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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! **************************************************************************************************
12MODULE 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
44CONTAINS
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
170END 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
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:55
cp_subsys_types::cp_subsys_type
represents a system: atoms, molecules, their pos,vel,...
Definition cp_subsys_types.F:89
distribution_1d_types::distribution_1d_type
structure to store local (to a processor) ordered lists of integers.
Definition distribution_1d_types.F:62
embed_types::embed_env_type
Embedding environment type.
Definition embed_types.F:127
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:126
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:763
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:161
molecule_types::molecule_type
Definition molecule_types.F:110
particle_types::particle_type
Definition particle_types.F:35