comp-chem/cp2k
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Default for SE/TB is now use Element symbol as atom name (#340)

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Juerg Hutter 2019-05-07 14:41:55 +02:00 • committed by GitHub
parent 158053f68c
commit dd18ba31a5
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5 changed files with 47 additions and 10 deletions
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6
src/cp_subsys_methods.F
View file

@ -87,11 +87,12 @@ CONTAINS
!> \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)
use_motion_section, qmmm, qmmm_env, exclusions, elkind)
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(cp_para_env_type), POINTER :: para_env
TYPE(section_vals_type), POINTER :: root_section
@ -101,6 +102,7 @@ CONTAINS
TYPE(qmmm_env_mm_type), OPTIONAL, POINTER :: qmmm_env
TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
POINTER :: exclusions
LOGICAL, INTENT(IN), OPTIONAL :: elkind
CHARACTER(len=*), PARAMETER :: routineN = 'cp_subsys_create', &
routineP = moduleN//':'//routineN
@ -159,7 +161,7 @@ CONTAINS
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)
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)

8
src/input_cp2k_subsys.F
View file

@ -1576,6 +1576,14 @@ CONTAINS
NULLIFY (keyword, print_key)
! Logical
CALL keyword_create(keyword, name="USE_ELEMENT_AS_KIND", &
description="Kinds are generated according to the element name."// &
" Default=True for SE and TB methods.", &
usage="USE_ELEMENT_AS_KIND logical", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(section, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, name="CHARGE_OCCUP", &
variants=(/"CHARGE_O"/), &
description="Read MM charges from the OCCUP field of PDB file.", &

13
src/qs_environment.F
View file

@ -246,8 +246,9 @@ CONTAINS
INTEGER :: ikind, method_id, natom, nkind
LOGICAL :: do_admm_rpa, do_et, do_exx, do_hfx, &
do_kpoints, mp2_present, my_qmmm, &
qmmm_decoupl, silent, use_ref_cell
do_kpoints, is_semi, mp2_present, &
my_qmmm, qmmm_decoupl, silent, &
use_ref_cell
REAL(KIND=dp), DIMENSION(:, :), POINTER :: rtmat
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell, my_cell_ref
@ -294,8 +295,11 @@ CONTAINS
CASE (do_method_rm1, do_method_am1, do_method_mndo, do_method_pdg, &
do_method_pm3, do_method_pm6, do_method_pm6fm, do_method_mndod, do_method_pnnl)
CALL init_se_intd_array()
is_semi = .TRUE.
CASE (do_method_xtb, do_method_dftb)
is_semi = .TRUE.
CASE DEFAULT
! Do nothing
is_semi = .FALSE.
END SELECT
CALL qs_subsys_create(subsys, para_env, &
@ -303,7 +307,8 @@ CONTAINS
subsys_section=subsys_section, &
use_motion_section=use_motion_section, &
root_section=root_section, &
cp_subsys=cp_subsys, cell=cell, cell_ref=cell_ref)
cp_subsys=cp_subsys, cell=cell, cell_ref=cell_ref, &
elkind=is_semi)
CALL qs_ks_env_create(ks_env)
CALL set_ks_env(ks_env, subsys=subsys)

7
src/qs_subsys_methods.F
View file

@ -63,9 +63,10 @@ CONTAINS
!> \param cp_subsys ...
!> \param cell ...
!> \param cell_ref ...
!> \param elkind ...
! **************************************************************************************************
SUBROUTINE qs_subsys_create(subsys, para_env, root_section, force_env_section, subsys_section, &
use_motion_section, cp_subsys, cell, cell_ref)
use_motion_section, cp_subsys, cell, cell_ref, elkind)
TYPE(qs_subsys_type), POINTER :: subsys
TYPE(cp_para_env_type), POINTER :: para_env
TYPE(section_vals_type), OPTIONAL, POINTER :: root_section
@ -73,6 +74,7 @@ CONTAINS
LOGICAL, INTENT(IN) :: use_motion_section
TYPE(cp_subsys_type), OPTIONAL, POINTER :: cp_subsys
TYPE(cell_type), OPTIONAL, POINTER :: cell, cell_ref
LOGICAL, INTENT(IN), OPTIONAL :: elkind
CHARACTER(len=*), PARAMETER :: routineN = 'qs_subsys_create', &
routineP = moduleN//':'//routineN
@ -95,7 +97,8 @@ CONTAINS
CALL cp_subsys_create(my_cp_subsys, para_env, root_section=root_section, &
force_env_section=force_env_section, &
subsys_section=subsys_section, &
use_motion_section=use_motion_section)
use_motion_section=use_motion_section, &
elkind=elkind)
ELSE
CPABORT("qs_subsys_create: cp_subsys or root_section needed")
END IF

23
src/topology.F
View file

@ -115,10 +115,11 @@ CONTAINS
!> \param subsys_section ...
!> \param use_motion_section ...
!> \param exclusions ...
!> \param elkind ...
! **************************************************************************************************
SUBROUTINE topology_control(atomic_kind_set, particle_set, molecule_kind_set, &
molecule_set, colvar_p, gci, root_section, para_env, qmmm, qmmm_env, &
force_env_section, subsys_section, use_motion_section, exclusions)
force_env_section, subsys_section, use_motion_section, exclusions, elkind)
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
@ -134,12 +135,14 @@ CONTAINS
LOGICAL, INTENT(IN) :: use_motion_section
TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
POINTER :: exclusions
LOGICAL, INTENT(IN), OPTIONAL :: elkind
CHARACTER(LEN=*), PARAMETER :: routineN = 'topology_control', &
routineP = moduleN//':'//routineN
INTEGER :: handle, iw, iw2
LOGICAL :: binary_coord_read, my_qmmm
LOGICAL :: binary_coord_read, el_as_kind, explicit, &
my_qmmm
TYPE(cp_logger_type), POINTER :: logger
TYPE(section_vals_type), POINTER :: cell_section, constraint_section, &
topology_section
@ -160,6 +163,17 @@ CONTAINS
my_qmmm = .FALSE.
IF (PRESENT(qmmm) .AND. PRESENT(qmmm_env)) my_qmmm = qmmm
IF (PRESENT(elkind)) THEN
CALL section_vals_val_get(topology_section, "USE_ELEMENT_AS_KIND", explicit=explicit)
IF (explicit) THEN
CALL section_vals_val_get(topology_section, "USE_ELEMENT_AS_KIND", l_val=el_as_kind)
ELSE
el_as_kind = elkind
END IF
ELSE
CALL section_vals_val_get(topology_section, "USE_ELEMENT_AS_KIND", l_val=el_as_kind)
END IF
! 1. Initialize the topology structure type
CALL init_topology(topology)
@ -186,6 +200,11 @@ CONTAINS
CALL connectivity_control(topology, para_env, my_qmmm, qmmm_env, subsys_section, &
force_env_section)
IF (el_as_kind) THEN
! redefine atom names with the name of the element
topology%atom_info%id_atmname(:) = topology%atom_info%id_element(:)
END IF
! 7. Pack everything into the molecular types
CALL topology_connectivity_pack(molecule_kind_set, molecule_set, &
topology, subsys_section)