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cp_subsys_methods.F
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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 Initialize a small environment for a particular calculation
10!> \par History
11!> 5.2004 created [fawzi]
12!> 9.2007 cleaned [tlaino] - University of Zurich
13!> \author Teodoro Laino
14! **************************************************************************************************
15MODULE cp_subsys_methods
16 USE atomic_kind_list_types, ONLY: atomic_kind_list_create,&
17 atomic_kind_list_release,&
18 atomic_kind_list_type
19 USE atomic_kind_types, ONLY: atomic_kind_type
20 USE atprop_types, ONLY: atprop_create
21 USE cell_methods, ONLY: write_cell
22 USE cell_types, ONLY: cell_retain,&
23 cell_type
24 USE colvar_methods, ONLY: colvar_read
25 USE cp_result_types, ONLY: cp_result_create
26 USE cp_subsys_types, ONLY: cp_subsys_get,&
27 cp_subsys_set,&
28 cp_subsys_type
29 USE exclusion_types, ONLY: exclusion_type
30 USE input_constants, ONLY: do_conn_off,&
31 do_stress_analytical,&
32 do_stress_diagonal_anal,&
33 do_stress_diagonal_numer,&
34 do_stress_none,&
35 do_stress_numerical
36 USE input_section_types, ONLY: section_vals_get,&
37 section_vals_get_subs_vals,&
38 section_vals_type,&
39 section_vals_val_get
40 USE kinds, ONLY: default_string_length,&
41 dp
42 USE message_passing, ONLY: mp_para_env_type
43 USE molecule_kind_list_types, ONLY: molecule_kind_list_create,&
44 molecule_kind_list_release,&
45 molecule_kind_list_type
46 USE molecule_kind_types, ONLY: molecule_kind_type
47 USE molecule_list_types, ONLY: molecule_list_create,&
48 molecule_list_release,&
49 molecule_list_type
50 USE molecule_types, ONLY: molecule_type
51 USE particle_list_types, ONLY: particle_list_create,&
52 particle_list_release,&
53 particle_list_type
54 USE particle_types, ONLY: particle_type
55 USE qmmm_types_low, ONLY: qmmm_env_mm_type
56 USE string_table, ONLY: id2str,&
57 s2s,&
58 str2id
59 USE topology, ONLY: connectivity_control,&
60 topology_control
61 USE topology_connectivity_util, ONLY: topology_connectivity_pack
62 USE topology_coordinate_util, ONLY: topology_coordinate_pack
63 USE topology_types, ONLY: deallocate_topology,&
64 init_topology,&
65 topology_parameters_type
66 USE topology_util, ONLY: check_subsys_element
67 USE virial_types, ONLY: virial_set
68#include "./base/base_uses.f90"
69
70 IMPLICIT NONE
71 PRIVATE
72
73 LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .false.
74 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cp_subsys_methods'
75
76 PUBLIC :: create_small_subsys, cp_subsys_create
77
78CONTAINS
79
80! **************************************************************************************************
81!> \brief Creates allocates and fills subsys from given input.
82!> \param subsys ...
83!> \param para_env ...
84!> \param root_section ...
85!> \param force_env_section ...
86!> \param subsys_section ...
87!> \param use_motion_section ...
88!> \param qmmm ...
89!> \param qmmm_env ...
90!> \param exclusions ...
91!> \param elkind ...
92!> \author Ole Schuett
93! **************************************************************************************************
94 SUBROUTINE cp_subsys_create(subsys, para_env, &
95 root_section, force_env_section, subsys_section, &
96 use_motion_section, qmmm, qmmm_env, exclusions, elkind)
97 TYPE(cp_subsys_type), POINTER :: subsys
98 TYPE(mp_para_env_type), POINTER :: para_env
99 TYPE(section_vals_type), POINTER :: root_section
100 TYPE(section_vals_type), OPTIONAL, POINTER :: force_env_section, subsys_section
101 LOGICAL, INTENT(IN), OPTIONAL :: use_motion_section
102 LOGICAL, OPTIONAL :: qmmm
103 TYPE(qmmm_env_mm_type), OPTIONAL, POINTER :: qmmm_env
104 TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
105 POINTER :: exclusions
106 LOGICAL, INTENT(IN), OPTIONAL :: elkind
107
108 INTEGER :: stress_tensor
109 INTEGER, DIMENSION(:), POINTER :: seed_vals
110 LOGICAL :: atomic_energy, my_use_motion_section, &
111 pv_availability, pv_diagonal, &
112 pv_numerical
113 TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
114 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
115 TYPE(molecule_kind_list_type), POINTER :: mol_kinds
116 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
117 TYPE(molecule_list_type), POINTER :: mols
118 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
119 TYPE(particle_list_type), POINTER :: particles
120 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
121 TYPE(section_vals_type), POINTER :: colvar_section, my_force_env_section, &
122 my_subsys_section
123
124 cpassert(.NOT. ASSOCIATED(subsys))
125 ALLOCATE (subsys)
126
127 CALL para_env%retain()
128 subsys%para_env => para_env
129
130 my_use_motion_section = .false.
131 IF (PRESENT(use_motion_section)) &
132 my_use_motion_section = use_motion_section
133
134 my_force_env_section => section_vals_get_subs_vals(root_section, "FORCE_EVAL")
135 IF (PRESENT(force_env_section)) &
136 my_force_env_section => force_env_section
137
138 my_subsys_section => section_vals_get_subs_vals(my_force_env_section, "SUBSYS")
139 IF (PRESENT(subsys_section)) &
140 my_subsys_section => subsys_section
141
142 CALL section_vals_val_get(my_subsys_section, "SEED", i_vals=seed_vals)
143 IF (SIZE(seed_vals) == 1) THEN
144 subsys%seed(:, :) = real(seed_vals(1), kind=dp)
145 ELSE IF (SIZE(seed_vals) == 6) THEN
146 subsys%seed(1:3, 1:2) = reshape(real(seed_vals(:), kind=dp), [3, 2])
147 ELSE
148 cpabort("Supply exactly 1 or 6 arguments for SEED in &SUBSYS only!")
149 END IF
150
151 colvar_section => section_vals_get_subs_vals(my_subsys_section, "COLVAR")
152
153 CALL cp_subsys_read_colvar(subsys, colvar_section)
154
155 ! *** Read the particle coordinates and allocate the atomic kind, ***
156 ! *** the molecule kind, and the molecule data structures ***
157 CALL topology_control(atomic_kind_set, particle_set, molecule_kind_set, molecule_set, &
158 subsys%colvar_p, subsys%gci, root_section, para_env, &
159 force_env_section=my_force_env_section, &
160 subsys_section=my_subsys_section, use_motion_section=my_use_motion_section, &
161 qmmm=qmmm, qmmm_env=qmmm_env, exclusions=exclusions, elkind=elkind, &
162 subsys=subsys)
163
164 CALL particle_list_create(particles, els_ptr=particle_set)
165 CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
166 CALL molecule_list_create(mols, els_ptr=molecule_set)
167 CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)
168
169 CALL cp_subsys_set(subsys, particles=particles, atomic_kinds=atomic_kinds, &
170 molecules=mols, molecule_kinds=mol_kinds)
171
172 CALL particle_list_release(particles)
173 CALL atomic_kind_list_release(atomic_kinds)
174 CALL molecule_list_release(mols)
175 CALL molecule_kind_list_release(mol_kinds)
176
177 ! Should we compute the virial?
178 CALL section_vals_val_get(my_force_env_section, "STRESS_TENSOR", i_val=stress_tensor)
179 SELECT CASE (stress_tensor)
180 CASE (do_stress_none)
181 pv_availability = .false.
182 pv_numerical = .false.
183 pv_diagonal = .false.
184 CASE (do_stress_analytical)
185 pv_availability = .true.
186 pv_numerical = .false.
187 pv_diagonal = .false.
188 CASE (do_stress_numerical)
189 pv_availability = .true.
190 pv_numerical = .true.
191 pv_diagonal = .false.
192 CASE (do_stress_diagonal_anal)
193 pv_availability = .true.
194 pv_numerical = .false.
195 pv_diagonal = .true.
196 CASE (do_stress_diagonal_numer)
197 pv_availability = .true.
198 pv_numerical = .true.
199 pv_diagonal = .true.
200 END SELECT
201
202 ALLOCATE (subsys%virial)
203 CALL virial_set(virial=subsys%virial, &
204 pv_availability=pv_availability, &
205 pv_numer=pv_numerical, &
206 pv_diagonal=pv_diagonal)
207
208 ! Should we compute atomic properties?
209 CALL atprop_create(subsys%atprop)
210 CALL section_vals_val_get(my_force_env_section, "PROPERTIES%ATOMIC%ENERGY", l_val=atomic_energy)
211 subsys%atprop%energy = atomic_energy
212
213 CALL cp_result_create(subsys%results)
214 END SUBROUTINE cp_subsys_create
215
216! **************************************************************************************************
217!> \brief reads the colvar section of the colvar
218!> \param subsys ...
219!> \param colvar_section ...
220!> \par History
221!> 2006.01 Joost VandeVondele
222! **************************************************************************************************
223 SUBROUTINE cp_subsys_read_colvar(subsys, colvar_section)
224 TYPE(cp_subsys_type), POINTER :: subsys
225 TYPE(section_vals_type), POINTER :: colvar_section
226
227 INTEGER :: ig, ncol
228
229 CALL section_vals_get(colvar_section, n_repetition=ncol)
230 ALLOCATE (subsys%colvar_p(ncol))
231 DO ig = 1, ncol
232 NULLIFY (subsys%colvar_p(ig)%colvar)
233 CALL colvar_read(subsys%colvar_p(ig)%colvar, ig, colvar_section, subsys%para_env)
234 END DO
235 END SUBROUTINE cp_subsys_read_colvar
236
237! **************************************************************************************************
238!> \brief updates the molecule information of the given subsys
239!> \param small_subsys the subsys to create
240!> \param big_subsys the superset of small_subsys
241!> \param small_cell the cell of small_subsys
242!> \param small_para_env the parallel environment for the new (small)
243!> subsys
244!> \param sub_atom_index indexes of the atoms that should be in small_subsys
245!> \param sub_atom_kind_name ...
246!> \param para_env ...
247!> \param force_env_section ...
248!> \param subsys_section ...
249!> \param ignore_outside_box ...
250!> \par History
251!> 05.2004 created [fawzi]
252!> \author Fawzi Mohamed, Teodoro Laino
253!> \note
254!> not really ready to be used with different para_envs for the small
255!> and big part
256!> qmmm_env_create() should be the only instance where this subroutine is called
257!> with small_cell distinct from big_subsys%cell; otherwise it could be possible
258!> to drop the small_cell as input parameter entirely.
259! **************************************************************************************************
260 SUBROUTINE create_small_subsys(small_subsys, big_subsys, small_cell, &
261 small_para_env, sub_atom_index, sub_atom_kind_name, &
262 para_env, force_env_section, subsys_section, ignore_outside_box)
263
264 TYPE(cp_subsys_type), POINTER :: small_subsys, big_subsys
265 TYPE(cell_type), POINTER :: small_cell
266 TYPE(mp_para_env_type), POINTER :: small_para_env
267 INTEGER, DIMENSION(:), INTENT(in) :: sub_atom_index
268 CHARACTER(len=default_string_length), &
269 DIMENSION(:), INTENT(in) :: sub_atom_kind_name
270 TYPE(mp_para_env_type), POINTER :: para_env
271 TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
272 LOGICAL, INTENT(in), OPTIONAL :: ignore_outside_box
273
274 CHARACTER(len=default_string_length) :: my_element, strtmp1
275 INTEGER :: iat, id_, nat
276 TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
277 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
278 TYPE(molecule_kind_list_type), POINTER :: mol_kinds
279 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
280 TYPE(molecule_list_type), POINTER :: mols
281 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
282 TYPE(particle_list_type), POINTER :: particles
283 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
284 TYPE(topology_parameters_type) :: topology
285
286 NULLIFY (mol_kinds, mols, particles, atomic_kinds, atomic_kind_set, particle_set, &
287 molecule_kind_set, molecule_set, particles, atomic_kinds)
288
289 cpassert(.NOT. ASSOCIATED(small_subsys))
290 cpassert(ASSOCIATED(big_subsys))
291 IF (big_subsys%para_env /= small_para_env) &
292 cpabort("big_subsys%para_env==small_para_env")
293
294 !-----------------------------------------------------------------------------
295 !-----------------------------------------------------------------------------
296 ! 1. Initialize the topology structure type
297 !-----------------------------------------------------------------------------
298 CALL init_topology(topology)
299
300 !-----------------------------------------------------------------------------
301 !-----------------------------------------------------------------------------
302 ! 2. Get the cell info
303 !-----------------------------------------------------------------------------
304 topology%cell => small_cell
305 CALL cell_retain(small_cell)
306 CALL write_cell(small_cell, subsys_section, tag="CELL")
307 CALL write_cell(small_cell, subsys_section, tag="CELL_REF")
308
309 !-----------------------------------------------------------------------------
310 !-----------------------------------------------------------------------------
311 ! 3. Initialize atom coords from the bigger system
312 !-----------------------------------------------------------------------------
313 nat = SIZE(sub_atom_index)
314 topology%natoms = nat
315 cpassert(.NOT. ASSOCIATED(topology%atom_info%r))
316 cpassert(.NOT. ASSOCIATED(topology%atom_info%id_atmname))
317 cpassert(.NOT. ASSOCIATED(topology%atom_info%id_molname))
318 cpassert(.NOT. ASSOCIATED(topology%atom_info%id_resname))
319 cpassert(.NOT. ASSOCIATED(topology%atom_info%atm_mass))
320 cpassert(.NOT. ASSOCIATED(topology%atom_info%atm_charge))
321 ALLOCATE (topology%atom_info%r(3, nat), topology%atom_info%id_atmname(nat), &
322 topology%atom_info%id_molname(nat), topology%atom_info%id_resname(nat), &
323 topology%atom_info%id_element(nat), topology%atom_info%atm_mass(nat), &
324 topology%atom_info%atm_charge(nat))
325
326 CALL cp_subsys_get(big_subsys, particles=particles)
327 DO iat = 1, nat
328 topology%atom_info%r(:, iat) = particles%els(sub_atom_index(iat))%r
329 topology%atom_info%id_atmname(iat) = str2id(s2s(sub_atom_kind_name(iat)))
330 topology%atom_info%id_molname(iat) = topology%atom_info%id_atmname(iat)
331 topology%atom_info%id_resname(iat) = topology%atom_info%id_atmname(iat)
332 !
333 ! Defining element
334 !
335 id_ = index(id2str(topology%atom_info%id_atmname(iat)), "_") - 1
336 IF (id_ == -1) id_ = len_trim(id2str(topology%atom_info%id_atmname(iat)))
337 strtmp1 = id2str(topology%atom_info%id_atmname(iat))
338 strtmp1 = strtmp1(1:id_)
339 CALL check_subsys_element(strtmp1, strtmp1, my_element, &
340 subsys_section, use_mm_map_first=.false.)
341 topology%atom_info%id_element(iat) = str2id(s2s(my_element))
342 topology%atom_info%atm_mass(iat) = 0._dp
343 topology%atom_info%atm_charge(iat) = 0._dp
344 END DO
345 topology%conn_type = do_conn_off
346
347 !-----------------------------------------------------------------------------
348 !-----------------------------------------------------------------------------
349 ! 4. Read in or generate the molecular connectivity
350 !-----------------------------------------------------------------------------
351 CALL connectivity_control(topology, para_env, subsys_section=subsys_section, &
352 force_env_section=force_env_section)
353
354 !-----------------------------------------------------------------------------
355 !-----------------------------------------------------------------------------
356 ! 5. Pack everything into the molecular types
357 !-----------------------------------------------------------------------------
358 CALL topology_connectivity_pack(molecule_kind_set, molecule_set, &
359 topology, subsys_section=subsys_section)
360
361 !-----------------------------------------------------------------------------
362 !-----------------------------------------------------------------------------
363 ! 6. Pack everything into the atomic types
364 !-----------------------------------------------------------------------------
365 CALL topology_coordinate_pack(particle_set, atomic_kind_set, &
366 molecule_kind_set, molecule_set, topology, subsys_section=subsys_section, &
367 force_env_section=force_env_section, ignore_outside_box=ignore_outside_box)
368
369 !-----------------------------------------------------------------------------
370 !-----------------------------------------------------------------------------
371 ! 7. Cleanup the topology structure type
372 !-----------------------------------------------------------------------------
373 CALL deallocate_topology(topology)
374
375 !-----------------------------------------------------------------------------
376 !-----------------------------------------------------------------------------
377 ! 8. Allocate new subsys
378 !-----------------------------------------------------------------------------
379 ALLOCATE (small_subsys)
380 CALL para_env%retain()
381 small_subsys%para_env => para_env
382 CALL particle_list_create(particles, els_ptr=particle_set)
383 CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
384 CALL molecule_list_create(mols, els_ptr=molecule_set)
385 CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)
386 CALL cp_subsys_set(small_subsys, particles=particles, atomic_kinds=atomic_kinds, &
387 molecules=mols, molecule_kinds=mol_kinds, cell=small_cell, &
388 cell_ref=small_cell, use_ref_cell=.false.)
389 CALL particle_list_release(particles)
390 CALL atomic_kind_list_release(atomic_kinds)
391 CALL molecule_list_release(mols)
392 CALL molecule_kind_list_release(mol_kinds)
393
394 ALLOCATE (small_subsys%virial)
395 CALL atprop_create(small_subsys%atprop)
396 CALL cp_result_create(small_subsys%results)
397 END SUBROUTINE create_small_subsys
398
399END MODULE cp_subsys_methods
atomic_kind_list_types
represent a simple array based list of the given type
Definition atomic_kind_list_types.F:15
atomic_kind_list_types::atomic_kind_list_release
subroutine, public atomic_kind_list_release(list)
releases a list (see doc/ReferenceCounting.html)
Definition atomic_kind_list_types.F:128
atomic_kind_list_types::atomic_kind_list_create
subroutine, public atomic_kind_list_create(list, els_ptr, owns_els, n_els)
creates a list
Definition atomic_kind_list_types.F:79
atomic_kind_types
Define the atomic kind types and their sub types.
Definition atomic_kind_types.F:23
atprop_types
Holds information on atomic properties.
Definition atprop_types.F:14
atprop_types::atprop_create
subroutine, public atprop_create(atprop_env)
...
Definition atprop_types.F:51
cell_methods
Handles all functions related to the CELL.
Definition cell_methods.F:15
cell_methods::write_cell
subroutine, public write_cell(cell, subsys_section, tag)
Write the cell parameters to the output unit.
Definition cell_methods.F:1035
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
cell_types::cell_retain
subroutine, public cell_retain(cell)
retains the given cell (see doc/ReferenceCounting.html)
Definition cell_types.F:547
colvar_methods
defines collective variables s({R}) and the derivative of this variable wrt R these can then be used ...
Definition colvar_methods.F:16
colvar_methods::colvar_read
recursive subroutine, public colvar_read(colvar, icol, colvar_section, para_env)
reads a colvar from the input
Definition colvar_methods.F:123
cp_result_types
set of type/routines to handle the storage of results in force_envs
Definition cp_result_types.F:18
cp_result_types::cp_result_create
subroutine, public cp_result_create(results)
Allocates and intitializes the cp_result.
Definition cp_result_types.F:96
cp_subsys_methods
Initialize a small environment for a particular calculation.
Definition cp_subsys_methods.F:15
cp_subsys_methods::create_small_subsys
subroutine, public 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)
updates the molecule information of the given subsys
Definition cp_subsys_methods.F:263
cp_subsys_methods::cp_subsys_create
subroutine, public cp_subsys_create(subsys, para_env, root_section, force_env_section, subsys_section, use_motion_section, qmmm, qmmm_env, exclusions, elkind)
Creates allocates and fills subsys from given input.
Definition cp_subsys_methods.F:97
cp_subsys_types
types that represent a subsys, i.e. a part of the system
Definition cp_subsys_types.F:16
cp_subsys_types::cp_subsys_set
subroutine, public cp_subsys_set(subsys, atomic_kinds, particles, local_particles, molecules, molecule_kinds, local_molecules, para_env, colvar_p, shell_particles, core_particles, gci, multipoles, results, cell, cell_ref, use_ref_cell)
sets various propreties of the subsys
Definition cp_subsys_types.F:210
cp_subsys_types::cp_subsys_get
subroutine, public cp_subsys_get(subsys, ref_count, atomic_kinds, atomic_kind_set, particles, particle_set, local_particles, molecules, molecule_set, molecule_kinds, molecule_kind_set, local_molecules, para_env, colvar_p, shell_particles, core_particles, gci, multipoles, natom, nparticle, ncore, nshell, nkind, atprop, virial, results, cell, cell_ref, use_ref_cell)
returns information about various attributes of the given subsys
Definition cp_subsys_types.F:364
exclusion_types
an exclusion type
Definition exclusion_types.F:10
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::do_stress_analytical
integer, parameter, public do_stress_analytical
Definition input_constants.F:449
input_constants::do_conn_off
integer, parameter, public do_conn_off
Definition input_constants.F:419
input_constants::do_stress_diagonal_anal
integer, parameter, public do_stress_diagonal_anal
Definition input_constants.F:449
input_constants::do_stress_diagonal_numer
integer, parameter, public do_stress_diagonal_numer
Definition input_constants.F:449
input_constants::do_stress_none
integer, parameter, public do_stress_none
Definition input_constants.F:449
input_constants::do_stress_numerical
integer, parameter, public do_stress_numerical
Definition input_constants.F:449
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
input_section_types::section_vals_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition input_section_types.F:731
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition input_section_types.F:704
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition input_section_types.F:1047
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
message_passing
Interface to the message passing library MPI.
Definition message_passing.F:23
molecule_kind_list_types
represent a simple array based list of the given type
Definition molecule_kind_list_types.F:15
molecule_kind_list_types::molecule_kind_list_create
subroutine, public molecule_kind_list_create(list, els_ptr, owns_els, n_els)
creates a list
Definition molecule_kind_list_types.F:79
molecule_kind_list_types::molecule_kind_list_release
subroutine, public molecule_kind_list_release(list)
releases a list (see doc/ReferenceCounting.html)
Definition molecule_kind_list_types.F:128
molecule_kind_types
Define the molecule kind structure types and the corresponding functionality.
Definition molecule_kind_types.F:16
molecule_list_types
represent a simple array based list of the given type
Definition molecule_list_types.F:15
molecule_list_types::molecule_list_create
subroutine, public molecule_list_create(list, els_ptr, owns_els, n_els)
creates a list
Definition molecule_list_types.F:80
molecule_list_types::molecule_list_release
subroutine, public molecule_list_release(list)
releases a list (see doc/ReferenceCounting.html)
Definition molecule_list_types.F:129
molecule_types
Define the data structure for the molecule information.
Definition molecule_types.F:16
particle_list_types
represent a simple array based list of the given type
Definition particle_list_types.F:15
particle_list_types::particle_list_create
subroutine, public particle_list_create(list, els_ptr, owns_els, n_els)
creates a list
Definition particle_list_types.F:80
particle_list_types::particle_list_release
subroutine, public particle_list_release(list)
releases a list (see doc/ReferenceCounting.html)
Definition particle_list_types.F:129
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
qmmm_types_low
Definition qmmm_types_low.F:13
string_table
generates a unique id number for a string (str2id) that can be used two compare two strings....
Definition string_table.F:22
string_table::s2s
character(len=default_string_length) function, public s2s(str)
converts a string in a string of default_string_length
Definition string_table.F:141
string_table::str2id
integer function, public str2id(str)
returns a unique id for a given string, and stores the string for later retrieval using the id.
Definition string_table.F:72
string_table::id2str
character(len=default_string_length) function, public id2str(id)
returns the string associated with a given id
Definition string_table.F:115
topology_connectivity_util
Collection of subroutine needed for topology related things.
Definition topology_connectivity_util.F:14
topology_connectivity_util::topology_connectivity_pack
subroutine, public topology_connectivity_pack(molecule_kind_set, molecule_set, topology, subsys_section)
topology connectivity pack
Definition topology_connectivity_util.F:65
topology_coordinate_util
Collection of subroutine needed for topology related things.
Definition topology_coordinate_util.F:13
topology_coordinate_util::topology_coordinate_pack
subroutine, public topology_coordinate_pack(particle_set, atomic_kind_set, molecule_kind_set, molecule_set, topology, qmmm, qmmm_env, subsys_section, force_env_section, exclusions, ignore_outside_box)
Take info readin from different file format and stuff it into compatible data structure in cp2k.
Definition topology_coordinate_util.F:87
topology_types
Definition topology_types.F:18
topology_types::deallocate_topology
subroutine, public deallocate_topology(topology)
Just DEALLOCATE all the stuff
Definition topology_types.F:392
topology_types::init_topology
subroutine, public init_topology(topology)
Just NULLIFY and zero all the stuff
Definition topology_types.F:206
topology_util
Collection of subroutine needed for topology related things.
Definition topology_util.F:13
topology_util::check_subsys_element
subroutine, public check_subsys_element(element_in, atom_name_in, element_out, subsys_section, use_mm_map_first)
Check and returns the ELEMENT label.
Definition topology_util.F:1144
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
topology::connectivity_control
subroutine, public connectivity_control(topology, para_env, qmmm, qmmm_env, subsys_section, force_env_section)
If reading in from external file, make sure its there first
Definition topology.F:310
topology::topology_control
subroutine, public topology_control(atomic_kind_set, particle_set, molecule_kind_set, molecule_set, colvar_p, gci, root_section, para_env, qmmm, qmmm_env, force_env_section, subsys_section, use_motion_section, exclusions, elkind, subsys)
...
Definition topology.F:133
virial_types
Definition virial_types.F:13
virial_types::virial_set
subroutine, public virial_set(virial, pv_total, pv_kinetic, pv_virial, pv_xc, pv_fock_4c, pv_constraint, pv_overlap, pv_ekinetic, pv_ppl, pv_ppnl, pv_ecore_overlap, pv_ehartree, pv_exc, pv_exx, pv_vdw, pv_mp2, pv_nlcc, pv_gapw, pv_lrigpw, pv_availability, pv_calculate, pv_numer, pv_diagonal)
...
Definition virial_types.F:192
atomic_kind_list_types::atomic_kind_list_type
represent a list of objects
Definition atomic_kind_list_types.F:45
atomic_kind_types::atomic_kind_type
Provides all information about an atomic kind.
Definition atomic_kind_types.F:45
cell_types::cell_type
Type defining parameters related to the simulation cell.
Definition cell_types.F:60
cp_subsys_types::cp_subsys_type
represents a system: atoms, molecules, their pos,vel,...
Definition cp_subsys_types.F:89
exclusion_types::exclusion_type
A type used to store lists of exclusions and onfos.
Definition exclusion_types.F:21
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:743
molecule_kind_list_types::molecule_kind_list_type
represent a list of objects
Definition molecule_kind_list_types.F:45
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:151
molecule_list_types::molecule_list_type
represent a list of objects
Definition molecule_list_types.F:46
molecule_types::molecule_type
Definition molecule_types.F:159
particle_list_types::particle_list_type
represent a list of objects
Definition particle_list_types.F:46
particle_types::particle_type
Definition particle_types.F:35
qmmm_types_low::qmmm_env_mm_type
...
Definition qmmm_types_low.F:238
topology_types::topology_parameters_type
Definition topology_types.F:143