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negf_control_types.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Input control types for NEGF based quantum transport calculations
10! **************************************************************************************************
11
12MODULE negf_control_types
13 USE cp_subsys_types, ONLY: cp_subsys_get,&
14 cp_subsys_type
15 USE input_constants, ONLY: negf_run
16 USE input_section_types, ONLY: section_vals_get,&
17 section_vals_get_subs_vals,&
18 section_vals_type,&
19 section_vals_val_get
20 USE kinds, ONLY: default_string_length,&
21 dp
22 USE mathconstants, ONLY: pi
23 USE molecule_kind_types, ONLY: get_molecule_kind,&
24 molecule_kind_type
25 USE molecule_types, ONLY: get_molecule,&
26 molecule_type
27 USE negf_alloc_types, ONLY: negf_allocatable_ivector
28 USE particle_types, ONLY: particle_type
29 USE physcon, ONLY: kelvin
30 USE string_utilities, ONLY: integer_to_string
31 USE util, ONLY: sort
32#include "./base/base_uses.f90"
33
34 IMPLICIT NONE
35 PRIVATE
36
37 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'negf_control_types'
38 LOGICAL, PARAMETER, PRIVATE :: debug_this_module = .true.
39
40 PUBLIC :: negf_control_type, negf_control_contact_type
41 PUBLIC :: negf_control_create, negf_control_release, read_negf_control
42
43! **************************************************************************************************
44!> \brief Input parameters related to a single contact.
45!> \author Sergey Chulkov
46! **************************************************************************************************
47 TYPE negf_control_contact_type
48 !> atoms belonging to bulk and screening regions
49 INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_bulk, atomlist_screening
50 !> atom belonging to the primary and secondary bulk unit cells
51 TYPE(negf_allocatable_ivector), ALLOCATABLE, &
52 DIMENSION(:) :: atomlist_cell
53 !> index of the sub_force_env which should be used for bulk calculation
54 INTEGER :: force_env_index = -1
55 !> contact Fermi level needs to be computed prior NEGF run
56 LOGICAL :: compute_fermi_level = .false.
57 !> when computing contact Fermi level, use the energy given in 'fermi_level' (instead of HOMO)
58 !> (instead of the HOMO energy) as a starting point
59 LOGICAL :: refine_fermi_level = .false.
60 !> Fermi level
61 REAL(kind=dp) :: fermi_level = -1.0_dp
62 !> temperature [in a.u.]
63 REAL(kind=dp) :: temperature = -1.0_dp
64 !> applied electric potential
65 REAL(kind=dp) :: v_external = 0.0_dp
66 END TYPE negf_control_contact_type
67
68! **************************************************************************************************
69!> \brief Input parameters related to the NEGF run.
70!> \author Sergey Chulkov
71! **************************************************************************************************
72 TYPE negf_control_type
73 !> input options for every contact
74 TYPE(negf_control_contact_type), ALLOCATABLE, &
75 DIMENSION(:) :: contacts
76 !> atoms belonging to the scattering region
77 INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_s
78 !> atoms belonging to the scattering region as well as atoms belonging to
79 !> screening regions of all the contacts
80 INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_s_screening
81 !> do not keep contact self-energy matrices
82 LOGICAL :: disable_cache = .false.
83 !> convergence criteria for adaptive integration methods
84 REAL(kind=dp) :: conv_density = -1.0_dp
85 !> convergence criteria for iterative Lopez-Sancho algorithm
86 REAL(kind=dp) :: conv_green = -1.0_dp
87 !> convergence criteria for self-consistent iterations
88 REAL(kind=dp) :: conv_scf = -1.0_dp
89 !> accuracy in mapping atoms between different force environments
90 REAL(kind=dp) :: eps_geometry = -1.0_dp
91 !> applied bias [in a.u.]
92 REAL(kind=dp) :: v_bias = -1.0_dp
93 !> integration lower bound [in a.u.]
94 REAL(kind=dp) :: energy_lbound = -1.0_dp
95 !> infinitesimal offset along the imaginary axis [in a.u.]
96 REAL(kind=dp) :: eta = -1.0_dp
97 !> initial guess to determine the actual Fermi level of bulk contacts [in a.u.]
98 REAL(kind=dp) :: homo_lumo_gap = -1.0_dp
99 !> number of residuals (poles of the Fermi function)
100 INTEGER :: delta_npoles = -1
101 !> offset along the x-axis away from the poles of the Fermi function [in units of kT]
102 INTEGER :: gamma_kt = -1
103 !> integration method
104 INTEGER :: integr_method = -1
105 !> minimal number of grid points along the closed contour
106 INTEGER :: integr_min_points = -1
107 !> maximal number of grid points along the closed contour
108 INTEGER :: integr_max_points = -1
109 !> maximal number of SCF iterations
110 INTEGER :: max_scf = -1
111 !> minimal number of MPI processes to be used to compute Green's function per energy point
112 INTEGER :: nprocs = -1
113 !> shift in Hartree potential [in a.u.]
114 REAL(kind=dp) :: v_shift = -1.0_dp
115 !> initial offset to determine the correct shift in Hartree potential [in a.u.]
116 REAL(kind=dp) :: v_shift_offset = -1.0_dp
117 !> maximal number of iteration to determine the shift in Hartree potential
118 INTEGER :: v_shift_maxiters = -1
119 END TYPE negf_control_type
120
121 PRIVATE :: read_negf_atomlist
122
123CONTAINS
124
125! **************************************************************************************************
126!> \brief allocate control options for Non-equilibrium Green's Function calculation
127!> \param negf_control an object to create
128!> \par History
129!> * 02.2017 created [Sergey Chulkov]
130! **************************************************************************************************
131 SUBROUTINE negf_control_create(negf_control)
132 TYPE(negf_control_type), POINTER :: negf_control
133
134 CHARACTER(len=*), PARAMETER :: routinen = 'negf_control_create'
135
136 INTEGER :: handle
137
138 cpassert(.NOT. ASSOCIATED(negf_control))
139 CALL timeset(routinen, handle)
140
141 ALLOCATE (negf_control)
142
143 CALL timestop(handle)
144 END SUBROUTINE negf_control_create
145
146! **************************************************************************************************
147!> \brief release memory allocated for NEGF control options
148!> \param negf_control an object to release
149!> \par History
150!> * 02.2017 created [Sergey Chulkov]
151! **************************************************************************************************
152 SUBROUTINE negf_control_release(negf_control)
153 TYPE(negf_control_type), POINTER :: negf_control
154
155 CHARACTER(len=*), PARAMETER :: routinen = 'negf_control_release'
156
157 INTEGER :: handle, i, j
158
159 CALL timeset(routinen, handle)
160
161 IF (ASSOCIATED(negf_control)) THEN
162 IF (ALLOCATED(negf_control%atomlist_S)) DEALLOCATE (negf_control%atomlist_S)
163 IF (ALLOCATED(negf_control%atomlist_S_screening)) DEALLOCATE (negf_control%atomlist_S_screening)
164
165 IF (ALLOCATED(negf_control%contacts)) THEN
166 DO i = SIZE(negf_control%contacts), 1, -1
167 IF (ALLOCATED(negf_control%contacts(i)%atomlist_bulk)) &
168 DEALLOCATE (negf_control%contacts(i)%atomlist_bulk)
169
170 IF (ALLOCATED(negf_control%contacts(i)%atomlist_screening)) &
171 DEALLOCATE (negf_control%contacts(i)%atomlist_screening)
172
173 IF (ALLOCATED(negf_control%contacts(i)%atomlist_cell)) THEN
174 DO j = SIZE(negf_control%contacts(i)%atomlist_cell), 1, -1
175 IF (ALLOCATED(negf_control%contacts(i)%atomlist_cell(j)%vector)) &
176 DEALLOCATE (negf_control%contacts(i)%atomlist_cell(j)%vector)
177 END DO
178 DEALLOCATE (negf_control%contacts(i)%atomlist_cell)
179 END IF
180 END DO
181
182 DEALLOCATE (negf_control%contacts)
183 END IF
184
185 DEALLOCATE (negf_control)
186 END IF
187
188 CALL timestop(handle)
189 END SUBROUTINE negf_control_release
190
191! **************************************************************************************************
192!> \brief Read NEGF input parameters.
193!> \param negf_control NEGF control parameters
194!> \param input root input section
195!> \param subsys subsystem environment
196! **************************************************************************************************
197 SUBROUTINE read_negf_control(negf_control, input, subsys)
198 TYPE(negf_control_type), POINTER :: negf_control
199 TYPE(section_vals_type), POINTER :: input
200 TYPE(cp_subsys_type), POINTER :: subsys
201
202 CHARACTER(len=*), PARAMETER :: routinen = 'read_negf_control'
203
204 CHARACTER(len=default_string_length) :: contact_id_str, eta_current_str, eta_max_str, &
205 npoles_current_str, npoles_min_str, temp_current_str, temp_min_str
206 INTEGER :: delta_npoles_min, handle, i2_rep, i_rep, &
207 n2_rep, n_rep, natoms_current, &
208 natoms_total, run_type
209 INTEGER, ALLOCATABLE, DIMENSION(:) :: inds
210 LOGICAL :: do_negf, is_explicit
211 REAL(kind=dp) :: eta_max, temp_current, temp_min
212 TYPE(section_vals_type), POINTER :: cell_section, contact_section, &
213 negf_section, region_section
214
215 CALL timeset(routinen, handle)
216
217 CALL section_vals_val_get(input, "GLOBAL%RUN_TYPE", i_val=run_type)
218 do_negf = run_type == negf_run
219
220 negf_section => section_vals_get_subs_vals(input, "NEGF")
221
222 contact_section => section_vals_get_subs_vals(negf_section, "CONTACT")
223 CALL section_vals_get(contact_section, n_repetition=n_rep, explicit=is_explicit)
224 IF ((.NOT. is_explicit) .AND. do_negf) THEN
225 CALL cp_abort(__location__, &
226 "At least one contact is needed for NEGF calculation.")
227 END IF
228
229 ALLOCATE (negf_control%contacts(n_rep))
230 DO i_rep = 1, n_rep
231 region_section => section_vals_get_subs_vals(contact_section, "SCREENING_REGION", i_rep_section=i_rep)
232 CALL section_vals_get(region_section, explicit=is_explicit)
233
234 IF ((.NOT. is_explicit) .AND. do_negf) THEN
235 WRITE (contact_id_str, '(I11)') i_rep
236 CALL cp_abort(__location__, &
237 "The screening region must be defined for the contact "//trim(adjustl(contact_id_str))//".")
238 END IF
239
240 IF (is_explicit) THEN
241 CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_screening, region_section, 1, subsys)
242 END IF
243
244 region_section => section_vals_get_subs_vals(contact_section, "BULK_REGION", i_rep_section=i_rep)
245
246 CALL section_vals_get(region_section, explicit=is_explicit)
247
248 IF ((.NOT. is_explicit) .AND. do_negf) THEN
249 WRITE (contact_id_str, '(I11)') i_rep
250 CALL cp_abort(__location__, &
251 "The bulk region must be defined for the contact "//trim(adjustl(contact_id_str))//".")
252 END IF
253
254 IF (is_explicit) THEN
255 CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_bulk, region_section, 1, subsys)
256 END IF
257
258 CALL section_vals_val_get(contact_section, "FORCE_EVAL_SECTION", &
259 i_val=negf_control%contacts(i_rep)%force_env_index, &
260 i_rep_section=i_rep)
261
262 cell_section => section_vals_get_subs_vals(region_section, "CELL")
263 CALL section_vals_get(cell_section, n_repetition=n2_rep, explicit=is_explicit)
264
265 IF (((.NOT. is_explicit) .OR. n2_rep /= 2) .AND. negf_control%contacts(i_rep)%force_env_index <= 0 .AND. do_negf) THEN
266 WRITE (contact_id_str, '(I11)') i_rep
267 CALL cp_abort(__location__, &
268 "You must either provide indices of atoms belonging to two adjacent bulk unit cells "// &
269 "(BULK_REGION/CELL) for the contact, or the index of the FORCE_EVAL section (FORCE_EVAL_SECTION) "// &
270 "which will be used to construct Kohn-Sham matrix for the bulk contact "// &
271 trim(adjustl(contact_id_str))//".")
272 END IF
273
274 IF (is_explicit .AND. n2_rep > 0) THEN
275 ALLOCATE (negf_control%contacts(i_rep)%atomlist_cell(n2_rep))
276
277 DO i2_rep = 1, n2_rep
278 CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_cell(i2_rep)%vector, cell_section, i2_rep, subsys)
279 END DO
280 END IF
281
282 CALL section_vals_val_get(contact_section, "REFINE_FERMI_LEVEL", &
283 l_val=negf_control%contacts(i_rep)%refine_fermi_level, &
284 i_rep_section=i_rep)
285
286 CALL section_vals_val_get(contact_section, "FERMI_LEVEL", &
287 r_val=negf_control%contacts(i_rep)%fermi_level, &
288 i_rep_section=i_rep, explicit=is_explicit)
289 negf_control%contacts(i_rep)%compute_fermi_level = (.NOT. is_explicit) .OR. &
290 negf_control%contacts(i_rep)%refine_fermi_level
291
292 IF (do_negf .AND. negf_control%contacts(i_rep)%force_env_index <= 0 .AND. &
293 (.NOT. (is_explicit .OR. negf_control%contacts(i_rep)%refine_fermi_level))) THEN
294 WRITE (contact_id_str, '(I11)') i_rep
295 CALL cp_warn(__location__, &
296 "There is no way to reasonably guess the Fermi level for the bulk contact "// &
297 trim(adjustl(contact_id_str))//" without running a separate bulk DFT calculation first. "// &
298 "Therefore, 0.0 Hartree will be used as an initial guess. It is strongly advised to enable "// &
299 "the REFINE_FERMI_LEVEL switch and to provide an initial guess using the FERMI_LEVEL keyword. "// &
300 "Alternatively, a bulk FORCE_EVAL_SECTION can be set up.")
301 END IF
302
303 CALL section_vals_val_get(contact_section, "TEMPERATURE", &
304 r_val=negf_control%contacts(i_rep)%temperature, &
305 i_rep_section=i_rep)
306 IF (negf_control%contacts(i_rep)%temperature <= 0.0_dp) THEN
307 CALL cp_abort(__location__, "Electronic temperature must be > 0")
308 END IF
309
310 CALL section_vals_val_get(contact_section, "ELECTRIC_POTENTIAL", &
311 r_val=negf_control%contacts(i_rep)%v_external, &
312 i_rep_section=i_rep)
313 END DO
314
315 region_section => section_vals_get_subs_vals(negf_section, "SCATTERING_REGION")
316 CALL section_vals_get(region_section, explicit=is_explicit)
317 IF (is_explicit) THEN
318 CALL read_negf_atomlist(negf_control%atomlist_S, region_section, 1, subsys)
319 END IF
320
321 CALL section_vals_val_get(negf_section, "DISABLE_CACHE", l_val=negf_control%disable_cache)
322
323 CALL section_vals_val_get(negf_section, "EPS_DENSITY", r_val=negf_control%conv_density)
324 CALL section_vals_val_get(negf_section, "EPS_GREEN", r_val=negf_control%conv_green)
325 CALL section_vals_val_get(negf_section, "EPS_SCF", r_val=negf_control%conv_scf)
326
327 CALL section_vals_val_get(negf_section, "EPS_GEO", r_val=negf_control%eps_geometry)
328
329 CALL section_vals_val_get(negf_section, "ENERGY_LBOUND", r_val=negf_control%energy_lbound)
330 CALL section_vals_val_get(negf_section, "ETA", r_val=negf_control%eta)
331 CALL section_vals_val_get(negf_section, "HOMO_LUMO_GAP", r_val=negf_control%homo_lumo_gap)
332 CALL section_vals_val_get(negf_section, "DELTA_NPOLES", i_val=negf_control%delta_npoles)
333 CALL section_vals_val_get(negf_section, "GAMMA_KT", i_val=negf_control%gamma_kT)
334
335 CALL section_vals_val_get(negf_section, "INTEGRATION_METHOD", i_val=negf_control%integr_method)
336 CALL section_vals_val_get(negf_section, "INTEGRATION_MIN_POINTS", i_val=negf_control%integr_min_points)
337 CALL section_vals_val_get(negf_section, "INTEGRATION_MAX_POINTS", i_val=negf_control%integr_max_points)
338
339 IF (negf_control%integr_max_points < negf_control%integr_min_points) &
340 negf_control%integr_max_points = negf_control%integr_min_points
341
342 CALL section_vals_val_get(negf_section, "MAX_SCF", i_val=negf_control%max_scf)
343
344 CALL section_vals_val_get(negf_section, "NPROC_POINT", i_val=negf_control%nprocs)
345
346 CALL section_vals_val_get(negf_section, "V_SHIFT", r_val=negf_control%v_shift)
347 CALL section_vals_val_get(negf_section, "V_SHIFT_OFFSET", r_val=negf_control%v_shift_offset)
348 CALL section_vals_val_get(negf_section, "V_SHIFT_MAX_ITERS", i_val=negf_control%v_shift_maxiters)
349
350 ! check consistency
351 IF (negf_control%eta < 0.0_dp) THEN
352 CALL cp_abort(__location__, "ETA must be >= 0")
353 END IF
354
355 IF (n_rep > 0) THEN
356 delta_npoles_min = nint(0.5_dp*(negf_control%eta/(pi*maxval(negf_control%contacts(:)%temperature)) + 1.0_dp))
357 ELSE
358 delta_npoles_min = 1
359 END IF
360
361 IF (negf_control%delta_npoles < delta_npoles_min) THEN
362 IF (n_rep > 0) THEN
363 eta_max = real(2*negf_control%delta_npoles - 1, kind=dp)*pi*maxval(negf_control%contacts(:)%temperature)
364 temp_current = maxval(negf_control%contacts(:)%temperature)*kelvin
365 temp_min = negf_control%eta/(pi*real(2*negf_control%delta_npoles - 1, kind=dp))*kelvin
366
367 WRITE (eta_current_str, '(ES11.4E2)') negf_control%eta
368 WRITE (eta_max_str, '(ES11.4E2)') eta_max
369 WRITE (npoles_current_str, '(I11)') negf_control%delta_npoles
370 WRITE (npoles_min_str, '(I11)') delta_npoles_min
371 WRITE (temp_current_str, '(F11.3)') temp_current
372 WRITE (temp_min_str, '(F11.3)') temp_min
373
374 CALL cp_abort(__location__, &
375 "Parameter DELTA_NPOLES must be at least "//trim(adjustl(npoles_min_str))// &
376 " (instead of "//trim(adjustl(npoles_current_str))// &
377 ") for given TEMPERATURE ("//trim(adjustl(temp_current_str))// &
378 " K) and ETA ("//trim(adjustl(eta_current_str))// &
379 "). Alternatively you can increase TEMPERATURE above "//trim(adjustl(temp_min_str))// &
380 " K, or decrease ETA below "//trim(adjustl(eta_max_str))// &
381 ". Please keep in mind that very tight ETA may result in dramatical precision loss"// &
382 " due to inversion of ill-conditioned matrices.")
383 ELSE
384 ! no leads have been defined, so calculation will abort anyway
385 negf_control%delta_npoles = delta_npoles_min
386 END IF
387 END IF
388
389 ! expand scattering region by adding atoms from contact screening regions
390 n_rep = SIZE(negf_control%contacts)
391 IF (ALLOCATED(negf_control%atomlist_S)) THEN
392 natoms_total = SIZE(negf_control%atomlist_S)
393 ELSE
394 natoms_total = 0
395 END IF
396
397 DO i_rep = 1, n_rep
398 IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) THEN
399 IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) &
400 natoms_total = natoms_total + SIZE(negf_control%contacts(i_rep)%atomlist_screening)
401 END IF
402 END DO
403
404 IF (natoms_total > 0) THEN
405 ALLOCATE (negf_control%atomlist_S_screening(natoms_total))
406 IF (ALLOCATED(negf_control%atomlist_S)) THEN
407 natoms_total = SIZE(negf_control%atomlist_S)
408 negf_control%atomlist_S_screening(1:natoms_total) = negf_control%atomlist_S(1:natoms_total)
409 ELSE
410 natoms_total = 0
411 END IF
412
413 DO i_rep = 1, n_rep
414 IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) THEN
415 natoms_current = SIZE(negf_control%contacts(i_rep)%atomlist_screening)
416
417 negf_control%atomlist_S_screening(natoms_total + 1:natoms_total + natoms_current) = &
418 negf_control%contacts(i_rep)%atomlist_screening(1:natoms_current)
419
420 natoms_total = natoms_total + natoms_current
421 END IF
422 END DO
423
424 ! sort and remove duplicated atoms
425 ALLOCATE (inds(natoms_total))
426 CALL sort(negf_control%atomlist_S_screening, natoms_total, inds)
427 DEALLOCATE (inds)
428
429 natoms_current = 1
430 DO i_rep = natoms_current + 1, natoms_total
431 IF (negf_control%atomlist_S_screening(i_rep) /= negf_control%atomlist_S_screening(natoms_current)) THEN
432 natoms_current = natoms_current + 1
433 negf_control%atomlist_S_screening(natoms_current) = negf_control%atomlist_S_screening(i_rep)
434 END IF
435 END DO
436
437 IF (natoms_current < natoms_total) THEN
438 CALL move_alloc(negf_control%atomlist_S_screening, inds)
439
440 ALLOCATE (negf_control%atomlist_S_screening(natoms_current))
441 negf_control%atomlist_S_screening(1:natoms_current) = inds(1:natoms_current)
442 DEALLOCATE (inds)
443 END IF
444 END IF
445
446 IF (do_negf .AND. SIZE(negf_control%contacts) > 2) THEN
447 CALL cp_abort(__location__, &
448 "General case (> 2 contacts) has not been implemented yet")
449 END IF
450
451 CALL timestop(handle)
452 END SUBROUTINE read_negf_control
453
454! **************************************************************************************************
455!> \brief Read region-specific list of atoms.
456!> \param atomlist list of atoms
457!> \param input_section input section which contains 'LIST' and 'MOLNAME' keywords
458!> \param i_rep_section repetition index of the input_section
459!> \param subsys subsystem environment
460! **************************************************************************************************
461 SUBROUTINE read_negf_atomlist(atomlist, input_section, i_rep_section, subsys)
462 INTEGER, ALLOCATABLE, DIMENSION(:), INTENT(out) :: atomlist
463 TYPE(section_vals_type), POINTER :: input_section
464 INTEGER, INTENT(in) :: i_rep_section
465 TYPE(cp_subsys_type), POINTER :: subsys
466
467 CHARACTER(len=*), PARAMETER :: routinen = 'read_negf_atomlist'
468
469 CHARACTER(len=default_string_length) :: index_str, natoms_str
470 CHARACTER(len=default_string_length), &
471 DIMENSION(:), POINTER :: cptr
472 INTEGER :: first_atom, handle, iatom, ikind, imol, iname, irep, last_atom, natoms_current, &
473 natoms_max, natoms_total, nkinds, nmols, nnames, nrep_list, nrep_molname
474 INTEGER, ALLOCATABLE, DIMENSION(:) :: inds
475 INTEGER, DIMENSION(:), POINTER :: iptr
476 LOGICAL :: is_list, is_molname
477 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
478 TYPE(molecule_kind_type), POINTER :: molecule_kind
479 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
480 TYPE(molecule_type), POINTER :: molecule
481 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
482
483 CALL timeset(routinen, handle)
484
485 CALL cp_subsys_get(subsys, particle_set=particle_set, &
486 molecule_set=molecule_set, &
487 molecule_kind_set=molecule_kind_set)
488 natoms_max = SIZE(particle_set)
489 nkinds = SIZE(molecule_kind_set)
490
491 CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, &
492 n_rep_val=nrep_list, explicit=is_list)
493 CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, &
494 n_rep_val=nrep_molname, explicit=is_molname)
495
496 ! compute the number of atoms in the NEGF region, and check the validity of giben atomic indices
497 natoms_total = 0
498 IF (is_list .AND. nrep_list > 0) THEN
499 DO irep = 1, nrep_list
500 CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, i_rep_val=irep, i_vals=iptr)
501
502 natoms_current = SIZE(iptr)
503 DO iatom = 1, natoms_current
504 IF (iptr(iatom) > natoms_max) THEN
505 CALL integer_to_string(iptr(iatom), index_str)
506 CALL integer_to_string(natoms_max, natoms_str)
507 CALL cp_abort(__location__, &
508 "NEGF: Atomic index "//trim(index_str)//" given in section "// &
509 trim(input_section%section%name)//" exceeds the maximum number of atoms ("// &
510 trim(natoms_str)//").")
511 END IF
512 END DO
513
514 natoms_total = natoms_total + natoms_current
515 END DO
516 END IF
517
518 IF (is_molname .AND. nrep_molname > 0) THEN
519 DO irep = 1, nrep_molname
520 CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, i_rep_val=irep, c_vals=cptr)
521 nnames = SIZE(cptr)
522
523 DO iname = 1, nnames
524 DO ikind = 1, nkinds
525 IF (molecule_kind_set(ikind)%name .EQ. cptr(iname)) EXIT
526 END DO
527
528 IF (ikind <= nkinds) THEN
529 molecule_kind => molecule_kind_set(ikind)
530 CALL get_molecule_kind(molecule_kind, nmolecule=nmols, molecule_list=iptr)
531
532 DO imol = 1, nmols
533 molecule => molecule_set(iptr(imol))
534 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
535 natoms_current = last_atom - first_atom + 1
536 natoms_total = natoms_total + natoms_current
537 END DO
538 ELSE
539 CALL cp_abort(__location__, &
540 "NEGF: A molecule with the name '"//trim(cptr(iname))//"' mentioned in section "// &
541 trim(input_section%section%name)//" has not been defined. Note that names are case sensitive.")
542 END IF
543 END DO
544 END DO
545 END IF
546
547 ! create a list of atomic indices
548 IF (natoms_total > 0) THEN
549 ALLOCATE (atomlist(natoms_total))
550
551 natoms_total = 0
552
553 IF (is_list .AND. nrep_list > 0) THEN
554 DO irep = 1, nrep_list
555 CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, i_rep_val=irep, i_vals=iptr)
556
557 natoms_current = SIZE(iptr)
558 atomlist(natoms_total + 1:natoms_total + natoms_current) = iptr(1:natoms_current)
559 natoms_total = natoms_total + natoms_current
560 END DO
561 END IF
562
563 IF (is_molname .AND. nrep_molname > 0) THEN
564 DO irep = 1, nrep_molname
565 CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, i_rep_val=irep, c_vals=cptr)
566 nnames = SIZE(cptr)
567
568 DO iname = 1, nnames
569 DO ikind = 1, nkinds
570 IF (molecule_kind_set(ikind)%name .EQ. cptr(iname)) EXIT
571 END DO
572
573 IF (ikind <= nkinds) THEN
574 molecule_kind => molecule_kind_set(ikind)
575 CALL get_molecule_kind(molecule_kind, nmolecule=nmols, molecule_list=iptr)
576
577 DO imol = 1, nmols
578 molecule => molecule_set(iptr(imol))
579 CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
580
581 DO natoms_current = first_atom, last_atom
582 natoms_total = natoms_total + 1
583 atomlist(natoms_total) = natoms_current
584 END DO
585 END DO
586 END IF
587 END DO
588 END DO
589 END IF
590
591 ! remove duplicated atoms
592 ALLOCATE (inds(natoms_total))
593 CALL sort(atomlist, natoms_total, inds)
594 DEALLOCATE (inds)
595
596 natoms_current = 1
597 DO iatom = natoms_current + 1, natoms_total
598 IF (atomlist(iatom) /= atomlist(natoms_current)) THEN
599 natoms_current = natoms_current + 1
600 atomlist(natoms_current) = atomlist(iatom)
601 END IF
602 END DO
603
604 IF (natoms_current < natoms_total) THEN
605 CALL move_alloc(atomlist, inds)
606
607 ALLOCATE (atomlist(natoms_current))
608 atomlist(1:natoms_current) = inds(1:natoms_current)
609 DEALLOCATE (inds)
610 END IF
611 END IF
612
613 CALL timestop(handle)
614 END SUBROUTINE read_negf_atomlist
615END MODULE negf_control_types
cp_subsys_types
types that represent a subsys, i.e. a part of the system
Definition cp_subsys_types.F:16
cp_subsys_types::cp_subsys_get
subroutine, public cp_subsys_get(subsys, ref_count, atomic_kinds, atomic_kind_set, particles, particle_set, local_particles, molecules, molecule_set, molecule_kinds, molecule_kind_set, local_molecules, para_env, colvar_p, shell_particles, core_particles, gci, multipoles, natom, nparticle, ncore, nshell, nkind, atprop, virial, results, cell)
returns information about various attributes of the given subsys
Definition cp_subsys_types.F:345
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::negf_run
integer, parameter, public negf_run
Definition input_constants.F:122
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
input_section_types::section_vals_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition input_section_types.F:731
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition input_section_types.F:704
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition input_section_types.F:1047
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
mathconstants
Definition of mathematical constants and functions.
Definition mathconstants.F:16
mathconstants::pi
real(kind=dp), parameter, public pi
Definition mathconstants.F:110
molecule_kind_types
Define the molecule kind structure types and the corresponding functionality.
Definition molecule_kind_types.F:16
molecule_kind_types::get_molecule_kind
subroutine, public get_molecule_kind(molecule_kind, atom_list, bond_list, bend_list, ub_list, impr_list, opbend_list, colv_list, fixd_list, g3x3_list, g4x6_list, vsite_list, torsion_list, shell_list, name, mass, charge, kind_number, natom, nbend, nbond, nub, nimpr, nopbend, nconstraint, nconstraint_fixd, nfixd, ncolv, ng3x3, ng4x6, nvsite, nfixd_restraint, ng3x3_restraint, ng4x6_restraint, nvsite_restraint, nrestraints, nmolecule, nsgf, nshell, ntorsion, molecule_list, nelectron, nelectron_alpha, nelectron_beta, bond_kind_set, bend_kind_set, ub_kind_set, impr_kind_set, opbend_kind_set, torsion_kind_set, molname_generated)
Get informations about a molecule kind.
Definition molecule_kind_types.F:510
molecule_types
Define the data structure for the molecule information.
Definition molecule_types.F:16
molecule_types::get_molecule
subroutine, public get_molecule(molecule, molecule_kind, lmi, lci, lg3x3, lg4x6, lcolv, first_atom, last_atom, first_shell, last_shell)
Get components from a molecule data set.
Definition molecule_types.F:277
negf_alloc_types
Allocatable vectors for NEGF based quantum transport calculations.
Definition negf_alloc_types.F:12
negf_control_types
Input control types for NEGF based quantum transport calculations.
Definition negf_control_types.F:12
negf_control_types::negf_control_create
subroutine, public negf_control_create(negf_control)
allocate control options for Non-equilibrium Green's Function calculation
Definition negf_control_types.F:132
negf_control_types::read_negf_control
subroutine, public read_negf_control(negf_control, input, subsys)
Read NEGF input parameters.
Definition negf_control_types.F:198
negf_control_types::negf_control_release
subroutine, public negf_control_release(negf_control)
release memory allocated for NEGF control options
Definition negf_control_types.F:153
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
physcon
Definition of physical constants:
Definition physcon.F:68
physcon::kelvin
real(kind=dp), parameter, public kelvin
Definition physcon.F:165
string_utilities
Utilities for string manipulations.
Definition string_utilities.F:16
string_utilities::integer_to_string
subroutine, public integer_to_string(inumber, string)
Converts an integer number to a string. The WRITE statement will return an error message,...
Definition string_utilities.F:3239
util
All kind of helpful little routines.
Definition util.F:14
cp_subsys_types::cp_subsys_type
represents a system: atoms, molecules, their pos,vel,...
Definition cp_subsys_types.F:89
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:161
molecule_types::molecule_type
Definition molecule_types.F:110
negf_alloc_types::negf_allocatable_ivector
Allocatable 1-D integer vector.
Definition negf_alloc_types.F:27
negf_control_types::negf_control_contact_type
Input parameters related to a single contact.
Definition negf_control_types.F:47
negf_control_types::negf_control_type
Input parameters related to the NEGF run.
Definition negf_control_types.F:72
particle_types::particle_type
Definition particle_types.F:35