comp-chem/cp2k
1
0
Fork 0
mirror of https://github.com/cp2k/cp2k.git synced 2026-07-29 06:35:28 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions

NEGF: New method to extract the matrix Hamiltonians for electrodes and minor changes.

Browse source
This commit is contained in:
Dmitry Ryndyk 2025-11-02 02:13:42 +01:00 • committed by Hans Pabst
parent e68414f036
commit 298f7c48fd
17 changed files with 2484 additions and 692 deletions
Download patch file Download diff file Expand all files Collapse all files

2
src/negf_alloc_types.F
View file

@ -25,7 +25,7 @@ MODULE negf_alloc_types
!> \brief Allocatable 1-D integer vector
! **************************************************************************************************
TYPE negf_allocatable_ivector
!> allocatable 1-D real vector
!> allocatable 1-D integer vector
INTEGER, ALLOCATABLE, DIMENSION(:) :: vector
END TYPE negf_allocatable_ivector

31
src/negf_atom_map.F
View file

@ -71,6 +71,10 @@ CONTAINS
!> \param eps_geometry accuracy in mapping atoms based on their Cartesian coordinates
!> \par History
!> * 08.2017 created [Sergey Chulkov]
!> * 10.2025 Centering of contact coordinates is added in the end. It is necessary to keep the
!> right order of indices in the real space image matrices. It is made only here, because
!> the mapping is based on the comparison of the coordinates. [Dmitry Ryndyk]
!> \note
! **************************************************************************************************
SUBROUTINE negf_map_atomic_indices(atom_map, atom_list, subsys_device, subsys_contact, eps_geometry)
TYPE(negf_atom_map_type), DIMENSION(:), &
@ -144,9 +148,36 @@ CONTAINS
CALL qs_kind_groups_release(kind_groups_contact)
CALL centering_contact_coordinates(subsys=subsys_contact)
CALL timestop(handle)
END SUBROUTINE negf_map_atomic_indices
! **************************************************************************************************
!> \brief Centering the atom coordinates of the primary unit cell of the bulk electrode.
!> \param subsys ...
!> \par History
!> * 10.2025 created [Dmitry Ryndyk]
!> \note It is necessary to keep the right order of indices in the real space image matrices.
! **************************************************************************************************
SUBROUTINE centering_contact_coordinates(subsys)
TYPE(qs_subsys_type), POINTER :: subsys
REAL(KIND=dp) :: shiftX, shiftY, shiftZ
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
CALL qs_subsys_get(subsys, particle_set=particle_set)
shiftX = (MAXVAL(particle_set(:)%r(1)) + MINVAL(particle_set(:)%r(1)))/2.0
shiftY = (MAXVAL(particle_set(:)%r(2)) + MINVAL(particle_set(:)%r(2)))/2.0
shiftZ = (MAXVAL(particle_set(:)%r(3)) + MINVAL(particle_set(:)%r(3)))/2.0
particle_set(:)%r(1) = particle_set(:)%r(1) - shiftX
particle_set(:)%r(2) = particle_set(:)%r(2) - shiftY
particle_set(:)%r(3) = particle_set(:)%r(3) - shiftZ
END SUBROUTINE centering_contact_coordinates
! **************************************************************************************************
!> \brief Group particles from 'particle_set' according to their atomic (QS) kind.
!> \param kind_groups kind groups that will be created

10
src/negf_control_types.F
View file

@ -47,17 +47,17 @@ MODULE negf_control_types
TYPE negf_control_contact_type
!> atoms belonging to bulk and screening regions
INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_bulk, atomlist_screening
!> atom belonging to the primary and secondary bulk unit cells
!> atoms belonging to the primary and secondary bulk unit cells
TYPE(negf_allocatable_ivector), ALLOCATABLE, &
DIMENSION(:) :: atomlist_cell
!> index of the sub_force_env which should be used for bulk calculation
INTEGER :: force_env_index = -1
!> contact Fermi level needs to be computed prior NEGF run
LOGICAL :: compute_fermi_level = .FALSE.
!> when computing contact Fermi level, use the energy given in 'fermi_level' (instead of HOMO)
!> (instead of the HOMO energy) as a starting point
!> to compute contact Fermi level starting from 'fermi_level'
!> (instead of the HOMO energy)
LOGICAL :: refine_fermi_level = .FALSE.
!> Fermi level
!> Fermi level or starting Fermi level
REAL(kind=dp) :: fermi_level = -1.0_dp
!> temperature [in a.u.]
REAL(kind=dp) :: temperature = -1.0_dp
@ -493,7 +493,7 @@ CONTAINS
CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, &
n_rep_val=nrep_molname, explicit=is_molname)
! compute the number of atoms in the NEGF region, and check the validity of giben atomic indices
! compute the number of atoms in the NEGF region, and check the validity of given atomic indices
natoms_total = 0
IF (is_list .AND. nrep_list > 0) THEN
DO irep = 1, nrep_list

44
src/negf_env_types.F
View file

@ -17,8 +17,7 @@ MODULE negf_env_types
dbcsr_deallocate_matrix,&
dbcsr_init_p,&
dbcsr_p_type,&
dbcsr_set,&
dbcsr_type
dbcsr_set
USE cp_fm_struct, ONLY: cp_fm_struct_create,&
cp_fm_struct_release,&
cp_fm_struct_type
@ -45,7 +44,6 @@ MODULE negf_env_types
USE negf_matrix_utils, ONLY: invert_cell_to_index,&
negf_copy_contact_matrix,&
negf_copy_sym_dbcsr_to_fm_submat,&
negf_reference_contact_matrix,&
number_of_atomic_orbitals
USE negf_subgroup_types, ONLY: negf_subgroup_env_type
USE negf_vectors, ONLY: contact_direction_vector,&
@ -260,18 +258,20 @@ CONTAINS
DO icontact = 1, ncontacts
IF (negf_control%contacts(icontact)%force_env_index > 0) THEN
IF (log_unit > 0) &
WRITE (log_unit, '(/,T2,A,T70,I11)') "NEGF| Construct the Kohn-Sham matrix for the contact ", icontact
WRITE (log_unit, '(/,T2,A,T70,I11)') "NEGF| Construct the Kohn-Sham matrix for the contact", icontact
CALL force_env_get(sub_force_env(negf_control%contacts(icontact)%force_env_index)%force_env, qs_env=qs_env_contact)
CALL qs_energies(qs_env_contact, consistent_energies=.FALSE., calc_forces=.FALSE.)
CALL negf_env_contact_init_matrices(contact_env=negf_env%contacts(icontact), sub_env=sub_env, &
qs_env_contact=qs_env_contact, matrix_s_device=matrix_s_kp(1, 1)%matrix)
qs_env_contact=qs_env_contact)
END IF
END DO
! obtain an initial KS-matrix for the scattering region
IF (log_unit > 0) &
WRITE (log_unit, '(/,T2,A,T70)') "NEGF| Construct the Kohn-Sham matrix for the entire system"
CALL qs_energies(qs_env, consistent_energies=.FALSE., calc_forces=.FALSE.)
! *** obtain relevant Kohn-Sham matrix blocks for each contact with no separate FORCE_ENV ***
@ -376,26 +376,26 @@ CONTAINS
!> \param contact_env NEGF environment for the contact (modified on exit)
!> \param sub_env NEGF parallel (sub)group environment
!> \param qs_env_contact QuickStep environment for the contact force environment
!> \param matrix_s_device overlap matrix from device force environment
!> \author Sergey Chulkov
!> \par History
!> * 10.2017 created [Sergey Chulkov]
!> * 10.2025 The subroutine is essentially modified. New functionality of negf_copy_contact_matrix.
!> [Dmitry Ryndyk]
! **************************************************************************************************
SUBROUTINE negf_env_contact_init_matrices(contact_env, sub_env, qs_env_contact, matrix_s_device)
SUBROUTINE negf_env_contact_init_matrices(contact_env, sub_env, qs_env_contact)
TYPE(negf_env_contact_type), INTENT(inout) :: contact_env
TYPE(negf_subgroup_env_type), INTENT(in) :: sub_env
TYPE(qs_environment_type), POINTER :: qs_env_contact
TYPE(dbcsr_type), POINTER :: matrix_s_device
CHARACTER(LEN=*), PARAMETER :: routineN = 'negf_env_contact_init_matrices'
INTEGER :: handle, iatom, ispin, nao, natoms, &
nimages, nspins
INTEGER, ALLOCATABLE, DIMENSION(:) :: atom_list0, atom_list1
INTEGER, ALLOCATABLE, DIMENSION(:, :) :: index_to_cell, is_same_cell
INTEGER, ALLOCATABLE, DIMENSION(:, :) :: index_to_cell
INTEGER, DIMENSION(:, :, :), POINTER :: cell_to_index
LOGICAL :: do_kpoints
TYPE(cp_fm_struct_type), POINTER :: fm_struct
TYPE(dbcsr_p_type), DIMENSION(:, :), POINTER :: matrix_ks_kp, matrix_s_kp, rho_ao_kp
TYPE(dbcsr_type), POINTER :: matrix_s_ref
TYPE(dft_control_type), POINTER :: dft_control
TYPE(kpoint_type), POINTER :: kpoints
TYPE(mp_para_env_type), POINTER :: para_env
@ -470,19 +470,6 @@ CONTAINS
CALL cp_fm_struct_release(fm_struct)
NULLIFY (matrix_s_ref)
CALL dbcsr_init_p(matrix_s_ref)
CALL dbcsr_copy(matrix_s_ref, matrix_s_kp(1, 1)%matrix)
CALL dbcsr_set(matrix_s_ref, 0.0_dp)
ALLOCATE (is_same_cell(natoms, natoms))
CALL negf_reference_contact_matrix(matrix_contact=matrix_s_ref, &
matrix_device=matrix_s_device, &
atom_list=contact_env%atomlist_cell0, &
atom_map=contact_env%atom_map_cell0, &
para_env=para_env)
! extract matrices: s_00, s_01
CALL negf_copy_contact_matrix(fm_cell0=contact_env%s_00, &
fm_cell1=contact_env%s_01, &
@ -491,7 +478,7 @@ CONTAINS
index_to_cell=index_to_cell, &
atom_list0=atom_list0, atom_list1=atom_list1, &
subsys=subsys, mpi_comm_global=para_env, &
is_same_cell=is_same_cell, matrix_ref=matrix_s_ref)
kpoints=kpoints)
! extract matrices: h_00, h_01, rho_00, rho_01
DO ispin = 1, nspins
@ -502,7 +489,7 @@ CONTAINS
index_to_cell=index_to_cell, &
atom_list0=atom_list0, atom_list1=atom_list1, &
subsys=subsys, mpi_comm_global=para_env, &
is_same_cell=is_same_cell)
kpoints=kpoints)
CALL negf_copy_contact_matrix(fm_cell0=contact_env%rho_00(ispin), &
fm_cell1=contact_env%rho_01(ispin), &
@ -511,12 +498,9 @@ CONTAINS
index_to_cell=index_to_cell, &
atom_list0=atom_list0, atom_list1=atom_list1, &
subsys=subsys, mpi_comm_global=para_env, &
is_same_cell=is_same_cell)
kpoints=kpoints)
END DO
DEALLOCATE (is_same_cell)
CALL dbcsr_deallocate_matrix(matrix_s_ref)
DEALLOCATE (index_to_cell)
DEALLOCATE (atom_list0, atom_list1)
CALL timestop(handle)

195
src/negf_matrix_utils.F
View file

@ -8,7 +8,6 @@
! **************************************************************************************************
!> \brief Helper routines to manipulate with matrices.
! **************************************************************************************************
MODULE negf_matrix_utils
USE cp_dbcsr_api, ONLY: &
dbcsr_add, dbcsr_copy, dbcsr_deallocate_matrix, dbcsr_get_block_p, dbcsr_get_info, &
@ -19,6 +18,8 @@ MODULE negf_matrix_utils
cp_fm_set_submatrix,&
cp_fm_type
USE kinds, ONLY: dp
USE kpoint_types, ONLY: get_kpoint_info,&
kpoint_type
USE message_passing, ONLY: mp_comm_type,&
mp_para_env_type,&
mp_request_type
@ -27,6 +28,13 @@ MODULE negf_matrix_utils
USE particle_methods, ONLY: get_particle_set
USE particle_types, ONLY: particle_type
USE qs_kind_types, ONLY: qs_kind_type
USE qs_neighbor_list_types, ONLY: get_iterator_info,&
get_neighbor_list_set_p,&
neighbor_list_iterate,&
neighbor_list_iterator_create,&
neighbor_list_iterator_p_type,&
neighbor_list_iterator_release,&
neighbor_list_set_p_type
USE qs_subsys_types, ONLY: qs_subsys_get,&
qs_subsys_type
#include "./base/base_uses.f90"
@ -285,15 +293,13 @@ CONTAINS
!> \param atom_list1 list of atoms which belong to the secondary contact unit cell
!> \param subsys QuickStep subsystem
!> \param mpi_comm_global global MPI communicator
!> \param 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)
!> \param matrix_ref reference DBCSR matrix
!> \param kpoints ...
!> \par History
!> * 10.2017 created [Sergey Chulkov]
!> * 10.2025 The subroutine is essentially modified. [Dmitry Ryndyk]
! **************************************************************************************************
SUBROUTINE 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)
atom_list0, atom_list1, subsys, mpi_comm_global, kpoints)
TYPE(cp_fm_type), INTENT(IN) :: fm_cell0, fm_cell1
INTEGER, INTENT(in) :: direction_axis
TYPE(dbcsr_p_type), DIMENSION(:), INTENT(in) :: matrix_kp
@ -301,21 +307,23 @@ CONTAINS
INTEGER, DIMENSION(:), INTENT(in) :: atom_list0, 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
CLASS(mp_comm_type), INTENT(in) :: mpi_comm_global
TYPE(kpoint_type), POINTER :: kpoints
CHARACTER(LEN=*), PARAMETER :: routineN = 'negf_copy_contact_matrix'
INTEGER :: direction_axis_abs, handle, iatom_col, &
iatom_row, image, natoms, nimages, &
phase, rep
LOGICAL :: found
REAL(kind=dp) :: error_diff, error_same
rep
LOGICAL :: found, do_symmetric
REAL(kind=dp), DIMENSION(:, :), POINTER :: block_dest, block_src
TYPE(dbcsr_p_type), ALLOCATABLE, DIMENSION(:) :: matrix_cells_raw
TYPE(dbcsr_type), POINTER :: matrix_cell_0, matrix_cell_1, &
matrix_cell_minus1
TYPE(dbcsr_type), POINTER :: matrix_cell_1, matrix_cell_minus1
INTEGER, DIMENSION(3) :: cell
TYPE(neighbor_list_set_p_type), DIMENSION(:), &
POINTER :: sab_nl
TYPE(neighbor_list_iterator_p_type), &
DIMENSION(:), POINTER :: nl_iterator
CALL timeset(routineN, handle)
@ -325,10 +333,8 @@ CONTAINS
direction_axis_abs = ABS(direction_axis)
! 0 -- primary unit cell;
! +- 1 -- upper- and lower-diagonal matrices for the secondary unit cell;
! when the distance between two atoms within the unit cell becomes bigger than
! the distance between the same atoms from different cell replicas, the third
! unit cell replica (+- 2) is also needed.
! +- 1 -- upper- and lower-diagonal matrices for neighbor-cell matrix elements;
! +- 2 -- for control
ALLOCATE (matrix_cells_raw(-2:2))
DO rep = -2, 2
NULLIFY (matrix_cells_raw(rep)%matrix)
@ -337,11 +343,14 @@ CONTAINS
CALL dbcsr_set(matrix_cells_raw(rep)%matrix, 0.0_dp)
END DO
NULLIFY (matrix_cell_0, matrix_cell_1, matrix_cell_minus1)
DO image = 1, nimages
rep = index_to_cell(direction_axis_abs, image)
CALL dbcsr_init_p(matrix_cell_0)
CALL dbcsr_copy(matrix_cell_0, matrix_kp(1)%matrix)
CALL dbcsr_set(matrix_cell_0, 0.0_dp)
IF (ABS(rep) <= 2) &
CALL dbcsr_add(matrix_cells_raw(rep)%matrix, matrix_kp(image)%matrix, 1.0_dp, 1.0_dp)
END DO
NULLIFY (matrix_cell_1, matrix_cell_minus1)
CALL dbcsr_init_p(matrix_cell_1)
CALL dbcsr_copy(matrix_cell_1, matrix_kp(1)%matrix)
@ -351,103 +360,55 @@ CONTAINS
CALL dbcsr_copy(matrix_cell_minus1, matrix_kp(1)%matrix)
CALL dbcsr_set(matrix_cell_minus1, 0.0_dp)
DO image = 1, nimages
rep = index_to_cell(direction_axis_abs, image)
CALL dbcsr_get_info(matrix_cell_1, nblkrows_total=natoms)
IF (ABS(rep) <= 2) &
CALL dbcsr_add(matrix_cells_raw(rep)%matrix, matrix_kp(image)%matrix, 1.0_dp, 1.0_dp)
END DO
CALL get_kpoint_info(kpoints, sab_nl=sab_nl)
CALL get_neighbor_list_set_p(neighbor_list_sets=sab_nl, symmetric=do_symmetric)
CALL neighbor_list_iterator_create(nl_iterator, sab_nl)
DO WHILE (neighbor_list_iterate(nl_iterator) == 0)
CALL get_iterator_info(nl_iterator, iatom=iatom_row, jatom=iatom_col, cell=cell)
CALL dbcsr_get_info(matrix_cell_0, nblkrows_total=natoms)
IF (PRESENT(matrix_ref)) THEN
! 0 -- atoms belong to the same cell or absent (zero) matrix block;
! +1 -- atoms belong to different cells
is_same_cell(:, :) = 0
DO iatom_col = 1, natoms
DO iatom_row = 1, iatom_col
CALL dbcsr_get_block_p(matrix=matrix_ref, &
row=iatom_row, col=iatom_col, &
block=block_src, found=found)
IF (found) THEN
! it should be much safe to rely on atomic indices (iatom / jatom) obtained using a neighbour list iterator:
! phase == 1 when iatom <= jatom, and phase == -1 when iatom > jatom
IF (MOD(iatom_col - iatom_row, 2) == 0) THEN
phase = 1
ELSE
phase = -1
END IF
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(0)%matrix, &
row=iatom_row, col=iatom_col, &
block=block_dest, found=found)
CPASSERT(found)
error_same = MAXVAL(ABS(block_dest(:, :) - block_src(:, :)))
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(phase)%matrix, &
row=iatom_row, col=iatom_col, &
block=block_dest, found=found)
CPASSERT(found)
error_diff = MAXVAL(ABS(block_dest(:, :) - block_src(:, :)))
IF (error_same <= error_diff) THEN
is_same_cell(iatom_row, iatom_col) = 0
ELSE
is_same_cell(iatom_row, iatom_col) = 1
END IF
END IF
END DO
END DO
END IF
DO iatom_col = 1, natoms
DO iatom_row = 1, iatom_col
CALL dbcsr_get_block_p(matrix=matrix_cell_0, &
IF (ABS(cell(direction_axis_abs)) == 1) THEN
IF (iatom_row <= iatom_col) THEN
! secondary unit cell, i <= j:
CALL dbcsr_get_block_p(matrix=matrix_cell_1, &
row=iatom_row, col=iatom_col, block=block_dest, found=found)
CPASSERT(found)
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(-cell(direction_axis_abs))%matrix, &
row=iatom_row, col=iatom_col, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
IF (found) THEN
! it should be much safe to rely on a neighbour list iterator
IF (MOD(iatom_col - iatom_row, 2) == 0) THEN
phase = 1
ELSE
phase = -1
END IF
rep = phase*is_same_cell(iatom_row, iatom_col)
CALL dbcsr_get_block_p(matrix=matrix_cell_minus1, &
row=iatom_row, col=iatom_col, block=block_dest, found=found)
CPASSERT(found)
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(cell(direction_axis_abs))%matrix, &
row=iatom_row, col=iatom_col, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
! primary unit cell:
! matrix(i,j) <- [0]%matrix(i,j) when i and j are from the same replica
! matrix(i,j) <- [phase]%matrix(i,j) when i and j are from different replicas
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(rep)%matrix, &
row=iatom_row, col=iatom_col, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
ELSE
! secondary unit cell, i > j:
CALL dbcsr_get_block_p(matrix=matrix_cell_1, &
row=iatom_col, col=iatom_row, block=block_dest, found=found)
CPASSERT(found)
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(-cell(direction_axis_abs))%matrix, &
row=iatom_col, col=iatom_row, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
! secondary unit cell, i <= j:
! matrix(i,j) <- [phase]%matrix(i,j) when i and j are from the same replica
! matrix(i,j) <- [2*phase]%matrix(i,j) when i and j are from different replicas
CALL dbcsr_get_block_p(matrix=matrix_cell_1, &
row=iatom_row, col=iatom_col, block=block_dest, found=found)
CPASSERT(found)
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(rep + phase)%matrix, &
row=iatom_row, col=iatom_col, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
CALL dbcsr_get_block_p(matrix=matrix_cell_minus1, &
row=iatom_col, col=iatom_row, block=block_dest, found=found)
CPASSERT(found)
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(cell(direction_axis_abs))%matrix, &
row=iatom_col, col=iatom_row, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
END IF
END IF
! secondary unit cell, i > j:
! matrix(i,j) <- [-phase]%matrix(i,j) when i and j are from the same replica
! matrix(i,j) <- [-2*phase]%matrix(i,j) when i and j are from different replicas
CALL dbcsr_get_block_p(matrix=matrix_cell_minus1, &
row=iatom_row, col=iatom_col, block=block_dest, found=found)
CPASSERT(found)
CALL dbcsr_get_block_p(matrix=matrix_cells_raw(rep - phase)%matrix, &
row=iatom_row, col=iatom_col, block=block_src, found=found)
CPASSERT(found)
block_dest(:, :) = block_src(:, :)
END IF
END DO
END DO
IF (direction_axis >= 0) THEN
@ -464,22 +425,20 @@ CONTAINS
! lower-diagonal part of fm_cell1
CALL negf_copy_sym_dbcsr_to_fm_submat(matrix_cell_1, fm_cell0, atom_list0, atom_list1, &
subsys, mpi_comm_global, do_upper_diag=.FALSE., do_lower=.TRUE.)
END IF
CALL cp_fm_scale_and_add(1.0_dp, fm_cell1, 1.0_dp, fm_cell0)
! symmetric matrix fm_cell0
CALL negf_copy_sym_dbcsr_to_fm_submat(matrix_cell_0, fm_cell0, atom_list0, atom_list0, &
CALL negf_copy_sym_dbcsr_to_fm_submat(matrix_cells_raw(0)%matrix, fm_cell0, atom_list0, atom_list0, &
subsys, mpi_comm_global, do_upper_diag=.TRUE., do_lower=.TRUE.)
CALL dbcsr_deallocate_matrix(matrix_cell_0)
CALL dbcsr_deallocate_matrix(matrix_cell_1)
CALL dbcsr_deallocate_matrix(matrix_cell_minus1)
DO rep = -2, 2
CALL dbcsr_deallocate_matrix(matrix_cells_raw(rep)%matrix)
END DO
DEALLOCATE (matrix_cells_raw)
CALL neighbor_list_iterator_release(nl_iterator)
CALL dbcsr_deallocate_matrix(matrix_cell_1)
CALL dbcsr_deallocate_matrix(matrix_cell_minus1)
CALL timestop(handle)
END SUBROUTINE negf_copy_contact_matrix

86
src/negf_methods.F
View file

@ -8,7 +8,6 @@
! **************************************************************************************************
!> \brief NEGF based quantum transport calculations
! **************************************************************************************************
MODULE negf_methods
USE bibliography, ONLY: Bailey2006,&
Papior2017,&
@ -157,11 +156,13 @@ CONTAINS
CHARACTER(LEN=*), PARAMETER :: routineN = 'do_negf'
CHARACTER(len=100) :: sfmt
CHARACTER(len=default_string_length) :: contact_id_str
INTEGER :: handle, icontact, ispin, log_unit, &
ncontacts, npoints, nspins, &
print_level, print_unit
LOGICAL :: should_output, verbose_output
INTEGER :: handle, i, icontact, ispin, j, k, &
log_unit, n, ncontacts, npoints, &
nspins, print_level, print_unit
LOGICAL :: debug_output, should_output, &
verbose_output
REAL(kind=dp) :: energy_max, energy_min
REAL(kind=dp), DIMENSION(2) :: current
TYPE(cp_blacs_env_type), POINTER :: blacs_env
@ -198,36 +199,82 @@ CONTAINS
NULLIFY (negf_control)
CALL negf_control_create(negf_control)
CALL read_negf_control(negf_control, root_section, cp_subsys)
CALL get_qs_env(qs_env, dft_control=dft_control)
! print unit, if log_unit > 0, otherwise no output
log_unit = cp_print_key_unit_nr(logger, negf_section, "PRINT%PROGRAM_RUN_INFO", extension=".Log")
IF (log_unit > 0) THEN
WRITE (log_unit, '(/,T2,79("-"))')
WRITE (log_unit, '(T27,A,T62)') "NEGF calculation is started"
WRITE (log_unit, '(T2,79("-"))')
END IF
! print levels, are used if log_unit > 0
IF (log_unit > 0) THEN
CALL section_vals_val_get(negf_section, "PRINT%PROGRAM_RUN_INFO%PRINT_LEVEL", i_val=print_level)
SELECT CASE (print_level)
CASE (high_print_level, debug_print_level)
CASE (high_print_level)
verbose_output = .TRUE.
CASE (debug_print_level)
verbose_output = .TRUE.
debug_output = .TRUE.
CASE DEFAULT
verbose_output = .FALSE.
debug_output = .FALSE.
END SELECT
END IF
IF (log_unit > 0) THEN
WRITE (log_unit, '(/,T2,A,T62)') "COMPUTE THE RELEVANT HAMILTONIAN MATRICES"
WRITE (log_unit, "(/,' THE RELEVANT HAMILTONIAN AND OVERLAP MATRICES FROM DFT')")
WRITE (log_unit, "( ' ------------------------------------------------------')")
END IF
CALL negf_sub_env_create(sub_env, negf_control, blacs_env, global_env%blacs_grid_layout, global_env%blacs_repeatable)
CALL negf_env_create(negf_env, sub_env, negf_control, force_env, negf_mixing_section, log_unit)
IF (log_unit > 0 .AND. verbose_output) THEN
IF (log_unit > 0) THEN
WRITE (log_unit, "(/,' NEGF| The initial Hamiltonian and Overlap matrices are calculated.')")
END IF
IF (log_unit > 0) THEN
DO icontact = 1, SIZE(negf_control%contacts)
WRITE (log_unit, "(/,' NEGF| Atoms in the contact region',I2,':',I4)") &
icontact, SIZE(negf_control%contacts(icontact)%atomlist_bulk)
WRITE (log_unit, "(16I5)") negf_control%contacts(icontact)%atomlist_bulk
WRITE (log_unit, "(/,' The electrode',I5)") icontact
WRITE (log_unit, "( ' ------------------')")
WRITE (log_unit, "(' From the force environment:',I16)") negf_control%contacts(icontact)%force_env_index
WRITE (log_unit, "(' Number of atoms:',I27)") SIZE(negf_control%contacts(icontact)%atomlist_bulk)
IF (verbose_output) WRITE (log_unit, "(' Atoms belonging to a contact:')")
IF (verbose_output) WRITE (log_unit, "(16I5)") negf_control%contacts(icontact)%atomlist_bulk
WRITE (log_unit, "(' Number of atoms in a primary unit cell:',I4)") SIZE(negf_env%contacts(icontact)%atomlist_cell0)
IF (verbose_output) WRITE (log_unit, "(' Atoms belonging to a primary unit cell:')")
IF (verbose_output) WRITE (log_unit, "(16I5)") negf_env%contacts(icontact)%atomlist_cell0
n = SIZE(negf_env%contacts(icontact)%h_00(1)%local_data, 1)
WRITE (sfmt, "('(',i0,'(E15.5))')") n
WRITE (log_unit, "(' The number of atomic orbtals:',I14)") n
! print the electrode Hamiltonians for check and debuging
IF (debug_output) THEN
DO k = 1, dft_control%nspins
WRITE (log_unit, "(' The H_00 electrode Hamiltonian for spin',I2)") k
DO i = 1, n
WRITE (log_unit, sfmt) (negf_env%contacts(icontact)%h_00(k)%local_data(i, j), j=1, n)
END DO
WRITE (log_unit, "(' The H_01 electrode Hamiltonian for spin',I2)") k
DO i = 1, n
WRITE (log_unit, sfmt) (negf_env%contacts(icontact)%h_01(k)%local_data(i, j), j=1, n)
END DO
END DO
WRITE (log_unit, "(' The S_00 overlap matrix')")
DO i = 1, n
WRITE (log_unit, sfmt) (negf_env%contacts(icontact)%s_00%local_data(i, j), j=1, n)
END DO
WRITE (log_unit, "(' The S_01 overlap matrix')")
DO i = 1, n
WRITE (log_unit, sfmt) (negf_env%contacts(icontact)%s_01%local_data(i, j), j=1, n)
END DO
END IF
END DO
WRITE (log_unit, "(/,' NEGF| Atoms in the full scattering region:',I4)") SIZE(negf_control%atomlist_S_screening)
WRITE (log_unit, "(16I5)") negf_control%atomlist_S_screening
WRITE (log_unit, "(/,' Atoms in the full scattering region:',I4)") SIZE(negf_control%atomlist_S_screening)
IF (verbose_output) WRITE (log_unit, "(16I5)") negf_control%atomlist_S_screening
WRITE (log_unit, *)
END IF
@ -344,6 +391,12 @@ CONTAINS
END IF
IF (log_unit > 0) THEN
WRITE (log_unit, '(/,T2,79("-"))')
WRITE (log_unit, '(T27,A,T62)') "NEGF calculation is finished"
WRITE (log_unit, '(T2,79("-"))')
END IF
CALL negf_env_release(negf_env)
CALL negf_sub_env_release(sub_env)
@ -475,8 +528,9 @@ CONTAINS
IF (log_unit > 0) THEN
WRITE (temperature_str, '(F11.3)') negf_control%contacts(contact_id)%temperature*kelvin
WRITE (log_unit, '(/,T2,A,I0,A)') "COMPUTE FERMI LEVEL OF CONTACT ", &
contact_id, " AT "//TRIM(ADJUSTL(temperature_str))//" KELVIN"
WRITE (log_unit, '(/,T2,A,I3)') "COMPUTE FERMI LEVEL OF CONTACT ", contact_id
WRITE (log_unit, "( ' ----------------------------------')")
WRITE (log_unit, '(A)') " Temperature "//TRIM(ADJUSTL(temperature_str))//" Kelvin"
WRITE (log_unit, '(/,T2,A,T60,F20.10,/)') "Electronic density of the isolated contact unit cell:", &
-1.0_dp*(nelectrons_qs_cell0 + nelectrons_qs_cell1)
WRITE (log_unit, '(T3,A)') "Step Integration method Time Fermi level Convergence (density)"
@ -746,6 +800,7 @@ CONTAINS
IF (log_unit > 0) THEN
WRITE (log_unit, '(/,T2,A)') "COMPUTE SHIFT IN HARTREE POTENTIAL"
WRITE (log_unit, "( ' ----------------------------------')")
WRITE (log_unit, '(/,T2,A,T55,F25.14,/)') "Initial electronic density of the scattering region:", -1.0_dp*nelectrons_ref
WRITE (log_unit, '(T3,A)') "Step Integration method Time V shift Convergence (density)"
WRITE (log_unit, '(T3,78("-"))')
@ -1049,6 +1104,7 @@ CONTAINS
IF (log_unit > 0) THEN
WRITE (log_unit, '(/,T2,A)') "NEGF SELF-CONSISTENT PROCEDURE"
WRITE (log_unit, "( ' ------------------------------')")
WRITE (log_unit, '(/,T2,A,T55,F25.14,/)') "Initial electronic density of the scattering region:", -1.0_dp*nelectrons
WRITE (log_unit, '(T3,A)') "Step Integration method Time Electronic density Convergence"
WRITE (log_unit, '(T3,78("-"))')

404
tests/QS/regtest-negf-1/H28-device-0-1_0.dos Normal file
View file

@ -0,0 +1,404 @@
# Density of states for the scattering region
# Energy (a.u.) Number of states [alpha + beta]
# ------------------------------------------------------------------------------
-0.55123988 9.29725255992E-004
-0.54848368 9.51486045544E-004
-0.54572748 9.74081374121E-004
-0.54297128 9.97556572903E-004
-0.54021508 1.02196018946E-003
-0.53745888 1.04734427130E-003
-0.53470268 1.07376467940E-003
-0.53194649 1.10128143555E-003
-0.52919029 1.12995910768E-003
-0.52643409 1.15986723812E-003
-0.52367789 1.19108082042E-003
-0.52092169 1.22368083103E-003
-0.51816549 1.25775482356E-003
-0.51540929 1.29339759399E-003
-0.51265309 1.33071192691E-003
-0.50989689 1.36980943444E-003
-0.50714069 1.41081150129E-003
-0.50438449 1.45385035178E-003
-0.50162829 1.49907025740E-003
-0.49887209 1.54662890668E-003
-0.49611589 1.59669896305E-003
-0.49335969 1.64946984114E-003
-0.49060349 1.70514973768E-003
-0.48784729 1.76396795996E-003
-0.48509110 1.82617760338E-003
-0.48233490 1.89205863999E-003
-0.47957870 1.96192149239E-003
-0.47682250 2.03611118337E-003
-0.47406630 2.11501217092E-003
-0.47131010 2.19905400276E-003
-0.46855390 2.28871795481E-003
-0.46579770 2.38454485673E-003
-0.46304150 2.48714435646E-003
-0.46028530 2.59720593774E-003
-0.45752910 2.71551208517E-003
-0.45477290 2.84295409448E-003
-0.45201670 2.98055116110E-003
-0.44926050 3.12947355713E-003
-0.44650430 3.29107094157E-003
-0.44374810 3.46690716216E-003
-0.44099190 3.65880332903E-003
-0.43823571 3.86889151509E-003
-0.43547951 4.09968222757E-003
-0.43272331 4.35414989326E-003
-0.42996711 4.63584214415E-003
-0.42721091 4.94902089203E-003
-0.42445471 5.29884636089E-003
-0.42169851 5.69161991255E-003
-0.41894231 6.13510845754E-003
-0.41618611 6.63898380315E-003
-0.41342991 7.21542663165E-003
-0.41067371 7.87997063929E-003
-0.40791751 8.65270419411E-003
-0.40516131 9.56001638813E-003
-0.40240511 1.06371933393E-002
-0.39964891 1.19323810817E-002
-0.39689271 1.35128179751E-002
-0.39413651 1.54749808133E-002
-0.39138032 1.79617825871E-002
-0.38862412 2.11931512244E-002
-0.38586792 2.55236280111E-002
-0.38311172 3.15588427186E-002
-0.38035552 4.04131740799E-002
-0.37759932 5.43509171817E-002
-0.37484312 7.86628045505E-002
-0.37208692 1.28660030032E-001
-0.36933072 2.69131175708E-001
-0.36657452 1.23548542843E+000
-0.36381832 4.54613541459E+002
-0.36106212 2.46726874553E+002
-0.35830592 1.88683860875E+002
-0.35554972 1.58956423992E+002
-0.35279352 1.39966036834E+002
-0.35003732 1.26442484680E+002
-0.34728113 1.16206893724E+002
-0.34452493 1.08139814739E+002
-0.34176873 1.01580036044E+002
-0.33901253 9.61068148960E+001
-0.33625633 9.14428221357E+001
-0.33350013 8.74013952310E+001
-0.33074393 8.38538074626E+001
-0.32798773 8.07089080770E+001
-0.32523153 7.78978604624E+001
-0.32247533 7.53679347851E+001
-0.31971913 7.30764509728E+001
-0.31696293 7.09883661848E+001
-0.31420673 6.90747037346E+001
-0.31145053 6.73115579461E+001
-0.30869433 6.56793260981E+001
-0.30593813 6.41620121357E+001
-0.30318193 6.27465595365E+001
-0.30042574 6.14222263614E+001
-0.29766954 6.01800328741E+001
-0.29491334 5.90123073404E+001
-0.29215714 5.79123414261E+001
-0.28940094 5.68741515000E+001
-0.28664474 5.58923300265E+001
-0.28388854 5.49619648469E+001
-0.28113234 5.40786023640E+001
-0.27837614 5.32382330855E+001
-0.27561994 5.24372827287E+001
-0.27286374 5.16725978437E+001
-0.27010754 5.09414204791E+001
-0.26735134 5.02413510221E+001
-0.26459514 4.95703016087E+001
-0.26183894 4.89264443442E+001
-0.25908274 4.83081591506E+001
-0.25632654 4.77139856506E+001
-0.25357035 4.71425824549E+001
-0.25081415 4.65926958572E+001
-0.24805795 4.60631385506E+001
-0.24530175 4.55527777604E+001
-0.24254555 4.50605312681E+001
-0.23978935 4.45853692459E+001
-0.23703315 4.41263196173E+001
-0.23427695 4.36824747767E+001
-0.23152075 4.32529979224E+001
-0.22876455 4.28371282206E+001
-0.22600835 4.24341894769E+001
-0.22325215 4.20493265000E+001
-0.22049595 4.16645424710E+001
-0.21773975 4.12969410741E+001
-0.21498355 4.09401705225E+001
-0.21222735 4.05938544751E+001
-0.20947115 4.02576400821E+001
-0.20671496 3.99311961692E+001
-0.20395876 3.96142063842E+001
-0.20120256 3.93063633529E+001
-0.19844636 3.90073646811E+001
-0.19569016 3.87169109389E+001
-0.19293396 3.84347054941E+001
-0.19017776 3.81604558969E+001
-0.18742156 3.78938764176E+001
-0.18466536 3.76346912908E+001
-0.18190916 3.73826382074E+001
-0.17915296 3.71374716460E+001
-0.17639676 3.68989656831E+001
-0.17364056 3.66669160217E+001
-0.17088436 3.64411410763E+001
-0.16812816 3.62214820332E+001
-0.16537196 3.60078019323E+001
-0.16261576 3.57999838563E+001
-0.15985957 3.55979284164E+001
-0.15710337 3.54015507334E+001
-0.15434717 3.52107771604E+001
-0.15159097 3.50255419795E+001
-0.14883477 3.48457842980E+001
-0.14607857 3.46714453371E+001
-0.14332237 3.45024662602E+001
-0.14056617 3.43387866530E+001
-0.13780997 3.41803436968E+001
-0.13505377 3.40270720408E+001
-0.13229757 3.38789043260E+001
-0.12954137 3.37357722960E+001
-0.12678517 3.35976083179E+001
-0.12402897 3.34643473028E+001
-0.12127277 3.33359286739E+001
-0.11851657 3.32122985154E+001
-0.11576038 3.30934114392E+001
-0.11300418 3.29792323617E+001
-0.11024798 3.28697378092E+001
-0.10749178 3.27649169563E+001
-0.10473558 3.26647720825E+001
-0.10197938 3.25693186398E+001
-0.09922318 3.24785848494E+001
-0.09646698 3.23926109165E+001
-0.09371078 3.23114478945E+001
-0.09095458 3.22351563132E+001
-0.08819838 3.21638046594E+001
-0.08544218 3.20974678159E+001
-0.08268598 3.20362255658E+001
-0.07992978 3.19801612643E+001
-0.07717358 3.19293607683E+001
-0.07441738 3.18839117037E+001
-0.07166118 3.18439031288E+001
-0.06890499 3.18094256354E+001
-0.06614879 3.17805719063E+001
-0.06339259 3.17574377255E+001
-0.06063639 3.17401234139E+001
-0.05788019 3.17287356396E+001
-0.05512399 3.17233895095E+001
-0.05236779 3.17242107708E+001
-0.04961159 3.17313376371E+001
-0.04685539 3.17449200174E+001
-0.04409919 3.17650941238E+001
-0.04134299 3.17932167981E+001
-0.03858679 3.18265858586E+001
-0.03583059 3.18680093758E+001
-0.03307439 3.19170616822E+001
-0.03031819 3.19740320586E+001
-0.02756199 3.20392612645E+001
-0.02480579 3.21131286277E+001
-0.02204960 3.21960512638E+001
-0.01929340 3.22884849581E+001
-0.01653720 3.23909255128E+001
-0.01378100 3.25039104227E+001
-0.01102480 3.26280209754E+001
-0.00826860 3.27638849464E+001
-0.00551240 3.29121801072E+001
-0.00275620 3.30736387980E+001
0.00000000 3.32490538487E+001
0.00275620 3.34392861631E+001
0.00551240 3.36452743177E+001
0.00826860 3.38680465784E+001
0.01102480 3.41087356649E+001
0.01378100 3.43685971226E+001
0.01653720 3.46490312031E+001
0.01929340 3.49516096793E+001
0.02204960 3.52781078999E+001
0.02480579 3.56305432479E+001
0.02756199 3.60112213182E+001
0.03031819 3.64227911585E+001
0.03307439 3.68683119079E+001
0.03583059 3.73513333656E+001
0.03858679 3.78759941648E+001
0.04134299 3.84471424524E+001
0.04409919 3.90704858893E+001
0.04685539 3.97527803819E+001
0.04961159 4.05020709542E+001
0.05236779 4.13280040069E+001
0.05512399 4.22422391081E+001
0.05788019 4.32590022828E+001
0.06063639 4.43958446237E+001
0.06339259 4.56747056905E+001
0.06614879 4.71234408942E+001
0.06890499 4.87780756597E+001
0.07166118 5.06862359497E+001
0.07441738 5.29125569777E+001
0.07717358 5.55475723179E+001
0.07992978 5.87230688764E+001
0.08268598 6.26402848912E+001
0.08544218 6.76258621746E+001
0.08819838 7.42547525137E+001
0.09095458 8.36609186243E+001
0.09371078 9.85061099523E+001
0.09646698 1.27311868398E+002
0.09922318 2.32639170571E+002
0.10197938 6.44077037392E-001
0.10473558 1.42624785572E-001
0.10749178 6.85270382717E-002
0.11024798 4.21156913044E-002
0.11300418 2.92611068846E-002
0.11576038 2.18831677247E-002
0.11851657 1.71893611384E-002
0.12127277 1.39846258022E-002
0.12402897 1.16808092857E-002
0.12678517 9.95823555530E-003
0.12954137 8.62972318721E-003
0.13229757 7.57912401549E-003
0.13505377 6.73093275435E-003
0.13780997 6.03415355952E-003
0.14056617 5.45322627939E-003
0.14332237 4.96267285719E-003
0.14607857 4.54380841883E-003
0.14883477 4.18264961408E-003
0.15159097 3.86854402491E-003
0.15434717 3.59324816883E-003
0.15710337 3.35029279868E-003
0.15985957 3.13453690263E-003
0.16261576 2.94184848665E-003
0.16537196 2.76887228533E-003
0.16812816 2.61285817640E-003
0.17088436 2.47153269574E-003
0.17364056 2.34300162060E-003
0.17639676 2.22567525998E-003
0.17915296 2.11821055356E-003
0.18190916 2.01946575945E-003
0.18466536 1.92846467311E-003
0.18742156 1.84436813537E-003
0.19017776 1.76645116715E-003
0.19293396 1.69408448583E-003
0.19569016 1.62671946138E-003
0.19844636 1.56387579375E-003
0.20120256 1.50513135843E-003
0.20395876 1.45011379129E-003
0.20671496 1.39849347741E-003
0.20947115 1.34997768030E-003
0.21222735 1.30430560231E-003
0.21498355 1.26124420987E-003
0.21773975 1.22058468988E-003
0.22049595 1.18213942951E-003
0.22325215 1.14573943223E-003
0.22600835 1.11123209864E-003
0.22876455 1.07847931412E-003
0.23152075 1.04735579508E-003
0.23427695 1.01774765446E-003
0.23703315 9.89551153332E-004
0.23978935 9.62671611463E-004
0.24254555 9.37022453751E-004
0.24530175 9.12524373414E-004
0.24805795 8.89104595664E-004
0.25081415 8.66696228200E-004
0.25357035 8.45237686899E-004
0.25632654 8.24672186805E-004
0.25908274 8.04947290000E-004
0.26183894 7.86014503122E-004
0.26459514 7.67828918336E-004
0.26735134 7.50348892428E-004
0.27010754 7.33535759411E-004
0.27286374 7.17353572667E-004
0.27561994 7.01768873168E-004
0.27837614 6.86750480765E-004
0.28113234 6.72269305953E-004
0.28388854 6.58298179794E-004
0.28664474 6.44811700027E-004
0.28940094 6.31786091598E-004
0.29215714 6.19199080063E-004
0.29491334 6.07029776531E-004
0.29766954 5.95258572918E-004
0.30042574 5.83867046485E-004
0.30318193 5.72837872704E-004
0.30593813 5.62154745627E-004
0.30869433 5.51802305020E-004
0.31145053 5.41766069613E-004
0.31420673 5.32032375866E-004
0.31696293 5.22588321743E-004
0.31971913 5.13421715016E-004
0.32247533 5.04521025692E-004
0.32523153 4.95875342174E-004
0.32798773 4.87474330839E-004
0.33074393 4.79308198708E-004
0.33350013 4.71367658951E-004
0.33625633 4.63643898981E-004
0.33901253 4.56128550903E-004
0.34176873 4.48813664133E-004
0.34452493 4.41691679995E-004
0.34728113 4.34755408139E-004
0.35003732 4.27998004623E-004
0.35279352 4.21412951534E-004
0.35554972 4.14994038011E-004
0.35830592 4.08735342578E-004
0.36106212 4.02631216665E-004
0.36381832 3.96676269236E-004
0.36657452 3.90865352436E-004
0.36933072 3.85193548181E-004
0.37208692 3.79656155615E-004
0.37484312 3.74248679378E-004
0.37759932 3.68966818617E-004
0.38035552 3.63806456691E-004
0.38311172 3.58763651516E-004
0.38586792 3.53834626508E-004
0.38862412 3.49015762080E-004
0.39138032 3.44303587652E-004
0.39413651 3.39694774143E-004
0.39689271 3.35186126908E-004
0.39964891 3.30774579088E-004
0.40240511 3.26457185353E-004
0.40516131 3.22231116002E-004
0.40791751 3.18093651404E-004
0.41067371 3.14042176752E-004
0.41342991 3.10074177113E-004
0.41618611 3.06187232756E-004
0.41894231 3.02379014732E-004
0.42169851 2.98647280702E-004
0.42445471 2.94989870992E-004
0.42721091 2.91404704852E-004
0.42996711 2.87889776925E-004
0.43272331 2.84443153897E-004
0.43547951 2.81062971323E-004
0.43823571 2.77747430618E-004
0.44099190 2.74494796207E-004
0.44374810 2.71303392817E-004
0.44650430 2.68171602908E-004
0.44926050 2.65097864229E-004
0.45201670 2.62080667507E-004
0.45477290 2.59118554237E-004
0.45752910 2.56210114591E-004
0.46028530 2.53353985425E-004
0.46304150 2.50548848380E-004
0.46579770 2.47793428078E-004
0.46855390 2.45086490405E-004
0.47131010 2.42426840871E-004
0.47406630 2.39813323047E-004
0.47682250 2.37244817083E-004
0.47957870 2.34720238280E-004
0.48233490 2.32238535744E-004
0.48509110 2.29798691088E-004
0.48784729 2.27399717198E-004
0.49060349 2.25040657059E-004
0.49335969 2.22720582625E-004
0.49611589 2.20438593741E-004
0.49887209 2.18193817120E-004
0.50162829 2.15985405353E-004
0.50438449 2.13812535973E-004
0.50714069 2.11674410548E-004
0.50989689 2.09570253824E-004
0.51265309 2.07499312899E-004
0.51540929 2.05460856426E-004
0.51816549 2.03454173864E-004
0.52092169 2.01478574746E-004
0.52367789 1.99533387983E-004
0.52643409 1.97617961200E-004
0.52919029 1.95731660093E-004
0.53194649 1.93873867813E-004
0.53470268 1.92043984380E-004
0.53745888 1.90241426114E-004
0.54021508 1.88465625093E-004
0.54297128 1.86716028632E-004
0.54572748 1.84992098776E-004
0.54848368 1.83293311825E-004
0.55123988 1.81619157865E-004

404
tests/QS/regtest-negf-1/H28-transm-0-1_0.transm Normal file
View file

@ -0,0 +1,404 @@
# Transmission coefficient (G0 = 2 e^2/h) for the scattering region
# Energy (a.u.) Transmission coefficient [alpha + beta]
# ------------------------------------------------------------------------------
-0.55123988 3.80877855732E-026
-0.54848368 3.59764213446E-026
-0.54572748 3.37854830987E-026
-0.54297128 3.15006101443E-026
-0.54021508 2.91072918567E-026
-0.53745888 2.65920045655E-026
-0.53470268 2.39441692896E-026
-0.53194649 2.11594152362E-026
-0.52919029 1.82449107615E-026
-0.52643409 1.52279596598E-026
-0.52367789 1.21697502326E-026
-0.52092169 9.18723872510E-027
-0.51816549 6.48789156630E-027
-0.51540929 4.42479869799E-027
-0.51265309 3.58414968024E-027
-0.50989689 4.92429560011E-027
-0.50714069 9.99735171363E-027
-0.50438449 2.13034281282E-026
-0.50162829 4.28589460966E-026
-0.49887209 8.11122240813E-026
-0.49611589 1.46425311252E-025
-0.49335969 2.55484212206E-025
-0.49060349 4.35240068838E-025
-0.48784729 7.29390274807E-025
-0.48509110 1.20910020066E-024
-0.48233490 1.99085186133E-024
-0.47957870 3.26635325090E-024
-0.47682250 5.35300476864E-024
-0.47406630 8.77966841557E-024
-0.47131010 1.44335387961E-023
-0.46855390 2.38136360830E-023
-0.46579770 3.94719474772E-023
-0.46304150 6.57877786803E-023
-0.46028530 1.10339341465E-022
-0.45752910 1.86356333992E-022
-0.45477290 3.17149293647E-022
-0.45201670 5.44192986028E-022
-0.44926050 9.42041274775E-022
-0.44650430 1.64616748977E-021
-0.44374810 2.90557093270E-021
-0.44099190 5.18347423992E-021
-0.43823571 9.35273272698E-021
-0.43547951 1.70805934816E-020
-0.43272331 3.15980997731E-020
-0.42996711 5.92642914645E-020
-0.42721091 1.12802905258E-019
-0.42445471 2.18128028481E-019
-0.42169851 4.29034916895E-019
-0.41894231 8.59523397092E-019
-0.41618611 1.75663676164E-018
-0.41342991 3.66892533046E-018
-0.41067371 7.84731824541E-018
-0.40791751 1.72293445105E-017
-0.40516131 3.89406781863E-017
-0.40240511 9.09029350715E-017
-0.39964891 2.20059023768E-016
-0.39689271 5.55161284294E-016
-0.39413651 1.46845951087E-015
-0.39138032 4.10403524323E-015
-0.38862412 1.22403354379E-014
-0.38586792 3.94791891529E-014
-0.38311172 1.40241540019E-013
-0.38035552 5.63341370008E-013
-0.37759932 2.66435540326E-012
-0.37484312 1.58689966983E-011
-0.37208692 1.35168551909E-010
-0.36933072 2.22062425195E-009
-0.36657452 2.26637104435E-007
-0.36381832 9.83724629128E-001
-0.36106212 9.92278527896E-001
-0.35830592 9.94045406137E-001
-0.35554972 9.94980911242E-001
-0.35279352 9.95599015127E-001
-0.35003732 9.96034274112E-001
-0.34728113 9.96355269535E-001
-0.34452493 9.96604530329E-001
-0.34176873 9.96807716948E-001
-0.33901253 9.96979311722E-001
-0.33625633 9.97127203874E-001
-0.33350013 9.97255927278E-001
-0.33074393 9.97368571599E-001
-0.32798773 9.97467658525E-001
-0.32523153 9.97555501461E-001
-0.32247533 9.97634135875E-001
-0.31971913 9.97705293649E-001
-0.31696293 9.97770341938E-001
-0.31420673 9.97830290384E-001
-0.31145053 9.97885846119E-001
-0.30869433 9.97937494409E-001
-0.30593813 9.97985581896E-001
-0.30318193 9.98030385967E-001
-0.30042574 9.98072162199E-001
-0.29766954 9.98111169045E-001
-0.29491334 9.98147673771E-001
-0.29215714 9.98181945916E-001
-0.28940094 9.98214244787E-001
-0.28664474 9.98244806392E-001
-0.28388854 9.98273833481E-001
-0.28113234 9.98301490522E-001
-0.27837614 9.98327903869E-001
-0.27561994 9.98353166287E-001
-0.27286374 9.98377344362E-001
-0.27010754 9.98400487141E-001
-0.26735134 9.98422634533E-001
-0.26459514 9.98443824328E-001
-0.26183894 9.98464097162E-001
-0.25908274 9.98483499200E-001
-0.25632654 9.98502082678E-001
-0.25357035 9.98519904723E-001
-0.25081415 9.98537025005E-001
-0.24805795 9.98553502832E-001
-0.24530175 9.98569394235E-001
-0.24254555 9.98584749487E-001
-0.23978935 9.98599611354E-001
-0.23703315 9.98614014224E-001
-0.23427695 9.98627984120E-001
-0.23152075 9.98641539478E-001
-0.22876455 9.98654692511E-001
-0.22600835 9.98667450779E-001
-0.22325215 9.98675276397E-001
-0.22049595 9.98691807832E-001
-0.21773975 9.98703412821E-001
-0.21498355 9.98714645986E-001
-0.21222735 9.98725516763E-001
-0.20947115 9.98736037695E-001
-0.20671496 9.98746224031E-001
-0.20395876 9.98756093172E-001
-0.20120256 9.98765663892E-001
-0.19844636 9.98774955420E-001
-0.19569016 9.98783986504E-001
-0.19293396 9.98792774531E-001
-0.19017776 9.98801334805E-001
-0.18742156 9.98809680020E-001
-0.18466536 9.98817819970E-001
-0.18190916 9.98825761500E-001
-0.17915296 9.98833508682E-001
-0.17639676 9.98841063184E-001
-0.17364056 9.98848424778E-001
-0.17088436 9.98855591953E-001
-0.16812816 9.98862562548E-001
-0.16537196 9.98869334382E-001
-0.16261576 9.98875905808E-001
-0.15985957 9.98882276170E-001
-0.15710337 9.98888446124E-001
-0.15434717 9.98894417823E-001
-0.15159097 9.98900194951E-001
-0.14883477 9.98905782611E-001
-0.14607857 9.98911187111E-001
-0.14332237 9.98916415638E-001
-0.14056617 9.98921475872E-001
-0.13780997 9.98926375571E-001
-0.13505377 9.98931122154E-001
-0.13229757 9.98935722301E-001
-0.12954137 9.98940181627E-001
-0.12678517 9.98944504417E-001
-0.12402897 9.98948693453E-001
-0.12127277 9.98952749935E-001
-0.11851657 9.98956673507E-001
-0.11576038 9.98960462357E-001
-0.11300418 9.98964113421E-001
-0.11024798 9.98967622630E-001
-0.10749178 9.98970985204E-001
-0.10473558 9.98974195990E-001
-0.10197938 9.98977249780E-001
-0.09922318 9.98980141632E-001
-0.09646698 9.98982867137E-001
-0.09371078 9.98985422650E-001
-0.09095458 9.98987805453E-001
-0.08819838 9.98990013841E-001
-0.08544218 9.98992047138E-001
-0.08268598 9.98993905637E-001
-0.07992978 9.98995590467E-001
-0.07717358 9.98997103395E-001
-0.07441738 9.98998446580E-001
-0.07166118 9.98999622290E-001
-0.06890499 9.99000632591E-001
-0.06614879 9.99001479035E-001
-0.06339259 9.99002162355E-001
-0.06063639 9.99002682186E-001
-0.05788019 9.99003036830E-001
-0.05512399 9.99003223063E-001
-0.05236779 9.99003236020E-001
-0.04961159 9.99003069137E-001
-0.04685539 9.99002714206E-001
-0.04409919 9.99002161776E-001
-0.04134299 9.99001375662E-001
-0.03858679 9.99000410049E-001
-0.03583059 9.98999189522E-001
-0.03307439 9.98997717751E-001
-0.03031819 9.98995980000E-001
-0.02756199 9.98993960969E-001
-0.02480579 9.98991645302E-001
-0.02204960 9.98989017840E-001
-0.01929340 9.98986063781E-001
-0.01653720 9.98982768755E-001
-0.01378100 9.98979118810E-001
-0.01102480 9.98975100286E-001
-0.00826860 9.98970699576E-001
-0.00551240 9.98965902763E-001
-0.00275620 9.98960695129E-001
0.00000000 9.98955060534E-001
0.00275620 9.98948980679E-001
0.00551240 9.98942434242E-001
0.00826860 9.98935395917E-001
0.01102480 9.98927835355E-001
0.01378100 9.98919716028E-001
0.01653720 9.98910994032E-001
0.01929340 9.98901616839E-001
0.02204960 9.98891521999E-001
0.02480579 9.98880635869E-001
0.02756199 9.98868872238E-001
0.03031819 9.98856130966E-001
0.03307439 9.98842296533E-001
0.03583059 9.98827236457E-001
0.03858679 9.98810799502E-001
0.04134299 9.98792813515E-001
0.04409919 9.98773082694E-001
0.04685539 9.98751383946E-001
0.04961159 9.98727461888E-001
0.05236779 9.98701021773E-001
0.05512399 9.98671719316E-001
0.05788019 9.98639145858E-001
0.06063639 9.98602806468E-001
0.06339259 9.98562087263E-001
0.06614879 9.98516205910E-001
0.06890499 9.98464135413E-001
0.07166118 9.98404484115E-001
0.07441738 9.98335301480E-001
0.07717358 9.98253752358E-001
0.07992978 9.98155545436E-001
0.08268598 9.98033870366E-001
0.08544218 9.97877265696E-001
0.08819838 9.97664885592E-001
0.09095458 9.97354391763E-001
0.09371078 9.96843621781E-001
0.09646698 9.95795251840E-001
0.09922318 9.91590689622E-001
0.10197938 1.31180785730E-006
0.10473558 4.51464127333E-008
0.10749178 6.32536352080E-009
0.11024798 1.44416637705E-009
0.11300418 4.26252351599E-010
0.11576038 1.47557965378E-010
0.11851657 5.69143896984E-011
0.12127277 2.37112686648E-011
0.12402897 1.04502608662E-011
0.12678517 4.79903671059E-012
0.12954137 2.26897092262E-012
0.13229757 1.09311417650E-012
0.13505377 5.31388907066E-013
0.13780997 2.57985064683E-013
0.14056617 1.23578176116E-013
0.14332237 5.74756657332E-014
0.14607857 2.53403215706E-014
0.14883477 1.01646934739E-014
0.15159097 3.41001861413E-015
0.15434717 7.58319100560E-016
0.15710337 2.64452520923E-017
0.15985957 1.21406174043E-016
0.16261576 5.09031526367E-016
0.16537196 9.40672154819E-016
0.16812816 1.31168929676E-015
0.17088436 1.58808802318E-015
0.17364056 1.76869046573E-015
0.17639676 1.86592628363E-015
0.17915296 1.89636937251E-015
0.18190916 1.87633990003E-015
0.18466536 1.82009509602E-015
0.18742156 1.73930128447E-015
0.19017776 1.64310273068E-015
0.19293396 1.53843540252E-015
0.19569016 1.43041062249E-015
0.19844636 1.32268677959E-015
0.20120256 1.21779545977E-015
0.20395876 1.11741244423E-015
0.20671496 1.02257534189E-015
0.20947115 9.33854298101E-016
0.21222735 8.51483560313E-016
0.21498355 7.75461443059E-016
0.21773975 7.05625340815E-016
0.22049595 6.41707351679E-016
0.22325215 5.83375019258E-016
0.22600835 5.30260767054E-016
0.22876455 4.81982816703E-016
0.23152075 4.38159745405E-016
0.23427695 3.98420331960E-016
0.23703315 3.62409944464E-016
0.23978935 3.29794415509E-016
0.24254555 3.00262114611E-016
0.24530175 2.73524747265E-016
0.24805795 2.49317273111E-016
0.25081415 2.27397232150E-016
0.25357035 2.07543690076E-016
0.25632654 1.89555955359E-016
0.25908274 1.73252177184E-016
0.26183894 1.58467900952E-016
0.26459514 1.45054634188E-016
0.26735134 1.32878458116E-016
0.27010754 1.21818707417E-016
0.27286374 1.11766731448E-016
0.27561994 1.02624743643E-016
0.27837614 9.43047612097E-017
0.28113234 8.67276340889E-017
0.28388854 7.98221600336E-017
0.28664474 7.35242813661E-017
0.28940094 6.77763581850E-017
0.29215714 6.25265124317E-017
0.29491334 5.77280371282E-017
0.29766954 5.33388651877E-017
0.30042574 4.93210924167E-017
0.30318193 4.56405496201E-017
0.30593813 4.22664190572E-017
0.30869433 3.91708908527E-017
0.31145053 3.63288553295E-017
0.31420673 3.37176275817E-017
0.31696293 3.13167009448E-017
0.31971913 2.91075263399E-017
0.32247533 2.70733147641E-017
0.32523153 2.51988604769E-017
0.32798773 2.34703826790E-017
0.33074393 2.18753837138E-017
0.33350013 2.04025220245E-017
0.33625633 1.90414982914E-017
0.33901253 1.77829533405E-017
0.34176873 1.66183765650E-017
0.34452493 1.55400237399E-017
0.34728113 1.45408432293E-017
0.35003732 1.36144096942E-017
0.35279352 1.27548645083E-017
0.35554972 1.19568621710E-017
0.35830592 1.12155220886E-017
0.36106212 1.05263851593E-017
0.36381832 9.88537466124E-018
0.36657452 9.28876099571E-018
0.36933072 8.73312988574E-018
0.37208692 8.21535367468E-018
0.37484312 7.73256540603E-018
0.37759932 7.28213540070E-018
0.38035552 6.86165007782E-018
0.38311172 6.46889279231E-018
0.38586792 6.10182648618E-018
0.38862412 5.75857797222E-018
0.39138032 5.43742368750E-018
0.39413651 5.13677677110E-018
0.39689271 4.85517533577E-018
0.39964891 4.59127181656E-018
0.40240511 4.34382329150E-018
0.40516131 4.11168268025E-018
0.40791751 3.89379073611E-018
0.41067371 3.68916875548E-018
0.41342991 3.49691193641E-018
0.41618611 3.31618332488E-018
0.41894231 3.14620829334E-018
0.42169851 2.98626950186E-018
0.42445471 2.83570229695E-018
0.42721091 2.69389050743E-018
0.42996711 2.56026260107E-018
0.43272331 2.43428816882E-018
0.43547951 2.31547470692E-018
0.43823571 2.20336467005E-018
0.44099190 2.09753277101E-018
0.44374810 1.99758350506E-018
0.44650430 1.90314887887E-018
0.44926050 1.81388632610E-018
0.45201670 1.72947679315E-018
0.45477290 1.64962298028E-018
0.45752910 1.57404772464E-018
0.46028530 1.50249251289E-018
0.46304150 1.43471611241E-018
0.46579770 1.37049331092E-018
0.46855390 1.30961375527E-018
0.47131010 1.25188088122E-018
0.47406630 1.19711092638E-018
0.47682250 1.14513201955E-018
0.47957870 1.09578333998E-018
0.48233490 1.04891434095E-018
0.48509110 1.00438403232E-018
0.48784729 9.62060317169E-019
0.49060349 9.21819378354E-019
0.49335969 8.83545110766E-019
0.49611589 8.47128595734E-019
0.49887209 8.12467614202E-019
0.50162829 7.79466195595E-019
0.50438449 7.48034199586E-019
0.50714069 7.18086928172E-019
0.50989689 6.89544765712E-019
0.51265309 6.62332844760E-019
0.51540929 6.36380735703E-019
0.51816549 6.11622158394E-019
0.52092169 5.87994714088E-019
0.52367789 5.65439636166E-019
0.52643409 5.43901558209E-019
0.52919029 5.23328298148E-019
0.53194649 5.03670657270E-019
0.53470268 4.84882232996E-019
0.53745888 4.66919244405E-019
0.54021508 4.49740369585E-019
0.54297128 4.33306593929E-019
0.54572748 4.17581068602E-019
0.54848368 4.02528978433E-019
0.55123988 3.88117418563E-019

238
tests/QS/regtest-negf-1/H28.inp Normal file
View file

@ -0,0 +1,238 @@
@SET Project H28
@SET V_bias_volt 0.0
@SET Temperature 10.0
# The following two parameters are computed automatically during the NEGF run.
# You can use keywords 'FERMI_LEVEL' to give this value and skip calculation
# or 'FERMI_LEVEL'+'REFINE_FERMI_LEVEL' to compute starting from this value.
# If 'FERMI_LEVEL' is not given, it is calculated automatically.
# 'V_SHIFT' is used to give initial value.
@SET Fermi_level -0.22306314
@SET V_shift 0.00011054
@SET basis_set_path BASIS_SET
! BASIS_MOLOPT BASIS_SET
@SET potential_path GTH_POTENTIALS
@SET xc_functional pade
!PBE pade
@SET cutoff 300
@SET added_mos -1
@SET max_scf 50
@SET eps_scf 1e-8
@SET lx 6.0
@SET ly 6.0
!---------------------------------------------------------------------------------------------------
&GLOBAL
EXTENDED_FFT_LENGTHS .true.
PREFERRED_DIAG_LIBRARY SL
PRINT_LEVEL LOW #SILENT #LOW #MEDIUM #HIGH #DEBUG
PROJECT ${Project}
RUN_TYPE NEGF
&END GLOBAL
&NEGF
# Integration lower bound (in Hartree)
ENERGY_LBOUND -2.0
!clenshaw-curtis simpson
# Maximum error in each matrix element of the density matrix
EPS_DENSITY 1e-5
# 'simpson' is slower, but works without FFTW3 library
# clenshaw-curtis is faster, but requires FFTW3 library
INTEGRATION_METHOD simpson
!EPS_SCF 1e-5
MAX_SCF 100
# Number of parallel processes per energy point.
# 'NPROC_POINT 1' means that if you run this job using 8 MPI processes,
# than Green's functions at up to 8 (8 / NPROC_POINT) energy points
# will be computed simultaneously.
#
NPROC_POINT 1
!EPS_GREEN 1e-5
!ETA 1e-7
# Boundary conditions define solution of the Poisson equation up to
# an additive constant, which affects Hamiltonian matrix elements within
# the NEGF procedure. The following parameters control evaluation of
# the correct shift in Hartree potential:
# * V_SHIFT -- initial guess for the shift
# * V_SHIFT_MAX_ITERS -- maximal number of iterations
V_SHIFT ${V_shift}
V_SHIFT_MAX_ITERS 100
&CONTACT
ELECTRIC_POTENTIAL [eV] ${V_bias_volt}/2
FERMI_LEVEL ${Fermi_level}
REFINE_FERMI_LEVEL
TEMPERATURE [K] ${Temperature}
&BULK_REGION
# Atomic indices (and/or names of molecular fragments) that belong to the electrode contact region.
!MOLNAME L1 L2
LIST 1..8
# List of atoms that belong to the primary and secondary unit cells of the 1st contact.
# Primary and secondary unit cells can be defined in any order.
# They should be adjusted to each other and should not overlap.
#
# As matrix blocks should correspond to ones for the electrode contact region,
# in actual calculation you may want to use a longer chain, e.g.
# L1 L2 L3 L4 L5 L6 .
# cell1 cell2
# Alternatively, instead of the below CELL sections, a separate bulk FORCE_EVAL section
# for the contact can be set up and the keyword FORCE_EVAL_SECTION should be set accordingly
# (see the test file regtest-negf-2/H28_k.inp).
&CELL
!MOLNAME L1
LIST 1..4
&END CELL
&CELL
!MOLNAME L2
LIST 5..8
&END CELL
&END BULK_REGION
&SCREENING_REGION
!MOLNAME L0
LIST 9..12
&END SCREENING_REGION
&END CONTACT
&CONTACT
ELECTRIC_POTENTIAL [eV] -${V_bias_volt}/2
FERMI_LEVEL ${Fermi_level}
REFINE_FERMI_LEVEL
TEMPERATURE [K] ${Temperature}
# the second semi-infinite electrode
&BULK_REGION
MOLNAME R1 R2
&CELL
MOLNAME R1
&END CELL
&CELL
MOLNAME R2
&END CELL
&END BULK_REGION
&SCREENING_REGION
MOLNAME R0
&END SCREENING_REGION
&END CONTACT
# Density mixing is not needed in zero-bias case, as NEGF self-consistent
# procedure will converge in one iteration. However, when an external bias
# is applied, a density mixing scheme in inverse space is typically
# much stable then the default direct mixing of new and old density matrices.
&MIXING
ALPHA 0.2
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&DOS
FILENAME device
FROM_ENERGY [eV] -15
N_GRIDPOINTS 401
TILL_ENERGY [eV] 15
&END DOS
&PROGRAM_RUN_INFO low
PRINT_LEVEL debug
! high debug
&END PROGRAM_RUN_INFO
&TRANSMISSION
FILENAME transm
FROM_ENERGY [eV] -15
N_GRIDPOINTS 401
TILL_ENERGY [eV] 15
&END TRANSMISSION
&END PRINT
&SCATTERING_REGION
MOLNAME S
!LIST 13..16
&END SCATTERING_REGION
#DISABLE_CACHE
&END NEGF
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&PRINT
&PDOS
COMPONENTS
NLUMO -1
&END PDOS
&END PRINT
&SCF
!atomic restart
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS restart
&MIXING
ALPHA 0.3
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART
&END RESTART
#&PROGRAM_RUN_INFO silent
#&END
#&DETAILED_ENERGY silent
#&END
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${Temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC ${lx} ${ly} 42.
PERIODIC xyz
&END CELL
&COORD
H 0.00000000 0.00000000 0.00000000 L2
H 0.00000000 0.00000000 1.50000000 L2
H 0.00000000 0.00000000 3.00000000 L2
H 0.00000000 0.00000000 4.50000000 L2
H 0.00000000 0.00000000 6.00000000 L1
H 0.00000000 0.00000000 7.50000000 L1
H 0.00000000 0.00000000 9.00000000 L1
H 0.00000000 0.00000000 10.50000000 L1
H 0.00000000 0.00000000 12.00000000 L0
H 0.00000000 0.00000000 13.50000000 L0
H 0.00000000 0.00000000 15.00000000 L0
H 0.00000000 0.00000000 16.50000000 L0
H 0.00000000 0.00000000 18.00000000 S
H 0.00000000 0.00000000 19.50000000 S
H 0.00000000 0.00000000 21.00000000 S
H 0.00000000 0.00000000 22.50000000 S
H 0.00000000 0.00000000 24.00000000 R0
H 0.00000000 0.00000000 25.50000000 R0
H 0.00000000 0.00000000 27.00000000 R0
H 0.00000000 0.00000000 28.50000000 R0
H 0.00000000 0.00000000 30.00000000 R1
H 0.00000000 0.00000000 31.50000000 R1
H 0.00000000 0.00000000 33.00000000 R1
H 0.00000000 0.00000000 34.50000000 R1
H 0.00000000 0.00000000 36.00000000 R2
H 0.00000000 0.00000000 37.50000000 R2
H 0.00000000 0.00000000 39.00000000 R2
H 0.00000000 0.00000000 40.50000000 R2
# H 0.00000000 0.00000000 42.00000000 R3
# H 0.00000000 0.00000000 43.50000000 R3
# H 0.00000000 0.00000000 45.00000000 R3
# H 0.00000000 0.00000000 46.50000000 R3
&END COORD
&KIND H
BASIS_SET SZV-GTH-PADE
! SZV-GTH-PADE DZV-ALL-PADE DZVP-ALL-PADE SZV-MOLOPT-GTH
POTENTIAL GTH-PADE-q1
!GTH-PADE-q1 GTH-PBE-q1
&END KIND
&END SUBSYS
&END FORCE_EVAL

2
tests/QS/regtest-negf-fft/TEST_FILES.toml → tests/QS/regtest-negf-1/TEST_FILES.toml
View file

@ -4,4 +4,4 @@
# 1 compares the last total energy in the file
# for details see cp2k/tools/do_regtest
#
"li_chain_kp.inp" = []
"H28.inp" = []

404
tests/QS/regtest-negf-2/H28_k-device-0-1_0.dos Normal file
View file

@ -0,0 +1,404 @@
# Density of states for the scattering region
# Energy (a.u.) Number of states [alpha + beta]
# ------------------------------------------------------------------------------
-0.55123988 9.29725193576E-004
-0.54848368 9.51485980692E-004
-0.54572748 9.74081306699E-004
-0.54297128 9.97556502769E-004
-0.54021508 1.02196011647E-003
-0.53745888 1.04734419528E-003
-0.53470268 1.07376460018E-003
-0.53194649 1.10128135293E-003
-0.52919029 1.12995902146E-003
-0.52643409 1.15986714809E-003
-0.52367789 1.19108072633E-003
-0.52092169 1.22368073263E-003
-0.51816549 1.25775472058E-003
-0.51540929 1.29339748613E-003
-0.51265309 1.33071181384E-003
-0.50989689 1.36980931581E-003
-0.50714069 1.41081137671E-003
-0.50438449 1.45385022083E-003
-0.50162829 1.49907011962E-003
-0.49887209 1.54662876157E-003
-0.49611589 1.59669881006E-003
-0.49335969 1.64946967966E-003
-0.49060349 1.70514956706E-003
-0.48784729 1.76396777945E-003
-0.48509110 1.82617741218E-003
-0.48233490 1.89205843721E-003
-0.47957870 1.96192127703E-003
-0.47682250 2.03611095432E-003
-0.47406630 2.11501192695E-003
-0.47131010 2.19905374249E-003
-0.46855390 2.28871767669E-003
-0.46579770 2.38454455902E-003
-0.46304150 2.48714403719E-003
-0.46028530 2.59720559469E-003
-0.45752910 2.71551171581E-003
-0.45477290 2.84295369592E-003
-0.45201670 2.98055073005E-003
-0.44926050 3.12947308978E-003
-0.44650430 3.29107043355E-003
-0.44374810 3.46690660838E-003
-0.44099190 3.65880272356E-003
-0.43823571 3.86889085097E-003
-0.43547951 4.09968149661E-003
-0.43272331 4.35414908573E-003
-0.42996711 4.63584124843E-003
-0.42721091 4.94901989412E-003
-0.42445471 5.29884524383E-003
-0.42169851 5.69161865558E-003
-0.41894231 6.13510703504E-003
-0.41618611 6.63898218312E-003
-0.41342991 7.21542477371E-003
-0.41067371 7.87996849182E-003
-0.40791751 8.65270169018E-003
-0.40516131 9.56001343956E-003
-0.40240511 1.06371898278E-002
-0.39964891 1.19323768453E-002
-0.39689271 1.35128127868E-002
-0.39413651 1.54749743457E-002
-0.39138032 1.79617743532E-002
-0.38862412 2.11931404702E-002
-0.38586792 2.55236135129E-002
-0.38311172 3.15588223700E-002
-0.38035552 4.04131439686E-002
-0.37759932 5.43508692700E-002
-0.37484312 7.86627198137E-002
-0.37208692 1.28659852704E-001
-0.36933072 2.69130670949E-001
-0.36657452 1.23548287361E+000
-0.36381832 4.54615092904E+002
-0.36106212 2.46727429656E+002
-0.35830592 1.88684019922E+002
-0.35554972 1.58956496792E+002
-0.35279352 1.39966090296E+002
-0.35003732 1.26442527544E+002
-0.34728113 1.16206926241E+002
-0.34452493 1.08139838687E+002
-0.34176873 1.01580054543E+002
-0.33901253 9.61068308499E+001
-0.33625633 9.14428374575E+001
-0.33350013 8.74014111197E+001
-0.33074393 8.38538317626E+001
-0.32798773 8.07089175398E+001
-0.32523153 7.78978705356E+001
-0.32247533 7.53679439969E+001
-0.31971913 7.30764590888E+001
-0.31696293 7.09883732923E+001
-0.31420673 6.90747100440E+001
-0.31145053 6.73115636857E+001
-0.30869433 6.56793314542E+001
-0.30593813 6.41620172278E+001
-0.30318193 6.27465644191E+001
-0.30042574 6.14222310409E+001
-0.29766954 6.01800373314E+001
-0.29491334 5.90123115519E+001
-0.29215714 5.79123453783E+001
-0.28940094 5.68741551964E+001
-0.28664474 5.58923334881E+001
-0.28388854 5.49619681073E+001
-0.28113234 5.40786054625E+001
-0.27837614 5.32382360597E+001
-0.27561994 5.24372856085E+001
-0.27286374 5.16726006482E+001
-0.27010754 5.09414232157E+001
-0.26735134 5.02413536877E+001
-0.26459514 4.95703041932E+001
-0.26183894 4.89264468345E+001
-0.25908274 4.83081615346E+001
-0.25632654 4.77139879204E+001
-0.25357035 4.71425846093E+001
-0.25081415 4.65926979027E+001
-0.24805795 4.60631405014E+001
-0.24530175 4.55527796370E+001
-0.24254555 4.50605330959E+001
-0.23978935 4.45853710536E+001
-0.23703315 4.41263214354E+001
-0.23427695 4.36824766393E+001
-0.23152075 4.32529998738E+001
-0.22876455 4.28371303449E+001
-0.22600835 4.24341920801E+001
-0.22325215 4.20495184671E+001
-0.22049595 4.16645432788E+001
-0.21773975 4.12969423383E+001
-0.21498355 4.09401719248E+001
-0.21222735 4.05938559251E+001
-0.20947115 4.02576415364E+001
-0.20671496 3.99311976015E+001
-0.20395876 3.96142077778E+001
-0.20120256 3.93063646976E+001
-0.19844636 3.90073659721E+001
-0.19569016 3.87169121756E+001
-0.19293396 3.84347066794E+001
-0.19017776 3.81604570362E+001
-0.18742156 3.78938775180E+001
-0.18466536 3.76346923600E+001
-0.18190916 3.73826392529E+001
-0.17915296 3.71374726746E+001
-0.17639676 3.68989667003E+001
-0.17364056 3.66669170313E+001
-0.17088436 3.64411420805E+001
-0.16812816 3.62214830323E+001
-0.16537196 3.60078029252E+001
-0.16261576 3.57999848405E+001
-0.15985957 3.55979293888E+001
-0.15710337 3.54015516904E+001
-0.15434717 3.52107780984E+001
-0.15159097 3.50255428953E+001
-0.14883477 3.48457851891E+001
-0.14607857 3.46714462020E+001
-0.14332237 3.45024670985E+001
-0.14056617 3.43387874652E+001
-0.13780997 3.41803444847E+001
-0.13505377 3.40270728066E+001
-0.13229757 3.38789050730E+001
-0.12954137 3.37357730275E+001
-0.12678517 3.35976090376E+001
-0.12402897 3.34643480139E+001
-0.12127277 3.33359293793E+001
-0.11851657 3.32122992171E+001
-0.11576038 3.30934121388E+001
-0.11300418 3.29792330596E+001
-0.11024798 3.28697385047E+001
-0.10749178 3.27649176481E+001
-0.10473558 3.26647727684E+001
-0.10197938 3.25693193171E+001
-0.09922318 3.24785855146E+001
-0.09646698 3.23926115663E+001
-0.09371078 3.23114485254E+001
-0.09095458 3.22351569223E+001
-0.08819838 3.21638052442E+001
-0.08544218 3.20974683746E+001
-0.08268598 3.20362260979E+001
-0.07992978 3.19801617699E+001
-0.07717358 3.19293612490E+001
-0.07441738 3.18839121621E+001
-0.07166118 3.18439035687E+001
-0.06890499 3.18094260618E+001
-0.06614879 3.17805723253E+001
-0.06339259 3.17574381443E+001
-0.06063639 3.17401238412E+001
-0.05788019 3.17287360857E+001
-0.05512399 3.17233899880E+001
-0.05236779 3.17242113011E+001
-0.04961159 3.17313382536E+001
-0.04685539 3.17449208030E+001
-0.04409919 3.17650954367E+001
-0.04134299 3.17932112477E+001
-0.03858679 3.18265855427E+001
-0.03583059 3.18680094153E+001
-0.03307439 3.19170618611E+001
-0.03031819 3.19740323152E+001
-0.02756199 3.20392615711E+001
-0.02480579 3.21131289675E+001
-0.02204960 3.21960516251E+001
-0.01929340 3.22884853315E+001
-0.01653720 3.23909258902E+001
-0.01378100 3.25039107971E+001
-0.01102480 3.26280213403E+001
-0.00826860 3.27638852963E+001
-0.00551240 3.29121804371E+001
-0.00275620 3.30736391037E+001
0.00000000 3.32490541265E+001
0.00275620 3.34392864103E+001
0.00551240 3.36452745320E+001
0.00826860 3.38680467582E+001
0.01102480 3.41087358094E+001
0.01378100 3.43685972314E+001
0.01653720 3.46490312763E+001
0.01929340 3.49516097173E+001
0.02204960 3.52781079047E+001
0.02480579 3.56305432212E+001
0.02756199 3.60112212630E+001
0.03031819 3.64227910782E+001
0.03307439 3.68683118067E+001
0.03583059 3.73513332487E+001
0.03858679 3.78759940379E+001
0.04134299 3.84471423214E+001
0.04409919 3.90704857595E+001
0.04685539 3.97527802571E+001
0.04961159 4.05020708345E+001
0.05236779 4.13280038858E+001
0.05512399 4.22422389688E+001
0.05788019 4.32590020921E+001
0.06063639 4.43958443237E+001
0.06339259 4.56747051876E+001
0.06614879 4.71234400434E+001
0.06890499 4.87780742440E+001
0.07166118 5.06862336521E+001
0.07441738 5.29125533431E+001
0.07717358 5.55475667025E+001
0.07992978 5.87230603809E+001
0.08268598 6.26402722750E+001
0.08544218 6.76258437599E+001
0.08819838 7.42547261342E+001
0.09095458 8.36608819061E+001
0.09371078 9.85060626402E+001
0.09646698 1.27311831897E+002
0.09922318 2.32639714396E+002
0.10197938 6.44074495535E-001
0.10473558 1.42624690187E-001
0.10749178 6.85270256805E-002
0.11024798 4.21156898829E-002
0.11300418 2.92611076421E-002
0.11576038 2.18831688704E-002
0.11851657 1.71893622460E-002
0.12127277 1.39846267757E-002
0.12402897 1.16808101182E-002
0.12678517 9.95823626299E-003
0.12954137 8.62972379021E-003
0.13229757 7.57912453215E-003
0.13505377 6.73093320005E-003
0.13780997 6.03415394673E-003
0.14056617 5.45322661814E-003
0.14332237 4.96267315551E-003
0.14607857 4.54380868320E-003
0.14883477 4.18264984973E-003
0.15159097 3.86854423609E-003
0.15434717 3.59324835905E-003
0.15710337 3.35029297081E-003
0.15985957 3.13453705906E-003
0.16261576 2.94184862939E-003
0.16537196 2.76887241606E-003
0.16812816 2.61285829655E-003
0.17088436 2.47153280653E-003
0.17364056 2.34300172306E-003
0.17639676 2.22567535500E-003
0.17915296 2.11821064193E-003
0.18190916 2.01946584183E-003
0.18466536 1.92846475009E-003
0.18742156 1.84436820745E-003
0.19017776 1.76645123479E-003
0.19293396 1.69408454943E-003
0.19569016 1.62671952129E-003
0.19844636 1.56387585028E-003
0.20120256 1.50513141187E-003
0.20395876 1.45011384187E-003
0.20671496 1.39849352537E-003
0.20947115 1.34997772583E-003
0.21222735 1.30430564559E-003
0.21498355 1.26124425107E-003
0.21773975 1.22058472914E-003
0.22049595 1.18213946698E-003
0.22325215 1.14573946802E-003
0.22600835 1.11123213286E-003
0.22876455 1.07847934687E-003
0.23152075 1.04735582646E-003
0.23427695 1.01774768455E-003
0.23703315 9.89551182217E-004
0.23978935 9.62671639211E-004
0.24254555 9.37022480429E-004
0.24530175 9.12524399084E-004
0.24805795 8.89104620381E-004
0.25081415 8.66696252018E-004
0.25357035 8.45237709866E-004
0.25632654 8.24672208966E-004
0.25908274 8.04947311398E-004
0.26183894 7.86014523796E-004
0.26459514 7.67828938322E-004
0.26735134 7.50348911760E-004
0.27010754 7.33535778121E-004
0.27286374 7.17353590786E-004
0.27561994 7.01768890722E-004
0.27837614 6.86750497781E-004
0.28113234 6.72269322455E-004
0.28388854 6.58298195806E-004
0.28664474 6.44811715571E-004
0.28940094 6.31786106693E-004
0.29215714 6.19199094729E-004
0.29491334 6.07029790785E-004
0.29766954 5.95258586778E-004
0.30042574 5.83867059968E-004
0.30318193 5.72837885824E-004
0.30593813 5.62154758399E-004
0.30869433 5.51802317458E-004
0.31145053 5.41766081729E-004
0.31420673 5.32032387674E-004
0.31696293 5.22588333253E-004
0.31971913 5.13421726240E-004
0.32247533 5.04521036639E-004
0.32523153 4.95875352856E-004
0.32798773 4.87474341265E-004
0.33074393 4.79308208886E-004
0.33350013 4.71367668891E-004
0.33625633 4.63643908691E-004
0.33901253 4.56128560390E-004
0.34176873 4.48813673404E-004
0.34452493 4.41691689059E-004
0.34728113 4.34755417002E-004
0.35003732 4.27998013292E-004
0.35279352 4.21412960014E-004
0.35554972 4.14994046309E-004
0.35830592 4.08735350700E-004
0.36106212 4.02631224616E-004
0.36381832 3.96676277021E-004
0.36657452 3.90865360061E-004
0.36933072 3.85193555650E-004
0.37208692 3.79656162933E-004
0.37484312 3.74248686549E-004
0.37759932 3.68966825646E-004
0.38035552 3.63806463582E-004
0.38311172 3.58763658273E-004
0.38586792 3.53834633134E-004
0.38862412 3.49015768579E-004
0.39138032 3.44303594028E-004
0.39413651 3.39694780399E-004
0.39689271 3.35186133047E-004
0.39964891 3.30774585114E-004
0.40240511 3.26457191268E-004
0.40516131 3.22231121810E-004
0.40791751 3.18093657107E-004
0.41067371 3.14042182353E-004
0.41342991 3.10074182615E-004
0.41618611 3.06187238161E-004
0.41894231 3.02379020043E-004
0.42169851 2.98647285921E-004
0.42445471 2.94989876121E-004
0.42721091 2.91404709894E-004
0.42996711 2.87889781882E-004
0.43272331 2.84443158771E-004
0.43547951 2.81062976115E-004
0.43823571 2.77747435331E-004
0.44099190 2.74494800843E-004
0.44374810 2.71303397378E-004
0.44650430 2.68171607394E-004
0.44926050 2.65097868644E-004
0.45201670 2.62080671851E-004
0.45477290 2.59118558513E-004
0.45752910 2.56210118800E-004
0.46028530 2.53353989568E-004
0.46304150 2.50548852458E-004
0.46579770 2.47793432094E-004
0.46855390 2.45086494359E-004
0.47131010 2.42426844765E-004
0.47406630 2.39813326883E-004
0.47682250 2.37244820861E-004
0.47957870 2.34720242002E-004
0.48233490 2.32238539411E-004
0.48509110 2.29798694700E-004
0.48784729 2.27399720758E-004
0.49060349 2.25040660567E-004
0.49335969 2.22720586082E-004
0.49611589 2.20438597149E-004
0.49887209 2.18193820479E-004
0.50162829 2.15985408665E-004
0.50438449 2.13812539238E-004
0.50714069 2.11674413767E-004
0.50989689 2.09570256999E-004
0.51265309 2.07499316029E-004
0.51540929 2.05460859513E-004
0.51816549 2.03454176909E-004
0.52092169 2.01478577749E-004
0.52367789 1.99533390946E-004
0.52643409 1.97617964124E-004
0.52919029 1.95731662977E-004
0.53194649 1.93873870659E-004
0.53470268 1.92043987188E-004
0.53745888 1.90241428885E-004
0.54021508 1.88465627829E-004
0.54297128 1.86716031331E-004
0.54572748 1.84992101440E-004
0.54848368 1.83293314455E-004
0.55123988 1.81619160462E-004

404
tests/QS/regtest-negf-2/H28_k-transm-0-1_0.transm Normal file
View file

@ -0,0 +1,404 @@
# Transmission coefficient (G0 = 2 e^2/h) for the scattering region
# Energy (a.u.) Transmission coefficient [alpha + beta]
# ------------------------------------------------------------------------------
-0.55123988 3.80877958658E-026
-0.54848368 3.59764317765E-026
-0.54572748 3.37854937265E-026
-0.54297128 3.15006210296E-026
-0.54021508 2.91073030650E-026
-0.53745888 2.65920161634E-026
-0.53470268 2.39441813406E-026
-0.53194649 2.11594277923E-026
-0.52919029 1.82449238498E-026
-0.52643409 1.52279732603E-026
-0.52367789 1.21697642422E-026
-0.52092169 9.18725289901E-027
-0.51816549 6.48790542536E-027
-0.51540929 4.42481138020E-027
-0.51265309 3.58415970426E-027
-0.50989689 4.92430048816E-027
-0.50714069 9.99734738928E-027
-0.50438449 2.13034079524E-026
-0.50162829 4.28588993198E-026
-0.49887209 8.11121333485E-026
-0.49611589 1.46425148565E-025
-0.49335969 2.55483932352E-025
-0.49060349 4.35239598661E-025
-0.48784729 7.29389495557E-025
-0.48509110 1.20909891883E-024
-0.48233490 1.99084976014E-024
-0.47957870 3.26634980907E-024
-0.47682250 5.35299912351E-024
-0.47406630 8.77965913068E-024
-0.47131010 1.44335234638E-023
-0.46855390 2.38136106394E-023
-0.46579770 3.94719050117E-023
-0.46304150 6.57877073494E-023
-0.46028530 1.10339220803E-022
-0.45752910 1.86356128322E-022
-0.45477290 3.17148940213E-022
-0.45201670 5.44192373364E-022
-0.44926050 9.42040202884E-022
-0.44650430 1.64616559595E-021
-0.44374810 2.90556755172E-021
-0.44099190 5.18346813697E-021
-0.43823571 9.35272158094E-021
-0.43547951 1.70805728702E-020
-0.43272331 3.15980611499E-020
-0.42996711 5.92642180590E-020
-0.42721091 1.12802763622E-019
-0.42445471 2.18127750727E-019
-0.42169851 4.29034362626E-019
-0.41894231 8.59522270014E-019
-0.41618611 1.75663442257E-018
-0.41342991 3.66892036722E-018
-0.41067371 7.84730745546E-018
-0.40791751 1.72293204202E-017
-0.40516131 3.89406227933E-017
-0.40240511 9.09028034607E-017
-0.39964891 2.20058699374E-016
-0.39689271 5.55160450845E-016
-0.39413651 1.46845726564E-015
-0.39138032 4.10402885463E-015
-0.38862412 1.22403160578E-014
-0.38586792 3.94791257124E-014
-0.38311172 1.40241312293E-013
-0.38035552 5.63340453839E-013
-0.37759932 2.66435114619E-012
-0.37484312 1.58689729390E-011
-0.37208692 1.35168389347E-010
-0.36933072 2.22062379755E-009
-0.36657452 2.26638604399E-007
-0.36381832 9.83723539301E-001
-0.36106212 9.92278507553E-001
-0.35830592 9.94045414168E-001
-0.35554972 9.94980909768E-001
-0.35279352 9.95599011629E-001
-0.35003732 9.96034272128E-001
-0.34728113 9.96355268823E-001
-0.34452493 9.96604529786E-001
-0.34176873 9.96807715913E-001
-0.33901253 9.96979310136E-001
-0.33625633 9.97127202006E-001
-0.33350013 9.97255925392E-001
-0.33074393 9.97368568745E-001
-0.32798773 9.97467658237E-001
-0.32523153 9.97555501265E-001
-0.32247533 9.97634135853E-001
-0.31971913 9.97705293709E-001
-0.31696293 9.97770341990E-001
-0.31420673 9.97830290375E-001
-0.31145053 9.97885846035E-001
-0.30869433 9.97937494264E-001
-0.30593813 9.97985581717E-001
-0.30318193 9.98030385784E-001
-0.30042574 9.98072162035E-001
-0.29766954 9.98111168910E-001
-0.29491334 9.98147673665E-001
-0.29215714 9.98181945830E-001
-0.28940094 9.98214244709E-001
-0.28664474 9.98244806311E-001
-0.28388854 9.98273833390E-001
-0.28113234 9.98301490416E-001
-0.27837614 9.98327903749E-001
-0.27561994 9.98353166159E-001
-0.27286374 9.98377344232E-001
-0.27010754 9.98400487016E-001
-0.26735134 9.98422634420E-001
-0.26459514 9.98443824229E-001
-0.26183894 9.98464097078E-001
-0.25908274 9.98483499128E-001
-0.25632654 9.98502082613E-001
-0.25357035 9.98519904657E-001
-0.25081415 9.98537024932E-001
-0.24805795 9.98553502746E-001
-0.24530175 9.98569394130E-001
-0.24254555 9.98584749359E-001
-0.23978935 9.98599611203E-001
-0.23703315 9.98614014050E-001
-0.23427695 9.98627983924E-001
-0.23152075 9.98641539262E-001
-0.22876455 9.98654692268E-001
-0.22600835 9.98667450465E-001
-0.22325215 9.98675106782E-001
-0.22049595 9.98691807846E-001
-0.21773975 9.98703412776E-001
-0.21498355 9.98714645936E-001
-0.21222735 9.98725516722E-001
-0.20947115 9.98736037666E-001
-0.20671496 9.98746224013E-001
-0.20395876 9.98756093164E-001
-0.20120256 9.98765663891E-001
-0.19844636 9.98774955423E-001
-0.19569016 9.98783986507E-001
-0.19293396 9.98792774532E-001
-0.19017776 9.98801334801E-001
-0.18742156 9.98809680009E-001
-0.18466536 9.98817819951E-001
-0.18190916 9.98825761474E-001
-0.17915296 9.98833508650E-001
-0.17639676 9.98841063147E-001
-0.17364056 9.98848424738E-001
-0.17088436 9.98855591911E-001
-0.16812816 9.98862562506E-001
-0.16537196 9.98869334342E-001
-0.16261576 9.98875905771E-001
-0.15985957 9.98882276136E-001
-0.15710337 9.98888446094E-001
-0.15434717 9.98894417798E-001
-0.15159097 9.98900194929E-001
-0.14883477 9.98905782592E-001
-0.14607857 9.98911187094E-001
-0.14332237 9.98916415621E-001
-0.14056617 9.98921475854E-001
-0.13780997 9.98926375551E-001
-0.13505377 9.98931122131E-001
-0.13229757 9.98935722275E-001
-0.12954137 9.98940181598E-001
-0.12678517 9.98944504383E-001
-0.12402897 9.98948693416E-001
-0.12127277 9.98952749895E-001
-0.11851657 9.98956673466E-001
-0.11576038 9.98960462316E-001
-0.11300418 9.98964113380E-001
-0.11024798 9.98967622591E-001
-0.10749178 9.98970985167E-001
-0.10473558 9.98974195956E-001
-0.10197938 9.98977249750E-001
-0.09922318 9.98980141606E-001
-0.09646698 9.98982867114E-001
-0.09371078 9.98985422631E-001
-0.09095458 9.98987805436E-001
-0.08819838 9.98990013825E-001
-0.08544218 9.98992047122E-001
-0.08268598 9.98993905620E-001
-0.07992978 9.98995590446E-001
-0.07717358 9.98997103368E-001
-0.07441738 9.98998446546E-001
-0.07166118 9.98999622247E-001
-0.06890499 9.99000632538E-001
-0.06614879 9.99001478970E-001
-0.06339259 9.99002162277E-001
-0.06063639 9.99002682093E-001
-0.05788019 9.99003036720E-001
-0.05512399 9.99003222935E-001
-0.05236779 9.99003235869E-001
-0.04961159 9.99003068952E-001
-0.04685539 9.99002713959E-001
-0.04409919 9.99002161336E-001
-0.04134299 9.99001377857E-001
-0.03858679 9.99000410231E-001
-0.03583059 9.98999189579E-001
-0.03307439 9.98997717768E-001
-0.03031819 9.98995979999E-001
-0.02756199 9.98993960960E-001
-0.02480579 9.98991645292E-001
-0.02204960 9.98989017832E-001
-0.01929340 9.98986063777E-001
-0.01653720 9.98982768757E-001
-0.01378100 9.98979118818E-001
-0.01102480 9.98975100300E-001
-0.00826860 9.98970699597E-001
-0.00551240 9.98965902790E-001
-0.00275620 9.98960695162E-001
0.00000000 9.98955060572E-001
0.00275620 9.98948980720E-001
0.00551240 9.98942434285E-001
0.00826860 9.98935395961E-001
0.01102480 9.98927835399E-001
0.01378100 9.98919716072E-001
0.01653720 9.98910994073E-001
0.01929340 9.98901616877E-001
0.02204960 9.98891522033E-001
0.02480579 9.98880635898E-001
0.02756199 9.98868872261E-001
0.03031819 9.98856130983E-001
0.03307439 9.98842296545E-001
0.03583059 9.98827236464E-001
0.03858679 9.98810799505E-001
0.04134299 9.98792813518E-001
0.04409919 9.98773082701E-001
0.04685539 9.98751383964E-001
0.04961159 9.98727461926E-001
0.05236779 9.98701021843E-001
0.05512399 9.98671719434E-001
0.05788019 9.98639146043E-001
0.06063639 9.98602806744E-001
0.06339259 9.98562087656E-001
0.06614879 9.98516206449E-001
0.06890499 9.98464136121E-001
0.07166118 9.98404485007E-001
0.07441738 9.98335302546E-001
0.07717358 9.98253753540E-001
0.07992978 9.98155546583E-001
0.08268598 9.98033871149E-001
0.08544218 9.97877265438E-001
0.08819838 9.97664882894E-001
0.09095458 9.97354383572E-001
0.09371078 9.96843600494E-001
0.09646698 9.95795192094E-001
0.09922318 9.91590372678E-001
0.10197938 1.31179214827E-006
0.10473558 4.51462174815E-008
0.10749178 6.32534659709E-009
0.11024798 1.44416351364E-009
0.11300418 4.26251662637E-010
0.11576038 1.47557758721E-010
0.11851657 5.69143175477E-011
0.12127277 2.37112405216E-011
0.12402897 1.04502489267E-011
0.12678517 4.79903130477E-012
0.12954137 2.26896834727E-012
0.13229757 1.09311290004E-012
0.13505377 5.31388255144E-013
0.13780997 2.57984724633E-013
0.14056617 1.23577996594E-013
0.14332237 5.74755708091E-014
0.14607857 2.53402719978E-014
0.14883477 1.01646684663E-014
0.15159097 3.41000694698E-015
0.15434717 7.58314624193E-016
0.15710337 2.64445658253E-017
0.15985957 1.21407391028E-016
0.16261576 5.09033604006E-016
0.16537196 9.40674525385E-016
0.16812816 1.31169166067E-015
0.17088436 1.58809023200E-015
0.17364056 1.76869245542E-015
0.17639676 1.86592803627E-015
0.17915296 1.89637089442E-015
0.18190916 1.87634120928E-015
0.18466536 1.82009621541E-015
0.18742156 1.73930223772E-015
0.19017776 1.64310354042E-015
0.19293396 1.53843608938E-015
0.19569016 1.43041120474E-015
0.19844636 1.32268727312E-015
0.20120256 1.21779587824E-015
0.20395876 1.11741279929E-015
0.20671496 1.02257564340E-015
0.20947115 9.33854554413E-016
0.21222735 8.51483778454E-016
0.21498355 7.75461628945E-016
0.21773975 7.05625499424E-016
0.22049595 6.41707487195E-016
0.22325215 5.83375135203E-016
0.22600835 5.30260866390E-016
0.22876455 4.81982901927E-016
0.23152075 4.38159818621E-016
0.23427695 3.98420394944E-016
0.23703315 3.62409998717E-016
0.23978935 3.29794462303E-016
0.24254555 3.00262155021E-016
0.24530175 2.73524782206E-016
0.24805795 2.49317303357E-016
0.25081415 2.27397258363E-016
0.25357035 2.07543712818E-016
0.25632654 1.89555975111E-016
0.25908274 1.73252194355E-016
0.26183894 1.58467915895E-016
0.26459514 1.45054647203E-016
0.26735134 1.32878469462E-016
0.27010754 1.21818717315E-016
0.27286374 1.11766740090E-016
0.27561994 1.02624751193E-016
0.27837614 9.43047678102E-017
0.28113234 8.67276398624E-017
0.28388854 7.98221650863E-017
0.28664474 7.35242857899E-017
0.28940094 6.77763620595E-017
0.29215714 6.25265158261E-017
0.29491334 5.77280401026E-017
0.29766954 5.33388677944E-017
0.30042574 4.93210947011E-017
0.30318193 4.56405516220E-017
0.30593813 4.22664208112E-017
0.30869433 3.91708923890E-017
0.31145053 3.63288566746E-017
0.31420673 3.37176287588E-017
0.31696293 3.13167019741E-017
0.31971913 2.91075272391E-017
0.32247533 2.70733155489E-017
0.32523153 2.51988611609E-017
0.32798773 2.34703832744E-017
0.33074393 2.18753842311E-017
0.33350013 2.04025224728E-017
0.33625633 1.90414986791E-017
0.33901253 1.77829536748E-017
0.34176873 1.66183768522E-017
0.34452493 1.55400239857E-017
0.34728113 1.45408434385E-017
0.35003732 1.36144098712E-017
0.35279352 1.27548646570E-017
0.35554972 1.19568622949E-017
0.35830592 1.12155221906E-017
0.36106212 1.05263852421E-017
0.36381832 9.88537472722E-018
0.36657452 9.28876104694E-018
0.36933072 8.73312992406E-018
0.37208692 8.21535370171E-018
0.37484312 7.73256542323E-018
0.37759932 7.28213540934E-018
0.38035552 6.86165007904E-018
0.38311172 6.46889278710E-018
0.38586792 6.10182647542E-018
0.38862412 5.75857795671E-018
0.39138032 5.43742366792E-018
0.39413651 5.13677674806E-018
0.39689271 4.85517530981E-018
0.39964891 4.59127178816E-018
0.40240511 4.34382326108E-018
0.40516131 4.11168264817E-018
0.40791751 3.89379070271E-018
0.41067371 3.68916872103E-018
0.41342991 3.49691190118E-018
0.41618611 3.31618328908E-018
0.41894231 3.14620825715E-018
0.42169851 2.98626946547E-018
0.42445471 2.83570226050E-018
0.42721091 2.69389047104E-018
0.42996711 2.56026256485E-018
0.43272331 2.43428813286E-018
0.43547951 2.31547467131E-018
0.43823571 2.20336463485E-018
0.44099190 2.09753273629E-018
0.44374810 1.99758347086E-018
0.44650430 1.90314884524E-018
0.44926050 1.81388629307E-018
0.45201670 1.72947676074E-018
0.45477290 1.64962294852E-018
0.45752910 1.57404769354E-018
0.46028530 1.50249248246E-018
0.46304150 1.43471608267E-018
0.46579770 1.37049328186E-018
0.46855390 1.30961372690E-018
0.47131010 1.25188085353E-018
0.47406630 1.19711089938E-018
0.47682250 1.14513199323E-018
0.47957870 1.09578331433E-018
0.48233490 1.04891431598E-018
0.48509110 1.00438400800E-018
0.48784729 9.62060293497E-019
0.49060349 9.21819355319E-019
0.49335969 8.83545088355E-019
0.49611589 8.47128573937E-019
0.49887209 8.12467593005E-019
0.50162829 7.79466174985E-019
0.50438449 7.48034179551E-019
0.50714069 7.18086908698E-019
0.50989689 6.89544746786E-019
0.51265309 6.62332826367E-019
0.51540929 6.36380717832E-019
0.51816549 6.11622141030E-019
0.52092169 5.87994697218E-019
0.52367789 5.65439619776E-019
0.52643409 5.43901542287E-019
0.52919029 5.23328282681E-019
0.53194649 5.03670642246E-019
0.53470268 4.84882218401E-019
0.53745888 4.66919230228E-019
0.54021508 4.49740355814E-019
0.54297128 4.33306580551E-019
0.54572748 4.17581055607E-019
0.54848368 4.02528965809E-019
0.55123988 3.88117406299E-019

427
tests/QS/regtest-negf-2/H28_k.inp Normal file
View file

@ -0,0 +1,427 @@
@SET Project H28_k
@SET V_bias_volt 0.0
@SET Temperature 10.0
# The following two parameters are computed automatically during the NEGF run.
# You can use keywords 'FERMI_LEVEL' to give this value and skip calculation
# or 'FERMI_LEVEL'+'REFINE_FERMI_LEVEL' to compute starting from this value.
# If 'FERMI_LEVEL' is not given, it is calculated automatically.
# 'V_SHIFT' is used to give initial value.
@SET Fermi_level -0.22306350 #-0.23822635 #-0.22306350 #
@SET V_shift 0.00011009 # 0.00010984 # 0.00011009 #
@SET basis_set_path BASIS_SET
! BASIS_MOLOPT BASIS_SET
@SET potential_path GTH_POTENTIALS
@SET xc_functional pade
!PBE pade
@SET cutoff 300
@SET added_mos -1
@SET max_scf 100
@SET eps_scf 1e-9
@SET lx 6.0
@SET ly 6.0
!--------------------------------------------------------------------------------------------------!
&GLOBAL
EXTENDED_FFT_LENGTHS .true.
PREFERRED_DIAG_LIBRARY SL
PRINT_LEVEL LOW #SILENT #LOW #MEDIUM #HIGH #DEBUG
PROJECT ${Project}
RUN_TYPE NEGF
&END GLOBAL
&MULTIPLE_FORCE_EVALS
# Order in which the input file parser internally stores different force environments.
#
# 'FORCE_EVAL_ORDER 1 2 3' means that the 1st force environment --
# which holds the entire system -- will have the internal index '0',
# while the 2nd and 3rd force environments -- which correspond to the
# 1st and 2nd semi-infinite electrodes respectively -- will have
# the internal indices '1' and '2'. Note that internal indices start from 0.
#
FORCE_EVAL_ORDER 1 2 3
# Different force environments contain non-identical molecular structures.
# By default, the input parser ignores 'subsys' sections from all but the force
# environment with the internal index '0'.
MULTIPLE_SUBSYS .true.
&END MULTIPLE_FORCE_EVALS
&NEGF
# Integration lower bound (in Hartree)
ENERGY_LBOUND -2.0
!clenshaw-curtis simpson
# Maximum error in each matrix element of the density matrix
EPS_DENSITY 1e-5
EPS_GREEN 1e-5
EPS_SCF 1e-5
ETA 1e-5
# 'simpson' is slower, but works without FFTW3 library
# clenshaw-curtis is faster, but requires FFTW3 library
INTEGRATION_METHOD simpson
MAX_SCF 100
# Number of parallel processes per energy point.
# 'NPROC_POINT 1' means that if you run this job using 8 MPI processes,
# than Green's functions at up to 8 (8 / NPROC_POINT) energy points
# will be computed simultaneously.
#
NPROC_POINT 1
# Boundary conditions define solution of the Poisson equation up to
# an additive constant, which affects Hamiltonian matrix elements within
# the NEGF procedure. The following parameters control evaluation of
# the correct shift in Hartree potential:
# * V_SHIFT -- initial guess for the shift
# * V_SHIFT_MAX_ITERS -- maximal number of iterations
V_SHIFT ${V_shift}
V_SHIFT_MAX_ITERS 100
&CONTACT
# REFINE_FERMI_LEVEL
ELECTRIC_POTENTIAL [eV] ${V_bias_volt}/2
FERMI_LEVEL ${Fermi_level}
# the force environment with the internal index '1' should be used
# to compute 'bulk' properties of this (1st) semi-infinite electrode.
FORCE_EVAL_SECTION 1
TEMPERATURE [K] ${Temperature}
&BULK_REGION
# This section is used to map matrix elements between the primary
# (with index 0) and the 'electrode' (with index 1) force environments.
#
# Atomic indices (and/or names of molecular fragments) are relative
# to the primary force environment.
MOLNAME L1 L2
!LIST 1..8
&CELL
MOLNAME L1
!LIST 5..8
&END CELL
&CELL
MOLNAME L2
!LIST 1..4
&END CELL
&END BULK_REGION
&SCREENING_REGION
MOLNAME L0
!LIST 9..12
&END SCREENING_REGION
&END CONTACT
&CONTACT
# REFINE_FERMI_LEVEL
ELECTRIC_POTENTIAL [eV] -${V_bias_volt}/2
FERMI_LEVEL ${Fermi_level}
# the second semi-infinite electrode
FORCE_EVAL_SECTION 2
TEMPERATURE [K] ${Temperature}
&BULK_REGION
MOLNAME R1 R2
&CELL
MOLNAME R1
&END CELL
&CELL
MOLNAME R2
&END CELL
&END BULK_REGION
&SCREENING_REGION
MOLNAME R0
&END SCREENING_REGION
&END CONTACT
# Density mixing is not needed in zero-bias case, as NEGF self-consistent
# procedure will converge in one iteration. However, when an external bias
# is applied, a density mixing scheme in inverse space is typically
# much stable then the default direct mixing of new and old density matrices.
&MIXING
ALPHA 0.2
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&DOS
FILENAME device
FROM_ENERGY [eV] -15
N_GRIDPOINTS 401
TILL_ENERGY [eV] 15
&END DOS
&PROGRAM_RUN_INFO low
PRINT_LEVEL debug
! high debug
&END PROGRAM_RUN_INFO
&TRANSMISSION
FILENAME transm
FROM_ENERGY [eV] -15
N_GRIDPOINTS 401
TILL_ENERGY [eV] 15
&END TRANSMISSION
&END PRINT
&SCATTERING_REGION
MOLNAME S
!LIST 13..16
&END SCATTERING_REGION
#DISABLE_CACHE
&END NEGF
# *** Primary force environment ***
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
!atomic restart
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS restart
&MIXING
ALPHA 0.3
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_0
&END RESTART
#&PROGRAM_RUN_INFO silent
#&END
#&DETAILED_ENERGY silent
#&END
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${Temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC ${lx} ${ly} 42.
PERIODIC xyz
&END CELL
&COORD
# H 0.00000000 0.00000000 10.50000000 L1
# H 0.00000000 0.00000000 9.00000000 L1
# H 0.00000000 0.00000000 7.50000000 L1
# H 0.00000000 0.00000000 6.00000000 L1
# H 0.00000000 0.00000000 4.50000000 L2
# H 0.00000000 0.00000000 3.00000000 L2
# H 0.00000000 0.00000000 1.50000000 L2
# H 0.00000000 0.00000000 0.00000000 L2
# H 0.00000000 0.00000000 16.50000000 L0
# H 0.00000000 0.00000000 15.00000000 L0
# H 0.00000000 0.00000000 13.50000000 L0
# H 0.00000000 0.00000000 12.00000000 L0
H 0.00000000 0.00000000 0.00000000 L2
H 0.00000000 0.00000000 1.50000000 L2
H 0.00000000 0.00000000 3.00000000 L2
H 0.00000000 0.00000000 4.50000000 L2
H 0.00000000 0.00000000 6.00000000 L1
H 0.00000000 0.00000000 7.50000000 L1
H 0.00000000 0.00000000 9.00000000 L1
H 0.00000000 0.00000000 10.50000000 L1
H 0.00000000 0.00000000 12.00000000 L0
H 0.00000000 0.00000000 13.50000000 L0
H 0.00000000 0.00000000 15.00000000 L0
H 0.00000000 0.00000000 16.50000000 L0
H 0.00000000 0.00000000 18.00000000 S
H 0.00000000 0.00000000 19.50000000 S
H 0.00000000 0.00000000 21.00000000 S
H 0.00000000 0.00000000 22.50000000 S
H 0.00000000 0.00000000 24.00000000 R0
H 0.00000000 0.00000000 25.50000000 R0
H 0.00000000 0.00000000 27.00000000 R0
H 0.00000000 0.00000000 28.50000000 R0
H 0.00000000 0.00000000 30.00000000 R1
H 0.00000000 0.00000000 31.50000000 R1
H 0.00000000 0.00000000 33.00000000 R1
H 0.00000000 0.00000000 34.50000000 R1
H 0.00000000 0.00000000 36.00000000 R2
H 0.00000000 0.00000000 37.50000000 R2
H 0.00000000 0.00000000 39.00000000 R2
H 0.00000000 0.00000000 40.50000000 R2
# H 0.00000000 0.00000000 42.00000000 R3
# H 0.00000000 0.00000000 43.50000000 R3
# H 0.00000000 0.00000000 45.00000000 R3
# H 0.00000000 0.00000000 46.50000000 R3
# H 0.00000000 0.00000000 48.00000000 R4
# H 0.00000000 0.00000000 49.50000000 R4
# H 0.00000000 0.00000000 51.00000000 R4
# H 0.00000000 0.00000000 52.50000000 R4
&END COORD
&KIND H
BASIS_SET SZV-GTH-PADE
! SZV-GTH-PADE DZV-ALL-PADE DZVP-ALL-PADE SZV-MOLOPT-GTH
POTENTIAL GTH-PADE-q1
!GTH-PADE-q1 GTH-PBE-q1
&END KIND
&END SUBSYS
&END FORCE_EVAL
# *** The 1st (left) semi-infinite electrode ***
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&KPOINTS
SCHEME MONKHORST-PACK 1 1 14
&END KPOINTS
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
!atomic restart
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS restart
&MIXING
ALPHA 0.2
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_1
&END RESTART
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${Temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
# &PRINT
# &S_CSR_WRITE
# REAL_SPACE
# FILENAME=L
# &END
# &KS_CSR_WRITE
# REAL_SPACE
# &END
# &END PRINT
&END DFT
&SUBSYS
# a primary unit cell of the 1st semi-infinite electrode
&CELL
ABC ${lx} ${ly} 6.00000000
PERIODIC xyz
&END CELL
&COORD
# H 0.00000000 0.00000000 10.50000000 L1
# H 0.00000000 0.00000000 9.00000000 L1
# H 0.00000000 0.00000000 7.50000000 L1
# H 0.00000000 0.00000000 6.00000000 L1
H 0.00000000 0.00000000 6.00000000 L1
H 0.00000000 0.00000000 7.50000000 L1
H 0.00000000 0.00000000 9.00000000 L1
H 0.00000000 0.00000000 10.50000000 L1
&END COORD
&KIND H
BASIS_SET SZV-GTH-PADE
! SZV-GTH-PADE DZV-ALL-PADE DZVP-ALL-PADE SZV-MOLOPT-GTH
POTENTIAL GTH-PADE-q1
!GTH-PADE-q1 GTH-PBE-q1
&END KIND
&TOPOLOGY
! COORD_FILE_FORMAT XYZ
! COORD_FILE_NAME ${COORD_FILE_NAME}.xyz
! &CENTER_COORDINATES
! CENTER_POINT 0. 0. 0.
! &END
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
# *** The 2nd (right) semi-infinite electrode ***
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&KPOINTS
SCHEME MONKHORST-PACK 1 1 14
&END KPOINTS
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
!atomic
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS restart
&MIXING
ALPHA 0.2
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_2
&END RESTART
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${Temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
# &PRINT
# &S_CSR_WRITE
# REAL_SPACE
# FILENAME=R
# &END
# &KS_CSR_WRITE
# REAL_SPACE
# &END
# &END PRINT
&END DFT
&SUBSYS
# a primary unit cell of the 2st semi-infinite electrode
&CELL
ABC ${lx} ${ly} 6.00000000
PERIODIC xyz
&END CELL
&COORD
# H 0.00000000 0.00000000 34.50000000 R1
# H 0.00000000 0.00000000 33.00000000 R1
# H 0.00000000 0.00000000 31.50000000 R1
# H 0.00000000 0.00000000 30.00000000 R1
H 0.00000000 0.00000000 30.00000000 R1
H 0.00000000 0.00000000 31.50000000 R1
H 0.00000000 0.00000000 33.00000000 R1
H 0.00000000 0.00000000 34.50000000 R1
# H 0.00000000 0.00000000 36.00000000 R2
# H 0.00000000 0.00000000 37.50000000 R2
# H 0.00000000 0.00000000 39.00000000 R2
# H 0.00000000 0.00000000 40.50000000 R2
# H 0.00000000 0.00000000 42.00000000 R3
# H 0.00000000 0.00000000 43.50000000 R3
# H 0.00000000 0.00000000 45.00000000 R3
# H 0.00000000 0.00000000 46.50000000 R3
&END COORD
&KIND H
BASIS_SET SZV-GTH-PADE
! SZV-GTH-PADE DZV-ALL-PADE DZVP-ALL-PADE SZV-MOLOPT-GTH
POTENTIAL GTH-PADE-q1
!GTH-PADE-q1 GTH-PBE-q1
&END KIND
&END SUBSYS
&END FORCE_EVAL

2
tests/QS/regtest-negf/TEST_FILES.toml → tests/QS/regtest-negf-2/TEST_FILES.toml
View file

@ -4,4 +4,4 @@
# 1 compares the last total energy in the file
# for details see cp2k/tools/do_regtest
#
"li_chain.inp" = []
"H28_k.inp" = []

320
tests/QS/regtest-negf-fft/li_chain_kp.inp
View file

@ -1,320 +0,0 @@
@SET project li_chain_kp
@SET v_bias_volt 0.0
@SET temperature 293.0
# The following two parameters are computed automatically during the NEGF run.
# You can uncomment keywords 'FERMI_LEVEL' and 'V_SHIFT' to skip these stages.
@SET fermi_level -0.08987575
@SET v_shift 0.00280782
@SET basis_set_path BASIS_MOLOPT
@SET potential_path GTH_POTENTIALS
@SET basis_set_li SZV-MOLOPT-SR-GTH
@SET potential_li GTH-PADE-q3
@SET xc_functional pade
@SET cutoff 100
@SET added_mos 100
@SET max_scf 50
@SET eps_scf 1e-4
@SET lx 5.0
@SET ly 5.0
&GLOBAL
EXTENDED_FFT_LENGTHS .true.
PRINT_LEVEL low
PROJECT ${project}
RUN_TYPE negf
&END GLOBAL
&MULTIPLE_FORCE_EVALS
# Order in which the input file parser internally stores different force environments.
#
# 'FORCE_EVAL_ORDER 1 2 3' means that the 1st force environment --
# which holds the entire system -- will have the internal index '0',
# while the 2nd and 3rd force environments -- which correspond to the
# 1st and 2nd semi-infinite electrodes respectively -- will have
# the internal indices '1' and '2'. Note that internal indices start from 0.
#
FORCE_EVAL_ORDER 1 2 3
# Different force environments contain non-identical molecular structures.
# By default, the input parser ignores 'subsys' sections from all but the force
# environment with the internal index '0'.
MULTIPLE_SUBSYS .true.
&END MULTIPLE_FORCE_EVALS
&NEGF
# Integration lower bound (in Hartree)
ENERGY_LBOUND -2.0
# Maximum error in each matrix element of the density matrix
EPS_DENSITY 1e-5
# faster, but requires FFTW3 library
INTEGRATION_METHOD clenshaw-curtis
MAX_SCF 16
# Number of parallel processes per energy point.
# 'NPROC_POINT 1' means that if you run this job using 8 MPI processes,
# than Green's functions at up to 8 (8 / NPROC_POINT) energy points
# will be computed simultaneously.
#
NPROC_POINT 1
# Boundary conditions define solution of the Poisson equation up to
# an additive constant, which affects Hamiltonian matrix elements within
# the NEGF procedure. The following parameters control evaluation of
# the correct shift in Hartree potential:
# * V_SHIFT -- initial guess for the shift
# * V_SHIFT_MAX_ITERS -- maximal number of iterations
#V_SHIFT ${v_shift}
V_SHIFT_MAX_ITERS 20
&CONTACT
# Uncomment the next line to skip refining the Fermi level for this contact
#FERMI_LEVEL ${fermi_level}
ELECTRIC_POTENTIAL [eV] ${v_bias_volt}/2
# the force environment with the internal index '1' should be used
# to compute 'bulk' properties of this (1st) semi-infinite electrode.
FORCE_EVAL_SECTION 1
TEMPERATURE [K] ${temperature}
&BULK_REGION
# This section is used to map matrix elements between the primary
# (with index 0) and the 'bulk' (with index 1) force environments.
#
# Atomic indices (and/or names of molecular fragments) are relative
# to the primary force environment.
MOLNAME L1 L2
&END BULK_REGION
&SCREENING_REGION
MOLNAME L0
&END SCREENING_REGION
&END CONTACT
&CONTACT
#FERMI_LEVEL ${fermi_level}
ELECTRIC_POTENTIAL [eV] -${v_bias_volt}/2
# the second semi-infinite electrode
FORCE_EVAL_SECTION 2
TEMPERATURE [K] ${temperature}
&BULK_REGION
MOLNAME R1 R2
&END BULK_REGION
&SCREENING_REGION
MOLNAME R0
&END SCREENING_REGION
&END CONTACT
# Density mixing is not needed in zero-bias case, as NEGF self-consistent
# procedure will converge in one iteration. However, when an external bias
# is applied, a density mixing scheme in inverse space is typically
# much stable then the default direct mixing of new and old density matrices.
&MIXING
ALPHA 0.2
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&DOS
FILENAME device
FROM_ENERGY -0.2
N_GRIDPOINTS 301
TILL_ENERGY 0.1
&END DOS
&TRANSMISSION
FILENAME transm
FROM_ENERGY -0.2
N_GRIDPOINTS 301
TILL_ENERGY 0.1
&END TRANSMISSION
&END PRINT
&SCATTERING_REGION
MOLNAME S
&END SCATTERING_REGION
&END NEGF
# *** Primary force environment ***
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS atomic
&MIXING
ALPHA 0.3
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_0
&END RESTART
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC ${lx} ${ly} 83.720
PERIODIC xyz
&END CELL
&COORD
Li 0.00000000 0.00000000 0.00000000 L2
Li 0.00000000 0.00000000 2.99000000 L2
Li 0.00000000 0.00000000 5.98000000 L2
Li 0.00000000 0.00000000 8.97000000 L2
Li 0.00000000 0.00000000 11.96000000 L1
Li 0.00000000 0.00000000 14.95000000 L1
Li 0.00000000 0.00000000 17.94000000 L1
Li 0.00000000 0.00000000 20.93000000 L1
Li 0.00000000 0.00000000 23.92000000 L0
Li 0.00000000 0.00000000 26.91000000 L0
Li 0.00000000 0.00000000 29.90000000 L0
Li 0.00000000 0.00000000 32.89000000 L0
Li 0.00000000 0.00000000 35.88000000 S
Li 0.00000000 0.00000000 38.87000000 S
Li 0.00000000 0.00000000 41.86000000 S
Li 0.00000000 0.00000000 44.85000000 S
Li 0.00000000 0.00000000 47.84000000 R0
Li 0.00000000 0.00000000 50.83000000 R0
Li 0.00000000 0.00000000 53.82000000 R0
Li 0.00000000 0.00000000 56.81000000 R0
Li 0.00000000 0.00000000 59.80000000 R1
Li 0.00000000 0.00000000 62.79000000 R1
Li 0.00000000 0.00000000 65.78000000 R1
Li 0.00000000 0.00000000 68.77000000 R1
Li 0.00000000 0.00000000 71.76000000 R2
Li 0.00000000 0.00000000 74.75000000 R2
Li 0.00000000 0.00000000 77.74000000 R2
Li 0.00000000 0.00000000 80.73000000 R2
&END COORD
&KIND Li
BASIS_SET ${basis_set_li}
POTENTIAL ${potential_li}
&END KIND
&END SUBSYS
&END FORCE_EVAL
# *** The 1st (left) semi-infinite electrode ***
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&KPOINTS
SCHEME MONKHORST-PACK 4 4 8
&END KPOINTS
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS atomic
&MIXING
ALPHA 0.3
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_1
&END RESTART
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
# a primary unit cell of the 1st semi-infinite electrode
&CELL
ABC ${lx} ${ly} 11.960
PERIODIC xyz
&END CELL
&COORD
Li 0.00000000 0.00000000 11.96000000 L1
Li 0.00000000 0.00000000 14.95000000 L1
Li 0.00000000 0.00000000 17.94000000 L1
Li 0.00000000 0.00000000 20.93000000 L1
&END COORD
&KIND Li
BASIS_SET ${basis_set_li}
POTENTIAL ${potential_li}
&END KIND
&END SUBSYS
&END FORCE_EVAL
# *** The 2nd (right) semi-infinite electrode ***
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&KPOINTS
SCHEME MONKHORST-PACK 4 4 8
&END KPOINTS
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS atomic
&MIXING
ALPHA 0.3
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_2
&END RESTART
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
# a primary unit cell of the 2nd semi-infinite electrode
&CELL
ABC ${lx} ${ly} 11.960
PERIODIC xyz
&END CELL
&COORD
Li 0.00000000 0.00000000 59.80000000 R1
Li 0.00000000 0.00000000 62.79000000 R1
Li 0.00000000 0.00000000 65.78000000 R1
Li 0.00000000 0.00000000 68.77000000 R1
&END COORD
&KIND Li
BASIS_SET ${basis_set_li}
POTENTIAL ${potential_li}
&END KIND
&END SUBSYS
&END FORCE_EVAL

199
tests/QS/regtest-negf/li_chain.inp
View file

@ -1,199 +0,0 @@
@SET project li_chain
@SET v_bias_volt 0.0
@SET temperature 293.0
# The following two parameters are computed automatically during the NEGF run.
# You can uncomment keywords 'FERMI_LEVEL' and 'V_SHIFT' to skip these stages.
@SET fermi_level -0.08987575
@SET v_shift 0.00280782
@SET basis_set_path BASIS_MOLOPT
@SET potential_path GTH_POTENTIALS
@SET basis_set_li SZV-MOLOPT-SR-GTH
@SET potential_li GTH-PADE-q3
@SET xc_functional pade
@SET cutoff 80
@SET added_mos 100
@SET max_scf 50
@SET eps_scf 1e-4
@SET lx 5.0
@SET ly 5.0
&GLOBAL
EXTENDED_FFT_LENGTHS .true.
PRINT_LEVEL low
PROJECT ${project}
RUN_TYPE negf
&END GLOBAL
&NEGF
# Integration lower bound (in Hartree)
ENERGY_LBOUND -2.0
# Maximum error in each matrix element of the density matrix
EPS_DENSITY 1e-5
# slower, but works without FFTW3 library
INTEGRATION_METHOD simpson
MAX_SCF 16
# Number of parallel processes per energy point.
# 'NPROC_POINT 1' means that if you run this job using 8 MPI processes,
# than Green's functions at up to 8 (8 / NPROC_POINT) energy points
# will be computed simultaneously.
#
NPROC_POINT 1
# Boundary conditions define solution of the Poisson equation up to
# an additive constant, which affects Hamiltonian matrix elements within
# the NEGF procedure. The following parameters control evaluation of
# the correct shift in Hartree potential:
# * V_SHIFT -- initial guess for the shift
# * V_SHIFT_MAX_ITERS -- maximal number of iterations
#V_SHIFT ${v_shift}
V_SHIFT_MAX_ITERS 20
&CONTACT
ELECTRIC_POTENTIAL [eV] ${v_bias_volt}/2
FERMI_LEVEL ${fermi_level}
TEMPERATURE [K] ${temperature}
&BULK_REGION
# Atomic indices (and/or names of molecular fragments) that belong to the bulk contact region.
MOLNAME L1 L2
# List of atoms that belong to the primary and secondary bulk unit cells
# of the 1st contact. Primary and secondary unit cells can be defined in any order.
# They should be adjusted to each other and should not overlap.
#
# As matrix blocks should correspond to ones for the bulk contact,
# in actual calculation you may want to use a longer chain, e.g.
# L1 L2 L3 L4 L5 L6 .
# cell1 cell2
# Alternatively, instead of the below CELL sections, a separate bulk FORCE_EVAL section
# for the contact can be set up and the keyword FORCE_EVAL_SECTION should be set accordingly
# (see the test file regtest-negf-fft/li_chain_kp.inp).
&CELL
MOLNAME L1
&END CELL
&CELL
MOLNAME L2
&END CELL
&END BULK_REGION
&SCREENING_REGION
MOLNAME L0
&END SCREENING_REGION
&END CONTACT
&CONTACT
ELECTRIC_POTENTIAL [eV] -${v_bias_volt}/2
FERMI_LEVEL ${fermi_level}
TEMPERATURE [K] ${temperature}
# the second semi-infinite electrode
&BULK_REGION
MOLNAME R1 R2
&CELL
MOLNAME R1
&END CELL
&CELL
MOLNAME R2
&END CELL
&END BULK_REGION
&SCREENING_REGION
MOLNAME R0
&END SCREENING_REGION
&END CONTACT
# Density mixing is not needed in zero-bias case, as NEGF self-consistent
# procedure will converge in one iteration. However, when an external bias
# is applied, a density mixing scheme in inverse space is typically
# much stable then the default direct mixing of new and old density matrices.
&MIXING
ALPHA 0.2
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&DOS
FILENAME device
FROM_ENERGY -0.2
N_GRIDPOINTS 301
TILL_ENERGY 0.1
&END DOS
&TRANSMISSION
FILENAME transm
FROM_ENERGY -0.2
N_GRIDPOINTS 301
TILL_ENERGY 0.1
&END TRANSMISSION
&END PRINT
&SCATTERING_REGION
MOLNAME S
&END SCATTERING_REGION
&END NEGF
&FORCE_EVAL
METHOD Quickstep
&DFT
BASIS_SET_FILE_NAME ${basis_set_path}
POTENTIAL_FILE_NAME ${potential_path}
&MGRID
CUTOFF ${cutoff}
&END MGRID
&POISSON
PERIODIC xyz
&END POISSON
&SCF
ADDED_MOS ${added_mos}
EPS_SCF ${eps_scf}
MAX_SCF ${max_scf}
SCF_GUESS atomic
&MIXING
ALPHA 0.3
METHOD broyden_mixing
NBUFFER 8
&END MIXING
&PRINT
&RESTART
FILENAME RESTART_0
&END RESTART
&END PRINT
&SMEAR
ELECTRONIC_TEMPERATURE [K] ${temperature}
METHOD fermi_dirac
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL ${xc_functional}
&END XC_FUNCTIONAL
&END XC
&END DFT
&SUBSYS
&CELL
ABC ${lx} ${ly} 83.720
PERIODIC xyz
&END CELL
&COORD
Li 0.00000000 0.00000000 0.00000000 L2
Li 0.00000000 0.00000000 2.99000000 L2
Li 0.00000000 0.00000000 5.98000000 L2
Li 0.00000000 0.00000000 8.97000000 L2
Li 0.00000000 0.00000000 11.96000000 L1
Li 0.00000000 0.00000000 14.95000000 L1
Li 0.00000000 0.00000000 17.94000000 L1
Li 0.00000000 0.00000000 20.93000000 L1
Li 0.00000000 0.00000000 23.92000000 L0
Li 0.00000000 0.00000000 26.91000000 L0
Li 0.00000000 0.00000000 29.90000000 L0
Li 0.00000000 0.00000000 32.89000000 L0
Li 0.00000000 0.00000000 35.88000000 S
Li 0.00000000 0.00000000 38.87000000 S
Li 0.00000000 0.00000000 41.86000000 S
Li 0.00000000 0.00000000 44.85000000 S
Li 0.00000000 0.00000000 47.84000000 R0
Li 0.00000000 0.00000000 50.83000000 R0
Li 0.00000000 0.00000000 53.82000000 R0
Li 0.00000000 0.00000000 56.81000000 R0
Li 0.00000000 0.00000000 59.80000000 R1
Li 0.00000000 0.00000000 62.79000000 R1
Li 0.00000000 0.00000000 65.78000000 R1
Li 0.00000000 0.00000000 68.77000000 R1
Li 0.00000000 0.00000000 71.76000000 R2
Li 0.00000000 0.00000000 74.75000000 R2
Li 0.00000000 0.00000000 77.74000000 R2
Li 0.00000000 0.00000000 80.73000000 R2
&END COORD
&KIND Li
BASIS_SET ${basis_set_li}
POTENTIAL ${potential_li}
&END KIND
&END SUBSYS
&END FORCE_EVAL

4
tests/TEST_DIRS
View file

@ -356,7 +356,8 @@ QS/regtest-double-hybrid-2 libint !ifx
QS/regtest-sccs-2
FE/regtest-3
QS/regtest-properties/resp
QS/regtest-negf-fft fftw3
QS/regtest-negf-1 fftw3
QS/regtest-negf-2 fftw3
NEB/regtest-1
QS/regtest-double-hybrid-stress-numer-meta libxc !ifx
QS/regtest-elpa-qr elpa mpiranks==1||mpiranks%2==0
@ -368,7 +369,6 @@ QS/regtest-double-hybrid-stress
DFTB/regtest-debug
optimize_input/regtest-1
DFTB/regtest-vdw
QS/regtest-negf
SWARM/regtest-glbopt-1
QS/regtest-cdft-hirshfeld-3
QS/regtest-linearscaling