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eip_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 Methods and functions on the EIP environment
10!> \par History
11!> 03.2006 initial create [tdk]
12!> \author Thomas D. Kuehne (tkuehne@phys.chem.ethz.ch)
13! **************************************************************************************************
14MODULE eip_environment
15 USE atomic_kind_types, ONLY: atomic_kind_type,&
16 get_atomic_kind
17 USE cell_methods, ONLY: read_cell,&
18 write_cell
19 USE cell_types, ONLY: cell_release,&
20 cell_type,&
21 get_cell
22 USE cp_subsys_methods, ONLY: cp_subsys_create
23 USE cp_subsys_types, ONLY: cp_subsys_set,&
24 cp_subsys_type
25 USE distribution_1d_types, ONLY: distribution_1d_release,&
26 distribution_1d_type
27 USE distribution_methods, ONLY: distribute_molecules_1d
28 USE eip_environment_types, ONLY: eip_env_set,&
29 eip_environment_type
30 USE input_section_types, ONLY: section_vals_get_subs_vals,&
31 section_vals_type,&
32 section_vals_val_get
33 USE kinds, ONLY: default_string_length,&
34 dp
35 USE message_passing, ONLY: mp_para_env_type
36 USE molecule_kind_types, ONLY: molecule_kind_type,&
37 write_molecule_kind_set
38 USE molecule_types, ONLY: molecule_type
39 USE particle_methods, ONLY: write_fist_particle_coordinates,&
40 write_particle_distances,&
41 write_structure_data
42 USE particle_types, ONLY: particle_type
43#include "./base/base_uses.f90"
44
45 IMPLICIT NONE
46
47 PRIVATE
48
49! *** Global parameters ***
50
51 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'eip_environment'
52
53! *** Public subroutines ***
54
55 PUBLIC :: eip_init
56
57CONTAINS
58
59! **************************************************************************************************
60!> \brief Initialize the eip environment
61!> \param eip_env The eip environment to retain
62!> \param root_section ...
63!> \param para_env ...
64!> \param force_env_section ...
65!> \param subsys_section ...
66!> \par History
67!> 03.2006 initial create [tdk]
68!> \author Thomas D. Kuehne (tkuehne@phys.chem.ethz.ch)
69! **************************************************************************************************
70 SUBROUTINE eip_init(eip_env, root_section, para_env, force_env_section, &
71 subsys_section)
72 TYPE(eip_environment_type), POINTER :: eip_env
73 TYPE(section_vals_type), POINTER :: root_section
74 TYPE(mp_para_env_type), POINTER :: para_env
75 TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
76
77 CHARACTER(len=*), PARAMETER :: routinen = 'eip_init'
78
79 INTEGER :: handle
80 LOGICAL :: use_ref_cell
81 REAL(kind=dp), DIMENSION(3) :: abc
82 TYPE(cell_type), POINTER :: cell, cell_ref
83 TYPE(cp_subsys_type), POINTER :: subsys
84 TYPE(section_vals_type), POINTER :: cell_section, colvar_section, eip_section
85
86 CALL timeset(routinen, handle)
87
88 cpassert(ASSOCIATED(eip_env))
89
90 ! nullifying pointers
91 NULLIFY (cell_section, colvar_section, eip_section, cell, cell_ref, &
92 subsys)
93
94 IF (.NOT. ASSOCIATED(subsys_section)) THEN
95 subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
96 END IF
97 cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
98 colvar_section => section_vals_get_subs_vals(subsys_section, "COLVAR")
99 eip_section => section_vals_get_subs_vals(force_env_section, "EIP")
100
101 CALL eip_env_set(eip_env=eip_env, eip_input=eip_section, &
102 force_env_input=force_env_section)
103
104 CALL read_cell(cell=cell, cell_ref=cell_ref, use_ref_cell=use_ref_cell, cell_section=cell_section, &
105 para_env=para_env)
106 CALL get_cell(cell=cell, abc=abc)
107 CALL write_cell(cell=cell, subsys_section=subsys_section)
108
109 CALL cp_subsys_create(subsys, para_env, root_section)
110
111 CALL eip_init_subsys(eip_env=eip_env, subsys=subsys, cell=cell, &
112 cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
113 subsys_section=subsys_section)
114
115 CALL cell_release(cell)
116 CALL cell_release(cell_ref)
117
118 CALL timestop(handle)
119
120 END SUBROUTINE eip_init
121
122! **************************************************************************************************
123!> \brief Initialize the eip environment
124!> \param eip_env The eip environment of matter
125!> \param subsys the subsys
126!> \param cell Pointer to the actual simulation cell
127!> \param cell_ref Pointer to the reference cell, used e.g. in NPT simulations
128!> \param use_ref_cell Logical which indicates if cell_ref is in use
129!> \param subsys_section ...
130!> \par History
131!> 03.2006 initial create [tdk]
132!> \author Thomas D. Kuehne (tkuehne@phys.chem.ethz.ch)
133! **************************************************************************************************
134 SUBROUTINE eip_init_subsys(eip_env, subsys, cell, cell_ref, use_ref_cell, subsys_section)
135 TYPE(eip_environment_type), POINTER :: eip_env
136 TYPE(cp_subsys_type), POINTER :: subsys
137 TYPE(cell_type), POINTER :: cell, cell_ref
138 LOGICAL, INTENT(in) :: use_ref_cell
139 TYPE(section_vals_type), POINTER :: subsys_section
140
141 CHARACTER(len=*), PARAMETER :: routinen = 'eip_init_subsys'
142
143 INTEGER :: handle, natom
144 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
145 TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
146 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
147 TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
148 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
149
150! ------------------------------------------------------------------------
151
152 CALL timeset(routinen, handle)
153
154 NULLIFY (atomic_kind_set, molecule_kind_set, particle_set, molecule_set, &
155 local_molecules, local_particles)
156
157 particle_set => subsys%particles%els
158 atomic_kind_set => subsys%atomic_kinds%els
159 molecule_kind_set => subsys%molecule_kinds%els
160 molecule_set => subsys%molecules%els
161
162! *** Print the molecule kind set ***
163 CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
164
165! *** Print the atomic coordinates
166 CALL write_fist_particle_coordinates(particle_set, subsys_section)
167 CALL write_particle_distances(particle_set, cell=cell, &
168 subsys_section=subsys_section)
169 CALL write_structure_data(particle_set, cell=cell, &
170 input_section=subsys_section)
171
172! *** Distribute molecules and atoms using the new data structures ***
173 CALL distribute_molecules_1d(atomic_kind_set=atomic_kind_set, &
174 particle_set=particle_set, &
175 local_particles=local_particles, &
176 molecule_kind_set=molecule_kind_set, &
177 molecule_set=molecule_set, &
178 local_molecules=local_molecules, &
179 force_env_section=eip_env%force_env_input)
180
181 natom = SIZE(particle_set)
182
183 ALLOCATE (eip_env%eip_forces(3, natom))
184
185 eip_env%eip_forces(:, :) = 0.0_dp
186
187 CALL cp_subsys_set(subsys, cell=cell)
188 CALL eip_env_set(eip_env=eip_env, subsys=subsys, &
189 cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
190 local_molecules=local_molecules, &
191 local_particles=local_particles)
192
193 CALL distribution_1d_release(local_particles)
194 CALL distribution_1d_release(local_molecules)
195
196 CALL eip_init_model(eip_env=eip_env)
197
198 CALL timestop(handle)
199
200 END SUBROUTINE eip_init_subsys
201
202! **************************************************************************************************
203!> \brief Initialize the empirical interatomic potnetial (force field) model
204!> \param eip_env The eip environment to retain
205!> \par History
206!> 03.2006 initial create [tdk]
207!> \author Thomas D. Kuehne (tkuehne@phys.chem.ethz.ch)
208! **************************************************************************************************
209 SUBROUTINE eip_init_model(eip_env)
210 TYPE(eip_environment_type), POINTER :: eip_env
211
212 CHARACTER(len=*), PARAMETER :: routinen = 'eip_init_model'
213
214 CHARACTER(LEN=default_string_length) :: eip_atomic_kind_name
215 INTEGER :: handle, i
216 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
217 TYPE(atomic_kind_type), POINTER :: atomic_kind_ptr
218 TYPE(section_vals_type), POINTER :: eip_section
219
220! ------------------------------------------------------------------------
221
222 CALL timeset(routinen, handle)
223
224 NULLIFY (atomic_kind_set, atomic_kind_ptr, eip_section)
225
226 eip_section => section_vals_get_subs_vals(eip_env%force_env_input, &
227 "EIP")
228
229 atomic_kind_set => eip_env%subsys%atomic_kinds%els
230
231 ! loop over all kinds
232 DO i = 1, SIZE(atomic_kind_set)
233 atomic_kind_ptr => eip_env%subsys%atomic_kinds%els(i)
234 CALL get_atomic_kind(atomic_kind=atomic_kind_ptr, &
235 name=eip_atomic_kind_name)
236 SELECT CASE (eip_atomic_kind_name)
237 CASE ("SI", "Si")
238 CALL section_vals_val_get(section_vals=eip_section, &
239 keyword_name="EIP-Model", &
240 i_val=eip_env%eip_model)
241 CASE DEFAULT
242 cpabort("EIP models for other elements than Si isn't implemented yet.")
243 END SELECT
244 END DO
245
246 CALL timestop(handle)
247
248 END SUBROUTINE eip_init_model
249
250END MODULE eip_environment
atomic_kind_types
Define the atomic kind types and their sub types.
Definition atomic_kind_types.F:23
atomic_kind_types::get_atomic_kind
subroutine, public get_atomic_kind(atomic_kind, fist_potential, element_symbol, name, mass, kind_number, natom, atom_list, rcov, rvdw, z, qeff, apol, cpol, mm_radius, shell, shell_active, damping)
Get attributes of an atomic kind.
Definition atomic_kind_types.F:138
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
eip_environment_types
The environment for the empirical interatomic potential methods.
Definition eip_environment_types.F:14
eip_environment_types::eip_env_set
subroutine, public eip_env_set(eip_env, eip_model, eip_energy, eip_energy_var, eip_forces, coord_avg, coord_var, count, subsys, atomic_kind_set, particle_set, local_particles, molecule_kind_set, molecule_set, local_molecules, eip_input, force_env_input, cell_ref, use_ref_cell, eip_kinetic_energy, eip_potential_energy)
Sets various attributes of the eip environment.
Definition eip_environment_types.F:278
eip_environment
Methods and functions on the EIP environment.
Definition eip_environment.F:14
eip_environment::eip_init
subroutine, public eip_init(eip_env, root_section, para_env, force_env_section, subsys_section)
Initialize the eip environment.
Definition eip_environment.F:72
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_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_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_methods
Define methods related to particle_type.
Definition particle_methods.F:14
particle_methods::write_fist_particle_coordinates
subroutine, public write_fist_particle_coordinates(particle_set, subsys_section, charges)
Write the atomic coordinates to the output unit.
Definition particle_methods.F:484
particle_methods::write_structure_data
subroutine, public write_structure_data(particle_set, cell, input_section)
Write structure data requested by a separate structure data input section to the output unit....
Definition particle_methods.F:786
particle_methods::write_particle_distances
subroutine, public write_particle_distances(particle_set, cell, subsys_section)
Write the matrix of the particle distances to the output unit.
Definition particle_methods.F:606
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
eip_environment_types::eip_environment_type
The empirical interatomic potential environment.
Definition eip_environment_types.F:83
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