Using a standard seed

Initial seeds in the form of line segments are supported. These seeds can be defined with the following parameters, where N refers to the number of seeds the user wants to define:

name	value	description
`seed_density`	N * real	Maximum density for the seed (in 1/m3)
`seed_rel_r0`	N * NDIM reals	relative start position (between 0 and 1)
`seed_rel_r1`	N * NDIM reals	relative end position (between 0 and 1)
`seed_charge_type`	N * integer	0 for neutral, 1 for positive ions, -1 for electrons
`seed_falloff`	N * string	Fall-off type for seed (sigmoid, gaussian, smoothstep, step, laser)
`seed_width`	N * real	Seed decay width (m)

Other settings that control the initial conditions are:

name	value	description
`background_density`	real	The background ion and electron density (1/m3)

Defining custom initial conditions

To define custom initial conditions, specify the following in your m_user.f90 file:

user_initial_conditions => my_init_cond

where my_init_cond is a routine (see m_user_methods::user_initial_conditions) that can modify the initial state in any way you like.

Finding the index of a species

To set the value of a particular species, first find its index with

i_species = af_find_cc_variable(tree, "species_name")

then you can for example set species density to zero (in 2D) with

box%cc(:, :, i_species) = 0.0_dp

Using a static grid for a specific region in the domain

The user can specify a specific region of the domain to have fixed grid spacing. The following flags are utilized for that purpose:

refine_regions_dr - equate to the value you want the minimum grid spacing in the region to be
refine_regions_rmin - mark the starting boundary of the region you want to have a static grid
refine_regions_rmax - mark the closing boundary of the region you want to have a static grid

The flag refine_regions_rmin should have two values if working in a two dimensional domain and three values if in a three dimensional domain. The same is the case for refine_regions_rmax. The values are separated by spaces. For example, having refine_regions_rmin = 0.0 0.0 and refine_regions_rmax = 6.0e-4 5.0e-2 in a cylindrically symmetric simulation corresponds to the region bounded by the lines r = 0.0, z = 0.0, r = 6.0e-4, and z = 5.0e-2.