-
Notifications
You must be signed in to change notification settings - Fork 0
/
atoms_input.F
473 lines (440 loc) · 24.3 KB
/
atoms_input.F
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
!--------------------------------------------------------------------------------------------------!
! CP2K: A general program to perform molecular dynamics simulations !
! Copyright 2000-2021 CP2K developers group <https://cp2k.org> !
! !
! SPDX-License-Identifier: GPL-2.0-or-later !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \par History
!> cjm, Feb-20-2001 : added all the extended variables to
!> system_type
!> gt 23-09-2002 : major changes. Pointer part is allocated/deallocated
!> and initialized here. Atomic coordinates can now be
!> read also from &COORD section in the input file.
!> If &COORD is not found, .dat file is read.
!> If & coord is found and .NOT. 'INIT', parsing of the .dat
!> is performed to get the proper coords/vel/eta variables
!> CJM 31-7-03 : Major rewrite. No more atype
! **************************************************************************************************
MODULE atoms_input
USE atomic_kind_types, ONLY: atomic_kind_type,&
get_atomic_kind
USE cell_types, ONLY: cell_type,&
pbc,&
scaled_to_real
USE cp_linked_list_input, ONLY: cp_sll_val_next,&
cp_sll_val_type
USE cp_log_handling, ONLY: cp_logger_get_default_io_unit,&
cp_to_string
USE cp_parser_methods, ONLY: read_float_object
USE cp_units, ONLY: cp_unit_to_cp2k
USE input_section_types, ONLY: section_vals_get,&
section_vals_get_subs_vals,&
section_vals_list_get,&
section_vals_remove_values,&
section_vals_type,&
section_vals_val_get
USE input_val_types, ONLY: val_get,&
val_type
USE kinds, ONLY: default_string_length,&
dp
USE memory_utilities, ONLY: reallocate
USE particle_types, ONLY: particle_type
USE shell_potential_types, ONLY: shell_kind_type
USE string_table, ONLY: id2str,&
s2s,&
str2id
USE string_utilities, ONLY: uppercase
USE topology_types, ONLY: atom_info_type,&
topology_parameters_type
#include "./base/base_uses.f90"
IMPLICIT NONE
PRIVATE
PUBLIC :: read_atoms_input, read_shell_coord_input
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'atoms_input'
CONTAINS
! **************************************************************************************************
!> \brief ...
!> \param topology ...
!> \param overwrite ...
!> \param subsys_section ...
!> \param save_mem ...
!> \author CJM
! **************************************************************************************************
SUBROUTINE read_atoms_input(topology, overwrite, subsys_section, save_mem)
TYPE(topology_parameters_type) :: topology
LOGICAL, INTENT(IN), OPTIONAL :: overwrite
TYPE(section_vals_type), POINTER :: subsys_section
LOGICAL, INTENT(IN), OPTIONAL :: save_mem
CHARACTER(len=*), PARAMETER :: routineN = 'read_atoms_input'
CHARACTER(len=2*default_string_length) :: line_att
CHARACTER(len=default_string_length) :: error_message, my_default_index, strtmp, &
unit_str
INTEGER :: default_id, end_c, handle, iatom, j, &
natom, output_unit, start_c, wrd
LOGICAL :: explicit, is_ok, my_overwrite, &
my_save_mem, scaled_coordinates
REAL(KIND=dp) :: r0(3), unit_conv
TYPE(atom_info_type), POINTER :: atom_info
TYPE(cell_type), POINTER :: cell
TYPE(cp_sll_val_type), POINTER :: list
TYPE(section_vals_type), POINTER :: coord_section
TYPE(val_type), POINTER :: val
my_overwrite = .FALSE.
my_save_mem = .FALSE.
error_message = ""
output_unit = cp_logger_get_default_io_unit()
IF (PRESENT(overwrite)) my_overwrite = overwrite
IF (PRESENT(save_mem)) my_save_mem = save_mem
NULLIFY (coord_section)
coord_section => section_vals_get_subs_vals(subsys_section, "COORD")
CALL section_vals_get(coord_section, explicit=explicit)
IF (.NOT. explicit) RETURN
CALL timeset(routineN, handle)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 1. get cell and topology%atom_info
!-----------------------------------------------------------------------------
atom_info => topology%atom_info
cell => topology%cell_muc
CALL section_vals_val_get(coord_section, "UNIT", c_val=unit_str)
CALL section_vals_val_get(coord_section, "SCALED", l_val=scaled_coordinates)
unit_conv = cp_unit_to_cp2k(1.0_dp, TRIM(unit_str))
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 2. Read in the coordinates from &COORD section in the input file
!-----------------------------------------------------------------------------
CALL section_vals_val_get(coord_section, "_DEFAULT_KEYWORD_", &
n_rep_val=natom)
topology%natoms = natom
IF (my_overwrite) THEN
CPASSERT(SIZE(atom_info%r, 2) == natom)
CALL cp_warn(__LOCATION__, &
"Overwriting coordinates. Active coordinates read from &COORD section."// &
" Active coordinates READ from &COORD section ")
CALL section_vals_list_get(coord_section, "_DEFAULT_KEYWORD_", list=list)
DO iatom = 1, natom
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
! Read name and atomic coordinates
start_c = 1
DO wrd = 1, 4
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (LEN_TRIM(line_att(start_c:end_c - 1)) == 0) &
CPABORT("incorrectly formatted line in coord section'"//line_att//"'")
IF (wrd == 1) THEN
atom_info%id_atmname(iatom) = str2id(s2s(line_att(start_c:end_c - 1)))
ELSE
READ (line_att(start_c:end_c - 1), *) atom_info%r(wrd - 1, iatom)
END IF
start_c = end_c
END DO
END DO
ELSE
! Element is assigned on the basis of the atm_name
topology%aa_element = .TRUE.
CALL reallocate(atom_info%id_molname, 1, natom)
CALL reallocate(atom_info%id_resname, 1, natom)
CALL reallocate(atom_info%resid, 1, natom)
CALL reallocate(atom_info%id_atmname, 1, natom)
CALL reallocate(atom_info%id_element, 1, natom)
CALL reallocate(atom_info%r, 1, 3, 1, natom)
CALL reallocate(atom_info%atm_mass, 1, natom)
CALL reallocate(atom_info%atm_charge, 1, natom)
CALL section_vals_list_get(coord_section, "_DEFAULT_KEYWORD_", list=list)
DO iatom = 1, natom
! we use only the first default_string_length characters of each line
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
default_id = str2id(s2s(""))
atom_info%id_molname(iatom) = default_id
atom_info%id_resname(iatom) = default_id
atom_info%resid(iatom) = 1
atom_info%id_atmname(iatom) = default_id
atom_info%id_element(iatom) = default_id
topology%molname_generated = .TRUE.
! Read name and atomic coordinates
start_c = 1
DO wrd = 1, 6
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (LEN_TRIM(line_att(start_c:end_c - 1)) == 0) &
CALL cp_abort(__LOCATION__, &
"Incorrectly formatted input line for atom "// &
TRIM(ADJUSTL(cp_to_string(iatom)))// &
" found in COORD section. Input line: <"// &
TRIM(line_att)//"> ")
SELECT CASE (wrd)
CASE (1)
atom_info%id_atmname(iatom) = str2id(s2s(line_att(start_c:end_c - 1)))
CASE (2:4)
CALL read_float_object(line_att(start_c:end_c - 1), &
atom_info%r(wrd - 1, iatom), error_message)
IF (LEN_TRIM(error_message) /= 0) &
CALL cp_abort(__LOCATION__, &
"Incorrectly formatted input line for atom "// &
TRIM(ADJUSTL(cp_to_string(iatom)))// &
" found in COORD section. "//TRIM(error_message)// &
" Input line: <"//TRIM(line_att)//"> ")
CASE (5)
READ (line_att(start_c:end_c - 1), *) strtmp
atom_info%id_molname(iatom) = str2id(strtmp)
atom_info%id_resname(iatom) = atom_info%id_molname(iatom)
topology%molname_generated = .FALSE.
CASE (6)
READ (line_att(start_c:end_c - 1), *) strtmp
atom_info%id_resname(iatom) = str2id(strtmp)
END SELECT
start_c = end_c
IF (start_c > LEN_TRIM(line_att)) EXIT
END DO
IF (topology%molname_generated) THEN
! Use defaults, if no molname was specified
WRITE (my_default_index, '(I0)') iatom
atom_info%id_molname(iatom) = str2id(s2s(TRIM(id2str(atom_info%id_atmname(iatom)))//TRIM(my_default_index)))
atom_info%id_resname(iatom) = atom_info%id_molname(iatom)
END IF
atom_info%id_element(iatom) = atom_info%id_atmname(iatom)
atom_info%atm_mass(iatom) = 0.0_dp
atom_info%atm_charge(iatom) = -HUGE(0.0_dp)
END DO
END IF
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 3. Convert coordinates into internal cp2k coordinates
!-----------------------------------------------------------------------------
DO iatom = 1, natom
IF (scaled_coordinates) THEN
r0 = atom_info%r(:, iatom)
CALL scaled_to_real(atom_info%r(:, iatom), r0, cell)
ELSE
atom_info%r(:, iatom) = atom_info%r(:, iatom)*unit_conv
END IF
END DO
IF (my_save_mem) CALL section_vals_remove_values(coord_section)
CALL timestop(handle)
END SUBROUTINE read_atoms_input
! **************************************************************************************************
!> \brief ...
!> \param particle_set ...
!> \param shell_particle_set ...
!> \param cell ...
!> \param subsys_section ...
!> \param core_particle_set ...
!> \param save_mem ...
!> \author MI
! **************************************************************************************************
SUBROUTINE read_shell_coord_input(particle_set, shell_particle_set, cell, &
subsys_section, core_particle_set, save_mem)
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set, shell_particle_set
TYPE(cell_type), POINTER :: cell
TYPE(section_vals_type), POINTER :: subsys_section
TYPE(particle_type), DIMENSION(:), OPTIONAL, &
POINTER :: core_particle_set
LOGICAL, INTENT(IN), OPTIONAL :: save_mem
CHARACTER(len=*), PARAMETER :: routineN = 'read_shell_coord_input'
CHARACTER(len=2*default_string_length) :: line_att
CHARACTER(len=default_string_length) :: name_kind, unit_str
CHARACTER(len=default_string_length), &
ALLOCATABLE, DIMENSION(:) :: at_name, at_name_c
INTEGER :: end_c, handle, ishell, j, nshell, &
output_unit, sh_index, start_c, wrd
INTEGER, ALLOCATABLE, DIMENSION(:) :: at_index, at_index_c
LOGICAL :: core_scaled_coordinates, explicit, &
is_ok, is_shell, my_save_mem, &
shell_scaled_coordinates
REAL(KIND=dp) :: dab, mass_com, rab(3), unit_conv_core, &
unit_conv_shell
REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: r, rc
TYPE(atomic_kind_type), POINTER :: atomic_kind
TYPE(cp_sll_val_type), POINTER :: list
TYPE(section_vals_type), POINTER :: core_coord_section, shell_coord_section
TYPE(shell_kind_type), POINTER :: shell
TYPE(val_type), POINTER :: val
my_save_mem = .FALSE.
NULLIFY (atomic_kind, list, shell_coord_section, shell, val)
output_unit = cp_logger_get_default_io_unit()
IF (PRESENT(save_mem)) my_save_mem = save_mem
NULLIFY (shell_coord_section, core_coord_section)
shell_coord_section => section_vals_get_subs_vals(subsys_section, "SHELL_COORD")
CALL section_vals_get(shell_coord_section, explicit=explicit)
IF (.NOT. explicit) RETURN
CALL timeset(routineN, handle)
CPASSERT(ASSOCIATED(particle_set))
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 2. Read in the coordinates from &SHELL_COORD section in the input file
!-----------------------------------------------------------------------------
CALL section_vals_val_get(shell_coord_section, "UNIT", c_val=unit_str)
CALL section_vals_val_get(shell_coord_section, "SCALED", l_val=shell_scaled_coordinates)
unit_conv_shell = cp_unit_to_cp2k(1.0_dp, TRIM(unit_str))
CALL section_vals_val_get(shell_coord_section, "_DEFAULT_KEYWORD_", &
n_rep_val=nshell)
IF (ASSOCIATED(shell_particle_set)) THEN
CPASSERT((SIZE(shell_particle_set, 1) == nshell))
ALLOCATE (r(3, nshell), at_name(nshell), at_index(nshell))
CALL cp_warn(__LOCATION__, &
"Overwriting shell coordinates. "// &
"Active coordinates READ from &SHELL_COORD section. ")
CALL section_vals_list_get(shell_coord_section, "_DEFAULT_KEYWORD_", list=list)
DO ishell = 1, nshell
! we use only the first default_string_length characters of each line
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
start_c = 1
DO wrd = 1, 5
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (wrd /= 5 .AND. end_c >= LEN(line_att) + 1) &
CPABORT("incorrectly formatted line in coord section'"//line_att//"'")
IF (wrd == 1) THEN
at_name(ishell) = line_att(start_c:end_c - 1)
CALL uppercase(at_name(ishell))
ELSE IF (wrd == 5) THEN
READ (line_att(start_c:end_c - 1), *) at_index(ishell)
ELSE
READ (line_att(start_c:end_c - 1), *) r(wrd - 1, ishell)
END IF
start_c = end_c
END DO
END DO
IF (PRESENT(core_particle_set)) THEN
CPASSERT(ASSOCIATED(core_particle_set))
core_coord_section => section_vals_get_subs_vals(subsys_section, "CORE_COORD")
CALL section_vals_get(core_coord_section, explicit=explicit)
IF (explicit) THEN
CALL section_vals_val_get(core_coord_section, "UNIT", c_val=unit_str)
CALL section_vals_val_get(core_coord_section, "SCALED", l_val=core_scaled_coordinates)
unit_conv_core = cp_unit_to_cp2k(1.0_dp, TRIM(unit_str))
CALL section_vals_val_get(core_coord_section, "_DEFAULT_KEYWORD_", &
n_rep_val=nshell)
CPASSERT((SIZE(core_particle_set, 1) == nshell))
ALLOCATE (rc(3, nshell), at_name_c(nshell), at_index_c(nshell))
CALL cp_warn(__LOCATION__, &
"Overwriting cores coordinates. "// &
" Active coordinates READ from &CORE_COORD section. ")
CALL section_vals_list_get(core_coord_section, "_DEFAULT_KEYWORD_", list=list)
DO ishell = 1, nshell
! we use only the first default_string_length characters of each line
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
start_c = 1
DO wrd = 1, 5
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (wrd /= 5 .AND. end_c >= LEN(line_att) + 1) &
CPABORT("incorrectly formatted line in coord section'"//line_att//"'")
IF (wrd == 1) THEN
at_name_c(ishell) = line_att(start_c:end_c - 1)
CALL uppercase(at_name_c(ishell))
ELSE IF (wrd == 5) THEN
READ (line_att(start_c:end_c - 1), *) at_index_c(ishell)
ELSE
READ (line_att(start_c:end_c - 1), *) rc(wrd - 1, ishell)
END IF
start_c = end_c
END DO
END DO
IF (my_save_mem) CALL section_vals_remove_values(core_coord_section)
END IF ! explicit
END IF ! core_particle_set
!-----------------------------------------------------------------------------
! 3. Check corrispondence and convert coordinates into internal cp2k coordinates
!-----------------------------------------------------------------------------
DO ishell = 1, nshell
atomic_kind => particle_set(at_index(ishell))%atomic_kind
CALL get_atomic_kind(atomic_kind=atomic_kind, &
name=name_kind, shell_active=is_shell, mass=mass_com, shell=shell)
CALL uppercase(name_kind)
IF ((TRIM(at_name(ishell)) == TRIM(name_kind)) .AND. is_shell) THEN
sh_index = particle_set(at_index(ishell))%shell_index
IF (shell_scaled_coordinates) THEN
CALL scaled_to_real(r(:, ishell), shell_particle_set(sh_index)%r(:), cell)
ELSE
shell_particle_set(sh_index)%r(:) = r(:, ishell)*unit_conv_shell
END IF
shell_particle_set(sh_index)%atom_index = at_index(ishell)
IF (PRESENT(core_particle_set) .AND. .NOT. explicit) THEN
core_particle_set(sh_index)%r(1) = (mass_com*particle_set(at_index(ishell))%r(1) - &
shell%mass_shell*shell_particle_set(sh_index)%r(1))/shell%mass_core
core_particle_set(sh_index)%r(2) = (mass_com*particle_set(at_index(ishell))%r(2) - &
shell%mass_shell*shell_particle_set(sh_index)%r(2))/shell%mass_core
core_particle_set(sh_index)%r(3) = (mass_com*particle_set(at_index(ishell))%r(3) - &
shell%mass_shell*shell_particle_set(sh_index)%r(3))/shell%mass_core
core_particle_set(sh_index)%atom_index = at_index(ishell)
rab = pbc(shell_particle_set(sh_index)%r, core_particle_set(sh_index)%r, cell)
ELSE IF (explicit) THEN
IF (core_scaled_coordinates) THEN
CALL scaled_to_real(rc(:, ishell), core_particle_set(sh_index)%r(:), cell)
ELSE
core_particle_set(sh_index)%r(:) = rc(:, ishell)*unit_conv_core
END IF
core_particle_set(sh_index)%atom_index = at_index_c(ishell)
rab = pbc(shell_particle_set(sh_index)%r, core_particle_set(sh_index)%r, cell)
CPASSERT(TRIM(at_name(ishell)) == TRIM(at_name_c(ishell)))
CPASSERT(at_index(ishell) == at_index_c(ishell))
ELSE
rab = pbc(shell_particle_set(sh_index)%r, particle_set(at_index(ishell))%r, cell)
END IF
dab = SQRT(rab(1)*rab(1) + rab(2)*rab(2) + rab(3)*rab(3))
IF (shell%max_dist > 0.0_dp .AND. shell%max_dist < dab) THEN
IF (output_unit > 0) THEN
WRITE (output_unit, *) "WARNING : shell and core for atom ", at_index(ishell), " seem to be too distant. "
END IF
END IF
ELSE
CPABORT("shell coordinate assigned to the wrong atom. check the shell indexes in the input")
END IF
END DO
DEALLOCATE (r, at_index, at_name)
DEALLOCATE (rc, at_index_c, at_name_c)
END IF
IF (my_save_mem) CALL section_vals_remove_values(shell_coord_section)
CALL timestop(handle)
END SUBROUTINE read_shell_coord_input
END MODULE atoms_input