Line data Source code
1 : !--------------------------------------------------------------------------------------------------!
2 : ! CP2K: A general program to perform molecular dynamics simulations !
3 : ! Copyright 2000-2024 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 cp_log_handling, ONLY: cp_get_default_logger,&
27 : cp_logger_type,&
28 : cp_to_string
29 : USE cp_output_handling, ONLY: cp_print_key_finished_output,&
30 : cp_print_key_unit_nr
31 : USE cp_units, ONLY: cp_unit_from_cp2k
32 : USE external_potential_types, ONLY: fist_potential_type,&
33 : get_potential
34 : USE input_constants, ONLY: dump_atomic,&
35 : dump_dcd,&
36 : dump_dcd_aligned_cell,&
37 : dump_pdb,&
38 : dump_xmol
39 : USE input_section_types, ONLY: section_vals_get_subs_vals,&
40 : section_vals_type,&
41 : section_vals_val_get
42 : USE kinds, ONLY: default_string_length,&
43 : dp,&
44 : sp
45 : USE mathconstants, ONLY: degree
46 : USE mathlib, ONLY: angle,&
47 : dihedral_angle
48 : USE memory_utilities, ONLY: reallocate
49 : USE particle_types, ONLY: get_particle_pos_or_vel,&
50 : particle_type
51 : USE physcon, ONLY: massunit
52 : USE qmmm_ff_fist, ONLY: qmmm_ff_precond_only_qm
53 : USE qs_kind_types, ONLY: get_qs_kind,&
54 : qs_kind_type
55 : USE shell_potential_types, ONLY: get_shell,&
56 : shell_kind_type
57 : USE string_utilities, ONLY: uppercase
58 : USE util, ONLY: sort,&
59 : sort_unique
60 : #include "./base/base_uses.f90"
61 :
62 : IMPLICIT NONE
63 :
64 : PRIVATE
65 :
66 : ! Public subroutines
67 :
68 : PUBLIC :: write_fist_particle_coordinates, &
69 : write_qs_particle_coordinates, &
70 : write_particle_distances, &
71 : write_particle_coordinates, &
72 : write_structure_data, &
73 : get_particle_set, &
74 : write_particle_matrix
75 :
76 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'particle_methods'
77 :
78 : CONTAINS
79 :
80 : ! **************************************************************************************************
81 : !> \brief Get the components of a particle set.
82 : !> \param particle_set ...
83 : !> \param qs_kind_set ...
84 : !> \param first_sgf ...
85 : !> \param last_sgf ...
86 : !> \param nsgf ...
87 : !> \param nmao ...
88 : !> \param basis ...
89 : !> \date 14.01.2002
90 : !> \par History
91 : !> - particle type cleaned (13.10.2003,MK)
92 : !> - refactoring and add basis set option (17.08.2010,jhu)
93 : !> \author MK
94 : !> \version 1.0
95 : ! **************************************************************************************************
96 164828 : SUBROUTINE get_particle_set(particle_set, qs_kind_set, first_sgf, last_sgf, nsgf, &
97 164828 : nmao, basis)
98 :
99 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
100 : TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
101 : INTEGER, DIMENSION(:), INTENT(INOUT), OPTIONAL :: first_sgf, last_sgf, nsgf, nmao
102 : TYPE(gto_basis_set_p_type), DIMENSION(:), OPTIONAL :: basis
103 :
104 : INTEGER :: ikind, iparticle, isgf, nparticle, ns
105 :
106 164828 : CPASSERT(ASSOCIATED(particle_set))
107 :
108 164828 : nparticle = SIZE(particle_set)
109 164828 : IF (PRESENT(first_sgf)) THEN
110 39468 : CPASSERT(SIZE(first_sgf) >= nparticle)
111 : END IF
112 164828 : IF (PRESENT(last_sgf)) THEN
113 33508 : CPASSERT(SIZE(last_sgf) >= nparticle)
114 : END IF
115 164828 : IF (PRESENT(nsgf)) THEN
116 124930 : CPASSERT(SIZE(nsgf) >= nparticle)
117 : END IF
118 164828 : IF (PRESENT(nmao)) THEN
119 14 : CPASSERT(SIZE(nmao) >= nparticle)
120 : END IF
121 :
122 164828 : IF (PRESENT(first_sgf) .OR. PRESENT(last_sgf) .OR. PRESENT(nsgf)) THEN
123 : isgf = 0
124 963787 : DO iparticle = 1, nparticle
125 799429 : CALL get_atomic_kind(particle_set(iparticle)%atomic_kind, kind_number=ikind)
126 799429 : IF (PRESENT(basis)) THEN
127 592069 : IF (ASSOCIATED(basis(ikind)%gto_basis_set)) THEN
128 592065 : CALL get_gto_basis_set(gto_basis_set=basis(ikind)%gto_basis_set, nsgf=ns)
129 : ELSE
130 4 : ns = 0
131 : END IF
132 : ELSE
133 207360 : CALL get_qs_kind(qs_kind_set(ikind), nsgf=ns)
134 : END IF
135 799429 : IF (PRESENT(nsgf)) nsgf(iparticle) = ns
136 799429 : IF (PRESENT(first_sgf)) first_sgf(iparticle) = isgf + 1
137 799429 : isgf = isgf + ns
138 1763686 : IF (PRESENT(last_sgf)) last_sgf(iparticle) = isgf
139 : END DO
140 : END IF
141 :
142 164828 : IF (PRESENT(first_sgf)) THEN
143 39468 : IF (SIZE(first_sgf) > nparticle) first_sgf(nparticle + 1) = isgf + 1
144 : END IF
145 :
146 164828 : IF (PRESENT(nmao)) THEN
147 86 : DO iparticle = 1, nparticle
148 72 : CALL get_atomic_kind(particle_set(iparticle)%atomic_kind, kind_number=ikind)
149 72 : CALL get_qs_kind(qs_kind_set(ikind), mao=ns)
150 86 : nmao(iparticle) = ns
151 : END DO
152 : END IF
153 :
154 164828 : END SUBROUTINE get_particle_set
155 :
156 : ! **************************************************************************************************
157 : !> \brief Should be able to write a few formats e.g. xmol, and some binary
158 : !> format (dcd) some format can be used for x,v,f
159 : !>
160 : !> FORMAT CONTENT UNITS x, v, f
161 : !> XMOL POS, VEL, FORCE, POS_VEL, POS_VEL_FORCE Angstrom, a.u., a.u.
162 : !>
163 : !> \param particle_set ...
164 : !> \param iunit ...
165 : !> \param output_format ...
166 : !> \param content ...
167 : !> \param title ...
168 : !> \param cell ...
169 : !> \param array ...
170 : !> \param unit_conv ...
171 : !> \param charge_occup ...
172 : !> \param charge_beta ...
173 : !> \param charge_extended ...
174 : !> \param print_kind ...
175 : !> \date 14.01.2002
176 : !> \author MK
177 : !> \version 1.0
178 : ! **************************************************************************************************
179 26987 : SUBROUTINE write_particle_coordinates(particle_set, iunit, output_format, &
180 26987 : content, title, cell, array, unit_conv, &
181 : charge_occup, charge_beta, &
182 : charge_extended, print_kind)
183 :
184 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
185 : INTEGER :: iunit, output_format
186 : CHARACTER(LEN=*) :: content, title
187 : TYPE(cell_type), OPTIONAL, POINTER :: cell
188 : REAL(KIND=dp), DIMENSION(:), INTENT(IN), OPTIONAL :: array
189 : REAL(KIND=dp), INTENT(IN), OPTIONAL :: unit_conv
190 : LOGICAL, INTENT(IN), OPTIONAL :: charge_occup, charge_beta, &
191 : charge_extended, print_kind
192 :
193 : CHARACTER(len=*), PARAMETER :: routineN = 'write_particle_coordinates'
194 :
195 : CHARACTER(LEN=120) :: line
196 : CHARACTER(LEN=2) :: element_symbol
197 : CHARACTER(LEN=4) :: name
198 : CHARACTER(LEN=default_string_length) :: atm_name, my_format
199 : INTEGER :: handle, iatom, natom
200 : LOGICAL :: dummy, my_charge_beta, &
201 : my_charge_extended, my_charge_occup, &
202 : my_print_kind
203 : REAL(KIND=dp) :: angle_alpha, angle_beta, angle_gamma, &
204 : factor, qeff
205 26987 : REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: arr
206 : REAL(KIND=dp), DIMENSION(3) :: abc, angles, f, r, v
207 : REAL(KIND=dp), DIMENSION(3, 3) :: h
208 26987 : REAL(KIND=sp), ALLOCATABLE, DIMENSION(:) :: x4, y4, z4
209 : TYPE(cell_type), POINTER :: cell_dcd
210 : TYPE(fist_potential_type), POINTER :: fist_potential
211 : TYPE(shell_kind_type), POINTER :: shell
212 :
213 26987 : CALL timeset(routineN, handle)
214 :
215 26987 : natom = SIZE(particle_set)
216 26987 : IF (PRESENT(array)) THEN
217 1773 : SELECT CASE (TRIM(content))
218 : CASE ("POS_VEL", "POS_VEL_FORCE")
219 1773 : CPABORT("Illegal usage")
220 : END SELECT
221 : END IF
222 26987 : factor = 1.0_dp
223 26987 : IF (PRESENT(unit_conv)) THEN
224 26836 : factor = unit_conv
225 : END IF
226 53901 : SELECT CASE (output_format)
227 : CASE (dump_xmol)
228 26914 : my_print_kind = .FALSE.
229 26914 : IF (PRESENT(print_kind)) my_print_kind = print_kind
230 26914 : WRITE (iunit, "(I8)") natom
231 26914 : WRITE (iunit, "(A)") TRIM(title)
232 1323030 : DO iatom = 1, natom
233 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
234 1296116 : element_symbol=element_symbol)
235 1296116 : IF (LEN_TRIM(element_symbol) == 0 .OR. my_print_kind) THEN
236 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
237 24 : name=atm_name)
238 24 : dummy = qmmm_ff_precond_only_qm(id1=atm_name)
239 24 : my_format = "(A,"
240 24 : atm_name = TRIM(atm_name)
241 : ELSE
242 1296092 : my_format = "(T2,A2,"
243 1296092 : atm_name = TRIM(element_symbol)
244 : END IF
245 26914 : SELECT CASE (TRIM(content))
246 : CASE ("POS")
247 1181019 : IF (PRESENT(array)) THEN
248 48271 : r(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
249 : ELSE
250 4530992 : r(:) = particle_set(iatom)%r(:)
251 : END IF
252 4724076 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), r(1:3)*factor
253 : CASE ("VEL")
254 85469 : IF (PRESENT(array)) THEN
255 0 : v(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
256 : ELSE
257 341876 : v(:) = particle_set(iatom)%v(:)
258 : END IF
259 341876 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), v(1:3)*factor
260 : CASE ("FORCE")
261 21019 : IF (PRESENT(array)) THEN
262 0 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
263 : ELSE
264 84076 : f(:) = particle_set(iatom)%f(:)
265 : END IF
266 84076 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), f(1:3)*factor
267 : CASE ("FORCE_MIXING_LABELS")
268 8609 : IF (PRESENT(array)) THEN
269 34436 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
270 : ELSE
271 0 : f(:) = particle_set(iatom)%f(:)
272 : END IF
273 1330552 : WRITE (iunit, TRIM(my_format)//"1X,3F20.10)") TRIM(atm_name), f(1:3)*factor
274 : END SELECT
275 : END DO
276 : CASE (dump_atomic)
277 170 : DO iatom = 1, natom
278 10 : SELECT CASE (TRIM(content))
279 : CASE ("POS")
280 160 : IF (PRESENT(array)) THEN
281 0 : r(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
282 : ELSE
283 640 : r(:) = particle_set(iatom)%r(:)
284 : END IF
285 640 : WRITE (iunit, "(3F20.10)") r(1:3)*factor
286 : CASE ("VEL")
287 0 : IF (PRESENT(array)) THEN
288 0 : v(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
289 : ELSE
290 0 : v(:) = particle_set(iatom)%v(:)
291 : END IF
292 0 : WRITE (iunit, "(3F20.10)") v(1:3)*factor
293 : CASE ("FORCE")
294 0 : IF (PRESENT(array)) THEN
295 0 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
296 : ELSE
297 0 : f(:) = particle_set(iatom)%f(:)
298 : END IF
299 0 : WRITE (iunit, "(3F20.10)") f(1:3)*factor
300 : CASE ("FORCE_MIXING_LABELS")
301 0 : IF (PRESENT(array)) THEN
302 0 : f(:) = array((iatom - 1)*3 + 1:(iatom - 1)*3 + 3)
303 : ELSE
304 0 : f(:) = particle_set(iatom)%f(:)
305 : END IF
306 160 : WRITE (iunit, "(3F20.10)") f(1:3)*factor
307 : END SELECT
308 : END DO
309 : CASE (dump_dcd, dump_dcd_aligned_cell)
310 4 : IF (.NOT. (PRESENT(cell))) THEN
311 0 : CPABORT("Cell is not present! Report this bug!")
312 : END IF
313 : CALL get_cell(cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, &
314 4 : abc=abc)
315 4 : IF (.NOT. cell%orthorhombic .AND. (output_format == dump_dcd_aligned_cell)) THEN
316 : ! In the case of a non-orthorhombic cell adopt a common convention
317 : ! for the orientation of the cell with respect to the Cartesian axes:
318 : ! Cell vector a is aligned with the x axis and the cell vector b lies
319 : ! in the xy plane.
320 0 : NULLIFY (cell_dcd)
321 0 : CALL cell_create(cell_dcd)
322 0 : CALL cell_clone(cell, cell_dcd, tag="CELL_DCD")
323 0 : angles(1) = angle_alpha/degree
324 0 : angles(2) = angle_beta/degree
325 0 : angles(3) = angle_gamma/degree
326 : CALL set_cell_param(cell_dcd, abc, angles, &
327 0 : do_init_cell=.TRUE.)
328 0 : h(1:3, 1:3) = MATMUL(cell_dcd%hmat(1:3, 1:3), cell%h_inv(1:3, 1:3))
329 0 : CALL cell_release(cell_dcd)
330 : END IF
331 12 : ALLOCATE (arr(3, natom))
332 4 : IF (PRESENT(array)) THEN
333 0 : arr(1:3, 1:natom) = RESHAPE(array, (/3, natom/))
334 : ELSE
335 8 : SELECT CASE (TRIM(content))
336 : CASE ("POS")
337 1156 : DO iatom = 1, natom
338 4612 : arr(1:3, iatom) = particle_set(iatom)%r(1:3)
339 : END DO
340 : CASE ("VEL")
341 0 : DO iatom = 1, natom
342 0 : arr(1:3, iatom) = particle_set(iatom)%v(1:3)
343 : END DO
344 : CASE ("FORCE")
345 0 : DO iatom = 1, natom
346 0 : arr(1:3, iatom) = particle_set(iatom)%f(1:3)
347 : END DO
348 : CASE DEFAULT
349 4 : CPABORT("Illegal DCD dump type")
350 : END SELECT
351 : END IF
352 12 : ALLOCATE (x4(natom))
353 12 : ALLOCATE (y4(natom))
354 12 : ALLOCATE (z4(natom))
355 4 : IF (.NOT. cell%orthorhombic .AND. (output_format == dump_dcd_aligned_cell)) THEN
356 0 : x4(1:natom) = REAL(MATMUL(h(1, 1:3), arr(1:3, 1:natom)), KIND=sp)
357 0 : y4(1:natom) = REAL(MATMUL(h(2, 1:3), arr(1:3, 1:natom)), KIND=sp)
358 0 : z4(1:natom) = REAL(MATMUL(h(3, 1:3), arr(1:3, 1:natom)), KIND=sp)
359 : ELSE
360 1156 : x4(1:natom) = REAL(arr(1, 1:natom), KIND=sp)
361 1156 : y4(1:natom) = REAL(arr(2, 1:natom), KIND=sp)
362 1156 : z4(1:natom) = REAL(arr(3, 1:natom), KIND=sp)
363 : END IF
364 4 : WRITE (iunit) abc(1)*factor, angle_gamma, abc(2)*factor, &
365 8 : angle_beta, angle_alpha, abc(3)*factor
366 1156 : WRITE (iunit) x4*REAL(factor, KIND=sp)
367 1156 : WRITE (iunit) y4*REAL(factor, KIND=sp)
368 1156 : WRITE (iunit) z4*REAL(factor, KIND=sp)
369 : ! Release work storage
370 4 : DEALLOCATE (arr)
371 4 : DEALLOCATE (x4)
372 4 : DEALLOCATE (y4)
373 8 : DEALLOCATE (z4)
374 : CASE (dump_pdb)
375 59 : my_charge_occup = .FALSE.
376 59 : IF (PRESENT(charge_occup)) my_charge_occup = charge_occup
377 59 : my_charge_beta = .FALSE.
378 59 : IF (PRESENT(charge_beta)) my_charge_beta = charge_beta
379 59 : my_charge_extended = .FALSE.
380 59 : IF (PRESENT(charge_extended)) my_charge_extended = charge_extended
381 59 : IF (LEN_TRIM(title) > 0) THEN
382 : WRITE (UNIT=iunit, FMT="(A6,T11,A)") &
383 59 : "REMARK", TRIM(title)
384 : END IF
385 59 : CALL get_cell(cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, abc=abc)
386 : ! COLUMNS DATA TYPE CONTENTS
387 : ! --------------------------------------------------
388 : ! 1 - 6 Record name "CRYST1"
389 : ! 7 - 15 Real(9.3) a (Angstroms)
390 : ! 16 - 24 Real(9.3) b (Angstroms)
391 : ! 25 - 33 Real(9.3) c (Angstroms)
392 : ! 34 - 40 Real(7.2) alpha (degrees)
393 : ! 41 - 47 Real(7.2) beta (degrees)
394 : ! 48 - 54 Real(7.2) gamma (degrees)
395 : ! 56 - 66 LString Space group
396 : ! 67 - 70 Integer Z value
397 : WRITE (UNIT=iunit, FMT="(A6,3F9.3,3F7.2)") &
398 236 : "CRYST1", abc(1:3)*factor, angle_alpha, angle_beta, angle_gamma
399 59 : WRITE (UNIT=line(1:6), FMT="(A6)") "ATOM "
400 2999 : DO iatom = 1, natom
401 2940 : line = ""
402 : ! COLUMNS DATA TYPE CONTENTS
403 : ! 1 - 6 Record name "ATOM "
404 : ! 7 - 11 Integer Atom serial number
405 : ! 13 - 16 Atom Atom name
406 : ! 17 Character Alternate location indicator
407 : ! 18 - 20 Residue name Residue name
408 : ! 22 Character Chain identifier
409 : ! 23 - 26 Integer Residue sequence number
410 : ! 27 AChar Code for insertion of residues
411 : ! 31 - 38 Real(8.3) Orthogonal coordinates for X in Angstrom
412 : ! 39 - 46 Real(8.3) Orthogonal coordinates for Y in Angstrom
413 : ! 47 - 54 Real(8.3) Orthogonal coordinates for Z in Angstrom
414 : ! 55 - 60 Real(6.2) Occupancy
415 : ! 61 - 66 Real(6.2) Temperature factor (Default = 0.0)
416 : ! 73 - 76 LString(4) Segment identifier, left-justified
417 : ! 77 - 78 LString(2) Element symbol, right-justified
418 : ! 79 - 80 LString(2) Charge on the atom
419 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
420 : element_symbol=element_symbol, name=atm_name, &
421 2940 : fist_potential=fist_potential, shell=shell)
422 2940 : IF (LEN_TRIM(element_symbol) == 0) THEN
423 0 : dummy = qmmm_ff_precond_only_qm(id1=atm_name)
424 : END IF
425 2940 : name = TRIM(atm_name)
426 2940 : IF (ASSOCIATED(fist_potential)) THEN
427 2940 : CALL get_potential(potential=fist_potential, qeff=qeff)
428 : ELSE
429 0 : qeff = 0.0_dp
430 : END IF
431 2940 : IF (ASSOCIATED(shell)) CALL get_shell(shell=shell, charge=qeff)
432 2940 : WRITE (UNIT=line(1:6), FMT="(A6)") "ATOM "
433 2940 : WRITE (UNIT=line(7:11), FMT="(I5)") MODULO(iatom, 100000)
434 2940 : WRITE (UNIT=line(13:16), FMT="(A4)") ADJUSTL(name)
435 : ! WRITE (UNIT=line(18:20),FMT="(A3)") TRIM(resname)
436 : ! WRITE (UNIT=line(23:26),FMT="(I4)") MODULO(idres,10000)
437 5880 : SELECT CASE (TRIM(content))
438 : CASE ("POS")
439 2940 : IF (PRESENT(array)) THEN
440 0 : r(1:3) = get_particle_pos_or_vel(iatom, particle_set, array)
441 : ELSE
442 11760 : r(:) = particle_set(iatom)%r(:)
443 : END IF
444 11760 : WRITE (UNIT=line(31:54), FMT="(3F8.3)") r(1:3)*factor
445 : CASE DEFAULT
446 2940 : CPABORT("PDB dump only for trajectory available")
447 : END SELECT
448 2940 : IF (my_charge_occup) THEN
449 2130 : WRITE (UNIT=line(55:60), FMT="(F6.2)") qeff
450 : ELSE
451 810 : WRITE (UNIT=line(55:60), FMT="(F6.2)") 0.0_dp
452 : END IF
453 2940 : IF (my_charge_beta) THEN
454 480 : WRITE (UNIT=line(61:66), FMT="(F6.2)") qeff
455 : ELSE
456 2460 : WRITE (UNIT=line(61:66), FMT="(F6.2)") 0.0_dp
457 : END IF
458 : ! WRITE (UNIT=line(73:76),FMT="(A4)") ADJUSTL(TRIM(molname))
459 2940 : WRITE (UNIT=line(77:78), FMT="(A2)") ADJUSTR(TRIM(element_symbol))
460 2940 : IF (my_charge_extended) THEN
461 330 : WRITE (UNIT=line(81:), FMT="(SP,F0.8)") qeff
462 : END IF
463 2999 : WRITE (UNIT=iunit, FMT="(A)") TRIM(line)
464 : END DO
465 59 : WRITE (UNIT=iunit, FMT="(A)") "END"
466 : CASE DEFAULT
467 27046 : CPABORT("Illegal dump type")
468 : END SELECT
469 :
470 26987 : CALL timestop(handle)
471 :
472 26987 : END SUBROUTINE write_particle_coordinates
473 :
474 : ! **************************************************************************************************
475 : !> \brief Write the atomic coordinates to the output unit.
476 : !> \param particle_set ...
477 : !> \param subsys_section ...
478 : !> \param charges ...
479 : !> \date 05.06.2000
480 : !> \author MK
481 : !> \version 1.0
482 : ! **************************************************************************************************
483 9761 : SUBROUTINE write_fist_particle_coordinates(particle_set, subsys_section, charges)
484 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
485 : TYPE(section_vals_type), POINTER :: subsys_section
486 : REAL(KIND=dp), DIMENSION(:), OPTIONAL :: charges
487 :
488 : CHARACTER(LEN=default_string_length) :: name, unit_str
489 : INTEGER :: iatom, ikind, iw, natom
490 : REAL(KIND=dp) :: conv, mass, qcore, qeff, qshell
491 : TYPE(cp_logger_type), POINTER :: logger
492 : TYPE(shell_kind_type), POINTER :: shell_kind
493 :
494 9761 : NULLIFY (logger)
495 9761 : NULLIFY (shell_kind)
496 :
497 9761 : logger => cp_get_default_logger()
498 : iw = cp_print_key_unit_nr(logger, subsys_section, &
499 9761 : "PRINT%ATOMIC_COORDINATES", extension=".coordLog")
500 :
501 9761 : CALL section_vals_val_get(subsys_section, "PRINT%ATOMIC_COORDINATES%UNIT", c_val=unit_str)
502 9761 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
503 9761 : CALL uppercase(unit_str)
504 9761 : IF (iw > 0) THEN
505 : WRITE (UNIT=iw, FMT="(/,/,T2,A)") &
506 2505 : "MODULE FIST: ATOMIC COORDINATES IN "//TRIM(unit_str)
507 : WRITE (UNIT=iw, FMT="(/,T4,A,T30,A,T44,A,T58,A,T66,A,T77,A)") &
508 2505 : "Atom Kind Name", "X", "Y", "Z", "q(eff)", "Mass"
509 2505 : natom = SIZE(particle_set)
510 362590 : DO iatom = 1, natom
511 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
512 : kind_number=ikind, &
513 : name=name, &
514 : mass=mass, &
515 : qeff=qeff, &
516 360085 : shell=shell_kind)
517 360085 : IF (PRESENT(charges)) qeff = charges(iatom)
518 360085 : IF (ASSOCIATED(shell_kind)) THEN
519 : CALL get_shell(shell=shell_kind, &
520 : charge_core=qcore, &
521 3426 : charge_shell=qshell)
522 3426 : qeff = qcore + qshell
523 : END IF
524 : WRITE (UNIT=iw, FMT="(T2,I6,1X,I4,1X,A7,3(1X,F13.6),2(1X,F8.4))") &
525 1802930 : iatom, ikind, name, particle_set(iatom)%r(1:3)*conv, qeff, mass/massunit
526 : END DO
527 2505 : WRITE (iw, "(A)") ""
528 : END IF
529 :
530 : CALL cp_print_key_finished_output(iw, logger, subsys_section, &
531 9761 : "PRINT%ATOMIC_COORDINATES")
532 :
533 9761 : END SUBROUTINE write_fist_particle_coordinates
534 :
535 : ! **************************************************************************************************
536 : !> \brief Write the atomic coordinates to the output unit.
537 : !> \param particle_set ...
538 : !> \param qs_kind_set ...
539 : !> \param subsys_section ...
540 : !> \param label ...
541 : !> \date 05.06.2000
542 : !> \author MK
543 : !> \version 1.0
544 : ! **************************************************************************************************
545 13326 : SUBROUTINE write_qs_particle_coordinates(particle_set, qs_kind_set, subsys_section, label)
546 :
547 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
548 : TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
549 : TYPE(section_vals_type), POINTER :: subsys_section
550 : CHARACTER(LEN=*), INTENT(IN) :: label
551 :
552 : CHARACTER(len=*), PARAMETER :: routineN = 'write_qs_particle_coordinates'
553 :
554 : CHARACTER(LEN=2) :: element_symbol
555 : CHARACTER(LEN=default_string_length) :: unit_str
556 : INTEGER :: handle, iatom, ikind, iw, natom, z
557 : REAL(KIND=dp) :: conv, mass, zeff
558 : TYPE(cp_logger_type), POINTER :: logger
559 :
560 13326 : CALL timeset(routineN, handle)
561 :
562 13326 : NULLIFY (logger)
563 13326 : logger => cp_get_default_logger()
564 : iw = cp_print_key_unit_nr(logger, subsys_section, &
565 13326 : "PRINT%ATOMIC_COORDINATES", extension=".coordLog")
566 :
567 13326 : CALL section_vals_val_get(subsys_section, "PRINT%ATOMIC_COORDINATES%UNIT", c_val=unit_str)
568 13326 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
569 13326 : CALL uppercase(unit_str)
570 13326 : IF (iw > 0) THEN
571 : WRITE (UNIT=iw, FMT="(/,/,T2,A)") &
572 3150 : "MODULE "//TRIM(label)//": ATOMIC COORDINATES IN "//TRIM(unit_str)
573 : WRITE (UNIT=iw, FMT="(/,T4,A,T30,A,T44,A,T58,A,T66,A,T77,A)") &
574 3150 : "Atom Kind Element", "X", "Y", "Z", "Z(eff)", "Mass"
575 3150 : natom = SIZE(particle_set)
576 19762 : DO iatom = 1, natom
577 : CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
578 : kind_number=ikind, &
579 : element_symbol=element_symbol, &
580 : mass=mass, &
581 16612 : z=z)
582 16612 : CALL get_qs_kind(qs_kind_set(ikind), zeff=zeff)
583 : WRITE (UNIT=iw, FMT="(T2,I6,1X,I4,1X,A2,1X,I4,3(1X,F13.6),2(1X,F8.4))") &
584 69598 : iatom, ikind, element_symbol, z, particle_set(iatom)%r(1:3)*conv, zeff, mass/massunit
585 : END DO
586 3150 : WRITE (iw, "(A)") ""
587 : END IF
588 :
589 : CALL cp_print_key_finished_output(iw, logger, subsys_section, &
590 13326 : "PRINT%ATOMIC_COORDINATES")
591 :
592 13326 : CALL timestop(handle)
593 :
594 13326 : END SUBROUTINE write_qs_particle_coordinates
595 :
596 : ! **************************************************************************************************
597 : !> \brief Write the matrix of the particle distances to the output unit.
598 : !> \param particle_set ...
599 : !> \param cell ...
600 : !> \param subsys_section ...
601 : !> \date 06.10.2000
602 : !> \author Matthias Krack
603 : !> \version 1.0
604 : ! **************************************************************************************************
605 9217 : SUBROUTINE write_particle_distances(particle_set, cell, subsys_section)
606 :
607 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
608 : TYPE(cell_type), POINTER :: cell
609 : TYPE(section_vals_type), POINTER :: subsys_section
610 :
611 : CHARACTER(len=*), PARAMETER :: routineN = 'write_particle_distances'
612 :
613 : CHARACTER(LEN=default_string_length) :: unit_str
614 : INTEGER :: handle, iatom, iw, jatom, natom
615 : INTEGER, DIMENSION(3) :: periodic
616 : LOGICAL :: explicit
617 : REAL(KIND=dp) :: conv, dab, dab_abort, dab_min, dab_warn
618 9217 : REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: distance_matrix
619 : REAL(KIND=dp), DIMENSION(3) :: rab
620 : TYPE(cp_logger_type), POINTER :: logger
621 :
622 9217 : CALL timeset(routineN, handle)
623 :
624 9217 : CPASSERT(ASSOCIATED(particle_set))
625 9217 : CPASSERT(ASSOCIATED(cell))
626 9217 : CPASSERT(ASSOCIATED(subsys_section))
627 :
628 9217 : NULLIFY (logger)
629 9217 : logger => cp_get_default_logger()
630 : iw = cp_print_key_unit_nr(logger, subsys_section, &
631 9217 : "PRINT%INTERATOMIC_DISTANCES", extension=".distLog")
632 :
633 9217 : CALL section_vals_val_get(subsys_section, "PRINT%INTERATOMIC_DISTANCES%UNIT", c_val=unit_str)
634 9217 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
635 : CALL section_vals_val_get(subsys_section, "PRINT%INTERATOMIC_DISTANCES%CHECK_INTERATOMIC_DISTANCES", &
636 9217 : r_val=dab_min, explicit=explicit)
637 :
638 9217 : dab_abort = 0.0_dp
639 9217 : dab_warn = 0.0_dp
640 9217 : natom = SIZE(particle_set)
641 :
642 : ! Compute interatomic distances only if their printout or check is explicitly requested
643 : ! Disable the default check for systems with more than 3000 atoms
644 9217 : IF (explicit .OR. (iw > 0) .OR. (natom <= 2000)) THEN
645 9175 : IF (dab_min > 0.0_dp) THEN
646 9171 : dab_warn = dab_min*conv
647 4 : ELSE IF (dab_min < 0.0_dp) THEN
648 0 : dab_abort = ABS(dab_min)*conv
649 : END IF
650 : END IF
651 :
652 9217 : IF ((iw > 0) .OR. (dab_abort > 0.0_dp) .OR. (dab_warn > 0.0_dp)) THEN
653 9171 : CALL get_cell(cell=cell, periodic=periodic)
654 9171 : IF (iw > 0) THEN
655 128 : ALLOCATE (distance_matrix(natom, natom))
656 72180 : distance_matrix(:, :) = 0.0_dp
657 : END IF
658 315890 : DO iatom = 1, natom
659 116776912 : DO jatom = iatom + 1, natom
660 : rab(:) = pbc(particle_set(iatom)%r(:), &
661 116461022 : particle_set(jatom)%r(:), cell)
662 116461022 : dab = SQRT(rab(1)*rab(1) + rab(2)*rab(2) + rab(3)*rab(3))*conv
663 116461022 : IF (dab_abort > 0.0_dp) THEN
664 : ! Stop the run for interatomic distances smaller than the requested threshold
665 0 : IF (dab < dab_abort) THEN
666 : CALL cp_abort(__LOCATION__, "The distance between the atoms "// &
667 : TRIM(ADJUSTL(cp_to_string(iatom, fmt="(I8)")))//" and "// &
668 : TRIM(ADJUSTL(cp_to_string(jatom, fmt="(I8)")))//" is only "// &
669 : TRIM(ADJUSTL(cp_to_string(dab, fmt="(F6.3)")))//" "// &
670 : TRIM(ADJUSTL(unit_str))//" and thus smaller than the requested threshold of "// &
671 : TRIM(ADJUSTL(cp_to_string(dab_abort, fmt="(F6.3)")))//" "// &
672 0 : TRIM(ADJUSTL(unit_str)))
673 : END IF
674 : END IF
675 116461022 : IF (dab < dab_warn) THEN
676 : ! Print warning for interatomic distances smaller than the requested threshold
677 : CALL cp_warn(__LOCATION__, "The distance between the atoms "// &
678 : TRIM(ADJUSTL(cp_to_string(iatom, fmt="(I8)")))//" and "// &
679 : TRIM(ADJUSTL(cp_to_string(jatom, fmt="(I8)")))//" is only "// &
680 : TRIM(ADJUSTL(cp_to_string(dab, fmt="(F6.3)")))//" "// &
681 : TRIM(ADJUSTL(unit_str))//" and thus smaller than the threshold of "// &
682 : TRIM(ADJUSTL(cp_to_string(dab_warn, fmt="(F6.3)")))//" "// &
683 912 : TRIM(ADJUSTL(unit_str)))
684 : END IF
685 116767741 : IF (iw > 0) THEN
686 35183 : distance_matrix(iatom, jatom) = dab
687 35183 : distance_matrix(jatom, iatom) = distance_matrix(iatom, jatom)
688 : END IF
689 : END DO
690 : END DO
691 9171 : IF (iw > 0) THEN
692 : ! Print the distance matrix
693 : WRITE (UNIT=iw, FMT="(/,/,T2,A)") &
694 32 : "INTERATOMIC DISTANCES IN "//TRIM(unit_str)
695 32 : CALL write_particle_matrix(distance_matrix, particle_set, iw)
696 32 : IF (ALLOCATED(distance_matrix)) DEALLOCATE (distance_matrix)
697 : END IF
698 : CALL cp_print_key_finished_output(iw, logger, subsys_section, &
699 9171 : "PRINT%INTERATOMIC_DISTANCES")
700 : END IF
701 :
702 9217 : CALL timestop(handle)
703 :
704 9217 : END SUBROUTINE write_particle_distances
705 :
706 : ! **************************************************************************************************
707 : !> \brief ...
708 : !> \param matrix ...
709 : !> \param particle_set ...
710 : !> \param iw ...
711 : !> \param el_per_part ...
712 : !> \param Ilist ...
713 : !> \param parts_per_line : number of particle columns to be printed in one line
714 : ! **************************************************************************************************
715 52 : SUBROUTINE write_particle_matrix(matrix, particle_set, iw, el_per_part, Ilist, parts_per_line)
716 : REAL(KIND=dp), DIMENSION(:, :) :: matrix
717 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
718 : INTEGER, INTENT(IN) :: iw
719 : INTEGER, INTENT(IN), OPTIONAL :: el_per_part
720 : INTEGER, DIMENSION(:), OPTIONAL, POINTER :: Ilist
721 : INTEGER, INTENT(IN), OPTIONAL :: parts_per_line
722 :
723 : CHARACTER(LEN=2) :: element_symbol
724 : CHARACTER(LEN=default_string_length) :: fmt_string1, fmt_string2
725 : INTEGER :: from, i, iatom, icol, jatom, katom, &
726 : my_el_per_part, my_parts_per_line, &
727 : natom, to
728 52 : INTEGER, DIMENSION(:), POINTER :: my_list
729 :
730 52 : my_el_per_part = 1
731 20 : IF (PRESENT(el_per_part)) my_el_per_part = el_per_part
732 52 : my_parts_per_line = 5
733 52 : IF (PRESENT(parts_per_line)) my_parts_per_line = MAX(parts_per_line, 1)
734 : WRITE (fmt_string1, FMT='(A,I0,A)') &
735 52 : "(/,T2,11X,", my_parts_per_line, "(4X,I5,4X))"
736 : WRITE (fmt_string2, FMT='(A,I0,A)') &
737 52 : "(T2,I5,2X,A2,2X,", my_parts_per_line, "(1X,F12.6))"
738 52 : IF (PRESENT(Ilist)) THEN
739 20 : natom = SIZE(Ilist)
740 : ELSE
741 32 : natom = SIZE(particle_set)
742 : END IF
743 156 : ALLOCATE (my_list(natom))
744 52 : IF (PRESENT(Ilist)) THEN
745 120 : my_list = Ilist
746 : ELSE
747 923 : DO i = 1, natom
748 923 : my_list(i) = i
749 : END DO
750 : END IF
751 52 : natom = natom*my_el_per_part
752 286 : DO jatom = 1, natom, my_parts_per_line
753 234 : from = jatom
754 234 : to = MIN(from + my_parts_per_line - 1, natom)
755 1275 : WRITE (UNIT=iw, FMT=TRIM(fmt_string1)) (icol, icol=from, to)
756 15441 : DO iatom = 1, natom
757 15155 : katom = iatom/my_el_per_part
758 15155 : IF (MOD(iatom, my_el_per_part) /= 0) katom = katom + 1
759 : CALL get_atomic_kind(atomic_kind=particle_set(my_list(katom))%atomic_kind, &
760 15155 : element_symbol=element_symbol)
761 : WRITE (UNIT=iw, FMT=TRIM(fmt_string2)) &
762 15155 : iatom, element_symbol, &
763 30544 : (matrix(iatom, icol), icol=from, to)
764 : END DO
765 : END DO
766 :
767 52 : DEALLOCATE (my_list)
768 :
769 52 : END SUBROUTINE write_particle_matrix
770 :
771 : ! **************************************************************************************************
772 : !> \brief Write structure data requested by a separate structure data input
773 : !> section to the output unit.
774 : !> input_section can be either motion_section or subsys_section.
775 : !>
776 : !> \param particle_set ...
777 : !> \param cell ...
778 : !> \param input_section ...
779 : !> \date 11.03.04
780 : !> \par History
781 : !> Recovered (23.03.06,MK)
782 : !> \author MK
783 : !> \version 1.0
784 : ! **************************************************************************************************
785 69297 : SUBROUTINE write_structure_data(particle_set, cell, input_section)
786 : TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
787 : TYPE(cell_type), POINTER :: cell
788 : TYPE(section_vals_type), POINTER :: input_section
789 :
790 : CHARACTER(LEN=*), PARAMETER :: routineN = 'write_structure_data'
791 :
792 : CHARACTER(LEN=default_string_length) :: string, unit_str
793 : INTEGER :: handle, i, i_rep, iw, n, n_rep, n_vals, &
794 : natom, new_size, old_size, wrk2(2), &
795 : wrk3(3), wrk4(4)
796 69297 : INTEGER, ALLOCATABLE, DIMENSION(:) :: work
797 69297 : INTEGER, DIMENSION(:), POINTER :: atomic_indices, index_list
798 : LOGICAL :: unique
799 : REAL(KIND=dp) :: conv, dab
800 : REAL(KIND=dp), DIMENSION(3) :: r, rab, rbc, rcd, s
801 : TYPE(cp_logger_type), POINTER :: logger
802 : TYPE(section_vals_type), POINTER :: section
803 :
804 69297 : CALL timeset(routineN, handle)
805 69297 : NULLIFY (atomic_indices)
806 69297 : NULLIFY (index_list)
807 69297 : NULLIFY (logger)
808 69297 : NULLIFY (section)
809 69297 : string = ""
810 :
811 69297 : logger => cp_get_default_logger()
812 : iw = cp_print_key_unit_nr(logger=logger, &
813 : basis_section=input_section, &
814 : print_key_path="PRINT%STRUCTURE_DATA", &
815 69297 : extension=".coordLog")
816 :
817 69297 : CALL section_vals_val_get(input_section, "PRINT%STRUCTURE_DATA%UNIT", c_val=unit_str)
818 69297 : conv = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
819 69297 : CALL uppercase(unit_str)
820 69297 : IF (iw > 0) THEN
821 553 : natom = SIZE(particle_set)
822 : section => section_vals_get_subs_vals(section_vals=input_section, &
823 553 : subsection_name="PRINT%STRUCTURE_DATA")
824 :
825 553 : WRITE (UNIT=iw, FMT="(/,T2,A)") "REQUESTED STRUCTURE DATA"
826 : ! Print the requested atomic position vectors
827 : CALL section_vals_val_get(section_vals=section, &
828 : keyword_name="POSITION", &
829 553 : n_rep_val=n_rep)
830 553 : IF (n_rep > 0) THEN
831 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
832 145 : "Position vectors r(i) of the atoms i in "//TRIM(unit_str)
833 145 : old_size = 0
834 848 : DO i_rep = 1, n_rep
835 : CALL section_vals_val_get(section_vals=section, &
836 : keyword_name="POSITION", &
837 : i_rep_val=i_rep, &
838 703 : i_vals=atomic_indices)
839 703 : n_vals = SIZE(atomic_indices)
840 703 : new_size = old_size + n_vals
841 703 : CALL reallocate(index_list, 1, new_size)
842 2903 : index_list(old_size + 1:new_size) = atomic_indices(1:n_vals)
843 848 : old_size = new_size
844 : END DO
845 435 : ALLOCATE (work(new_size))
846 145 : CALL sort(index_list, new_size, work)
847 145 : DEALLOCATE (work)
848 1245 : DO i = 1, new_size
849 1100 : WRITE (UNIT=string, FMT="(A,I0,A)") "(", index_list(i), ")"
850 1100 : IF ((index_list(i) < 1) .OR. (index_list(i) > natom)) THEN
851 : WRITE (UNIT=iw, FMT="(T3,A)") &
852 30 : "Invalid atomic index "//TRIM(string)//" specified. Print request is ignored."
853 30 : CYCLE
854 : END IF
855 1070 : IF (i > 1) THEN
856 : ! Skip redundant indices
857 935 : IF (index_list(i) == index_list(i - 1)) CYCLE
858 : END IF
859 : WRITE (UNIT=iw, FMT="(T3,A,T20,A,3F13.6)") &
860 4425 : "r"//TRIM(string), "=", pbc(particle_set(index_list(i))%r(1:3), cell)*conv
861 : END DO
862 145 : DEALLOCATE (index_list)
863 : END IF
864 :
865 : ! Print the requested atomic position vectors in scaled coordinates
866 : CALL section_vals_val_get(section_vals=section, &
867 : keyword_name="POSITION_SCALED", &
868 553 : n_rep_val=n_rep)
869 553 : IF (n_rep > 0) THEN
870 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
871 27 : "Position vectors s(i) of the atoms i in scaled coordinates"
872 27 : old_size = 0
873 84 : DO i_rep = 1, n_rep
874 : CALL section_vals_val_get(section_vals=section, &
875 : keyword_name="POSITION_SCALED", &
876 : i_rep_val=i_rep, &
877 57 : i_vals=atomic_indices)
878 57 : n_vals = SIZE(atomic_indices)
879 57 : new_size = old_size + n_vals
880 57 : CALL reallocate(index_list, 1, new_size)
881 965 : index_list(old_size + 1:new_size) = atomic_indices(1:n_vals)
882 84 : old_size = new_size
883 : END DO
884 81 : ALLOCATE (work(new_size))
885 27 : CALL sort(index_list, new_size, work)
886 27 : DEALLOCATE (work)
887 481 : DO i = 1, new_size
888 454 : WRITE (UNIT=string, FMT="(A,I0,A)") "(", index_list(i), ")"
889 454 : IF ((index_list(i) < 1) .OR. (index_list(i) > natom)) THEN
890 : WRITE (UNIT=iw, FMT="(T3,A)") &
891 30 : "Invalid atomic index "//TRIM(string)//" specified. Print request is ignored."
892 30 : CYCLE
893 : END IF
894 424 : IF (i > 1) THEN
895 : ! Skip redundant indices
896 407 : IF (index_list(i) == index_list(i - 1)) CYCLE
897 : END IF
898 424 : r(1:3) = pbc(particle_set(index_list(i))%r(1:3), cell)
899 424 : CALL real_to_scaled(s, r, cell)
900 : WRITE (UNIT=iw, FMT="(T3,A,T20,A,3F13.6)") &
901 451 : "s"//TRIM(string), "=", s(1:3)
902 : END DO
903 27 : DEALLOCATE (index_list)
904 : END IF
905 :
906 : ! Print the requested distances
907 : CALL section_vals_val_get(section_vals=section, &
908 : keyword_name="DISTANCE", &
909 553 : n_rep_val=n)
910 553 : IF (n > 0) THEN
911 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
912 : "Distance vector r(i,j) between the atom i and j in "// &
913 128 : TRIM(unit_str)
914 353 : DO i = 1, n
915 : CALL section_vals_val_get(section_vals=section, &
916 : keyword_name="DISTANCE", &
917 : i_rep_val=i, &
918 225 : i_vals=atomic_indices)
919 225 : string = ""
920 : WRITE (UNIT=string, FMT="(A,2(I0,A))") &
921 225 : "(", atomic_indices(1), ",", atomic_indices(2), ")"
922 675 : wrk2 = atomic_indices
923 225 : CALL sort_unique(wrk2, unique)
924 353 : IF (((wrk2(1) >= 1) .AND. (wrk2(SIZE(wrk2)) <= natom)) .AND. unique) THEN
925 : rab(:) = pbc(particle_set(atomic_indices(1))%r(:), &
926 225 : particle_set(atomic_indices(2))%r(:), cell)
927 225 : dab = SQRT(rab(1)*rab(1) + rab(2)*rab(2) + rab(3)*rab(3))
928 : WRITE (UNIT=iw, FMT="(T3,A,T20,A,3F13.6,3X,A,F13.6)") &
929 900 : "r"//TRIM(string), "=", rab(:)*conv, &
930 450 : "|r| =", dab*conv
931 : ELSE
932 : WRITE (UNIT=iw, FMT="(T3,A)") &
933 0 : "Invalid atomic indices "//TRIM(string)//" specified. Print request is ignored."
934 : END IF
935 : END DO
936 : END IF
937 :
938 : ! Print the requested angles
939 : CALL section_vals_val_get(section_vals=section, &
940 : keyword_name="ANGLE", &
941 553 : n_rep_val=n)
942 553 : IF (n > 0) THEN
943 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
944 : "Angle a(i,j,k) between the atomic distance vectors r(j,i) and "// &
945 67 : "r(j,k) in DEGREE"
946 139 : DO i = 1, n
947 : CALL section_vals_val_get(section_vals=section, &
948 : keyword_name="ANGLE", &
949 : i_rep_val=i, &
950 72 : i_vals=atomic_indices)
951 72 : string = ""
952 : WRITE (UNIT=string, FMT="(A,3(I0,A))") &
953 72 : "(", atomic_indices(1), ",", atomic_indices(2), ",", atomic_indices(3), ")"
954 288 : wrk3 = atomic_indices
955 72 : CALL sort_unique(wrk3, unique)
956 139 : IF (((wrk3(1) >= 1) .AND. (wrk3(SIZE(wrk3)) <= natom)) .AND. unique) THEN
957 : rab(:) = pbc(particle_set(atomic_indices(1))%r(:), &
958 67 : particle_set(atomic_indices(2))%r(:), cell)
959 : rbc(:) = pbc(particle_set(atomic_indices(2))%r(:), &
960 67 : particle_set(atomic_indices(3))%r(:), cell)
961 : WRITE (UNIT=iw, FMT="(T3,A,T26,A,F9.3)") &
962 268 : "a"//TRIM(string), "=", angle(-rab, rbc)*degree
963 : ELSE
964 : WRITE (UNIT=iw, FMT="(T3,A)") &
965 5 : "Invalid atomic indices "//TRIM(string)//" specified. Print request is ignored."
966 : END IF
967 : END DO
968 : END IF
969 :
970 : ! Print the requested dihedral angles
971 : CALL section_vals_val_get(section_vals=section, &
972 : keyword_name="DIHEDRAL_ANGLE", &
973 553 : n_rep_val=n)
974 553 : IF (n > 0) THEN
975 : WRITE (UNIT=iw, FMT="(/,T3,A,/)") &
976 : "Dihedral angle d(i,j,k,l) between the planes (i,j,k) and (j,k,l) "// &
977 5 : "in DEGREE"
978 15 : DO i = 1, n
979 : CALL section_vals_val_get(section_vals=section, &
980 : keyword_name="DIHEDRAL_ANGLE", &
981 : i_rep_val=i, &
982 10 : i_vals=atomic_indices)
983 10 : string = ""
984 : WRITE (UNIT=string, FMT="(A,4(I0,A))") &
985 10 : "(", atomic_indices(1), ",", atomic_indices(2), ",", &
986 20 : atomic_indices(3), ",", atomic_indices(4), ")"
987 50 : wrk4 = atomic_indices
988 10 : CALL sort_unique(wrk4, unique)
989 15 : IF (((wrk4(1) >= 1) .AND. (wrk4(SIZE(wrk4)) <= natom)) .AND. unique) THEN
990 : rab(:) = pbc(particle_set(atomic_indices(1))%r(:), &
991 0 : particle_set(atomic_indices(2))%r(:), cell)
992 : rbc(:) = pbc(particle_set(atomic_indices(2))%r(:), &
993 0 : particle_set(atomic_indices(3))%r(:), cell)
994 : rcd(:) = pbc(particle_set(atomic_indices(3))%r(:), &
995 0 : particle_set(atomic_indices(4))%r(:), cell)
996 : WRITE (UNIT=iw, FMT="(T3,A,T26,A,F9.3)") &
997 0 : "d"//TRIM(string), "=", dihedral_angle(rab, rbc, rcd)*degree
998 : ELSE
999 : WRITE (UNIT=iw, FMT="(T3,A)") &
1000 10 : "Invalid atomic indices "//TRIM(string)//" specified. Print request is ignored."
1001 : END IF
1002 : END DO
1003 : END IF
1004 : END IF
1005 : CALL cp_print_key_finished_output(iw, logger, input_section, &
1006 69297 : "PRINT%STRUCTURE_DATA")
1007 :
1008 69297 : CALL timestop(handle)
1009 :
1010 69297 : END SUBROUTINE write_structure_data
1011 :
1012 0 : END MODULE particle_methods
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