(git:ccc2433)
cp_subsys_methods.F
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1 !--------------------------------------------------------------------------------------------------!
2 ! CP2K: A general program to perform molecular dynamics simulations !
3 ! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4 ! !
5 ! SPDX-License-Identifier: GPL-2.0-or-later !
6 !--------------------------------------------------------------------------------------------------!
7 
8 ! **************************************************************************************************
9 !> \brief 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 ! **************************************************************************************************
15 MODULE 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_types, ONLY: cell_retain,&
22  cell_type
23  USE colvar_methods, ONLY: colvar_read
24  USE cp_result_types, ONLY: cp_result_create
25  USE cp_subsys_types, ONLY: cp_subsys_get,&
26  cp_subsys_set,&
27  cp_subsys_type
28  USE exclusion_types, ONLY: exclusion_type
29  USE input_constants, ONLY: do_conn_off,&
30  do_stress_analytical,&
31  do_stress_diagonal_anal,&
32  do_stress_diagonal_numer,&
33  do_stress_none,&
34  do_stress_numerical
35  USE input_section_types, ONLY: section_vals_get,&
36  section_vals_get_subs_vals,&
37  section_vals_type,&
38  section_vals_val_get
39  USE kinds, ONLY: default_string_length,&
40  dp
41  USE message_passing, ONLY: mp_para_env_type
42  USE molecule_kind_list_types, ONLY: molecule_kind_list_create,&
43  molecule_kind_list_release,&
44  molecule_kind_list_type
45  USE molecule_kind_types, ONLY: molecule_kind_type
46  USE molecule_list_types, ONLY: molecule_list_create,&
47  molecule_list_release,&
48  molecule_list_type
49  USE molecule_types, ONLY: molecule_type
50  USE particle_list_types, ONLY: particle_list_create,&
51  particle_list_release,&
52  particle_list_type
53  USE particle_types, ONLY: particle_type
54  USE qmmm_types_low, ONLY: qmmm_env_mm_type
55  USE string_table, ONLY: id2str,&
56  s2s,&
57  str2id
58  USE topology, ONLY: connectivity_control,&
59  topology_control
60  USE topology_connectivity_util, ONLY: topology_connectivity_pack
61  USE topology_coordinate_util, ONLY: topology_coordinate_pack
62  USE topology_types, ONLY: deallocate_topology,&
63  init_topology,&
64  topology_parameters_type
65  USE topology_util, ONLY: check_subsys_element
66  USE virial_types, ONLY: virial_set
67 #include "./base/base_uses.f90"
68 
69  IMPLICIT NONE
70  PRIVATE
71 
72  LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .false.
73  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cp_subsys_methods'
74 
75  PUBLIC :: create_small_subsys, cp_subsys_create
76 
77 CONTAINS
78 
79 ! **************************************************************************************************
80 !> \brief Creates allocates and fills subsys from given input.
81 !> \param subsys ...
82 !> \param para_env ...
83 !> \param root_section ...
84 !> \param force_env_section ...
85 !> \param subsys_section ...
86 !> \param use_motion_section ...
87 !> \param qmmm ...
88 !> \param qmmm_env ...
89 !> \param exclusions ...
90 !> \param elkind ...
91 !> \author Ole Schuett
92 ! **************************************************************************************************
93  SUBROUTINE cp_subsys_create(subsys, para_env, &
94  root_section, force_env_section, subsys_section, &
95  use_motion_section, qmmm, qmmm_env, exclusions, elkind)
96  TYPE(cp_subsys_type), POINTER :: subsys
97  TYPE(mp_para_env_type), POINTER :: para_env
98  TYPE(section_vals_type), POINTER :: root_section
99  TYPE(section_vals_type), OPTIONAL, POINTER :: force_env_section, subsys_section
100  LOGICAL, INTENT(IN), OPTIONAL :: use_motion_section
101  LOGICAL, OPTIONAL :: qmmm
102  TYPE(qmmm_env_mm_type), OPTIONAL, POINTER :: qmmm_env
103  TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
104  POINTER :: exclusions
105  LOGICAL, INTENT(IN), OPTIONAL :: elkind
106 
107  INTEGER :: stress_tensor
108  INTEGER, DIMENSION(:), POINTER :: seed_vals
109  LOGICAL :: atomic_energy, atomic_stress, &
110  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 
163  CALL particle_list_create(particles, els_ptr=particle_set)
164  CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
165  CALL molecule_list_create(mols, els_ptr=molecule_set)
166  CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)
167 
168  CALL cp_subsys_set(subsys, particles=particles, atomic_kinds=atomic_kinds, &
169  molecules=mols, molecule_kinds=mol_kinds)
170 
171  CALL particle_list_release(particles)
172  CALL atomic_kind_list_release(atomic_kinds)
173  CALL molecule_list_release(mols)
174  CALL molecule_kind_list_release(mol_kinds)
175 
176  ! Should we compute the virial?
177  CALL section_vals_val_get(my_force_env_section, "STRESS_TENSOR", i_val=stress_tensor)
178  SELECT CASE (stress_tensor)
179  CASE (do_stress_none)
180  pv_availability = .false.
181  pv_numerical = .false.
182  pv_diagonal = .false.
183  CASE (do_stress_analytical)
184  pv_availability = .true.
185  pv_numerical = .false.
186  pv_diagonal = .false.
187  CASE (do_stress_numerical)
188  pv_availability = .true.
189  pv_numerical = .true.
190  pv_diagonal = .false.
191  CASE (do_stress_diagonal_anal)
192  pv_availability = .true.
193  pv_numerical = .false.
194  pv_diagonal = .true.
195  CASE (do_stress_diagonal_numer)
196  pv_availability = .true.
197  pv_numerical = .true.
198  pv_diagonal = .true.
199  END SELECT
200 
201  ALLOCATE (subsys%virial)
202  CALL virial_set(virial=subsys%virial, &
203  pv_availability=pv_availability, &
204  pv_numer=pv_numerical, &
205  pv_diagonal=pv_diagonal)
206 
207  ! Should we compute atomic properties?
208  CALL atprop_create(subsys%atprop)
209  CALL section_vals_val_get(my_force_env_section, "PROPERTIES%ATOMIC%ENERGY", l_val=atomic_energy)
210  subsys%atprop%energy = atomic_energy
211  CALL section_vals_val_get(my_force_env_section, "PROPERTIES%ATOMIC%PRESSURE", l_val=atomic_stress)
212  IF (atomic_stress) THEN
213  cpassert(pv_availability)
214  cpassert(.NOT. pv_numerical)
215  END IF
216  subsys%atprop%stress = atomic_stress
217 
218  CALL cp_result_create(subsys%results)
219  END SUBROUTINE cp_subsys_create
220 
221 ! **************************************************************************************************
222 !> \brief reads the colvar section of the colvar
223 !> \param subsys ...
224 !> \param colvar_section ...
225 !> \par History
226 !> 2006.01 Joost VandeVondele
227 ! **************************************************************************************************
228  SUBROUTINE cp_subsys_read_colvar(subsys, colvar_section)
229  TYPE(cp_subsys_type), POINTER :: subsys
230  TYPE(section_vals_type), POINTER :: colvar_section
231 
232  INTEGER :: ig, ncol
233 
234  CALL section_vals_get(colvar_section, n_repetition=ncol)
235  ALLOCATE (subsys%colvar_p(ncol))
236  DO ig = 1, ncol
237  NULLIFY (subsys%colvar_p(ig)%colvar)
238  CALL colvar_read(subsys%colvar_p(ig)%colvar, ig, colvar_section, subsys%para_env)
239  END DO
240  END SUBROUTINE cp_subsys_read_colvar
241 
242 ! **************************************************************************************************
243 !> \brief updates the molecule information of the given subsys
244 !> \param small_subsys the subsys to create
245 !> \param big_subsys the superset of small_subsys
246 !> \param small_cell ...
247 !> \param small_para_env the parallel environment for the new (small)
248 !> subsys
249 !> \param sub_atom_index indexes of the atoms that should be in small_subsys
250 !> \param sub_atom_kind_name ...
251 !> \param para_env ...
252 !> \param force_env_section ...
253 !> \param subsys_section ...
254 !> \param ignore_outside_box ...
255 !> \par History
256 !> 05.2004 created [fawzi]
257 !> \author Fawzi Mohamed, Teodoro Laino
258 !> \note
259 !> not really ready to be used with different para_envs for the small
260 !> and big part
261 ! **************************************************************************************************
262  SUBROUTINE create_small_subsys(small_subsys, big_subsys, small_cell, &
263  small_para_env, sub_atom_index, sub_atom_kind_name, &
264  para_env, force_env_section, subsys_section, ignore_outside_box)
265 
266  TYPE(cp_subsys_type), POINTER :: small_subsys, big_subsys
267  TYPE(cell_type), POINTER :: small_cell
268  TYPE(mp_para_env_type), POINTER :: small_para_env
269  INTEGER, DIMENSION(:), INTENT(in) :: sub_atom_index
270  CHARACTER(len=default_string_length), &
271  DIMENSION(:), INTENT(in) :: sub_atom_kind_name
272  TYPE(mp_para_env_type), POINTER :: para_env
273  TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
274  LOGICAL, INTENT(in), OPTIONAL :: ignore_outside_box
275 
276  CHARACTER(len=default_string_length) :: my_element, strtmp1
277  INTEGER :: iat, id_, nat
278  TYPE(atomic_kind_list_type), POINTER :: atomic_kinds
279  TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
280  TYPE(molecule_kind_list_type), POINTER :: mol_kinds
281  TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
282  TYPE(molecule_list_type), POINTER :: mols
283  TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
284  TYPE(particle_list_type), POINTER :: particles
285  TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
286  TYPE(topology_parameters_type) :: topology
287 
288  NULLIFY (mol_kinds, mols, particles, atomic_kinds, atomic_kind_set, particle_set, &
289  molecule_kind_set, molecule_set, particles, atomic_kinds)
290 
291  cpassert(.NOT. ASSOCIATED(small_subsys))
292  cpassert(ASSOCIATED(big_subsys))
293  IF (big_subsys%para_env /= small_para_env) &
294  cpabort("big_subsys%para_env==small_para_env")
295 
296  !-----------------------------------------------------------------------------
297  !-----------------------------------------------------------------------------
298  ! 1. Initialize the topology structure type
299  !-----------------------------------------------------------------------------
300  CALL init_topology(topology)
301 
302  !-----------------------------------------------------------------------------
303  !-----------------------------------------------------------------------------
304  ! 2. Get the cell info
305  !-----------------------------------------------------------------------------
306  topology%cell => small_cell
307  CALL cell_retain(small_cell)
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)
388  CALL particle_list_release(particles)
389  CALL atomic_kind_list_release(atomic_kinds)
390  CALL molecule_list_release(mols)
391  CALL molecule_kind_list_release(mol_kinds)
392 
393  ALLOCATE (small_subsys%virial)
394  CALL atprop_create(small_subsys%atprop)
395  CALL cp_result_create(small_subsys%results)
396  END SUBROUTINE create_small_subsys
397 
398 END 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:53
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:542
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:265
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:96
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)
sets various propreties of the subsys
Definition: cp_subsys_types.F:205
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)
returns information about various attributes of the given subsys
Definition: cp_subsys_types.F:345
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:441
input_constants::do_conn_off
integer, parameter, public do_conn_off
Definition: input_constants.F:412
input_constants::do_stress_diagonal_anal
integer, parameter, public do_stress_diagonal_anal
Definition: input_constants.F:441
input_constants::do_stress_diagonal_numer
integer, parameter, public do_stress_diagonal_numer
Definition: input_constants.F:441
input_constants::do_stress_none
integer, parameter, public do_stress_none
Definition: input_constants.F:441
input_constants::do_stress_numerical
integer, parameter, public do_stress_numerical
Definition: input_constants.F:441
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:724
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:697
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:1040
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:390
topology_types::init_topology
subroutine, public init_topology(topology)
Just NULLIFY and zero all the stuff
Definition: topology_types.F:205
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:1135
topology
Control for reading in different topologies and coordinates.
Definition: topology.F:13
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)
...
Definition: topology.F:125
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:285
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
topology_types::topology_parameters_type
Definition: topology_types.F:142