!--------------------------------------------------------------------------------------------------!
!   CP2K: A general program to perform molecular dynamics simulations                              !
!   Copyright 2000-2025 CP2K developers group <https://cp2k.org>                                   !
!                                                                                                  !
!   SPDX-License-Identifier: GPL-2.0-or-later                                                      !
!--------------------------------------------------------------------------------------------------!

! **************************************************************************************************
!> \brief Initialize a small environment for a particular calculation
!> \par History
!>      5.2004 created [fawzi]
!>      9.2007 cleaned [tlaino] - University of Zurich
!> \author Teodoro Laino
! **************************************************************************************************
MODULE cp_subsys_methods
   USE atomic_kind_list_types,          ONLY: atomic_kind_list_create,&
                                              atomic_kind_list_release,&
                                              atomic_kind_list_type
   USE atomic_kind_types,               ONLY: atomic_kind_type
   USE atprop_types,                    ONLY: atprop_create
   USE cell_types,                      ONLY: cell_retain,&
                                              cell_type
   USE colvar_methods,                  ONLY: colvar_read
   USE cp_result_types,                 ONLY: cp_result_create
   USE cp_subsys_types,                 ONLY: cp_subsys_get,&
                                              cp_subsys_set,&
                                              cp_subsys_type
   USE exclusion_types,                 ONLY: exclusion_type
   USE input_constants,                 ONLY: do_conn_off,&
                                              do_stress_analytical,&
                                              do_stress_diagonal_anal,&
                                              do_stress_diagonal_numer,&
                                              do_stress_none,&
                                              do_stress_numerical
   USE input_section_types,             ONLY: section_vals_get,&
                                              section_vals_get_subs_vals,&
                                              section_vals_type,&
                                              section_vals_val_get
   USE kinds,                           ONLY: default_string_length,&
                                              dp
   USE message_passing,                 ONLY: mp_para_env_type
   USE molecule_kind_list_types,        ONLY: molecule_kind_list_create,&
                                              molecule_kind_list_release,&
                                              molecule_kind_list_type
   USE molecule_kind_types,             ONLY: molecule_kind_type
   USE molecule_list_types,             ONLY: molecule_list_create,&
                                              molecule_list_release,&
                                              molecule_list_type
   USE molecule_types,                  ONLY: molecule_type
   USE particle_list_types,             ONLY: particle_list_create,&
                                              particle_list_release,&
                                              particle_list_type
   USE particle_types,                  ONLY: particle_type
   USE qmmm_types_low,                  ONLY: qmmm_env_mm_type
   USE string_table,                    ONLY: id2str,&
                                              s2s,&
                                              str2id
   USE topology,                        ONLY: connectivity_control,&
                                              topology_control
   USE topology_connectivity_util,      ONLY: topology_connectivity_pack
   USE topology_coordinate_util,        ONLY: topology_coordinate_pack
   USE topology_types,                  ONLY: deallocate_topology,&
                                              init_topology,&
                                              topology_parameters_type
   USE topology_util,                   ONLY: check_subsys_element
   USE virial_types,                    ONLY: virial_set
#include "./base/base_uses.f90"

   IMPLICIT NONE
   PRIVATE

   LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .FALSE.
   CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cp_subsys_methods'

   PUBLIC :: create_small_subsys, cp_subsys_create

CONTAINS

! **************************************************************************************************
!> \brief Creates allocates and fills subsys from given input.
!> \param subsys ...
!> \param para_env ...
!> \param root_section ...
!> \param force_env_section ...
!> \param subsys_section ...
!> \param use_motion_section ...
!> \param qmmm ...
!> \param qmmm_env ...
!> \param exclusions ...
!> \param elkind ...
!> \author Ole Schuett
! **************************************************************************************************
   SUBROUTINE cp_subsys_create(subsys, para_env, &
                               root_section, force_env_section, subsys_section, &
                               use_motion_section, qmmm, qmmm_env, exclusions, elkind)
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(section_vals_type), POINTER                   :: root_section
      TYPE(section_vals_type), OPTIONAL, POINTER         :: force_env_section, subsys_section
      LOGICAL, INTENT(IN), OPTIONAL                      :: use_motion_section
      LOGICAL, OPTIONAL                                  :: qmmm
      TYPE(qmmm_env_mm_type), OPTIONAL, POINTER          :: qmmm_env
      TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
         POINTER                                         :: exclusions
      LOGICAL, INTENT(IN), OPTIONAL                      :: elkind

      INTEGER                                            :: stress_tensor
      INTEGER, DIMENSION(:), POINTER                     :: seed_vals
      LOGICAL                                            :: atomic_energy, my_use_motion_section, &
                                                            pv_availability, pv_diagonal, &
                                                            pv_numerical
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(molecule_kind_list_type), POINTER             :: mol_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: mols
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(particle_list_type), POINTER                  :: particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: particle_set
      TYPE(section_vals_type), POINTER                   :: colvar_section, my_force_env_section, &
                                                            my_subsys_section

      CPASSERT(.NOT. ASSOCIATED(subsys))
      ALLOCATE (subsys)

      CALL para_env%retain()
      subsys%para_env => para_env

      my_use_motion_section = .FALSE.
      IF (PRESENT(use_motion_section)) &
         my_use_motion_section = use_motion_section

      my_force_env_section => section_vals_get_subs_vals(root_section, "FORCE_EVAL")
      IF (PRESENT(force_env_section)) &
         my_force_env_section => force_env_section

      my_subsys_section => section_vals_get_subs_vals(my_force_env_section, "SUBSYS")
      IF (PRESENT(subsys_section)) &
         my_subsys_section => subsys_section

      CALL section_vals_val_get(my_subsys_section, "SEED", i_vals=seed_vals)
      IF (SIZE(seed_vals) == 1) THEN
         subsys%seed(:, :) = REAL(seed_vals(1), KIND=dp)
      ELSE IF (SIZE(seed_vals) == 6) THEN
         subsys%seed(1:3, 1:2) = RESHAPE(REAL(seed_vals(:), KIND=dp), (/3, 2/))
      ELSE
         CPABORT("Supply exactly 1 or 6 arguments for SEED in &SUBSYS only!")
      END IF

      colvar_section => section_vals_get_subs_vals(my_subsys_section, "COLVAR")

      CALL cp_subsys_read_colvar(subsys, colvar_section)

      !   *** Read the particle coordinates and allocate the atomic kind, ***
      !   *** the molecule kind, and the molecule data structures         ***
      CALL topology_control(atomic_kind_set, particle_set, molecule_kind_set, molecule_set, &
                            subsys%colvar_p, subsys%gci, root_section, para_env, &
                            force_env_section=my_force_env_section, &
                            subsys_section=my_subsys_section, use_motion_section=my_use_motion_section, &
                            qmmm=qmmm, qmmm_env=qmmm_env, exclusions=exclusions, elkind=elkind)

      CALL particle_list_create(particles, els_ptr=particle_set)
      CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
      CALL molecule_list_create(mols, els_ptr=molecule_set)
      CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)

      CALL cp_subsys_set(subsys, particles=particles, atomic_kinds=atomic_kinds, &
                         molecules=mols, molecule_kinds=mol_kinds)

      CALL particle_list_release(particles)
      CALL atomic_kind_list_release(atomic_kinds)
      CALL molecule_list_release(mols)
      CALL molecule_kind_list_release(mol_kinds)

      ! Should we compute the virial?
      CALL section_vals_val_get(my_force_env_section, "STRESS_TENSOR", i_val=stress_tensor)
      SELECT CASE (stress_tensor)
      CASE (do_stress_none)
         pv_availability = .FALSE.
         pv_numerical = .FALSE.
         pv_diagonal = .FALSE.
      CASE (do_stress_analytical)
         pv_availability = .TRUE.
         pv_numerical = .FALSE.
         pv_diagonal = .FALSE.
      CASE (do_stress_numerical)
         pv_availability = .TRUE.
         pv_numerical = .TRUE.
         pv_diagonal = .FALSE.
      CASE (do_stress_diagonal_anal)
         pv_availability = .TRUE.
         pv_numerical = .FALSE.
         pv_diagonal = .TRUE.
      CASE (do_stress_diagonal_numer)
         pv_availability = .TRUE.
         pv_numerical = .TRUE.
         pv_diagonal = .TRUE.
      END SELECT

      ALLOCATE (subsys%virial)
      CALL virial_set(virial=subsys%virial, &
                      pv_availability=pv_availability, &
                      pv_numer=pv_numerical, &
                      pv_diagonal=pv_diagonal)

      ! Should we compute atomic properties?
      CALL atprop_create(subsys%atprop)
      CALL section_vals_val_get(my_force_env_section, "PROPERTIES%ATOMIC%ENERGY", l_val=atomic_energy)
      subsys%atprop%energy = atomic_energy

      CALL cp_result_create(subsys%results)
   END SUBROUTINE cp_subsys_create

! **************************************************************************************************
!> \brief reads the colvar section of the colvar
!> \param subsys ...
!> \param colvar_section ...
!> \par History
!>      2006.01 Joost VandeVondele
! **************************************************************************************************
   SUBROUTINE cp_subsys_read_colvar(subsys, colvar_section)
      TYPE(cp_subsys_type), POINTER                      :: subsys
      TYPE(section_vals_type), POINTER                   :: colvar_section

      INTEGER                                            :: ig, ncol

      CALL section_vals_get(colvar_section, n_repetition=ncol)
      ALLOCATE (subsys%colvar_p(ncol))
      DO ig = 1, ncol
         NULLIFY (subsys%colvar_p(ig)%colvar)
         CALL colvar_read(subsys%colvar_p(ig)%colvar, ig, colvar_section, subsys%para_env)
      END DO
   END SUBROUTINE cp_subsys_read_colvar

! **************************************************************************************************
!> \brief updates the molecule information of the given subsys
!> \param small_subsys the subsys to create
!> \param big_subsys the superset of small_subsys
!> \param small_cell ...
!> \param small_para_env the parallel environment for the new (small)
!>        subsys
!> \param sub_atom_index indexes of the atoms that should be in small_subsys
!> \param sub_atom_kind_name ...
!> \param para_env ...
!> \param force_env_section ...
!> \param subsys_section ...
!> \param ignore_outside_box ...
!> \par History
!>      05.2004 created [fawzi]
!> \author Fawzi Mohamed, Teodoro Laino
!> \note
!>      not really ready to be used with different para_envs for the small
!>      and big part
! **************************************************************************************************
   SUBROUTINE create_small_subsys(small_subsys, big_subsys, small_cell, &
                                  small_para_env, sub_atom_index, sub_atom_kind_name, &
                                  para_env, force_env_section, subsys_section, ignore_outside_box)

      TYPE(cp_subsys_type), POINTER                      :: small_subsys, big_subsys
      TYPE(cell_type), POINTER                           :: small_cell
      TYPE(mp_para_env_type), POINTER                    :: small_para_env
      INTEGER, DIMENSION(:), INTENT(in)                  :: sub_atom_index
      CHARACTER(len=default_string_length), &
         DIMENSION(:), INTENT(in)                        :: sub_atom_kind_name
      TYPE(mp_para_env_type), POINTER                    :: para_env
      TYPE(section_vals_type), POINTER                   :: force_env_section, subsys_section
      LOGICAL, INTENT(in), OPTIONAL                      :: ignore_outside_box

      CHARACTER(len=default_string_length)               :: my_element, strtmp1
      INTEGER                                            :: iat, id_, nat
      TYPE(atomic_kind_list_type), POINTER               :: atomic_kinds
      TYPE(atomic_kind_type), DIMENSION(:), POINTER      :: atomic_kind_set
      TYPE(molecule_kind_list_type), POINTER             :: mol_kinds
      TYPE(molecule_kind_type), DIMENSION(:), POINTER    :: molecule_kind_set
      TYPE(molecule_list_type), POINTER                  :: mols
      TYPE(molecule_type), DIMENSION(:), POINTER         :: molecule_set
      TYPE(particle_list_type), POINTER                  :: particles
      TYPE(particle_type), DIMENSION(:), POINTER         :: particle_set
      TYPE(topology_parameters_type)                     :: topology

      NULLIFY (mol_kinds, mols, particles, atomic_kinds, atomic_kind_set, particle_set, &
               molecule_kind_set, molecule_set, particles, atomic_kinds)

      CPASSERT(.NOT. ASSOCIATED(small_subsys))
      CPASSERT(ASSOCIATED(big_subsys))
      IF (big_subsys%para_env /= small_para_env) &
         CPABORT("big_subsys%para_env==small_para_env")

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 1. Initialize the topology structure type
      !-----------------------------------------------------------------------------
      CALL init_topology(topology)

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 2. Get the cell info
      !-----------------------------------------------------------------------------
      topology%cell => small_cell
      CALL cell_retain(small_cell)

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 3. Initialize atom coords from the bigger system
      !-----------------------------------------------------------------------------
      nat = SIZE(sub_atom_index)
      topology%natoms = nat
      CPASSERT(.NOT. ASSOCIATED(topology%atom_info%r))
      CPASSERT(.NOT. ASSOCIATED(topology%atom_info%id_atmname))
      CPASSERT(.NOT. ASSOCIATED(topology%atom_info%id_molname))
      CPASSERT(.NOT. ASSOCIATED(topology%atom_info%id_resname))
      CPASSERT(.NOT. ASSOCIATED(topology%atom_info%atm_mass))
      CPASSERT(.NOT. ASSOCIATED(topology%atom_info%atm_charge))
      ALLOCATE (topology%atom_info%r(3, nat), topology%atom_info%id_atmname(nat), &
                topology%atom_info%id_molname(nat), topology%atom_info%id_resname(nat), &
                topology%atom_info%id_element(nat), topology%atom_info%atm_mass(nat), &
                topology%atom_info%atm_charge(nat))

      CALL cp_subsys_get(big_subsys, particles=particles)
      DO iat = 1, nat
         topology%atom_info%r(:, iat) = particles%els(sub_atom_index(iat))%r
         topology%atom_info%id_atmname(iat) = str2id(s2s(sub_atom_kind_name(iat)))
         topology%atom_info%id_molname(iat) = topology%atom_info%id_atmname(iat)
         topology%atom_info%id_resname(iat) = topology%atom_info%id_atmname(iat)
         !
         ! Defining element
         !
         id_ = INDEX(id2str(topology%atom_info%id_atmname(iat)), "_") - 1
         IF (id_ == -1) id_ = LEN_TRIM(id2str(topology%atom_info%id_atmname(iat)))
         strtmp1 = id2str(topology%atom_info%id_atmname(iat))
         strtmp1 = strtmp1(1:id_)
         CALL check_subsys_element(strtmp1, strtmp1, my_element, &
                                   subsys_section, use_mm_map_first=.FALSE.)
         topology%atom_info%id_element(iat) = str2id(s2s(my_element))
         topology%atom_info%atm_mass(iat) = 0._dp
         topology%atom_info%atm_charge(iat) = 0._dp
      END DO
      topology%conn_type = do_conn_off

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 4. Read in or generate the molecular connectivity
      !-----------------------------------------------------------------------------
      CALL connectivity_control(topology, para_env, subsys_section=subsys_section, &
                                force_env_section=force_env_section)

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 5. Pack everything into the molecular types
      !-----------------------------------------------------------------------------
      CALL topology_connectivity_pack(molecule_kind_set, molecule_set, &
                                      topology, subsys_section=subsys_section)

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 6. Pack everything into the atomic types
      !-----------------------------------------------------------------------------
      CALL topology_coordinate_pack(particle_set, atomic_kind_set, &
                                    molecule_kind_set, molecule_set, topology, subsys_section=subsys_section, &
                                    force_env_section=force_env_section, ignore_outside_box=ignore_outside_box)

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 7. Cleanup the topology structure type
      !-----------------------------------------------------------------------------
      CALL deallocate_topology(topology)

      !-----------------------------------------------------------------------------
      !-----------------------------------------------------------------------------
      ! 8. Allocate new subsys
      !-----------------------------------------------------------------------------
      ALLOCATE (small_subsys)
      CALL para_env%retain()
      small_subsys%para_env => para_env
      CALL particle_list_create(particles, els_ptr=particle_set)
      CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)
      CALL molecule_list_create(mols, els_ptr=molecule_set)
      CALL molecule_kind_list_create(mol_kinds, els_ptr=molecule_kind_set)
      CALL cp_subsys_set(small_subsys, particles=particles, atomic_kinds=atomic_kinds, &
                         molecules=mols, molecule_kinds=mol_kinds)
      CALL particle_list_release(particles)
      CALL atomic_kind_list_release(atomic_kinds)
      CALL molecule_list_release(mols)
      CALL molecule_kind_list_release(mol_kinds)

      ALLOCATE (small_subsys%virial)
      CALL atprop_create(small_subsys%atprop)
      CALL cp_result_create(small_subsys%results)
   END SUBROUTINE create_small_subsys

END MODULE cp_subsys_methods
