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atoms_input.F
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atoms_input.F
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!--------------------------------------------------------------------------------------------------!
! CP2K: A general program to perform molecular dynamics simulations !
! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
! !
! SPDX-License-Identifier: GPL-2.0-or-later !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \par History
!> cjm, Feb-20-2001 : added all the extended variables to
!> system_type
!> gt 23-09-2002 : major changes. Pointer part is allocated/deallocated
!> and initialized here. Atomic coordinates can now be
!> read also from &COORD section in the input file.
!> If &COORD is not found, .dat file is read.
!> If & coord is found and .NOT. 'INIT', parsing of the .dat
!> is performed to get the proper coords/vel/eta variables
!> CJM 31-7-03 : Major rewrite. No more atype
! **************************************************************************************************
MODULE atoms_input
USE atomic_kind_types, ONLY: atomic_kind_type,&
get_atomic_kind
USE cell_types, ONLY: cell_type,&
pbc,&
scaled_to_real
USE cp_linked_list_input, ONLY: cp_sll_val_next,&
cp_sll_val_type
USE cp_log_handling, ONLY: cp_logger_get_default_io_unit,&
cp_to_string
USE cp_parser_methods, ONLY: read_float_object
USE cp_units, ONLY: cp_unit_to_cp2k
USE input_section_types, ONLY: section_vals_get,&
section_vals_get_subs_vals,&
section_vals_list_get,&
section_vals_remove_values,&
section_vals_type,&
section_vals_val_get
USE input_val_types, ONLY: val_get,&
val_type
USE kinds, ONLY: default_string_length,&
dp
USE memory_utilities, ONLY: reallocate
USE particle_types, ONLY: particle_type
USE shell_potential_types, ONLY: shell_kind_type
USE string_table, ONLY: id2str,&
s2s,&
str2id
USE string_utilities, ONLY: uppercase
USE topology_types, ONLY: atom_info_type,&
topology_parameters_type
#include "./base/base_uses.f90"
IMPLICIT NONE
PRIVATE
PUBLIC :: read_atoms_input, read_shell_coord_input
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'atoms_input'
CONTAINS
! **************************************************************************************************
!> \brief ...
!> \param topology ...
!> \param overwrite ...
!> \param subsys_section ...
!> \param save_mem ...
!> \author CJM
! **************************************************************************************************
SUBROUTINE read_atoms_input(topology, overwrite, subsys_section, save_mem)
TYPE(topology_parameters_type) :: topology
LOGICAL, INTENT(IN), OPTIONAL :: overwrite
TYPE(section_vals_type), POINTER :: subsys_section
LOGICAL, INTENT(IN), OPTIONAL :: save_mem
CHARACTER(len=*), PARAMETER :: routineN = 'read_atoms_input'
CHARACTER(len=2*default_string_length) :: line_att
CHARACTER(len=default_string_length) :: error_message, my_default_index, strtmp, &
unit_str
INTEGER :: default_id, end_c, handle, iatom, j, &
natom, output_unit, start_c, wrd
LOGICAL :: explicit, is_ok, my_overwrite, &
my_save_mem, scaled_coordinates
REAL(KIND=dp) :: r0(3), unit_conv
TYPE(atom_info_type), POINTER :: atom_info
TYPE(cell_type), POINTER :: cell
TYPE(cp_sll_val_type), POINTER :: list
TYPE(section_vals_type), POINTER :: coord_section
TYPE(val_type), POINTER :: val
my_overwrite = .FALSE.
my_save_mem = .FALSE.
error_message = ""
output_unit = cp_logger_get_default_io_unit()
IF (PRESENT(overwrite)) my_overwrite = overwrite
IF (PRESENT(save_mem)) my_save_mem = save_mem
NULLIFY (coord_section)
coord_section => section_vals_get_subs_vals(subsys_section, "COORD")
CALL section_vals_get(coord_section, explicit=explicit)
IF (.NOT. explicit) RETURN
CALL timeset(routineN, handle)
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 1. get cell and topology%atom_info
!-----------------------------------------------------------------------------
atom_info => topology%atom_info
cell => topology%cell_muc
CALL section_vals_val_get(coord_section, "UNIT", c_val=unit_str)
CALL section_vals_val_get(coord_section, "SCALED", l_val=scaled_coordinates)
unit_conv = cp_unit_to_cp2k(1.0_dp, TRIM(unit_str))
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 2. Read in the coordinates from &COORD section in the input file
!-----------------------------------------------------------------------------
CALL section_vals_val_get(coord_section, "_DEFAULT_KEYWORD_", &
n_rep_val=natom)
topology%natoms = natom
IF (my_overwrite) THEN
CPASSERT(SIZE(atom_info%r, 2) == natom)
CALL cp_warn(__LOCATION__, &
"Overwriting coordinates. Active coordinates read from &COORD section."// &
" Active coordinates READ from &COORD section ")
CALL section_vals_list_get(coord_section, "_DEFAULT_KEYWORD_", list=list)
DO iatom = 1, natom
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
! Read name and atomic coordinates
start_c = 1
DO wrd = 1, 4
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (LEN_TRIM(line_att(start_c:end_c - 1)) == 0) &
CPABORT("incorrectly formatted line in coord section'"//line_att//"'")
IF (wrd == 1) THEN
atom_info%id_atmname(iatom) = str2id(s2s(line_att(start_c:end_c - 1)))
ELSE
READ (line_att(start_c:end_c - 1), *) atom_info%r(wrd - 1, iatom)
END IF
start_c = end_c
END DO
END DO
ELSE
! Element is assigned on the basis of the atm_name
topology%aa_element = .TRUE.
CALL reallocate(atom_info%id_molname, 1, natom)
CALL reallocate(atom_info%id_resname, 1, natom)
CALL reallocate(atom_info%resid, 1, natom)
CALL reallocate(atom_info%id_atmname, 1, natom)
CALL reallocate(atom_info%id_element, 1, natom)
CALL reallocate(atom_info%r, 1, 3, 1, natom)
CALL reallocate(atom_info%atm_mass, 1, natom)
CALL reallocate(atom_info%atm_charge, 1, natom)
CALL section_vals_list_get(coord_section, "_DEFAULT_KEYWORD_", list=list)
DO iatom = 1, natom
! we use only the first default_string_length characters of each line
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
default_id = str2id(s2s(""))
atom_info%id_molname(iatom) = default_id
atom_info%id_resname(iatom) = default_id
atom_info%resid(iatom) = 1
atom_info%id_atmname(iatom) = default_id
atom_info%id_element(iatom) = default_id
topology%molname_generated = .TRUE.
! Read name and atomic coordinates
start_c = 1
DO wrd = 1, 6
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (LEN_TRIM(line_att(start_c:end_c - 1)) == 0) &
CALL cp_abort(__LOCATION__, &
"Incorrectly formatted input line for atom "// &
TRIM(ADJUSTL(cp_to_string(iatom)))// &
" found in COORD section. Input line: <"// &
TRIM(line_att)//"> ")
SELECT CASE (wrd)
CASE (1)
atom_info%id_atmname(iatom) = str2id(s2s(line_att(start_c:end_c - 1)))
CASE (2:4)
CALL read_float_object(line_att(start_c:end_c - 1), &
atom_info%r(wrd - 1, iatom), error_message)
IF (LEN_TRIM(error_message) /= 0) &
CALL cp_abort(__LOCATION__, &
"Incorrectly formatted input line for atom "// &
TRIM(ADJUSTL(cp_to_string(iatom)))// &
" found in COORD section. "//TRIM(error_message)// &
" Input line: <"//TRIM(line_att)//"> ")
CASE (5)
READ (line_att(start_c:end_c - 1), *) strtmp
atom_info%id_molname(iatom) = str2id(strtmp)
atom_info%id_resname(iatom) = atom_info%id_molname(iatom)
topology%molname_generated = .FALSE.
CASE (6)
READ (line_att(start_c:end_c - 1), *) strtmp
atom_info%id_resname(iatom) = str2id(strtmp)
END SELECT
start_c = end_c
IF (start_c > LEN_TRIM(line_att)) EXIT
END DO
IF (topology%molname_generated) THEN
! Use defaults, if no molname was specified
WRITE (my_default_index, '(I0)') iatom
atom_info%id_molname(iatom) = str2id(s2s(TRIM(id2str(atom_info%id_atmname(iatom)))//TRIM(my_default_index)))
atom_info%id_resname(iatom) = atom_info%id_molname(iatom)
END IF
atom_info%id_element(iatom) = atom_info%id_atmname(iatom)
atom_info%atm_mass(iatom) = 0.0_dp
atom_info%atm_charge(iatom) = -HUGE(0.0_dp)
END DO
END IF
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 3. Convert coordinates into internal cp2k coordinates
!-----------------------------------------------------------------------------
DO iatom = 1, natom
IF (scaled_coordinates) THEN
r0 = atom_info%r(:, iatom)
CALL scaled_to_real(atom_info%r(:, iatom), r0, cell)
ELSE
atom_info%r(:, iatom) = atom_info%r(:, iatom)*unit_conv
END IF
END DO
IF (my_save_mem) CALL section_vals_remove_values(coord_section)
CALL timestop(handle)
END SUBROUTINE read_atoms_input
! **************************************************************************************************
!> \brief ...
!> \param particle_set ...
!> \param shell_particle_set ...
!> \param cell ...
!> \param subsys_section ...
!> \param core_particle_set ...
!> \param save_mem ...
!> \author MI
! **************************************************************************************************
SUBROUTINE read_shell_coord_input(particle_set, shell_particle_set, cell, &
subsys_section, core_particle_set, save_mem)
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set, shell_particle_set
TYPE(cell_type), POINTER :: cell
TYPE(section_vals_type), POINTER :: subsys_section
TYPE(particle_type), DIMENSION(:), OPTIONAL, &
POINTER :: core_particle_set
LOGICAL, INTENT(IN), OPTIONAL :: save_mem
CHARACTER(len=*), PARAMETER :: routineN = 'read_shell_coord_input'
CHARACTER(len=2*default_string_length) :: line_att
CHARACTER(len=default_string_length) :: name_kind, unit_str
CHARACTER(len=default_string_length), &
ALLOCATABLE, DIMENSION(:) :: at_name, at_name_c
INTEGER :: end_c, handle, ishell, j, nshell, &
output_unit, sh_index, start_c, wrd
INTEGER, ALLOCATABLE, DIMENSION(:) :: at_index, at_index_c
LOGICAL :: core_scaled_coordinates, explicit, &
is_ok, is_shell, my_save_mem, &
shell_scaled_coordinates
REAL(KIND=dp) :: dab, mass_com, rab(3), unit_conv_core, &
unit_conv_shell
REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: r, rc
TYPE(atomic_kind_type), POINTER :: atomic_kind
TYPE(cp_sll_val_type), POINTER :: list
TYPE(section_vals_type), POINTER :: core_coord_section, shell_coord_section
TYPE(shell_kind_type), POINTER :: shell
TYPE(val_type), POINTER :: val
my_save_mem = .FALSE.
NULLIFY (atomic_kind, list, shell_coord_section, shell, val)
output_unit = cp_logger_get_default_io_unit()
IF (PRESENT(save_mem)) my_save_mem = save_mem
NULLIFY (shell_coord_section, core_coord_section)
shell_coord_section => section_vals_get_subs_vals(subsys_section, "SHELL_COORD")
CALL section_vals_get(shell_coord_section, explicit=explicit)
IF (.NOT. explicit) RETURN
CALL timeset(routineN, handle)
CPASSERT(ASSOCIATED(particle_set))
!-----------------------------------------------------------------------------
!-----------------------------------------------------------------------------
! 2. Read in the coordinates from &SHELL_COORD section in the input file
!-----------------------------------------------------------------------------
CALL section_vals_val_get(shell_coord_section, "UNIT", c_val=unit_str)
CALL section_vals_val_get(shell_coord_section, "SCALED", l_val=shell_scaled_coordinates)
unit_conv_shell = cp_unit_to_cp2k(1.0_dp, TRIM(unit_str))
CALL section_vals_val_get(shell_coord_section, "_DEFAULT_KEYWORD_", &
n_rep_val=nshell)
IF (ASSOCIATED(shell_particle_set)) THEN
CPASSERT((SIZE(shell_particle_set, 1) == nshell))
ALLOCATE (r(3, nshell), at_name(nshell), at_index(nshell))
CALL cp_warn(__LOCATION__, &
"Overwriting shell coordinates. "// &
"Active coordinates READ from &SHELL_COORD section. ")
CALL section_vals_list_get(shell_coord_section, "_DEFAULT_KEYWORD_", list=list)
DO ishell = 1, nshell
! we use only the first default_string_length characters of each line
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
start_c = 1
DO wrd = 1, 5
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (wrd /= 5 .AND. end_c >= LEN(line_att) + 1) &
CPABORT("incorrectly formatted line in coord section'"//line_att//"'")
IF (wrd == 1) THEN
at_name(ishell) = line_att(start_c:end_c - 1)
CALL uppercase(at_name(ishell))
ELSE IF (wrd == 5) THEN
READ (line_att(start_c:end_c - 1), *) at_index(ishell)
ELSE
READ (line_att(start_c:end_c - 1), *) r(wrd - 1, ishell)
END IF
start_c = end_c
END DO
END DO
IF (PRESENT(core_particle_set)) THEN
CPASSERT(ASSOCIATED(core_particle_set))
core_coord_section => section_vals_get_subs_vals(subsys_section, "CORE_COORD")
CALL section_vals_get(core_coord_section, explicit=explicit)
IF (explicit) THEN
CALL section_vals_val_get(core_coord_section, "UNIT", c_val=unit_str)
CALL section_vals_val_get(core_coord_section, "SCALED", l_val=core_scaled_coordinates)
unit_conv_core = cp_unit_to_cp2k(1.0_dp, TRIM(unit_str))
CALL section_vals_val_get(core_coord_section, "_DEFAULT_KEYWORD_", &
n_rep_val=nshell)
CPASSERT((SIZE(core_particle_set, 1) == nshell))
ALLOCATE (rc(3, nshell), at_name_c(nshell), at_index_c(nshell))
CALL cp_warn(__LOCATION__, &
"Overwriting cores coordinates. "// &
"Active coordinates READ from &CORE_COORD section. ")
CALL section_vals_list_get(core_coord_section, "_DEFAULT_KEYWORD_", list=list)
DO ishell = 1, nshell
! we use only the first default_string_length characters of each line
is_ok = cp_sll_val_next(list, val)
CALL val_get(val, c_val=line_att)
start_c = 1
DO wrd = 1, 5
DO j = start_c, LEN(line_att)
IF (line_att(j:j) /= ' ') THEN
start_c = j
EXIT
END IF
END DO
end_c = LEN(line_att) + 1
DO j = start_c, LEN(line_att)
IF (line_att(j:j) == ' ') THEN
end_c = j
EXIT
END IF
END DO
IF (wrd /= 5 .AND. end_c >= LEN(line_att) + 1) &
CPABORT("incorrectly formatted line in coord section'"//line_att//"'")
IF (wrd == 1) THEN
at_name_c(ishell) = line_att(start_c:end_c - 1)
CALL uppercase(at_name_c(ishell))
ELSE IF (wrd == 5) THEN
READ (line_att(start_c:end_c - 1), *) at_index_c(ishell)
ELSE
READ (line_att(start_c:end_c - 1), *) rc(wrd - 1, ishell)
END IF
start_c = end_c
END DO
END DO
IF (my_save_mem) CALL section_vals_remove_values(core_coord_section)
END IF ! explicit
END IF ! core_particle_set
!-----------------------------------------------------------------------------
! 3. Check corrispondence and convert coordinates into internal cp2k coordinates
!-----------------------------------------------------------------------------
DO ishell = 1, nshell
atomic_kind => particle_set(at_index(ishell))%atomic_kind
CALL get_atomic_kind(atomic_kind=atomic_kind, &
name=name_kind, shell_active=is_shell, mass=mass_com, shell=shell)
CALL uppercase(name_kind)
IF ((TRIM(at_name(ishell)) == TRIM(name_kind)) .AND. is_shell) THEN
sh_index = particle_set(at_index(ishell))%shell_index
IF (shell_scaled_coordinates) THEN
CALL scaled_to_real(r(:, ishell), shell_particle_set(sh_index)%r(:), cell)
ELSE
shell_particle_set(sh_index)%r(:) = r(:, ishell)*unit_conv_shell
END IF
shell_particle_set(sh_index)%atom_index = at_index(ishell)
IF (PRESENT(core_particle_set) .AND. .NOT. explicit) THEN
core_particle_set(sh_index)%r(1) = (mass_com*particle_set(at_index(ishell))%r(1) - &
shell%mass_shell*shell_particle_set(sh_index)%r(1))/shell%mass_core
core_particle_set(sh_index)%r(2) = (mass_com*particle_set(at_index(ishell))%r(2) - &
shell%mass_shell*shell_particle_set(sh_index)%r(2))/shell%mass_core
core_particle_set(sh_index)%r(3) = (mass_com*particle_set(at_index(ishell))%r(3) - &
shell%mass_shell*shell_particle_set(sh_index)%r(3))/shell%mass_core
core_particle_set(sh_index)%atom_index = at_index(ishell)
rab = pbc(shell_particle_set(sh_index)%r, core_particle_set(sh_index)%r, cell)
ELSE IF (explicit) THEN
IF (core_scaled_coordinates) THEN
CALL scaled_to_real(rc(:, ishell), core_particle_set(sh_index)%r(:), cell)
ELSE
core_particle_set(sh_index)%r(:) = rc(:, ishell)*unit_conv_core
END IF
core_particle_set(sh_index)%atom_index = at_index_c(ishell)
rab = pbc(shell_particle_set(sh_index)%r, core_particle_set(sh_index)%r, cell)
CPASSERT(TRIM(at_name(ishell)) == TRIM(at_name_c(ishell)))
CPASSERT(at_index(ishell) == at_index_c(ishell))
ELSE
rab = pbc(shell_particle_set(sh_index)%r, particle_set(at_index(ishell))%r, cell)
END IF
dab = SQRT(rab(1)*rab(1) + rab(2)*rab(2) + rab(3)*rab(3))
IF (shell%max_dist > 0.0_dp .AND. shell%max_dist < dab) THEN
IF (output_unit > 0) THEN
WRITE (output_unit, *) "WARNING : shell and core for atom ", at_index(ishell), " seem to be too distant."
END IF
END IF
ELSE
CPABORT("shell coordinate assigned to the wrong atom. check the shell indexes in the input")
END IF
END DO
DEALLOCATE (r, at_index, at_name)
DEALLOCATE (rc, at_index_c, at_name_c)
END IF
IF (my_save_mem) CALL section_vals_remove_values(shell_coord_section)
CALL timestop(handle)
END SUBROUTINE read_shell_coord_input
END MODULE atoms_input