-
Notifications
You must be signed in to change notification settings - Fork 1
/
cp_subsys_methods.F
391 lines (349 loc) · 20.3 KB
/
cp_subsys_methods.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
!--------------------------------------------------------------------------------------------------!
! CP2K: A general program to perform molecular dynamics simulations !
! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
! !
! SPDX-License-Identifier: GPL-2.0-or-later !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \brief Initialize a small environment for a particular calculation
!> \par History
!> 5.2004 created [fawzi]
!> 9.2007 cleaned [tlaino] - University of Zurich
!> \author Teodoro Laino
! **************************************************************************************************
MODULE cp_subsys_methods
USE atomic_kind_list_types, ONLY: atomic_kind_list_create,&
atomic_kind_list_release,&
atomic_kind_list_type
USE atomic_kind_types, ONLY: atomic_kind_type
USE atprop_types, ONLY: atprop_create
USE cell_types, ONLY: cell_retain,&
cell_type
USE colvar_methods, ONLY: colvar_read
USE cp_result_types, ONLY: cp_result_create
USE cp_subsys_types, ONLY: cp_subsys_get,&
cp_subsys_set,&
cp_subsys_type
USE exclusion_types, ONLY: exclusion_type
USE input_constants, ONLY: do_conn_off,&
do_stress_analytical,&
do_stress_diagonal_anal,&
do_stress_diagonal_numer,&
do_stress_none,&
do_stress_numerical
USE input_section_types, ONLY: section_vals_get,&
section_vals_get_subs_vals,&
section_vals_type,&
section_vals_val_get
USE kinds, ONLY: default_string_length,&
dp
USE message_passing, ONLY: mp_para_env_type
USE molecule_kind_list_types, ONLY: molecule_kind_list_create,&
molecule_kind_list_release,&
molecule_kind_list_type
USE molecule_kind_types, ONLY: molecule_kind_type
USE molecule_list_types, ONLY: molecule_list_create,&
molecule_list_release,&
molecule_list_type
USE molecule_types, ONLY: molecule_type
USE particle_list_types, ONLY: particle_list_create,&
particle_list_release,&
particle_list_type
USE particle_types, ONLY: particle_type
USE qmmm_types_low, ONLY: qmmm_env_mm_type
USE string_table, ONLY: id2str,&
s2s,&
str2id
USE topology, ONLY: connectivity_control,&
topology_control
USE topology_connectivity_util, ONLY: topology_connectivity_pack
USE topology_coordinate_util, ONLY: topology_coordinate_pack
USE topology_types, ONLY: deallocate_topology,&
init_topology,&
topology_parameters_type
USE topology_util, ONLY: check_subsys_element
USE virial_types, ONLY: virial_set
#include "./base/base_uses.f90"
IMPLICIT NONE
PRIVATE
LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .FALSE.
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cp_subsys_methods'
PUBLIC :: create_small_subsys, cp_subsys_create
CONTAINS
! **************************************************************************************************
!> \brief Creates allocates and fills subsys from given input.
!> \param subsys ...
!> \param para_env ...
!> \param root_section ...
!> \param force_env_section ...
!> \param subsys_section ...
!> \param use_motion_section ...
!> \param qmmm ...
!> \param qmmm_env ...
!> \param exclusions ...
!> \param elkind ...
!> \author Ole Schuett
! **************************************************************************************************
SUBROUTINE cp_subsys_create(subsys, para_env, &
root_section, force_env_section, subsys_section, &
use_motion_section, qmmm, qmmm_env, exclusions, elkind)
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(mp_para_env_type), POINTER :: para_env
TYPE(section_vals_type), POINTER :: root_section
TYPE(section_vals_type), OPTIONAL, POINTER :: force_env_section, subsys_section
LOGICAL, INTENT(IN), OPTIONAL :: use_motion_section
LOGICAL, OPTIONAL :: qmmm
TYPE(qmmm_env_mm_type), OPTIONAL, POINTER :: qmmm_env
TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
POINTER :: exclusions
LOGICAL, INTENT(IN), OPTIONAL :: elkind
INTEGER :: stress_tensor
INTEGER, DIMENSION(:), POINTER :: seed_vals
LOGICAL :: atomic_energy, my_use_motion_section, &
pv_availability, pv_diagonal, &
pv_numerical
TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(molecule_kind_list_type), POINTER :: mol_kinds
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
TYPE(molecule_list_type), POINTER :: mols
TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
TYPE(particle_list_type), POINTER :: particles
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
TYPE(section_vals_type), POINTER :: colvar_section, my_force_env_section, &
my_subsys_section
CPASSERT(.NOT. ASSOCIATED(subsys))
ALLOCATE (subsys)
CALL para_env%retain()
subsys%para_env => para_env
my_use_motion_section = .FALSE.
IF (PRESENT(use_motion_section)) &
my_use_motion_section = use_motion_section
my_force_env_section => section_vals_get_subs_vals(root_section, "FORCE_EVAL")
IF (PRESENT(force_env_section)) &
my_force_env_section => force_env_section
my_subsys_section => section_vals_get_subs_vals(my_force_env_section, "SUBSYS")
IF (PRESENT(subsys_section)) &
my_subsys_section => subsys_section
CALL section_vals_val_get(my_subsys_section, "SEED", i_vals=seed_vals)
IF (SIZE(seed_vals) == 1) THEN
subsys%seed(:, :) = REAL(seed_vals(1), KIND=dp)
ELSE IF (SIZE(seed_vals) == 6) THEN
subsys%seed(1:3, 1:2) = RESHAPE(REAL(seed_vals(:), KIND=dp), (/3, 2/))
ELSE
CPABORT("Supply exactly 1 or 6 arguments for SEED in &SUBSYS only!")
END IF
colvar_section => section_vals_get_subs_vals(my_subsys_section, "COLVAR")
CALL cp_subsys_read_colvar(subsys, colvar_section)
! *** Read the particle coordinates and allocate the atomic kind, ***
! *** the molecule kind, and the molecule data structures ***
CALL topology_control(atomic_kind_set, particle_set, molecule_kind_set, molecule_set, &
subsys%colvar_p, subsys%gci, root_section, para_env, &
force_env_section=my_force_env_section, &
subsys_section=my_subsys_section, use_motion_section=my_use_motion_section, &
qmmm=qmmm, qmmm_env=qmmm_env, exclusions=exclusions, elkind=elkind)
CALL particle_list_create(particles, els_ptr=particle_set)
CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
CALL molecule_list_create(mols, els_ptr=molecule_set)
CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)
CALL cp_subsys_set(subsys, particles=particles, atomic_kinds=atomic_kinds, &
molecules=mols, molecule_kinds=mol_kinds)
CALL particle_list_release(particles)
CALL atomic_kind_list_release(atomic_kinds)
CALL molecule_list_release(mols)
CALL molecule_kind_list_release(mol_kinds)
! Should we compute the virial?
CALL section_vals_val_get(my_force_env_section, "STRESS_TENSOR", i_val=stress_tensor)
SELECT CASE (stress_tensor)
CASE (do_stress_none)
pv_availability = .FALSE.
pv_numerical = .FALSE.
pv_diagonal = .FALSE.
CASE (do_stress_analytical)
pv_availability = .TRUE.
pv_numerical = .FALSE.
pv_diagonal = .FALSE.
CASE (do_stress_numerical)
pv_availability = .TRUE.
pv_numerical = .TRUE.
pv_diagonal = .FALSE.
CASE (do_stress_diagonal_anal)
pv_availability = .TRUE.
pv_numerical = .FALSE.
pv_diagonal = .TRUE.
CASE (do_stress_diagonal_numer)
pv_availability = .TRUE.
pv_numerical = .TRUE.
pv_diagonal = .TRUE.
END SELECT
ALLOCATE (subsys%virial)
CALL virial_set(virial=subsys%virial, &
pv_availability=pv_availability, &
pv_numer=pv_numerical, &
pv_diagonal=pv_diagonal)
! Should we compute atomic properties?
CALL atprop_create(subsys%atprop)
CALL section_vals_val_get(my_force_env_section, "PROPERTIES%ATOMIC%ENERGY", l_val=atomic_energy)
subsys%atprop%energy = atomic_energy
CALL cp_result_create(subsys%results)
END SUBROUTINE cp_subsys_create
! **************************************************************************************************
!> \brief reads the colvar section of the colvar
!> \param subsys ...
!> \param colvar_section ...
!> \par History
!> 2006.01 Joost VandeVondele
! **************************************************************************************************
SUBROUTINE cp_subsys_read_colvar(subsys, colvar_section)
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(section_vals_type), POINTER :: colvar_section
INTEGER :: ig, ncol
CALL section_vals_get(colvar_section, n_repetition=ncol)
ALLOCATE (subsys%colvar_p(ncol))
DO ig = 1, ncol
NULLIFY (subsys%colvar_p(ig)%colvar)
CALL colvar_read(subsys%colvar_p(ig)%colvar, ig, colvar_section, subsys%para_env)
END DO
END SUBROUTINE cp_subsys_read_colvar
! **************************************************************************************************
!> \brief updates the molecule information of the given subsys
!> \param small_subsys the subsys to create
!> \param big_subsys the superset of small_subsys
!> \param small_cell ...
!> \param small_para_env the parallel environment for the new (small)
!> subsys
!> \param sub_atom_index indexes of the atoms that should be in small_subsys
!> \param sub_atom_kind_name ...
!> \param para_env ...
!> \param force_env_section ...
!> \param subsys_section ...
!> \param ignore_outside_box ...
!> \par History
!> 05.2004 created [fawzi]
!> \author Fawzi Mohamed, Teodoro Laino
!> \note
!> not really ready to be used with different para_envs for the small
!> and big part
! **************************************************************************************************
SUBROUTINE create_small_subsys(small_subsys, big_subsys, small_cell, &
small_para_env, sub_atom_index, sub_atom_kind_name, &
para_env, force_env_section, subsys_section, ignore_outside_box)
TYPE(cp_subsys_type), POINTER :: small_subsys, big_subsys
TYPE(cell_type), POINTER :: small_cell
TYPE(mp_para_env_type), POINTER :: small_para_env
INTEGER, DIMENSION(:), INTENT(in) :: sub_atom_index
CHARACTER(len=default_string_length), &
DIMENSION(:), INTENT(in) :: sub_atom_kind_name
TYPE(mp_para_env_type), POINTER :: para_env
TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
LOGICAL, INTENT(in), OPTIONAL :: ignore_outside_box
CHARACTER(len=default_string_length) :: my_element, strtmp1
INTEGER :: iat, id_, nat
TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(molecule_kind_list_type), POINTER :: mol_kinds
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
TYPE(molecule_list_type), POINTER :: mols
TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
TYPE(particle_list_type), POINTER :: particles
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
TYPE(topology_parameters_type) :: topology
NULLIFY (mol_kinds, mols, particles, atomic_kinds, atomic_kind_set, particle_set, &
molecule_kind_set, molecule_set, particles, atomic_kinds)
CPASSERT(.NOT. ASSOCIATED(small_subsys))
CPASSERT(ASSOCIATED(big_subsys))
IF (big_subsys%para_env /= small_para_env) &
CPABORT("big_subsys%para_env==small_para_env")
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 1. Initialize the topology structure type
!-----------------------------------------------------------------------------
CALL init_topology(topology)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 2. Get the cell info
!-----------------------------------------------------------------------------
topology%cell => small_cell
CALL cell_retain(small_cell)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 3. Initialize atom coords from the bigger system
!-----------------------------------------------------------------------------
nat = SIZE(sub_atom_index)
topology%natoms = nat
CPASSERT(.NOT. ASSOCIATED(topology%atom_info%r))
CPASSERT(.NOT. ASSOCIATED(topology%atom_info%id_atmname))
CPASSERT(.NOT. ASSOCIATED(topology%atom_info%id_molname))
CPASSERT(.NOT. ASSOCIATED(topology%atom_info%id_resname))
CPASSERT(.NOT. ASSOCIATED(topology%atom_info%atm_mass))
CPASSERT(.NOT. ASSOCIATED(topology%atom_info%atm_charge))
ALLOCATE (topology%atom_info%r(3, nat), topology%atom_info%id_atmname(nat), &
topology%atom_info%id_molname(nat), topology%atom_info%id_resname(nat), &
topology%atom_info%id_element(nat), topology%atom_info%atm_mass(nat), &
topology%atom_info%atm_charge(nat))
CALL cp_subsys_get(big_subsys, particles=particles)
DO iat = 1, nat
topology%atom_info%r(:, iat) = particles%els(sub_atom_index(iat))%r
topology%atom_info%id_atmname(iat) = str2id(s2s(sub_atom_kind_name(iat)))
topology%atom_info%id_molname(iat) = topology%atom_info%id_atmname(iat)
topology%atom_info%id_resname(iat) = topology%atom_info%id_atmname(iat)
!
! Defining element
!
id_ = INDEX(id2str(topology%atom_info%id_atmname(iat)), "_") - 1
IF (id_ == -1) id_ = LEN_TRIM(id2str(topology%atom_info%id_atmname(iat)))
strtmp1 = id2str(topology%atom_info%id_atmname(iat))
strtmp1 = strtmp1(1:id_)
CALL check_subsys_element(strtmp1, strtmp1, my_element, &
subsys_section, use_mm_map_first=.FALSE.)
topology%atom_info%id_element(iat) = str2id(s2s(my_element))
topology%atom_info%atm_mass(iat) = 0._dp
topology%atom_info%atm_charge(iat) = 0._dp
END DO
topology%conn_type = do_conn_off
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 4. Read in or generate the molecular connectivity
!-----------------------------------------------------------------------------
CALL connectivity_control(topology, para_env, subsys_section=subsys_section, &
force_env_section=force_env_section)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 5. Pack everything into the molecular types
!-----------------------------------------------------------------------------
CALL topology_connectivity_pack(molecule_kind_set, molecule_set, &
topology, subsys_section=subsys_section)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 6. Pack everything into the atomic types
!-----------------------------------------------------------------------------
CALL topology_coordinate_pack(particle_set, atomic_kind_set, &
molecule_kind_set, molecule_set, topology, subsys_section=subsys_section, &
force_env_section=force_env_section, ignore_outside_box=ignore_outside_box)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 7. Cleanup the topology structure type
!-----------------------------------------------------------------------------
CALL deallocate_topology(topology)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 8. Allocate new subsys
!-----------------------------------------------------------------------------
ALLOCATE (small_subsys)
CALL para_env%retain()
small_subsys%para_env => para_env
CALL particle_list_create(particles, els_ptr=particle_set)
CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
CALL molecule_list_create(mols, els_ptr=molecule_set)
CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)
CALL cp_subsys_set(small_subsys, particles=particles, atomic_kinds=atomic_kinds, &
molecules=mols, molecule_kinds=mol_kinds)
CALL particle_list_release(particles)
CALL atomic_kind_list_release(atomic_kinds)
CALL molecule_list_release(mols)
CALL molecule_kind_list_release(mol_kinds)
ALLOCATE (small_subsys%virial)
CALL atprop_create(small_subsys%atprop)
CALL cp_result_create(small_subsys%results)
END SUBROUTINE create_small_subsys
END MODULE cp_subsys_methods