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 Handles all functions related to the CELL
10 : !> \par History
11 : !> 11.2008 Teodoro Laino [tlaino] - deeply cleaning cell_type from units
12 : !> 10.2014 Moved many routines to cell_types.F.
13 : !> \author Matthias KracK (16.01.2002, based on a earlier version of CJM, JGH)
14 : ! **************************************************************************************************
15 : MODULE cell_methods
16 : USE cell_types, ONLY: &
17 : cell_clone, cell_release, cell_sym_cubic, cell_sym_hexagonal_gamma_120, &
18 : cell_sym_hexagonal_gamma_60, cell_sym_monoclinic, cell_sym_monoclinic_gamma_ab, &
19 : cell_sym_none, cell_sym_orthorhombic, cell_sym_rhombohedral, cell_sym_tetragonal_ab, &
20 : cell_sym_tetragonal_ac, cell_sym_tetragonal_bc, cell_sym_triclinic, cell_type, get_cell, &
21 : plane_distance, use_perd_none, use_perd_x, use_perd_xy, use_perd_xyz, use_perd_xz, &
22 : use_perd_y, use_perd_yz, use_perd_z
23 : USE cp_log_handling, ONLY: cp_get_default_logger,&
24 : cp_logger_type
25 : USE cp_output_handling, ONLY: cp_print_key_finished_output,&
26 : cp_print_key_unit_nr
27 : USE cp_parser_methods, ONLY: parser_get_next_line,&
28 : parser_get_object,&
29 : parser_search_string
30 : USE cp_parser_types, ONLY: cp_parser_type,&
31 : parser_create,&
32 : parser_release
33 : USE cp_units, ONLY: cp_unit_from_cp2k,&
34 : cp_unit_to_cp2k
35 : USE input_constants, ONLY: &
36 : do_cell_cif, do_cell_cp2k, do_cell_extxyz, do_cell_pdb, do_cell_xsc, do_coord_cif, &
37 : do_coord_cp2k, do_coord_pdb, do_coord_xyz
38 : USE input_cp2k_subsys, ONLY: create_cell_section
39 : USE input_enumeration_types, ONLY: enum_i2c,&
40 : enumeration_type
41 : USE input_keyword_types, ONLY: keyword_get,&
42 : keyword_type
43 : USE input_section_types, ONLY: &
44 : section_get_keyword, section_release, section_type, section_vals_get, &
45 : section_vals_get_subs_vals, section_vals_type, section_vals_val_get, section_vals_val_set, &
46 : section_vals_val_unset
47 : USE kinds, ONLY: default_path_length,&
48 : default_string_length,&
49 : dp
50 : USE machine, ONLY: default_output_unit
51 : USE mathconstants, ONLY: degree,&
52 : sqrt3
53 : USE mathlib, ONLY: angle,&
54 : det_3x3,&
55 : inv_3x3
56 : USE message_passing, ONLY: mp_para_env_type
57 : USE string_utilities, ONLY: uppercase
58 : #include "./base/base_uses.f90"
59 :
60 : IMPLICIT NONE
61 :
62 : PRIVATE
63 :
64 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cell_methods'
65 :
66 : PUBLIC :: cell_create, &
67 : init_cell, &
68 : read_cell, &
69 : read_cell_cif, &
70 : read_cell_cp2k, &
71 : read_cell_extxyz, &
72 : read_cell_pdb, &
73 : read_cell_xsc, &
74 : set_cell_param, &
75 : write_cell, &
76 : write_cell_low
77 :
78 : CONTAINS
79 :
80 : ! **************************************************************************************************
81 : !> \brief allocates and initializes a cell
82 : !> \param cell the cell to initialize
83 : !> \param hmat the h matrix that defines the cell
84 : !> \param periodic periodicity of the cell
85 : !> \param tag ...
86 : !> \par History
87 : !> 09.2003 created [fawzi]
88 : !> \author Fawzi Mohamed
89 : ! **************************************************************************************************
90 82855 : SUBROUTINE cell_create(cell, hmat, periodic, tag)
91 :
92 : TYPE(cell_type), POINTER :: cell
93 : REAL(KIND=dp), DIMENSION(3, 3), INTENT(IN), &
94 : OPTIONAL :: hmat
95 : INTEGER, DIMENSION(3), INTENT(IN), OPTIONAL :: periodic
96 : CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: tag
97 :
98 0 : CPASSERT(.NOT. ASSOCIATED(cell))
99 2485650 : ALLOCATE (cell)
100 82855 : cell%ref_count = 1
101 82855 : IF (PRESENT(periodic)) THEN
102 1340 : cell%perd = periodic
103 : ELSE
104 330080 : cell%perd = 1
105 : END IF
106 : cell%orthorhombic = .FALSE.
107 : cell%symmetry_id = cell_sym_none
108 82855 : IF (PRESENT(hmat)) CALL init_cell(cell, hmat)
109 82855 : IF (PRESENT(tag)) cell%tag = tag
110 :
111 82855 : END SUBROUTINE cell_create
112 :
113 : ! **************************************************************************************************
114 : !> \brief Initialise/readjust a simulation cell after hmat has been changed
115 : !> \param cell ...
116 : !> \param hmat ...
117 : !> \param periodic ...
118 : !> \date 16.01.2002
119 : !> \author Matthias Krack
120 : !> \version 1.0
121 : ! **************************************************************************************************
122 346263 : SUBROUTINE init_cell(cell, hmat, periodic)
123 :
124 : TYPE(cell_type), POINTER :: cell
125 : REAL(KIND=dp), DIMENSION(3, 3), INTENT(IN), &
126 : OPTIONAL :: hmat
127 : INTEGER, DIMENSION(3), INTENT(IN), OPTIONAL :: periodic
128 :
129 : REAL(KIND=dp), PARAMETER :: eps_hmat = 1.0E-14_dp
130 :
131 : INTEGER :: dim
132 : REAL(KIND=dp) :: a, acosa, acosah, acosg, alpha, asina, &
133 : asinah, asing, beta, gamma, norm, &
134 : norm_c
135 : REAL(KIND=dp), DIMENSION(3) :: abc
136 :
137 346263 : CPASSERT(ASSOCIATED(cell))
138 :
139 450915 : IF (PRESENT(hmat)) cell%hmat(:, :) = hmat(:, :)
140 346347 : IF (PRESENT(periodic)) cell%perd(:) = periodic(:)
141 :
142 346263 : cell%deth = ABS(det_3x3(cell%hmat))
143 :
144 346263 : IF (cell%deth < 1.0E-10_dp) THEN
145 0 : CALL write_cell_low(cell, "angstrom", default_output_unit)
146 : CALL cp_abort(__LOCATION__, &
147 : "An invalid set of cell vectors was specified. "// &
148 0 : "The cell volume is too small")
149 : END IF
150 :
151 350329 : SELECT CASE (cell%symmetry_id)
152 : CASE (cell_sym_cubic, &
153 : cell_sym_tetragonal_ab, &
154 : cell_sym_tetragonal_ac, &
155 : cell_sym_tetragonal_bc, &
156 : cell_sym_orthorhombic)
157 4066 : CALL get_cell(cell=cell, abc=abc)
158 4066 : abc(2) = plane_distance(0, 1, 0, cell=cell)
159 4066 : abc(3) = plane_distance(0, 0, 1, cell=cell)
160 4066 : SELECT CASE (cell%symmetry_id)
161 : CASE (cell_sym_cubic)
162 5376 : abc(1:3) = SUM(abc(1:3))/3.0_dp
163 : CASE (cell_sym_tetragonal_ab, &
164 : cell_sym_tetragonal_ac, &
165 : cell_sym_tetragonal_bc)
166 4066 : SELECT CASE (cell%symmetry_id)
167 : CASE (cell_sym_tetragonal_ab)
168 1322 : a = 0.5_dp*(abc(1) + abc(2))
169 1322 : abc(1) = a
170 1322 : abc(2) = a
171 : CASE (cell_sym_tetragonal_ac)
172 633 : a = 0.5_dp*(abc(1) + abc(3))
173 633 : abc(1) = a
174 633 : abc(3) = a
175 : CASE (cell_sym_tetragonal_bc)
176 612 : a = 0.5_dp*(abc(2) + abc(3))
177 612 : abc(2) = a
178 2567 : abc(3) = a
179 : END SELECT
180 : END SELECT
181 4066 : cell%hmat(1, 1) = abc(1); cell%hmat(1, 2) = 0.0_dp; cell%hmat(1, 3) = 0.0_dp
182 4066 : cell%hmat(2, 1) = 0.0_dp; cell%hmat(2, 2) = abc(2); cell%hmat(2, 3) = 0.0_dp
183 4066 : cell%hmat(3, 1) = 0.0_dp; cell%hmat(3, 2) = 0.0_dp; cell%hmat(3, 3) = abc(3)
184 : CASE (cell_sym_hexagonal_gamma_60, cell_sym_hexagonal_gamma_120)
185 2638 : CALL get_cell(cell=cell, abc=abc)
186 2638 : a = 0.5_dp*(abc(1) + abc(2))
187 2638 : acosg = 0.5_dp*a
188 2638 : asing = sqrt3*acosg
189 2638 : IF (cell%symmetry_id == cell_sym_hexagonal_gamma_120) acosg = -acosg
190 2638 : cell%hmat(1, 1) = a; cell%hmat(1, 2) = acosg; cell%hmat(1, 3) = 0.0_dp
191 2638 : cell%hmat(2, 1) = 0.0_dp; cell%hmat(2, 2) = asing; cell%hmat(2, 3) = 0.0_dp
192 2638 : cell%hmat(3, 1) = 0.0_dp; cell%hmat(3, 2) = 0.0_dp; cell%hmat(3, 3) = abc(3)
193 : CASE (cell_sym_rhombohedral)
194 665 : CALL get_cell(cell=cell, abc=abc)
195 2660 : a = SUM(abc(1:3))/3.0_dp
196 : alpha = (angle(cell%hmat(:, 3), cell%hmat(:, 2)) + &
197 : angle(cell%hmat(:, 1), cell%hmat(:, 3)) + &
198 665 : angle(cell%hmat(:, 1), cell%hmat(:, 2)))/3.0_dp
199 665 : acosa = a*COS(alpha)
200 665 : asina = a*SIN(alpha)
201 665 : acosah = a*COS(0.5_dp*alpha)
202 665 : asinah = a*SIN(0.5_dp*alpha)
203 665 : norm = acosa/acosah
204 665 : norm_c = SQRT(1.0_dp - norm*norm)
205 665 : cell%hmat(1, 1) = a; cell%hmat(1, 2) = acosa; cell%hmat(1, 3) = acosah*norm
206 665 : cell%hmat(2, 1) = 0.0_dp; cell%hmat(2, 2) = asina; cell%hmat(2, 3) = asinah*norm
207 665 : cell%hmat(3, 1) = 0.0_dp; cell%hmat(3, 2) = 0.0_dp; cell%hmat(3, 3) = a*norm_c
208 : CASE (cell_sym_monoclinic)
209 873 : CALL get_cell(cell=cell, abc=abc)
210 873 : beta = angle(cell%hmat(:, 1), cell%hmat(:, 3))
211 873 : cell%hmat(1, 1) = abc(1); cell%hmat(1, 2) = 0.0_dp; cell%hmat(1, 3) = abc(3)*COS(beta)
212 873 : cell%hmat(2, 1) = 0.0_dp; cell%hmat(2, 2) = abc(2); cell%hmat(2, 3) = 0.0_dp
213 873 : cell%hmat(3, 1) = 0.0_dp; cell%hmat(3, 2) = 0.0_dp; cell%hmat(3, 3) = abc(3)*SIN(beta)
214 : CASE (cell_sym_monoclinic_gamma_ab)
215 : ! Cell symmetry with a = b, alpha = beta = 90 degree and gammma not equal 90 degree
216 742 : CALL get_cell(cell=cell, abc=abc)
217 742 : a = 0.5_dp*(abc(1) + abc(2))
218 742 : gamma = angle(cell%hmat(:, 1), cell%hmat(:, 2))
219 742 : acosg = a*COS(gamma)
220 742 : asing = a*SIN(gamma)
221 742 : cell%hmat(1, 1) = a; cell%hmat(1, 2) = acosg; cell%hmat(1, 3) = 0.0_dp
222 742 : cell%hmat(2, 1) = 0.0_dp; cell%hmat(2, 2) = asing; cell%hmat(2, 3) = 0.0_dp
223 347005 : cell%hmat(3, 1) = 0.0_dp; cell%hmat(3, 2) = 0.0_dp; cell%hmat(3, 3) = abc(3)
224 : CASE (cell_sym_triclinic)
225 : ! Nothing to do
226 : END SELECT
227 :
228 : ! Do we have an (almost) orthorhombic cell?
229 : IF ((ABS(cell%hmat(1, 2)) < eps_hmat) .AND. (ABS(cell%hmat(1, 3)) < eps_hmat) .AND. &
230 : (ABS(cell%hmat(2, 1)) < eps_hmat) .AND. (ABS(cell%hmat(2, 3)) < eps_hmat) .AND. &
231 346263 : (ABS(cell%hmat(3, 1)) < eps_hmat) .AND. (ABS(cell%hmat(3, 2)) < eps_hmat)) THEN
232 320624 : cell%orthorhombic = .TRUE.
233 : ELSE
234 25639 : cell%orthorhombic = .FALSE.
235 : END IF
236 :
237 : ! Retain an exact orthorhombic cell
238 : ! (off-diagonal elements must remain zero identically to keep QS fast)
239 346263 : IF (cell%orthorhombic) THEN
240 320624 : cell%hmat(1, 2) = 0.0_dp
241 320624 : cell%hmat(1, 3) = 0.0_dp
242 320624 : cell%hmat(2, 1) = 0.0_dp
243 320624 : cell%hmat(2, 3) = 0.0_dp
244 320624 : cell%hmat(3, 1) = 0.0_dp
245 320624 : cell%hmat(3, 2) = 0.0_dp
246 : END IF
247 :
248 1385052 : dim = COUNT(cell%perd == 1)
249 346263 : IF ((dim == 1) .AND. (.NOT. cell%orthorhombic)) THEN
250 0 : CPABORT("Non-orthorhombic and not periodic")
251 : END IF
252 :
253 : ! Update deth and hmat_inv with enforced symmetry
254 346263 : cell%deth = ABS(det_3x3(cell%hmat))
255 346263 : IF (cell%deth < 1.0E-10_dp) THEN
256 : CALL cp_abort(__LOCATION__, &
257 : "An invalid set of cell vectors was obtained after applying "// &
258 0 : "the requested cell symmetry. The cell volume is too small")
259 : END IF
260 4501419 : cell%h_inv = inv_3x3(cell%hmat)
261 :
262 346263 : END SUBROUTINE init_cell
263 :
264 : ! **************************************************************************************************
265 : !> \brief ...
266 : !> \param cell ...
267 : !> \param cell_ref ...
268 : !> \param use_ref_cell ...
269 : !> \param cell_section ...
270 : !> \param topology_section ...
271 : !> \param check_for_ref ...
272 : !> \param para_env ...
273 : !> \par History
274 : !> 03.2005 created [teo]
275 : !> 03.2026 revamped logic with pdb and extxyz parsers
276 : !> \author Teodoro Laino
277 : ! **************************************************************************************************
278 185373 : RECURSIVE SUBROUTINE read_cell(cell, cell_ref, use_ref_cell, cell_section, &
279 : topology_section, check_for_ref, para_env)
280 :
281 : TYPE(cell_type), POINTER :: cell, cell_ref
282 : LOGICAL, INTENT(INOUT), OPTIONAL :: use_ref_cell
283 : TYPE(section_vals_type), OPTIONAL, POINTER :: cell_section, topology_section
284 : LOGICAL, INTENT(IN), OPTIONAL :: check_for_ref
285 : TYPE(mp_para_env_type), POINTER :: para_env
286 :
287 : REAL(KIND=dp), PARAMETER :: eps = EPSILON(0.0_dp)
288 :
289 : CHARACTER(LEN=default_path_length) :: cell_file_name, coord_file_name
290 : INTEGER :: cell_file_format, coord_file_format, &
291 : my_per
292 20597 : INTEGER, DIMENSION(:), POINTER :: multiple_unit_cell
293 : LOGICAL :: cell_read_a, cell_read_abc, cell_read_alpha_beta_gamma, cell_read_b, cell_read_c, &
294 : cell_read_file, my_check_ref, tmp_comb_abc, tmp_comb_cell, tmp_comb_top, topo_read_coord
295 : REAL(KIND=dp), DIMENSION(3) :: read_ang, read_len
296 : REAL(KIND=dp), DIMENSION(3, 3) :: read_mat
297 20597 : REAL(KIND=dp), DIMENSION(:), POINTER :: cell_par
298 : TYPE(cell_type), POINTER :: cell_tmp
299 : TYPE(section_vals_type), POINTER :: cell_ref_section
300 :
301 20597 : my_check_ref = .TRUE.
302 20597 : NULLIFY (cell_ref_section, cell_par, cell_tmp, multiple_unit_cell)
303 : ! cell_tmp is only for transferring matrix of cell vectors from
304 : ! individual file parser subroutines to read_mat here, assuming
305 : ! that unit conversion has been done in those subroutines.
306 20597 : CALL cell_create(cell_tmp)
307 20597 : IF (.NOT. ASSOCIATED(cell)) CALL cell_create(cell, tag="CELL")
308 20597 : IF (.NOT. ASSOCIATED(cell_ref)) CALL cell_create(cell_ref, tag="CELL_REF")
309 20597 : IF (PRESENT(check_for_ref)) my_check_ref = check_for_ref
310 :
311 20597 : cell%deth = 0.0_dp
312 20597 : cell%orthorhombic = .FALSE.
313 82388 : cell%perd(:) = 1
314 20597 : cell%symmetry_id = cell_sym_none
315 267761 : cell%hmat(:, :) = 0.0_dp
316 267761 : cell%h_inv(:, :) = 0.0_dp
317 : cell_read_file = .FALSE.
318 : cell_read_a = .FALSE.
319 : cell_read_b = .FALSE.
320 : cell_read_c = .FALSE.
321 : cell_read_abc = .FALSE.
322 : cell_read_alpha_beta_gamma = .FALSE.
323 20597 : read_mat(:, :) = 0.0_dp
324 20597 : read_ang(:) = 0.0_dp
325 20597 : read_len(:) = 0.0_dp
326 :
327 : ! Precedence of retrieving cell information from input:
328 : ! 1. CELL/CELL_FILE_NAME
329 : ! 2. CELL/ABC and optionally CELL/ALPHA_BETA_GAMMA
330 : ! 3. CELL/A, CELL/B, CELL/C
331 : ! 4. TOPOLOGY/COORD_FILE_NAME, if topology_section is present
332 : ! The actual order of processing is 4 -> 1 -> 2 -> 3, with
333 : ! case 4 merged to case 1 (if file format permits) first.
334 : ! Store data into either read_mat or read_ang and read_len
335 : ! in CP2K units, which will be converted to cell%hmat and A, B, C.
336 20597 : CALL section_vals_val_get(cell_section, "A", explicit=cell_read_a)
337 20597 : CALL section_vals_val_get(cell_section, "B", explicit=cell_read_b)
338 20597 : CALL section_vals_val_get(cell_section, "C", explicit=cell_read_c)
339 20597 : CALL section_vals_val_get(cell_section, "ABC", explicit=cell_read_abc)
340 20597 : CALL section_vals_val_get(cell_section, "ALPHA_BETA_GAMMA", explicit=cell_read_alpha_beta_gamma)
341 20597 : CALL section_vals_val_get(cell_section, "CELL_FILE_NAME", explicit=cell_read_file)
342 :
343 : ! Case 4
344 20597 : tmp_comb_top = (.NOT. (cell_read_file .OR. cell_read_abc))
345 11691 : tmp_comb_top = (tmp_comb_top .AND. (.NOT. cell_read_a))
346 0 : tmp_comb_top = (tmp_comb_top .AND. (.NOT. cell_read_b))
347 0 : tmp_comb_top = (tmp_comb_top .AND. (.NOT. cell_read_c))
348 : IF (tmp_comb_top) THEN
349 : CALL cp_warn(__LOCATION__, &
350 : "None of the keywords CELL_FILE_NAME, ABC, or A, B, C "// &
351 : "are specified in CELL section. CP2K will now attempt to read "// &
352 : "TOPOLOGY/COORD_FILE_NAME if its format can be parsed for "// &
353 0 : "cell information.")
354 0 : IF (ASSOCIATED(topology_section)) THEN
355 0 : CALL section_vals_val_get(topology_section, "COORD_FILE_NAME", explicit=topo_read_coord)
356 0 : IF (topo_read_coord) THEN
357 0 : CALL section_vals_val_get(topology_section, "COORD_FILE_NAME", c_val=coord_file_name)
358 0 : CALL section_vals_val_get(topology_section, "COORD_FILE_FORMAT", i_val=coord_file_format)
359 0 : SELECT CASE (coord_file_format) ! Add formats with both cell and coord parser manually
360 : CASE (do_coord_cif)
361 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_NAME", c_val=coord_file_name)
362 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_FORMAT", i_val=do_cell_cif)
363 : CASE (do_coord_cp2k)
364 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_NAME", c_val=coord_file_name)
365 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_FORMAT", i_val=do_cell_cp2k)
366 : CASE (do_coord_pdb)
367 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_NAME", c_val=coord_file_name)
368 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_FORMAT", i_val=do_cell_pdb)
369 : CASE (do_coord_xyz)
370 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_NAME", c_val=coord_file_name)
371 0 : CALL section_vals_val_set(cell_section, "CELL_FILE_FORMAT", i_val=do_cell_extxyz)
372 : CASE DEFAULT
373 : CALL cp_abort(__LOCATION__, &
374 : "COORD_FILE_FORMAT is not set to one of the implemented "// &
375 0 : "CELL_FILE_FORMAT options and cannot be parsed for cell information!")
376 : END SELECT
377 : ELSE
378 : CALL cp_abort(__LOCATION__, &
379 0 : "COORD_FILE_NAME is not set, so no cell information is available!")
380 : END IF
381 : ELSE
382 : CALL cp_warn(__LOCATION__, &
383 : "TOPOLOGY section is not available, so COORD_FILE_NAME cannot "// &
384 0 : "be parsed for cell information in lieu of missing CELL settings.")
385 : END IF
386 : END IF
387 : ! Former logic in SUBROUTINE read_cell_from_external_file is moved here
388 20597 : CALL section_vals_val_get(cell_section, "CELL_FILE_NAME", explicit=cell_read_file)
389 20597 : IF (cell_read_file) THEN ! Case 1
390 16 : tmp_comb_cell = (cell_read_abc .OR. (cell_read_a .OR. (cell_read_b .OR. cell_read_c)))
391 : IF (tmp_comb_cell) &
392 : CALL cp_warn(__LOCATION__, &
393 : "Cell Information provided through A, B, C, or ABC in conjunction "// &
394 : "with CELL_FILE_NAME. The definition in external file will override "// &
395 0 : "other ones.")
396 16 : CALL section_vals_val_get(cell_section, "CELL_FILE_NAME", c_val=cell_file_name)
397 16 : CALL section_vals_val_get(cell_section, "CELL_FILE_FORMAT", i_val=cell_file_format)
398 2 : SELECT CASE (cell_file_format)
399 : CASE (do_cell_cp2k)
400 2 : CALL read_cell_cp2k(cell_file_name, cell_tmp, para_env)
401 : CASE (do_cell_xsc)
402 0 : CALL read_cell_xsc(cell_file_name, cell_tmp, para_env)
403 : CASE (do_cell_extxyz)
404 2 : CALL read_cell_extxyz(cell_file_name, cell_tmp, para_env)
405 : CASE (do_cell_pdb)
406 2 : CALL read_cell_pdb(cell_file_name, cell_tmp, para_env)
407 : CASE (do_cell_cif)
408 10 : CALL read_cell_cif(cell_file_name, cell_tmp, para_env)
409 : CASE DEFAULT
410 : CALL cp_abort(__LOCATION__, &
411 : "CELL_FILE_FORMAT is not set to one of the implemented "// &
412 16 : "options and cannot be parsed for cell information!")
413 : END SELECT
414 208 : read_mat = cell_tmp%hmat
415 : ELSE
416 20581 : IF (cell_read_abc) THEN ! Case 2
417 8890 : CALL section_vals_val_get(cell_section, "ABC", r_vals=cell_par)
418 35560 : read_len = cell_par
419 8890 : CALL section_vals_val_get(cell_section, "ALPHA_BETA_GAMMA", r_vals=cell_par)
420 35560 : read_ang = cell_par
421 8890 : IF (cell_read_a .OR. cell_read_b .OR. cell_read_c) &
422 : CALL cp_warn(__LOCATION__, &
423 : "Cell information provided through vectors A, B or C in conjunction with ABC. "// &
424 0 : "The definition of the ABC keyword will override the one provided by A, B and C.")
425 : ELSE ! Case 3
426 11691 : tmp_comb_abc = ((cell_read_a .EQV. cell_read_b) .AND. (cell_read_b .EQV. cell_read_c))
427 : IF (tmp_comb_abc) THEN
428 11691 : CALL section_vals_val_get(cell_section, "A", r_vals=cell_par)
429 46764 : read_mat(:, 1) = cell_par(:)
430 11691 : CALL section_vals_val_get(cell_section, "B", r_vals=cell_par)
431 46764 : read_mat(:, 2) = cell_par(:)
432 11691 : CALL section_vals_val_get(cell_section, "C", r_vals=cell_par)
433 46764 : read_mat(:, 3) = cell_par(:)
434 11691 : IF (cell_read_alpha_beta_gamma) &
435 : CALL cp_warn(__LOCATION__, &
436 : "The keyword ALPHA_BETA_GAMMA is ignored because it was used without the "// &
437 0 : "keyword ABC.")
438 : ELSE
439 : CALL cp_abort(__LOCATION__, &
440 : "Neither of the keywords CELL_FILE_NAME or ABC are specified, "// &
441 0 : "and cell vector settings in A, B, C are incomplete!")
442 : END IF
443 : END IF
444 : END IF
445 20597 : CALL cell_release(cell_tmp)
446 :
447 : ! Convert read_mat or read_len and read_ang to actual cell%hmat
448 127525 : IF (ANY(read_mat(:, :) > eps)) THEN
449 : ! Make a warning before storing cell vectors that
450 : ! do not form a triangular matrix.
451 : IF ((ABS(read_mat(2, 1)) > eps) .OR. &
452 11707 : (ABS(read_mat(3, 1)) > eps) .OR. &
453 : (ABS(read_mat(3, 2)) > eps)) &
454 : CALL cp_warn(__LOCATION__, &
455 : "Cell vectors are read but cell matrix is not "// &
456 : "a lower triangle, not conforming to the program "// &
457 : "convention that A lies along the X-axis and "// &
458 868 : "B is in the XY plane.")
459 152191 : cell%hmat = read_mat
460 : ELSE
461 17780 : IF (ANY(read_ang(:) > eps) .AND. ANY(read_len(:) > eps)) THEN
462 : CALL set_cell_param(cell, cell_length=read_len, cell_angle=read_ang, &
463 8890 : do_init_cell=.FALSE.)
464 : ELSE
465 : CALL cp_abort(__LOCATION__, &
466 0 : "No meaningful cell information is read from parser!")
467 : END IF
468 : END IF
469 : ! Reset cell section so that only A, B, C are kept
470 20597 : CALL reset_cell_section_by_cell_mat(cell, cell_section)
471 :
472 : ! Multiple unit cell
473 20597 : CALL section_vals_val_get(cell_section, "MULTIPLE_UNIT_CELL", i_vals=multiple_unit_cell)
474 81508 : IF (ANY(multiple_unit_cell /= 1)) CALL set_multiple_unit_cell(cell, multiple_unit_cell)
475 :
476 20597 : CALL section_vals_val_get(cell_section, "PERIODIC", i_val=my_per)
477 0 : SELECT CASE (my_per)
478 : CASE (use_perd_x)
479 0 : cell%perd = [1, 0, 0]
480 : CASE (use_perd_y)
481 0 : cell%perd = [0, 1, 0]
482 : CASE (use_perd_z)
483 32 : cell%perd = [0, 0, 1]
484 : CASE (use_perd_xy)
485 112 : cell%perd = [1, 1, 0]
486 : CASE (use_perd_xz)
487 48 : cell%perd = [1, 0, 1]
488 : CASE (use_perd_yz)
489 192 : cell%perd = [0, 1, 1]
490 : CASE (use_perd_xyz)
491 52972 : cell%perd = [1, 1, 1]
492 : CASE (use_perd_none)
493 29032 : cell%perd = [0, 0, 0]
494 : CASE DEFAULT
495 20597 : CPABORT("")
496 : END SELECT
497 :
498 : ! Load requested cell symmetry
499 20597 : CALL section_vals_val_get(cell_section, "SYMMETRY", i_val=cell%symmetry_id)
500 :
501 : ! Initialize cell
502 20597 : CALL init_cell(cell)
503 :
504 20597 : IF (my_check_ref) THEN
505 : ! Recursive check for reference cell requested
506 20151 : cell_ref_section => section_vals_get_subs_vals(cell_section, "CELL_REF")
507 20151 : IF (parsed_cp2k_input(cell_ref_section, check_this_section=.TRUE.)) THEN
508 52 : IF (PRESENT(use_ref_cell)) use_ref_cell = .TRUE.
509 : CALL read_cell(cell_ref, cell_ref, use_ref_cell=use_ref_cell, &
510 : cell_section=cell_ref_section, check_for_ref=.FALSE., &
511 52 : para_env=para_env)
512 : ELSE
513 20099 : CALL cell_clone(cell, cell_ref, tag="CELL_REF")
514 20099 : IF (PRESENT(use_ref_cell)) use_ref_cell = .FALSE.
515 : END IF
516 : END IF
517 :
518 20597 : END SUBROUTINE read_cell
519 :
520 : ! **************************************************************************************************
521 : !> \brief utility function to ease the transition to the new input.
522 : !> returns true if the new input was parsed
523 : !> \param input_file the parsed input file
524 : !> \param check_this_section ...
525 : !> \return ...
526 : !> \author fawzi
527 : ! **************************************************************************************************
528 20151 : FUNCTION parsed_cp2k_input(input_file, check_this_section) RESULT(res)
529 :
530 : TYPE(section_vals_type), POINTER :: input_file
531 : LOGICAL, INTENT(IN), OPTIONAL :: check_this_section
532 : LOGICAL :: res
533 :
534 : LOGICAL :: my_check
535 : TYPE(section_vals_type), POINTER :: glob_section
536 :
537 20151 : my_check = .FALSE.
538 20151 : IF (PRESENT(check_this_section)) my_check = check_this_section
539 20151 : res = ASSOCIATED(input_file)
540 20151 : IF (res) THEN
541 20151 : CPASSERT(input_file%ref_count > 0)
542 20151 : IF (.NOT. my_check) THEN
543 0 : glob_section => section_vals_get_subs_vals(input_file, "GLOBAL")
544 0 : CALL section_vals_get(glob_section, explicit=res)
545 : ELSE
546 20151 : CALL section_vals_get(input_file, explicit=res)
547 : END IF
548 : END IF
549 :
550 20151 : END FUNCTION parsed_cp2k_input
551 :
552 : ! **************************************************************************************************
553 : !> \brief Sets the cell using the internal parameters (a,b,c) (alpha,beta,gamma)
554 : !> using the convention: a parallel to the x axis, b in the x-y plane and
555 : !> and c univoquely determined; gamma is the angle between a and b; beta
556 : !> is the angle between c and a and alpha is the angle between c and b
557 : !> \param cell ...
558 : !> \param cell_length ...
559 : !> \param cell_angle ...
560 : !> \param periodic ...
561 : !> \param do_init_cell ...
562 : !> \date 03.2008
563 : !> \author Teodoro Laino
564 : ! **************************************************************************************************
565 8918 : SUBROUTINE set_cell_param(cell, cell_length, cell_angle, periodic, do_init_cell)
566 :
567 : TYPE(cell_type), POINTER :: cell
568 : REAL(KIND=dp), DIMENSION(3), INTENT(IN) :: cell_length, cell_angle
569 : INTEGER, DIMENSION(3), INTENT(IN), OPTIONAL :: periodic
570 : LOGICAL, INTENT(IN) :: do_init_cell
571 :
572 : REAL(KIND=dp), PARAMETER :: eps = EPSILON(0.0_dp)
573 :
574 : REAL(KIND=dp) :: cos_alpha, cos_beta, cos_gamma, sin_gamma
575 :
576 8918 : CPASSERT(ASSOCIATED(cell))
577 35672 : CPASSERT(ALL(cell_angle /= 0.0_dp))
578 :
579 8918 : cos_gamma = COS(cell_angle(3)); IF (ABS(cos_gamma) < eps) cos_gamma = 0.0_dp
580 8918 : IF (ABS(ABS(cos_gamma) - 1.0_dp) < eps) cos_gamma = SIGN(1.0_dp, cos_gamma)
581 8918 : sin_gamma = SIN(cell_angle(3)); IF (ABS(sin_gamma) < eps) sin_gamma = 0.0_dp
582 8918 : IF (ABS(ABS(sin_gamma) - 1.0_dp) < eps) sin_gamma = SIGN(1.0_dp, sin_gamma)
583 8918 : cos_beta = COS(cell_angle(2)); IF (ABS(cos_beta) < eps) cos_beta = 0.0_dp
584 8918 : IF (ABS(ABS(cos_beta) - 1.0_dp) < eps) cos_beta = SIGN(1.0_dp, cos_beta)
585 8918 : cos_alpha = COS(cell_angle(1)); IF (ABS(cos_alpha) < eps) cos_alpha = 0.0_dp
586 8918 : IF (ABS(ABS(cos_alpha) - 1.0_dp) < eps) cos_alpha = SIGN(1.0_dp, cos_alpha)
587 :
588 35672 : cell%hmat(:, 1) = [1.0_dp, 0.0_dp, 0.0_dp]
589 35672 : cell%hmat(:, 2) = [cos_gamma, sin_gamma, 0.0_dp]
590 35672 : cell%hmat(:, 3) = [cos_beta, (cos_alpha - cos_gamma*cos_beta)/sin_gamma, 0.0_dp]
591 8918 : cell%hmat(3, 3) = SQRT(1.0_dp - cell%hmat(1, 3)**2 - cell%hmat(2, 3)**2)
592 :
593 35672 : cell%hmat(:, 1) = cell%hmat(:, 1)*cell_length(1)
594 35672 : cell%hmat(:, 2) = cell%hmat(:, 2)*cell_length(2)
595 35672 : cell%hmat(:, 3) = cell%hmat(:, 3)*cell_length(3)
596 :
597 8918 : IF (do_init_cell) THEN
598 28 : IF (PRESENT(periodic)) THEN
599 28 : CALL init_cell(cell=cell, periodic=periodic)
600 : ELSE
601 0 : CALL init_cell(cell=cell)
602 : END IF
603 : END IF
604 :
605 8918 : END SUBROUTINE set_cell_param
606 :
607 : ! **************************************************************************************************
608 : !> \brief Setup of the multiple unit_cell
609 : !> \param cell ...
610 : !> \param multiple_unit_cell ...
611 : !> \date 05.2009
612 : !> \author Teodoro Laino [tlaino]
613 : !> \version 1.0
614 : ! **************************************************************************************************
615 300 : SUBROUTINE set_multiple_unit_cell(cell, multiple_unit_cell)
616 :
617 : TYPE(cell_type), POINTER :: cell
618 : INTEGER, DIMENSION(:), POINTER :: multiple_unit_cell
619 :
620 300 : CPASSERT(ASSOCIATED(cell))
621 :
622 : ! Abort, if one of the value is set to zero
623 1200 : IF (ANY(multiple_unit_cell <= 0)) &
624 : CALL cp_abort(__LOCATION__, &
625 : "CELL%MULTIPLE_UNIT_CELL accepts only integer values larger than 0! "// &
626 0 : "A value of 0 or negative is meaningless!")
627 :
628 : ! Scale abc according to user request
629 1200 : cell%hmat(:, 1) = cell%hmat(:, 1)*multiple_unit_cell(1)
630 1200 : cell%hmat(:, 2) = cell%hmat(:, 2)*multiple_unit_cell(2)
631 1200 : cell%hmat(:, 3) = cell%hmat(:, 3)*multiple_unit_cell(3)
632 :
633 300 : END SUBROUTINE set_multiple_unit_cell
634 :
635 : ! **************************************************************************************************
636 : !> \brief Reads cell information from CIF file
637 : !> \param cif_file_name ...
638 : !> \param cell ...
639 : !> \param para_env ...
640 : !> \date 12.2008
641 : !> \par Format Information implemented:
642 : !> _cell_length_a
643 : !> _cell_length_b
644 : !> _cell_length_c
645 : !> _cell_angle_alpha
646 : !> _cell_angle_beta
647 : !> _cell_angle_gamma
648 : !>
649 : !> \author Teodoro Laino [tlaino]
650 : !> moved from topology_cif (1/2019 JHU)
651 : ! **************************************************************************************************
652 48 : SUBROUTINE read_cell_cif(cif_file_name, cell, para_env)
653 :
654 : CHARACTER(len=*) :: cif_file_name
655 : TYPE(cell_type), POINTER :: cell
656 : TYPE(mp_para_env_type), POINTER :: para_env
657 :
658 : CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_cif'
659 :
660 : INTEGER :: handle
661 : INTEGER, DIMENSION(3) :: periodic
662 : LOGICAL :: found
663 : REAL(KIND=dp), DIMENSION(3) :: cell_angles, cell_lengths
664 : TYPE(cp_parser_type) :: parser
665 :
666 24 : CALL timeset(routineN, handle)
667 :
668 : CALL parser_create(parser, cif_file_name, &
669 24 : para_env=para_env, apply_preprocessing=.FALSE.)
670 :
671 : ! Parsing cell infos
672 96 : periodic = 1
673 : ! Check for _cell_length_a
674 : CALL parser_search_string(parser, "_cell_length_a", ignore_case=.FALSE., found=found, &
675 24 : begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
676 24 : IF (.NOT. found) &
677 0 : CPABORT("The field (_cell_length_a) was not found in CIF file! ")
678 24 : CALL cif_get_real(parser, cell_lengths(1))
679 24 : cell_lengths(1) = cp_unit_to_cp2k(cell_lengths(1), "angstrom")
680 :
681 : ! Check for _cell_length_b
682 : CALL parser_search_string(parser, "_cell_length_b", ignore_case=.FALSE., found=found, &
683 24 : begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
684 24 : IF (.NOT. found) &
685 0 : CPABORT("The field (_cell_length_b) was not found in CIF file! ")
686 24 : CALL cif_get_real(parser, cell_lengths(2))
687 24 : cell_lengths(2) = cp_unit_to_cp2k(cell_lengths(2), "angstrom")
688 :
689 : ! Check for _cell_length_c
690 : CALL parser_search_string(parser, "_cell_length_c", ignore_case=.FALSE., found=found, &
691 24 : begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
692 24 : IF (.NOT. found) &
693 0 : CPABORT("The field (_cell_length_c) was not found in CIF file! ")
694 24 : CALL cif_get_real(parser, cell_lengths(3))
695 24 : cell_lengths(3) = cp_unit_to_cp2k(cell_lengths(3), "angstrom")
696 :
697 : ! Check for _cell_angle_alpha
698 : CALL parser_search_string(parser, "_cell_angle_alpha", ignore_case=.FALSE., found=found, &
699 24 : begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
700 24 : IF (.NOT. found) &
701 0 : CPABORT("The field (_cell_angle_alpha) was not found in CIF file! ")
702 24 : CALL cif_get_real(parser, cell_angles(1))
703 24 : cell_angles(1) = cp_unit_to_cp2k(cell_angles(1), "deg")
704 :
705 : ! Check for _cell_angle_beta
706 : CALL parser_search_string(parser, "_cell_angle_beta", ignore_case=.FALSE., found=found, &
707 24 : begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
708 24 : IF (.NOT. found) &
709 0 : CPABORT("The field (_cell_angle_beta) was not found in CIF file! ")
710 24 : CALL cif_get_real(parser, cell_angles(2))
711 24 : cell_angles(2) = cp_unit_to_cp2k(cell_angles(2), "deg")
712 :
713 : ! Check for _cell_angle_gamma
714 : CALL parser_search_string(parser, "_cell_angle_gamma", ignore_case=.FALSE., found=found, &
715 24 : begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
716 24 : IF (.NOT. found) &
717 0 : CPABORT("The field (_cell_angle_gamma) was not found in CIF file! ")
718 24 : CALL cif_get_real(parser, cell_angles(3))
719 24 : cell_angles(3) = cp_unit_to_cp2k(cell_angles(3), "deg")
720 :
721 : ! Create cell
722 : CALL set_cell_param(cell, cell_lengths, cell_angles, periodic=periodic, &
723 24 : do_init_cell=.TRUE.)
724 :
725 24 : CALL parser_release(parser)
726 :
727 24 : CALL timestop(handle)
728 :
729 72 : END SUBROUTINE read_cell_cif
730 :
731 : ! **************************************************************************************************
732 : !> \brief Reads REAL from the CIF file.. This wrapper is needed in order to
733 : !> treat properly the accuracy specified in the CIF file, i.e. 3.45(6)
734 : !> \param parser ...
735 : !> \param r ...
736 : !> \date 12.2008
737 : !> \author Teodoro Laino [tlaino]
738 : ! **************************************************************************************************
739 144 : SUBROUTINE cif_get_real(parser, r)
740 :
741 : TYPE(cp_parser_type), INTENT(INOUT) :: parser
742 : REAL(KIND=dp), INTENT(OUT) :: r
743 :
744 : CHARACTER(LEN=default_string_length) :: s_tag
745 : INTEGER :: iln
746 :
747 144 : CALL parser_get_object(parser, s_tag)
748 144 : iln = LEN_TRIM(s_tag)
749 144 : IF (INDEX(s_tag, "(") /= 0) iln = INDEX(s_tag, "(") - 1
750 144 : READ (s_tag(1:iln), *) r
751 :
752 144 : END SUBROUTINE cif_get_real
753 :
754 : ! **************************************************************************************************
755 : !> \brief Reads cell information from comment line of extended xyz file
756 : !> \param extxyz_file_name ...
757 : !> \param cell ...
758 : !> \param para_env ...
759 : !> \date 03.2026
760 : !> \par Extended xyz format has comment on the second line in the form as
761 : !> Lattice="Ax Ay Az Bx By Bz Cx Cy Cz"
762 : !> where Ax, Ay, Az are three Cartesian components of cell vector A,
763 : !> Bx, By, Bz are components of B, Cx, Cy, Cz are components of C,
764 : !> all in the unit of angstrom.
765 : ! **************************************************************************************************
766 4 : SUBROUTINE read_cell_extxyz(extxyz_file_name, cell, para_env)
767 :
768 : CHARACTER(len=*) :: extxyz_file_name
769 : TYPE(cell_type), POINTER :: cell
770 : TYPE(mp_para_env_type), POINTER :: para_env
771 :
772 : CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_extxyz'
773 :
774 : INTEGER :: handle, i, id1, id2, j
775 : REAL(KIND=dp), DIMENSION(3, 3) :: hmat
776 : TYPE(cp_parser_type) :: parser
777 :
778 2 : CALL timeset(routineN, handle)
779 :
780 : CALL parser_create(parser, extxyz_file_name, &
781 2 : para_env=para_env, apply_preprocessing=.FALSE.)
782 2 : CALL parser_get_next_line(parser, 2)
783 2 : CALL uppercase(parser%input_line)
784 2 : id1 = INDEX(parser%input_line, "LATTICE=")
785 2 : IF (id1 > 0) THEN
786 2 : id2 = INDEX(parser%input_line(id1 + 9:), '"')
787 2 : READ (parser%input_line(id1 + 9:id1 + id2 + 7), *) hmat(:, 1), hmat(:, 2), hmat(:, 3)
788 8 : DO i = 1, 3
789 26 : DO j = 1, 3
790 24 : cell%hmat(j, i) = cp_unit_to_cp2k(hmat(j, i), "angstrom")
791 : END DO
792 : END DO
793 :
794 : ELSE
795 : CALL cp_abort(__LOCATION__, &
796 : "The field (lattice=) was not found on comment line "// &
797 : "of XYZ file, so cell information cannot be set via "// &
798 0 : "extended XYZ specification! ")
799 : END IF
800 :
801 2 : CALL parser_release(parser)
802 :
803 2 : CALL timestop(handle)
804 :
805 6 : END SUBROUTINE read_cell_extxyz
806 :
807 : ! **************************************************************************************************
808 : !> \brief Reads cell information from CRYST1 record of PDB file
809 : !> \param pdb_file_name ...
810 : !> \param cell ...
811 : !> \param para_env ...
812 : !> \date 03.2026
813 : !> \par CRYST1 record may contain space group and Z value at the end,
814 : !> but here only the first entries are read:
815 : !> COLUMNS DATA TYPE FIELD DEFINITION
816 : !> -------------------------------------------------------------
817 : !> 1 - 6 Record name "CRYST1"
818 : !> 7 - 15 Real(9.3) a a (Angstroms).
819 : !> 16 - 24 Real(9.3) b b (Angstroms).
820 : !> 25 - 33 Real(9.3) c c (Angstroms).
821 : !> 34 - 40 Real(7.2) alpha alpha (degrees).
822 : !> 41 - 47 Real(7.2) beta beta (degrees).
823 : !> 48 - 54 Real(7.2) gamma gamma (degrees).
824 : ! **************************************************************************************************
825 4 : SUBROUTINE read_cell_pdb(pdb_file_name, cell, para_env)
826 :
827 : CHARACTER(len=*) :: pdb_file_name
828 : TYPE(cell_type), POINTER :: cell
829 : TYPE(mp_para_env_type), POINTER :: para_env
830 :
831 : CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_pdb'
832 :
833 : CHARACTER(LEN=default_string_length) :: cryst
834 : INTEGER :: handle, i
835 : INTEGER, DIMENSION(3) :: periodic
836 : LOGICAL :: found
837 : REAL(KIND=dp), DIMENSION(3) :: cell_angles, cell_lengths
838 : TYPE(cp_parser_type) :: parser
839 :
840 2 : CALL timeset(routineN, handle)
841 :
842 : CALL parser_create(parser, pdb_file_name, &
843 2 : para_env=para_env, apply_preprocessing=.FALSE.)
844 :
845 : CALL parser_search_string(parser, "CRYST1", ignore_case=.FALSE., found=found, &
846 2 : begin_line=.TRUE., search_from_begin_of_file=.TRUE.)
847 2 : IF (.NOT. found) &
848 0 : CPABORT("The field (CRYST1) was not found in PDB file! ")
849 :
850 8 : periodic = 1
851 2 : READ (parser%input_line, *) cryst, cell_lengths(:), cell_angles(:)
852 8 : DO i = 1, 3
853 6 : cell_lengths(i) = cp_unit_to_cp2k(cell_lengths(i), "angstrom")
854 8 : cell_angles(i) = cp_unit_to_cp2k(cell_angles(i), "deg")
855 : END DO
856 : CALL set_cell_param(cell, cell_lengths, cell_angles, periodic=periodic, &
857 2 : do_init_cell=.TRUE.)
858 :
859 2 : CALL parser_release(parser)
860 :
861 2 : CALL timestop(handle)
862 :
863 6 : END SUBROUTINE read_cell_pdb
864 :
865 : ! **************************************************************************************************
866 : !> \brief Reads cell information from cp2k file
867 : !> \param cp2k_file_name ...
868 : !> \param cell ...
869 : !> \param para_env ...
870 : !> \date 03.2026
871 : !> \par Isolated from former read_cell_from_external_file
872 : ! **************************************************************************************************
873 4 : SUBROUTINE read_cell_cp2k(cp2k_file_name, cell, para_env)
874 :
875 : CHARACTER(len=*) :: cp2k_file_name
876 : TYPE(cell_type), POINTER :: cell
877 : TYPE(mp_para_env_type), POINTER :: para_env
878 :
879 : CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_cp2k'
880 :
881 : INTEGER :: handle, i, idum, j
882 : LOGICAL :: my_end
883 : REAL(KIND=dp) :: xdum
884 : REAL(KIND=dp), DIMENSION(3, 3) :: hmat
885 : TYPE(cp_parser_type) :: parser
886 :
887 2 : CALL timeset(routineN, handle)
888 :
889 : CALL parser_create(parser, cp2k_file_name, &
890 2 : para_env=para_env, apply_preprocessing=.FALSE.)
891 :
892 2 : CALL parser_get_next_line(parser, 1)
893 2 : my_end = .FALSE.
894 24 : DO WHILE (.NOT. my_end)
895 22 : READ (parser%input_line, *) idum, xdum, hmat(:, 1), hmat(:, 2), hmat(:, 3)
896 24 : CALL parser_get_next_line(parser, 1, at_end=my_end)
897 : END DO
898 8 : DO i = 1, 3
899 26 : DO j = 1, 3
900 24 : cell%hmat(j, i) = cp_unit_to_cp2k(hmat(j, i), "angstrom")
901 : END DO
902 : END DO
903 :
904 2 : CALL parser_release(parser)
905 :
906 2 : CALL timestop(handle)
907 :
908 6 : END SUBROUTINE read_cell_cp2k
909 :
910 : ! **************************************************************************************************
911 : !> \brief Reads cell information from xsc file
912 : !> \param xsc_file_name ...
913 : !> \param cell ...
914 : !> \param para_env ...
915 : !> \date 03.2026
916 : !> \par Isolated from former read_cell_from_external_file
917 : ! **************************************************************************************************
918 0 : SUBROUTINE read_cell_xsc(xsc_file_name, cell, para_env)
919 :
920 : CHARACTER(len=*) :: xsc_file_name
921 : TYPE(cell_type), POINTER :: cell
922 : TYPE(mp_para_env_type), POINTER :: para_env
923 :
924 : CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_xsc'
925 :
926 : INTEGER :: handle, i, idum, j
927 : REAL(KIND=dp), DIMENSION(3, 3) :: hmat
928 : TYPE(cp_parser_type) :: parser
929 :
930 0 : CALL timeset(routineN, handle)
931 :
932 : CALL parser_create(parser, xsc_file_name, &
933 0 : para_env=para_env, apply_preprocessing=.FALSE.)
934 :
935 0 : CALL parser_get_next_line(parser, 1)
936 0 : READ (parser%input_line, *) idum, hmat(:, 1), hmat(:, 2), hmat(:, 3)
937 0 : DO i = 1, 3
938 0 : DO j = 1, 3
939 0 : cell%hmat(j, i) = cp_unit_to_cp2k(hmat(j, i), "angstrom")
940 : END DO
941 : END DO
942 :
943 0 : CALL parser_release(parser)
944 :
945 0 : CALL timestop(handle)
946 :
947 0 : END SUBROUTINE read_cell_xsc
948 :
949 : ! **************************************************************************************************
950 : !> \brief Reset cell section by matrix in cell-type pointer
951 : !> \param cell ...
952 : !> \param cell_section ...
953 : !> \date 03.2026
954 : !> \par Alternative keywords for cell settings will be unset
955 : !> except MULTIPLE_UNIT_CELL, PERIODIC and SYMMETRY.
956 : ! **************************************************************************************************
957 20597 : SUBROUTINE reset_cell_section_by_cell_mat(cell, cell_section)
958 :
959 : TYPE(cell_type), POINTER :: cell
960 : TYPE(section_vals_type), POINTER :: cell_section
961 :
962 20597 : REAL(KIND=dp), DIMENSION(:), POINTER :: cell_par
963 :
964 20597 : CALL section_vals_val_unset(cell_section, "CELL_FILE_NAME")
965 20597 : CALL section_vals_val_unset(cell_section, "CELL_FILE_FORMAT")
966 20597 : CALL section_vals_val_unset(cell_section, "ABC")
967 20597 : CALL section_vals_val_unset(cell_section, "ALPHA_BETA_GAMMA")
968 20597 : CALL section_vals_val_unset(cell_section, "A")
969 20597 : CALL section_vals_val_unset(cell_section, "B")
970 20597 : CALL section_vals_val_unset(cell_section, "C")
971 20597 : ALLOCATE (cell_par(3))
972 164776 : cell_par = cell%hmat(:, 1)
973 20597 : CALL section_vals_val_set(cell_section, "A", r_vals_ptr=cell_par)
974 20597 : ALLOCATE (cell_par(3))
975 164776 : cell_par = cell%hmat(:, 2)
976 20597 : CALL section_vals_val_set(cell_section, "B", r_vals_ptr=cell_par)
977 20597 : ALLOCATE (cell_par(3))
978 164776 : cell_par = cell%hmat(:, 3)
979 20597 : CALL section_vals_val_set(cell_section, "C", r_vals_ptr=cell_par)
980 :
981 20597 : END SUBROUTINE reset_cell_section_by_cell_mat
982 :
983 : ! **************************************************************************************************
984 : !> \brief Write the cell parameters to the output unit.
985 : !> \param cell ...
986 : !> \param subsys_section ...
987 : !> \param tag ...
988 : !> \date 02.06.2000
989 : !> \par History
990 : !> - 11.2008 Teodoro Laino [tlaino] - rewrite and enabling user driven units
991 : !> \author Matthias Krack
992 : !> \version 1.0
993 : ! **************************************************************************************************
994 37507 : SUBROUTINE write_cell(cell, subsys_section, tag)
995 :
996 : TYPE(cell_type), POINTER :: cell
997 : TYPE(section_vals_type), POINTER :: subsys_section
998 : CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: tag
999 :
1000 : CHARACTER(LEN=default_string_length) :: label, unit_str
1001 : INTEGER :: output_unit
1002 : TYPE(cp_logger_type), POINTER :: logger
1003 :
1004 37507 : NULLIFY (logger)
1005 37507 : logger => cp_get_default_logger()
1006 37507 : IF (PRESENT(tag)) THEN
1007 9994 : label = TRIM(tag)//"|"
1008 : ELSE
1009 27513 : label = TRIM(cell%tag)//"|"
1010 : END IF
1011 :
1012 37507 : output_unit = cp_print_key_unit_nr(logger, subsys_section, "PRINT%CELL", extension=".Log")
1013 37507 : CALL section_vals_val_get(subsys_section, "PRINT%CELL%UNIT", c_val=unit_str)
1014 37507 : CALL write_cell_low(cell, unit_str, output_unit, label)
1015 37507 : CALL cp_print_key_finished_output(output_unit, logger, subsys_section, "PRINT%CELL")
1016 :
1017 37507 : END SUBROUTINE write_cell
1018 :
1019 : ! **************************************************************************************************
1020 : !> \brief Write the cell parameters to the output unit
1021 : !> \param cell ...
1022 : !> \param unit_str ...
1023 : !> \param output_unit ...
1024 : !> \param label ...
1025 : !> \date 17.05.2023
1026 : !> \par History
1027 : !> - Extracted from write_cell (17.05.2023, MK)
1028 : !> \version 1.0
1029 : ! **************************************************************************************************
1030 37507 : SUBROUTINE write_cell_low(cell, unit_str, output_unit, label)
1031 :
1032 : TYPE(cell_type), POINTER :: cell
1033 : CHARACTER(LEN=*), INTENT(IN) :: unit_str
1034 : INTEGER, INTENT(IN) :: output_unit
1035 : CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: label
1036 :
1037 : CHARACTER(LEN=12) :: tag
1038 : CHARACTER(LEN=3) :: string
1039 : CHARACTER(LEN=default_string_length) :: my_label
1040 : REAL(KIND=dp) :: alpha, beta, gamma, val
1041 : REAL(KIND=dp), DIMENSION(3) :: abc
1042 : TYPE(enumeration_type), POINTER :: enum
1043 : TYPE(keyword_type), POINTER :: keyword
1044 : TYPE(section_type), POINTER :: section
1045 :
1046 37507 : NULLIFY (enum)
1047 37507 : NULLIFY (keyword)
1048 37507 : NULLIFY (section)
1049 :
1050 49047 : IF (output_unit > 0) THEN
1051 11540 : CALL get_cell(cell=cell, abc=abc, alpha=alpha, beta=beta, gamma=gamma, tag=tag)
1052 11540 : IF (PRESENT(label)) THEN
1053 11540 : my_label = label
1054 : ELSE
1055 0 : my_label = TRIM(tag)//"|"
1056 : END IF
1057 11540 : val = cp_unit_from_cp2k(cell%deth, TRIM(unit_str)//"^3")
1058 : WRITE (UNIT=output_unit, FMT="(/,T2,A,T61,F20.6)") &
1059 11540 : TRIM(my_label)//" Volume ["//TRIM(unit_str)//"^3]:", val
1060 11540 : val = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
1061 : WRITE (UNIT=output_unit, FMT="(T2,A,T30,3F10.3,3X,A6,F12.6)") &
1062 46160 : TRIM(my_label)//" Vector a ["//TRIM(unit_str)//"]:", cell%hmat(:, 1)*val, &
1063 11540 : "|a| = ", abc(1)*val, &
1064 46160 : TRIM(my_label)//" Vector b ["//TRIM(unit_str)//"]:", cell%hmat(:, 2)*val, &
1065 11540 : "|b| = ", abc(2)*val, &
1066 46160 : TRIM(my_label)//" Vector c ["//TRIM(unit_str)//"]:", cell%hmat(:, 3)*val, &
1067 23080 : "|c| = ", abc(3)*val
1068 : WRITE (UNIT=output_unit, FMT="(T2,A,T69,F12.6)") &
1069 11540 : TRIM(my_label)//" Angle (b,c), alpha [degree]: ", alpha, &
1070 11540 : TRIM(my_label)//" Angle (a,c), beta [degree]: ", beta, &
1071 23080 : TRIM(my_label)//" Angle (a,b), gamma [degree]: ", gamma
1072 11540 : IF (cell%symmetry_id /= cell_sym_none) THEN
1073 1464 : CALL create_cell_section(section)
1074 1464 : keyword => section_get_keyword(section, "SYMMETRY")
1075 1464 : CALL keyword_get(keyword, enum=enum)
1076 : WRITE (UNIT=output_unit, FMT="(T2,A,T61,A20)") &
1077 1464 : TRIM(my_label)//" Requested initial symmetry: ", &
1078 2928 : ADJUSTR(TRIM(enum_i2c(enum, cell%symmetry_id)))
1079 1464 : CALL section_release(section)
1080 : END IF
1081 11540 : IF (cell%orthorhombic) THEN
1082 : WRITE (UNIT=output_unit, FMT="(T2,A,T78,A3)") &
1083 8179 : TRIM(my_label)//" Numerically orthorhombic: ", "YES"
1084 : ELSE
1085 : WRITE (UNIT=output_unit, FMT="(T2,A,T78,A3)") &
1086 3361 : TRIM(my_label)//" Numerically orthorhombic: ", " NO"
1087 : END IF
1088 46160 : IF (SUM(cell%perd(1:3)) == 0) THEN
1089 : WRITE (UNIT=output_unit, FMT="(T2,A,T77,A4)") &
1090 2469 : TRIM(my_label)//" Periodicity", "NONE"
1091 : ELSE
1092 9071 : string = ""
1093 9071 : IF (cell%perd(1) == 1) string = TRIM(string)//"X"
1094 9071 : IF (cell%perd(2) == 1) string = TRIM(string)//"Y"
1095 9071 : IF (cell%perd(3) == 1) string = TRIM(string)//"Z"
1096 : WRITE (UNIT=output_unit, FMT="(T2,A,T78,A3)") &
1097 9071 : TRIM(my_label)//" Periodicity", ADJUSTR(string)
1098 : END IF
1099 : END IF
1100 :
1101 37507 : END SUBROUTINE write_cell_low
1102 :
1103 : END MODULE cell_methods
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