mesh_oct_m Module Reference

This module defines the meshes, which are used in Octopus. More...

Detailed Description

This module defines the meshes, which are used in Octopus.

Data Types
type	mesh_line_t
	This data type defines a line, and a regular grid defined on this line (or rather, on a portion of this line). NB: only works for 2D grids. More...
type	mesh_plane_t
	define a grid on a plane. More...
type	mesh_t
	Describes mesh distribution to nodes. More...

Functions/Subroutines
subroutine	mesh_init (this)
subroutine, public	mesh_double_box (space, mesh, alpha, db)
	finds the dimension of a box doubled in the non-periodic dimensions More...
subroutine, public	mesh_write_info (this, iunit, namespace)
pure subroutine, public	mesh_r (mesh, ip, rr, origin, coords)
	return the distance to the origin for a given grid point More...
subroutine	mesh_r_global (mesh, ipg, rr, origin, coords)
	return the distance to the origin for a given grid point More...
integer function, public	mesh_nearest_point (mesh, pos, dmin, rankmin)
	Returns the index of the point which is nearest to a given vector position pos. More...
subroutine, public	mesh_discretize_values_to_mesh (mesh, values)
	Assign a set of values to their nearest discrete points on the mesh. More...
real(real64) function, public	mesh_gcutoff (mesh)
	mesh_gcutoff returns the "natural" band limitation of the grid mesh, in terms of the maximum G vector. For a cubic regular grid, it is M_PI/spacing. More...
subroutine, public	mesh_write_fingerprint (mesh, dir, filename, mpi_grp, namespace, ierr)
subroutine, public	mesh_read_fingerprint (mesh, dir, filename, mpi_grp, namespace, read_np_part, read_np, bits, type, offset, nn, ierr)
	This function reads the fingerprint of a mesh written in filename. If the meshes are equal (same fingerprint) return values are 0, otherwise it returns the size of the mesh stored. fingerprint cannot be read, it returns ierr /= 0. More...
subroutine, public	mesh_check_dump_compatibility (mesh, dir, filename, namespace, mpi_grp, grid_changed, grid_reordered, map, ierr)
recursive subroutine, public	mesh_end (this)
integer(int64) function, public	mesh_periodic_point (mesh, space, ip)
	This function returns the point inside the grid corresponding to a boundary point when PBCs are used. In case the point does not have a correspondence (i.e. other BCs are used in that direction), the same point is returned. Note that this function returns a global point number when parallelization in domains is used. More...
integer(int64) function, public	mesh_periodic_point_global (mesh, space, ipg_in)
real(real64) pure function, public	mesh_global_memory (mesh)
real(real64) pure function, public	mesh_local_memory (mesh)
real(real64) function, dimension(1:mesh%box%dim), public	mesh_x_global (mesh, ipg)
	Given a global point index, this function returns the coordinates of the point. More...
subroutine, public	mesh_check_symmetries (mesh, symm, periodic_dim)
integer(int64) function, public	mesh_global_index_from_coords (mesh, ix)
	This function returns the true global index of the point for a given vector of integer coordinates. More...
subroutine, public	mesh_global_index_to_coords (mesh, ipg, ix)
	Given a global point index, this function returns the set of integer coordinates of the point. More...
integer function, public	mesh_local_index_from_coords (mesh, ix)
	This function returns the local index of the point for a given vector of integer coordinates. More...
subroutine, public	mesh_local_index_to_coords (mesh, ip, ix)
	Given a local point index, this function returns the set of integer coordinates of the point. More...
integer(int64) function, public	mesh_local2global (mesh, ip)
	This function returns the global mesh index for a given local index. More...
integer function, public	mesh_global2local (mesh, ipg)
	This function returns the local mesh index for a given global index. More...
subroutine, public	mesh_minmaxloc (mesh, min_or_max, rank_min_or_max, op)
	Given a local min/max this returns the global min/max and the rank where this is located. More...
real(real64) function, dimension(space%dim)	mesh_red_min (mesh, space)
	Helper routine to compute the minimal index of the mesh in reduced coordinate. More...
subroutine	dmesh_allreduce_0 (mesh, aa)
subroutine	dmesh_allreduce_1 (mesh, aa, dim)
subroutine	dmesh_allreduce_2 (mesh, aa, dim)
subroutine	dmesh_allreduce_3 (mesh, aa, dim)
subroutine	dmesh_allreduce_4 (mesh, aa)
subroutine	dmesh_allreduce_5 (mesh, aa)
subroutine	dmesh_allreduce_6 (mesh, aa)
subroutine	zmesh_allreduce_0 (mesh, aa)
subroutine	zmesh_allreduce_1 (mesh, aa, dim)
subroutine	zmesh_allreduce_2 (mesh, aa, dim)
subroutine	zmesh_allreduce_3 (mesh, aa, dim)
subroutine	zmesh_allreduce_4 (mesh, aa)
subroutine	zmesh_allreduce_5 (mesh, aa)
subroutine	zmesh_allreduce_6 (mesh, aa)
subroutine	imesh_allreduce_0 (mesh, aa)
subroutine	imesh_allreduce_1 (mesh, aa, dim)
subroutine	imesh_allreduce_2 (mesh, aa, dim)
subroutine	imesh_allreduce_3 (mesh, aa, dim)
subroutine	imesh_allreduce_4 (mesh, aa)
subroutine	imesh_allreduce_5 (mesh, aa)
subroutine	imesh_allreduce_6 (mesh, aa)
subroutine	lmesh_allreduce_0 (mesh, aa)
subroutine	lmesh_allreduce_1 (mesh, aa, dim)
subroutine	lmesh_allreduce_2 (mesh, aa, dim)
subroutine	lmesh_allreduce_3 (mesh, aa, dim)
subroutine	lmesh_allreduce_4 (mesh, aa)
subroutine	lmesh_allreduce_5 (mesh, aa)
subroutine	lmesh_allreduce_6 (mesh, aa)

Function/Subroutine Documentation

mesh_init()

subroutine mesh_oct_m::mesh_init ( class(mesh_t), intent(inout)  this )

private

Definition at line 277 of file mesh.F90.

mesh_double_box()

subroutine, public mesh_oct_m::mesh_double_box	(	class(space_t), intent(in)	space,
		type(mesh_t), intent(in)	mesh,
		real(real64), intent(in)	alpha,
		integer, dimension(:), intent(out), contiguous	db
	)

finds the dimension of a box doubled in the non-periodic dimensions

Parameters

[in]

alpha

enlargement factor for double box

Definition at line 289 of file mesh.F90.

mesh_write_info()

subroutine, public mesh_oct_m::mesh_write_info	(	class(mesh_t), intent(in)	this,
		integer, intent(in), optional	iunit,
		type(namespace_t), intent(in), optional	namespace
	)

Definition at line 314 of file mesh.F90.

mesh_r()

pure subroutine, public mesh_oct_m::mesh_r	(	class(mesh_t), intent(in)	mesh,
		integer, intent(in)	ip,
		real(real64), intent(out)	rr,
		real(real64), dimension(:), intent(in), optional	origin,
		real(real64), dimension(:), intent(out), optional	coords
	)

return the distance to the origin for a given grid point

Parameters

[in]	ip	point index
[out]	rr	distance with respect to the origin as given by the next parameter
[in]	origin	origin(sbdim), default (0,0,0)
[out]	coords	coords(sbdim), optional output of shifted coordinates

Definition at line 346 of file mesh.F90.

mesh_r_global()

subroutine mesh_oct_m::mesh_r_global ( class(mesh_t), intent(in)  mesh, integer(int64), intent(in)  ipg, real(real64), intent(out)  rr, real(real64), dimension(:), intent(in), optional, contiguous  origin, real(real64), dimension(:), intent(out), optional, contiguous  coords  )

private

return the distance to the origin for a given grid point

Parameters

[in]	ipg	global point index
[out]	rr	distance with respect to the origin as given by the next parameter
[in]	origin	origin(sbdim), default (0,0,0)
[out]	coords	coords(sbdim), optional output of shifted coordinates

Definition at line 366 of file mesh.F90.

mesh_nearest_point()

integer function, public mesh_oct_m::mesh_nearest_point	(	class(mesh_t), intent(in)	mesh,
		real(real64), dimension(:), intent(in)	pos,
		real(real64), intent(out)	dmin,
		integer, intent(out)	rankmin
	)

Returns the index of the point which is nearest to a given vector position pos.

Returns the index of the point, ind. This index is domain-specific, and is only meaningful rankmin.

Parameters

[in]	pos	Position vector
[out]	dmin	Distance between pos and this nearest mesh point
[out]	rankmin	Rank of the processor that holds the point

Definition at line 390 of file mesh.F90.

mesh_discretize_values_to_mesh()

subroutine, public mesh_oct_m::mesh_discretize_values_to_mesh	(	class(mesh_t), intent(in)	mesh,
		real(real64), dimension(:, :), intent(inout), contiguous	values
	)

Assign a set of values to their nearest discrete points on the mesh.

Parameters

[in]	mesh	mesh instance
[in,out]	values	In: Values of shape(dim, nvalues)

Definition at line 420 of file mesh.F90.

mesh_gcutoff()

real(real64) function, public mesh_oct_m::mesh_gcutoff

(

class(mesh_t), intent(in)

mesh

)

mesh_gcutoff returns the "natural" band limitation of the grid mesh, in terms of the maximum G vector. For a cubic regular grid, it is M_PI/spacing.

Definition at line 454 of file mesh.F90.

mesh_write_fingerprint()

subroutine, public mesh_oct_m::mesh_write_fingerprint	(	type(mesh_t), intent(in)	mesh,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	filename,
		type(mpi_grp_t), intent(in)	mpi_grp,
		type(namespace_t), intent(in)	namespace,
		integer, intent(out)	ierr
	)

Definition at line 464 of file mesh.F90.

mesh_read_fingerprint()

subroutine, public mesh_oct_m::mesh_read_fingerprint	(	type(mesh_t), intent(in)	mesh,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	filename,
		type(mpi_grp_t), intent(in)	mpi_grp,
		type(namespace_t), intent(in)	namespace,
		integer(int64), intent(out)	read_np_part,
		integer(int64), intent(out)	read_np,
		integer, intent(out)	bits,
		integer, intent(out)	type,
		integer, dimension(1:mesh%idx%dim), intent(out)	offset,
		integer, dimension(1:mesh%idx%dim), intent(out)	nn,
		integer, intent(out)	ierr
	)

This function reads the fingerprint of a mesh written in filename. If the meshes are equal (same fingerprint) return values are 0, otherwise it returns the size of the mesh stored. fingerprint cannot be read, it returns ierr /= 0.

Definition at line 512 of file mesh.F90.

mesh_check_dump_compatibility()

subroutine, public mesh_oct_m::mesh_check_dump_compatibility	(	type(mesh_t), intent(in)	mesh,
		character(len=*), intent(in)	dir,
		character(len=*), intent(in)	filename,
		type(namespace_t), intent(in)	namespace,
		type(mpi_grp_t), intent(in)	mpi_grp,
		logical, intent(out)	grid_changed,
		logical, intent(out)	grid_reordered,
		integer(int64), dimension(:), intent(out), allocatable	map,
		integer, intent(out)	ierr
	)

Definition at line 600 of file mesh.F90.

mesh_end()

recursive subroutine, public mesh_oct_m::mesh_end

(

class(mesh_t), intent(inout)

this

)

Definition at line 690 of file mesh.F90.

mesh_periodic_point()

integer(int64) function, public mesh_oct_m::mesh_periodic_point	(	class(mesh_t), intent(in)	mesh,
		class(space_t), intent(in)	space,
		integer, intent(in)	ip
	)

This function returns the point inside the grid corresponding to a boundary point when PBCs are used. In case the point does not have a correspondence (i.e. other BCs are used in that direction), the same point is returned. Note that this function returns a global point number when parallelization in domains is used.

Parameters

[in]

ip

local point for which periodic copy is searched

Definition at line 732 of file mesh.F90.

mesh_periodic_point_global()

integer(int64) function, public mesh_oct_m::mesh_periodic_point_global	(	class(mesh_t), intent(in)	mesh,
		class(space_t), intent(in)	space,
		integer(int64), intent(in)	ipg_in
	)

Parameters

[in]

ipg_in

local point for which periodic copy is searched

Definition at line 766 of file mesh.F90.

mesh_global_memory()

real(real64) pure function, public mesh_oct_m::mesh_global_memory

(

class(mesh_t), intent(in)

mesh

)

Definition at line 799 of file mesh.F90.

mesh_local_memory()

real(real64) pure function, public mesh_oct_m::mesh_local_memory

(

class(mesh_t), intent(in)

mesh

)

Definition at line 810 of file mesh.F90.

mesh_x_global()

real(real64) function, dimension(1:mesh%box%dim), public mesh_oct_m::mesh_x_global	(	class(mesh_t), intent(in)	mesh,
		integer(int64), intent(in)	ipg
	)

Given a global point index, this function returns the coordinates of the point.

Definition at line 825 of file mesh.F90.

mesh_check_symmetries()

subroutine, public mesh_oct_m::mesh_check_symmetries	(	class(mesh_t), intent(in)	mesh,
		type(symmetries_t), intent(in)	symm,
		integer, intent(in)	periodic_dim
	)

Definition at line 843 of file mesh.F90.

mesh_global_index_from_coords()

integer(int64) function, public mesh_oct_m::mesh_global_index_from_coords	(	class(mesh_t), intent(in)	mesh,
		integer, dimension(:), intent(in)	ix
	)

This function returns the true global index of the point for a given vector of integer coordinates.

Definition at line 927 of file mesh.F90.

mesh_global_index_to_coords()

subroutine, public mesh_oct_m::mesh_global_index_to_coords	(	type(mesh_t), intent(in)	mesh,
		integer(int64), intent(in)	ipg,
		integer, dimension(:), intent(out), contiguous	ix
	)

Given a global point index, this function returns the set of integer coordinates of the point.

Definition at line 936 of file mesh.F90.

mesh_local_index_from_coords()

integer function, public mesh_oct_m::mesh_local_index_from_coords	(	type(mesh_t), intent(in)	mesh,
		integer, dimension(:), intent(in)	ix
	)

This function returns the local index of the point for a given vector of integer coordinates.

Definition at line 946 of file mesh.F90.

mesh_local_index_to_coords()

subroutine, public mesh_oct_m::mesh_local_index_to_coords	(	type(mesh_t), intent(in)	mesh,
		integer, intent(in)	ip,
		integer, dimension(:), intent(out), contiguous	ix
	)

Given a local point index, this function returns the set of integer coordinates of the point.

Definition at line 958 of file mesh.F90.

mesh_local2global()

integer(int64) function, public mesh_oct_m::mesh_local2global	(	type(mesh_t), intent(in)	mesh,
		integer, intent(in)	ip
	)

This function returns the global mesh index for a given local index.

Definition at line 970 of file mesh.F90.

mesh_global2local()

integer function, public mesh_oct_m::mesh_global2local	(	type(mesh_t), intent(in)	mesh,
		integer(int64), intent(in)	ipg
	)

This function returns the local mesh index for a given global index.

If ip < 1 or ip > np, the point is not available on the local process

Definition at line 980 of file mesh.F90.

mesh_minmaxloc()

subroutine, public mesh_oct_m::mesh_minmaxloc	(	type(mesh_t), intent(in)	mesh,
		real(real64), intent(inout)	min_or_max,
		integer, intent(out)	rank_min_or_max,
		type(mpi_op), intent(in)	op
	)

Given a local min/max this returns the global min/max and the rank where this is located.

Parameters

[in,out]	min_or_max	On entry, the local value, on exit the global value
[out]	rank_min_or_max	On exit, the rank where the min/max is located
[in]	op	MPI_MINLOC or MPI_MAXLOC

Definition at line 989 of file mesh.F90.

mesh_red_min()

real(real64) function, dimension(space%dim) mesh_oct_m::mesh_red_min ( class(mesh_t), intent(in)  mesh, type(space_t), intent(in)  space  )

private

Helper routine to compute the minimal index of the mesh in reduced coordinate.

Definition at line 1014 of file mesh.F90.

dmesh_allreduce_0()

subroutine mesh_oct_m::dmesh_allreduce_0 ( class(mesh_t), intent(in)  mesh, real(real64), intent(inout)  aa  )

private

Definition at line 1102 of file mesh.F90.

dmesh_allreduce_1()

subroutine mesh_oct_m::dmesh_allreduce_1 ( class(mesh_t), intent(in)  mesh, real(real64), dimension(:), intent(inout), contiguous  aa, integer, intent(in), optional  dim  )

private

Definition at line 1110 of file mesh.F90.

dmesh_allreduce_2()

subroutine mesh_oct_m::dmesh_allreduce_2 ( class(mesh_t), intent(in)  mesh, real(real64), dimension(:, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(2)

Definition at line 1119 of file mesh.F90.

dmesh_allreduce_3()

subroutine mesh_oct_m::dmesh_allreduce_3 ( class(mesh_t), intent(in)  mesh, real(real64), dimension(:, :, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(3)

Definition at line 1128 of file mesh.F90.

dmesh_allreduce_4()

subroutine mesh_oct_m::dmesh_allreduce_4 ( class(mesh_t), intent(in)  mesh, real(real64), dimension(:, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1137 of file mesh.F90.

dmesh_allreduce_5()

subroutine mesh_oct_m::dmesh_allreduce_5 ( class(mesh_t), intent(in)  mesh, real(real64), dimension(:, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1145 of file mesh.F90.

dmesh_allreduce_6()

subroutine mesh_oct_m::dmesh_allreduce_6 ( class(mesh_t), intent(in)  mesh, real(real64), dimension(:, :, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1153 of file mesh.F90.

zmesh_allreduce_0()

subroutine mesh_oct_m::zmesh_allreduce_0 ( class(mesh_t), intent(in)  mesh, complex(real64), intent(inout)  aa  )

private

Definition at line 1234 of file mesh.F90.

zmesh_allreduce_1()

subroutine mesh_oct_m::zmesh_allreduce_1 ( class(mesh_t), intent(in)  mesh, complex(real64), dimension(:), intent(inout), contiguous  aa, integer, intent(in), optional  dim  )

private

Definition at line 1242 of file mesh.F90.

zmesh_allreduce_2()

subroutine mesh_oct_m::zmesh_allreduce_2 ( class(mesh_t), intent(in)  mesh, complex(real64), dimension(:, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(2)

Definition at line 1251 of file mesh.F90.

zmesh_allreduce_3()

subroutine mesh_oct_m::zmesh_allreduce_3 ( class(mesh_t), intent(in)  mesh, complex(real64), dimension(:, :, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(3)

Definition at line 1260 of file mesh.F90.

zmesh_allreduce_4()

subroutine mesh_oct_m::zmesh_allreduce_4 ( class(mesh_t), intent(in)  mesh, complex(real64), dimension(:, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1269 of file mesh.F90.

zmesh_allreduce_5()

subroutine mesh_oct_m::zmesh_allreduce_5 ( class(mesh_t), intent(in)  mesh, complex(real64), dimension(:, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1277 of file mesh.F90.

zmesh_allreduce_6()

subroutine mesh_oct_m::zmesh_allreduce_6 ( class(mesh_t), intent(in)  mesh, complex(real64), dimension(:, :, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1285 of file mesh.F90.

imesh_allreduce_0()

subroutine mesh_oct_m::imesh_allreduce_0 ( class(mesh_t), intent(in)  mesh, integer, intent(inout)  aa  )

private

Definition at line 1366 of file mesh.F90.

imesh_allreduce_1()

subroutine mesh_oct_m::imesh_allreduce_1 ( class(mesh_t), intent(in)  mesh, integer, dimension(:), intent(inout), contiguous  aa, integer, intent(in), optional  dim  )

private

Definition at line 1374 of file mesh.F90.

imesh_allreduce_2()

subroutine mesh_oct_m::imesh_allreduce_2 ( class(mesh_t), intent(in)  mesh, integer, dimension(:, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(2)

Definition at line 1383 of file mesh.F90.

imesh_allreduce_3()

subroutine mesh_oct_m::imesh_allreduce_3 ( class(mesh_t), intent(in)  mesh, integer, dimension(:, :, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(3)

Definition at line 1392 of file mesh.F90.

imesh_allreduce_4()

subroutine mesh_oct_m::imesh_allreduce_4 ( class(mesh_t), intent(in)  mesh, integer, dimension(:, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1401 of file mesh.F90.

imesh_allreduce_5()

subroutine mesh_oct_m::imesh_allreduce_5 ( class(mesh_t), intent(in)  mesh, integer, dimension(:, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1409 of file mesh.F90.

imesh_allreduce_6()

subroutine mesh_oct_m::imesh_allreduce_6 ( class(mesh_t), intent(in)  mesh, integer, dimension(:, :, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1417 of file mesh.F90.

lmesh_allreduce_0()

subroutine mesh_oct_m::lmesh_allreduce_0 ( class(mesh_t), intent(in)  mesh, integer(int64), intent(inout)  aa  )

private

Definition at line 1499 of file mesh.F90.

lmesh_allreduce_1()

subroutine mesh_oct_m::lmesh_allreduce_1 ( class(mesh_t), intent(in)  mesh, integer(int64), dimension(:), intent(inout), contiguous  aa, integer, intent(in), optional  dim  )

private

Definition at line 1507 of file mesh.F90.

lmesh_allreduce_2()

subroutine mesh_oct_m::lmesh_allreduce_2 ( class(mesh_t), intent(in)  mesh, integer(int64), dimension(:, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(2)

Definition at line 1516 of file mesh.F90.

lmesh_allreduce_3()

subroutine mesh_oct_m::lmesh_allreduce_3 ( class(mesh_t), intent(in)  mesh, integer(int64), dimension(:, :, :), intent(inout), contiguous  aa, integer, dimension(:), intent(in), optional  dim  )

private

Parameters

[in]

dim

(3)

Definition at line 1525 of file mesh.F90.

lmesh_allreduce_4()

subroutine mesh_oct_m::lmesh_allreduce_4 ( class(mesh_t), intent(in)  mesh, integer(int64), dimension(:, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1534 of file mesh.F90.

lmesh_allreduce_5()

subroutine mesh_oct_m::lmesh_allreduce_5 ( class(mesh_t), intent(in)  mesh, integer(int64), dimension(:, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1542 of file mesh.F90.

lmesh_allreduce_6()

subroutine mesh_oct_m::lmesh_allreduce_6 ( class(mesh_t), intent(in)  mesh, integer(int64), dimension(:, :, :, :, :, :), intent(inout), contiguous  aa  )

private

Definition at line 1550 of file mesh.F90.