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qs_subsys_methods.F
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1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Routines that work on qs_subsys_type
10!> \author Ole Schuett
11! **************************************************************************************************
12MODULE qs_subsys_methods
13 USE atom_types, ONLY: lmat
14 USE atomic_kind_types, ONLY: atomic_kind_type,&
15 get_atomic_kind
16 USE basis_set_types, ONLY: get_gto_basis_set,&
17 gto_basis_set_type
18 USE cell_methods, ONLY: cell_create,&
19 read_cell,&
20 write_cell
21 USE cell_types, ONLY: cell_clone,&
22 cell_release,&
23 cell_type
24 USE cp_subsys_methods, ONLY: cp_subsys_create
25 USE cp_subsys_types, ONLY: cp_subsys_get,&
26 cp_subsys_release,&
27 cp_subsys_set,&
28 cp_subsys_type
29 USE external_potential_types, ONLY: all_potential_type,&
30 get_potential,&
31 gth_potential_type,&
32 sgp_potential_type
33 USE input_section_types, ONLY: section_vals_get_subs_vals,&
34 section_vals_type
35 USE kinds, ONLY: dp
36 USE message_passing, ONLY: mp_para_env_type
37 USE molecule_kind_types, ONLY: get_molecule_kind,&
38 molecule_kind_type,&
39 set_molecule_kind
40 USE qs_cneo_types, ONLY: cneo_potential_type,&
41 get_cneo_potential
42 USE qs_kind_types, ONLY: create_qs_kind_set,&
43 get_qs_kind,&
44 init_atom_electronic_state,&
45 qs_kind_type
46 USE qs_subsys_types, ONLY: qs_subsys_set,&
47 qs_subsys_type
48#include "./base/base_uses.f90"
49
50 IMPLICIT NONE
51 PRIVATE
52
53 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'qs_subsys_methods'
54
55 PUBLIC :: qs_subsys_create
56
57CONTAINS
58
59! **************************************************************************************************
60!> \brief Creates a qs_subsys. Optionally an existsing cp_subsys is used.
61!> \param subsys ...
62!> \param para_env ...
63!> \param root_section ...
64!> \param force_env_section ...
65!> \param subsys_section ...
66!> \param use_motion_section ...
67!> \param cp_subsys ...
68!> \param cell ...
69!> \param cell_ref ...
70!> \param elkind ...
71!> \param silent ...
72! **************************************************************************************************
73 SUBROUTINE qs_subsys_create(subsys, para_env, root_section, force_env_section, subsys_section, &
74 use_motion_section, cp_subsys, cell, cell_ref, elkind, silent)
75 TYPE(qs_subsys_type), INTENT(OUT) :: subsys
76 TYPE(mp_para_env_type), POINTER :: para_env
77 TYPE(section_vals_type), OPTIONAL, POINTER :: root_section
78 TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
79 LOGICAL, INTENT(IN) :: use_motion_section
80 TYPE(cp_subsys_type), OPTIONAL, POINTER :: cp_subsys
81 TYPE(cell_type), OPTIONAL, POINTER :: cell, cell_ref
82 LOGICAL, INTENT(IN), OPTIONAL :: elkind, silent
83
84 LOGICAL :: be_silent, use_ref_cell
85 TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
86 TYPE(cell_type), POINTER :: my_cell, my_cell_ref
87 TYPE(cp_subsys_type), POINTER :: my_cp_subsys
88 TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
89 TYPE(section_vals_type), POINTER :: cell_section, kind_section
90
91 NULLIFY (atomic_kind_set, qs_kind_set, cell_section, kind_section, my_cell, my_cell_ref, my_cp_subsys)
92
93 be_silent = .false.
94 IF (PRESENT(silent)) be_silent = silent
95 ! create cp_subsys
96 IF (PRESENT(cp_subsys)) THEN
97 my_cp_subsys => cp_subsys
98 ELSE IF (PRESENT(root_section)) THEN
99 CALL cp_subsys_create(my_cp_subsys, para_env, root_section=root_section, &
100 force_env_section=force_env_section, &
101 subsys_section=subsys_section, &
102 use_motion_section=use_motion_section, &
103 elkind=elkind)
104 ELSE
105 cpabort("qs_subsys_create: cp_subsys or root_section needed")
106 END IF
107
108 ! create cp_subsys%cell
109 !TODO: moved to cp_subsys_create(), needs further disentanglement of cell_ref.
110 use_ref_cell = .false.
111 IF (PRESENT(cell)) THEN
112 my_cell => cell
113 IF (PRESENT(cell_ref)) THEN
114 my_cell_ref => cell_ref
115 use_ref_cell = .true.
116 ELSE
117 CALL cell_create(my_cell_ref)
118 CALL cell_clone(my_cell, my_cell_ref, tag="CELL_REF")
119 END IF
120 ELSE
121 cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
122 CALL read_cell(my_cell, my_cell_ref, use_ref_cell=use_ref_cell, &
123 cell_section=cell_section, para_env=para_env)
124 END IF
125 CALL cp_subsys_set(my_cp_subsys, cell=my_cell)
126 CALL write_cell(my_cell, subsys_section)
127 CALL write_cell(my_cell_ref, subsys_section)
128
129 ! setup qs_kinds
130 CALL cp_subsys_get(my_cp_subsys, atomic_kind_set=atomic_kind_set)
131 kind_section => section_vals_get_subs_vals(subsys_section, "KIND")
132 CALL create_qs_kind_set(qs_kind_set, atomic_kind_set, kind_section, &
133 para_env, force_env_section, be_silent)
134
135 CALL num_ao_el_per_molecule(my_cp_subsys%molecule_kinds%els, &
136 qs_kind_set)
137
138 CALL qs_subsys_set(subsys, &
139 cp_subsys=my_cp_subsys, &
140 cell_ref=my_cell_ref, &
141 use_ref_cell=use_ref_cell, &
142 qs_kind_set=qs_kind_set)
143
144 IF (.NOT. PRESENT(cell)) CALL cell_release(my_cell)
145 IF (.NOT. PRESENT(cell_ref)) CALL cell_release(my_cell_ref)
146 IF (.NOT. PRESENT(cp_subsys)) CALL cp_subsys_release(my_cp_subsys)
147
148 END SUBROUTINE qs_subsys_create
149
150! **************************************************************************************************
151!> \brief Read a molecule kind data set from the input file.
152!> \param molecule_kind_set ...
153!> \param qs_kind_set ...
154!> \date 22.11.2004
155!> \par History
156!> Rustam Z. Khaliullin 10.2014 - charges and electrons of molecules
157!> are now in agreement with atomic guess
158!> \author MI
159!> \version 1.0
160! **************************************************************************************************
161 SUBROUTINE num_ao_el_per_molecule(molecule_kind_set, qs_kind_set)
162
163 TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
164 TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
165
166 INTEGER :: arbitrary_spin, iatom, ikind, imol, &
167 n_ao, natom, nmol_kind, nsgf, nspins, &
168 z_molecule
169 INTEGER, DIMENSION(0:lmat, 10) :: ne_core, ne_elem, ne_explicit
170 INTEGER, DIMENSION(2) :: n_occ_alpha_and_beta
171 REAL(kind=dp) :: charge_molecule, zeff, zeff_correction
172 REAL(kind=dp), DIMENSION(0:lmat, 10, 2) :: edelta
173 TYPE(all_potential_type), POINTER :: all_potential
174 TYPE(atomic_kind_type), POINTER :: atomic_kind
175 TYPE(cneo_potential_type), POINTER :: cneo_potential
176 TYPE(gth_potential_type), POINTER :: gth_potential
177 TYPE(gto_basis_set_type), POINTER :: orb_basis_set
178 TYPE(molecule_kind_type), POINTER :: molecule_kind
179 TYPE(sgp_potential_type), POINTER :: sgp_potential
180
181 IF (ASSOCIATED(molecule_kind_set)) THEN
182
183 nspins = 2
184 nmol_kind = SIZE(molecule_kind_set, 1)
185 natom = 0
186
187 ! *** Initialize the molecule kind data structure ***
188 arbitrary_spin = 1
189 DO imol = 1, nmol_kind
190
191 molecule_kind => molecule_kind_set(imol)
192 CALL get_molecule_kind(molecule_kind=molecule_kind, &
193 natom=natom)
194 !nelectron = 0
195 n_ao = 0
196 n_occ_alpha_and_beta(1:nspins) = 0
197 z_molecule = 0
198
199 DO iatom = 1, natom
200
201 atomic_kind => molecule_kind%atom_list(iatom)%atomic_kind
202 CALL get_atomic_kind(atomic_kind, kind_number=ikind)
203 CALL get_qs_kind(qs_kind_set(ikind), &
204 basis_set=orb_basis_set, &
205 all_potential=all_potential, &
206 gth_potential=gth_potential, &
207 sgp_potential=sgp_potential, &
208 cneo_potential=cneo_potential)
209
210 ! Obtain the electronic state of the atom
211 ! The same state is used to calculate the ATOMIC GUESS
212 ! It is great that we are consistent with ATOMIC_GUESS
213 CALL init_atom_electronic_state(atomic_kind=atomic_kind, &
214 qs_kind=qs_kind_set(ikind), &
215 ncalc=ne_explicit, &
216 ncore=ne_core, &
217 nelem=ne_elem, &
218 edelta=edelta)
219
220 ! If &BS section is used ATOMIC_GUESS is calculated twice
221 ! for two separate wfns with their own alpha-beta combinations
222 ! This is done to break the spin symmetry of the initial wfn
223 ! For now, only alpha part of &BS is used to count electrons on
224 ! molecules
225 ! Get the number of explicit electrons (i.e. with orbitals)
226 ! For now, only the total number of electrons can be obtained
227 ! from init_atom_electronic_state
228 n_occ_alpha_and_beta(arbitrary_spin) = &
229 n_occ_alpha_and_beta(arbitrary_spin) + sum(ne_explicit) + &
230 sum(nint(2*edelta(:, :, arbitrary_spin)))
231 ! We need a way to specify the number of alpha and beta electrons
232 ! on each molecule (i.e. multiplicity is not enough)
233 !n_occ(ispin) = n_occ(ispin) + SUM(ne_explicit) + SUM(NINT(2*edelta(:, :, ispin)))
234
235 IF (ASSOCIATED(all_potential)) THEN
236 CALL get_potential(potential=all_potential, zeff=zeff, &
237 zeff_correction=zeff_correction)
238 ELSE IF (ASSOCIATED(gth_potential)) THEN
239 CALL get_potential(potential=gth_potential, zeff=zeff, &
240 zeff_correction=zeff_correction)
241 ELSE IF (ASSOCIATED(sgp_potential)) THEN
242 CALL get_potential(potential=sgp_potential, zeff=zeff, &
243 zeff_correction=zeff_correction)
244 ELSE IF (ASSOCIATED(cneo_potential)) THEN
245 CALL get_cneo_potential(potential=cneo_potential, zeff=zeff)
246 zeff_correction = 0.0_dp
247 ELSE
248 zeff = 0.0_dp
249 zeff_correction = 0.0_dp
250 END IF
251 z_molecule = z_molecule + nint(zeff - zeff_correction)
252
253 ! this one does not work because nelem is not adjusted in the symmetry breaking code
254 !CALL get_atomic_kind(atomic_kind,z=z)
255 !z_molecule=z_molecule+z
256
257 IF (ASSOCIATED(orb_basis_set)) THEN
258 CALL get_gto_basis_set(gto_basis_set=orb_basis_set, nsgf=nsgf)
259 ELSE
260 nsgf = 0
261 END IF
262 n_ao = n_ao + nsgf
263
264 END DO ! iatom
265
266 ! At this point we have the number of electrons (alpha+beta) on the molecule
267 ! as they are seen by the ATOMIC GUESS routines
268 charge_molecule = real(z_molecule - n_occ_alpha_and_beta(arbitrary_spin), dp)
269 CALL set_molecule_kind(molecule_kind=molecule_kind, &
270 nelectron=n_occ_alpha_and_beta(arbitrary_spin), &
271 charge=charge_molecule, &
272 nsgf=n_ao)
273
274 END DO ! imol
275 END IF
276
277 END SUBROUTINE num_ao_el_per_molecule
278
279END MODULE qs_subsys_methods
external_potential_types::get_potential
Definition external_potential_types.F:276
atom_types
Define the atom type and its sub types.
Definition atom_types.F:15
atom_types::lmat
integer, parameter, public lmat
Definition atom_types.F:67
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
basis_set_types
Definition basis_set_types.F:15
basis_set_types::get_gto_basis_set
subroutine, public get_gto_basis_set(gto_basis_set, name, aliases, norm_type, kind_radius, ncgf, nset, nsgf, cgf_symbol, sgf_symbol, norm_cgf, set_radius, lmax, lmin, lx, ly, lz, m, ncgf_set, npgf, nsgf_set, nshell, cphi, pgf_radius, sphi, scon, zet, first_cgf, first_sgf, l, last_cgf, last_sgf, n, gcc, maxco, maxl, maxpgf, maxsgf_set, maxshell, maxso, nco_sum, npgf_sum, nshell_sum, maxder, short_kind_radius, npgf_seg_sum)
...
Definition basis_set_types.F:630
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:273
cell_methods::write_cell
subroutine, public write_cell(cell, subsys_section, tag)
Write the cell parameters to the output unit.
Definition cell_methods.F:732
cell_methods::cell_create
subroutine, public cell_create(cell, hmat, periodic, tag)
allocates and initializes a cell
Definition cell_methods.F:86
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::cell_clone
subroutine, public cell_clone(cell_in, cell_out, tag)
Clone cell variable.
Definition cell_types.F:107
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_release
subroutine, public cp_subsys_release(subsys)
releases a subsys (see doc/ReferenceCounting.html)
Definition cp_subsys_types.F:150
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
external_potential_types
Definition of the atomic potential types.
Definition external_potential_types.F:14
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
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::get_molecule_kind
subroutine, public get_molecule_kind(molecule_kind, atom_list, bond_list, bend_list, ub_list, impr_list, opbend_list, colv_list, fixd_list, g3x3_list, g4x6_list, vsite_list, torsion_list, shell_list, name, mass, charge, kind_number, natom, nbend, nbond, nub, nimpr, nopbend, nconstraint, nconstraint_fixd, nfixd, ncolv, ng3x3, ng4x6, nvsite, nfixd_restraint, ng3x3_restraint, ng4x6_restraint, nvsite_restraint, nrestraints, nmolecule, nsgf, nshell, ntorsion, molecule_list, nelectron, nelectron_alpha, nelectron_beta, bond_kind_set, bend_kind_set, ub_kind_set, impr_kind_set, opbend_kind_set, torsion_kind_set, molname_generated)
Get informations about a molecule kind.
Definition molecule_kind_types.F:504
molecule_kind_types::set_molecule_kind
subroutine, public set_molecule_kind(molecule_kind, name, mass, charge, kind_number, molecule_list, atom_list, nbond, bond_list, nbend, bend_list, nub, ub_list, nimpr, impr_list, nopbend, opbend_list, ntorsion, torsion_list, fixd_list, ncolv, colv_list, ng3x3, g3x3_list, ng4x6, nfixd, g4x6_list, nvsite, vsite_list, ng3x3_restraint, ng4x6_restraint, nfixd_restraint, nshell, shell_list, nvsite_restraint, bond_kind_set, bend_kind_set, ub_kind_set, torsion_kind_set, impr_kind_set, opbend_kind_set, nelectron, nsgf, molname_generated)
Set the components of a molecule kind.
Definition molecule_kind_types.F:773
qs_cneo_types
Types used by CNEO-DFT (see J. Chem. Theory Comput. 2025, 21, 16, 7865–7877)
Definition qs_cneo_types.F:15
qs_cneo_types::get_cneo_potential
subroutine, public get_cneo_potential(potential, z, zeff, mass, elec_conf, nsgf, nne, npsgf, nsotot, my_gcc_h, my_gcc_s, ovlp, kin, utrans, distance, harmonics, qlm_gg, gg, vgg, n2oindex, o2nindex, rad2l, oorad2l)
...
Definition qs_cneo_types.F:264
qs_kind_types
Define the quickstep kind type and their sub types.
Definition qs_kind_types.F:23
qs_kind_types::get_qs_kind
subroutine, public get_qs_kind(qs_kind, basis_set, basis_type, ncgf, nsgf, all_potential, tnadd_potential, gth_potential, sgp_potential, upf_potential, cneo_potential, se_parameter, dftb_parameter, xtb_parameter, dftb3_param, zatom, zeff, elec_conf, mao, lmax_dftb, alpha_core_charge, ccore_charge, core_charge, core_charge_radius, paw_proj_set, paw_atom, hard_radius, hard0_radius, max_rad_local, covalent_radius, vdw_radius, gpw_type_forced, harmonics, max_iso_not0, max_s_harm, grid_atom, ngrid_ang, ngrid_rad, lmax_rho0, dft_plus_u_atom, l_of_dft_plus_u, n_of_dft_plus_u, u_minus_j, u_of_dft_plus_u, j_of_dft_plus_u, alpha_of_dft_plus_u, beta_of_dft_plus_u, j0_of_dft_plus_u, occupation_of_dft_plus_u, dispersion, bs_occupation, magnetization, no_optimize, addel, laddel, naddel, orbitals, max_scf, eps_scf, smear, u_ramping, u_minus_j_target, eps_u_ramping, init_u_ramping_each_scf, reltmat, ghost, floating, name, element_symbol, pao_basis_size, pao_model_file, pao_potentials, pao_descriptors, nelec)
Get attributes of an atomic kind.
Definition qs_kind_types.F:466
qs_kind_types::init_atom_electronic_state
subroutine, public init_atom_electronic_state(atomic_kind, qs_kind, ncalc, ncore, nelem, edelta)
...
Definition qs_kind_types.F:3392
qs_kind_types::create_qs_kind_set
subroutine, public create_qs_kind_set(qs_kind_set, atomic_kind_set, kind_section, para_env, force_env_section, silent)
Read an atomic kind set data set from the input file.
Definition qs_kind_types.F:2807
qs_subsys_methods
Routines that work on qs_subsys_type.
Definition qs_subsys_methods.F:12
qs_subsys_methods::qs_subsys_create
subroutine, public qs_subsys_create(subsys, para_env, root_section, force_env_section, subsys_section, use_motion_section, cp_subsys, cell, cell_ref, elkind, silent)
Creates a qs_subsys. Optionally an existsing cp_subsys is used.
Definition qs_subsys_methods.F:75
qs_subsys_types
types that represent a quickstep subsys
Definition qs_subsys_types.F:12
qs_subsys_types::qs_subsys_set
subroutine, public qs_subsys_set(subsys, cp_subsys, local_particles, local_molecules, cell, cell_ref, use_ref_cell, energy, force, qs_kind_set, nelectron_total, nelectron_spin)
...
Definition qs_subsys_types.F:226
atomic_kind_types::atomic_kind_type
Provides all information about an atomic kind.
Definition atomic_kind_types.F:45
basis_set_types::gto_basis_set_type
Definition basis_set_types.F:72
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
external_potential_types::all_potential_type
Definition external_potential_types.F:70
external_potential_types::gth_potential_type
Definition external_potential_types.F:116
external_potential_types::sgp_potential_type
Definition external_potential_types.F:172
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:763
molecule_kind_types::molecule_kind_type
Definition molecule_kind_types.F:148
qs_cneo_types::cneo_potential_type
Definition qs_cneo_types.F:53
qs_kind_types::qs_kind_type
Provides all information about a quickstep kind.
Definition qs_kind_types.F:177
qs_subsys_types::qs_subsys_type
Definition qs_subsys_types.F:56