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Refactor: when calling cp_subsys_create() do not call read_cell() again (#5048)

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HE Zilong 2026-04-13 18:34:27 +08:00 • committed by GitHub
parent 0e652e763d
commit 563e6d5d46
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11 changed files with 156 additions and 225 deletions
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3
src/cp_subsys_methods.F
View file

@ -157,7 +157,8 @@ 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, elkind=elkind)
qmmm=qmmm, qmmm_env=qmmm_env, exclusions=exclusions, elkind=elkind, &
subsys=subsys)
CALL particle_list_create(particles, els_ptr=particle_set)
CALL atomic_kind_list_create(atomic_kinds, els_ptr=atomic_kind_set)

54
src/eip_environment.F
View file

@ -14,14 +14,9 @@
MODULE eip_environment
USE atomic_kind_types, ONLY: atomic_kind_type,&
get_atomic_kind
USE cell_methods, ONLY: read_cell,&
write_cell
USE cell_types, ONLY: cell_release,&
cell_type,&
get_cell
USE cell_types, ONLY: cell_type
USE cp_subsys_methods, ONLY: cp_subsys_create
USE cp_subsys_types, ONLY: cp_subsys_set,&
cp_subsys_type
USE cp_subsys_types, ONLY: cp_subsys_type
USE distribution_1d_types, ONLY: distribution_1d_release,&
distribution_1d_type
USE distribution_methods, ONLY: distribute_molecules_1d
@ -77,44 +72,30 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'eip_init'
INTEGER :: handle
LOGICAL :: use_ref_cell
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(section_vals_type), POINTER :: cell_section, colvar_section, eip_section
TYPE(section_vals_type), POINTER :: colvar_section, eip_section
CALL timeset(routineN, handle)
CPASSERT(ASSOCIATED(eip_env))
! nullifying pointers
NULLIFY (cell_section, colvar_section, eip_section, cell, cell_ref, &
subsys)
NULLIFY (colvar_section, eip_section, subsys)
IF (.NOT. ASSOCIATED(subsys_section)) THEN
subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
END IF
cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
colvar_section => section_vals_get_subs_vals(subsys_section, "COLVAR")
eip_section => section_vals_get_subs_vals(force_env_section, "EIP")
CALL eip_env_set(eip_env=eip_env, eip_input=eip_section, &
force_env_input=force_env_section)
CALL read_cell(cell=cell, cell_ref=cell_ref, use_ref_cell=use_ref_cell, cell_section=cell_section, &
para_env=para_env)
CALL get_cell(cell=cell, abc=abc)
CALL write_cell(cell=cell, subsys_section=subsys_section)
CALL cp_subsys_create(subsys, para_env, root_section)
CALL eip_init_subsys(eip_env=eip_env, subsys=subsys, cell=cell, &
cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
CALL eip_init_subsys(eip_env=eip_env, subsys=subsys, &
subsys_section=subsys_section)
CALL cell_release(cell)
CALL cell_release(cell_ref)
CALL timestop(handle)
END SUBROUTINE eip_init
@ -123,25 +104,21 @@ CONTAINS
!> \brief Initialize the eip environment
!> \param eip_env The eip environment of matter
!> \param subsys the subsys
!> \param cell Pointer to the actual simulation cell
!> \param cell_ref Pointer to the reference cell, used e.g. in NPT simulations
!> \param use_ref_cell Logical which indicates if cell_ref is in use
!> \param subsys_section ...
!> \par History
!> 03.2006 initial create [tdk]
!> \author Thomas D. Kuehne (tkuehne@phys.chem.ethz.ch)
! **************************************************************************************************
SUBROUTINE eip_init_subsys(eip_env, subsys, cell, cell_ref, use_ref_cell, subsys_section)
SUBROUTINE eip_init_subsys(eip_env, subsys, subsys_section)
TYPE(eip_environment_type), POINTER :: eip_env
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(cell_type), POINTER :: cell, cell_ref
LOGICAL, INTENT(in) :: use_ref_cell
TYPE(section_vals_type), POINTER :: subsys_section
CHARACTER(len=*), PARAMETER :: routineN = 'eip_init_subsys'
INTEGER :: handle, natom
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell, my_cell_ref
TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
@ -152,21 +129,28 @@ CONTAINS
CALL timeset(routineN, handle)
NULLIFY (atomic_kind_set, molecule_kind_set, particle_set, molecule_set, &
local_molecules, local_particles)
my_cell, my_cell_ref, local_molecules, local_particles)
particle_set => subsys%particles%els
atomic_kind_set => subsys%atomic_kinds%els
molecule_kind_set => subsys%molecule_kinds%els
molecule_set => subsys%molecules%els
my_cell => subsys%cell
my_cell_ref => subsys%cell_ref
! *** Set up cell ***
CALL eip_env_set(eip_env=eip_env, subsys=subsys, &
cell_ref=my_cell_ref, &
use_ref_cell=subsys%use_ref_cell)
! *** Print the molecule kind set ***
CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
! *** Print the atomic coordinates
CALL write_fist_particle_coordinates(particle_set, subsys_section)
CALL write_particle_distances(particle_set, cell=cell, &
CALL write_particle_distances(particle_set, cell=my_cell, &
subsys_section=subsys_section)
CALL write_structure_data(particle_set, cell=cell, &
CALL write_structure_data(particle_set, cell=my_cell, &
input_section=subsys_section)
! *** Distribute molecules and atoms using the new data structures ***
@ -184,9 +168,7 @@ CONTAINS
eip_env%eip_forces(:, :) = 0.0_dp
CALL cp_subsys_set(subsys, cell=cell)
CALL eip_env_set(eip_env=eip_env, subsys=subsys, &
cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
CALL eip_env_set(eip_env=eip_env, &
local_molecules=local_molecules, &
local_particles=local_particles)

47
src/embed_environment.F
View file

@ -11,14 +11,9 @@
! **************************************************************************************************
MODULE embed_environment
USE atomic_kind_types, ONLY: atomic_kind_type
USE cell_methods, ONLY: read_cell,&
write_cell
USE cell_types, ONLY: cell_release,&
cell_type,&
get_cell
USE cell_types, ONLY: cell_type
USE cp_subsys_methods, ONLY: cp_subsys_create
USE cp_subsys_types, ONLY: cp_subsys_set,&
cp_subsys_type
USE cp_subsys_types, ONLY: cp_subsys_type
USE distribution_1d_types, ONLY: distribution_1d_release,&
distribution_1d_type
USE distribution_methods, ONLY: distribute_molecules_1d
@ -26,7 +21,6 @@ MODULE embed_environment
set_embed_env
USE input_section_types, ONLY: section_vals_get_subs_vals,&
section_vals_type
USE kinds, ONLY: dp
USE message_passing, ONLY: mp_para_env_type
USE molecule_kind_types, ONLY: molecule_kind_type,&
write_molecule_kind_set
@ -66,39 +60,23 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'embed_init'
INTEGER :: handle
LOGICAL :: use_ref_cell
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(section_vals_type), POINTER :: cell_section, subsys_section
TYPE(section_vals_type), POINTER :: subsys_section
CALL timeset(routineN, handle)
NULLIFY (subsys, cell, cell_ref)
NULLIFY (cell_section)
NULLIFY (subsys)
subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
CALL set_embed_env(embed_env, input=force_env_section)
CALL cp_subsys_create(subsys, para_env, root_section, &
force_env_section=force_env_section, &
use_motion_section=use_motion_section)
CALL read_cell(cell, cell_ref, use_ref_cell=use_ref_cell, &
cell_section=cell_section, para_env=para_env)
CALL get_cell(cell, abc=abc)
! Print the cell parameters ***
CALL write_cell(cell, subsys_section)
CALL write_cell(cell_ref, subsys_section)
CALL embed_init_subsys(embed_env, subsys, cell, cell_ref, &
CALL embed_init_subsys(embed_env, subsys, &
force_env_section, subsys_section)
CALL cell_release(cell)
CALL cell_release(cell_ref)
CALL timestop(handle)
END SUBROUTINE embed_init
@ -108,36 +86,35 @@ CONTAINS
!> embed environment.
!> \param embed_env ...
!> \param subsys ...
!> \param cell ...
!> \param cell_ref ...
!> \param force_env_section ...
!> \param subsys_section ...
!> \date 02.2018
!> \author Vladimir Rybkin
! **************************************************************************************************
SUBROUTINE embed_init_subsys(embed_env, subsys, cell, cell_ref, &
force_env_section, subsys_section)
SUBROUTINE embed_init_subsys(embed_env, subsys, force_env_section, &
subsys_section)
TYPE(embed_env_type), INTENT(INOUT) :: embed_env
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
CHARACTER(len=*), PARAMETER :: routineN = 'embed_init_subsys'
INTEGER :: handle
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell_ref
TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
CALL timeset(routineN, handle)
NULLIFY (local_molecules, local_particles)
NULLIFY (local_molecules, local_particles, my_cell_ref)
particle_set => subsys%particles%els
atomic_kind_set => subsys%atomic_kinds%els
molecule_set => subsys%molecules%els
molecule_kind_set => subsys%molecule_kinds%els
my_cell_ref => subsys%cell_ref
! Print the molecule kind set
CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
@ -151,12 +128,10 @@ CONTAINS
local_molecules=local_molecules, &
force_env_section=force_env_section)
CALL cp_subsys_set(subsys, cell=cell)
! set the embed_env
CALL set_embed_env(embed_env=embed_env, subsys=subsys)
CALL set_embed_env(embed_env=embed_env, &
cell_ref=cell_ref, &
cell_ref=my_cell_ref, &
local_molecules=local_molecules, &
local_particles=local_particles)

54
src/fist_environment.F
View file

@ -16,11 +16,7 @@ MODULE fist_environment
Dick1958,&
Mitchell1993,&
cite_reference
USE cell_methods, ONLY: read_cell,&
write_cell
USE cell_types, ONLY: cell_release,&
cell_type,&
get_cell
USE cell_types, ONLY: cell_type
USE cp_log_handling, ONLY: cp_get_default_logger,&
cp_logger_type
USE cp_output_handling, ONLY: cp_print_key_finished_output,&
@ -53,7 +49,6 @@ MODULE fist_environment
USE header, ONLY: fist_header
USE input_section_types, ONLY: section_vals_get_subs_vals,&
section_vals_type
USE kinds, ONLY: dp
USE message_passing, ONLY: mp_para_env_type
USE molecule_kind_types, ONLY: molecule_kind_type,&
write_molecule_kind_set
@ -104,8 +99,6 @@ CONTAINS
INTEGER :: handle, iw
LOGICAL :: qmmm, shell_adiabatic, shell_present
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(cp_logger_type), POINTER :: logger
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(ewald_environment_type), POINTER :: ewald_env
@ -115,21 +108,19 @@ CONTAINS
TYPE(particle_list_type), POINTER :: core_particles, shell_particles
TYPE(particle_type), DIMENSION(:), POINTER :: core_particle_set, shell_particle_set
TYPE(qmmm_env_mm_type), POINTER :: qmmm_env
TYPE(section_vals_type), POINTER :: cell_section, ewald_section, mm_section, &
TYPE(section_vals_type), POINTER :: ewald_section, mm_section, &
poisson_section
CALL timeset(routineN, handle)
logger => cp_get_default_logger()
NULLIFY (subsys, cell, cell_ref)
NULLIFY (ewald_env, fist_nonbond_env, qmmm_env, cell_section, &
NULLIFY (ewald_env, fist_nonbond_env, qmmm_env, subsys, &
poisson_section, shell_particle_set, shell_particles, &
core_particle_set, core_particles, exclusions)
IF (.NOT. ASSOCIATED(subsys_section)) THEN
subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
END IF
mm_section => section_vals_get_subs_vals(force_env_section, "MM")
cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
poisson_section => section_vals_get_subs_vals(mm_section, "POISSON")
ewald_section => section_vals_get_subs_vals(poisson_section, "EWALD")
@ -140,13 +131,6 @@ CONTAINS
CALL fist_header(iw)
CALL cp_print_key_finished_output(iw, logger, mm_section, "PRINT%PROGRAM_BANNER")
CALL read_cell(cell, cell_ref, cell_section=cell_section, para_env=para_env)
CALL get_cell(cell, abc=abc)
! Print the cell parameters
CALL write_cell(cell, subsys_section)
CALL write_cell(cell_ref, subsys_section)
! Create the ewald environment
ALLOCATE (ewald_env)
CALL ewald_env_create(ewald_env, para_env)
@ -173,7 +157,7 @@ CONTAINS
ewald_env, fist_nonbond_env, root_section, para_env, qmmm=qmmm, &
qmmm_env=qmmm_env, subsys_section=subsys_section, &
mm_section=mm_section, shell_particle_set=shell_particle_set, &
core_particle_set=core_particle_set, cell=cell)
core_particle_set=core_particle_set, cell=subsys%cell)
NULLIFY (shell_particles, core_particles)
IF (ASSOCIATED(shell_particle_set)) THEN
@ -194,12 +178,9 @@ CONTAINS
CALL particle_list_release(shell_particles)
CALL particle_list_release(core_particles)
CALL fist_init_subsys(fist_env, subsys, cell, cell_ref, fist_nonbond_env, ewald_env, &
CALL fist_init_subsys(fist_env, subsys, fist_nonbond_env, ewald_env, &
force_env_section, subsys_section, prev_subsys)
CALL cell_release(cell)
CALL cell_release(cell_ref)
CALL timestop(handle)
END SUBROUTINE fist_init
@ -209,8 +190,6 @@ CONTAINS
!> FIST environment.
!> \param fist_env ...
!> \param subsys ...
!> \param cell ...
!> \param cell_ref ...
!> \param fist_nonbond_env ...
!> \param ewald_env ...
!> \param force_env_section ...
@ -220,13 +199,12 @@ CONTAINS
!> \author MK
!> \version 1.0
! **************************************************************************************************
SUBROUTINE fist_init_subsys(fist_env, subsys, cell, cell_ref, fist_nonbond_env, &
SUBROUTINE fist_init_subsys(fist_env, subsys, fist_nonbond_env, &
ewald_env, force_env_section, subsys_section, &
prev_subsys)
TYPE(fist_environment_type), POINTER :: fist_env
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(fist_nonbond_env_type), POINTER :: fist_nonbond_env
TYPE(ewald_environment_type), POINTER :: ewald_env
TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
@ -237,6 +215,7 @@ CONTAINS
INTEGER :: handle, max_multipole
LOGICAL :: do_multipoles
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell, my_cell_ref
TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles, &
prev_local_molecules
TYPE(ewald_pw_type), POINTER :: ewald_pw
@ -248,11 +227,14 @@ CONTAINS
TYPE(section_vals_type), POINTER :: grid_print_section
CALL timeset(routineN, handle)
NULLIFY (thermo, ewald_pw, local_molecules, local_particles, multipoles)
NULLIFY (thermo, ewald_pw, local_molecules, local_particles, &
multipoles, my_cell, my_cell_ref)
particle_set => subsys%particles%els
atomic_kind_set => subsys%atomic_kinds%els
molecule_set => subsys%molecules%els
molecule_kind_set => subsys%molecule_kinds%els
my_cell => subsys%cell
my_cell_ref => subsys%cell_ref
IF (PRESENT(prev_subsys)) THEN
prev_molecule_kind_set => prev_subsys%molecule_kinds%els
@ -271,11 +253,11 @@ CONTAINS
! Print the atomic coordinates
CALL write_fist_particle_coordinates(particle_set, subsys_section, &
fist_nonbond_env%charges)
CALL write_particle_distances(particle_set, cell, subsys_section)
CALL write_structure_data(particle_set, cell=cell, input_section=subsys_section)
CALL write_particle_distances(particle_set, my_cell, subsys_section)
CALL write_structure_data(particle_set, cell=my_cell, input_section=subsys_section)
! Print symmetry information
CALL write_symmetry(particle_set, cell, subsys_section)
CALL write_symmetry(particle_set, my_cell, subsys_section)
! Distribute molecules and atoms using the new data structures ***
CALL distribute_molecules_1d(atomic_kind_set=atomic_kind_set, &
@ -292,10 +274,10 @@ CONTAINS
grid_print_section => section_vals_get_subs_vals(force_env_section, &
"PRINT%GRID_INFORMATION")
ALLOCATE (ewald_pw)
CALL ewald_pw_create(ewald_pw, ewald_env, cell, cell_ref, grid_print_section)
CALL ewald_pw_create(ewald_pw, ewald_env, my_cell, my_cell_ref, grid_print_section)
! Initialize ewald grids
CALL ewald_pw_grid_update(ewald_pw, ewald_env, cell%hmat)
CALL ewald_pw_grid_update(ewald_pw, ewald_env, my_cell%hmat)
! Possibly Initialize the multipole environment
CALL ewald_env_get(ewald_env, do_multipoles=do_multipoles, &
@ -304,11 +286,11 @@ CONTAINS
ALLOCATE (multipoles)
CALL create_multipole_type(multipoles, particle_set, subsys_section, max_multipole)
END IF
CALL cp_subsys_set(subsys, multipoles=multipoles, cell=cell)
CALL cp_subsys_set(subsys, multipoles=multipoles)
! Set the fist_env
CALL fist_env_set(fist_env=fist_env, &
cell_ref=cell_ref, &
cell_ref=my_cell_ref, &
local_molecules=local_molecules, &
local_particles=local_particles, &
ewald_env=ewald_env, ewald_pw=ewald_pw, &

3
src/input_cp2k_subsys.F
View file

@ -87,7 +87,8 @@ CONTAINS
"2. The lengths and angles of cell vectors set by ABC and ALPHA_BETA_GAMMA;"//newline// &
"3. The vectors set by A, B, C together;"//newline// &
"4. If none above exist, the external file set by TOPOLOGY/COORD_FILE_NAME with "// &
"certain TOPOLOGY/COORD_FILE_FORMAT may also be parsed.")
"certain TOPOLOGY/COORD_FILE_FORMAT may also be parsed. This behavior has NOT "// &
"been fully tested for BSSE as well as QM/MM calculations.")
CALL create_cell_section_low(section, periodic)
NULLIFY (subsection)

45
src/ipi_environment.F
View file

@ -13,14 +13,9 @@
! **************************************************************************************************
MODULE ipi_environment
USE atomic_kind_types, ONLY: atomic_kind_type
USE cell_methods, ONLY: read_cell,&
write_cell
USE cell_types, ONLY: cell_release,&
cell_type,&
get_cell
USE cell_types, ONLY: cell_type
USE cp_subsys_methods, ONLY: cp_subsys_create
USE cp_subsys_types, ONLY: cp_subsys_set,&
cp_subsys_type
USE cp_subsys_types, ONLY: cp_subsys_type
USE distribution_1d_types, ONLY: distribution_1d_release,&
distribution_1d_type
USE distribution_methods, ONLY: distribute_molecules_1d
@ -75,38 +70,25 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'ipi_init'
INTEGER :: handle
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(section_vals_type), POINTER :: cell_section, driver_section, &
motion_section
TYPE(section_vals_type), POINTER :: driver_section, motion_section
CALL timeset(routineN, handle)
CPASSERT(ASSOCIATED(ipi_env))
! nullifying pointers
NULLIFY (cell_section, cell, cell_ref, subsys)
NULLIFY (subsys)
IF (.NOT. ASSOCIATED(subsys_section)) THEN
subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
END IF
cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
CALL ipi_env_set(ipi_env=ipi_env, force_env_input=force_env_section)
CALL read_cell(cell=cell, cell_ref=cell_ref, &
cell_section=cell_section, para_env=para_env)
CALL get_cell(cell=cell, abc=abc)
CALL write_cell(cell=cell, subsys_section=subsys_section)
CALL cp_subsys_create(subsys, para_env, root_section)
CALL ipi_init_subsys(ipi_env=ipi_env, subsys=subsys, cell=cell, &
cell_ref=cell_ref, subsys_section=subsys_section)
CALL cell_release(cell)
CALL cell_release(cell_ref)
CALL ipi_init_subsys(ipi_env=ipi_env, subsys=subsys, subsys_section=subsys_section)
motion_section => section_vals_get_subs_vals(root_section, "MOTION")
driver_section => section_vals_get_subs_vals(motion_section, "DRIVER")
@ -120,23 +102,21 @@ CONTAINS
!> \brief Initialize the ipi environment
!> \param ipi_env The ipi environment
!> \param subsys the subsys
!> \param cell Pointer to the actual simulation cell
!> \param cell_ref Pointer to the reference cell, used e.g. in NPT simulations
!> \param subsys_section ...
!> \par History
!> 03.2024 initial create
!> \author Sebastian Seidenath (sebastian.seidenath@uni-jena.de)
! **************************************************************************************************
SUBROUTINE ipi_init_subsys(ipi_env, subsys, cell, cell_ref, subsys_section)
SUBROUTINE ipi_init_subsys(ipi_env, subsys, subsys_section)
TYPE(ipi_environment_type), POINTER :: ipi_env
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(section_vals_type), POINTER :: subsys_section
CHARACTER(len=*), PARAMETER :: routineN = 'ipi_init_subsys'
INTEGER :: handle, natom
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell, my_cell_ref
TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
@ -145,21 +125,23 @@ CONTAINS
CALL timeset(routineN, handle)
NULLIFY (atomic_kind_set, molecule_kind_set, particle_set, molecule_set, &
local_molecules, local_particles)
local_molecules, local_particles, my_cell, my_cell_ref)
particle_set => subsys%particles%els
atomic_kind_set => subsys%atomic_kinds%els
molecule_kind_set => subsys%molecule_kinds%els
molecule_set => subsys%molecules%els
my_cell => subsys%cell
my_cell_ref => subsys%cell_ref
! *** Print the molecule kind set ***
CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
! *** Print the atomic coordinates ***
CALL write_fist_particle_coordinates(particle_set, subsys_section)
CALL write_particle_distances(particle_set, cell=cell, &
CALL write_particle_distances(particle_set, cell=my_cell, &
subsys_section=subsys_section)
CALL write_structure_data(particle_set, cell=cell, &
CALL write_structure_data(particle_set, cell=my_cell, &
input_section=subsys_section)
! *** Distribute molecules and atoms using the new data structures ***
@ -176,9 +158,8 @@ CONTAINS
ALLOCATE (ipi_env%ipi_forces(3, natom))
ipi_env%ipi_forces(:, :) = 0.0_dp
CALL cp_subsys_set(subsys, cell=cell)
CALL ipi_env_set(ipi_env=ipi_env, subsys=subsys, &
cell_ref=cell_ref, &
cell_ref=my_cell_ref, &
local_molecules=local_molecules, &
local_particles=local_particles)

47
src/mixed_environment.F
View file

@ -11,20 +11,14 @@
! **************************************************************************************************
MODULE mixed_environment
USE atomic_kind_types, ONLY: atomic_kind_type
USE cell_methods, ONLY: read_cell,&
write_cell
USE cell_types, ONLY: cell_release,&
cell_type,&
get_cell
USE cell_types, ONLY: cell_type
USE cp_subsys_methods, ONLY: cp_subsys_create
USE cp_subsys_types, ONLY: cp_subsys_set,&
cp_subsys_type
USE cp_subsys_types, ONLY: cp_subsys_type
USE distribution_1d_types, ONLY: distribution_1d_release,&
distribution_1d_type
USE distribution_methods, ONLY: distribute_molecules_1d
USE input_section_types, ONLY: section_vals_get_subs_vals,&
section_vals_type
USE kinds, ONLY: dp
USE message_passing, ONLY: mp_para_env_type
USE mixed_energy_types, ONLY: allocate_mixed_energy,&
mixed_energy_type
@ -68,39 +62,23 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'mixed_init'
INTEGER :: handle
LOGICAL :: use_ref_cell
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(section_vals_type), POINTER :: cell_section, subsys_section
TYPE(section_vals_type), POINTER :: subsys_section
CALL timeset(routineN, handle)
NULLIFY (subsys, cell, cell_ref)
NULLIFY (cell_section)
NULLIFY (subsys)
subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
CALL set_mixed_env(mixed_env, input=force_env_section)
CALL cp_subsys_create(subsys, para_env, root_section, &
force_env_section=force_env_section, &
use_motion_section=use_motion_section)
CALL read_cell(cell, cell_ref, use_ref_cell=use_ref_cell, &
cell_section=cell_section, para_env=para_env)
CALL get_cell(cell, abc=abc)
! Print the cell parameters ***
CALL write_cell(cell, subsys_section)
CALL write_cell(cell_ref, subsys_section)
CALL mixed_init_subsys(mixed_env, subsys, cell, cell_ref, &
CALL mixed_init_subsys(mixed_env, subsys, &
force_env_section, subsys_section)
CALL cell_release(cell)
CALL cell_release(cell_ref)
CALL timestop(handle)
END SUBROUTINE mixed_init
@ -110,26 +88,24 @@ CONTAINS
!> mixed environment.
!> \param mixed_env ...
!> \param subsys ...
!> \param cell ...
!> \param cell_ref ...
!> \param force_env_section ...
!> \param subsys_section ...
!> \date 11.06
!> \author fschiff
!> \version 1.0
! **************************************************************************************************
SUBROUTINE mixed_init_subsys(mixed_env, subsys, cell, cell_ref, &
force_env_section, subsys_section)
SUBROUTINE mixed_init_subsys(mixed_env, subsys, force_env_section, &
subsys_section)
TYPE(mixed_environment_type), INTENT(INOUT) :: mixed_env
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(cell_type), POINTER :: cell, cell_ref
TYPE(section_vals_type), POINTER :: force_env_section, subsys_section
CHARACTER(len=*), PARAMETER :: routineN = 'mixed_init_subsys'
INTEGER :: handle
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell_ref
TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
TYPE(mixed_energy_type), POINTER :: mixed_energy
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
@ -137,11 +113,12 @@ CONTAINS
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
CALL timeset(routineN, handle)
NULLIFY (mixed_energy, local_molecules, local_particles)
NULLIFY (mixed_energy, local_molecules, local_particles, my_cell_ref)
particle_set => subsys%particles%els
atomic_kind_set => subsys%atomic_kinds%els
molecule_set => subsys%molecules%els
molecule_kind_set => subsys%molecule_kinds%els
my_cell_ref => subsys%cell_ref
! Create the mixed_energy_type
CALL allocate_mixed_energy(mixed_energy)
@ -158,12 +135,10 @@ CONTAINS
local_molecules=local_molecules, &
force_env_section=force_env_section)
CALL cp_subsys_set(subsys, cell=cell)
! set the mixed_env
CALL set_mixed_env(mixed_env=mixed_env, subsys=subsys)
CALL set_mixed_env(mixed_env=mixed_env, &
cell_ref=cell_ref, &
cell_ref=my_cell_ref, &
local_molecules=local_molecules, &
local_particles=local_particles, &
mixed_energy=mixed_energy)

57
src/nnp_environment.F
View file

@ -18,11 +18,7 @@ MODULE nnp_environment
Schran2020a,&
Schran2020b,&
cite_reference
USE cell_methods, ONLY: read_cell,&
write_cell
USE cell_types, ONLY: cell_release,&
cell_type,&
get_cell
USE cell_types, ONLY: cell_type
USE cp_log_handling, ONLY: cp_get_default_logger,&
cp_logger_get_default_unit_nr,&
cp_logger_type
@ -33,8 +29,7 @@ MODULE nnp_environment
parser_release,&
parser_reset
USE cp_subsys_methods, ONLY: cp_subsys_create
USE cp_subsys_types, ONLY: cp_subsys_set,&
cp_subsys_type
USE cp_subsys_types, ONLY: cp_subsys_type
USE distribution_1d_types, ONLY: distribution_1d_release,&
distribution_1d_type
USE distribution_methods, ONLY: distribute_molecules_1d
@ -98,11 +93,9 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'nnp_init'
INTEGER :: handle
LOGICAL :: explicit, use_ref_cell
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cell_type), POINTER :: cell, cell_ref
LOGICAL :: explicit
TYPE(cp_subsys_type), POINTER :: subsys
TYPE(section_vals_type), POINTER :: cell_section, nnp_section
TYPE(section_vals_type), POINTER :: nnp_section
CALL timeset(routineN, handle)
CALL cite_reference(Behler2007)
@ -112,12 +105,11 @@ CONTAINS
CPASSERT(ASSOCIATED(nnp_env))
NULLIFY (cell_section, nnp_section, cell, cell_ref, subsys)
NULLIFY (nnp_section, subsys)
IF (.NOT. ASSOCIATED(subsys_section)) THEN
subsys_section => section_vals_get_subs_vals(force_env_section, "SUBSYS")
END IF
cell_section => section_vals_get_subs_vals(subsys_section, "CELL")
nnp_section => section_vals_get_subs_vals(force_env_section, "NNP")
CALL section_vals_get(nnp_section, explicit=explicit)
IF (.NOT. explicit) THEN
@ -127,22 +119,13 @@ CONTAINS
CALL nnp_env_set(nnp_env=nnp_env, nnp_input=nnp_section, &
force_env_input=force_env_section)
CALL read_cell(cell=cell, cell_ref=cell_ref, use_ref_cell=use_ref_cell, cell_section=cell_section, &
para_env=para_env)
CALL get_cell(cell=cell, abc=abc)
CALL write_cell(cell=cell, subsys_section=subsys_section)
CALL cp_subsys_create(subsys, para_env, root_section, &
force_env_section=force_env_section, subsys_section=subsys_section, &
use_motion_section=use_motion_section)
CALL nnp_init_subsys(nnp_env=nnp_env, subsys=subsys, cell=cell, &
cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
CALL nnp_init_subsys(nnp_env=nnp_env, subsys=subsys, &
subsys_section=subsys_section)
CALL cell_release(cell)
CALL cell_release(cell_ref)
CALL timestop(handle)
END SUBROUTINE nnp_init
@ -151,24 +134,20 @@ CONTAINS
!> \brief Read and initialize all the information for neural network potentials
!> \param nnp_env ...
!> \param subsys ...
!> \param cell ...
!> \param cell_ref ...
!> \param use_ref_cell ...
!> \param subsys_section ...
!> \date 2020-10-10
!> \author Christoph Schran (christoph.schran@rub.de)
! **************************************************************************************************
SUBROUTINE nnp_init_subsys(nnp_env, subsys, cell, cell_ref, use_ref_cell, subsys_section)
SUBROUTINE nnp_init_subsys(nnp_env, subsys, subsys_section)
TYPE(nnp_type), INTENT(INOUT), POINTER :: nnp_env
TYPE(cp_subsys_type), INTENT(IN), POINTER :: subsys
TYPE(cell_type), INTENT(INOUT), POINTER :: cell, cell_ref
LOGICAL, INTENT(IN) :: use_ref_cell
TYPE(section_vals_type), INTENT(IN), POINTER :: subsys_section
CHARACTER(len=*), PARAMETER :: routineN = 'nnp_init_subsys'
INTEGER :: handle, natom
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(cell_type), POINTER :: my_cell, my_cell_ref
TYPE(distribution_1d_type), POINTER :: local_molecules, local_particles
TYPE(molecule_kind_type), DIMENSION(:), POINTER :: molecule_kind_set
TYPE(molecule_type), DIMENSION(:), POINTER :: molecule_set
@ -176,22 +155,29 @@ CONTAINS
CALL timeset(routineN, handle)
NULLIFY (atomic_kind_set, molecule_kind_set, particle_set, molecule_set, &
local_molecules, local_particles)
NULLIFY (atomic_kind_set, molecule_kind_set, my_cell, my_cell_ref, &
particle_set, molecule_set, local_molecules, local_particles)
particle_set => subsys%particles%els
atomic_kind_set => subsys%atomic_kinds%els
molecule_kind_set => subsys%molecule_kinds%els
molecule_set => subsys%molecules%els
my_cell => subsys%cell
my_cell_ref => subsys%cell_ref
!Print the molecule kind set
CALL write_molecule_kind_set(molecule_kind_set, subsys_section)
!Set up cell
CALL nnp_env_set(nnp_env=nnp_env, subsys=subsys, &
cell=my_cell, cell_ref=my_cell_ref, &
use_ref_cell=subsys%use_ref_cell)
!Print the atomic coordinates
CALL write_fist_particle_coordinates(particle_set, subsys_section)
CALL write_particle_distances(particle_set, cell=cell, &
CALL write_particle_distances(particle_set, cell=my_cell, &
subsys_section=subsys_section)
CALL write_structure_data(particle_set, cell=cell, &
CALL write_structure_data(particle_set, cell=my_cell, &
input_section=subsys_section)
!Distribute molecules and atoms using the new data structures
@ -220,10 +206,7 @@ CONTAINS
ALLOCATE (nnp_env%sort(natom))
ALLOCATE (nnp_env%sort_inv(natom))
CALL cp_subsys_set(subsys, cell=cell)
CALL nnp_env_set(nnp_env=nnp_env, subsys=subsys, &
cell_ref=cell_ref, use_ref_cell=use_ref_cell, &
CALL nnp_env_set(nnp_env=nnp_env, &
local_molecules=local_molecules, &
local_particles=local_particles)

10
src/qs_subsys_methods.F
View file

@ -107,6 +107,16 @@ CONTAINS
! create cp_subsys%cell
!TODO: moved to cp_subsys_create(), needs further disentanglement of cell_ref.
![NB] subroutines qs_init() and qs_init_subsys() may pass cell and cell_ref to
! qs_subsys_create() here, and two places where qs_init() is called are tricky:
! 1. For QM/MM calculation, qmmm_env_create() passes "qm_cell_small" from
! setup_qmmm_vars_qm() to qs_init() and subsequently to my_cell here;
! 2. For BSSE calculation, eval_bsse_energy_low() calls create_small_subsys()
! to create cp_subsys_type "subsys_loc" and then calls qs_init() with
! subsys_loc, but create_small_subsys() does not set subsys_loc%cell.
! If not for these, it would have been easy to set my_cell => my_cp_subsys%cell
! and my_cell_ref => my_cp_subsys%cell_ref so as to avoid re-read the cell_section
! when cell and cell_ref are not passed as input here.
use_ref_cell = .FALSE.
IF (PRESENT(cell)) THEN
my_cell => cell

32
src/subsys/cp_subsys_types.F
View file

@ -108,7 +108,8 @@ MODULE cp_subsys_types
TYPE(atprop_type), POINTER :: atprop => Null()
TYPE(virial_type), POINTER :: virial => Null()
TYPE(cp_result_type), POINTER :: results => Null()
TYPE(cell_type), POINTER :: cell => Null()
TYPE(cell_type), POINTER :: cell => Null(), cell_ref => Null()
LOGICAL :: use_ref_cell = .FALSE.
END TYPE cp_subsys_type
! **************************************************************************************************
@ -172,6 +173,7 @@ CONTAINS
IF (ASSOCIATED(subsys%virial)) DEALLOCATE (subsys%virial)
CALL cp_result_release(subsys%results)
CALL cell_release(subsys%cell)
CALL cell_release(subsys%cell_ref)
DEALLOCATE (subsys)
END IF
NULLIFY (subsys)
@ -195,13 +197,16 @@ CONTAINS
!> \param multipoles ...
!> \param results ...
!> \param cell ...
!> \param cell_ref ...
!> \param use_ref_cell ...
!> \par History
!> 08.2003 created [fawzi]
!> \author Fawzi Mohamed
! **************************************************************************************************
SUBROUTINE 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)
colvar_p, shell_particles, core_particles, gci, multipoles, &
results, cell, cell_ref, use_ref_cell)
TYPE(cp_subsys_type), INTENT(INOUT) :: subsys
TYPE(atomic_kind_list_type), OPTIONAL, POINTER :: atomic_kinds
TYPE(particle_list_type), OPTIONAL, POINTER :: particles
@ -216,7 +221,8 @@ CONTAINS
TYPE(global_constraint_type), OPTIONAL, POINTER :: gci
TYPE(multipole_type), OPTIONAL, POINTER :: multipoles
TYPE(cp_result_type), OPTIONAL, POINTER :: results
TYPE(cell_type), OPTIONAL, POINTER :: cell
TYPE(cell_type), OPTIONAL, POINTER :: cell, cell_ref
LOGICAL, OPTIONAL :: use_ref_cell
CPASSERT(subsys%ref_count > 0)
IF (PRESENT(multipoles)) THEN
@ -299,6 +305,17 @@ CONTAINS
subsys%cell => cell
END IF
END IF
IF (PRESENT(cell_ref)) THEN
IF (ASSOCIATED(cell_ref)) THEN
CALL cell_retain(cell_ref)
CALL cell_release(subsys%cell_ref)
subsys%cell_ref => cell_ref
subsys%use_ref_cell = .TRUE.
END IF
END IF
IF (PRESENT(use_ref_cell)) THEN
subsys%use_ref_cell = use_ref_cell
END IF
END SUBROUTINE cp_subsys_set
! **************************************************************************************************
@ -330,6 +347,8 @@ CONTAINS
!> \param virial ...
!> \param results ...
!> \param cell ...
!> \param cell_ref ...
!> \param use_ref_cell ...
!> \par History
!> 08.2003 created [fawzi]
!> 22.11.2010 (MK)
@ -341,7 +360,7 @@ CONTAINS
molecule_kind_set, local_molecules, para_env, colvar_p, &
shell_particles, core_particles, gci, multipoles, &
natom, nparticle, ncore, nshell, nkind, atprop, virial, &
results, cell)
results, cell, cell_ref, use_ref_cell)
TYPE(cp_subsys_type), INTENT(IN) :: subsys
INTEGER, INTENT(out), OPTIONAL :: ref_count
TYPE(atomic_kind_list_type), OPTIONAL, POINTER :: atomic_kinds
@ -368,7 +387,8 @@ CONTAINS
TYPE(atprop_type), OPTIONAL, POINTER :: atprop
TYPE(virial_type), OPTIONAL, POINTER :: virial
TYPE(cp_result_type), OPTIONAL, POINTER :: results
TYPE(cell_type), OPTIONAL, POINTER :: cell
TYPE(cell_type), OPTIONAL, POINTER :: cell, cell_ref
LOGICAL, OPTIONAL :: use_ref_cell
INTEGER :: n_atom, n_core, n_shell
@ -399,6 +419,8 @@ CONTAINS
IF (PRESENT(atprop)) atprop => subsys%atprop
IF (PRESENT(results)) results => subsys%results
IF (PRESENT(cell)) cell => subsys%cell
IF (PRESENT(cell_ref)) cell_ref => subsys%cell_ref
IF (PRESENT(use_ref_cell)) use_ref_cell = subsys%use_ref_cell
IF (PRESENT(nkind)) nkind = SIZE(subsys%atomic_kinds%els)
IF (PRESENT(natom) .OR. PRESENT(nparticle) .OR. PRESENT(nshell)) THEN

29
src/topology.F
View file

@ -16,7 +16,9 @@ MODULE topology
USE cell_methods, ONLY: cell_create,&
read_cell,&
write_cell
USE cell_types, ONLY: cell_retain,&
USE cell_types, ONLY: cell_clone,&
cell_release,&
cell_retain,&
cell_type
USE colvar_types, ONLY: colvar_p_type,&
colvar_setup,&
@ -26,6 +28,8 @@ MODULE topology
cp_logger_type
USE cp_output_handling, ONLY: cp_print_key_finished_output,&
cp_print_key_unit_nr
USE cp_subsys_types, ONLY: cp_subsys_set,&
cp_subsys_type
USE exclusion_types, ONLY: exclusion_type
USE input_constants, ONLY: &
do_conn_amb7, do_conn_g87, do_conn_g96, do_conn_generate, do_conn_mol_set, do_conn_off, &
@ -120,10 +124,12 @@ CONTAINS
!> \param use_motion_section ...
!> \param exclusions ...
!> \param elkind ...
!> \param subsys ...
! **************************************************************************************************
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, elkind)
force_env_section, subsys_section, use_motion_section, &
exclusions, elkind, subsys)
TYPE(atomic_kind_type), DIMENSION(:), POINTER :: atomic_kind_set
TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
@ -140,12 +146,14 @@ CONTAINS
TYPE(exclusion_type), DIMENSION(:), OPTIONAL, &
POINTER :: exclusions
LOGICAL, INTENT(IN), OPTIONAL :: elkind
TYPE(cp_subsys_type), OPTIONAL, POINTER :: subsys
CHARACTER(LEN=*), PARAMETER :: routineN = 'topology_control'
INTEGER :: handle, iw, iw2
LOGICAL :: binary_coord_read, el_as_kind, explicit, &
my_qmmm
TYPE(cell_type), POINTER :: my_cell, my_cell_ref
TYPE(cp_logger_type), POINTER :: logger
TYPE(section_vals_type), POINTER :: cell_section, constraint_section, &
topology_section
@ -181,10 +189,21 @@ CONTAINS
CALL init_topology(topology)
! 2. Get the cell info
CALL read_cell(topology%cell, topology%cell_ref, cell_section=cell_section, &
para_env=para_env)
CALL write_cell(topology%cell, subsys_section, tag="CELL_TOP")
NULLIFY (my_cell, my_cell_ref)
CALL read_cell(my_cell, my_cell_ref, cell_section=cell_section, &
topology_section=topology_section, para_env=para_env)
IF (.NOT. ASSOCIATED(topology%cell)) CALL cell_create(topology%cell)
IF (.NOT. ASSOCIATED(topology%cell_ref)) CALL cell_create(topology%cell_ref)
CALL cell_clone(my_cell, topology%cell)
CALL cell_clone(my_cell_ref, topology%cell_ref)
CALL setup_cell_muc(topology%cell_muc, topology%cell, subsys_section)
IF (PRESENT(subsys)) THEN ! subsys is passed from cp_subsys_create
CALL cp_subsys_set(subsys, cell=my_cell, cell_ref=my_cell_ref)
END IF
CALL write_cell(my_cell, subsys_section, tag="CELL")
CALL write_cell(my_cell_ref, subsys_section, tag="CELL_REF")
CALL cell_release(my_cell)
CALL cell_release(my_cell_ref)
! 3. Read in the topology section in the input file if any
CALL read_topology_section(topology, topology_section)