    required when ``warpx.B_ext_grid_init_style="parse_B_ext_grid_function"``
    and when ``warpx.E_ext_grid_init_style="parse_E_ext_grid_function"``, respectively.
    External uniform and constant electrostatic and magnetostatic field added
    to the grid at initialization. Use with caution as these fields are used for
    the field solver. In particular, do not use any other boundary condition
    than periodic.

*  ``particles.B_ext_particle_init_style`` (string) optional (default is "default")
     This parameter determines the type of initialization for the external
     magnetic field that is applied directly to the particles at every timestep.
     The "default" style sets the external B-field (Bx,By,Bz) to (0.0,0.0,0.0).
     The string can be set to "constant" if a constant external B-field is applied
     every timestep. If this parameter is set to "constant", then an additional
     parameter, namely, ``particles.B_external_particle`` must be specified in
     the input file.
     To parse a mathematical function for the external B-field, use the option
     ``parse_B_ext_particle_function``. This option requires additional parameters
     in the input file, namely,
     ``particles.Bx_external_particle_function(x,y,z,t)``,
     ``particles.By_external_particle_function(x,y,z,t)``,
     ``particles.Bz_external_particle_function(x,y,z,t)`` to apply the external B-field
     on the particles. Constants required in the mathematical expression can be set
     using ``my_constants``. For a two-dimensional simulation, it is assumed that
     the first and second dimensions are `x` and `z`, respectively, and the
     value of the `By` component is set to zero.
     Note that the current implementation of the parser for B-field on particles
     does not work with RZ and the code will abort with an error message.

*    ``particles.E_ext_particle_init_style`` (string) optional (default is "default")
     This parameter determines the type of initialization for the external
     electric field that is applied directly to the particles at every timestep.
     The "default" style set the external E-field (Ex,Ey,Ez) to (0.0,0.0,0.0).
     The string can be set to "constant" if a constant external E-field is to be
     used in the simulation at every timestep. If this parameter is set to "constant",
     then an additional parameter, namely, ``particles.E_external_particle`` must be
     specified in the input file.
     To parse a mathematical function for the external E-field, use the option
     ``parse_E_ext_particle_function``. This option requires additional
     parameters in the input file, namely,
     ``particles.Ex_external_particle_function(x,y,z,t)``,
     ``particles.Ey_external_particle_function(x,y,z,t)``,
     ``particles.Ez_external_particle_function(x,y,z,t)`` to apply the external E-field
     on the particles. Constants required in the mathematical expression can be set
     using ``my_constants``. For a two-dimensional simulation, similar to the B-field,
     it is assumed that the first and second dimensions are `x` and `z`, respectively,
     and the value of the `Ey` component is set to zero.
     The current implementation of the parser for the E-field on particles does not work
     with RZ and the code will abort with an error message.

* ``particles.E_external_particle`` & ``particles.B_external_particle`` (list of `float`) optional (default `0. 0. 0.`)
    Two separate parameters which add an externally applied uniform E-field or
    B-field to each particle which is then added to the field values gathered
    from the grid in the PIC cycle.

Collision initialization
------------------------

WarpX provides a relativistic elastic Monte Carlo binary collision model,
following the algorithm given by `Perez et al. (Phys. Plasmas 19, 083104, 2012) <https://doi.org/10.1063/1.4742167>`_.

* ``collisions.ncollisions`` (`int`) optional (default `0`)
    Number of collision types.

* ``collisions.collision_names`` (`strings`, separated by spaces)
    The name of each collision type. It must be provided if ``collisions.ncollisions`` is not zero.
    This is then used in the rest of the input deck;
    in this documentation we use ``<collision_name>`` as a placeholder.
    The number of strings provided should match the number of collision types,
    i.e. ``collisions.ncollisions``.

* ``<collision_name>.species`` (`strings`, two species names separated by spaces)
    The names of two species, between which the collision will be considered.
    It must be provided if ``collisions.ncollisions`` is not zero, and
    the number of provided ``<collision_name>.species`` should match
    the number of collision types, i.e. ``collisions.ncollisions``.

* ``<collision_name>.CoulombLog`` (`float`) optional
    A provided fixed Coulomb logarithm of the collision type
    ``<collision_name>``.
    If this is not provided, or if a non-positive value is provided,
    a Coulomb logarithm will be computed automatically according to the algorithm.

Numerics and algorithms
-----------------------

* ``warpx.cfl`` (`float`)
    The ratio between the actual timestep that is used in the simulation
    and the Courant-Friedrichs-Lewy (CFL) limit. (e.g. for `warpx.cfl=1`,
    the timestep will be exactly equal to the CFL limit.)

* ``warpx.use_filter`` (`0 or 1`)
    Whether to smooth the charge and currents on the mesh, after depositing
    them from the macroparticles. This uses a bilinear filter
    (see the sub-section **Filtering** in :doc:`../theory/theory`).

* ``warpx.filter_npass_each_dir`` (`3 int`) optional (default `1 1 1`)
    Number of passes along each direction for the bilinear filter.
    In 2D simulations, only the first two values are read.

* ``algo.current_deposition`` (`string`, optional)
    The algorithm for current deposition. Available options are:

     - ``esirkepov``: the charge-conserving Esirkepov algorithm
       (see `Esirkepov, Comp. Phys. Comm. (2001) <https://www.sciencedirect.com/science/article/pii/S0010465500002289>`__)
     - ``direct``: simpler current deposition algorithm, described in
       the section :doc:`../theory/picsar_theory`. Note that this algorithm is not strictly charge-conserving.

    If ``algo.current_deposition`` is not specified, the default is
    ``esirkepov`` (unless WarpX is compiled with ``USE_PSATD=TRUE``, in which
    case the default is ``direct``).

* ``algo.charge_deposition`` (`string`, optional)
    The algorithm for the charge density deposition. Available options are:

     - ``standard``: standard charge deposition algorithm, described in
       the section :doc:`../theory/picsar_theory`.

* ``algo.field_gathering`` (`string`, optional)
    The algorithm for field gathering. Available options are:

     - ``energy-conserving``: gathers directly from the grid points (either staggered
       or nodal gridpoints depending on ``warpx.do_nodal``).
     - ``momentum-conserving``: first average the fields from the grid points to
       the nodes, and then gather from the nodes.

     If ``algo.field_gathering`` is not specified, the default is ``energy-conserving``.
     If ``warpx.do_nodal`` is ``true``, then ``energy-conserving`` and ``momentum-conserving``
     are equivalent.


* ``algo.particle_pusher`` (`string`, optional)
    The algorithm for the particle pusher. Available options are:

     - ``boris``: Boris pusher.
     - ``vay``: Vay pusher (see `Vay, Phys. Plasmas (2008) <https://aip.scitation.org/doi/10.1063/1.2837054>`__)
     - ``higuera``: Higuera-Cary pusher (see `Higuera and Cary, Phys. Plasmas (2017) <https://aip.scitation.org/doi/10.1063/1.4979989>`__)

     If ``algo.particle_pusher`` is not specified, ``boris`` is the default.

* ``algo.maxwell_fdtd_solver`` (`string`, optional)
    The algorithm for the FDTD Maxwell field solver. Available options are:

     - ``yee``: Yee FDTD solver.
     - ``ckc``: (not available in ``RZ`` geometry) Cole-Karkkainen solver with Cowan
       coefficients (see `Cowan, PRSTAB 16 (2013) <https://journals.aps.org/prab/abstract/10.1103/PhysRevSTAB.16.041303>`__)

     If ``algo.maxwell_fdtd_solver`` is not specified, ``yee`` is the default.

* ``interpolation.nox``, ``interpolation.noy``, ``interpolation.noz`` (`integer`)
    The order of the shape factors for the macroparticles, for the 3 dimensions of space.
    Lower-order shape factors result in faster simulations, but more noisy results,

    Note that the implementation in WarpX is more efficient when these 3 numbers are equal,
    and when they are between 1 and 3.

* ``warpx.do_dive_cleaning`` (`0` or `1` ; default: 0)
    Whether to use modified Maxwell equations that progressively eliminate
    the error in :math:`div(E)-\rho`. This can be useful when using a current
    deposition algorithm which is not strictly charge-conserving, or when
    using mesh refinement. These modified Maxwell equation will cause the error
    to propagate (at the speed of light) to the boundaries of the simulation
    domain, where it can be absorbed.

* ``warpx.do_nodal`` (`0` or `1` ; default: 0)
    Whether to use a nodal grid (i.e. all fields are defined at the
    same points in space) or a staggered grid (i.e. Yee grid ; different
    fields are defined at different points in space)

* ``warpx.do_subcycling`` (`0` or `1`; default: 0)
    Whether or not to use sub-cycling. Different refinement levels have a
    different cell size, which results in different Courant–Friedrichs–Lewy
    (CFL) limits for the time step. By default, when using mesh refinement,
    the same time step is used for all levels. This time step is
    taken as the CFL limit of the finest level. Hence, for coarser
    levels, the timestep is only a fraction of the CFL limit for this
    level, which may lead to numerical artifacts. With sub-cycling, each level
    evolves with its own time step, set to its own CFL limit. In practice, it
    means that when level 0 performs one iteration, level 1 performs two
    iterations. Currently, this option is only supported when
    ``amr.max_level = 1``. More information can be found at
    https://ieeexplore.ieee.org/document/8659392.

* ``psatd.nox``, ``psatd.noy``, ``pstad.noz`` (`integer`) optional (default `16` for all)
    The order of accuracy of the spatial derivatives, when using the code compiled with a PSATD solver.

* ``psatd.nx_guard`, ``psatd.ny_guard``, ``psatd.nz_guard`` (`integer`) optional
    The number of guard cells to use with PSATD solver.
    If not set by users, these values are calculated automatically and determined *empirically* and
    would be equal the order of the solver for nodal grid, and half the order of the solver for staggered.

* ``psatd.periodic_single_box_fft`` (`0` or `1`; default: 0)
    If true, this will *not* incorporate the guard cells into the box over which FFTs are performed.
    This is only valid when WarpX is run with periodic boundaries and a single box.
    In this case, using `psatd.periodic_single_box_fft` is equivalent to using a global FFT over the whole domain.
    Therefore, all the approximations that are usually made when using local FFTs with guard cells
    (for problems with multiple boxes) become exact in the case of the periodic, single-box FFT without guard cells.

* ``psatd.fftw_plan_measure`` (`0` or `1`)
    Defines whether the parameters of FFTW plans will be initialized by
    measuring and optimizing performance (``FFTW_MEASURE`` mode; activated by default here).
    If ``psatd.fftw_plan_measure`` is set to ``0``, then the best parameters of FFTW
    plans will simply be estimated (``FFTW_ESTIMATE`` mode).
    See `this section of the FFTW documentation <http://www.fftw.org/fftw3_doc/Planner-Flags.html>`__
    for more information.

* ``pstad.v_galilean`` (`3 floats`, in units of the speed of light; default `0. 0. 0.`)
    Defines the galilean velocity.
    Non-zero `v_galilean` activates Galilean algorithm, which suppresses the Numerical Cherenkov instability
    in boosted-frame simulation. This requires the code to be compiled with `USE_PSATD=TRUE`.
    (see the sub-section Numerical Stability and alternate formulation
    in a Galilean frame in :doc:`../theory/boosted-frame`).
    It also requires the use of the `direct` current deposition option
    `algo.current_deposition = direct` (does not work with Esirkepov algorithm).

* ``warpx.override_sync_int`` (`integer`) optional (default `10`)
    Number of time steps between synchronization of sources (`rho` and `J`) on
    grid nodes at box boundaries. Since the grid nodes at the interface between
    two neighbor boxes are duplicated in both boxes, an instability can occur
    if they have too different values. This option makes sure that they are
    synchronized periodically.

* ``warpx.use_hybrid_QED`` ('bool'; default: 0)
    Will use the Hybird QED Maxwell solver when pushing fields: a QED correction is added to the
    field solver to solve non-linear Maxwell's equations, according to [Quantum Electrodynamics
    vacuum polarization solver, P. Carneiro et al., `ArXiv 2016 <https://arxiv.org/abs/1607.04224>`__].
    Note that this option can only be used with the PSATD build. Furthermore,
    warpx.do_nodal must be set to `1` which is not its default value.

 * ``warpx.quantum_xi`` ('float'; default: 1.3050122.e-52)
     Overwrites the actual quantum parameter used in Maxwell's QED equations. Assigning a
     value here will make the simulation unphysical, but will allow QED effects to become more apparent.
     Note that this option will only have an effect if the warpx.use_Hybrid_QED flag is also triggered.

 * ``warpx.do_device_synchronize_before_profile`` (`bool`) optional (default `1`)
    When running in an accelerated platform, whether to call a deviceSynchronize around profiling regions.
    This allows the profiler to give meaningful timers, but (hardly) slows down the simulation.

 * ``warpx.sort_int`` (`int`) optional (defaults: ``-1`` on CPU; ``4`` on GPU)
     If ``<=0``, do not sort particles. If ``>0``, sort particles by bin every ``sort_int`` iteration.
     It is turned on on GPUs for performance reasons (to improve memory locality).

 * ``warpx.sort_bin_size`` (list of `int`) optional (default ``4 4 4``)
     If ``sort_int > 0`` particles are sorted in bins of ``sort_bin_size`` cells.
     In 2D, only the first two elements are read.

Boundary conditions
-------------------

* ``warpx.do_pml`` (`0` or `1`; default: 1)
    Whether to add Perfectly Matched Layers (PML) around the simulation box,
    and around the refinement patches. See the section :doc:`../../theory/PML`
    for more details.

* ``warpx.pml_ncells`` (`int`; default: 10)
    The depth of the PML, in number of cells.

* ``warpx.pml_delta`` (`int`; default: 10)
    The characteristic depth, in number of cells, over which
    the absorption coefficients of the PML increases.

* ``warpx.do_pml_in_domain`` (`int`; default: 0)
    Whether to create the PML inside the simulation area or outside. If inside,
    it allows the user to propagate particles in PML and to use extended PML

* ``warpx.do_pml_has_particles`` (`int`; default: 0)
    Whether to propagate particles in PML or not. Can only be done if PML are in simulation domain,
    i.e. if `warpx.do_pml_in_domain = 1`.

* ``warpx.do_pml_j_damping`` (`int`; default: 0)
    Whether to damp current in PML. Can only be used if particles are propagated in PML,
    i.e. if `warpx.do_pml_has_particles = 1`.

* ``warpx.do_pml_Lo`` (`2 ints in 2D`, `3 ints in 3D`; default: `1 1 1`)
    The directions along which one wants a pml boundary condition for lower boundaries on mother grid.

* ``warpx.do_pml_Hi`` (`2 floats in 2D`, `3 floats in 3D`; default: `1 1 1`)
    The directions along which one wants a pml boundary condition for upper boundaries on mother grid.

Diagnostics and output
----------------------

* ``amr.plot_int`` (`integer`) optional
    The number of PIC cycles (interval) in between two consecutive `plotfile` data dumps.
    Use a negative number to disable data dumping.
    This is ``-1`` (disabled) by default.

    * ``<species_name>.random_fraction`` (`float`) optional
        If provided ``<species_name>.random_fraction = a``,
        only `a` fraction of the particle data of this species will be dumped randomly,
        i.e. if `rand() < a`, this particle will be dumped,
        where `rand()` denotes a random number generator.
        The value `a` provided should be between 0 and 1.

    * ``<species_name>.uniform_stride`` (`int`) optional
        If provided ``<species_name>.uniform_stride = n``,
        every `n` particle of this species will be dumped, selected uniformly.
        The value provided should be an integer greater than or equal to 0.

    * ``<species_name>.plot_filter_function(t,x,y,z,ux,uy,uz)`` (`string`) optional
        Users can provide an expression returning a boolean for whether a particle is dumped (the exact test is whether the return value is `> 0.5`).
        `t` represents the physical time in seconds during the simulation.
        `x, y, z` represent particle positions in the unit of meter.
        `ux, uy, uz` represent particle velocities in the unit of
        :math:`\gamma v/c`, where
        :math:`\gamma` is the Lorentz factor,
        :math:`v/c` is the particle velocity normalized by the speed of light.
        E.g. If provided `(x>0.0)*(uz<10.0)` only those particles located at
        positions `x` greater than `0`, and those having velocity `uz` less than 10,
        will be dumped.

* ``warpx.openpmd_int`` (`integer`) optional
    The number of PIC cycles (interval) in between two consecutive `openPMD <https://www.openPMD.org>`_ data dumps.
    Requires to build WarpX with ``USE_OPENPMD=TRUE`` (see :ref:`instructions <building-openpmd>`).
    This is ``-1`` (disabled) by default.

* ``warpx.openpmd_backend`` (``bp``, ``h5`` or ``json``) optional
    `I/O backend <https://openpmd-api.readthedocs.io/en/latest/backends/overview.html>`_ for `openPMD <https://www.openPMD.org>`_ data dumps.
    ``bp`` is the `ADIOS I/O library <https://csmd.ornl.gov/adios>`_, ``h5`` is the `HDF5 format <https://www.hdfgroup.org/solutions/hdf5/>`_, and ``json`` is a `simple text format <https://en.wikipedia.org/wiki/JSON>`_.
    ``json`` only works with serial/single-rank jobs.
    When WarpX is compiled with openPMD support, the first available backend in the order given above is taken.

* ``warpx.do_back_transformed_diagnostics`` (`0` or `1`)
    Whether to use the **back-transformed diagnostics** (i.e. diagnostics that
    perform on-the-fly conversion to the laboratory frame, when running
    boosted-frame simulations)

* ``warpx.lab_data_directory`` (`string`)
    The directory in which to save the lab frame data when using the
    **back-transformed diagnostics**. If not specified, the default is
    is `lab_frame_data`.

* ``warpx.num_snapshots_lab`` (`integer`)
    Only used when ``warpx.do_back_transformed_diagnostics`` is ``1``.
    The number of lab-frame snapshots that will be written.

* ``warpx.dt_snapshots_lab`` (`float`, in seconds)
    Only used when ``warpx.do_back_transformed_diagnostics`` is ``1``.
    The time interval inbetween the lab-frame snapshots (where this
    time interval is expressed in the laboratory frame).

* ``warpx.dz_snapshots_lab`` (`float`, in meters)
    Only used when ``warpx.do_back_transformed_diagnostics`` is ``1``.
    Distance between the lab-frame snapshots (expressed in the laboratory
    frame). ``dt_snapshots_lab`` is then computed by
    ``dt_snapshots_lab = dz_snapshots_lab/c``. Either `dt_snapshots_lab`
    or `dz_snapshot_lab` is required.

* ``warpx.do_back_transformed_fields`` (`0 or 1`)
    Whether to use the **back-transformed diagnostics** for the fields.

* ``warpx.back_transformed_diag_fields`` (space-separated list of `string`)
    Which fields to dumped in back-transformed diagnostics. Choices are
    'Ex', 'Ey', Ez', 'Bx', 'By', Bz', 'jx', 'jy', jz' and 'rho'. Example:
    ``warpx.back_transformed_diag_fields = Ex Ez By``. By default, all fields
    are dumped.

* ``warpx.plot_raw_fields`` (`0` or `1`) optional (default `0`)
    By default, the fields written in the plot files are averaged on the nodes.
    When ```warpx.plot_raw_fields`` is `1`, then the raw (i.e. unaveraged)
    fields are also saved in the plot files.

* ``warpx.plot_raw_fields_guards`` (`0` or `1`)
    Only used when ``warpx.plot_raw_fields`` is ``1``.
    Whether to include the guard cells in the output of the raw fields.

* ``warpx.plot_finepatch`` (`0` or `1`)
    Only used when mesh refinement is activated and ``warpx.plot_raw_fields`` is ``1``.
    Whether to output the data of the fine patch, in the plot files.

* ``warpx.plot_crsepatch`` (`0` or `1`)
    Only used when mesh refinement is activated and ``warpx.plot_raw_fields`` is ``1``.
    Whether to output the data of the coarse patch, in the plot files.

* ``warpx.plot_coarsening_ratio`` (`int` ; default: `1`)
    Reduce size of the field output by this ratio in each dimension.
    (This is done by averaging the field.) ``plot_coarsening_ratio`` should
    be an integer divisor of ``blocking_factor``.

* ``amr.plot_file`` (`string`)
    Root for output file names. Supports sub-directories. Default `diags/plotfiles/plt`

* ``warpx.fields_to_plot`` (`list of strings`)
    Fields written to plotfiles. Possible values: ``Ex`` ``Ey`` ``Ez``
    ``Bx`` ``By`` ``Bz`` ``jx`` ``jy`` ``jz`` ``part_per_cell`` ``rho``
    ``F`` ``part_per_grid`` ``part_per_proc`` ``divE`` ``divB``.
    Default is
    ``warpx.fields_to_plot = Ex Ey Ez Bx By Bz jx jy jz part_per_cell``.

* ``slice.dom_lo`` and ``slice.dom_hi`` (`2 floats in 2D`, `3 floats in 3D`; in meters similar to the units of the simulation box.)
    The extent of the slice are defined by the co-ordinates of the lower
    corner (``slice.dom_lo``) and upper corner (``slice.dom_hi``).
    The slice could be 1D, 2D, or 3D, aligned with the co-ordinate axes
    and the first axis of the coordinates is x. For example: if for a
    3D simulation, an x-z slice is to be extracted at y = 0.0,
    then the y-value of slice.dom_lo and slice.dom_hi must be equal to 0.0

* ``slice.coarsening_ratio`` (`2 integers in 2D`, `3 integers in 3D`; default `1`)
    The coarsening ratio input must be greater than 0. Default is 1 in all directions.
    In the directions that is reduced, i.e., for an x-z slice in 3D,
    the reduced y-dimension has a default coarsening ratio equal to 1.

* ``slice.plot_int`` (`integer`)
    The number of PIC cycles inbetween two consecutive data dumps for the slice. Use a
    negative number to disable slice generation and slice data dumping.

* ``slice.num_slice_snapshots_lab`` (`integer`)
    Only used when ``warpx.do_back_transformed_diagnostics`` is ``1``.
    The number of back-transformed field and particle data that
    will be written for the reduced domain defined by ``slice.dom_lo``
    and ``slice.dom_hi``. Note that the 'slice' is a reduced
    diagnostic which could be 1D, 2D, or 3D, aligned with the co-ordinate axes.
    These slices can be visualized using read_raw_data.py and the HDF5 format can
    be visualized using the h5py library. Please see the documentation on visualization
    for further details.

* ``slice.dt_slice_snapshots_lab`` (`float`, in seconds)
    Only used when ``warpx.do_back_transformed_diagnostics`` is ``1``.
    The time interval between the back-transformed reduced diagnostics (where this
    time interval is expressed in the laboratory frame).

* ``slice.particle_slice_width_lab`` (`float`, in meters)
    Only used when ``warpx.do_back_transformed_diagnostics`` is ``1`` and
    ``slice.num_slice_snapshots_lab`` is non-zero. Particles are
    copied from the full back-transformed diagnostic to the reduced
    slice diagnostic if there are within the user-defined width from
    the slice region defined by ``slice.dom_lo`` and ``slice.dom_hi``.

* ``warpx.reduced_diags_names`` (`strings`, separated by spaces)
    The names given by the user of simple reduced diagnostics.
    Also the names of the output `.txt` files.
    This reduced diagnostics aims to produce simple outputs
    of the time history of some physical quantities.
    If ``warpx.reduced_diags_names`` is not provided in the input file,
    no reduced diagnostics will be done.
    This is then used in the rest of the input deck;
    in this documentation we use `<reduced_diags_name>` as a placeholder.

* ``<reduced_diags_name>.type`` (`string`)
    The type of reduced diagnostics associated with this `<reduced_diags_name>`.
    For example, ``ParticleEnergy`` and ``FieldEnergy``.
    All available types will be described below in detail.
    For all reduced diagnostics,
    the first and the second columns in the output file are
    the time step and the corresponding physical time in seconds, respectively.

    * ``ParticleEnergy``
        This type computes both the total and the mean
        relativistic particle kinetic energy among all species.

        .. math::

            E_p = \sum_{i=1}^N ( \sqrt{ p_i^2 c^2 + m_0^2 c^4 } - m_0 c^2 ) w_i

        where :math:`p` is the relativistic momentum,
        :math:`c` is the speed of light,
        :math:`m_0` is the rest mass,
        :math:`N` is the number of particles,
        :math:`w` is the individual particle weight.

        The output columns are
        total :math:`E_p` of all species,
        :math:`E_p` of each species,
        total mean energy :math:`E_p / \sum w_i`,
        mean energy of each species.

    * ``FieldEnergy``
        This type computes the electric and magnetic field energy.

        .. math::

            E_f = \sum [ \varepsilon_0 E^2 / 2 + B^2 / ( 2 \mu_0 ) ] \Delta V

        where
        :math:`E` is the electric field,
        :math:`B` is the magnetic field,
        :math:`\varepsilon_0` is the vacuum permittivity,
        :math:`\mu_0` is the vacuum permeability,
        :math:`\Delta V` is the cell volume (or area for 2D),
        the sum is over all cells.

        The output columns are
        total field energy :math:`E_f`,
        :math:`E` field energy,
        :math:`B` field energy, at mesh refinement levels from 0 to :math:`n`.

    * ``BeamRelevant``
        This type computes properties of a particle beam relevant for particle accelerators,
        like position, momentum, emittance, etc.

        ``<reduced_diags_name>.species`` must be provided,
        such that the diagnostics are done for this (beam-like) species only.

        The output columns (for 3D-XYZ) are the following, where the average is done over
        the whole species (typical usage: the particle beam is in a separate species):

        [1], [2], [3]: The mean values of beam positions (m)
        :math:`\langle x \rangle`, :math:`\langle y \rangle`,
        :math:`\langle z \rangle`.

        [4], [5], [6]: The mean values of beam relativistic momenta (kg m/s)
        :math:`\langle p_x \rangle`, :math:`\langle p_y \rangle`,
        :math:`\langle p_z \rangle`.

        [7]: The mean Lorentz factor :math:`\langle \gamma \rangle`.

        [8], [9], [10]: The RMS values of beam positions (m)
        :math:`\delta_x = \sqrt{ \langle (x - \langle x \rangle)^2 \rangle }`,
        :math:`\delta_y = \sqrt{ \langle (y - \langle y \rangle)^2 \rangle }`,
        :math:`\delta_z = \sqrt{ \langle (z - \langle z \rangle)^2 \rangle }`.

        [11], [12], [13]: The RMS values of beam relativistic momenta (kg m/s)
        :math:`\delta_{px} = \sqrt{ \langle (p_x - \langle p_x \rangle)^2 \rangle }`,
        :math:`\delta_{py} = \sqrt{ \langle (p_y - \langle p_y \rangle)^2 \rangle }`,
        :math:`\delta_{pz} = \sqrt{ \langle (p_z - \langle p_z \rangle)^2 \rangle }`.

        [14]: The RMS value of the Lorentz factor
        :math:`\sqrt{ \langle (\gamma - \langle \gamma \rangle)^2 \rangle }`.

        [15], [16], [17]: beam projected transverse RMS normalized emittance (m)
        :math:`\epsilon_x = \dfrac{1}{mc} \sqrt{\delta_x^2 \delta_{px}^2 -
        \Big\langle (x-\langle x \rangle) (p_x-\langle p_x \rangle) \Big\rangle^2}`,
        :math:`\epsilon_y = \dfrac{1}{mc} \sqrt{\delta_y^2 \delta_{py}^2 -
        \Big\langle (y-\langle y \rangle) (p_y-\langle p_y \rangle) \Big\rangle^2}`,
        :math:`\epsilon_z = \dfrac{1}{mc} \sqrt{\delta_z^2 \delta_{pz}^2 -
        \Big\langle (z-\langle z \rangle) (p_z-\langle p_z \rangle) \Big\rangle^2}`.

        [18]: The charge of the beam (C).

        For 2D-XZ,
        :math:`\langle y \rangle`,
        :math:`\delta_y`, and
        :math:`\epsilon_y` will not be outputed.

    * ``LoadBalanceCosts``
        This type computes the cost, used in load balancing, for each box on the domain.
        The cost :math:`c` is computed as

        .. math::

            c = n_{\text{particle}} \cdot w_{\text{particle}} + n_{\text{cell}} \cdot w_{\text{cell}},

        where
        :math:`n_{\text{particle}}` is the number of particles on the box,
        :math:`w_{\text{particle}}` is the particle cost weight factor (controlled by ``algo.costs_heuristic_particles_wt``),
        :math:`n_{\text{cell}}` is the number of cells on the box, and
        :math:`w_{\text{cell}}` is the cell cost weight factor (controlled by ``algo.costs_heuristic_cells_wt``).

    * ``ParticleHistogram``
        This type computes a user defined particle histogram.

        * ``<reduced_diags_name>.species`` (`string`)
            A species name must be provided,
            such that the diagnostics are done for this species.

        * ``<reduced_diags_name>.histogram_function(t,x,y,z,ux,uy,uz)`` (`string`)
            A histogram function must be provided.
            `t` represents the physical time in seconds during the simulation.
            `x, y, z` represent particle positions in the unit of meter.
            `ux, uy, uz` represent the particle velocities in the unit of
            :math:`\gamma v/c`, where
            :math:`\gamma` is the Lorentz factor,
            :math:`v/c` is the particle velocity normalized by the speed of light.
            E.g.
            ``x`` produces the position (density) distribution in `x`.
            ``ux`` produces the velocity distribution in `x`,
            ``sqrt(ux*ux+uy*uy+uz*uz)`` produces the speed distribution.
            The default value of the histogram without normalization is
            :math:`f = \sum\limits_{i=1}^N w_i`, where
            :math:`\sum\limits_{i=1}^N` is the sum over :math:`N` particles
            in that bin,
            :math:`w_i` denotes the weight of the ith particle.

        * ``<reduced_diags_name>.bin_number`` (`int` > 0)
            This is the number of bins used for the histogram.

        * ``<reduced_diags_name>.bin_max`` (`float`)
            This is the maximum value of the bins.

        * ``<reduced_diags_name>.bin_min`` (`float`)
            This is the minimum value of the bins.

        * ``<reduced_diags_name>.normalization`` (optional)
            This provides options to normalize the histogram:

            ``unity_particle_weight``
            uses unity particle weight to compute the histogram,
            such that the values of the histogram are
            the number of counted macroparticles in that bin,
            i.e.  :math:`f = \sum\limits_{i=1}^N 1`,
            :math:`N` is the number of particles in that bin.

            ``max_to_unity`` will normalize the histogram such that
            its maximum value is one.

            ``area_to_unity`` will normalize the histogram such that
            the area under the histogram is one,
            so the histogram is also the probability density function.

            If nothing is provided,
            the macroparticle weight will be used to compute
            the histogram, and no normalization will be done.

        The output columns are
        values of the 1st bin, the 2nd bin, ..., the nth bin.
        An example input file and a loading pything script of
        using the histogram reduced diagnostics
        are given in ``Examples/Tests/initial_distribution/``.

* ``<reduced_diags_name>.frequency`` (`int`)
    The output frequency (every # time steps).

* ``<reduced_diags_name>.path`` (`string`) optional (default `./diags/reducedfiles/`)
    The path that the output file will be stored.

* ``<reduced_diags_name>.extension`` (`string`) optional (default `txt`)
    The extension of the output file.

* ``<reduced_diags_name>.separator`` (`string`) optional (default a `whitespace`)
    The separator between row values in the output file.
    The default separator is a whitespace.

Lookup tables and other settings for QED modules (implementation in progress)
----------------------------------------------------------
Lookup tables store pre-computed values for functions used by the QED modules.
**Implementation of this feature is in progress. It requires `picsar` on the `QED` branch and to compile with QED=TRUE**

* ``qed_bw.lookup_table_mode`` (`string`)
    There are three options to prepare the lookup table required by the Breit-Wheeler module:

    * ``dummy_builtin``:  a built-in table is used (Warning: the quality of the table is very low,
      so this option has to be used only for test purposes).

    * ``generate``: a new table is generated. This option requires Boost math library
      (version >= 1.67) and to compile with QED_TABLE_GEN=TRUE. All
      the following parameters must be specified:

        * ``qed_bw.chi_min`` (`float`): minimum chi parameter to be considered by the engine

        * ``qed_bw.tab_dndt_chi_min`` (`float`): minimum chi parameter for lookup table 1 (
          used for the evolution of the optical depth of the photons)

        * ``qed_bw.tab_dndt_chi_max`` (`float`): maximum chi parameter for lookup table 1

        * ``qed_bw.tab_dndt_how_many`` (`int`): number of points to be used for lookup table 1

        * ``qed_bw.tab_pair_chi_min`` (`float`): minimum chi parameter for lookup table 2 (
          used for pair generation)

        * ``qed_bw.tab_pair_chi_max`` (`float`): maximum chi parameter for lookup table 2

        * ``qed_bw.tab_pair_chi_how_many`` (`int`): number of points to be used for chi axis in lookup table 2

        * ``qed_bw.tab_pair_frac_how_many`` (`int`): number of points to be used for the second axis in lookup table 2
          (the second axis is the ratio between the energy of the less energetic particle of the pair and the
          energy of the photon).

        * ``qed_bw.save_table_in`` (`string`): where to save the lookup table

    * ``load``: a lookup table is loaded from a pre-generated binary file. The following parameter
      must be specified:

        * ``qed_bw.load_table_from`` (`string`): name of the lookup table file to read from.

* ``qed_qs.lookup_table_mode`` (`string`)
    There are three options to prepare the lookup table required by the Quantum Synchrotron module:

    * ``dummy_builtin``:  a built-in table is used (Warning: the quality of the table is very low,
      so this option has to be used only for test purposes).

    * ``generate``: a new table is generated. This option requires Boost math library
      (version >= 1.67) and to compile with QED_TABLE_GEN=TRUE. All
      the following parameters must be specified:

        * ``qed_qs.chi_min`` (`float`): minimum chi parameter to be considered by the engine

        * ``qed_qs.tab_dndt_chi_min`` (`float`): minimum chi parameter for lookup table 1 (
          used for the evolution of the optical depth of electrons and positrons)

        * ``qed_qs.tab_dndt_chi_max`` (`float`): maximum chi parameter for lookup table 1

        * ``qed_qs.tab_dndt_how_many`` (`int`): number of points to be used for lookup table 1

        * ``qed_qs.tab_em_chi_min`` (`float`): minimum chi parameter for lookup table 2 (
          used for photon emission)

        * ``qed_qs.tab_em_chi_max`` (`float`): maximum chi parameter for lookup table 2

        * ``qed_qs.tab_em_chi_how_many`` (`int`): number of points to be used for chi axis in lookup table 2

        * ``qed_qs.tab_em_prob_how_many`` (`int`): number of points to be used for the second axis in lookup table 2
          (the second axis is a cumulative probability).

        * ``qed_bw.save_table_in`` (`string`): where to save the lookup table

    * ``load``: a lookup table is loaded from a pre-generated binary file. The following parameter
      must be specified:

        * ``qed_qs.load_table_from`` (`string`): name of the lookup table file to read from.

* ``qed_qs.photon_creation_energy_threshold`` (`float`) optional (default `2*me*c^2`)
    Energy threshold for photon particle creation in SI units.

Checkpoints and restart
-----------------------
WarpX supports checkpoints/restart via AMReX.

* ``amr.check_int`` (`integer`)
    The number of iterations between two consecutive checkpoints. Use a
    negative number to disable checkpoints.

* ``amr.restart`` (`string`)
    Name of the checkpoint file to restart from. Returns an error if the folder does not exist
    or if it is not properly formatted.