m_a2_core Module Reference

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	a2_init (tree, n_cell, n_var_cell, n_var_face, dr, r_min, lvl_limit, n_boxes, coarsen_to, coord, cc_names, fc_names, mem_limit_gb)
	Initialize a 2d tree type. More...
subroutine, public	a2_set_cc_methods (tree, iv, bc, rb, prolong, restrict)
	Set the methods for a cell-centered variable. More...
subroutine, public	a2_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, public	a2_set_base (tree, n_boxes, ix_list, nb_list)
	Create the base level of the tree, ix_list(:, id) stores the spatial index of box(id), nb_list(:, id) stores the neighbors of box(id). The connection between neighbors is handled automatically, so only boundary conditions have to be specified. Periodic boundaries only have to be specified from one side. A default value of af_no_box in the nb_list is converted to a physical boundary with index of -1. More...
subroutine, public	a2_tidy_up (tree, max_hole_frac, n_clean_min)
	Reorder and resize the list of boxes. More...
subroutine	set_leaves_parents (boxes, level)
	Create a list of leaves and a list of parents for a level. More...
subroutine, public	a2_init_box (box, n_cell, n_cc, n_fc)
	Mark box as active and allocate data storage for a box, for its cell- and face-centered data. More...
subroutine, public	a2_resize_box_storage (tree, new_size)
	Resize box storage to new_size. More...
subroutine, public	a2_adjust_refinement (tree, ref_subr, ref_info, ref_buffer, keep_buffer)
	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	set_ref_info (tree, ref_flags, ref_info)
	Set information about the refinement for all "normal" levels (>= 1) More...
subroutine	cell_to_ref_flags (cell_flags, nc, ref_flags, tree, id, ref_buffer, keep_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 (boxes, id)
	Remove the children of box id. More...
subroutine, public	a2_consistent_fluxes (tree, f_ixs)
	Restrict fluxes from children to parents on refinement boundaries. 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

a2_init()

subroutine, public m_a2_core::a2_init	(	type(a2_t), intent(inout)	tree,
		integer, intent(in)	n_cell,
		integer, intent(in)	n_var_cell,
		integer, intent(in)	n_var_face,
		real(dp), intent(in)	dr,
		real(dp), dimension(2), intent(in), optional	r_min,
		integer, intent(in), optional	lvl_limit,
		integer, intent(in), optional	n_boxes,
		integer, intent(in), optional	coarsen_to,
		integer, intent(in), optional	coord,
		character(len=*), dimension(:), intent(in), optional	cc_names,
		character(len=*), dimension(:), intent(in), optional	fc_names,
		real(dp), intent(in), optional	mem_limit_gb
	)

Initialize a 2d tree type.

Parameters

[in,out]	tree	The tree to initialize
[in]	n_cell	Boxes have n_cell^dim cells
[in]	n_var_cell	Number of cell-centered variables
[in]	n_var_face	Number of face-centered variables
[in]	dr	spacing of a cell at lvl 1
[in]	r_min	Lowest coordinate of box at 1,1. Default is (0, 0)
[in]	coarsen_to	Create additional coarse grids down to this size. Default is -1 (which means don't do this)
[in]	lvl_limit	Maximum number of levels. Default is 30
[in]	n_boxes	Allocate initial storage for n_boxes. Default is 1000
[in]	coord	Select coordinate type
[in]	mem_limit_gb	Memory limit in GByte
[in]	cc_names	Names of cell-centered variables
[in]	fc_names	Names of face-centered variables

Todo:

remove subtree in future

Definition at line 25 of file m_a2_core.f90.

a2_set_cc_methods()

subroutine, public m_a2_core::a2_set_cc_methods	(	type(a2_t), intent(inout)	tree,
		integer, intent(in)	iv,
		procedure(a2_subr_bc)	bc,
		procedure(a2_subr_rb), optional	rb,
		procedure(a2_subr_prolong), optional	prolong,
		procedure(a2_subr_restrict), optional	restrict
	)

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

Definition at line 137 of file m_a2_core.f90.

a2_destroy()

subroutine, public m_a2_core::a2_destroy

(

type(a2_t), intent(inout)

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 175 of file m_a2_core.f90.

a2_set_base()

subroutine, public m_a2_core::a2_set_base	(	type(a2_t), intent(inout)	tree,
		integer, intent(in)	n_boxes,
		integer, dimension(2, n_boxes), intent(in)	ix_list,
		integer, dimension(a2_num_neighbors, n_boxes), intent(inout), optional	nb_list
	)

Create the base level of the tree, ix_list(:, id) stores the spatial index of box(id), nb_list(:, id) stores the neighbors of box(id). The connection between neighbors is handled automatically, so only boundary conditions have to be specified. Periodic boundaries only have to be specified from one side. A default value of af_no_box in the nb_list is converted to a physical boundary with index of -1.

Parameters

[in,out]	tree	Tree for which we set the base
[in]	n_boxes	Number of boxes on coarse grid
[in]	ix_list	List of spatial indices for the initial boxes
[in,out]	nb_list	Neighbors for the initial boxes

Definition at line 197 of file m_a2_core.f90.

a2_tidy_up()

subroutine, public m_a2_core::a2_tidy_up	(	type(a2_t), intent(inout)	tree,
		real(dp), intent(in)	max_hole_frac,
		integer, intent(in)	n_clean_min
	)

Reorder and resize the list of boxes.

Parameters

[in,out]	tree	The tree to tidy up
[in]	max_hole_frac	Maximum fraction of holes in boxes array
[in]	n_clean_min	Reorganize memory if at least this many boxes can be cleaned up

Definition at line 429 of file m_a2_core.f90.

set_leaves_parents()

subroutine m_a2_core::set_leaves_parents	(	type(box2_t), dimension(:), intent(in)	boxes,
		type(lvl_t), intent(inout)	level
	)

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 515 of file m_a2_core.f90.

a2_init_box()

subroutine, public m_a2_core::a2_init_box	(	type(box2_t), intent(inout)	box,
		integer, intent(in)	n_cell,
		integer, intent(in)	n_cc,
		integer, intent(in)	n_fc
	)

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

Parameters

[in,out]	box	Box for which we allocate memory
[in]	n_cell	Number of cells per dimension in the box
[in]	n_cc	Number of cell-centered variables
[in]	n_fc	Number of face-centered variables

Definition at line 550 of file m_a2_core.f90.

a2_resize_box_storage()

subroutine, public m_a2_core::a2_resize_box_storage	(	type(a2_t), intent(inout)	tree,
		integer, intent(in)	new_size
	)

Resize box storage to new_size.

Parameters

[in,out]	tree	Tree to resize
[in]	new_size	New size for the array boxes(:)

Definition at line 633 of file m_a2_core.f90.

a2_adjust_refinement()

subroutine, public m_a2_core::a2_adjust_refinement	(	type(a2_t), intent(inout)	tree,
		procedure(a2_subr_ref)	ref_subr,
		type(ref_info_t), intent(inout)	ref_info,
		integer, intent(in), optional	ref_buffer,
		logical, intent(in), optional	keep_buffer
	)

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]	keep_buffer	Use buffer for 'keep refinement' flags

Definition at line 659 of file m_a2_core.f90.

set_ref_info()

subroutine m_a2_core::set_ref_info	(	type(a2_t), intent(in)	tree,
		integer, dimension(:), intent(in)	ref_flags,
		type(ref_info_t), intent(inout)	ref_info
	)

Set information about the refinement for all "normal" levels (>= 1)

Definition at line 826 of file m_a2_core.f90.

cell_to_ref_flags()

subroutine m_a2_core::cell_to_ref_flags	(	integer, dimension(nc, nc), intent(in)	cell_flags,
		integer, intent(in)	nc,
		integer, dimension(:), intent(inout)	ref_flags,
		type(a2_t), intent(in)	tree,
		integer, intent(in)	id,
		integer, intent(in)	ref_buffer,
		logical, intent(in)	keep_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).

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
[in]	keep_buffer	Buffer around 'keep refinement' flags

Definition at line 1044 of file m_a2_core.f90.

remove_children()

subroutine m_a2_core::remove_children	(	type(box2_t), dimension(:), intent(inout)	boxes,
		integer, intent(in)	id
	)

Remove the children of box id.

Parameters

[in,out]	boxes	List of all boxes
[in]	id	Id of box whose children will be removed

Definition at line 1103 of file m_a2_core.f90.

a2_consistent_fluxes()

subroutine, public m_a2_core::a2_consistent_fluxes	(	type(a2_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 1199 of file m_a2_core.f90.