Line data Source code
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 :
12 : MODULE 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 : !> atoms 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
56 : LOGICAL :: compute_fermi_level = .FALSE.
57 : !> to refine contact Fermi level using NEGF
58 : LOGICAL :: refine_fermi_level = .FALSE.
59 : !> to shift energies to common zero level
60 : LOGICAL :: shift_fermi_level = .FALSE.
61 : !> Fermi level or starting Fermi level
62 : REAL(kind=dp) :: fermi_level = -1.0_dp
63 : !> Fermi level shifted to the common zero-energy level
64 : REAL(kind=dp) :: fermi_level_shifted = -1.0_dp
65 : !> temperature [in a.u.]
66 : REAL(kind=dp) :: temperature = -1.0_dp
67 : !> applied electric potential
68 : REAL(kind=dp) :: v_external = 0.0_dp
69 : END TYPE negf_control_contact_type
70 :
71 : ! **************************************************************************************************
72 : !> \brief Input parameters related to the NEGF run.
73 : !> \author Sergey Chulkov
74 : ! **************************************************************************************************
75 : TYPE negf_control_type
76 : !> input options for every contact
77 : TYPE(negf_control_contact_type), ALLOCATABLE, &
78 : DIMENSION(:) :: contacts
79 : !> atoms belonging to the scattering region
80 : INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_S
81 : !> atoms belonging to the scattering region as well as atoms belonging to
82 : !> screening regions of all the contacts
83 : INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_S_screening
84 : !> do not keep contact self-energy matrices
85 : LOGICAL :: disable_cache = .FALSE.
86 : !> convergence criteria for adaptive integration methods
87 : REAL(kind=dp) :: conv_density = -1.0_dp
88 : !> convergence criteria for iterative Lopez-Sancho algorithm
89 : REAL(kind=dp) :: conv_green = -1.0_dp
90 : !> convergence criteria for self-consistent iterations
91 : REAL(kind=dp) :: conv_scf = -1.0_dp
92 : !> accuracy in mapping atoms between different force environments
93 : REAL(kind=dp) :: eps_geometry = -1.0_dp
94 : !> applied bias [in a.u.]
95 : REAL(kind=dp) :: v_bias = -1.0_dp
96 : !> integration lower bound [in a.u.]
97 : REAL(kind=dp) :: energy_lbound = -1.0_dp
98 : !> infinitesimal offset along the imaginary axis [in a.u.]
99 : REAL(kind=dp) :: eta = -1.0_dp
100 : !> initial guess to determine the actual Fermi level of bulk contacts [in a.u.]
101 : REAL(kind=dp) :: homo_lumo_gap = -1.0_dp
102 : !> number of residuals (poles of the Fermi function)
103 : INTEGER :: delta_npoles = -1
104 : !> offset along the x-axis away from the poles of the Fermi function [in units of kT]
105 : INTEGER :: gamma_kT = -1
106 : !> integration method
107 : INTEGER :: integr_method = -1
108 : !> minimal number of grid points along the closed contour
109 : INTEGER :: integr_min_points = -1
110 : !> maximal number of grid points along the closed contour
111 : INTEGER :: integr_max_points = -1
112 : !> maximal number of SCF iterations
113 : INTEGER :: max_scf = -1
114 : !> minimal number of MPI processes to be used to compute Green's function per energy point
115 : INTEGER :: nprocs = -1
116 : !> shift in Hartree potential [in a.u.]
117 : REAL(kind=dp) :: v_shift = -1.0_dp
118 : !> initial offset to determine the correct shift in Hartree potential [in a.u.]
119 : REAL(kind=dp) :: v_shift_offset = -1.0_dp
120 : !> maximal number of iteration to determine the shift in Hartree potential
121 : INTEGER :: v_shift_maxiters = -1
122 : END TYPE negf_control_type
123 :
124 : PRIVATE :: read_negf_atomlist
125 :
126 : CONTAINS
127 :
128 : ! **************************************************************************************************
129 : !> \brief allocate control options for Non-equilibrium Green's Function calculation
130 : !> \param negf_control an object to create
131 : !> \par History
132 : !> * 02.2017 created [Sergey Chulkov]
133 : ! **************************************************************************************************
134 8 : SUBROUTINE negf_control_create(negf_control)
135 : TYPE(negf_control_type), POINTER :: negf_control
136 :
137 : CHARACTER(len=*), PARAMETER :: routineN = 'negf_control_create'
138 :
139 : INTEGER :: handle
140 :
141 4 : CPASSERT(.NOT. ASSOCIATED(negf_control))
142 4 : CALL timeset(routineN, handle)
143 :
144 4 : ALLOCATE (negf_control)
145 :
146 4 : CALL timestop(handle)
147 4 : END SUBROUTINE negf_control_create
148 :
149 : ! **************************************************************************************************
150 : !> \brief release memory allocated for NEGF control options
151 : !> \param negf_control an object to release
152 : !> \par History
153 : !> * 02.2017 created [Sergey Chulkov]
154 : ! **************************************************************************************************
155 4 : SUBROUTINE negf_control_release(negf_control)
156 : TYPE(negf_control_type), POINTER :: negf_control
157 :
158 : CHARACTER(len=*), PARAMETER :: routineN = 'negf_control_release'
159 :
160 : INTEGER :: handle, i, j
161 :
162 4 : CALL timeset(routineN, handle)
163 :
164 4 : IF (ASSOCIATED(negf_control)) THEN
165 4 : IF (ALLOCATED(negf_control%atomlist_S)) DEALLOCATE (negf_control%atomlist_S)
166 4 : IF (ALLOCATED(negf_control%atomlist_S_screening)) DEALLOCATE (negf_control%atomlist_S_screening)
167 :
168 4 : IF (ALLOCATED(negf_control%contacts)) THEN
169 12 : DO i = SIZE(negf_control%contacts), 1, -1
170 8 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_bulk)) &
171 8 : DEALLOCATE (negf_control%contacts(i)%atomlist_bulk)
172 :
173 8 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_screening)) &
174 8 : DEALLOCATE (negf_control%contacts(i)%atomlist_screening)
175 :
176 12 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_cell)) THEN
177 24 : DO j = SIZE(negf_control%contacts(i)%atomlist_cell), 1, -1
178 16 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_cell(j)%vector)) &
179 24 : DEALLOCATE (negf_control%contacts(i)%atomlist_cell(j)%vector)
180 : END DO
181 24 : DEALLOCATE (negf_control%contacts(i)%atomlist_cell)
182 : END IF
183 : END DO
184 :
185 12 : DEALLOCATE (negf_control%contacts)
186 : END IF
187 :
188 4 : DEALLOCATE (negf_control)
189 : END IF
190 :
191 4 : CALL timestop(handle)
192 4 : END SUBROUTINE negf_control_release
193 :
194 : ! **************************************************************************************************
195 : !> \brief Read NEGF input parameters.
196 : !> \param negf_control NEGF control parameters
197 : !> \param input root input section
198 : !> \param subsys subsystem environment
199 : ! **************************************************************************************************
200 4 : SUBROUTINE read_negf_control(negf_control, input, subsys)
201 : TYPE(negf_control_type), POINTER :: negf_control
202 : TYPE(section_vals_type), POINTER :: input
203 : TYPE(cp_subsys_type), POINTER :: subsys
204 :
205 : CHARACTER(len=*), PARAMETER :: routineN = 'read_negf_control'
206 :
207 : CHARACTER(len=default_string_length) :: contact_id_str, eta_current_str, eta_max_str, &
208 : npoles_current_str, npoles_min_str, temp_current_str, temp_min_str
209 : INTEGER :: delta_npoles_min, handle, i2_rep, i_rep, &
210 : n2_rep, n_rep, natoms_current, &
211 : natoms_total, run_type
212 4 : INTEGER, ALLOCATABLE, DIMENSION(:) :: inds
213 : LOGICAL :: do_negf, is_explicit
214 : REAL(kind=dp) :: eta_max, temp_current, temp_min
215 : TYPE(section_vals_type), POINTER :: cell_section, contact_section, &
216 : negf_section, region_section
217 :
218 4 : CALL timeset(routineN, handle)
219 :
220 4 : CALL section_vals_val_get(input, "GLOBAL%RUN_TYPE", i_val=run_type)
221 4 : do_negf = run_type == negf_run
222 :
223 4 : negf_section => section_vals_get_subs_vals(input, "NEGF")
224 :
225 4 : contact_section => section_vals_get_subs_vals(negf_section, "CONTACT")
226 4 : CALL section_vals_get(contact_section, n_repetition=n_rep, explicit=is_explicit)
227 4 : IF ((.NOT. is_explicit) .AND. do_negf) THEN
228 : CALL cp_abort(__LOCATION__, &
229 0 : "At least one contact is needed for NEGF calculation.")
230 : END IF
231 :
232 20 : ALLOCATE (negf_control%contacts(n_rep))
233 12 : DO i_rep = 1, n_rep
234 8 : region_section => section_vals_get_subs_vals(contact_section, "SCREENING_REGION", i_rep_section=i_rep)
235 8 : CALL section_vals_get(region_section, explicit=is_explicit)
236 :
237 8 : IF ((.NOT. is_explicit) .AND. do_negf) THEN
238 0 : WRITE (contact_id_str, '(I11)') i_rep
239 : CALL cp_abort(__LOCATION__, &
240 0 : "The screening region must be defined for the contact "//TRIM(ADJUSTL(contact_id_str))//".")
241 : END IF
242 :
243 8 : IF (is_explicit) THEN
244 8 : CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_screening, region_section, 1, subsys)
245 : END IF
246 :
247 8 : region_section => section_vals_get_subs_vals(contact_section, "BULK_REGION", i_rep_section=i_rep)
248 :
249 8 : CALL section_vals_get(region_section, explicit=is_explicit)
250 :
251 8 : IF ((.NOT. is_explicit) .AND. do_negf) THEN
252 0 : WRITE (contact_id_str, '(I11)') i_rep
253 : CALL cp_abort(__LOCATION__, &
254 0 : "The bulk region must be defined for the contact "//TRIM(ADJUSTL(contact_id_str))//".")
255 : END IF
256 :
257 8 : IF (is_explicit) THEN
258 8 : CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_bulk, region_section, 1, subsys)
259 : END IF
260 :
261 : CALL section_vals_val_get(contact_section, "FORCE_EVAL_SECTION", &
262 : i_val=negf_control%contacts(i_rep)%force_env_index, &
263 8 : i_rep_section=i_rep)
264 :
265 8 : cell_section => section_vals_get_subs_vals(region_section, "CELL")
266 8 : CALL section_vals_get(cell_section, n_repetition=n2_rep, explicit=is_explicit)
267 :
268 8 : IF (((.NOT. is_explicit) .OR. n2_rep /= 2) .AND. negf_control%contacts(i_rep)%force_env_index <= 0 .AND. do_negf) THEN
269 0 : WRITE (contact_id_str, '(I11)') i_rep
270 : CALL cp_abort(__LOCATION__, &
271 : "You must either provide indices of atoms belonging to two adjacent bulk unit cells "// &
272 : "(BULK_REGION/CELL) for the contact, or the index of the FORCE_EVAL section (FORCE_EVAL_SECTION) "// &
273 : "which will be used to construct Kohn-Sham matrix for the bulk contact "// &
274 0 : TRIM(ADJUSTL(contact_id_str))//".")
275 : END IF
276 :
277 8 : IF (is_explicit .AND. n2_rep > 0) THEN
278 40 : ALLOCATE (negf_control%contacts(i_rep)%atomlist_cell(n2_rep))
279 :
280 24 : DO i2_rep = 1, n2_rep
281 24 : CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_cell(i2_rep)%vector, cell_section, i2_rep, subsys)
282 : END DO
283 : END IF
284 :
285 : CALL section_vals_val_get(contact_section, "REFINE_FERMI_LEVEL", &
286 : l_val=negf_control%contacts(i_rep)%refine_fermi_level, &
287 8 : i_rep_section=i_rep)
288 :
289 : CALL section_vals_val_get(contact_section, "FERMI_LEVEL", &
290 : r_val=negf_control%contacts(i_rep)%fermi_level, &
291 8 : i_rep_section=i_rep, explicit=is_explicit)
292 8 : IF (.NOT. is_explicit) negf_control%contacts(i_rep)%refine_fermi_level = .FALSE.
293 : negf_control%contacts(i_rep)%compute_fermi_level = (.NOT. is_explicit) .OR. &
294 8 : negf_control%contacts(i_rep)%refine_fermi_level
295 :
296 : CALL section_vals_val_get(contact_section, "FERMI_LEVEL_SHIFTED", &
297 : r_val=negf_control%contacts(i_rep)%fermi_level_shifted, &
298 8 : i_rep_section=i_rep, explicit=is_explicit)
299 8 : IF (is_explicit) negf_control%contacts(i_rep)%shift_fermi_level = .TRUE.
300 :
301 : CALL section_vals_val_get(contact_section, "TEMPERATURE", &
302 : r_val=negf_control%contacts(i_rep)%temperature, &
303 8 : i_rep_section=i_rep)
304 8 : IF (negf_control%contacts(i_rep)%temperature <= 0.0_dp) THEN
305 0 : CALL cp_abort(__LOCATION__, "Electronic temperature must be > 0")
306 : END IF
307 :
308 : CALL section_vals_val_get(contact_section, "ELECTRIC_POTENTIAL", &
309 : r_val=negf_control%contacts(i_rep)%v_external, &
310 52 : i_rep_section=i_rep)
311 : END DO
312 :
313 4 : region_section => section_vals_get_subs_vals(negf_section, "SCATTERING_REGION")
314 4 : CALL section_vals_get(region_section, explicit=is_explicit)
315 4 : IF (is_explicit) THEN
316 4 : CALL read_negf_atomlist(negf_control%atomlist_S, region_section, 1, subsys)
317 : END IF
318 :
319 4 : CALL section_vals_val_get(negf_section, "DISABLE_CACHE", l_val=negf_control%disable_cache)
320 :
321 4 : CALL section_vals_val_get(negf_section, "EPS_DENSITY", r_val=negf_control%conv_density)
322 4 : CALL section_vals_val_get(negf_section, "EPS_GREEN", r_val=negf_control%conv_green)
323 4 : CALL section_vals_val_get(negf_section, "EPS_SCF", r_val=negf_control%conv_scf)
324 :
325 4 : CALL section_vals_val_get(negf_section, "EPS_GEO", r_val=negf_control%eps_geometry)
326 :
327 4 : CALL section_vals_val_get(negf_section, "ENERGY_LBOUND", r_val=negf_control%energy_lbound)
328 4 : CALL section_vals_val_get(negf_section, "ETA", r_val=negf_control%eta)
329 4 : CALL section_vals_val_get(negf_section, "HOMO_LUMO_GAP", r_val=negf_control%homo_lumo_gap)
330 4 : CALL section_vals_val_get(negf_section, "DELTA_NPOLES", i_val=negf_control%delta_npoles)
331 4 : CALL section_vals_val_get(negf_section, "GAMMA_KT", i_val=negf_control%gamma_kT)
332 :
333 4 : CALL section_vals_val_get(negf_section, "INTEGRATION_METHOD", i_val=negf_control%integr_method)
334 4 : CALL section_vals_val_get(negf_section, "INTEGRATION_MIN_POINTS", i_val=negf_control%integr_min_points)
335 4 : CALL section_vals_val_get(negf_section, "INTEGRATION_MAX_POINTS", i_val=negf_control%integr_max_points)
336 :
337 4 : IF (negf_control%integr_max_points < negf_control%integr_min_points) &
338 0 : negf_control%integr_max_points = negf_control%integr_min_points
339 :
340 4 : CALL section_vals_val_get(negf_section, "MAX_SCF", i_val=negf_control%max_scf)
341 :
342 4 : CALL section_vals_val_get(negf_section, "NPROC_POINT", i_val=negf_control%nprocs)
343 :
344 4 : CALL section_vals_val_get(negf_section, "V_SHIFT", r_val=negf_control%v_shift)
345 4 : CALL section_vals_val_get(negf_section, "V_SHIFT_OFFSET", r_val=negf_control%v_shift_offset)
346 4 : CALL section_vals_val_get(negf_section, "V_SHIFT_MAX_ITERS", i_val=negf_control%v_shift_maxiters)
347 :
348 : ! check consistency
349 4 : IF (negf_control%eta < 0.0_dp) THEN
350 0 : CALL cp_abort(__LOCATION__, "ETA must be >= 0")
351 : END IF
352 :
353 4 : IF (n_rep > 0) THEN
354 16 : delta_npoles_min = NINT(0.5_dp*(negf_control%eta/(pi*MAXVAL(negf_control%contacts(:)%temperature)) + 1.0_dp))
355 : ELSE
356 0 : delta_npoles_min = 1
357 : END IF
358 :
359 4 : IF (negf_control%delta_npoles < delta_npoles_min) THEN
360 0 : IF (n_rep > 0) THEN
361 0 : eta_max = REAL(2*negf_control%delta_npoles - 1, kind=dp)*pi*MAXVAL(negf_control%contacts(:)%temperature)
362 0 : temp_current = MAXVAL(negf_control%contacts(:)%temperature)*kelvin
363 0 : temp_min = negf_control%eta/(pi*REAL(2*negf_control%delta_npoles - 1, kind=dp))*kelvin
364 :
365 0 : WRITE (eta_current_str, '(ES11.4E2)') negf_control%eta
366 0 : WRITE (eta_max_str, '(ES11.4E2)') eta_max
367 0 : WRITE (npoles_current_str, '(I11)') negf_control%delta_npoles
368 0 : WRITE (npoles_min_str, '(I11)') delta_npoles_min
369 0 : WRITE (temp_current_str, '(F11.3)') temp_current
370 0 : WRITE (temp_min_str, '(F11.3)') temp_min
371 :
372 : CALL cp_abort(__LOCATION__, &
373 : "Parameter DELTA_NPOLES must be at least "//TRIM(ADJUSTL(npoles_min_str))// &
374 : " (instead of "//TRIM(ADJUSTL(npoles_current_str))// &
375 : ") for given TEMPERATURE ("//TRIM(ADJUSTL(temp_current_str))// &
376 : " K) and ETA ("//TRIM(ADJUSTL(eta_current_str))// &
377 : "). Alternatively you can increase TEMPERATURE above "//TRIM(ADJUSTL(temp_min_str))// &
378 : " K, or decrease ETA below "//TRIM(ADJUSTL(eta_max_str))// &
379 : ". Please keep in mind that very tight ETA may result in dramatical precision loss"// &
380 0 : " due to inversion of ill-conditioned matrices.")
381 : ELSE
382 : ! no leads have been defined, so calculation will abort anyway
383 0 : negf_control%delta_npoles = delta_npoles_min
384 : END IF
385 : END IF
386 :
387 : ! expand scattering region by adding atoms from contact screening regions
388 4 : n_rep = SIZE(negf_control%contacts)
389 4 : IF (ALLOCATED(negf_control%atomlist_S)) THEN
390 4 : natoms_total = SIZE(negf_control%atomlist_S)
391 : ELSE
392 0 : natoms_total = 0
393 : END IF
394 :
395 12 : DO i_rep = 1, n_rep
396 12 : IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) THEN
397 : IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) &
398 8 : natoms_total = natoms_total + SIZE(negf_control%contacts(i_rep)%atomlist_screening)
399 : END IF
400 : END DO
401 :
402 4 : IF (natoms_total > 0) THEN
403 12 : ALLOCATE (negf_control%atomlist_S_screening(natoms_total))
404 4 : IF (ALLOCATED(negf_control%atomlist_S)) THEN
405 4 : natoms_total = SIZE(negf_control%atomlist_S)
406 20 : negf_control%atomlist_S_screening(1:natoms_total) = negf_control%atomlist_S(1:natoms_total)
407 : ELSE
408 0 : natoms_total = 0
409 : END IF
410 :
411 12 : DO i_rep = 1, n_rep
412 12 : IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) THEN
413 8 : natoms_current = SIZE(negf_control%contacts(i_rep)%atomlist_screening)
414 :
415 : negf_control%atomlist_S_screening(natoms_total + 1:natoms_total + natoms_current) = &
416 40 : negf_control%contacts(i_rep)%atomlist_screening(1:natoms_current)
417 :
418 8 : natoms_total = natoms_total + natoms_current
419 : END IF
420 : END DO
421 :
422 : ! sort and remove duplicated atoms
423 12 : ALLOCATE (inds(natoms_total))
424 4 : CALL sort(negf_control%atomlist_S_screening, natoms_total, inds)
425 4 : DEALLOCATE (inds)
426 :
427 4 : natoms_current = 1
428 48 : DO i_rep = natoms_current + 1, natoms_total
429 48 : IF (negf_control%atomlist_S_screening(i_rep) /= negf_control%atomlist_S_screening(natoms_current)) THEN
430 44 : natoms_current = natoms_current + 1
431 44 : negf_control%atomlist_S_screening(natoms_current) = negf_control%atomlist_S_screening(i_rep)
432 : END IF
433 : END DO
434 :
435 4 : IF (natoms_current < natoms_total) THEN
436 0 : CALL MOVE_ALLOC(negf_control%atomlist_S_screening, inds)
437 :
438 0 : ALLOCATE (negf_control%atomlist_S_screening(natoms_current))
439 0 : negf_control%atomlist_S_screening(1:natoms_current) = inds(1:natoms_current)
440 0 : DEALLOCATE (inds)
441 : END IF
442 : END IF
443 :
444 4 : IF (do_negf .AND. SIZE(negf_control%contacts) > 2) THEN
445 : CALL cp_abort(__LOCATION__, &
446 0 : "General case (> 2 contacts) has not been implemented yet")
447 : END IF
448 :
449 4 : CALL timestop(handle)
450 12 : END SUBROUTINE read_negf_control
451 :
452 : ! **************************************************************************************************
453 : !> \brief Read region-specific list of atoms.
454 : !> \param atomlist list of atoms
455 : !> \param input_section input section which contains 'LIST' and 'MOLNAME' keywords
456 : !> \param i_rep_section repetition index of the input_section
457 : !> \param subsys subsystem environment
458 : ! **************************************************************************************************
459 36 : SUBROUTINE read_negf_atomlist(atomlist, input_section, i_rep_section, subsys)
460 : INTEGER, ALLOCATABLE, DIMENSION(:), INTENT(out) :: atomlist
461 : TYPE(section_vals_type), POINTER :: input_section
462 : INTEGER, INTENT(in) :: i_rep_section
463 : TYPE(cp_subsys_type), POINTER :: subsys
464 :
465 : CHARACTER(len=*), PARAMETER :: routineN = 'read_negf_atomlist'
466 :
467 : CHARACTER(len=default_string_length) :: index_str, natoms_str
468 : CHARACTER(len=default_string_length), &
469 36 : DIMENSION(:), POINTER :: cptr
470 : INTEGER :: first_atom, handle, iatom, ikind, imol, iname, irep, last_atom, natoms_current, &
471 : natoms_max, natoms_total, nkinds, nmols, nnames, nrep_list, nrep_molname
472 36 : INTEGER, ALLOCATABLE, DIMENSION(:) :: inds
473 36 : INTEGER, DIMENSION(:), POINTER :: iptr
474 : LOGICAL :: is_list, is_molname
475 36 : TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
476 : TYPE(molecule_kind_type), POINTER :: molecule_kind
477 36 : TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
478 : TYPE(molecule_type), POINTER :: molecule
479 36 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
480 :
481 36 : CALL timeset(routineN, handle)
482 :
483 : CALL cp_subsys_get(subsys, particle_set=particle_set, &
484 : molecule_set=molecule_set, &
485 36 : molecule_kind_set=molecule_kind_set)
486 36 : natoms_max = SIZE(particle_set)
487 36 : nkinds = SIZE(molecule_kind_set)
488 :
489 : CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, &
490 36 : n_rep_val=nrep_list, explicit=is_list)
491 : CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, &
492 36 : n_rep_val=nrep_molname, explicit=is_molname)
493 :
494 : ! compute the number of atoms in the NEGF region, and check the validity of given atomic indices
495 36 : natoms_total = 0
496 36 : IF (is_list .AND. nrep_list > 0) THEN
497 16 : DO irep = 1, nrep_list
498 8 : CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, i_rep_val=irep, i_vals=iptr)
499 :
500 8 : natoms_current = SIZE(iptr)
501 48 : DO iatom = 1, natoms_current
502 48 : IF (iptr(iatom) > natoms_max) THEN
503 0 : CALL integer_to_string(iptr(iatom), index_str)
504 0 : CALL integer_to_string(natoms_max, natoms_str)
505 : CALL cp_abort(__LOCATION__, &
506 : "NEGF: Atomic index "//TRIM(index_str)//" given in section "// &
507 : TRIM(input_section%section%name)//" exceeds the maximum number of atoms ("// &
508 0 : TRIM(natoms_str)//").")
509 : END IF
510 : END DO
511 :
512 16 : natoms_total = natoms_total + natoms_current
513 : END DO
514 : END IF
515 :
516 36 : IF (is_molname .AND. nrep_molname > 0) THEN
517 56 : DO irep = 1, nrep_molname
518 28 : CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, i_rep_val=irep, c_vals=cptr)
519 28 : nnames = SIZE(cptr)
520 :
521 90 : DO iname = 1, nnames
522 158 : DO ikind = 1, nkinds
523 158 : IF (molecule_kind_set(ikind)%name == cptr(iname)) EXIT
524 : END DO
525 :
526 62 : IF (ikind <= nkinds) THEN
527 34 : molecule_kind => molecule_kind_set(ikind)
528 34 : CALL get_molecule_kind(molecule_kind, nmolecule=nmols, molecule_list=iptr)
529 :
530 68 : DO imol = 1, nmols
531 34 : molecule => molecule_set(iptr(imol))
532 34 : CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
533 34 : natoms_current = last_atom - first_atom + 1
534 68 : natoms_total = natoms_total + natoms_current
535 : END DO
536 : ELSE
537 : CALL cp_abort(__LOCATION__, &
538 : "NEGF: A molecule with the name '"//TRIM(cptr(iname))//"' mentioned in section "// &
539 0 : TRIM(input_section%section%name)//" has not been defined. Note that names are case sensitive.")
540 : END IF
541 : END DO
542 : END DO
543 : END IF
544 :
545 : ! create a list of atomic indices
546 36 : IF (natoms_total > 0) THEN
547 108 : ALLOCATE (atomlist(natoms_total))
548 :
549 36 : natoms_total = 0
550 :
551 36 : IF (is_list .AND. nrep_list > 0) THEN
552 16 : DO irep = 1, nrep_list
553 8 : CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, i_rep_val=irep, i_vals=iptr)
554 :
555 8 : natoms_current = SIZE(iptr)
556 48 : atomlist(natoms_total + 1:natoms_total + natoms_current) = iptr(1:natoms_current)
557 16 : natoms_total = natoms_total + natoms_current
558 : END DO
559 : END IF
560 :
561 36 : IF (is_molname .AND. nrep_molname > 0) THEN
562 56 : DO irep = 1, nrep_molname
563 28 : CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, i_rep_val=irep, c_vals=cptr)
564 28 : nnames = SIZE(cptr)
565 :
566 90 : DO iname = 1, nnames
567 158 : DO ikind = 1, nkinds
568 158 : IF (molecule_kind_set(ikind)%name == cptr(iname)) EXIT
569 : END DO
570 :
571 62 : IF (ikind <= nkinds) THEN
572 34 : molecule_kind => molecule_kind_set(ikind)
573 34 : CALL get_molecule_kind(molecule_kind, nmolecule=nmols, molecule_list=iptr)
574 :
575 68 : DO imol = 1, nmols
576 34 : molecule => molecule_set(iptr(imol))
577 34 : CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
578 :
579 204 : DO natoms_current = first_atom, last_atom
580 136 : natoms_total = natoms_total + 1
581 170 : atomlist(natoms_total) = natoms_current
582 : END DO
583 : END DO
584 : END IF
585 : END DO
586 : END DO
587 : END IF
588 :
589 : ! remove duplicated atoms
590 108 : ALLOCATE (inds(natoms_total))
591 36 : CALL sort(atomlist, natoms_total, inds)
592 36 : DEALLOCATE (inds)
593 :
594 36 : natoms_current = 1
595 176 : DO iatom = natoms_current + 1, natoms_total
596 176 : IF (atomlist(iatom) /= atomlist(natoms_current)) THEN
597 140 : natoms_current = natoms_current + 1
598 140 : atomlist(natoms_current) = atomlist(iatom)
599 : END IF
600 : END DO
601 :
602 36 : IF (natoms_current < natoms_total) THEN
603 0 : CALL MOVE_ALLOC(atomlist, inds)
604 :
605 0 : ALLOCATE (atomlist(natoms_current))
606 0 : atomlist(1:natoms_current) = inds(1:natoms_current)
607 0 : DEALLOCATE (inds)
608 : END IF
609 : END IF
610 :
611 36 : CALL timestop(handle)
612 36 : END SUBROUTINE read_negf_atomlist
613 0 : END MODULE negf_control_types
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