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

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

.. warning::

   This section is currently in development.


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

* ``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.

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_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.

* ``warpx.n_current_deposition_buffer`` (`integer`)
    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 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.

* ``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.

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

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>.charge`` (`float`)
    The charge of one `physical` particle of this species.

* ``<species_name>.mass`` (`float`)
    The mass of one `physical` particle of this species.

* ``<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``.

    * ``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`),
      and optional argument ``<species_name>.do_symmetrize`` (whether to
      symmetrize the beam in the x and y directions).

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

* ``<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.

* ``<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``.

    * ``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 linear 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 linear 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 linear 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>.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_boosted_frame_diags`` (`0` or `1` optional, default `1`)
    Only used when ``warpx.do_boosted_frame_diagnostic=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).

* ``<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`).

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.

*  ``<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`)

* ``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``.

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``.

* ``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:

     - ``standard``: gathers directly from the grid points (either staggered
       or nodal gridpoints depending on ``warpx.do_nodal``).

* ``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>`__)

     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.hybrid_mpi_decomposition`` (`0` or `1`; default: 0)
    Whether to use a different MPI decomposition for the particle-grid operations
    (deposition and gather) and for the PSATD solver. If `1`, the FFT will
    be performed over MPI groups.

* ``psatd.ngroups_fft`` (`integer`)
    The number of MPI groups that are created for the FFT, when using the code compiled with a PSATD solver
    (and only if `hybrid_mpi_decomposition` is `1`).
    The FFTs are global within one MPI group and use guard cell exchanges in between MPI groups.
    (If ``ngroups_fft`` is larger than the number of MPI ranks used,
    than the actual number of MPI ranks is used instead.)

* ``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.

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`)
    The number of PIC cycles inbetween two consecutive data dumps. Use a
    negative number to disable data dumping.

* ``warpx.dump_plotfiles`` (`0` or `1`) optional
    Whether to dump the simulation data in
    `AMReX plotfile <https://amrex-codes.github.io/amrex/docs_html/IO.html>`__
    format. This is ``1`` by default, unless WarpX is compiled with openPMD support.

* ``warpx.dump_openpmd`` (`0` or `1`) optional
    Whether to dump the simulation data in
    `openPMD <https://github.com/openPMD>`__ format.
    When WarpX is compiled with openPMD support, this is ``1`` by default.

* ``warpx.openpmd_backend`` (``h5``, ``bp`` or ``json``) optional
    I/O backend for
    `openPMD <https://github.com/openPMD>`__ dumps.
    When WarpX is compiled with openPMD support, this is ``h5`` by default.
    ``json`` only works with serial/single-rank jobs.

* ``warpx.do_boosted_frame_diagnostic`` (`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_boosted_frame_diagnostic`` is ``1``.
    The number of lab-frame snapshots that will be written.

* ``warpx.dt_snapshots_lab`` (`float`, in seconds)
    Only used when ``warpx.do_boosted_frame_diagnostic`` 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_boosted_frame_diagnostic`` 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_boosted_frame_fields`` (`0 or 1`)
    Whether to use the **back-transformed diagnostics** for the fields.

* ``warpx.boosted_frame_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.boosted_frame_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.

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.