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embed_environment.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 embed environment: clone of the mixed environment
10 !> \author Vladimir Rybkin
11 ! **************************************************************************************************
12 MODULE embed_environment
13  USE atomic_kind_types, ONLY: atomic_kind_type
14  USE cell_methods, ONLY: read_cell,&
15  write_cell
16  USE cell_types, ONLY: cell_release,&
17  cell_type,&
18  get_cell
19  USE cp_subsys_methods, ONLY: cp_subsys_create
20  USE cp_subsys_types, ONLY: cp_subsys_set,&
21  cp_subsys_type
22  USE distribution_1d_types, ONLY: distribution_1d_release,&
23  distribution_1d_type
24  USE distribution_methods, ONLY: distribute_molecules_1d
25  USE embed_types, ONLY: embed_env_type,&
26  set_embed_env
27  USE input_section_types, ONLY: section_vals_get_subs_vals,&
28  section_vals_type
29  USE kinds, ONLY: dp
30  USE message_passing, ONLY: mp_para_env_type
31  USE molecule_kind_types, ONLY: molecule_kind_type,&
32  write_molecule_kind_set
33  USE molecule_types, ONLY: molecule_type
34  USE particle_types, ONLY: particle_type
35 #include "./base/base_uses.f90"
36 
37  IMPLICIT NONE
38 
39  PRIVATE
40 
41  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'embed_environment'
42  PUBLIC :: embed_init
43 
44 CONTAINS
45 
46 ! **************************************************************************************************
47 !> \brief reads the input and database file for embedding
48 !> \param embed_env ...
49 !> \param root_section ...
50 !> \param para_env ...
51 !> \param force_env_section ...
52 !> \param use_motion_section ...
53 !> \par Used By
54 !> embed_main
55 !> \author Vladimir Rybkin
56 ! **************************************************************************************************
57  SUBROUTINE embed_init(embed_env, root_section, para_env, force_env_section, &
58  use_motion_section)
59 
60  TYPE(embed_env_type), INTENT(INOUT) :: embed_env
61  TYPE(section_vals_type), POINTER :: root_section
62  TYPE(mp_para_env_type), POINTER :: para_env
63  TYPE(section_vals_type), POINTER :: force_env_section
64  LOGICAL, INTENT(IN) :: use_motion_section
65 
66  CHARACTER(len=*), PARAMETER :: routinen = 'embed_init'
67 
68  INTEGER :: handle
69  LOGICAL :: use_ref_cell
70  REAL(kind=dp), DIMENSION(3) :: abc
71  TYPE(cell_type), POINTER :: cell, cell_ref
72  TYPE(cp_subsys_type), POINTER :: subsys
73  TYPE(section_vals_type), POINTER :: cell_section, subsys_section
74 
75  CALL timeset(routinen, handle)
76 
77  NULLIFY (subsys, cell, cell_ref)
78  NULLIFY (cell_section)
79 
80  subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
81  cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
82 
83  CALL set_embed_env(embed_env, input=force_env_section)
84  CALL cp_subsys_create(subsys, para_env, root_section, &
85  force_env_section=force_env_section, &
86  use_motion_section=use_motion_section)
87 
88  CALL read_cell(cell, cell_ref, use_ref_cell=use_ref_cell, &
89  cell_section=cell_section, para_env=para_env)
90  CALL get_cell(cell, abc=abc)
91 
92  ! Print the cell parameters ***
93  CALL write_cell(cell, subsys_section)
94  CALL write_cell(cell_ref, subsys_section)
95 
96  CALL embed_init_subsys(embed_env, subsys, cell, cell_ref, &
97  force_env_section, subsys_section)
98 
99  CALL cell_release(cell)
100  CALL cell_release(cell_ref)
101 
102  CALL timestop(handle)
103 
104  END SUBROUTINE embed_init
105 
106 ! **************************************************************************************************
107 !> \brief Read the input and the database files for the setup of the
108 !> embed environment.
109 !> \param embed_env ...
110 !> \param subsys ...
111 !> \param cell ...
112 !> \param cell_ref ...
113 !> \param force_env_section ...
114 !> \param subsys_section ...
115 !> \date 02.2018
116 !> \author Vladimir Rybkin
117 ! **************************************************************************************************
118  SUBROUTINE embed_init_subsys(embed_env, subsys, cell, cell_ref, &
119  force_env_section, subsys_section)
120 
121  TYPE(embed_env_type), INTENT(INOUT) :: embed_env
122  TYPE(cp_subsys_type), POINTER :: subsys
123  TYPE(cell_type), POINTER :: cell, cell_ref
124  TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
125 
126  CHARACTER(len=*), PARAMETER :: routinen = 'embed_init_subsys'
127 
128  INTEGER :: handle
129  TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
130  TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
131  TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
132  TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
133  TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
134 
135  CALL timeset(routinen, handle)
136  NULLIFY (local_molecules, local_particles)
137  particle_set => subsys%particles%els
138  atomic_kind_set => subsys%atomic_kinds%els
139  molecule_set => subsys%molecules%els
140  molecule_kind_set => subsys%molecule_kinds%els
141 
142  ! Print the molecule kind set
143  CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
144 
145  ! Distribute molecules and atoms using the new data structures ***
146  CALL distribute_molecules_1d(atomic_kind_set=atomic_kind_set, &
147  particle_set=particle_set, &
148  local_particles=local_particles, &
149  molecule_kind_set=molecule_kind_set, &
150  molecule_set=molecule_set, &
151  local_molecules=local_molecules, &
152  force_env_section=force_env_section)
153 
154  CALL cp_subsys_set(subsys, cell=cell)
155 
156  ! set the embed_env
157  CALL set_embed_env(embed_env=embed_env, subsys=subsys)
158  CALL set_embed_env(embed_env=embed_env, &
159  cell_ref=cell_ref, &
160  local_molecules=local_molecules, &
161  local_particles=local_particles)
162 
163  CALL distribution_1d_release(local_particles)
164  CALL distribution_1d_release(local_molecules)
165 
166  CALL timestop(handle)
167 
168  END SUBROUTINE embed_init_subsys
169 
170 END MODULE embed_environment
atomic_kind_types
Define the atomic kind types and their sub types.
Definition: atomic_kind_types.F:23
cell_methods
Handles all functions related to the CELL.
Definition: cell_methods.F:15
cell_methods::read_cell
recursive subroutine, public read_cell(cell, cell_ref, use_ref_cell, cell_section, check_for_ref, para_env)
...
Definition: cell_methods.F:272
cell_methods::write_cell
subroutine, public write_cell(cell, subsys_section, tag)
Write the cell parameters to the output unit.
Definition: cell_methods.F:731
cell_types
Handles all functions related to the CELL.
Definition: cell_types.F:15
cell_types::cell_release
subroutine, public cell_release(cell)
releases the given cell (see doc/ReferenceCounting.html)
Definition: cell_types.F:559
cell_types::get_cell
subroutine, public get_cell(cell, alpha, beta, gamma, deth, orthorhombic, abc, periodic, h, h_inv, symmetry_id, tag)
Get informations about a simulation cell.
Definition: cell_types.F:195
cp_subsys_methods
Initialize a small environment for a particular calculation.
Definition: cp_subsys_methods.F:15
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
distribution_1d_types
stores a lists of integer that are local to a processor. The idea is that these integers represent ob...
Definition: distribution_1d_types.F:24
distribution_1d_types::distribution_1d_release
subroutine, public distribution_1d_release(distribution_1d)
releases the given distribution_1d
Definition: distribution_1d_types.F:149
distribution_methods
Distribution methods for atoms, particles, or molecules.
Definition: distribution_methods.F:15
distribution_methods::distribute_molecules_1d
subroutine, public distribute_molecules_1d(atomic_kind_set, particle_set, local_particles, molecule_kind_set, molecule_set, local_molecules, force_env_section, prev_molecule_kind_set, prev_local_molecules)
Distribute molecules and particles.
Definition: distribution_methods.F:108
embed_environment
initialize embed environment: clone of the mixed environment
Definition: embed_environment.F:12
embed_environment::embed_init
subroutine, public embed_init(embed_env, root_section, para_env, force_env_section, use_motion_section)
reads the input and database file for embedding
Definition: embed_environment.F:59
embed_types
Definition: embed_types.F:8
embed_types::set_embed_env
subroutine, public set_embed_env(embed_env, atomic_kind_set, particle_set, local_particles, local_molecules, molecule_kind_set, molecule_set, cell_ref, subsys, input, sub_para_env)
...
Definition: embed_types.F:231
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
kinds
Defines the basic variable types.
Definition: kinds.F:23
kinds::dp
integer, parameter, public dp
Definition: kinds.F:34
message_passing
Interface to the message passing library MPI.
Definition: message_passing.F:23
molecule_kind_types
Define the molecule kind structure types and the corresponding functionality.
Definition: molecule_kind_types.F:16
molecule_kind_types::write_molecule_kind_set
subroutine, public write_molecule_kind_set(molecule_kind_set, subsys_section)
Write a moleculeatomic kind set data set to the output unit.
Definition: molecule_kind_types.F:966
molecule_types
Define the data structure for the molecule information.
Definition: molecule_types.F:16
particle_types
Define the data structure for the particle information.
Definition: particle_types.F:19