Line data Source code
1 : !--------------------------------------------------------------------------------------------------!
2 : ! CP2K: A general program to perform molecular dynamics simulations !
3 : ! Copyright 2000-2026 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 : !> to read/write H and S from/to file
62 : LOGICAL :: read_write_HS = .FALSE.
63 : !> if restart from files is really done
64 : LOGICAL :: is_restart = .FALSE.
65 : !> Fermi level or starting Fermi level
66 : REAL(kind=dp) :: fermi_level = -1.0_dp
67 : !> Fermi level shifted to the common zero-energy level
68 : REAL(kind=dp) :: fermi_level_shifted = -1.0_dp
69 : !> temperature [in a.u.]
70 : REAL(kind=dp) :: temperature = -1.0_dp
71 : !> applied electric potential
72 : REAL(kind=dp) :: v_external = 0.0_dp
73 : END TYPE negf_control_contact_type
74 :
75 : ! **************************************************************************************************
76 : !> \brief Input parameters related to the NEGF run.
77 : !> \author Sergey Chulkov
78 : ! **************************************************************************************************
79 : TYPE negf_control_type
80 : !> input options for every contact
81 : TYPE(negf_control_contact_type), ALLOCATABLE, &
82 : DIMENSION(:) :: contacts
83 : !> atoms belonging to the scattering region
84 : INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_S
85 : !> atoms belonging to the scattering region as well as atoms belonging to
86 : !> screening regions of all the contacts
87 : INTEGER, ALLOCATABLE, DIMENSION(:) :: atomlist_S_screening
88 : !> to read/write H and S from/to file
89 : LOGICAL :: read_write_HS = .FALSE.
90 : !> to update the atomic Hamiltonian during NEGF self-consistent cycle
91 : LOGICAL :: update_HS = .FALSE.
92 : !> if dft of entire system is done
93 : LOGICAL :: is_dft_entire = .FALSE.
94 : !> if restart from files is really done
95 : LOGICAL :: is_restart = .FALSE.
96 : !> the common restart file projectname-negf.restart is written if any of is_restart is .TRUE.
97 : LOGICAL :: write_common_restart_file = .FALSE.
98 : !> do not keep contact self-energy matrices
99 : LOGICAL :: disable_cache = .FALSE.
100 : !> convergence criteria for adaptive integration methods
101 : REAL(kind=dp) :: conv_density = -1.0_dp
102 : !> convergence criteria for iterative Lopez-Sancho algorithm
103 : REAL(kind=dp) :: conv_green = -1.0_dp
104 : !> convergence criteria for self-consistent iterations
105 : REAL(kind=dp) :: conv_scf = -1.0_dp
106 : !> accuracy in mapping atoms between different force environments
107 : REAL(kind=dp) :: eps_geometry = -1.0_dp
108 : !> applied bias [in a.u.]
109 : REAL(kind=dp) :: v_bias = -1.0_dp
110 : !> integration lower bound [in a.u.]
111 : REAL(kind=dp) :: energy_lbound = -1.0_dp
112 : !> infinitesimal offset along the imaginary axis [in a.u.]
113 : REAL(kind=dp) :: eta = -1.0_dp
114 : !> initial guess to determine the actual Fermi level of bulk contacts [in a.u.]
115 : REAL(kind=dp) :: homo_lumo_gap = -1.0_dp
116 : !> number of residuals (poles of the Fermi function)
117 : INTEGER :: delta_npoles = -1
118 : !> offset along the x-axis away from the poles of the Fermi function [in units of kT]
119 : INTEGER :: gamma_kT = -1
120 : !> integration method
121 : INTEGER :: integr_method = -1
122 : !> minimal number of grid points along the closed contour
123 : INTEGER :: integr_min_points = -1
124 : !> maximal number of grid points along the closed contour
125 : INTEGER :: integr_max_points = -1
126 : !> maximal number of SCF iterations
127 : INTEGER :: max_scf = -1
128 : !> minimal number of MPI processes to be used to compute Green's function per energy point
129 : INTEGER :: nprocs = -1
130 : !> shift in Hartree potential [in a.u.]
131 : REAL(kind=dp) :: v_shift = -1.0_dp
132 : !> initial offset to determine the correct shift in Hartree potential [in a.u.]
133 : REAL(kind=dp) :: v_shift_offset = -1.0_dp
134 : !> maximal number of iteration to determine the shift in Hartree potential
135 : INTEGER :: v_shift_maxiters = -1
136 : END TYPE negf_control_type
137 :
138 : PRIVATE :: read_negf_atomlist
139 :
140 : CONTAINS
141 :
142 : ! **************************************************************************************************
143 : !> \brief allocate control options for Non-equilibrium Green's Function calculation
144 : !> \param negf_control an object to create
145 : !> \par History
146 : !> * 02.2017 created [Sergey Chulkov]
147 : ! **************************************************************************************************
148 8 : SUBROUTINE negf_control_create(negf_control)
149 : TYPE(negf_control_type), POINTER :: negf_control
150 :
151 : CHARACTER(len=*), PARAMETER :: routineN = 'negf_control_create'
152 :
153 : INTEGER :: handle
154 :
155 4 : CPASSERT(.NOT. ASSOCIATED(negf_control))
156 4 : CALL timeset(routineN, handle)
157 :
158 4 : ALLOCATE (negf_control)
159 :
160 4 : CALL timestop(handle)
161 4 : END SUBROUTINE negf_control_create
162 :
163 : ! **************************************************************************************************
164 : !> \brief release memory allocated for NEGF control options
165 : !> \param negf_control an object to release
166 : !> \par History
167 : !> * 02.2017 created [Sergey Chulkov]
168 : ! **************************************************************************************************
169 4 : SUBROUTINE negf_control_release(negf_control)
170 : TYPE(negf_control_type), POINTER :: negf_control
171 :
172 : CHARACTER(len=*), PARAMETER :: routineN = 'negf_control_release'
173 :
174 : INTEGER :: handle, i, j
175 :
176 4 : CALL timeset(routineN, handle)
177 :
178 4 : IF (ASSOCIATED(negf_control)) THEN
179 4 : IF (ALLOCATED(negf_control%atomlist_S)) DEALLOCATE (negf_control%atomlist_S)
180 4 : IF (ALLOCATED(negf_control%atomlist_S_screening)) DEALLOCATE (negf_control%atomlist_S_screening)
181 :
182 4 : IF (ALLOCATED(negf_control%contacts)) THEN
183 12 : DO i = SIZE(negf_control%contacts), 1, -1
184 8 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_bulk)) &
185 8 : DEALLOCATE (negf_control%contacts(i)%atomlist_bulk)
186 :
187 8 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_screening)) &
188 8 : DEALLOCATE (negf_control%contacts(i)%atomlist_screening)
189 :
190 12 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_cell)) THEN
191 24 : DO j = SIZE(negf_control%contacts(i)%atomlist_cell), 1, -1
192 16 : IF (ALLOCATED(negf_control%contacts(i)%atomlist_cell(j)%vector)) &
193 24 : DEALLOCATE (negf_control%contacts(i)%atomlist_cell(j)%vector)
194 : END DO
195 24 : DEALLOCATE (negf_control%contacts(i)%atomlist_cell)
196 : END IF
197 : END DO
198 :
199 12 : DEALLOCATE (negf_control%contacts)
200 : END IF
201 :
202 4 : DEALLOCATE (negf_control)
203 : END IF
204 :
205 4 : CALL timestop(handle)
206 4 : END SUBROUTINE negf_control_release
207 :
208 : ! **************************************************************************************************
209 : !> \brief Read NEGF input parameters.
210 : !> \param negf_control NEGF control parameters
211 : !> \param input root input section
212 : !> \param subsys subsystem environment
213 : ! **************************************************************************************************
214 4 : SUBROUTINE read_negf_control(negf_control, input, subsys)
215 : TYPE(negf_control_type), POINTER :: negf_control
216 : TYPE(section_vals_type), POINTER :: input
217 : TYPE(cp_subsys_type), POINTER :: subsys
218 :
219 : CHARACTER(len=*), PARAMETER :: routineN = 'read_negf_control'
220 :
221 : CHARACTER(len=default_string_length) :: contact_id_str, eta_current_str, eta_max_str, &
222 : npoles_current_str, npoles_min_str, temp_current_str, temp_min_str
223 : INTEGER :: delta_npoles_min, handle, i2_rep, i_rep, &
224 : n2_rep, n_rep, natoms_current, &
225 : natoms_total, run_type
226 4 : INTEGER, ALLOCATABLE, DIMENSION(:) :: inds
227 : LOGICAL :: do_negf, is_explicit
228 : REAL(kind=dp) :: eta_max, temp_current, temp_min
229 : TYPE(section_vals_type), POINTER :: cell_section, contact_section, &
230 : negf_section, region_section, &
231 : subsection
232 :
233 4 : CALL timeset(routineN, handle)
234 :
235 4 : CALL section_vals_val_get(input, "GLOBAL%RUN_TYPE", i_val=run_type)
236 4 : do_negf = run_type == negf_run
237 :
238 4 : negf_section => section_vals_get_subs_vals(input, "NEGF")
239 :
240 4 : contact_section => section_vals_get_subs_vals(negf_section, "CONTACT")
241 4 : CALL section_vals_get(contact_section, n_repetition=n_rep, explicit=is_explicit)
242 4 : IF ((.NOT. is_explicit) .AND. do_negf) THEN
243 : CALL cp_abort(__LOCATION__, &
244 0 : "At least one contact is needed for NEGF calculation.")
245 : END IF
246 :
247 20 : ALLOCATE (negf_control%contacts(n_rep))
248 12 : DO i_rep = 1, n_rep
249 8 : region_section => section_vals_get_subs_vals(contact_section, "SCREENING_REGION", i_rep_section=i_rep)
250 8 : CALL section_vals_get(region_section, explicit=is_explicit)
251 :
252 8 : IF ((.NOT. is_explicit) .AND. do_negf) THEN
253 0 : WRITE (contact_id_str, '(I11)') i_rep
254 : CALL cp_abort(__LOCATION__, &
255 0 : "The screening region must be defined for the contact "//TRIM(ADJUSTL(contact_id_str))//".")
256 : END IF
257 :
258 8 : IF (is_explicit) THEN
259 8 : CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_screening, region_section, 1, subsys)
260 : END IF
261 :
262 8 : region_section => section_vals_get_subs_vals(contact_section, "BULK_REGION", i_rep_section=i_rep)
263 :
264 8 : CALL section_vals_get(region_section, explicit=is_explicit)
265 :
266 8 : IF ((.NOT. is_explicit) .AND. do_negf) THEN
267 0 : WRITE (contact_id_str, '(I11)') i_rep
268 : CALL cp_abort(__LOCATION__, &
269 0 : "The bulk region must be defined for the contact "//TRIM(ADJUSTL(contact_id_str))//".")
270 : END IF
271 :
272 8 : IF (is_explicit) THEN
273 8 : CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_bulk, region_section, 1, subsys)
274 : END IF
275 :
276 : CALL section_vals_val_get(contact_section, "FORCE_EVAL_SECTION", &
277 : i_val=negf_control%contacts(i_rep)%force_env_index, &
278 8 : i_rep_section=i_rep)
279 :
280 8 : cell_section => section_vals_get_subs_vals(region_section, "CELL")
281 8 : CALL section_vals_get(cell_section, n_repetition=n2_rep, explicit=is_explicit)
282 :
283 8 : IF (((.NOT. is_explicit) .OR. n2_rep /= 2) .AND. negf_control%contacts(i_rep)%force_env_index <= 0 .AND. do_negf) THEN
284 0 : WRITE (contact_id_str, '(I11)') i_rep
285 : CALL cp_abort(__LOCATION__, &
286 : "You must either provide indices of atoms belonging to two adjacent bulk unit cells "// &
287 : "(BULK_REGION/CELL) for the contact, or the index of the FORCE_EVAL section (FORCE_EVAL_SECTION) "// &
288 : "which will be used to construct Kohn-Sham matrix for the bulk contact "// &
289 0 : TRIM(ADJUSTL(contact_id_str))//".")
290 : END IF
291 :
292 8 : IF (is_explicit .AND. n2_rep > 0) THEN
293 40 : ALLOCATE (negf_control%contacts(i_rep)%atomlist_cell(n2_rep))
294 :
295 24 : DO i2_rep = 1, n2_rep
296 24 : CALL read_negf_atomlist(negf_control%contacts(i_rep)%atomlist_cell(i2_rep)%vector, cell_section, i2_rep, subsys)
297 : END DO
298 : END IF
299 :
300 : CALL section_vals_val_get(contact_section, "REFINE_FERMI_LEVEL", &
301 : l_val=negf_control%contacts(i_rep)%refine_fermi_level, &
302 8 : i_rep_section=i_rep)
303 :
304 : CALL section_vals_val_get(contact_section, "FERMI_LEVEL", &
305 : r_val=negf_control%contacts(i_rep)%fermi_level, &
306 8 : i_rep_section=i_rep, explicit=is_explicit)
307 8 : IF (.NOT. is_explicit) negf_control%contacts(i_rep)%refine_fermi_level = .FALSE.
308 : negf_control%contacts(i_rep)%compute_fermi_level = (.NOT. is_explicit) .OR. &
309 8 : negf_control%contacts(i_rep)%refine_fermi_level
310 :
311 : CALL section_vals_val_get(contact_section, "FERMI_LEVEL_SHIFTED", &
312 : r_val=negf_control%contacts(i_rep)%fermi_level_shifted, &
313 8 : i_rep_section=i_rep, explicit=is_explicit)
314 8 : IF (is_explicit) negf_control%contacts(i_rep)%shift_fermi_level = .TRUE.
315 :
316 : CALL section_vals_val_get(contact_section, "TEMPERATURE", &
317 : r_val=negf_control%contacts(i_rep)%temperature, &
318 8 : i_rep_section=i_rep)
319 8 : IF (negf_control%contacts(i_rep)%temperature <= 0.0_dp) THEN
320 0 : CALL cp_abort(__LOCATION__, "Electronic temperature must be > 0")
321 : END IF
322 :
323 : CALL section_vals_val_get(contact_section, "ELECTRIC_POTENTIAL", &
324 : r_val=negf_control%contacts(i_rep)%v_external, &
325 8 : i_rep_section=i_rep)
326 :
327 8 : subsection => section_vals_get_subs_vals(contact_section, "RESTART", i_rep_section=i_rep)
328 :
329 : CALL section_vals_val_get(subsection, "READ_WRITE_HS", &
330 : l_val=negf_control%contacts(i_rep)%read_write_HS, &
331 8 : explicit=is_explicit)
332 52 : IF (is_explicit) negf_control%contacts(i_rep)%read_write_HS = .TRUE.
333 :
334 : END DO
335 :
336 4 : region_section => section_vals_get_subs_vals(negf_section, "SCATTERING_REGION")
337 4 : CALL section_vals_get(region_section, explicit=is_explicit)
338 4 : IF (is_explicit) THEN
339 4 : CALL read_negf_atomlist(negf_control%atomlist_S, region_section, 1, subsys)
340 : END IF
341 :
342 4 : subsection => section_vals_get_subs_vals(negf_section, "SCATTERING_REGION%RESTART")
343 : CALL section_vals_val_get(subsection, "READ_WRITE_HS", &
344 : l_val=negf_control%read_write_HS, &
345 4 : explicit=is_explicit)
346 4 : IF (is_explicit) negf_control%read_write_HS = .TRUE.
347 :
348 4 : CALL section_vals_val_get(negf_section, "DISABLE_CACHE", l_val=negf_control%disable_cache)
349 :
350 4 : CALL section_vals_val_get(negf_section, "EPS_DENSITY", r_val=negf_control%conv_density)
351 4 : CALL section_vals_val_get(negf_section, "EPS_GREEN", r_val=negf_control%conv_green)
352 4 : CALL section_vals_val_get(negf_section, "EPS_SCF", r_val=negf_control%conv_scf)
353 :
354 4 : CALL section_vals_val_get(negf_section, "EPS_GEO", r_val=negf_control%eps_geometry)
355 :
356 4 : CALL section_vals_val_get(negf_section, "ENERGY_LBOUND", r_val=negf_control%energy_lbound)
357 4 : CALL section_vals_val_get(negf_section, "ETA", r_val=negf_control%eta)
358 4 : CALL section_vals_val_get(negf_section, "HOMO_LUMO_GAP", r_val=negf_control%homo_lumo_gap)
359 4 : CALL section_vals_val_get(negf_section, "DELTA_NPOLES", i_val=negf_control%delta_npoles)
360 4 : CALL section_vals_val_get(negf_section, "GAMMA_KT", i_val=negf_control%gamma_kT)
361 :
362 4 : CALL section_vals_val_get(negf_section, "INTEGRATION_METHOD", i_val=negf_control%integr_method)
363 4 : CALL section_vals_val_get(negf_section, "INTEGRATION_MIN_POINTS", i_val=negf_control%integr_min_points)
364 4 : CALL section_vals_val_get(negf_section, "INTEGRATION_MAX_POINTS", i_val=negf_control%integr_max_points)
365 :
366 4 : IF (negf_control%integr_max_points < negf_control%integr_min_points) &
367 0 : negf_control%integr_max_points = negf_control%integr_min_points
368 :
369 4 : CALL section_vals_val_get(negf_section, "MAX_SCF", i_val=negf_control%max_scf)
370 :
371 4 : CALL section_vals_val_get(negf_section, "NPROC_POINT", i_val=negf_control%nprocs)
372 :
373 4 : CALL section_vals_val_get(negf_section, "V_SHIFT", r_val=negf_control%v_shift)
374 4 : CALL section_vals_val_get(negf_section, "V_SHIFT_OFFSET", r_val=negf_control%v_shift_offset)
375 4 : CALL section_vals_val_get(negf_section, "V_SHIFT_MAX_ITERS", i_val=negf_control%v_shift_maxiters)
376 :
377 4 : CALL section_vals_val_get(negf_section, "UPDATE_HS", l_val=negf_control%update_HS)
378 :
379 : ! check consistency
380 4 : IF (negf_control%eta < 0.0_dp) THEN
381 0 : CALL cp_abort(__LOCATION__, "ETA must be >= 0")
382 : END IF
383 :
384 4 : IF (n_rep > 0) THEN
385 16 : delta_npoles_min = NINT(0.5_dp*(negf_control%eta/(pi*MAXVAL(negf_control%contacts(:)%temperature)) + 1.0_dp))
386 : ELSE
387 0 : delta_npoles_min = 1
388 : END IF
389 :
390 4 : IF (negf_control%delta_npoles < delta_npoles_min) THEN
391 0 : IF (n_rep > 0) THEN
392 0 : eta_max = REAL(2*negf_control%delta_npoles - 1, kind=dp)*pi*MAXVAL(negf_control%contacts(:)%temperature)
393 0 : temp_current = MAXVAL(negf_control%contacts(:)%temperature)*kelvin
394 0 : temp_min = negf_control%eta/(pi*REAL(2*negf_control%delta_npoles - 1, kind=dp))*kelvin
395 :
396 0 : WRITE (eta_current_str, '(ES11.4E2)') negf_control%eta
397 0 : WRITE (eta_max_str, '(ES11.4E2)') eta_max
398 0 : WRITE (npoles_current_str, '(I11)') negf_control%delta_npoles
399 0 : WRITE (npoles_min_str, '(I11)') delta_npoles_min
400 0 : WRITE (temp_current_str, '(F11.3)') temp_current
401 0 : WRITE (temp_min_str, '(F11.3)') temp_min
402 :
403 : CALL cp_abort(__LOCATION__, &
404 : "Parameter DELTA_NPOLES must be at least "//TRIM(ADJUSTL(npoles_min_str))// &
405 : " (instead of "//TRIM(ADJUSTL(npoles_current_str))// &
406 : ") for given TEMPERATURE ("//TRIM(ADJUSTL(temp_current_str))// &
407 : " K) and ETA ("//TRIM(ADJUSTL(eta_current_str))// &
408 : "). Alternatively you can increase TEMPERATURE above "//TRIM(ADJUSTL(temp_min_str))// &
409 : " K, or decrease ETA below "//TRIM(ADJUSTL(eta_max_str))// &
410 : ". Please keep in mind that very tight ETA may result in dramatical precision loss"// &
411 0 : " due to inversion of ill-conditioned matrices.")
412 : ELSE
413 : ! no leads have been defined, so calculation will abort anyway
414 0 : negf_control%delta_npoles = delta_npoles_min
415 : END IF
416 : END IF
417 :
418 : ! expand scattering region by adding atoms from contact screening regions
419 4 : n_rep = SIZE(negf_control%contacts)
420 4 : IF (ALLOCATED(negf_control%atomlist_S)) THEN
421 4 : natoms_total = SIZE(negf_control%atomlist_S)
422 : ELSE
423 0 : natoms_total = 0
424 : END IF
425 :
426 12 : DO i_rep = 1, n_rep
427 12 : IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) THEN
428 : IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) &
429 8 : natoms_total = natoms_total + SIZE(negf_control%contacts(i_rep)%atomlist_screening)
430 : END IF
431 : END DO
432 :
433 4 : IF (natoms_total > 0) THEN
434 12 : ALLOCATE (negf_control%atomlist_S_screening(natoms_total))
435 4 : IF (ALLOCATED(negf_control%atomlist_S)) THEN
436 4 : natoms_total = SIZE(negf_control%atomlist_S)
437 20 : negf_control%atomlist_S_screening(1:natoms_total) = negf_control%atomlist_S(1:natoms_total)
438 : ELSE
439 0 : natoms_total = 0
440 : END IF
441 :
442 12 : DO i_rep = 1, n_rep
443 12 : IF (ALLOCATED(negf_control%contacts(i_rep)%atomlist_screening)) THEN
444 8 : natoms_current = SIZE(negf_control%contacts(i_rep)%atomlist_screening)
445 :
446 : negf_control%atomlist_S_screening(natoms_total + 1:natoms_total + natoms_current) = &
447 40 : negf_control%contacts(i_rep)%atomlist_screening(1:natoms_current)
448 :
449 8 : natoms_total = natoms_total + natoms_current
450 : END IF
451 : END DO
452 :
453 : ! sort and remove duplicated atoms
454 12 : ALLOCATE (inds(natoms_total))
455 4 : CALL sort(negf_control%atomlist_S_screening, natoms_total, inds)
456 4 : DEALLOCATE (inds)
457 :
458 4 : natoms_current = 1
459 48 : DO i_rep = natoms_current + 1, natoms_total
460 48 : IF (negf_control%atomlist_S_screening(i_rep) /= negf_control%atomlist_S_screening(natoms_current)) THEN
461 44 : natoms_current = natoms_current + 1
462 44 : negf_control%atomlist_S_screening(natoms_current) = negf_control%atomlist_S_screening(i_rep)
463 : END IF
464 : END DO
465 :
466 4 : IF (natoms_current < natoms_total) THEN
467 0 : CALL MOVE_ALLOC(negf_control%atomlist_S_screening, inds)
468 :
469 0 : ALLOCATE (negf_control%atomlist_S_screening(natoms_current))
470 0 : negf_control%atomlist_S_screening(1:natoms_current) = inds(1:natoms_current)
471 0 : DEALLOCATE (inds)
472 : END IF
473 : END IF
474 :
475 4 : IF (do_negf .AND. SIZE(negf_control%contacts) > 2) THEN
476 : CALL cp_abort(__LOCATION__, &
477 0 : "General case (> 2 contacts) has not been implemented yet")
478 : END IF
479 :
480 4 : CALL timestop(handle)
481 16 : END SUBROUTINE read_negf_control
482 :
483 : ! **************************************************************************************************
484 : !> \brief Read region-specific list of atoms.
485 : !> \param atomlist list of atoms
486 : !> \param input_section input section which contains 'LIST' and 'MOLNAME' keywords
487 : !> \param i_rep_section repetition index of the input_section
488 : !> \param subsys subsystem environment
489 : ! **************************************************************************************************
490 36 : SUBROUTINE read_negf_atomlist(atomlist, input_section, i_rep_section, subsys)
491 : INTEGER, ALLOCATABLE, DIMENSION(:), INTENT(out) :: atomlist
492 : TYPE(section_vals_type), POINTER :: input_section
493 : INTEGER, INTENT(in) :: i_rep_section
494 : TYPE(cp_subsys_type), POINTER :: subsys
495 :
496 : CHARACTER(len=*), PARAMETER :: routineN = 'read_negf_atomlist'
497 :
498 : CHARACTER(len=default_string_length) :: index_str, natoms_str
499 : CHARACTER(len=default_string_length), &
500 36 : DIMENSION(:), POINTER :: cptr
501 : INTEGER :: first_atom, handle, iatom, ikind, imol, iname, irep, last_atom, natoms_current, &
502 : natoms_max, natoms_total, nkinds, nmols, nnames, nrep_list, nrep_molname
503 36 : INTEGER, ALLOCATABLE, DIMENSION(:) :: inds
504 36 : INTEGER, DIMENSION(:), POINTER :: iptr
505 : LOGICAL :: is_list, is_molname
506 36 : TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
507 : TYPE(molecule_kind_type), POINTER :: molecule_kind
508 36 : TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
509 : TYPE(molecule_type), POINTER :: molecule
510 36 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
511 :
512 36 : CALL timeset(routineN, handle)
513 :
514 : CALL cp_subsys_get(subsys, particle_set=particle_set, &
515 : molecule_set=molecule_set, &
516 36 : molecule_kind_set=molecule_kind_set)
517 36 : natoms_max = SIZE(particle_set)
518 36 : nkinds = SIZE(molecule_kind_set)
519 :
520 : CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, &
521 36 : n_rep_val=nrep_list, explicit=is_list)
522 : CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, &
523 36 : n_rep_val=nrep_molname, explicit=is_molname)
524 :
525 : ! compute the number of atoms in the NEGF region, and check the validity of given atomic indices
526 36 : natoms_total = 0
527 36 : IF (is_list .AND. nrep_list > 0) THEN
528 16 : DO irep = 1, nrep_list
529 8 : CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, i_rep_val=irep, i_vals=iptr)
530 :
531 8 : natoms_current = SIZE(iptr)
532 48 : DO iatom = 1, natoms_current
533 48 : IF (iptr(iatom) > natoms_max) THEN
534 0 : CALL integer_to_string(iptr(iatom), index_str)
535 0 : CALL integer_to_string(natoms_max, natoms_str)
536 : CALL cp_abort(__LOCATION__, &
537 : "NEGF: Atomic index "//TRIM(index_str)//" given in section "// &
538 : TRIM(input_section%section%name)//" exceeds the maximum number of atoms ("// &
539 0 : TRIM(natoms_str)//").")
540 : END IF
541 : END DO
542 :
543 16 : natoms_total = natoms_total + natoms_current
544 : END DO
545 : END IF
546 :
547 36 : IF (is_molname .AND. nrep_molname > 0) THEN
548 56 : DO irep = 1, nrep_molname
549 28 : CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, i_rep_val=irep, c_vals=cptr)
550 28 : nnames = SIZE(cptr)
551 :
552 90 : DO iname = 1, nnames
553 158 : DO ikind = 1, nkinds
554 158 : IF (molecule_kind_set(ikind)%name == cptr(iname)) EXIT
555 : END DO
556 :
557 62 : IF (ikind <= nkinds) THEN
558 34 : molecule_kind => molecule_kind_set(ikind)
559 34 : CALL get_molecule_kind(molecule_kind, nmolecule=nmols, molecule_list=iptr)
560 :
561 68 : DO imol = 1, nmols
562 34 : molecule => molecule_set(iptr(imol))
563 34 : CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
564 34 : natoms_current = last_atom - first_atom + 1
565 68 : natoms_total = natoms_total + natoms_current
566 : END DO
567 : ELSE
568 : CALL cp_abort(__LOCATION__, &
569 : "NEGF: A molecule with the name '"//TRIM(cptr(iname))//"' mentioned in section "// &
570 0 : TRIM(input_section%section%name)//" has not been defined. Note that names are case sensitive.")
571 : END IF
572 : END DO
573 : END DO
574 : END IF
575 :
576 : ! create a list of atomic indices
577 36 : IF (natoms_total > 0) THEN
578 108 : ALLOCATE (atomlist(natoms_total))
579 :
580 36 : natoms_total = 0
581 :
582 36 : IF (is_list .AND. nrep_list > 0) THEN
583 16 : DO irep = 1, nrep_list
584 8 : CALL section_vals_val_get(input_section, "LIST", i_rep_section=i_rep_section, i_rep_val=irep, i_vals=iptr)
585 :
586 8 : natoms_current = SIZE(iptr)
587 48 : atomlist(natoms_total + 1:natoms_total + natoms_current) = iptr(1:natoms_current)
588 16 : natoms_total = natoms_total + natoms_current
589 : END DO
590 : END IF
591 :
592 36 : IF (is_molname .AND. nrep_molname > 0) THEN
593 56 : DO irep = 1, nrep_molname
594 28 : CALL section_vals_val_get(input_section, "MOLNAME", i_rep_section=i_rep_section, i_rep_val=irep, c_vals=cptr)
595 28 : nnames = SIZE(cptr)
596 :
597 90 : DO iname = 1, nnames
598 158 : DO ikind = 1, nkinds
599 158 : IF (molecule_kind_set(ikind)%name == cptr(iname)) EXIT
600 : END DO
601 :
602 62 : IF (ikind <= nkinds) THEN
603 34 : molecule_kind => molecule_kind_set(ikind)
604 34 : CALL get_molecule_kind(molecule_kind, nmolecule=nmols, molecule_list=iptr)
605 :
606 68 : DO imol = 1, nmols
607 34 : molecule => molecule_set(iptr(imol))
608 34 : CALL get_molecule(molecule, first_atom=first_atom, last_atom=last_atom)
609 :
610 204 : DO natoms_current = first_atom, last_atom
611 136 : natoms_total = natoms_total + 1
612 170 : atomlist(natoms_total) = natoms_current
613 : END DO
614 : END DO
615 : END IF
616 : END DO
617 : END DO
618 : END IF
619 :
620 : ! remove duplicated atoms
621 108 : ALLOCATE (inds(natoms_total))
622 36 : CALL sort(atomlist, natoms_total, inds)
623 36 : DEALLOCATE (inds)
624 :
625 36 : natoms_current = 1
626 176 : DO iatom = natoms_current + 1, natoms_total
627 176 : IF (atomlist(iatom) /= atomlist(natoms_current)) THEN
628 140 : natoms_current = natoms_current + 1
629 140 : atomlist(natoms_current) = atomlist(iatom)
630 : END IF
631 : END DO
632 :
633 36 : IF (natoms_current < natoms_total) THEN
634 0 : CALL MOVE_ALLOC(atomlist, inds)
635 :
636 0 : ALLOCATE (atomlist(natoms_current))
637 0 : atomlist(1:natoms_current) = inds(1:natoms_current)
638 0 : DEALLOCATE (inds)
639 : END IF
640 : END IF
641 :
642 36 : CALL timestop(handle)
643 36 : END SUBROUTINE read_negf_atomlist
644 0 : END MODULE negf_control_types
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