Helper routines to manipulate with matrices. More...

Functions/Subroutines
integer function, public	number_of_atomic_orbitals (subsys, atom_list)
	Compute the number of atomic orbitals of the given set of atoms. More...

subroutine, public	negf_copy_fm_submat_to_dbcsr (fm, matrix, atomlist_row, atomlist_col, subsys)
	Populate relevant blocks of the DBCSR matrix using data from a ScaLAPACK matrix. Irrelevant blocks of the DBCSR matrix are kept untouched. More...

subroutine, public	negf_copy_sym_dbcsr_to_fm_submat (matrix, fm, atomlist_row, atomlist_col, subsys, mpi_comm_global, do_upper_diag, do_lower)
	Extract part of the DBCSR matrix based on selected atoms and copy it into a dense matrix. More...

subroutine, public	negf_copy_contact_matrix (fm_cell0, fm_cell1, direction_axis, matrix_kp, index_to_cell, atom_list0, atom_list1, subsys, mpi_comm_global, is_same_cell, matrix_ref)
	Driver routine to extract diagonal and off-diagonal blocks from a symmetric DBCSR matrix. More...

subroutine, public	negf_reference_contact_matrix (matrix_contact, matrix_device, atom_list, atom_map, para_env)
	Extract part of the DBCSR matrix based on selected atoms and copy it into another DBCSR matrix. More...

subroutine, public	invert_cell_to_index (cell_to_index, nimages, index_to_cell)
	Invert cell_to_index mapping between unit cells and DBCSR matrix images. More...

pure integer function, public	get_index_by_cell (cell, cell_to_index)
	Helper routine to obtain index of a DBCSR matrix image by its unit cell replica. Can be used with any usin cell. More...

Detailed Description

Helper routines to manipulate with matrices.

Function/Subroutine Documentation

◆ number_of_atomic_orbitals()

integer function, public negf_matrix_utils::number_of_atomic_orbitals	(	type(qs_subsys_type), pointer	subsys,
		integer, dimension(:), intent(in), optional	atom_list
	)

Compute the number of atomic orbitals of the given set of atoms.

Parameters

subsys	QuickStep subsystem
atom_list	list of selected atom; when absent all the atoms are taken into account

Returns: number of atomic orbitals

History

02.2017 created [Sergey Chulkov]

Definition at line 54 of file negf_matrix_utils.F.

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◆ negf_copy_fm_submat_to_dbcsr()

subroutine, public negf_matrix_utils::negf_copy_fm_submat_to_dbcsr	(	type(cp_fm_type), intent(in)	fm,
		type(dbcsr_type), pointer	matrix,
		integer, dimension(:), intent(in)	atomlist_row,
		integer, dimension(:), intent(in)	atomlist_col,
		type(qs_subsys_type), pointer	subsys
	)

Populate relevant blocks of the DBCSR matrix using data from a ScaLAPACK matrix. Irrelevant blocks of the DBCSR matrix are kept untouched.

Parameters

fm	dense matrix to copy
matrix	DBCSR matrix (modified on exit)
atomlist_row	set of atomic indices along the 1st (row) dimension
atomlist_col	set of atomic indices along the 2nd (column) dimension
subsys	subsystem environment

History

02.2017 created [Sergey Chulkov]

Definition at line 93 of file negf_matrix_utils.F.

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◆ negf_copy_sym_dbcsr_to_fm_submat()

subroutine, public negf_matrix_utils::negf_copy_sym_dbcsr_to_fm_submat	(	type(dbcsr_type), pointer	matrix,
		type(cp_fm_type), intent(in)	fm,
		integer, dimension(:), intent(in)	atomlist_row,
		integer, dimension(:), intent(in)	atomlist_col,
		type(qs_subsys_type), pointer	subsys,
		class(mp_comm_type), intent(in)	mpi_comm_global,
		logical, intent(in)	do_upper_diag,
		logical, intent(in)	do_lower
	)

Extract part of the DBCSR matrix based on selected atoms and copy it into a dense matrix.

Parameters

matrix	DBCSR matrix
fm	dense matrix (created and initialised on exit)
atomlist_row	set of atomic indices along the 1st (row) dimension
atomlist_col	set of atomic indices along the 2nd (column) dimension
subsys	subsystem environment
mpi_comm_global	MPI communicator which was used to distribute blocks of the DBCSR matrix. If missed, assume that both DBCSR and ScaLapack matrices are distributed across the same set of processors
do_upper_diag	initialise upper-triangular part of the dense matrix as well as diagonal elements
do_lower	initialise lower-triangular part of the dense matrix

History

02.2017 created [Sergey Chulkov]

Note: A naive implementation that copies relevant local DBCSR blocks into a 2-D matrix, performs collective summation, and then distributes the result. This approach seems to be optimal when processors are arranged into several independent MPI subgroups due to the fact that every subgroup automatically holds the copy of the dense matrix at the end, so we can avoid the final replication stage.

Definition at line 179 of file negf_matrix_utils.F.

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◆ negf_copy_contact_matrix()

subroutine, public negf_matrix_utils::negf_copy_contact_matrix	(	type(cp_fm_type), intent(in)	fm_cell0,
		type(cp_fm_type), intent(in)	fm_cell1,
		integer, intent(in)	direction_axis,
		type(dbcsr_p_type), dimension(:), intent(in)	matrix_kp,
		integer, dimension(:, :), intent(in)	index_to_cell,
		integer, dimension(:), intent(in)	atom_list0,
		integer, dimension(:), intent(in)	atom_list1,
		type(qs_subsys_type), pointer	subsys,
		class(mp_comm_type), intent(in)	mpi_comm_global,
		integer, dimension(:, :), intent(inout)	is_same_cell,
		type(dbcsr_type), optional, pointer	matrix_ref
	)

Driver routine to extract diagonal and off-diagonal blocks from a symmetric DBCSR matrix.

Parameters

fm_cell0	extracted diagonal matrix block
fm_cell1	extracted off-diagonal matrix block
direction_axis	axis towards the secondary unit cell
matrix_kp	set of DBCSR matrices
index_to_cell	inverted mapping between unit cells and DBCSR matrix images
atom_list0	list of atoms which belong to the primary contact unit cell
atom_list1	list of atoms which belong to the secondary contact unit cell
subsys	QuickStep subsystem
mpi_comm_global	global MPI communicator
is_same_cell	for every atomic pair indicates whether or not both atoms are assigned to the same (0) or different (-1) unit cells (initialised when the optional argument 'matrix_ref' is given)
matrix_ref	reference DBCSR matrix

History

10.2017 created [Sergey Chulkov]

Definition at line 295 of file negf_matrix_utils.F.

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◆ negf_reference_contact_matrix()

subroutine, public negf_matrix_utils::negf_reference_contact_matrix	(	type(dbcsr_type), pointer	matrix_contact,
		type(dbcsr_type), pointer	matrix_device,
		integer, dimension(:), intent(in)	atom_list,
		type(negf_atom_map_type), dimension(:), intent(in)	atom_map,
		type(mp_para_env_type), pointer	para_env
	)

Extract part of the DBCSR matrix based on selected atoms and copy it into another DBCSR matrix.

Parameters

matrix_contact	extracted DBCSR matrix
matrix_device	original DBCSR matrix
atom_list	list of selected atoms
atom_map	atomic map between device and contact force environments
para_env	parallel environment

Definition at line 496 of file negf_matrix_utils.F.

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◆ invert_cell_to_index()

subroutine, public negf_matrix_utils::invert_cell_to_index	(	integer, dimension(:, :, :), pointer	cell_to_index,
		integer, intent(in)	nimages,
		integer, dimension(3, nimages), intent(out)	index_to_cell
	)

Invert cell_to_index mapping between unit cells and DBCSR matrix images.

Parameters

cell_to_index	mapping: unit_cell -> image_index
nimages	number of images
index_to_cell	inverted mapping: image_index -> unit_cell

History

10.2017 created [Sergey Chulkov]

Definition at line 738 of file negf_matrix_utils.F.

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◆ get_index_by_cell()

pure integer function, public negf_matrix_utils::get_index_by_cell	(	integer, dimension(3), intent(in)	cell,
		integer, dimension(:, :, :), pointer	cell_to_index
	)

Helper routine to obtain index of a DBCSR matrix image by its unit cell replica. Can be used with any usin cell.

Parameters

cell	indices of the unit cell
cell_to_index	mapping: unit_cell -> image_index

Returns: DBCSR matrix images (0 means there are no non-zero matrix elements in the image)

History

10.2017 created [Sergey Chulkov]

Definition at line 780 of file negf_matrix_utils.F.

Functions/Subroutines

Detailed Description

Function/Subroutine Documentation

◆ number_of_atomic_orbitals()

◆ negf_copy_fm_submat_to_dbcsr()

◆ negf_copy_sym_dbcsr_to_fm_submat()

◆ negf_copy_contact_matrix()

◆ negf_reference_contact_matrix()

◆ invert_cell_to_index()

◆ get_index_by_cell()