This module contains the core routines of Afivo, namely those that deal with initializing and changing the quadtree/octree mesh. More...

Functions/Subroutines
subroutine, public	af_add_cc_variable (tree, name, write_out, n_copies, ix, write_binary)
	Add cell-centered variable. More...

subroutine, public	af_add_fc_variable (tree, name, ix, write_binary)
	Add face-centered variable. More...

integer function, public	af_find_cc_variable (tree, name)
	Find index of cell-centered variable. More...

integer function, public	af_find_fc_variable (tree, name)
	Find index of face-centered variable. More...

subroutine, public	af_init (tree, n_cell, r_max, grid_size, periodic, r_min, coord, mem_limit_gb, box_limit)
	Initialize a NDIM-d octree/quadtree grid. More...

subroutine	af_set_coarse_grid (tree, coarse_grid_size, periodic_dims)
	Create the coarse grid. More...

subroutine, public	af_set_cc_methods (tree, iv, bc, rb, prolong, restrict, bc_custom, funcval, prolong_limiter)
	Set the methods for a cell-centered variable. More...

subroutine, public	af_destroy (tree)
	"Destroy" the data in a tree. Since we don't use pointers, you can also just let a tree get out of scope More...

subroutine	create_index_array (nx, periodic, id_array)
	Create an array for easy lookup of indices. More...

subroutine	set_leaves_parents (boxes, level)
	Create a list of leaves and a list of parents for a level. More...

subroutine, public	af_init_box (tree, id)
	Mark box as active and allocate data storage for a box, for its cell- and face-centered data. More...

subroutine	af_deactivate_box (box)
	Mark box as inactive, but keep storage for cell- and face-centered data to avoid reallocating this. More...

subroutine	set_neighbs (boxes, id)

integer function	find_neighb (boxes, id, dix)
	Get the id of all neighbors of boxes(id), through its parent. More...

subroutine, public	af_refine_up_to_lvl (tree, lvl)
	Refine a tree up to a given refinement lvl. More...

subroutine, public	af_adjust_refinement (tree, ref_subr, ref_info, ref_buffer, ref_links)
	Adjust the refinement of a tree using the user-supplied ref_subr. The optional argument ref_buffer controls over how many cells neighbors are affected by refinement flags. More...

subroutine	auto_restrict (tree, id)
	Try to automatically restrict to box with index id. More...

subroutine	auto_prolong (tree, ref_info)
	Try to automatically prolong to all new boxes. More...

subroutine	get_free_ids (tree, ids)
	Get free ids from the boxes(:) array to store new boxes in. These ids are always consecutive. More...

subroutine	consistent_ref_flags (tree, ref_flags, ref_subr, ref_buffer, ref_links)
	Given the refinement function, return consistent refinement flags, that ensure that the tree is still balanced. Furthermore, it cannot derefine the base level, and it cannot refine above af_max_lvl. The argument ref_flags is changed: for boxes that will be refined it holds af_refine, for boxes that will be derefined it holds af_derefine. More...

subroutine	ensure_two_one_balance (tree, ref_flags)
	Adjust refinement flags to ensure 2-1 balance is maintained. More...

subroutine	handle_derefinement_flags (tree, ref_flags)

subroutine	cell_to_ref_flags (cell_flags, nc, ref_flags, tree, id, ref_buffer)
	Given the cell refinement flags of a box, set the refinement flag for that box and potentially also its neighbors (in case of refinement near a boundary). More...

subroutine	remove_children (tree, id)
	Remove the children of box id. More...

subroutine	add_children (tree, id, c_ids)
	Add children to box id, using the indices in c_ids. More...

subroutine	set_child_ids (p_ids, c_ids, boxes)
	Create a list c_ids(:) of all the children of p_ids(:). This is used after a level has been refined. More...

subroutine, public	af_consistent_fluxes (tree, f_ixs)
	Restrict fluxes from children to parents on refinement boundaries. More...

subroutine	flux_from_children (boxes, id, nb, f_ixs)
	The neighbor nb has no children and id does, so set flux on the neighbor from our children. This ensures flux consistency at refinement boundary. More...

Detailed Description

This module contains the core routines of Afivo, namely those that deal with initializing and changing the quadtree/octree mesh.

Function/Subroutine Documentation

◆ af_add_cc_variable()

subroutine, public m_af_core::af_add_cc_variable	(	type(af_t), intent(inout)	tree,
		character(len=*), intent(in)	name,
		logical, intent(in), optional	write_out,
		integer, intent(in), optional	n_copies,
		integer, intent(out), optional	ix,
		logical, intent(in), optional	write_binary
	)

Add cell-centered variable.

Todo:: ix as third argument?

Parameters

[in,out]	tree	Tree to add variable to
[in]	name	Name of the variable
[in]	write_out	Include variable in output
[in]	write_binary	Include variable in binary output (for restarting)
[in]	n_copies	How many copies of variable to store (default: 1)
[out]	ix	On output: index of variable

Definition at line 26 of file m_af_core.f90.

◆ af_add_fc_variable()

subroutine, public m_af_core::af_add_fc_variable	(	type(af_t), intent(inout)	tree,
		character(len=*), intent(in)	name,
		integer, intent(out), optional	ix,
		logical, intent(in), optional	write_binary
	)

Add face-centered variable.

Parameters

[in,out]	tree	Tree to add variable to
[in]	name	Name of the variable
[out]	ix	On output: index of variable
[in]	write_binary	Include variable in binary output

Definition at line 76 of file m_af_core.f90.

◆ af_find_cc_variable()

integer function, public m_af_core::af_find_cc_variable	(	type(af_t), intent(in)	tree,
		character(len=*), intent(in)	name
	)

Find index of cell-centered variable.

Definition at line 102 of file m_af_core.f90.

◆ af_find_fc_variable()

integer function, public m_af_core::af_find_fc_variable	(	type(af_t), intent(in)	tree,
		character(len=*), intent(in)	name
	)

Find index of face-centered variable.

Definition at line 120 of file m_af_core.f90.

◆ af_init()

subroutine, public m_af_core::af_init	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	n_cell,
		real(dp), dimension(ndim), intent(in)	r_max,
		integer, dimension(ndim), intent(in)	grid_size,
		logical, dimension(ndim), intent(in), optional	periodic,
		real(dp), dimension(ndim), intent(in), optional	r_min,
		integer, intent(in), optional	coord,
		real(dp), intent(in), optional	mem_limit_gb,
		integer, intent(in), optional	box_limit
	)

Initialize a NDIM-d octree/quadtree grid.

Parameters

[in,out]	tree	The tree to initialize
[in]	n_cell	Boxes have n_cell^dim cells
[in]	r_max	Maximal coordinates of the domain
[in]	grid_size	Size of the coarse grid
[in]	periodic	True for periodic dimensions
[in]	r_min	Lowest coordinate, default is (0., 0., 0.)
[in]	coord	Select coordinate type
[in]	mem_limit_gb	Memory limit in GByte
[in]	box_limit	Maximum number of boxes (overrides mem_limit_gb)

Definition at line 138 of file m_af_core.f90.

◆ af_set_coarse_grid()

subroutine m_af_core::af_set_coarse_grid	(	type(af_t), intent(inout)	tree,
		integer, dimension(ndim), intent(in)	coarse_grid_size,
		logical, dimension(ndim), intent(in), optional	periodic_dims
	)

private

Create the coarse grid.

Parameters

[in,out]	tree	Tree for which we set the base
[in]	coarse_grid_size	Size of coarse grid (in cells)
[in]	periodic_dims	Whether dimensions are periodic (default: false)

Definition at line 206 of file m_af_core.f90.

◆ af_set_cc_methods()

subroutine, public m_af_core::af_set_cc_methods	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	iv,
		procedure(af_subr_bc), optional	bc,
		procedure(af_subr_rb), optional	rb,
		procedure(af_subr_prolong), optional	prolong,
		procedure(af_subr_restrict), optional	restrict,
		procedure(af_subr_bc_custom), optional	bc_custom,
		procedure(af_subr_funcval), optional	funcval,
		integer, intent(in), optional	prolong_limiter
	)

Set the methods for a cell-centered variable.

Parameters

[in,out]	tree	Tree to operate on
[in]	iv	Index of variable
	bc	Boundary condition method
	rb	Refinement boundary method
	prolong	Prolongation method
	restrict	Restriction method
	bc_custom	Custom b.c. method
	funcval	Variable defined by function Type of limiter to use for prolongation (of values or ghost cells)

Definition at line 343 of file m_af_core.f90.

◆ af_destroy()

subroutine, public m_af_core::af_destroy ( type(af_t), intent(out) tree )

"Destroy" the data in a tree. Since we don't use pointers, you can also just let a tree get out of scope

Definition at line 431 of file m_af_core.f90.

◆ create_index_array()

subroutine m_af_core::create_index_array	(	integer, dimension(ndim), intent(in)	nx,
		logical, dimension(ndim), intent(in)	periodic,
		integer, dimension(dtimes(:)), intent(inout), allocatable	id_array
	)

private

Create an array for easy lookup of indices.

Definition at line 436 of file m_af_core.f90.

◆ set_leaves_parents()

subroutine m_af_core::set_leaves_parents	(	type(box_t), dimension(:), intent(in)	boxes,
		type(lvl_t), intent(inout)	level
	)

private

Create a list of leaves and a list of parents for a level.

Parameters

[in]	boxes	List of boxes
[in,out]	level	Level type which contains the indices of boxes

Definition at line 504 of file m_af_core.f90.

◆ af_init_box()

subroutine, public m_af_core::af_init_box	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	id
	)

Mark box as active and allocate data storage for a box, for its cell- and face-centered data.

Parameters

[in] id Box id

Definition at line 539 of file m_af_core.f90.

◆ af_deactivate_box()

subroutine m_af_core::af_deactivate_box ( type(box_t), intent(inout) box )

private

Mark box as inactive, but keep storage for cell- and face-centered data to avoid reallocating this.

Definition at line 583 of file m_af_core.f90.

◆ set_neighbs()

subroutine m_af_core::set_neighbs	(	type(box_t), dimension(:), intent(inout)	boxes,
		integer, intent(in)	id
	)

private

Definition at line 595 of file m_af_core.f90.

◆ find_neighb()

integer function m_af_core::find_neighb	(	type(box_t), dimension(:), intent(in)	boxes,
		integer, intent(in)	id,
		integer, dimension(ndim), intent(in)	dix
	)

private

Get the id of all neighbors of boxes(id), through its parent.

Parameters

[in]	boxes	List with all the boxes
[in]	id	Box whose neighbor we are looking for

Definition at line 636 of file m_af_core.f90.

◆ af_refine_up_to_lvl()

subroutine, public m_af_core::af_refine_up_to_lvl	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	lvl
	)

Refine a tree up to a given refinement lvl.

Parameters

[in,out]	tree	The tree to adjust
[in]	lvl	Refine up to this lvl

Definition at line 664 of file m_af_core.f90.

◆ af_adjust_refinement()

subroutine, public m_af_core::af_adjust_refinement	(	type(af_t), intent(inout)	tree,
		procedure(af_subr_ref)	ref_subr,
		type(ref_info_t), intent(inout)	ref_info,
		integer, intent(in), optional	ref_buffer,
		integer, dimension(:, :), intent(in), optional	ref_links
	)

Adjust the refinement of a tree using the user-supplied ref_subr. The optional argument ref_buffer controls over how many cells neighbors are affected by refinement flags.

On input, the tree should be balanced. On output, the tree is still balanced, and its refinement is updated (with at most one level per call).

Parameters

[in,out]	tree	The tree to adjust
	ref_subr	Refinement function
[in,out]	ref_info	Information about refinement
[in]	ref_buffer	Buffer width (in cells)
[in]	ref_links	Lists of linked boxes which should have the same refinement

Definition at line 697 of file m_af_core.f90.

◆ auto_restrict()

subroutine m_af_core::auto_restrict	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	id
	)

private

Try to automatically restrict to box with index id.

Definition at line 825 of file m_af_core.f90.

◆ auto_prolong()

subroutine m_af_core::auto_prolong	(	type(af_t), intent(inout)	tree,
		type(ref_info_t), intent(in)	ref_info
	)

private

Try to automatically prolong to all new boxes.

Definition at line 843 of file m_af_core.f90.

◆ get_free_ids()

subroutine m_af_core::get_free_ids	(	type(af_t), intent(inout)	tree,
		integer, dimension(:), intent(out)	ids
	)

Get free ids from the boxes(:) array to store new boxes in. These ids are always consecutive.

Parameters

[out] ids Array which will be filled with free box ids

Todo:: when doing AMR in parallel, perhaps move some of the code outside the critical construct

Definition at line 885 of file m_af_core.f90.

◆ consistent_ref_flags()

subroutine m_af_core::consistent_ref_flags	(	type(af_t), intent(inout)	tree,
		integer, dimension(:), intent(inout)	ref_flags,
		procedure(af_subr_ref)	ref_subr,
		integer, intent(in)	ref_buffer,
		integer, dimension(:, :), intent(in), optional	ref_links
	)

private

Given the refinement function, return consistent refinement flags, that ensure that the tree is still balanced. Furthermore, it cannot derefine the base level, and it cannot refine above af_max_lvl. The argument ref_flags is changed: for boxes that will be refined it holds af_refine, for boxes that will be derefined it holds af_derefine.

Parameters

[in,out]	tree	Tree for which we set refinement flags
[in,out]	ref_flags	List of refinement flags for all boxes(:)
	ref_subr	User-supplied refinement function.
[in]	ref_buffer	Buffer width (in cells)
[in]	ref_links	Lists of linked boxes which should have the same refinement

Definition at line 929 of file m_af_core.f90.

◆ ensure_two_one_balance()

subroutine m_af_core::ensure_two_one_balance	(	type(af_t), intent(inout)	tree,
		integer, dimension(:), intent(inout)	ref_flags
	)

Adjust refinement flags to ensure 2-1 balance is maintained.

Definition at line 1016 of file m_af_core.f90.

◆ handle_derefinement_flags()

subroutine m_af_core::handle_derefinement_flags	(	type(af_t), intent(inout)	tree,
		integer, dimension(:), intent(inout)	ref_flags
	)

private

Definition at line 1059 of file m_af_core.f90.

◆ cell_to_ref_flags()

subroutine m_af_core::cell_to_ref_flags	(	integer, dimension(dtimes(nc)), intent(in)	cell_flags,
		integer, intent(in)	nc,
		integer, dimension(:), intent(inout)	ref_flags,
		type(af_t), intent(in)	tree,
		integer, intent(in)	id,
		integer, intent(in)	ref_buffer
	)

private

Given the cell refinement flags of a box, set the refinement flag for that box and potentially also its neighbors (in case of refinement near a boundary).

Parameters

[in]	nc	n_cell for the box
[in]	cell_flags	Cell refinement flags
[in,out]	ref_flags	Box refinement flags for this thread
[in]	tree	Full tree
[in]	id	Which box is considered
[in]	ref_buffer	Buffer cells around refinement

Definition at line 1095 of file m_af_core.f90.

◆ remove_children()

subroutine m_af_core::remove_children	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	id
	)

Remove the children of box id.

Parameters

[in] id Id of box whose children will be removed

Definition at line 1151 of file m_af_core.f90.

◆ add_children()

subroutine m_af_core::add_children	(	type(af_t), intent(inout)	tree,
		integer, intent(in)	id,
		integer, dimension(af_num_children), intent(in)	c_ids
	)

private

Add children to box id, using the indices in c_ids.

Parameters

[in]	id	Id of box that gets children
[in]	c_ids	Free ids for the children

Definition at line 1188 of file m_af_core.f90.

◆ set_child_ids()

subroutine m_af_core::set_child_ids	(	integer, dimension(:), intent(in)	p_ids,
		integer, dimension(:), intent(inout), allocatable	c_ids,
		type(box_t), dimension(:), intent(in)	boxes
	)

private

Create a list c_ids(:) of all the children of p_ids(:). This is used after a level has been refined.

Parameters

[in]	p_ids	All the parents ids
[in,out]	c_ids	Output: all the children's ids
[in]	boxes	List of all the boxes

Definition at line 1237 of file m_af_core.f90.

◆ af_consistent_fluxes()

subroutine, public m_af_core::af_consistent_fluxes	(	type(af_t), intent(inout)	tree,
		integer, dimension(:), intent(in)	f_ixs
	)

Restrict fluxes from children to parents on refinement boundaries.

Parameters

[in,out]	tree	Tree to operate on
[in]	f_ixs	Indices of the fluxes

Definition at line 1257 of file m_af_core.f90.

◆ flux_from_children()

subroutine m_af_core::flux_from_children	(	type(box_t), dimension(:), intent(inout)	boxes,
		integer, intent(in)	id,
		integer, intent(in)	nb,
		integer, dimension(:), intent(in)	f_ixs
	)

private

The neighbor nb has no children and id does, so set flux on the neighbor from our children. This ensures flux consistency at refinement boundary.

Parameters

[in,out]	boxes	List of all the boxes
[in]	id	Id of box for which we set fluxes
[in]	nb	Direction in which fluxes are set
[in]	f_ixs	Indices of the fluxes

Definition at line 1286 of file m_af_core.f90.

Functions/Subroutines

Detailed Description

Function/Subroutine Documentation

◆ af_add_cc_variable()

◆ af_add_fc_variable()

◆ af_find_cc_variable()

◆ af_find_fc_variable()

◆ af_init()

◆ af_set_coarse_grid()

◆ af_set_cc_methods()

◆ af_destroy()

◆ create_index_array()

◆ set_leaves_parents()

◆ af_init_box()

◆ af_deactivate_box()

◆ set_neighbs()

◆ find_neighb()

◆ af_refine_up_to_lvl()

◆ af_adjust_refinement()

◆ auto_restrict()

◆ auto_prolong()

◆ get_free_ids()

◆ consistent_ref_flags()

◆ ensure_two_one_balance()

◆ handle_derefinement_flags()

◆ cell_to_ref_flags()

◆ remove_children()

◆ add_children()

◆ set_child_ids()

◆ af_consistent_fluxes()

◆ flux_from_children()