treelmesh_module

TREe based ELemental Mesh module, providing the definition and methods to act on a octree based mesh.

The mesh may either be externally generated by seeder or some simple mesh configurations can also be created internally. In case of an external mesh from seeder, the directory containing the mesh needs to be provided in the configuration:

  mesh = '/path/to/mesh/'

Note that the string provided here is used as a prefix. Thus, if the mesh is in a directory it needs to end in a path seperator. The default is 'mesh/', which results in the application to look for the mesh in the mesh subdirectory in the working directory of the application.

Internal meshes are defined in a table, where the first option describes which of the predefined meshes is to be generated, then there needs to be a definition of the universe (or root) cube within which the octree lives. This is given by an origin and then the length by which it extends along each axis. Further options may be required by the respective predefined mesh types. An example for a fully periodic uniform cubical mesh:

  mesh = {
    predefined = 'cube',
    origin = {0., 0., 0.},
    length = 10.,
    refinementLevel = 4
  }

The following predefined meshes are available:

'cube' create a fully periodic cube without boundary conditions and uniform element sizes by refining the root element (universe). For this kind of mesh you need to provide an refinementLevel which defines how often the encompassing cube should be bisected in each dimension leading to meshes with 8^refinementLevel elements.
'slice' create a slice of the fully periodic cube with uniform elements. For the slice you need to provide the refinementLevel, as for the cube. The resulting mesh will consist of 4^refinementLevel elements.
'line' creates a periodic line. For this kind of mesh it is possible to specify either an refinementLevel to create meshes with 2^refinementLevel elements, or the number of elements in the mesh by setting element_count.
'line_bounded' create a line with boundary conditions in west (on the left) and east (on the right). For this mesh the length needs to be defined by element_count.

The mesh is stored in treelmesh_type. The definition is designed to be used for parallel executions. It includes a reference to tem_global_type and the number of elements, which were loaded on the local partition, as well as the first and last tree ID of each partition in the current communicator. This enables the determination of any tree ID's position among the processes, independent of their actual existence. This is important to identify the location of neighbor elements when creating connectivity lists for the linearized element lists locally on each process within the solvers.

apes_schematic

Uses

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Graph Key

Nodes of different colours represent the following:

Solid arrows point from a submodule to the (sub)module which it is descended from. Dashed arrows point from a module or program unit to modules which it uses.

Used by

treelmesh_module		w	hvs_ascii_module
		w
		w	hvs_output_module
		w
		w	hvs_vtk_module
		w
		w	hvs_vtk_module
		w
		w	tem_adaptation_module
		w
		w	tem_bc_prop_module
		w
		w	tem_canonicalND_module
		w
		w	tem_color_prop_module
		w
		w	tem_construction_module
		w
		w	tem_convergence_module
		w
		w	tem_cube_module
		w
		w	tem_face_module
		w
		w	tem_geometry_module
		w
		w	tem_interpolation_module
		w
		w	tem_intersection_module
		w
		w	tem_logical_operation_var_module
		w
		w	tem_meshInfo_module
		w
		w	tem_operation_var_module
		w
		w	tem_pointData_module
		w
		w	tem_reduction_spatial_module
		w
		w	tem_refining_module
		w
		w	tem_restart_module
		w
		w	tem_shape_module
		w
		w	tem_spacetime_fun_module
		w
		w	tem_spacetime_var_module
		w
		w	tem_spatial_module
		w
		w	tem_spongeLayer_module
		w
		w	tem_subres_prop_module
		w
		w	tem_subTree_module
		w
		w	tem_subTree_type_module
		w
		w	tem_surfaceData_module
		w
		w	tem_tracking_module
		w
	w	tem_varSys_module
	w
	w	tem_vrtx_module
	w

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Derived Types

type, public :: treelmesh_type

declaration of the overall mesh on the local partition

Components

Type	Visibility	Attributes		Name		Initial
type(tem_global_type),	public		::	global			This entry provides some global informations on the mesh, which is needed across all partitions.
integer,	public		::	nElems
integer(kind=long_k),	public		::	elemOffset
integer(kind=long_k),	public,	allocatable	::	Part_First(:)			List of treeIDs of the first element on each partition, has a length of global%nParts
integer(kind=long_k),	public,	allocatable	::	Part_Last(:)			List of treeIDs of the last element on each partition, has a length of global%nParts
integer(kind=long_k),	public,	allocatable	::	treeID(:)			The treeIDs of each element (the array has a length of nElems) these IDs identify the element in the complete mesh, with a breadth-first numbering scheme. Allowing easy computation of parents and children. [treeid] \ref treeID Read more…
integer(kind=long_k),	public,	allocatable	::	ElemPropertyBits(:)			Bit field of element properties for each element (the array has a length of nElems), each bit in the 8 byte integer indicates the presence or absence of a given property, which are further described in the Property component. Read more…
type(tem_property_type),	public,	pointer	::	Property(:)	=>	null()	declaration of additional elemental properties, the array has a length of global%nProperties, each property provides a list of local element indices of elements with this property.
type(tem_path_type),	public,	allocatable	::	pathList(:)			Path for all elements in the treeID array
character(len=pathLen),	public		::	weights_file	=	''	Name of the file that contains weight information for each element to allow load balancing. If empty string, balancing will be deactivated.
character(len=pathLen),	public		::	write_weights			File to write weights to after simulation. Defaults to the same name as weights_file, if you do not want to have the input file overwritten, you can provide a different file to write to by setting write_weights accordingly in the configuration.
real(kind=rk),	public		::	levelWeight(globalMaxLevels)			Level weights as provided by the solver.

Functions

private function tem_CoordOf_2d_Id(Id2d, level) result(coord)

Arguments

Type	Intent	Optional	Attributes		Name
integer(kind=long_k),	intent(in)			::	Id2d	input element ID
integer,	intent(in)			::	level

Return Value integer, (4)

coordinate of element return value

Subroutines

public subroutine load_tem(me, conf, myPart, nParts, comm, levelWeight, meshDir, parent)

Load the treelmesh

Arguments

Type	Intent	Optional		Name
type(treelmesh_type),	intent(out)		::	me	Structure to load the mesh to
type(flu_State)			::	conf	Directory containing the mesh informations
integer,	intent(in)		::	myPart	Partition to use on the calling process (= MPI Rank in comm)
integer,	intent(in)		::	nParts	Number of partitions, the mesh is partitioned into (= Number of MPI processes in comm).
integer,	intent(in)		::	comm	MPI Communicator to use now defaults to the one given in the tree%global%comm
real(kind=rk),	intent(in),	optional	::	levelWeight(globalMaxLevels)	Balancing weight for elements on different levels. If these weights are present, the mesh is partitioned initially according to the given weights. This can not be combined with given offsets. If offset is also provided they will overwrite the levelWeight distribution.
character(len=*),	intent(out),	optional	::	meshDir	output Mesh directory name
integer,	intent(in),	optional	::	parent	optional parent handle

public subroutine unload_treelmesh(me)

Unload the treelmesh

Arguments

Type	Intent	Optional	Attributes		Name
type(treelmesh_type),	intent(inout)			::	me	Structure to load the mesh to

public subroutine free_treelmesh(me)

Completely free the memory of the treelmesh again.

Arguments

Type	Intent	Optional	Attributes		Name
type(treelmesh_type),	intent(inout)			::	me	Structure to free

public subroutine tem_load_internal(me, conf, thandle, myPart, nParts, comm)

Load an internally generated mesh

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(out)	::	me	Structure to load the mesh to
type(flu_State)		::	conf	Directory containing the mesh informations
integer,	intent(in)	::	thandle	Handle for the table to read the description of the mesh from.
integer,	intent(in)	::	myPart	Partition to use on the calling process (= MPI Rank in comm)
integer,	intent(in)	::	nParts	Number of partitions, the mesh is partitioned into (= Number of MPI processes in comm).
integer,	intent(in)	::	comm	MPI Communicator to use

public subroutine load_treelmesh(me, nParts)

This subroutine reads a mesh in treelm format from disk at the specified directory name.

Arguments

Type	Intent	Optional	Attributes		Name
type(treelmesh_type),	intent(inout)			::	me	Structure to load the mesh to
integer,	intent(in)			::	nParts	Directory containing the mesh informations Partition to use on the calling process (= MPI Rank in comm) Number of partitions, the mesh is partitioned into (= Number of MPI processes in comm).

public subroutine dump_treelmesh(me, root_only)

Write a given mesh to disk. it is stored to the directory given in the tem_global_type.

Arguments

Type	Intent	Optional	Attributes		Name
type(treelmesh_type),	intent(inout)			::	me	Mesh to dump to disk
logical,	intent(in),	optional		::	root_only	root dump global mesh when true and all process dump its own mesh when false

public subroutine generate_treelm_cube(me, origin, length, level, myPart, nParts, comm)

G e n e r a t e

p r e d e f i n e d

c u b e

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(out)	::	me	Mesh to generate
real(kind=rk),	intent(in)	::	origin(3)	Corner of the cube
real(kind=rk),	intent(in)	::	length	Length of cube
integer,	intent(in)	::	level	Resolution level
integer,	intent(in)	::	myPart	Partition of the caller (starts with 0)
integer,	intent(in)	::	nParts	Number of partitions
integer,	intent(in)	::	comm	communicator to be used

public subroutine treelmesh_fromList(me, tIDlist, comm, dirname)

This subroutine creates a simple mesh based on a treeID list requires the setting of me%global before hand Works on the communicator specified in me%global%comm

Arguments

Type	Intent	Optional		Name
type(treelmesh_type),	intent(inout)		::	me	Structure to load the mesh to
integer(kind=long_k),	intent(in)		::	tIDlist(:)	treeID list to generate the global list in the mesh from
integer,	intent(in),	optional	::	comm	MPI Communicator to use, defaults to the one in me%global%comm if not specified
character(len=*),	intent(in),	optional	::	dirname	Directory to store the mesh in. Is taken to be me%global%dirname if not specified

public subroutine dump_meshHeader(me)

write mesh information

Arguments

Type	Intent	Optional	Attributes		Name
type(treelmesh_type),	intent(in)			::	me	fluid tree from mesh

public subroutine tem_load_weights(me, weights, success)

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(in)	::	me
real(kind=rk),	intent(out)	::	weights(me%nElems)
logical,	intent(out)	::	success

public subroutine tem_dump_weights(me, filename, weights)

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(in)	::	me
character(len=*),	intent(in)	::	filename	Weights file name
real(kind=rk),	intent(in)	::	weights(me%nElems)

public subroutine exchange_elements(me, sparta)

Exchange mesh elements with other process The following data within treelmesh_type is updated in this routine: treeID, ElemPropertyBits, Part_First, Part_Last Data pathList is deallocated.

Arguments

Type	Intent	Optional	Attributes		Name
type(treelmesh_type),	intent(inout)			::	me	Tree Mesh type nElems and offset should be ready before this routine
type(tem_sparta_type),	intent(in)			::	sparta	How many elements to exchange with other processes

private subroutine generate_treelm_slice(me, origin, length, level, myPart, nParts, comm)

G e n e r a t e

p r e d e f i n e d

s l i c e

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(out)	::	me	Mesh to generate
real(kind=rk),	intent(in)	::	origin(3)	Corner of the cube
real(kind=rk),	intent(in)	::	length	Length of cube
integer,	intent(in)	::	level	Resolution level
integer,	intent(in)	::	myPart	Partition of the caller (starts with 0)
integer,	intent(in)	::	nParts	Number of partitions
integer,	intent(in)	::	comm	communicator to be used

private subroutine generate_treelm_line(me, origin, length, level, myPart, nParts, comm)

G e n e r a t e

p r e d e f i n e d

l i n e

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(out)	::	me	Mesh to generate
real(kind=rk),	intent(in)	::	origin(3)	Corner of the cube
real(kind=rk),	intent(in)	::	length	Length of cube
integer,	intent(in)	::	level	Resolution level
integer,	intent(in)	::	myPart	Partition of the caller (starts with 0)
integer,	intent(in)	::	nParts	Number of partitions
integer,	intent(in)	::	comm	communicator to be used

private subroutine generate_treelm_elements(me, origin, length, elementcount, myPart, nParts, comm, predefined, bclabel)

Generate a predefined line with a given number of elements

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(out)	::	me	Mesh to generate
real(kind=rk),	intent(in)	::	origin(3)	Corner of the cube
real(kind=rk),	intent(in)	::	length	Length of cube
integer,	intent(in)	::	elementcount	Number of elements in the line
integer,	intent(in)	::	myPart	Partition of the caller (starts with 0)
integer,	intent(in)	::	nParts	Number of partitions
integer,	intent(in)	::	comm	communicator to be used
character(len=*),	intent(in)	::	predefined	Label describing the internal mesh.
character(len=*),	intent(in)	::	bclabel	Label describing the boundary conditions to set for this mesh.

private subroutine generate_treelm_single(me, origin, length, myPart, nParts, comm)

G e n e r a t e

p r e d e f i n e d

s i n g l e

e l e m e n t

Arguments

Type	Intent		Name
type(treelmesh_type),	intent(out)	::	me	Mesh to generate
real(kind=rk),	intent(in)	::	origin(3)	Corner of the cube
real(kind=rk),	intent(in)	::	length	Length of cube
integer,	intent(in)	::	myPart	Partition of the caller (starts with 0)
integer,	intent(in)	::	nParts	Number of partitions
integer,	intent(in)	::	comm	communicator to be used

treelmesh_module Module

Contents

Derived Types

Functions

Subroutines

Uses

Used by

Derived Types

type, public :: treelmesh_type

Components

Functions

private function tem_CoordOf_2d_Id(Id2d, level) result(coord)

Arguments

Return Value integer, (4)

Subroutines

public subroutine load_tem(me, conf, myPart, nParts, comm, levelWeight, meshDir, parent)

Arguments

public subroutine unload_treelmesh(me)

Arguments

public subroutine free_treelmesh(me)

Arguments

public subroutine tem_load_internal(me, conf, thandle, myPart, nParts, comm)

Arguments

public subroutine load_treelmesh(me, nParts)

Arguments

public subroutine dump_treelmesh(me, root_only)

Arguments

public subroutine generate_treelm_cube(me, origin, length, level, myPart, nParts, comm)

Arguments

public subroutine treelmesh_fromList(me, tIDlist, comm, dirname)

Arguments

public subroutine dump_meshHeader(me)

Arguments

public subroutine tem_load_weights(me, weights, success)

Arguments

public subroutine tem_dump_weights(me, filename, weights)

Arguments

public subroutine exchange_elements(me, sparta)

Arguments

private subroutine generate_treelm_slice(me, origin, length, level, myPart, nParts, comm)

Arguments

private subroutine generate_treelm_line(me, origin, length, level, myPart, nParts, comm)

Arguments

private subroutine generate_treelm_elements(me, origin, length, elementcount, myPart, nParts, comm, predefined, bclabel)

Arguments

private subroutine generate_treelm_single(me, origin, length, myPart, nParts, comm)

Arguments