da/dad/qmmm__create_8F_source.html

 !--------------------------------------------------------------------------------------------------!

 !   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                                                      !

 !--------------------------------------------------------------------------------------------------!


 ! **************************************************************************************************

 !> \brief Initialize a QM/MM calculation

 !> \par History

 !>      5.2004 created [fawzi]

 !> \author Fawzi Mohamed

 ! **************************************************************************************************

 MODULE qmmm_create

    USE bibliography,                    ONLY: golze2013,&

                                               laino2005,&

                                               laino2006,&

                                               cite_reference

    USE cell_methods,                    ONLY: write_cell

    USE cell_types,                      ONLY: cell_clone,&

                                               cell_release,&

                                               cell_type,&

                                               get_cell

    USE cp_log_handling,                 ONLY: cp_get_default_logger,&

                                               cp_logger_type

    USE cp_output_handling,              ONLY: cp_print_key_finished_output,&

                                               cp_print_key_unit_nr

    USE cp_subsys_methods,               ONLY: create_small_subsys

    USE cp_subsys_types,                 ONLY: cp_subsys_release,&

                                               cp_subsys_type

    USE fist_environment,                ONLY: fist_init

    USE fist_environment_types,          ONLY: fist_env_create,&

                                               fist_env_get,&

                                               fist_env_set,&

                                               fist_environment_type

    USE fist_nonbond_env_types,          ONLY: fist_nonbond_env_type

    USE global_types,                    ONLY: global_environment_type

    USE header,                          ONLY: qmmm_header

    USE input_constants,                 ONLY: &

         do_fist, do_multipole_section_off, do_multipole_section_on, do_qmmm, &

         do_qmmm_center_every_step, do_qmmm_center_never, do_qmmm_center_pbc_aware, &

         do_qmmm_center_setup_only, do_qmmm_none, do_qs

    USE input_section_types,             ONLY: section_vals_get,&

                                               section_vals_get_subs_vals,&

                                               section_vals_type,&

                                               section_vals_val_get,&

                                               section_vals_val_set

    USE kinds,                           ONLY: default_string_length,&

                                               dp

    USE message_passing,                 ONLY: mp_para_env_type

    USE pw_env_types,                    ONLY: pw_env_type

    USE qmmm_init,                       ONLY: &

         assign_mm_charges_and_radius, move_or_add_atoms, print_image_charge_info, &

         print_qmmm_charges, print_qmmm_links, qmmm_init_gaussian_type, &

         qmmm_init_periodic_potential, qmmm_init_potential, setup_origin_mm_cell, setup_qmmm_links, &

         setup_qmmm_vars_mm, setup_qmmm_vars_qm

    USE qmmm_links_methods,              ONLY: qmmm_link_imomm_coord

    USE qmmm_pw_grid,                    ONLY: qmmm_pw_grid_init

    USE qmmm_types,                      ONLY: qmmm_env_type

    USE qmmm_types_low,                  ONLY: add_set_release,&

                                               add_set_type,&

                                               add_shell_type,&

                                               qmmm_env_mm_create,&

                                               qmmm_env_mm_type,&

                                               qmmm_env_qm_create,&

                                               qmmm_env_qm_type,&

                                               qmmm_links_type

    USE qs_environment,                  ONLY: qs_init

    USE qs_environment_types,            ONLY: get_qs_env,&

                                               qs_env_create,&

                                               qs_environment_type,&

                                               set_qs_env

 #include "./base/base_uses.f90"


    IMPLICIT NONE

    PRIVATE


    LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .true.

    CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'qmmm_create'


    PUBLIC :: qmmm_env_create


 CONTAINS


 ! **************************************************************************************************

 !> \brief ...

 !> \param qmmm_env ...

 !> \param root_section ...

 !> \param para_env ...

 !> \param globenv ...

 !> \param force_env_section ...

 !> \param qmmm_section ...

 !> \param subsys_section ...

 !> \param use_motion_section ...

 !> \param prev_subsys ...

 !> \param ignore_outside_box ...

 !> \par History

 !>      05.2004 created [fawzi]

 !> \author Fawzi Mohamed

 ! **************************************************************************************************

    SUBROUTINE qmmm_env_create(qmmm_env, root_section, para_env, globenv, &

                               force_env_section, qmmm_section, subsys_section, use_motion_section, prev_subsys, &

                               ignore_outside_box)

       TYPE(qmmm_env_type), INTENT(OUT)                   :: qmmm_env

       TYPE(section_vals_type), POINTER                   :: root_section

       TYPE(mp_para_env_type), POINTER                    :: para_env

       TYPE(global_environment_type), POINTER             :: globenv

       TYPE(section_vals_type), POINTER                   :: force_env_section, qmmm_section, &

                                                             subsys_section

       LOGICAL, INTENT(IN)                                :: use_motion_section

       TYPE(cp_subsys_type), OPTIONAL, POINTER            :: prev_subsys

       LOGICAL, INTENT(in), OPTIONAL                      :: ignore_outside_box


       CHARACTER(len=*), PARAMETER                        :: routinen = 'qmmm_env_create'


       CHARACTER(len=default_string_length), &

          DIMENSION(:), POINTER                           :: qm_atom_type

       INTEGER                                            :: center_i, delta_charge, handle, iw, iw2, &

                                                             orig_charge, qmmm_coupl_type, &

                                                             use_multipole

       INTEGER, DIMENSION(:), POINTER                     :: mm_atom_index, mm_link_atoms, &

                                                             qm_atom_index

       LOGICAL                                            :: add_mm_charges, explicit, &

                                                             move_mm_charges, nocompatibility, &

                                                             qmmm_link, qmmm_link_imomm, shell_model

       REAL(dp), DIMENSION(:), POINTER                    :: mm_atom_chrg, mm_el_pot_radius, &

                                                             mm_el_pot_radius_corr

       REAL(kind=dp)                                      :: eps_mm_rspace

       REAL(kind=dp), DIMENSION(3)                        :: abc_mm, abc_qm

       REAL(kind=dp), DIMENSION(:), POINTER               :: fist_scale_charge_link, &

                                                             mm_link_scale_factor

       TYPE(add_set_type), POINTER                        :: added_charges

       TYPE(add_shell_type), POINTER                      :: added_shells

       TYPE(cell_type), POINTER                           :: mm_cell, qm_cell_small, super_cell

       TYPE(cp_logger_type), POINTER                      :: logger

       TYPE(cp_subsys_type), POINTER                      :: subsys_mm, subsys_qm

       TYPE(fist_environment_type), POINTER               :: fist_env

       TYPE(fist_nonbond_env_type), POINTER               :: fist_nonbond_env

       TYPE(pw_env_type), POINTER                         :: pw_env

       TYPE(qmmm_env_mm_type), POINTER                    :: qmmm_env_mm

       TYPE(qmmm_env_qm_type), POINTER                    :: qmmm_env_qm

       TYPE(qmmm_links_type), POINTER                     :: qmmm_links

       TYPE(qs_environment_type), POINTER                 :: qs_env

       TYPE(section_vals_type), POINTER                   :: multipole_section, print_gen, &

                                                             print_section, qmmm_periodic


       CALL timeset(routinen, handle)


       NULLIFY (qm_atom_index, mm_atom_index, qm_atom_type)

       NULLIFY (qmmm_env_qm, subsys_mm, subsys_qm, mm_cell, qm_cell_small)

       NULLIFY (mm_atom_chrg, mm_el_pot_radius, qmmm_env_mm, fist_env)

       NULLIFY (mm_link_atoms, mm_link_scale_factor, qmmm_links, added_charges, added_shells)

       NULLIFY (fist_scale_charge_link, print_section, fist_nonbond_env)

       NULLIFY (print_gen, logger, mm_el_pot_radius_corr, super_cell, pw_env)


       logger => cp_get_default_logger()


       ! citations

       CALL cite_reference(laino2005)


       ! Input section...

       IF (.NOT. ASSOCIATED(subsys_section)) THEN

          subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")

       END IF

       qmmm_periodic => section_vals_get_subs_vals(qmmm_section, "PERIODIC")

       multipole_section => section_vals_get_subs_vals(qmmm_section, "PERIODIC%MULTIPOLE")

       print_section => section_vals_get_subs_vals(qmmm_section, "PRINT")

       print_gen => section_vals_get_subs_vals(print_section, "PROGRAM_RUN_INFO")

       iw = cp_print_key_unit_nr(logger, print_gen, "", extension=".log")


       ! Create QM/MM Environments..

       ALLOCATE (qmmm_env_qm)

       CALL qmmm_env_qm_create(qmmm_env_qm)

       ALLOCATE (qmmm_env_mm)

       CALL qmmm_env_mm_create(qmmm_env_mm)


       ! Set up QM/MM Options

       CALL setup_qmmm_vars_mm(qmmm_section, &

                               qmmm_env_mm, &

                               qm_atom_index, &

                               mm_link_atoms, &

                               mm_link_scale_factor, &

                               fist_scale_charge_link, &

                               qmmm_coupl_type, &

                               qmmm_link)


       qmmm_env_mm%qm_atom_index => qm_atom_index

       qmmm_env_mm%mm_link_atoms => mm_link_atoms

       qmmm_env_mm%mm_link_scale_factor => mm_link_scale_factor

       qmmm_env_mm%fist_scale_charge_link => fist_scale_charge_link

       qmmm_env_mm%qmmm_coupl_type = qmmm_coupl_type

       qmmm_env_mm%qmmm_link = qmmm_link

       ! Center the qm subsys into the qm box

       CALL section_vals_val_get(qmmm_section, "CENTER", i_val=center_i)

       IF (center_i == do_qmmm_center_never) THEN

          qmmm_env_qm%center_qm_subsys = .false.

          qmmm_env_qm%center_qm_subsys0 = .false.

       ELSE IF (center_i == do_qmmm_center_setup_only) THEN

          qmmm_env_qm%center_qm_subsys = .false.

          qmmm_env_qm%center_qm_subsys0 = .true.

       ELSE IF (center_i == do_qmmm_center_every_step) THEN

          qmmm_env_qm%center_qm_subsys = .true.

          qmmm_env_qm%center_qm_subsys0 = .true.

       ELSE

          cpabort("Unknown type of CENTER! ")

       END IF


       CALL section_vals_val_get(qmmm_section, "CENTER_TYPE", i_val=center_i)

       qmmm_env_qm%center_qm_subsys_pbc_aware = (center_i == do_qmmm_center_pbc_aware)


       ! Compatibility with the QM/MM in CPMD code

       CALL section_vals_val_get(qmmm_section, "NOCOMPATIBILITY", l_val=nocompatibility)

       qmmm_env_qm%compatibility = .NOT. nocompatibility


       ! Parallel scheme for the long range

       CALL section_vals_val_get(qmmm_section, "PARALLEL_SCHEME", &

                                 i_val=qmmm_env_qm%par_scheme)


       ! Periodic boundary condition calculation

       CALL section_vals_get(qmmm_periodic, explicit=explicit)

       qmmm_env_qm%periodic = explicit

       !multipole section is switched on by default; switched off only if explicitly stated

       IF (qmmm_env_qm%periodic) qmmm_env_qm%multipole = .true.

       CALL section_vals_get(multipole_section, explicit=explicit)

       CALL section_vals_val_get(multipole_section, "_SECTION_PARAMETERS_", i_val=use_multipole)

       IF (explicit .AND. use_multipole == do_multipole_section_off) qmmm_env_qm%multipole = .false.

       IF (explicit .AND. use_multipole == do_multipole_section_on) qmmm_env_qm%multipole = .true.

       IF (qmmm_env_qm%periodic .AND. qmmm_env_qm%multipole) CALL cite_reference(laino2006)

       IF (qmmm_coupl_type == do_qmmm_none) THEN

          IF (qmmm_env_qm%periodic) &

             CALL cp_warn(__location__, &

                          "QMMM periodic calculation with coupling NONE was requested! "// &

                          "Switching off the periodic keyword since periodic and non-periodic "// &

                          "calculation with coupling NONE represent the same method! ")

          qmmm_env_qm%periodic = .false.

       END IF


       ! First Initialize Fist...

       CALL section_vals_val_set(force_env_section, "METHOD", i_val=do_fist)

       ALLOCATE (fist_env)

       CALL fist_env_create(fist_env, para_env=para_env)

       CALL fist_env_set(fist_env, qmmm=.true., qmmm_env=qmmm_env_mm)

       CALL fist_init(fist_env, root_section, para_env, force_env_section, &

                      subsys_section, use_motion_section, prev_subsys=prev_subsys)

       CALL fist_env_get(fist_env, subsys=subsys_mm, cell=mm_cell)

       mm_cell%tag = "CELL_MM"


       ! Set up QM/MM Options

       CALL setup_qmmm_vars_qm(qmmm_section, &

                               qmmm_env_qm, &

                               subsys_mm, &

                               qm_atom_type, &

                               qm_atom_index, &

                               mm_atom_index, &

                               qm_cell_small, &

                               qmmm_coupl_type, &

                               eps_mm_rspace, &

                               qmmm_link, &

                               para_env)


       qmmm_env_qm%qm_atom_index => qm_atom_index

       qmmm_env_qm%mm_atom_index => mm_atom_index

       qmmm_env_qm%eps_mm_rspace = eps_mm_rspace

       qmmm_env_qm%qmmm_coupl_type = qmmm_coupl_type

       qmmm_env_qm%qmmm_link = qmmm_link

       qmmm_env_qm%num_qm_atoms = SIZE(qm_atom_index)

       qmmm_env_qm%num_mm_atoms = SIZE(mm_atom_index)

       IF (qmmm_env_qm%image_charge) THEN

          qmmm_env_qm%num_image_mm_atoms = SIZE(qmmm_env_qm%image_charge_pot%image_mm_list)

          CALL cite_reference(golze2013)

       END IF


       ! Duplicate structure for link atoms

       IF (qmmm_link) THEN

          IF (ASSOCIATED(mm_link_atoms)) THEN

             ALLOCATE (qmmm_env_qm%mm_link_atoms(SIZE(mm_link_atoms)))

             qmmm_env_qm%mm_link_atoms = mm_link_atoms

          END IF

       END IF

       IF (iw > 0) THEN

          WRITE (iw, '(A,I26)') " Number of QM atoms: ", qmmm_env_qm%num_qm_atoms

          WRITE (iw, '(A,I26)') " Number of MM atoms: ", qmmm_env_qm%num_mm_atoms

          IF (qmmm_env_qm%image_charge) THEN

             WRITE (iw, '(A,I8)') " Number of MM atoms with image charge: ", &

                qmmm_env_qm%num_image_mm_atoms

          END IF

          CALL write_cell(mm_cell, subsys_section)

       END IF

       CALL get_cell(qm_cell_small, abc=abc_qm)

       CALL get_cell(mm_cell, abc=abc_mm)


       IF (qmmm_env_qm%image_charge) THEN

          IF (any(abs(abc_mm - abc_qm) > 1.0e-12)) &

             cpabort("QM and MM box need to have the same size when using image charges")

       END IF


       ! Assign charges and mm_el_pot_radius from fist_topology

       CALL fist_env_get(fist_env, fist_nonbond_env=fist_nonbond_env)

       ALLOCATE (mm_atom_chrg(SIZE(mm_atom_index)))

       ALLOCATE (mm_el_pot_radius(SIZE(mm_atom_index)))

       ALLOCATE (mm_el_pot_radius_corr(SIZE(mm_atom_index)))

       mm_atom_chrg = 0.0_dp

       mm_el_pot_radius = 0.0_dp

       mm_el_pot_radius_corr = 0.0_dp


       CALL assign_mm_charges_and_radius(subsys=subsys_mm, &

                                         charges=fist_nonbond_env%charges, &

                                         mm_atom_chrg=mm_atom_chrg, &

                                         mm_el_pot_radius=mm_el_pot_radius, &

                                         mm_el_pot_radius_corr=mm_el_pot_radius_corr, &

                                         mm_atom_index=mm_atom_index, &

                                         mm_link_atoms=mm_link_atoms, &

                                         mm_link_scale_factor=mm_link_scale_factor, &

                                         added_shells=added_shells, &

                                         shell_model=shell_model)


       qmmm_env_qm%mm_atom_chrg => mm_atom_chrg

       qmmm_env_qm%mm_el_pot_radius => mm_el_pot_radius

       qmmm_env_qm%mm_el_pot_radius_corr => mm_el_pot_radius_corr

       qmmm_env_qm%added_shells => added_shells


       qmmm_link_imomm = .false.

       IF (qmmm_link) THEN

          CALL setup_qmmm_links(qmmm_section, qmmm_links, mm_el_pot_radius, &

                                mm_el_pot_radius_corr, mm_atom_index, iw)

          qmmm_env_qm%qmmm_links => qmmm_links


          CALL print_qmmm_links(qmmm_section, qmmm_links)


          CALL add_set_release(qmmm_env_qm%added_charges)

          CALL move_or_add_atoms(qmmm_section, move_mm_charges, add_mm_charges, &

                                 mm_atom_chrg, mm_el_pot_radius, mm_el_pot_radius_corr, &

                                 added_charges, mm_atom_index)

          qmmm_env_qm%move_mm_charges = move_mm_charges

          qmmm_env_qm%add_mm_charges = add_mm_charges

          qmmm_env_qm%added_charges => added_charges

          IF (ASSOCIATED(qmmm_links%imomm)) qmmm_link_imomm = (SIZE(qmmm_links%imomm) /= 0)

       END IF


       CALL print_qmmm_charges(mm_atom_index, mm_atom_chrg, mm_el_pot_radius, &

                               mm_el_pot_radius_corr, qmmm_env_qm%added_charges, &

                               qmmm_env_qm%added_shells, qmmm_section, nocompatibility, shell_model)

       IF (qmmm_env_qm%image_charge) THEN

          CALL print_image_charge_info(qmmm_env_qm, qmmm_section)

       END IF


       CALL section_vals_val_get(qmmm_section, "DELTA_CHARGE", i_val=delta_charge)

       CALL section_vals_val_get(force_env_section, "DFT%CHARGE", i_val=orig_charge)

       CALL section_vals_val_set(force_env_section, "DFT%CHARGE", i_val=orig_charge + delta_charge)


       CALL section_vals_val_set(force_env_section, "METHOD", i_val=do_qs)

       CALL create_small_subsys(subsys_qm, &

                                big_subsys=subsys_mm, small_para_env=para_env, &

                                small_cell=qm_cell_small, sub_atom_index=qm_atom_index, &

                                sub_atom_kind_name=qm_atom_type, para_env=para_env, &

                                force_env_section=force_env_section, subsys_section=subsys_section, &

                                ignore_outside_box=ignore_outside_box)

       IF (qmmm_link_imomm) CALL qmmm_link_imomm_coord(qmmm_links, subsys_qm%particles%els, &

                                                       qm_atom_index)

       ALLOCATE (qs_env)

       CALL qs_env_create(qs_env, globenv)

       CALL qs_init(qs_env, para_env, root_section, globenv=globenv, cp_subsys=subsys_qm, &

                    cell=qm_cell_small, qmmm=.true., qmmm_env_qm=qmmm_env_qm, &

                    force_env_section=force_env_section, subsys_section=subsys_section, &

                    use_motion_section=use_motion_section)

       CALL cp_subsys_release(subsys_qm)


       IF (qmmm_env_qm%periodic) THEN

          IF (.NOT. ASSOCIATED(super_cell)) THEN

             ALLOCATE (super_cell)

          END IF

          CALL cell_clone(mm_cell, super_cell, tag="SUPER_CELL")

          CALL set_qs_env(qs_env, super_cell=super_cell, qmmm_periodic=qmmm_env_qm%periodic)

          CALL cell_release(super_cell)

       END IF

       CALL section_vals_val_set(force_env_section, "DFT%CHARGE", i_val=orig_charge)

       CALL cp_print_key_finished_output(iw, logger, print_gen, "")

       iw2 = cp_print_key_unit_nr(logger, qmmm_section, "PRINT%PROGRAM_BANNER", &

                                  extension=".qmmmLog")

       CALL qmmm_header(iw2)

       CALL cp_print_key_finished_output(iw2, logger, qmmm_section, &

                                         "PRINT%PROGRAM_BANNER")

       !

       ! Initialize MM Potential fitted with Gaussian

       !

       CALL qmmm_init_gaussian_type(qmmm_env_qm=qmmm_env_qm, &

                                    para_env=para_env, &

                                    qs_env=qs_env, &

                                    mm_atom_chrg=mm_atom_chrg, &

                                    added_charges=qmmm_env_qm%added_charges, &

                                    added_shells=qmmm_env_qm%added_shells, &

                                    print_section=print_section, &

                                    qmmm_section=qmmm_section)

       !

       ! Initialize the MM potential stored on vector

       !

       CALL qmmm_init_potential(qmmm_env_qm=qmmm_env_qm, &

                                mm_cell=mm_cell, &

                                added_charges=qmmm_env_qm%added_charges, &

                                added_shells=qmmm_env_qm%added_shells, &

                                print_section=print_section)

       !

       ! Initialize the qmmm_pw_grid

       !

       CALL get_qs_env(qs_env, pw_env=pw_env)

       CALL qmmm_pw_grid_init(qmmm_env=qmmm_env_qm, &

                              pw_env=pw_env)

       !

       ! Initialize the MM periodic potential

       !

       CALL qmmm_init_periodic_potential(qmmm_env_qm=qmmm_env_qm, &

                                         qm_cell_small=qm_cell_small, &

                                         mm_cell=mm_cell, &

                                         para_env=para_env, &

                                         qs_env=qs_env, &

                                         added_charges=qmmm_env_qm%added_charges, &

                                         added_shells=qmmm_env_qm%added_shells, &

                                         qmmm_periodic=qmmm_periodic, &

                                         print_section=print_section, &

                                         mm_atom_chrg=mm_atom_chrg)

       !

       ! Preparing for PBC...

       !

       CALL setup_origin_mm_cell(qmmm_section, qmmm_env_qm, qm_cell_small, &

                                 dr=pw_env%pw_pools(pw_env%auxbas_grid)%pool%pw_grid%dr)


       CALL cell_release(qm_cell_small)


       ! assemble the actual qmmm_env

       qmmm_env%qs_env => qs_env

       qmmm_env%fist_env => fist_env

       qmmm_env%qm => qmmm_env_qm


       CALL section_vals_val_set(force_env_section, "METHOD", i_val=do_qmmm)

       DEALLOCATE (qm_atom_type)


       CALL timestop(handle)


    END SUBROUTINE qmmm_env_create


 END MODULE qmmm_create

bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition: bibliography.F:28

bibliography::laino2006
integer, save, public laino2006
Definition: bibliography.F:43

bibliography::golze2013
integer, save, public golze2013
Definition: bibliography.F:43

bibliography::laino2005
integer, save, public laino2005
Definition: bibliography.F:43

cell_methods
Handles all functions related to the CELL.
Definition: cell_methods.F:15

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::cell_clone
subroutine, public cell_clone(cell_in, cell_out, tag)
Clone cell variable.
Definition: cell_types.F:107

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_log_handling
various routines to log and control the output. The idea is that decisions about where to log should ...
Definition: cp_log_handling.F:41

cp_log_handling::cp_get_default_logger
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
Definition: cp_log_handling.F:234

cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition: cp_output_handling.F:25

cp_output_handling::cp_print_key_unit_nr
integer function, public cp_print_key_unit_nr(logger, basis_section, print_key_path, extension, middle_name, local, log_filename, ignore_should_output, file_form, file_position, file_action, file_status, do_backup, on_file, is_new_file, mpi_io, fout)
...
Definition: cp_output_handling.F:803

cp_output_handling::cp_print_key_finished_output
subroutine, public cp_print_key_finished_output(unit_nr, logger, basis_section, print_key_path, local, ignore_should_output, on_file, mpi_io)
should be called after you finish working with a unit obtained with cp_print_key_unit_nr,...
Definition: cp_output_handling.F:1013

cp_subsys_methods
Initialize a small environment for a particular calculation.
Definition: cp_subsys_methods.F:15

cp_subsys_methods::create_small_subsys
subroutine, public 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)
updates the molecule information of the given subsys
Definition: cp_subsys_methods.F:265

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

fist_environment_types
Definition: fist_environment_types.F:15

fist_environment_types::fist_env_get
subroutine, public fist_env_get(fist_env, atomic_kind_set, particle_set, ewald_pw, local_particles, local_molecules, molecule_kind_set, molecule_set, cell, cell_ref, ewald_env, fist_nonbond_env, thermo, para_env, subsys, qmmm, qmmm_env, input, shell_model, shell_model_ad, shell_particle_set, core_particle_set, multipoles, results, exclusions, efield)
Purpose: Get the FIST environment.
Definition: fist_environment_types.F:140

fist_environment_types::fist_env_create
subroutine, public fist_env_create(fist_env, para_env)
allocates and intitializes a fist_env
Definition: fist_environment_types.F:413

fist_environment_types::fist_env_set
subroutine, public fist_env_set(fist_env, atomic_kind_set, particle_set, ewald_pw, local_particles, local_molecules, molecule_kind_set, molecule_set, cell_ref, ewald_env, fist_nonbond_env, thermo, subsys, qmmm, qmmm_env, input, shell_model, shell_model_ad, exclusions, efield)
Set the FIST environment.
Definition: fist_environment_types.F:277

fist_environment
initialize fist environment
Definition: fist_environment.F:12

fist_environment::fist_init
subroutine, public fist_init(fist_env, root_section, para_env, force_env_section, subsys_section, use_motion_section, prev_subsys)
reads the input and database file for fist
Definition: fist_environment.F:95

fist_nonbond_env_types
Definition: fist_nonbond_env_types.F:13

global_types
Define type storing the global information of a run. Keep the amount of stored data small....
Definition: global_types.F:21

header
Definition: header.F:13

header::qmmm_header
subroutine, public qmmm_header(iw)
...
Definition: header.F:96

input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition: input_constants.F:17

input_constants::do_qmmm_none
integer, parameter, public do_qmmm_none
Definition: input_constants.F:384

input_constants::do_qmmm_center_every_step
integer, parameter, public do_qmmm_center_every_step
Definition: input_constants.F:289

input_constants::do_qmmm_center_pbc_aware
integer, parameter, public do_qmmm_center_pbc_aware
Definition: input_constants.F:293

input_constants::do_qmmm_center_never
integer, parameter, public do_qmmm_center_never
Definition: input_constants.F:289

input_constants::do_multipole_section_off
integer, parameter, public do_multipole_section_off
Definition: input_constants.F:271

input_constants::do_fist
integer, parameter, public do_fist
Definition: input_constants.F:48

input_constants::do_qmmm
integer, parameter, public do_qmmm
Definition: input_constants.F:48

input_constants::do_qmmm_center_setup_only
integer, parameter, public do_qmmm_center_setup_only
Definition: input_constants.F:289

input_constants::do_multipole_section_on
integer, parameter, public do_multipole_section_on
Definition: input_constants.F:271

input_constants::do_qs
integer, parameter, public do_qs
Definition: input_constants.F:48

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_val_set
subroutine, public section_vals_val_set(section_vals, keyword_name, i_rep_section, i_rep_val, val, l_val, i_val, r_val, c_val, l_vals_ptr, i_vals_ptr, r_vals_ptr, c_vals_ptr)
sets the requested value
Definition: input_section_types.F:1216

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_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition: input_section_types.F:697

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

pw_env_types
container for various plainwaves related things
Definition: pw_env_types.F:14

qmmm_create
Initialize a QM/MM calculation.
Definition: qmmm_create.F:14

qmmm_create::qmmm_env_create
subroutine, public qmmm_env_create(qmmm_env, root_section, para_env, globenv, force_env_section, qmmm_section, subsys_section, use_motion_section, prev_subsys, ignore_outside_box)
...
Definition: qmmm_create.F:104

qmmm_init
Initialize a QM/MM calculation.
Definition: qmmm_init.F:14

qmmm_init::setup_qmmm_vars_qm
subroutine, public setup_qmmm_vars_qm(qmmm_section, qmmm_env, subsys_mm, qm_atom_type, qm_atom_index, mm_atom_index, qm_cell_small, qmmm_coupl_type, eps_mm_rspace, qmmm_link, para_env)
...
Definition: qmmm_init.F:633

qmmm_init::setup_qmmm_links
subroutine, public setup_qmmm_links(qmmm_section, qmmm_links, mm_el_pot_radius, mm_el_pot_radius_corr, mm_atom_index, iw)
this routine sets up all variables to treat qmmm links
Definition: qmmm_init.F:1120

qmmm_init::qmmm_init_gaussian_type
subroutine, public qmmm_init_gaussian_type(qmmm_env_qm, para_env, mm_atom_chrg, qs_env, added_charges, added_shells, print_section, qmmm_section)
...
Definition: qmmm_init.F:368

qmmm_init::move_or_add_atoms
subroutine, public move_or_add_atoms(qmmm_section, move_mm_charges, add_mm_charges, mm_atom_chrg, mm_el_pot_radius, mm_el_pot_radius_corr, added_charges, mm_atom_index)
this routine sets up all variables to treat qmmm links
Definition: qmmm_init.F:1240

qmmm_init::assign_mm_charges_and_radius
subroutine, public assign_mm_charges_and_radius(subsys, charges, mm_atom_chrg, mm_el_pot_radius, mm_el_pot_radius_corr, mm_atom_index, mm_link_atoms, mm_link_scale_factor, added_shells, shell_model)
Assigns charges and radius to evaluate the MM electrostatic potential.
Definition: qmmm_init.F:115

qmmm_init::setup_origin_mm_cell
subroutine, public setup_origin_mm_cell(qmmm_section, qmmm_env, qm_cell_small, dr)
this routine sets up the origin of the MM cell respect to the origin of the QM cell....
Definition: qmmm_init.F:1416

qmmm_init::qmmm_init_periodic_potential
subroutine, public qmmm_init_periodic_potential(qmmm_env_qm, qm_cell_small, mm_cell, para_env, qs_env, added_charges, added_shells, qmmm_periodic, print_section, mm_atom_chrg)
...
Definition: qmmm_init.F:523

qmmm_init::print_qmmm_charges
subroutine, public print_qmmm_charges(mm_atom_index, mm_atom_chrg, mm_el_pot_radius, mm_el_pot_radius_corr, added_charges, added_shells, qmmm_section, nocompatibility, shell_model)
Print info on charges generating the qmmm potential..
Definition: qmmm_init.F:212

qmmm_init::print_qmmm_links
subroutine, public print_qmmm_links(qmmm_section, qmmm_links)
Print info on qm/mm links.
Definition: qmmm_init.F:307

qmmm_init::setup_qmmm_vars_mm
subroutine, public setup_qmmm_vars_mm(qmmm_section, qmmm_env, qm_atom_index, mm_link_atoms, mm_link_scale_factor, fist_scale_charge_link, qmmm_coupl_type, qmmm_link)
...
Definition: qmmm_init.F:857

qmmm_init::print_image_charge_info
subroutine, public print_image_charge_info(qmmm_env, qmmm_section)
Print info on image charges.
Definition: qmmm_init.F:1562

qmmm_init::qmmm_init_potential
subroutine, public qmmm_init_potential(qmmm_env_qm, mm_cell, added_charges, added_shells, print_section)
...
Definition: qmmm_init.F:467

qmmm_links_methods
A collection of methods to treat the QM/MM links.
Definition: qmmm_links_methods.F:14

qmmm_links_methods::qmmm_link_imomm_coord
subroutine, public qmmm_link_imomm_coord(qmmm_links, particles, qm_atom_index)
correct the position for qm/mm IMOMM link type
Definition: qmmm_links_methods.F:47

qmmm_pw_grid
sets variables for the qmmm pool of pw_types
Definition: qmmm_pw_grid.F:12

qmmm_pw_grid::qmmm_pw_grid_init
subroutine, public qmmm_pw_grid_init(qmmm_env, pw_env)
Initialize the qmmm pool of pw_r3d_rs_type. Then Main difference w.r.t. QS pw_r3d_rs_type pools is th...
Definition: qmmm_pw_grid.F:53

qmmm_types_low
Definition: qmmm_types_low.F:13

qmmm_types_low::qmmm_env_mm_create
subroutine, public qmmm_env_mm_create(qmmm_env)
...
Definition: qmmm_types_low.F:259

qmmm_types_low::qmmm_env_qm_create
subroutine, public qmmm_env_qm_create(qmmm_env)
...
Definition: qmmm_types_low.F:311

qmmm_types_low::add_set_release
subroutine, public add_set_release(added_charges)
deallocates the add_set_release
Definition: qmmm_types_low.F:565

qmmm_types
Basic container type for QM/MM.
Definition: qmmm_types.F:12

qs_environment_types
Definition: qs_environment_types.F:14

qs_environment_types::get_qs_env
subroutine, public get_qs_env(qs_env, atomic_kind_set, qs_kind_set, cell, super_cell, cell_ref, use_ref_cell, kpoints, dft_control, mos, sab_orb, sab_all, qmmm, qmmm_periodic, sac_ae, sac_ppl, sac_lri, sap_ppnl, sab_vdw, sab_scp, sap_oce, sab_lrc, sab_se, sab_xtbe, sab_tbe, sab_core, sab_xb, sab_xtb_nonbond, sab_almo, sab_kp, sab_kp_nosym, particle_set, energy, force, matrix_h, matrix_h_im, matrix_ks, matrix_ks_im, matrix_vxc, run_rtp, rtp, matrix_h_kp, matrix_h_im_kp, matrix_ks_kp, matrix_ks_im_kp, matrix_vxc_kp, kinetic_kp, matrix_s_kp, matrix_w_kp, matrix_s_RI_aux_kp, matrix_s, matrix_s_RI_aux, matrix_w, matrix_p_mp2, matrix_p_mp2_admm, rho, rho_xc, pw_env, ewald_env, ewald_pw, active_space, mpools, input, para_env, blacs_env, scf_control, rel_control, kinetic, qs_charges, vppl, rho_core, rho_nlcc, rho_nlcc_g, ks_env, ks_qmmm_env, wf_history, scf_env, local_particles, local_molecules, distribution_2d, dbcsr_dist, molecule_kind_set, molecule_set, subsys, cp_subsys, oce, local_rho_set, rho_atom_set, task_list, task_list_soft, rho0_atom_set, rho0_mpole, rhoz_set, ecoul_1c, rho0_s_rs, rho0_s_gs, do_kpoints, has_unit_metric, requires_mo_derivs, mo_derivs, mo_loc_history, nkind, natom, nelectron_total, nelectron_spin, efield, neighbor_list_id, linres_control, xas_env, virial, cp_ddapc_env, cp_ddapc_ewald, outer_scf_history, outer_scf_ihistory, x_data, et_coupling, dftb_potential, results, se_taper, se_store_int_env, se_nddo_mpole, se_nonbond_env, admm_env, lri_env, lri_density, exstate_env, ec_env, dispersion_env, gcp_env, vee, rho_external, external_vxc, mask, mp2_env, bs_env, kg_env, WannierCentres, atprop, ls_scf_env, do_transport, transport_env, v_hartree_rspace, s_mstruct_changed, rho_changed, potential_changed, forces_up_to_date, mscfg_env, almo_scf_env, gradient_history, variable_history, embed_pot, spin_embed_pot, polar_env, mos_last_converged, rhs)
Get the QUICKSTEP environment.
Definition: qs_environment_types.F:502

qs_environment_types::set_qs_env
subroutine, public set_qs_env(qs_env, super_cell, mos, qmmm, qmmm_periodic, ewald_env, ewald_pw, mpools, rho_external, external_vxc, mask, scf_control, rel_control, qs_charges, ks_env, ks_qmmm_env, wf_history, scf_env, active_space, input, oce, rho_atom_set, rho0_atom_set, rho0_mpole, run_rtp, rtp, rhoz_set, rhoz_tot, ecoul_1c, has_unit_metric, requires_mo_derivs, mo_derivs, mo_loc_history, efield, linres_control, xas_env, cp_ddapc_env, cp_ddapc_ewald, outer_scf_history, outer_scf_ihistory, x_data, et_coupling, dftb_potential, se_taper, se_store_int_env, se_nddo_mpole, se_nonbond_env, admm_env, ls_scf_env, do_transport, transport_env, lri_env, lri_density, exstate_env, ec_env, dispersion_env, gcp_env, mp2_env, bs_env, kg_env, force, kpoints, WannierCentres, almo_scf_env, gradient_history, variable_history, embed_pot, spin_embed_pot, polar_env, mos_last_converged, rhs)
Set the QUICKSTEP environment.
Definition: qs_environment_types.F:1035

qs_environment_types::qs_env_create
subroutine, public qs_env_create(qs_env, globenv)
allocates and intitializes a qs_env
Definition: qs_environment_types.F:1351

qs_environment
Definition: qs_environment.F:19

qs_environment::qs_init
subroutine, public qs_init(qs_env, para_env, root_section, globenv, cp_subsys, kpoint_env, cell, cell_ref, qmmm, qmmm_env_qm, force_env_section, subsys_section, use_motion_section)
Read the input and the database files for the setup of the QUICKSTEP environment.
Definition: qs_environment.F:237