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 Define methods related to particle_type
10 : !> \par History
11 : !> 10.2014 Move routines out of particle_types.F [Ole Schuett]
12 : !> \author Ole Schuett
13 : ! **************************************************************************************************
14 : MODULE particle_methods
15 : USE atomic_kind_types, ONLY: get_atomic_kind
16 : USE basis_set_types, ONLY: get_gto_basis_set,&
17 : gto_basis_set_p_type
18 : USE cell_methods, ONLY: cell_create,&
19 : set_cell_param
20 : USE cell_types, ONLY: cell_clone,&
21 : cell_release,&
22 : cell_type,&
23 : get_cell,&
24 : pbc,&
25 : real_to_scaled
26 : USE cp2k_info, ONLY: compile_revision,&
27 : cp2k_version,&
28 : r_cwd,&
29 : r_host_name,&
30 : r_user_name
31 : USE cp_log_handling, ONLY: cp_get_default_logger,&
32 : cp_logger_get_default_io_unit,&
33 : cp_logger_type,&
34 : cp_to_string
35 : USE cp_output_handling, ONLY: cp_print_key_finished_output,&
36 : cp_print_key_generate_filename,&
37 : cp_print_key_unit_nr
38 : USE cp_units, ONLY: cp_unit_from_cp2k
39 : USE external_potential_types, ONLY: fist_potential_type,&
40 : get_potential
41 : USE input_constants, ONLY: dump_atomic,&
42 : dump_dcd,&
43 : dump_dcd_aligned_cell,&
44 : dump_extxyz,&
45 : dump_pdb,&
46 : dump_xmol
47 : USE input_cp2k_subsys, ONLY: create_cell_section
48 : USE input_enumeration_types, ONLY: enum_i2c,&
49 : enumeration_type
50 : USE input_keyword_types, ONLY: keyword_get,&
51 : keyword_type
52 : USE input_section_types, ONLY: section_get_keyword,&
53 : section_release,&
54 : section_type,&
55 : section_vals_get_subs_vals,&
56 : section_vals_type,&
57 : section_vals_val_get
58 : USE kinds, ONLY: default_path_length,&
59 : default_string_length,&
60 : dp,&
61 : sp
62 : USE machine, ONLY: m_timestamp,&
63 : timestamp_length
64 : USE mathconstants, ONLY: degree
65 : USE mathlib, ONLY: angle,&
66 : dihedral_angle,&
67 : gcd
68 : USE memory_utilities, ONLY: reallocate
69 : USE particle_types, ONLY: get_particle_pos_or_vel,&
70 : particle_type
71 : USE periodic_table, ONLY: nelem
72 : USE physcon, ONLY: massunit
73 : USE qmmm_ff_fist, ONLY: qmmm_ff_precond_only_qm
74 : USE qs_kind_types, ONLY: get_qs_kind,&
75 : qs_kind_type
76 : USE shell_potential_types, ONLY: get_shell,&
77 : shell_kind_type
78 : USE string_utilities, ONLY: uppercase
79 : USE util, ONLY: sort,&
80 : sort_unique
81 : #include "./base/base_uses.f90"
82 :
83 : IMPLICIT NONE
84 :
85 : PRIVATE
86 :
87 : ! Public subroutines
88 :
89 : PUBLIC :: write_fist_particle_coordinates, &
90 : write_qs_particle_coordinates, &
91 : write_particle_distances, &
92 : write_particle_coordinates, &
93 : write_structure_data, &
94 : get_particle_set, &
95 : write_particle_matrix, &
96 : write_final_structure
97 :
98 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'particle_methods'
99 :
100 : CONTAINS
101 :
102 : ! **************************************************************************************************
103 : !> \brief Get the components of a particle set.
104 : !> \param particle_set ...
105 : !> \param qs_kind_set ...
106 : !> \param first_sgf ...
107 : !> \param last_sgf ...
108 : !> \param nsgf ...
109 : !> \param nmao ...
110 : !> \param basis ...
111 : !> \param ncgf ...
112 : !> \date 14.01.2002
113 : !> \par History
114 : !> - particle type cleaned (13.10.2003,MK)
115 : !> - refactoring and add basis set option (17.08.2010,jhu)
116 : !> \author MK
117 : !> \version 1.0
118 : ! **************************************************************************************************
119 195967 : SUBROUTINE get_particle_set(particle_set, qs_kind_set, first_sgf, last_sgf, nsgf, &
120 195967 : nmao, basis, ncgf)
121 :
122 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
123 : TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
124 : INTEGER, DIMENSION(:), INTENT(INOUT), OPTIONAL :: first_sgf, last_sgf, nsgf, nmao
125 : TYPE(gto_basis_set_p_type), DIMENSION(:), OPTIONAL :: basis
126 : INTEGER, DIMENSION(:), INTENT(INOUT), OPTIONAL :: ncgf
127 :
128 : INTEGER :: ikind, iparticle, isgf, nparticle, ns
129 :
130 195967 : CPASSERT(ASSOCIATED(particle_set))
131 :
132 195967 : nparticle = SIZE(particle_set)
133 195967 : IF (PRESENT(first_sgf)) THEN
134 42649 : CPASSERT(SIZE(first_sgf) >= nparticle)
135 : END IF
136 195967 : IF (PRESENT(last_sgf)) THEN
137 33955 : CPASSERT(SIZE(last_sgf) >= nparticle)
138 : END IF
139 195967 : IF (PRESENT(nsgf)) THEN
140 152868 : CPASSERT(SIZE(nsgf) >= nparticle)
141 : END IF
142 195967 : IF (PRESENT(nmao)) THEN
143 14 : CPASSERT(SIZE(nmao) >= nparticle)
144 : END IF
145 195967 : IF (PRESENT(ncgf)) THEN
146 4 : CPASSERT(SIZE(ncgf) >= nparticle)
147 : END IF
148 :
149 195967 : IF (PRESENT(first_sgf) .OR. PRESENT(last_sgf) .OR. PRESENT(nsgf)) THEN
150 : isgf = 0
151 1110268 : DO iparticle = 1, nparticle
152 914799 : CALL get_atomic_kind(particle_set(iparticle)%atomic_kind, kind_number=ikind)
153 914799 : IF (PRESENT(basis)) THEN
154 684943 : IF (ASSOCIATED(basis(ikind)%gto_basis_set)) THEN
155 684939 : CALL get_gto_basis_set(gto_basis_set=basis(ikind)%gto_basis_set, nsgf=ns)
156 : ELSE
157 4 : ns = 0
158 : END IF
159 : ELSE
160 229856 : CALL get_qs_kind(qs_kind_set(ikind), nsgf=ns)
161 : END IF
162 914799 : IF (PRESENT(nsgf)) nsgf(iparticle) = ns
163 914799 : IF (PRESENT(first_sgf)) first_sgf(iparticle) = isgf + 1
164 914799 : isgf = isgf + ns
165 2025565 : IF (PRESENT(last_sgf)) last_sgf(iparticle) = isgf
166 : END DO
167 : END IF
168 :
169 195967 : IF (PRESENT(ncgf)) THEN
170 12 : DO iparticle = 1, nparticle
171 8 : CALL get_atomic_kind(particle_set(iparticle)%atomic_kind, kind_number=ikind)
172 8 : IF (PRESENT(basis)) THEN
173 8 : IF (ASSOCIATED(basis(ikind)%gto_basis_set)) THEN
174 8 : CALL get_gto_basis_set(gto_basis_set=basis(ikind)%gto_basis_set, ncgf=ns)
175 : ELSE
176 0 : ns = 0
177 : END IF
178 : ELSE
179 0 : CALL get_qs_kind(qs_kind_set(ikind), ncgf=ns)
180 : END IF
181 20 : ncgf(iparticle) = ns
182 : END DO
183 : END IF
184 :
185 195967 : IF (PRESENT(first_sgf)) THEN
186 42649 : IF (SIZE(first_sgf) > nparticle) first_sgf(nparticle + 1) = isgf + 1
187 : END IF
188 :
189 195967 : IF (PRESENT(nmao)) THEN
190 86 : DO iparticle = 1, nparticle
191 72 : CALL get_atomic_kind(particle_set(iparticle)%atomic_kind, kind_number=ikind)
192 72 : CALL get_qs_kind(qs_kind_set(ikind), mao=ns)
193 86 : nmao(iparticle) = ns
194 : END DO
195 : END IF
196 :
197 195967 : END SUBROUTINE get_particle_set
198 :
199 : ! **************************************************************************************************
200 : !> \brief Should be able to write a few formats e.g. xmol, and some binary
201 : !> format (dcd) some format can be used for x,v,f
202 : !>
203 : !> FORMAT CONTENT UNITS x, v, f
204 : !> XMOL POS, VEL, FORCE, POS_VEL, POS_VEL_FORCE Angstrom, a.u., a.u.
205 : !>
206 : !> \param particle_set ...
207 : !> \param iunit ...
208 : !> \param output_format ...
209 : !> \param content ...
210 : !> \param title ...
211 : !> \param cell ...
212 : !> \param array ...
213 : !> \param unit_conv ...
214 : !> \param charge_occup ...
215 : !> \param charge_beta ...
216 : !> \param charge_extended ...
217 : !> \param print_kind ...
218 : !> \date 14.01.2002
219 : !> \author MK
220 : !> \version 1.0
221 : ! **************************************************************************************************
222 27261 : SUBROUTINE write_particle_coordinates(particle_set, iunit, output_format, &
223 27261 : content, title, cell, array, unit_conv, &
224 : charge_occup, charge_beta, &
225 : charge_extended, print_kind)
226 :
227 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
228 : INTEGER :: iunit, output_format
229 : CHARACTER(LEN=*) :: content, title
230 : TYPE(cell_type), OPTIONAL, POINTER :: cell
231 : REAL(KIND=dp), DIMENSION(:), INTENT(IN), OPTIONAL :: array
232 : REAL(KIND=dp), INTENT(IN), OPTIONAL :: unit_conv
233 : LOGICAL, INTENT(IN), OPTIONAL :: charge_occup, charge_beta, &
234 : charge_extended, print_kind
235 :
236 : CHARACTER(len=*), PARAMETER :: routineN = 'write_particle_coordinates'
237 :
238 : CHARACTER(LEN=120) :: line
239 : CHARACTER(LEN=2) :: element_symbol
240 : CHARACTER(LEN=4) :: name
241 : CHARACTER(LEN=default_string_length) :: atm_name, my_format
242 : INTEGER :: handle, iatom, natom
243 : LOGICAL :: dummy, my_charge_beta, &
244 : my_charge_extended, my_charge_occup, &
245 : my_print_kind
246 : REAL(KIND=dp) :: angle_alpha, angle_beta, angle_gamma, &
247 : factor, qeff
248 27261 : REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: arr
249 : REAL(KIND=dp), DIMENSION(3) :: abc, angles, f, r, v
250 : REAL(KIND=dp), DIMENSION(3, 3) :: h
251 27261 : REAL(KIND=sp), ALLOCATABLE, DIMENSION(:) :: x4, y4, z4
252 : TYPE(cell_type), POINTER :: cell_dcd
253 : TYPE(fist_potential_type), POINTER :: fist_potential
254 : TYPE(shell_kind_type), POINTER :: shell
255 :
256 27261 : CALL timeset(routineN, handle)
257 :
258 27261 : natom = SIZE(particle_set)
259 27261 : IF (PRESENT(array)) THEN
260 1847 : SELECT CASE (TRIM(content))
261 : CASE ("POS_VEL", "POS_VEL_FORCE")
262 1847 : CPABORT("Illegal usage")
263 : END SELECT
264 : END IF
265 27261 : factor = 1.0_dp
266 27261 : IF (PRESENT(unit_conv)) THEN
267 27110 : factor = unit_conv
268 : END IF
269 54449 : SELECT CASE (output_format)
270 : CASE (dump_xmol, dump_extxyz)
271 27188 : my_print_kind = .FALSE.
272 27188 : IF (PRESENT(print_kind)) my_print_kind = print_kind
273 27188 : WRITE (iunit, "(I8)") natom
274 27188 : WRITE (iunit, "(A)") TRIM(title)
275 1347992 : DO iatom = 1, natom
276 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
277 1320804 : element_symbol=element_symbol)
278 1320804 : IF (LEN_TRIM(element_symbol) == 0 .OR. my_print_kind) THEN
279 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
280 24 : name=atm_name)
281 24 : dummy = qmmm_ff_precond_only_qm(id1=atm_name)
282 24 : my_format = "(A,"
283 24 : atm_name = TRIM(atm_name)
284 : ELSE
285 1320780 : my_format = "(T2,A2,"
286 1320780 : atm_name = TRIM(element_symbol)
287 : END IF
288 27188 : SELECT CASE (TRIM(content))
289 : CASE ("POS")
290 1205468 : IF (PRESENT(array)) THEN
291 53902 : r(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
292 : ELSE
293 4606264 : r(:) = particle_set(iatom)%r(:)
294 : END IF
295 4821872 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), r(1:3)*factor
296 : CASE ("VEL")
297 85772 : IF (PRESENT(array)) THEN
298 0 : v(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
299 : ELSE
300 343088 : v(:) = particle_set(iatom)%v(:)
301 : END IF
302 343088 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), v(1:3)*factor
303 : CASE ("FORCE")
304 20955 : IF (PRESENT(array)) THEN
305 0 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
306 : ELSE
307 83820 : f(:) = particle_set(iatom)%f(:)
308 : END IF
309 83820 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), f(1:3)*factor
310 : CASE ("FORCE_MIXING_LABELS")
311 8609 : IF (PRESENT(array)) THEN
312 34436 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
313 : ELSE
314 0 : f(:) = particle_set(iatom)%f(:)
315 : END IF
316 1355240 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), f(1:3)*factor
317 : END SELECT
318 : END DO
319 : CASE (dump_atomic)
320 170 : DO iatom = 1, natom
321 10 : SELECT CASE (TRIM(content))
322 : CASE ("POS")
323 160 : IF (PRESENT(array)) THEN
324 0 : r(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
325 : ELSE
326 640 : r(:) = particle_set(iatom)%r(:)
327 : END IF
328 640 : WRITE (iunit, "(3F20.10)") r(1:3)*factor
329 : CASE ("VEL")
330 0 : IF (PRESENT(array)) THEN
331 0 : v(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
332 : ELSE
333 0 : v(:) = particle_set(iatom)%v(:)
334 : END IF
335 0 : WRITE (iunit, "(3F20.10)") v(1:3)*factor
336 : CASE ("FORCE")
337 0 : IF (PRESENT(array)) THEN
338 0 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
339 : ELSE
340 0 : f(:) = particle_set(iatom)%f(:)
341 : END IF
342 0 : WRITE (iunit, "(3F20.10)") f(1:3)*factor
343 : CASE ("FORCE_MIXING_LABELS")
344 0 : IF (PRESENT(array)) THEN
345 0 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
346 : ELSE
347 0 : f(:) = particle_set(iatom)%f(:)
348 : END IF
349 160 : WRITE (iunit, "(3F20.10)") f(1:3)*factor
350 : END SELECT
351 : END DO
352 : CASE (dump_dcd, dump_dcd_aligned_cell)
353 4 : IF (.NOT. (PRESENT(cell))) THEN
354 0 : CPABORT("Cell is not present! Report this bug!")
355 : END IF
356 : CALL get_cell(cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, &
357 4 : abc=abc)
358 4 : IF (.NOT. cell%orthorhombic .AND. (output_format == dump_dcd_aligned_cell)) THEN
359 : ! In the case of a non-orthorhombic cell adopt a common convention
360 : ! for the orientation of the cell with respect to the Cartesian axes:
361 : ! Cell vector a is aligned with the x axis and the cell vector b lies
362 : ! in the xy plane.
363 0 : NULLIFY (cell_dcd)
364 0 : CALL cell_create(cell_dcd)
365 0 : CALL cell_clone(cell, cell_dcd, tag="CELL_DCD")
366 0 : angles(1) = angle_alpha/degree
367 0 : angles(2) = angle_beta/degree
368 0 : angles(3) = angle_gamma/degree
369 : CALL set_cell_param(cell_dcd, abc, angles, &
370 0 : do_init_cell=.TRUE.)
371 0 : h(1:3, 1:3) = MATMUL(cell_dcd%hmat(1:3, 1:3), cell%h_inv(1:3, 1:3))
372 0 : CALL cell_release(cell_dcd)
373 : END IF
374 12 : ALLOCATE (arr(3, natom))
375 4 : IF (PRESENT(array)) THEN
376 0 : arr(1:3, 1:natom) = RESHAPE(array, [3, natom])
377 : ELSE
378 8 : SELECT CASE (TRIM(content))
379 : CASE ("POS")
380 1156 : DO iatom = 1, natom
381 4612 : arr(1:3, iatom) = particle_set(iatom)%r(1:3)
382 : END DO
383 : CASE ("VEL")
384 0 : DO iatom = 1, natom
385 0 : arr(1:3, iatom) = particle_set(iatom)%v(1:3)
386 : END DO
387 : CASE ("FORCE")
388 0 : DO iatom = 1, natom
389 0 : arr(1:3, iatom) = particle_set(iatom)%f(1:3)
390 : END DO
391 : CASE DEFAULT
392 4 : CPABORT("Illegal DCD dump type")
393 : END SELECT
394 : END IF
395 12 : ALLOCATE (x4(natom))
396 8 : ALLOCATE (y4(natom))
397 8 : ALLOCATE (z4(natom))
398 4 : IF (.NOT. cell%orthorhombic .AND. (output_format == dump_dcd_aligned_cell)) THEN
399 0 : x4(1:natom) = REAL(MATMUL(h(1, 1:3), arr(1:3, 1:natom)), KIND=sp)
400 0 : y4(1:natom) = REAL(MATMUL(h(2, 1:3), arr(1:3, 1:natom)), KIND=sp)
401 0 : z4(1:natom) = REAL(MATMUL(h(3, 1:3), arr(1:3, 1:natom)), KIND=sp)
402 : ELSE
403 1156 : x4(1:natom) = REAL(arr(1, 1:natom), KIND=sp)
404 1156 : y4(1:natom) = REAL(arr(2, 1:natom), KIND=sp)
405 1156 : z4(1:natom) = REAL(arr(3, 1:natom), KIND=sp)
406 : END IF
407 4 : WRITE (iunit) abc(1)*factor, angle_gamma, abc(2)*factor, &
408 8 : angle_beta, angle_alpha, abc(3)*factor
409 1156 : WRITE (iunit) x4*REAL(factor, KIND=sp)
410 1156 : WRITE (iunit) y4*REAL(factor, KIND=sp)
411 1156 : WRITE (iunit) z4*REAL(factor, KIND=sp)
412 : ! Release work storage
413 4 : DEALLOCATE (arr)
414 4 : DEALLOCATE (x4)
415 4 : DEALLOCATE (y4)
416 8 : DEALLOCATE (z4)
417 : CASE (dump_pdb)
418 59 : my_charge_occup = .FALSE.
419 59 : IF (PRESENT(charge_occup)) my_charge_occup = charge_occup
420 59 : my_charge_beta = .FALSE.
421 59 : IF (PRESENT(charge_beta)) my_charge_beta = charge_beta
422 59 : my_charge_extended = .FALSE.
423 59 : IF (PRESENT(charge_extended)) my_charge_extended = charge_extended
424 59 : IF (LEN_TRIM(title) > 0) THEN
425 : WRITE (UNIT=iunit, FMT="(A6,T11,A)") &
426 59 : "REMARK", TRIM(title)
427 : END IF
428 59 : CALL get_cell(cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, abc=abc)
429 : ! COLUMNS DATA TYPE CONTENTS
430 : ! --------------------------------------------------
431 : ! 1 - 6 Record name "CRYST1"
432 : ! 7 - 15 Real(9.3) a (Angstroms)
433 : ! 16 - 24 Real(9.3) b (Angstroms)
434 : ! 25 - 33 Real(9.3) c (Angstroms)
435 : ! 34 - 40 Real(7.2) alpha (degrees)
436 : ! 41 - 47 Real(7.2) beta (degrees)
437 : ! 48 - 54 Real(7.2) gamma (degrees)
438 : ! 56 - 66 LString Space group
439 : ! 67 - 70 Integer Z value
440 : WRITE (UNIT=iunit, FMT="(A6,3F9.3,3F7.2)") &
441 236 : "CRYST1", abc(1:3)*factor, angle_alpha, angle_beta, angle_gamma
442 59 : WRITE (UNIT=line(1:6), FMT="(A6)") "ATOM "
443 2999 : DO iatom = 1, natom
444 2940 : line = ""
445 : ! COLUMNS DATA TYPE CONTENTS
446 : ! 1 - 6 Record name "ATOM "
447 : ! 7 - 11 Integer Atom serial number
448 : ! 13 - 16 Atom Atom name
449 : ! 17 Character Alternate location indicator
450 : ! 18 - 20 Residue name Residue name
451 : ! 22 Character Chain identifier
452 : ! 23 - 26 Integer Residue sequence number
453 : ! 27 AChar Code for insertion of residues
454 : ! 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstrom
455 : ! 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstrom
456 : ! 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstrom
457 : ! 55 - 60 Real(6.2) Occupancy
458 : ! 61 - 66 Real(6.2) Temperature factor (Default = 0.0)
459 : ! 73 - 76 LString(4) Segment identifier, left-justified
460 : ! 77 - 78 LString(2) Element symbol, right-justified
461 : ! 79 - 80 LString(2) Charge on the atom
462 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
463 : element_symbol=element_symbol, name=atm_name, &
464 2940 : fist_potential=fist_potential, shell=shell)
465 2940 : IF (LEN_TRIM(element_symbol) == 0) THEN
466 0 : dummy = qmmm_ff_precond_only_qm(id1=atm_name)
467 : END IF
468 2940 : name = TRIM(atm_name)
469 2940 : IF (ASSOCIATED(fist_potential)) THEN
470 2940 : CALL get_potential(potential=fist_potential, qeff=qeff)
471 : ELSE
472 0 : qeff = 0.0_dp
473 : END IF
474 2940 : IF (ASSOCIATED(shell)) CALL get_shell(shell=shell, charge=qeff)
475 2940 : WRITE (UNIT=line(1:6), FMT="(A6)") "ATOM "
476 2940 : WRITE (UNIT=line(7:11), FMT="(I5)") MODULO(iatom, 100000)
477 2940 : WRITE (UNIT=line(13:16), FMT="(A4)") ADJUSTL(name)
478 : ! WRITE (UNIT=line(18:20),FMT="(A3)") TRIM(resname)
479 : ! WRITE (UNIT=line(23:26),FMT="(I4)") MODULO(idres,10000)
480 5880 : SELECT CASE (TRIM(content))
481 : CASE ("POS")
482 2940 : IF (PRESENT(array)) THEN
483 0 : r(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
484 : ELSE
485 11760 : r(:) = particle_set(iatom)%r(:)
486 : END IF
487 11760 : WRITE (UNIT=line(31:54), FMT="(3F8.3)") r(1:3)*factor
488 : CASE DEFAULT
489 2940 : CPABORT("PDB dump only for trajectory available")
490 : END SELECT
491 2940 : IF (my_charge_occup) THEN
492 2130 : WRITE (UNIT=line(55:60), FMT="(F6.2)") qeff
493 : ELSE
494 810 : WRITE (UNIT=line(55:60), FMT="(F6.2)") 0.0_dp
495 : END IF
496 2940 : IF (my_charge_beta) THEN
497 480 : WRITE (UNIT=line(61:66), FMT="(F6.2)") qeff
498 : ELSE
499 2460 : WRITE (UNIT=line(61:66), FMT="(F6.2)") 0.0_dp
500 : END IF
501 : ! WRITE (UNIT=line(73:76),FMT="(A4)") ADJUSTL(TRIM(molname))
502 2940 : WRITE (UNIT=line(77:78), FMT="(A2)") ADJUSTR(TRIM(element_symbol))
503 2940 : IF (my_charge_extended) THEN
504 330 : WRITE (UNIT=line(81:), FMT="(SP,F0.8)") qeff
505 : END IF
506 2999 : WRITE (UNIT=iunit, FMT="(A)") TRIM(line)
507 : END DO
508 59 : WRITE (UNIT=iunit, FMT="(A)") "END"
509 : CASE DEFAULT
510 27320 : CPABORT("Illegal dump type")
511 : END SELECT
512 :
513 27261 : CALL timestop(handle)
514 :
515 27261 : END SUBROUTINE write_particle_coordinates
516 :
517 : ! **************************************************************************************************
518 : !> \brief Write the atomic coordinates to the output unit.
519 : !> \param particle_set ...
520 : !> \param subsys_section ...
521 : !> \param charges ...
522 : !> \date 05.06.2000
523 : !> \author MK
524 : !> \version 1.0
525 : ! **************************************************************************************************
526 9689 : SUBROUTINE write_fist_particle_coordinates(particle_set, subsys_section, charges)
527 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
528 : TYPE(section_vals_type), POINTER :: subsys_section
529 : REAL(KIND=dp), DIMENSION(:), OPTIONAL :: charges
530 :
531 : CHARACTER(LEN=default_string_length) :: name, unit_str
532 : INTEGER :: iatom, ikind, iw, natom
533 : REAL(KIND=dp) :: conv, mass, qcore, qeff, qshell
534 : TYPE(cp_logger_type), POINTER :: logger
535 : TYPE(shell_kind_type), POINTER :: shell_kind
536 :
537 9689 : NULLIFY (logger)
538 9689 : NULLIFY (shell_kind)
539 :
540 9689 : logger => cp_get_default_logger()
541 : iw = cp_print_key_unit_nr(logger, subsys_section, &
542 9689 : "PRINT%ATOMIC_COORDINATES", extension=".coordLog")
543 :
544 9689 : CALL section_vals_val_get(subsys_section, "PRINT%ATOMIC_COORDINATES%UNIT", c_val=unit_str)
545 9689 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
546 9689 : CALL uppercase(unit_str)
547 9689 : IF (iw > 0) THEN
548 : WRITE (UNIT=iw, FMT="(/,/,T2,A)") &
549 2504 : "MODULE FIST: ATOMIC COORDINATES IN "//TRIM(unit_str)
550 : WRITE (UNIT=iw, FMT="(/,T4,A,T30,A,T44,A,T58,A,T66,A,T77,A)") &
551 2504 : "Atom Kind Name", "X", "Y", "Z", "q(eff)", "Mass"
552 2504 : natom = SIZE(particle_set)
553 362909 : DO iatom = 1, natom
554 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
555 : kind_number=ikind, &
556 : name=name, &
557 : mass=mass, &
558 : qeff=qeff, &
559 360405 : shell=shell_kind)
560 360405 : IF (PRESENT(charges)) qeff = charges(iatom)
561 360405 : IF (ASSOCIATED(shell_kind)) THEN
562 : CALL get_shell(shell=shell_kind, &
563 : charge_core=qcore, &
564 3426 : charge_shell=qshell)
565 3426 : qeff = qcore + qshell
566 : END IF
567 : WRITE (UNIT=iw, FMT="(T2,I6,1X,I4,1X,A7,3(1X,F13.6),2(1X,F8.4))") &
568 1804529 : iatom, ikind, name, particle_set(iatom)%r(1:3)*conv, qeff, mass/massunit
569 : END DO
570 2504 : WRITE (iw, "(A)") ""
571 : END IF
572 :
573 : CALL cp_print_key_finished_output(iw, logger, subsys_section, &
574 9689 : "PRINT%ATOMIC_COORDINATES")
575 :
576 9689 : END SUBROUTINE write_fist_particle_coordinates
577 :
578 : ! **************************************************************************************************
579 : !> \brief Write the atomic coordinates to the output unit.
580 : !> \param particle_set ...
581 : !> \param qs_kind_set ...
582 : !> \param subsys_section ...
583 : !> \param label ...
584 : !> \date 05.06.2000
585 : !> \author MK
586 : !> \version 1.0
587 : ! **************************************************************************************************
588 19228 : SUBROUTINE write_qs_particle_coordinates(particle_set, qs_kind_set, subsys_section, label)
589 :
590 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
591 : TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
592 : TYPE(section_vals_type), POINTER :: subsys_section
593 : CHARACTER(LEN=*), INTENT(IN) :: label
594 :
595 : CHARACTER(len=*), PARAMETER :: routineN = 'write_qs_particle_coordinates'
596 :
597 : CHARACTER(LEN=2) :: element_symbol
598 : CHARACTER(LEN=default_string_length) :: unit_str
599 : INTEGER :: handle, iatom, ikind, iw, natom, z
600 : REAL(KIND=dp) :: conv, mass, zeff
601 : TYPE(cp_logger_type), POINTER :: logger
602 :
603 19228 : CALL timeset(routineN, handle)
604 :
605 19228 : NULLIFY (logger)
606 19228 : logger => cp_get_default_logger()
607 : iw = cp_print_key_unit_nr(logger, subsys_section, &
608 19228 : "PRINT%ATOMIC_COORDINATES", extension=".coordLog")
609 :
610 19228 : CALL section_vals_val_get(subsys_section, "PRINT%ATOMIC_COORDINATES%UNIT", c_val=unit_str)
611 19228 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
612 19228 : CALL uppercase(unit_str)
613 19228 : IF (iw > 0) THEN
614 : WRITE (UNIT=iw, FMT="(/,/,T2,A)") &
615 4460 : "MODULE "//TRIM(label)//": ATOMIC COORDINATES IN "//TRIM(unit_str)
616 : WRITE (UNIT=iw, FMT="(/,T4,A,T30,A,T44,A,T58,A,T66,A,T77,A)") &
617 4460 : "Atom Kind Element", "X", "Y", "Z", "Z(eff)", "Mass"
618 4460 : natom = SIZE(particle_set)
619 26381 : DO iatom = 1, natom
620 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
621 : kind_number=ikind, &
622 : element_symbol=element_symbol, &
623 : mass=mass, &
624 21921 : z=z)
625 21921 : CALL get_qs_kind(qs_kind_set(ikind), zeff=zeff)
626 : WRITE (UNIT=iw, FMT="(T2,I6,1X,I4,1X,A2,1X,I4,3(1X,F13.6),2(1X,F8.4))") &
627 92144 : iatom, ikind, element_symbol, z, particle_set(iatom)%r(1:3)*conv, zeff, mass/massunit
628 : END DO
629 4460 : WRITE (iw, "(A)") ""
630 : END IF
631 :
632 : CALL cp_print_key_finished_output(iw, logger, subsys_section, &
633 19228 : "PRINT%ATOMIC_COORDINATES")
634 :
635 19228 : CALL timestop(handle)
636 :
637 19228 : END SUBROUTINE write_qs_particle_coordinates
638 :
639 : ! **************************************************************************************************
640 : !> \brief Write the matrix of the particle distances to the output unit.
641 : !> \param particle_set ...
642 : !> \param cell ...
643 : !> \param subsys_section ...
644 : !> \date 06.10.2000
645 : !> \author Matthias Krack
646 : !> \version 1.0
647 : ! **************************************************************************************************
648 11191 : SUBROUTINE write_particle_distances(particle_set, cell, subsys_section)
649 :
650 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
651 : TYPE(cell_type), POINTER :: cell
652 : TYPE(section_vals_type), POINTER :: subsys_section
653 :
654 : CHARACTER(len=*), PARAMETER :: routineN = 'write_particle_distances'
655 :
656 : CHARACTER(LEN=default_string_length) :: unit_str
657 : INTEGER :: handle, iatom, iw, jatom, natom
658 : INTEGER, DIMENSION(3) :: periodic
659 : LOGICAL :: explicit
660 : REAL(KIND=dp) :: conv, dab, dab_abort, dab_min, dab_warn
661 11191 : REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: distance_matrix
662 : REAL(KIND=dp), DIMENSION(3) :: rab
663 : TYPE(cp_logger_type), POINTER :: logger
664 :
665 11191 : CALL timeset(routineN, handle)
666 :
667 11191 : CPASSERT(ASSOCIATED(particle_set))
668 11191 : CPASSERT(ASSOCIATED(cell))
669 11191 : CPASSERT(ASSOCIATED(subsys_section))
670 :
671 11191 : NULLIFY (logger)
672 11191 : logger => cp_get_default_logger()
673 : iw = cp_print_key_unit_nr(logger, subsys_section, &
674 11191 : "PRINT%INTERATOMIC_DISTANCES", extension=".distLog")
675 :
676 11191 : CALL section_vals_val_get(subsys_section, "PRINT%INTERATOMIC_DISTANCES%UNIT", c_val=unit_str)
677 11191 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
678 : CALL section_vals_val_get(subsys_section, "PRINT%INTERATOMIC_DISTANCES%CHECK_INTERATOMIC_DISTANCES", &
679 11191 : r_val=dab_min, explicit=explicit)
680 :
681 11191 : dab_abort = 0.0_dp
682 11191 : dab_warn = 0.0_dp
683 11191 : natom = SIZE(particle_set)
684 :
685 : ! Compute interatomic distances only if their printout or check is explicitly requested
686 : ! Disable the default check for systems with more than 3000 atoms
687 11191 : IF (explicit .OR. (iw > 0) .OR. (natom <= 2000)) THEN
688 11149 : IF (dab_min > 0.0_dp) THEN
689 11145 : dab_warn = dab_min*conv
690 4 : ELSE IF (dab_min < 0.0_dp) THEN
691 0 : dab_abort = ABS(dab_min)*conv
692 : END IF
693 : END IF
694 :
695 11191 : IF ((iw > 0) .OR. (dab_abort > 0.0_dp) .OR. (dab_warn > 0.0_dp)) THEN
696 11145 : CALL get_cell(cell=cell, periodic=periodic)
697 11145 : IF (iw > 0) THEN
698 132 : ALLOCATE (distance_matrix(natom, natom))
699 33 : distance_matrix(:, :) = 0.0_dp
700 : END IF
701 332452 : DO iatom = 1, natom
702 119870238 : DO jatom = iatom + 1, natom
703 : rab(:) = pbc(particle_set(iatom)%r(:), &
704 119537786 : particle_set(jatom)%r(:), cell)
705 119537786 : dab = SQRT(rab(1)*rab(1) + rab(2)*rab(2) + rab(3)*rab(3))*conv
706 119537786 : IF (dab_abort > 0.0_dp) THEN
707 : ! Stop the run for interatomic distances smaller than the requested threshold
708 0 : IF (dab < dab_abort) THEN
709 : CALL cp_abort(__LOCATION__, "The distance between the atoms "// &
710 : TRIM(ADJUSTL(cp_to_string(iatom, fmt="(I8)")))//" and "// &
711 : TRIM(ADJUSTL(cp_to_string(jatom, fmt="(I8)")))//" is only "// &
712 : TRIM(ADJUSTL(cp_to_string(dab, fmt="(F6.3)")))//" "// &
713 : TRIM(ADJUSTL(unit_str))//" and thus smaller than the requested threshold of "// &
714 : TRIM(ADJUSTL(cp_to_string(dab_abort, fmt="(F6.3)")))//" "// &
715 0 : TRIM(ADJUSTL(unit_str)))
716 : END IF
717 : END IF
718 119537786 : IF (dab < dab_warn) THEN
719 : ! Print warning for interatomic distances smaller than the requested threshold
720 : CALL cp_warn(__LOCATION__, "The distance between the atoms "// &
721 : TRIM(ADJUSTL(cp_to_string(iatom, fmt="(I8)")))//" and "// &
722 : TRIM(ADJUSTL(cp_to_string(jatom, fmt="(I8)")))//" is only "// &
723 : TRIM(ADJUSTL(cp_to_string(dab, fmt="(F6.3)")))//" "// &
724 : TRIM(ADJUSTL(unit_str))//" and thus smaller than the threshold of "// &
725 : TRIM(ADJUSTL(cp_to_string(dab_warn, fmt="(F6.3)")))//" "// &
726 910 : TRIM(ADJUSTL(unit_str)))
727 : END IF
728 119859093 : IF (iw > 0) THEN
729 35186 : distance_matrix(iatom, jatom) = dab
730 35186 : distance_matrix(jatom, iatom) = distance_matrix(iatom, jatom)
731 : END IF
732 : END DO
733 : END DO
734 11145 : IF (iw > 0) THEN
735 : ! Print the distance matrix
736 : WRITE (UNIT=iw, FMT="(/,/,T2,A)") &
737 33 : "INTERATOMIC DISTANCES IN "//TRIM(unit_str)
738 33 : CALL write_particle_matrix(distance_matrix, particle_set, iw)
739 33 : IF (ALLOCATED(distance_matrix)) DEALLOCATE (distance_matrix)
740 : END IF
741 : CALL cp_print_key_finished_output(iw, logger, subsys_section, &
742 11145 : "PRINT%INTERATOMIC_DISTANCES")
743 : END IF
744 :
745 11191 : CALL timestop(handle)
746 :
747 11191 : END SUBROUTINE write_particle_distances
748 :
749 : ! **************************************************************************************************
750 : !> \brief ...
751 : !> \param matrix ...
752 : !> \param particle_set ...
753 : !> \param iw ...
754 : !> \param el_per_part ...
755 : !> \param Ilist ...
756 : !> \param parts_per_line : number of particle columns to be printed in one line
757 : ! **************************************************************************************************
758 63 : SUBROUTINE write_particle_matrix(matrix, particle_set, iw, el_per_part, Ilist, parts_per_line)
759 : REAL(KIND=dp), DIMENSION(:, :) :: matrix
760 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
761 : INTEGER, INTENT(IN) :: iw
762 : INTEGER, INTENT(IN), OPTIONAL :: el_per_part
763 : INTEGER, DIMENSION(:), OPTIONAL, POINTER :: Ilist
764 : INTEGER, INTENT(IN), OPTIONAL :: parts_per_line
765 :
766 : CHARACTER(LEN=2) :: element_symbol
767 : CHARACTER(LEN=default_string_length) :: fmt_string1, fmt_string2
768 : INTEGER :: from, i, iatom, icol, jatom, katom, &
769 : my_el_per_part, my_parts_per_line, &
770 : natom, to
771 63 : INTEGER, DIMENSION(:), POINTER :: my_list
772 :
773 63 : my_el_per_part = 1
774 30 : IF (PRESENT(el_per_part)) my_el_per_part = el_per_part
775 63 : my_parts_per_line = 5
776 63 : IF (PRESENT(parts_per_line)) my_parts_per_line = MAX(parts_per_line, 1)
777 : WRITE (fmt_string1, FMT='(A,I0,A)') &
778 63 : "(/,T2,9X,", my_parts_per_line, "(4X,I6,4X))"
779 : WRITE (fmt_string2, FMT='(A,I0,A)') &
780 63 : "(T2,I5,1X,A2,1X,", my_parts_per_line, "(1X,ES13.6E2))"
781 63 : IF (PRESENT(Ilist)) THEN
782 30 : natom = SIZE(Ilist)
783 : ELSE
784 33 : natom = SIZE(particle_set)
785 : END IF
786 189 : ALLOCATE (my_list(natom))
787 63 : IF (PRESENT(Ilist)) THEN
788 180 : my_list = Ilist
789 : ELSE
790 927 : DO i = 1, natom
791 927 : my_list(i) = i
792 : END DO
793 : END IF
794 63 : natom = natom*my_el_per_part
795 317 : DO jatom = 1, natom, my_parts_per_line
796 254 : from = jatom
797 254 : to = MIN(from + my_parts_per_line - 1, natom)
798 1373 : WRITE (UNIT=iw, FMT=TRIM(fmt_string1)) (icol, icol=from, to)
799 15622 : DO iatom = 1, natom
800 15305 : katom = iatom/my_el_per_part
801 15305 : IF (MOD(iatom, my_el_per_part) /= 0) katom = katom + 1
802 : CALL get_atomic_kind(atomic_kind=particle_set(my_list(katom))%atomic_kind, &
803 15305 : element_symbol=element_symbol)
804 : WRITE (UNIT=iw, FMT=TRIM(fmt_string2)) &
805 15305 : iatom, element_symbol, &
806 30864 : (matrix(iatom, icol), icol=from, to)
807 : END DO
808 : END DO
809 :
810 63 : DEALLOCATE (my_list)
811 :
812 63 : END SUBROUTINE write_particle_matrix
813 :
814 : ! **************************************************************************************************
815 : !> \brief Write structure data requested by a separate structure data input
816 : !> section to the output unit.
817 : !> input_section can be either motion_section or subsys_section.
818 : !>
819 : !> \param particle_set ...
820 : !> \param cell ...
821 : !> \param input_section ...
822 : !> \date 11.03.04
823 : !> \par History
824 : !> Recovered (23.03.06,MK)
825 : !> \author MK
826 : !> \version 1.0
827 : ! **************************************************************************************************
828 62299 : SUBROUTINE write_structure_data(particle_set, cell, input_section)
829 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
830 : TYPE(cell_type), POINTER :: cell
831 : TYPE(section_vals_type), POINTER :: input_section
832 :
833 : CHARACTER(LEN=*), PARAMETER :: routineN = 'write_structure_data'
834 :
835 : CHARACTER(LEN=default_string_length) :: string, unit_str
836 : INTEGER :: handle, i, i_rep, iw, n, n_rep, n_vals, &
837 : natom, new_size, old_size, wrk2(2), &
838 : wrk3(3), wrk4(4)
839 62299 : INTEGER, ALLOCATABLE, DIMENSION(:) :: work
840 62299 : INTEGER, DIMENSION(:), POINTER :: atomic_indices, index_list
841 : LOGICAL :: unique
842 : REAL(KIND=dp) :: conv, dab
843 : REAL(KIND=dp), DIMENSION(3) :: r, rab, rbc, rcd, s
844 : TYPE(cp_logger_type), POINTER :: logger
845 : TYPE(section_vals_type), POINTER :: section
846 :
847 62299 : CALL timeset(routineN, handle)
848 62299 : NULLIFY (atomic_indices)
849 62299 : NULLIFY (index_list)
850 62299 : NULLIFY (logger)
851 62299 : NULLIFY (section)
852 62299 : string = ""
853 :
854 62299 : logger => cp_get_default_logger()
855 : iw = cp_print_key_unit_nr(logger=logger, &
856 : basis_section=input_section, &
857 : print_key_path="PRINT%STRUCTURE_DATA", &
858 62299 : extension=".coordLog")
859 :
860 62299 : CALL section_vals_val_get(input_section, "PRINT%STRUCTURE_DATA%UNIT", c_val=unit_str)
861 62299 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
862 62299 : CALL uppercase(unit_str)
863 62299 : IF (iw > 0) THEN
864 568 : natom = SIZE(particle_set)
865 : section => section_vals_get_subs_vals(section_vals=input_section, &
866 568 : subsection_name="PRINT%STRUCTURE_DATA")
867 :
868 568 : WRITE (UNIT=iw, FMT="(/,T2,A)") "REQUESTED STRUCTURE DATA"
869 : ! Print the requested atomic position vectors
870 : CALL section_vals_val_get(section_vals=section, &
871 : keyword_name="POSITION", &
872 568 : n_rep_val=n_rep)
873 568 : IF (n_rep > 0) THEN
874 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
875 145 : "Position vectors r(i) of the atoms i in "//TRIM(unit_str)
876 145 : old_size = 0
877 848 : DO i_rep = 1, n_rep
878 : CALL section_vals_val_get(section_vals=section, &
879 : keyword_name="POSITION", &
880 : i_rep_val=i_rep, &
881 703 : i_vals=atomic_indices)
882 703 : n_vals = SIZE(atomic_indices)
883 703 : new_size = old_size + n_vals
884 703 : CALL reallocate(index_list, 1, new_size)
885 2903 : index_list(old_size + 1:new_size) = atomic_indices(1:n_vals)
886 848 : old_size = new_size
887 : END DO
888 435 : ALLOCATE (work(new_size))
889 145 : CALL sort(index_list, new_size, work)
890 145 : DEALLOCATE (work)
891 1245 : DO i = 1, new_size
892 1100 : WRITE (UNIT=string, FMT="(A,I0,A)") "(", index_list(i), ")"
893 1100 : IF ((index_list(i) < 1) .OR. (index_list(i) > natom)) THEN
894 : WRITE (UNIT=iw, FMT="(T3,A)") &
895 30 : "Invalid atomic index "//TRIM(string)//" specified. Print request is ignored."
896 30 : CYCLE
897 : END IF
898 1070 : IF (i > 1) THEN
899 : ! Skip redundant indices
900 935 : IF (index_list(i) == index_list(i - 1)) CYCLE
901 : END IF
902 : WRITE (UNIT=iw, FMT="(T3,A,T20,A,3F13.6)") &
903 4425 : "r"//TRIM(string), "=", pbc(particle_set(index_list(i))%r(1:3), cell)*conv
904 : END DO
905 145 : DEALLOCATE (index_list)
906 : END IF
907 :
908 : ! Print the requested atomic position vectors in scaled coordinates
909 : CALL section_vals_val_get(section_vals=section, &
910 : keyword_name="POSITION_SCALED", &
911 568 : n_rep_val=n_rep)
912 568 : IF (n_rep > 0) THEN
913 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
914 27 : "Position vectors s(i) of the atoms i in scaled coordinates"
915 27 : old_size = 0
916 84 : DO i_rep = 1, n_rep
917 : CALL section_vals_val_get(section_vals=section, &
918 : keyword_name="POSITION_SCALED", &
919 : i_rep_val=i_rep, &
920 57 : i_vals=atomic_indices)
921 57 : n_vals = SIZE(atomic_indices)
922 57 : new_size = old_size + n_vals
923 57 : CALL reallocate(index_list, 1, new_size)
924 965 : index_list(old_size + 1:new_size) = atomic_indices(1:n_vals)
925 84 : old_size = new_size
926 : END DO
927 81 : ALLOCATE (work(new_size))
928 27 : CALL sort(index_list, new_size, work)
929 27 : DEALLOCATE (work)
930 481 : DO i = 1, new_size
931 454 : WRITE (UNIT=string, FMT="(A,I0,A)") "(", index_list(i), ")"
932 454 : IF ((index_list(i) < 1) .OR. (index_list(i) > natom)) THEN
933 : WRITE (UNIT=iw, FMT="(T3,A)") &
934 30 : "Invalid atomic index "//TRIM(string)//" specified. Print request is ignored."
935 30 : CYCLE
936 : END IF
937 424 : IF (i > 1) THEN
938 : ! Skip redundant indices
939 407 : IF (index_list(i) == index_list(i - 1)) CYCLE
940 : END IF
941 424 : r(1:3) = pbc(particle_set(index_list(i))%r(1:3), cell)
942 424 : CALL real_to_scaled(s, r, cell)
943 : WRITE (UNIT=iw, FMT="(T3,A,T20,A,3F13.6)") &
944 451 : "s"//TRIM(string), "=", s(1:3)
945 : END DO
946 27 : DEALLOCATE (index_list)
947 : END IF
948 :
949 : ! Print the requested distances
950 : CALL section_vals_val_get(section_vals=section, &
951 : keyword_name="DISTANCE", &
952 568 : n_rep_val=n)
953 568 : IF (n > 0) THEN
954 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
955 : "Distance vector r(i,j) between the atom i and j in "// &
956 129 : TRIM(unit_str)
957 355 : DO i = 1, n
958 : CALL section_vals_val_get(section_vals=section, &
959 : keyword_name="DISTANCE", &
960 : i_rep_val=i, &
961 226 : i_vals=atomic_indices)
962 226 : string = ""
963 : WRITE (UNIT=string, FMT="(A,2(I0,A))") &
964 226 : "(", atomic_indices(1), ",", atomic_indices(2), ")"
965 678 : wrk2 = atomic_indices
966 226 : CALL sort_unique(wrk2, unique)
967 355 : IF (((wrk2(1) >= 1) .AND. (wrk2(SIZE(wrk2)) <= natom)) .AND. unique) THEN
968 : rab(:) = pbc(particle_set(atomic_indices(1))%r(:), &
969 226 : particle_set(atomic_indices(2))%r(:), cell)
970 226 : dab = SQRT(rab(1)*rab(1) + rab(2)*rab(2) + rab(3)*rab(3))
971 : WRITE (UNIT=iw, FMT="(T3,A,T20,A,3F13.6,3X,A,F13.6)") &
972 904 : "r"//TRIM(string), "=", rab(:)*conv, &
973 452 : "|r| =", dab*conv
974 : ELSE
975 : WRITE (UNIT=iw, FMT="(T3,A)") &
976 0 : "Invalid atomic indices "//TRIM(string)//" specified. Print request is ignored."
977 : END IF
978 : END DO
979 : END IF
980 :
981 : ! Print the requested angles
982 : CALL section_vals_val_get(section_vals=section, &
983 : keyword_name="ANGLE", &
984 568 : n_rep_val=n)
985 568 : IF (n > 0) THEN
986 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
987 : "Angle a(i,j,k) between the atomic distance vectors r(j,i) and "// &
988 67 : "r(j,k) in DEGREE"
989 139 : DO i = 1, n
990 : CALL section_vals_val_get(section_vals=section, &
991 : keyword_name="ANGLE", &
992 : i_rep_val=i, &
993 72 : i_vals=atomic_indices)
994 72 : string = ""
995 : WRITE (UNIT=string, FMT="(A,3(I0,A))") &
996 72 : "(", atomic_indices(1), ",", atomic_indices(2), ",", atomic_indices(3), ")"
997 288 : wrk3 = atomic_indices
998 72 : CALL sort_unique(wrk3, unique)
999 139 : IF (((wrk3(1) >= 1) .AND. (wrk3(SIZE(wrk3)) <= natom)) .AND. unique) THEN
1000 : rab(:) = pbc(particle_set(atomic_indices(1))%r(:), &
1001 67 : particle_set(atomic_indices(2))%r(:), cell)
1002 : rbc(:) = pbc(particle_set(atomic_indices(2))%r(:), &
1003 67 : particle_set(atomic_indices(3))%r(:), cell)
1004 : WRITE (UNIT=iw, FMT="(T3,A,T26,A,F9.3)") &
1005 268 : "a"//TRIM(string), "=", angle(-rab, rbc)*degree
1006 : ELSE
1007 : WRITE (UNIT=iw, FMT="(T3,A)") &
1008 5 : "Invalid atomic indices "//TRIM(string)//" specified. Print request is ignored."
1009 : END IF
1010 : END DO
1011 : END IF
1012 :
1013 : ! Print the requested dihedral angles
1014 : CALL section_vals_val_get(section_vals=section, &
1015 : keyword_name="DIHEDRAL_ANGLE", &
1016 568 : n_rep_val=n)
1017 568 : IF (n > 0) THEN
1018 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
1019 : "Dihedral angle d(i,j,k,l) between the planes (i,j,k) and (j,k,l) "// &
1020 5 : "in DEGREE"
1021 15 : DO i = 1, n
1022 : CALL section_vals_val_get(section_vals=section, &
1023 : keyword_name="DIHEDRAL_ANGLE", &
1024 : i_rep_val=i, &
1025 10 : i_vals=atomic_indices)
1026 10 : string = ""
1027 : WRITE (UNIT=string, FMT="(A,4(I0,A))") &
1028 10 : "(", atomic_indices(1), ",", atomic_indices(2), ",", &
1029 20 : atomic_indices(3), ",", atomic_indices(4), ")"
1030 50 : wrk4 = atomic_indices
1031 10 : CALL sort_unique(wrk4, unique)
1032 15 : IF (((wrk4(1) >= 1) .AND. (wrk4(SIZE(wrk4)) <= natom)) .AND. unique) THEN
1033 : rab(:) = pbc(particle_set(atomic_indices(1))%r(:), &
1034 0 : particle_set(atomic_indices(2))%r(:), cell)
1035 : rbc(:) = pbc(particle_set(atomic_indices(2))%r(:), &
1036 0 : particle_set(atomic_indices(3))%r(:), cell)
1037 : rcd(:) = pbc(particle_set(atomic_indices(3))%r(:), &
1038 0 : particle_set(atomic_indices(4))%r(:), cell)
1039 : WRITE (UNIT=iw, FMT="(T3,A,T26,A,F9.3)") &
1040 0 : "d"//TRIM(string), "=", dihedral_angle(rab, rbc, rcd)*degree
1041 : ELSE
1042 : WRITE (UNIT=iw, FMT="(T3,A)") &
1043 10 : "Invalid atomic indices "//TRIM(string)//" specified. Print request is ignored."
1044 : END IF
1045 : END DO
1046 : END IF
1047 : END IF
1048 : CALL cp_print_key_finished_output(iw, logger, input_section, &
1049 62299 : "PRINT%STRUCTURE_DATA")
1050 :
1051 62299 : CALL timestop(handle)
1052 :
1053 62299 : END SUBROUTINE write_structure_data
1054 :
1055 : ! **************************************************************************************************
1056 : !> \brief Write the final geometry and cell information to files
1057 : !> \param particle_set pointer to particles with atm_name, element_symbol and position
1058 : !> \param cell pointer to cell with abc, angle_alpha, angle_beta, angle_gamma and deth
1059 : !> \param input_section pointer to motion_section which has PRINT%FINAL_STRUCTURE
1060 : !> \param conv flag for whether convergence is achieved or not in optimization
1061 : !> \param keep_angles flag for whether cell optimization keeps initial angles
1062 : !> \param keep_symmetry flag for whether cell optimization keeps initial symmetry
1063 : !> \param keep_volume flag for whether cell optimization keeps initial volume
1064 : !> \param gopt_env_label the geometry optimization label "GEO_OPT", "CELL_OPT", ...
1065 : !> \param constraint_label label for directions with constraint in cell optimization
1066 : !> \par Intended to be invoked in gopt_f_methods:write_final_info.
1067 : !> This implementation does not consider higher space groups even if
1068 : !> one is detected, and the chemical formulae are neither written in
1069 : !> the sorted "Hill notation" nor expressed in groups of molecules.
1070 : !> Other potentially useful but yet to be written information includes:
1071 : !> the external pressure from CELL_OPT/EXTERNAL_POTENTIAL and the
1072 : !> stress tensor (virial) for CELL_OPT;
1073 : !> the fixed atoms from MOTION/CONSTRAINT/FIXED_ATOMS for all.
1074 : !>
1075 : !> History
1076 : !> 04.2026 - Created as write_final_cif
1077 : !> 05.2026 - Generalized to write_final_structure and enable extxyz
1078 : !> 06.2026 - Adopted write_particle_coordinates for handling kind in extxyz
1079 : !> \author HE Zilong
1080 : !> \version 1.0
1081 : ! **************************************************************************************************
1082 1077 : SUBROUTINE write_final_structure(particle_set, cell, input_section, conv, &
1083 : keep_angles, keep_symmetry, keep_volume, &
1084 : gopt_env_label, constraint_label)
1085 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
1086 : TYPE(cell_type), INTENT(IN), POINTER :: cell
1087 : TYPE(section_vals_type), INTENT(IN), POINTER :: input_section
1088 : LOGICAL, INTENT(IN) :: conv, keep_angles, keep_symmetry, &
1089 : keep_volume
1090 : CHARACTER(LEN=default_string_length), INTENT(IN) :: gopt_env_label
1091 : CHARACTER(LEN=4), INTENT(IN) :: constraint_label
1092 :
1093 : CHARACTER(len=*), PARAMETER :: routineN = 'write_final_structure'
1094 :
1095 : CHARACTER(LEN=1) :: conv_str
1096 : CHARACTER(LEN=2) :: element_symbol
1097 1077 : CHARACTER(LEN=2), ALLOCATABLE :: element_list(:)
1098 : CHARACTER(LEN=5) :: pbc_str
1099 1077 : CHARACTER(LEN=:), ALLOCATABLE :: formula_structural, formula_sum
1100 : CHARACTER(LEN=default_path_length) :: cell_str, record, title
1101 : CHARACTER(LEN=default_string_length) :: atm_name, f_cif, f_cif_label, &
1102 : f_cif_type_symbol
1103 1077 : CHARACTER(LEN=default_string_length), ALLOCATABLE :: cif_label(:), cif_type_symbol(:)
1104 : CHARACTER(LEN=timestamp_length) :: timestamp
1105 : INTEGER :: elem_seen, file_unit, gcd_all, handle, i, iatom, ielem, natom, output_unit, &
1106 : symmetry_id, w_cif_label, w_cif_type_symbol
1107 1077 : INTEGER, ALLOCATABLE :: count_list(:)
1108 : LOGICAL :: dummy, elem_in_list, orthorhombic, &
1109 : print_kind, write_cif, write_xyz
1110 : REAL(KIND=dp) :: angle_alpha, angle_beta, angle_gamma, &
1111 : deth, unit_conv
1112 : REAL(KIND=dp), DIMENSION(3) :: abc, r, s
1113 : REAL(KIND=dp), DIMENSION(3, 3) :: hmat
1114 : TYPE(cp_logger_type), POINTER :: logger
1115 : TYPE(enumeration_type), POINTER :: enum
1116 : TYPE(keyword_type), POINTER :: symmetry_keyword
1117 : TYPE(section_type), POINTER :: tmp_cell_section
1118 : TYPE(section_vals_type), POINTER :: print_key
1119 :
1120 1077 : CALL timeset(routineN, handle)
1121 :
1122 1077 : NULLIFY (enum, logger, symmetry_keyword, print_key, tmp_cell_section)
1123 1077 : logger => cp_get_default_logger()
1124 1077 : output_unit = cp_logger_get_default_io_unit(logger)
1125 1077 : print_key => section_vals_get_subs_vals(input_section, "PRINT%FINAL_STRUCTURE")
1126 1077 : conv_str = "F"
1127 1077 : IF (conv) conv_str(1:1) = "T"
1128 :
1129 : ! Collect cell information
1130 1077 : pbc_str = "F F F"
1131 : CALL get_cell(cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, &
1132 : deth=deth, orthorhombic=orthorhombic, abc=abc, h=hmat, &
1133 1077 : symmetry_id=symmetry_id)
1134 1077 : IF (cell%perd(1) == 1) pbc_str(1:1) = "T"
1135 1077 : IF (cell%perd(2) == 1) pbc_str(3:3) = "T"
1136 1077 : IF (cell%perd(3) == 1) pbc_str(5:5) = "T"
1137 1077 : CALL create_cell_section(tmp_cell_section)
1138 1077 : symmetry_keyword => section_get_keyword(tmp_cell_section, "SYMMETRY")
1139 1077 : CALL keyword_get(symmetry_keyword, enum=enum)
1140 : ! cell_str is default_path_length which is longer
1141 : ! than default_string_length and should be enough
1142 : WRITE (UNIT=cell_str, FMT="(9(1X,F19.10))") &
1143 1077 : cp_unit_from_cp2k(hmat(1, 1), "angstrom"), &
1144 1077 : cp_unit_from_cp2k(hmat(2, 1), "angstrom"), &
1145 1077 : cp_unit_from_cp2k(hmat(3, 1), "angstrom"), &
1146 1077 : cp_unit_from_cp2k(hmat(1, 2), "angstrom"), &
1147 1077 : cp_unit_from_cp2k(hmat(2, 2), "angstrom"), &
1148 1077 : cp_unit_from_cp2k(hmat(3, 2), "angstrom"), &
1149 1077 : cp_unit_from_cp2k(hmat(1, 3), "angstrom"), &
1150 1077 : cp_unit_from_cp2k(hmat(2, 3), "angstrom"), &
1151 2154 : cp_unit_from_cp2k(hmat(3, 3), "angstrom")
1152 :
1153 : ! Collect atom information
1154 1077 : natom = SIZE(particle_set)
1155 1077 : ALLOCATE (element_list(nelem + 1), count_list(nelem + 1))
1156 1077 : count_list(:) = 0
1157 4308 : ALLOCATE (cif_label(natom), cif_type_symbol(natom))
1158 1077 : elem_seen = 0
1159 1077 : w_cif_type_symbol = 0
1160 1077 : w_cif_label = 0
1161 37309 : atom_loop: DO iatom = 1, natom
1162 36232 : elem_in_list = .FALSE.
1163 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
1164 36232 : name=atm_name, element_symbol=element_symbol)
1165 36232 : cif_type_symbol(iatom) = TRIM(atm_name)
1166 : ! From write_particle_coordinates above it seems possible
1167 : ! for some atoms to have empty element symbols; whatever
1168 : ! these are, do not count them in the chemical formula
1169 36232 : IF (LEN_TRIM(element_symbol) == 0) THEN
1170 0 : dummy = qmmm_ff_precond_only_qm(id1=atm_name)
1171 0 : cif_label(iatom) = TRIM(atm_name)//TRIM(ADJUSTL(cp_to_string(iatom)))
1172 : ELSE
1173 36232 : cif_label(iatom) = TRIM(element_symbol)//TRIM(ADJUSTL(cp_to_string(iatom)))
1174 60836 : elem_loop: DO ielem = 1, elem_seen
1175 60836 : IF (element_list(ielem) == element_symbol) THEN
1176 34151 : elem_in_list = .TRUE.
1177 34151 : count_list(ielem) = count_list(ielem) + 1
1178 : EXIT elem_loop
1179 : END IF
1180 : END DO elem_loop
1181 : IF (.NOT. elem_in_list) THEN
1182 2081 : elem_seen = elem_seen + 1
1183 2081 : element_list(elem_seen) = element_symbol
1184 2081 : count_list(elem_seen) = 1
1185 : END IF
1186 : END IF
1187 36232 : IF (LEN_TRIM(cif_type_symbol(iatom)) > w_cif_type_symbol) &
1188 : w_cif_type_symbol = LEN_TRIM(cif_type_symbol(iatom))
1189 36232 : IF (LEN_TRIM(cif_label(iatom)) > w_cif_label) &
1190 1077 : w_cif_label = LEN_TRIM(cif_label(iatom))
1191 : END DO atom_loop
1192 :
1193 : ! Determine the format of each line in cif considering width of cif_type_symbol and cif_label
1194 : ! The fields are, in order:
1195 : ! _atom_site_type_symbol, _atom_site_label, _atom_site_symmetry_multiplicity,
1196 : ! _atom_site_fract_x, _atom_site_fract_y, _atom_site_fract_z, _atom_site_occupancy
1197 : ! in which:
1198 : ! _atom_site_type_symbol is taken as atm_name
1199 : ! _atom_site_label is taken as element_symbol//iatom
1200 : ! _atom_site_symmetry_multiplicity and _atom_site_occupancy are always 1
1201 1077 : f_cif_type_symbol = "A"//TRIM(ADJUSTL(cp_to_string(w_cif_type_symbol + 4)))
1202 1077 : f_cif_label = "A"//TRIM(ADJUSTL(cp_to_string(w_cif_label + 4)))
1203 1077 : f_cif = "(T3,"//TRIM(f_cif_type_symbol)//","//TRIM(f_cif_label)//",I4,3F14.8,F8.2)"
1204 :
1205 : ! Determine formula_sum
1206 1077 : CPASSERT(elem_seen > 0)
1207 1077 : CPASSERT(count_list(1) > 0)
1208 1077 : formula_sum = "'"
1209 3158 : DO ielem = 1, elem_seen
1210 2081 : formula_sum = formula_sum//TRIM(ADJUSTL(element_list(ielem)))
1211 2081 : formula_sum = formula_sum//TRIM(ADJUSTL(cp_to_string(count_list(ielem))))
1212 3158 : formula_sum = formula_sum//" "
1213 : END DO
1214 1077 : formula_sum = TRIM(ADJUSTL(formula_sum))//"'"
1215 :
1216 : ! Determine formula_structural and Z
1217 1077 : gcd_all = count_list(1)
1218 3158 : DO ielem = 1, elem_seen
1219 3158 : IF (count_list(ielem) /= 0) THEN
1220 2081 : gcd_all = gcd(gcd_all, count_list(ielem))
1221 : END IF
1222 : END DO
1223 64028 : IF (gcd_all > 1) count_list = count_list/gcd_all
1224 1077 : formula_structural = "'"
1225 3158 : DO ielem = 1, elem_seen
1226 2081 : formula_structural = formula_structural//TRIM(ADJUSTL(element_list(ielem)))
1227 2081 : formula_structural = formula_structural//TRIM(ADJUSTL(cp_to_string(count_list(ielem))))
1228 3158 : formula_structural = formula_structural//" "
1229 : END DO
1230 1077 : formula_structural = TRIM(ADJUSTL(formula_structural))//"'"
1231 :
1232 : ! Write XYZ
1233 1077 : CALL section_vals_val_get(print_key, "PRINT_XYZ", l_val=write_xyz)
1234 1077 : CALL section_vals_val_get(print_key, "PRINT_ATOM_KIND", l_val=print_kind)
1235 1077 : IF (write_xyz) THEN
1236 : ! Print a message to log
1237 : record = cp_print_key_generate_filename(logger, print_key, &
1238 : extension=".xyz", &
1239 1077 : my_local=.FALSE.)
1240 1077 : IF (output_unit > 0) THEN
1241 581 : IF (conv) THEN
1242 : WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
1243 221 : routineN//": Optimization converged, writing XYZ file gladly:"
1244 : ELSE
1245 : WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
1246 360 : routineN//": Optimization not yet converged, writing XYZ file anyway:"
1247 : END IF
1248 581 : WRITE (UNIT=output_unit, FMT="(T3,A)") TRIM(record)
1249 : END IF
1250 :
1251 : ! Prepare title
1252 : WRITE (UNIT=title, FMT="(A)") &
1253 : 'Lattice="'//TRIM(ADJUSTL(cell_str))//'" '// &
1254 : 'Properties=species:S:1:pos:R:3 '// &
1255 : 'pbc="'//pbc_str//'" '// &
1256 1077 : 'Converged='//conv_str
1257 : ! Extended XYZ uses angstrom for positions
1258 1077 : unit_conv = cp_unit_from_cp2k(1.0_dp, "angstrom")
1259 : ! Prepare file unit and write to it
1260 : file_unit = cp_print_key_unit_nr(logger, input_section, "PRINT%FINAL_STRUCTURE", &
1261 : file_status="REPLACE", file_form="FORMATTED", &
1262 1077 : extension=".xyz")
1263 1077 : IF (file_unit > 0) &
1264 : CALL write_particle_coordinates(particle_set, file_unit, dump_extxyz, "POS", title, &
1265 581 : cell=cell, unit_conv=unit_conv, print_kind=print_kind)
1266 : END IF
1267 :
1268 : ! Write CIF
1269 1077 : CALL section_vals_val_get(print_key, "PRINT_CIF", l_val=write_cif)
1270 1077 : IF (write_cif) THEN
1271 : ! Print a message to log
1272 : record = cp_print_key_generate_filename(logger, print_key, &
1273 : extension=".cif", &
1274 1077 : my_local=.FALSE.)
1275 1077 : IF (output_unit > 0) THEN
1276 581 : IF (conv) THEN
1277 : WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
1278 221 : routineN//": Optimization converged, writing CIF file gladly:"
1279 : ELSE
1280 : WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
1281 360 : routineN//": Optimization not yet converged, writing CIF file anyway:"
1282 : END IF
1283 581 : WRITE (UNIT=output_unit, FMT="(T3,A)") TRIM(record)
1284 : END IF
1285 :
1286 : ! Make timestamp for the file
1287 1077 : CALL m_timestamp(timestamp)
1288 :
1289 : ! Prepare file unit and write to it
1290 : file_unit = cp_print_key_unit_nr(logger, input_section, "PRINT%FINAL_STRUCTURE", &
1291 : file_status="REPLACE", file_form="FORMATTED", &
1292 1077 : extension=".cif")
1293 1077 : IF (file_unit > 0) THEN
1294 : ! Generic information
1295 : WRITE (UNIT=file_unit, FMT="(A)") &
1296 581 : "# CIF file created by CP2K "//TRIM(moduleN)//":"//TRIM(routineN)
1297 : WRITE (UNIT=file_unit, FMT="(A)") &
1298 581 : "data_"//TRIM(logger%iter_info%project_name)
1299 : WRITE (UNIT=file_unit, FMT="(A,T39,A)") &
1300 581 : "_audit_creation_date", timestamp(:10)
1301 : WRITE (UNIT=file_unit, FMT="(A,/,A,/,A)") &
1302 581 : "_audit_creation_method", ";", &
1303 1162 : TRIM(cp2k_version)//" (revision "//TRIM(compile_revision)//")"
1304 : WRITE (UNIT=file_unit, FMT="(A,/,A,/,A,/,A)") &
1305 581 : "Project name "//TRIM(logger%iter_info%project_name), &
1306 581 : "submitted by "//TRIM(r_user_name)//"@"//TRIM(r_host_name), &
1307 581 : "processed in "//TRIM(r_cwd), &
1308 1162 : "generated at "//TRIM(timestamp)
1309 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1310 581 : "- Optimization type: "//TRIM(gopt_env_label)
1311 581 : IF (conv) THEN
1312 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1313 221 : "- Optimization converged: TRUE"
1314 : ELSE
1315 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1316 360 : "- Optimization converged: FALSE"
1317 : END IF
1318 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1319 581 : "- Requested initial cell symmetry: "//TRIM(enum_i2c(enum, symmetry_id))
1320 581 : IF (orthorhombic) THEN
1321 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1322 470 : "- Cell is numerically orthorhombic: TRUE"
1323 : ELSE
1324 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1325 111 : "- Cell is numerically orthorhombic: FALSE"
1326 : END IF
1327 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1328 581 : "- Periodicity of cell: "//TRIM(pbc_str)
1329 581 : IF (gopt_env_label == "CELL_OPT") THEN
1330 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1331 102 : "- Cell is subject to optimization: TRUE"
1332 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1333 102 : "- Cell has constraint on direction: "//TRIM(ADJUSTL(constraint_label))
1334 102 : IF (keep_angles) THEN
1335 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1336 16 : "- Keep angles between the cell vectors during optimization: TRUE"
1337 : ELSE
1338 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1339 86 : "- Keep angles between the cell vectors during optimization: FALSE"
1340 : END IF
1341 102 : IF (keep_symmetry) THEN
1342 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1343 21 : "- Keep initial cell symmetry during optimization: TRUE"
1344 : ELSE
1345 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1346 81 : "- Keep initial cell symmetry during optimization: FALSE"
1347 : END IF
1348 102 : IF (keep_volume) THEN
1349 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1350 3 : "- Keep initial cell volume during optimization: TRUE"
1351 : ELSE
1352 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1353 99 : "- Keep initial cell volume during optimization: FALSE"
1354 : END IF
1355 : ELSE
1356 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1357 479 : "- Cell is subject to optimization: FALSE"
1358 : END IF
1359 : WRITE (UNIT=file_unit, FMT="(T2,A)") &
1360 581 : "- Final cell vectors A, B, C by rows [angstrom]:"
1361 2324 : DO i = 1, 3
1362 : WRITE (UNIT=file_unit, FMT="(T3,3(1X,F19.10))") &
1363 1743 : cp_unit_from_cp2k(hmat(1, i), "angstrom"), &
1364 1743 : cp_unit_from_cp2k(hmat(2, i), "angstrom"), &
1365 4067 : cp_unit_from_cp2k(hmat(3, i), "angstrom")
1366 : END DO
1367 581 : WRITE (UNIT=file_unit, FMT="(A)") ";"
1368 : ! Data of cell and geometry
1369 : WRITE (UNIT=file_unit, FMT="(/,A,T44,A)") &
1370 581 : "_symmetry_space_group_name_H-M", "'P 1'"
1371 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1372 581 : "_cell_length_a", cp_unit_from_cp2k(abc(1), "angstrom")
1373 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1374 581 : "_cell_length_b", cp_unit_from_cp2k(abc(2), "angstrom")
1375 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1376 581 : "_cell_length_c", cp_unit_from_cp2k(abc(3), "angstrom")
1377 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1378 581 : "_cell_angle_alpha", angle_alpha
1379 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1380 581 : "_cell_angle_beta", angle_beta
1381 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1382 581 : "_cell_angle_gamma", angle_gamma
1383 : WRITE (UNIT=file_unit, FMT="(A,T48,A)") &
1384 581 : "_symmetry_Int_Tables_number", "1"
1385 : WRITE (UNIT=file_unit, FMT="(A,T36,A)") &
1386 581 : "_chemical_formula_structural", formula_structural
1387 : WRITE (UNIT=file_unit, FMT="(A,T36,A)") &
1388 581 : "_chemical_formula_sum", formula_sum
1389 : WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
1390 581 : "_cell_volume", cp_unit_from_cp2k(ABS(deth), "angstrom^3")
1391 : WRITE (UNIT=file_unit, FMT="(A,T41,I8)") &
1392 581 : "_cell_formula_units_Z", gcd_all
1393 : WRITE (UNIT=file_unit, FMT="(A,/,T2,A,/,T2,A,/,T3,A)") &
1394 581 : "loop_", "_symmetry_equiv_pos_site_id", &
1395 1162 : "_symmetry_equiv_pos_as_xyz", "1 'x, y, z'"
1396 : WRITE (UNIT=file_unit, FMT="(A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A)") &
1397 581 : "loop_", "_atom_site_type_symbol", "_atom_site_label", &
1398 581 : "_atom_site_symmetry_multiplicity", "_atom_site_fract_x", &
1399 1162 : "_atom_site_fract_y", "_atom_site_fract_z", "_atom_site_occupancy"
1400 19332 : DO iatom = 1, natom
1401 : ! positive_range=.TRUE. makes r(1:3) in [0, cell%hmat(i,i)] and
1402 : ! s(1:3) in [0, 1], so there is no need to MODULO s(1:3) by 1.0
1403 18751 : r(1:3) = pbc(particle_set(iatom)%r(1:3), cell, positive_range=.TRUE.)
1404 18751 : CALL real_to_scaled(s, r, cell)
1405 : WRITE (UNIT=file_unit, FMT=TRIM(f_cif)) &
1406 19332 : cif_type_symbol(iatom), cif_label(iatom), 1, s(1:3), 1.0_dp
1407 : END DO
1408 : END IF
1409 : END IF
1410 :
1411 : ! Finish
1412 0 : DEALLOCATE (element_list, count_list, formula_structural, &
1413 1077 : formula_sum, cif_label, cif_type_symbol)
1414 1077 : CALL section_release(tmp_cell_section)
1415 : CALL cp_print_key_finished_output(file_unit, logger, input_section, &
1416 1077 : "PRINT%FINAL_STRUCTURE")
1417 1077 : IF (output_unit > 0) &
1418 : WRITE (UNIT=output_unit, FMT='(/,T2,A)') &
1419 581 : routineN//": Done!"
1420 :
1421 1077 : CALL timestop(handle)
1422 :
1423 4308 : END SUBROUTINE write_final_structure
1424 :
1425 14640 : END MODULE particle_methods
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