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topology_input.F
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topology_input.F
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!--------------------------------------------------------------------------------------------------!
! CP2K: A general program to perform molecular dynamics simulations !
! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
! !
! SPDX-License-Identifier: GPL-2.0-or-later !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \brief Reads the input sections "topology"
!> \par History
!> JGH (26-01-2002) Added read_topology_section
!> \author JGH
! **************************************************************************************************
MODULE topology_input
USE colvar_types, ONLY: colvar_clone,&
colvar_p_type
USE cp_log_handling, ONLY: cp_logger_get_default_io_unit,&
cp_to_string
USE input_constants, ONLY: do_conn_generate,&
do_conn_mol_set,&
do_conn_off,&
do_conn_user,&
do_constr_none,&
do_coord_off
USE input_section_types, ONLY: section_vals_get,&
section_vals_get_subs_vals,&
section_vals_type,&
section_vals_val_get,&
section_vals_val_unset
USE kinds, ONLY: default_string_length,&
dp
USE memory_utilities, ONLY: reallocate
USE topology_types, ONLY: constraint_info_type,&
topology_parameters_type
#include "./base/base_uses.f90"
IMPLICIT NONE
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_input'
PRIVATE
PUBLIC :: read_topology_section, read_constraints_section
CONTAINS
! **************************************************************************************************
!> \brief reads the input section topology
!> \param topology ...
!> \param topology_section ...
!> \par History
!> none
!> \author JGH (26-01-2002)
! **************************************************************************************************
SUBROUTINE read_topology_section(topology, topology_section)
TYPE(topology_parameters_type) :: topology
TYPE(section_vals_type), POINTER :: topology_section
CHARACTER(len=*), PARAMETER :: routineN = 'read_topology_section'
INTEGER :: handle, ival
CALL timeset(routineN, handle)
CALL section_vals_val_get(topology_section, "CHARGE_OCCUP", l_val=topology%charge_occup)
CALL section_vals_val_get(topology_section, "CHARGE_BETA", l_val=topology%charge_beta)
CALL section_vals_val_get(topology_section, "CHARGE_EXTENDED", l_val=topology%charge_extended)
ival = COUNT((/topology%charge_occup, topology%charge_beta, topology%charge_extended/))
IF (ival > 1) &
CPABORT("Only one between <CHARGE_OCCUP,CHARGE_BETA,CHARGE_EXTENDED> can be defined! ")
CALL section_vals_val_get(topology_section, "PARA_RES", l_val=topology%para_res)
CALL section_vals_val_get(topology_section, "GENERATE%REORDER", l_val=topology%reorder_atom)
CALL section_vals_val_get(topology_section, "GENERATE%CREATE_MOLECULES", l_val=topology%create_molecules)
CALL section_vals_val_get(topology_section, "MOL_CHECK", l_val=topology%molecules_check)
CALL section_vals_val_get(topology_section, "USE_G96_VELOCITY", l_val=topology%use_g96_velocity)
CALL section_vals_val_get(topology_section, "COORD_FILE_FORMAT", i_val=topology%coord_type)
SELECT CASE (topology%coord_type)
CASE (do_coord_off)
! Do Nothing
CASE DEFAULT
topology%coordinate = .TRUE.
CALL section_vals_val_get(topology_section, "COORD_FILE_NAME", c_val=topology%coord_file_name)
END SELECT
CALL section_vals_val_get(topology_section, "CONN_FILE_FORMAT", i_val=topology%conn_type)
SELECT CASE (topology%conn_type)
CASE (do_conn_off, do_conn_generate, do_conn_mol_set, do_conn_user)
! Do Nothing
CASE DEFAULT
CALL section_vals_val_get(topology_section, "CONN_FILE_NAME", c_val=topology%conn_file_name)
END SELECT
CALL section_vals_val_get(topology_section, "EXCLUDE_VDW", i_val=topology%exclude_vdw)
CALL section_vals_val_get(topology_section, "EXCLUDE_EI", i_val=topology%exclude_ei)
CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM", i_val=topology%bondparm_type)
CALL section_vals_val_get(topology_section, "GENERATE%BONDPARM_FACTOR", r_val=topology%bondparm_factor)
CALL timestop(handle)
END SUBROUTINE read_topology_section
! **************************************************************************************************
!> \brief Read all the distance parameters. Put them in the
!> constraint_distance array.
!> \param topology ...
!> \param colvar_p ...
!> \param constraint_section ...
!> \par History
!> JGH (26-01-2002) Distance parameters are now stored in tables. The position
!> within the table is used as handle for the topology
!> teo Read the CONSTRAINT section within the new input style
!> \author teo
! **************************************************************************************************
SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section)
TYPE(topology_parameters_type), INTENT(INOUT) :: topology
TYPE(colvar_p_type), DIMENSION(:), POINTER :: colvar_p
TYPE(section_vals_type), POINTER :: constraint_section
CHARACTER(LEN=default_string_length), &
DIMENSION(:), POINTER :: tmpstringlist
INTEGER :: icolvar, ig, isize, isize_old, itype, &
jg, msize, msize_old, n_rep, ncons, &
nrep
INTEGER, DIMENSION(:), POINTER :: ilist, tmplist
LOGICAL :: explicit
REAL(KIND=dp), DIMENSION(:), POINTER :: rlist
TYPE(constraint_info_type), POINTER :: cons_info
TYPE(section_vals_type), POINTER :: collective_section, fix_atom_section, &
g3x3_section, g4x6_section, &
hbonds_section, vsite_section
cons_info => topology%cons_info
IF (ASSOCIATED(constraint_section)) THEN
hbonds_section => section_vals_get_subs_vals(constraint_section, "HBONDS")
g3x3_section => section_vals_get_subs_vals(constraint_section, "G3X3")
g4x6_section => section_vals_get_subs_vals(constraint_section, "G4X6")
vsite_section => section_vals_get_subs_vals(constraint_section, "VIRTUAL_SITE")
fix_atom_section => section_vals_get_subs_vals(constraint_section, "FIXED_ATOMS")
collective_section => section_vals_get_subs_vals(constraint_section, "COLLECTIVE")
! HBONDS
CALL section_vals_get(hbonds_section, explicit=topology%const_hydr)
CALL check_restraint(hbonds_section, &
is_restraint=cons_info%hbonds_restraint, &
k0=cons_info%hbonds_k0, &
label="HBONDS")
! G3X3
CALL section_vals_get(g3x3_section, explicit=explicit, n_repetition=ncons)
IF (explicit) THEN
topology%const_33 = .TRUE.
cons_info%nconst_g33 = ncons
!
ALLOCATE (cons_info%const_g33_mol(ncons))
ALLOCATE (cons_info%const_g33_molname(ncons))
ALLOCATE (cons_info%const_g33_a(ncons))
ALLOCATE (cons_info%const_g33_b(ncons))
ALLOCATE (cons_info%const_g33_c(ncons))
ALLOCATE (cons_info%const_g33_dab(ncons))
ALLOCATE (cons_info%const_g33_dac(ncons))
ALLOCATE (cons_info%const_g33_dbc(ncons))
ALLOCATE (cons_info%g33_intermolecular(ncons))
ALLOCATE (cons_info%g33_restraint(ncons))
ALLOCATE (cons_info%g33_k0(ncons))
ALLOCATE (cons_info%g33_exclude_qm(ncons))
ALLOCATE (cons_info%g33_exclude_mm(ncons))
DO ig = 1, ncons
CALL check_restraint(g3x3_section, &
is_restraint=cons_info%g33_restraint(ig), &
k0=cons_info%g33_k0(ig), &
i_rep_section=ig, &
label="G3X3")
cons_info%const_g33_mol(ig) = 0
cons_info%const_g33_molname(ig) = "UNDEF"
! Exclude QM or MM
CALL section_vals_val_get(g3x3_section, "EXCLUDE_QM", i_rep_section=ig, &
l_val=cons_info%g33_exclude_qm(ig))
CALL section_vals_val_get(g3x3_section, "EXCLUDE_MM", i_rep_section=ig, &
l_val=cons_info%g33_exclude_mm(ig))
! Intramolecular restraint
CALL section_vals_val_get(g3x3_section, "INTERMOLECULAR", i_rep_section=ig, &
l_val=cons_info%g33_intermolecular(ig))
! If it is intramolecular let's unset (in case user did it)
! the molecule and molname field
IF (cons_info%g33_intermolecular(ig)) THEN
CALL section_vals_val_unset(g3x3_section, "MOLECULE", i_rep_section=ig)
CALL section_vals_val_unset(g3x3_section, "MOLNAME", i_rep_section=ig)
END IF
! Let's tag to which molecule we want to apply constraints
CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(g3x3_section, "MOLECULE", i_rep_section=ig, &
i_val=cons_info%const_g33_mol(ig))
END IF
CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(g3x3_section, "MOLNAME", i_rep_section=ig, &
c_val=cons_info%const_g33_molname(ig))
END IF
IF ((cons_info%const_g33_mol(ig) /= 0) .AND. (cons_info%const_g33_molname(ig) /= "UNDEF")) THEN
CPABORT("")
END IF
IF ((cons_info%const_g33_mol(ig) == 0) .AND. (cons_info%const_g33_molname(ig) == "UNDEF") .AND. &
(.NOT. cons_info%g33_intermolecular(ig))) THEN
CPABORT("")
END IF
CALL section_vals_val_get(g3x3_section, "ATOMS", i_rep_section=ig, &
i_vals=ilist)
CALL section_vals_val_get(g3x3_section, "DISTANCES", i_rep_section=ig, &
r_vals=rlist)
cons_info%const_g33_a(ig) = ilist(1)
cons_info%const_g33_b(ig) = ilist(2)
cons_info%const_g33_c(ig) = ilist(3)
cons_info%const_g33_dab(ig) = rlist(1)
cons_info%const_g33_dac(ig) = rlist(2)
cons_info%const_g33_dbc(ig) = rlist(3)
END DO
END IF
! G4X6
CALL section_vals_get(g4x6_section, explicit=explicit, n_repetition=ncons)
IF (explicit) THEN
topology%const_46 = .TRUE.
cons_info%nconst_g46 = ncons
!
ALLOCATE (cons_info%const_g46_mol(ncons))
ALLOCATE (cons_info%const_g46_molname(ncons))
ALLOCATE (cons_info%const_g46_a(ncons))
ALLOCATE (cons_info%const_g46_b(ncons))
ALLOCATE (cons_info%const_g46_c(ncons))
ALLOCATE (cons_info%const_g46_d(ncons))
ALLOCATE (cons_info%const_g46_dab(ncons))
ALLOCATE (cons_info%const_g46_dac(ncons))
ALLOCATE (cons_info%const_g46_dbc(ncons))
ALLOCATE (cons_info%const_g46_dad(ncons))
ALLOCATE (cons_info%const_g46_dbd(ncons))
ALLOCATE (cons_info%const_g46_dcd(ncons))
ALLOCATE (cons_info%g46_intermolecular(ncons))
ALLOCATE (cons_info%g46_restraint(ncons))
ALLOCATE (cons_info%g46_k0(ncons))
ALLOCATE (cons_info%g46_exclude_qm(ncons))
ALLOCATE (cons_info%g46_exclude_mm(ncons))
DO ig = 1, ncons
CALL check_restraint(g4x6_section, &
is_restraint=cons_info%g46_restraint(ig), &
k0=cons_info%g46_k0(ig), &
i_rep_section=ig, &
label="G4X6")
cons_info%const_g46_mol(ig) = 0
cons_info%const_g46_molname(ig) = "UNDEF"
! Exclude QM or MM
CALL section_vals_val_get(g4x6_section, "EXCLUDE_QM", i_rep_section=ig, &
l_val=cons_info%g46_exclude_qm(ig))
CALL section_vals_val_get(g4x6_section, "EXCLUDE_MM", i_rep_section=ig, &
l_val=cons_info%g46_exclude_mm(ig))
! Intramolecular restraint
CALL section_vals_val_get(g4x6_section, "INTERMOLECULAR", i_rep_section=ig, &
l_val=cons_info%g46_intermolecular(ig))
! If it is intramolecular let's unset (in case user did it)
! the molecule and molname field
IF (cons_info%g46_intermolecular(ig)) THEN
CALL section_vals_val_unset(g4x6_section, "MOLECULE", i_rep_section=ig)
CALL section_vals_val_unset(g4x6_section, "MOLNAME", i_rep_section=ig)
END IF
! Let's tag to which molecule we want to apply constraints
CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(g4x6_section, "MOLECULE", i_rep_section=ig, &
i_val=cons_info%const_g46_mol(ig))
END IF
CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(g4x6_section, "MOLNAME", i_rep_section=ig, &
c_val=cons_info%const_g46_molname(ig))
END IF
IF ((cons_info%const_g46_mol(ig) /= 0) .AND. (cons_info%const_g46_molname(ig) /= "UNDEF")) THEN
CPABORT("")
END IF
IF ((cons_info%const_g46_mol(ig) == 0) .AND. (cons_info%const_g46_molname(ig) == "UNDEF") .AND. &
(.NOT. cons_info%g46_intermolecular(ig))) THEN
CPABORT("")
END IF
CALL section_vals_val_get(g4x6_section, "ATOMS", i_rep_section=ig, &
i_vals=ilist)
CALL section_vals_val_get(g4x6_section, "DISTANCES", i_rep_section=ig, &
r_vals=rlist)
cons_info%const_g46_a(ig) = ilist(1)
cons_info%const_g46_b(ig) = ilist(2)
cons_info%const_g46_c(ig) = ilist(3)
cons_info%const_g46_d(ig) = ilist(4)
cons_info%const_g46_dab(ig) = rlist(1)
cons_info%const_g46_dac(ig) = rlist(2)
cons_info%const_g46_dad(ig) = rlist(3)
cons_info%const_g46_dbc(ig) = rlist(4)
cons_info%const_g46_dbd(ig) = rlist(5)
cons_info%const_g46_dcd(ig) = rlist(6)
END DO
END IF
! virtual
CALL section_vals_get(vsite_section, explicit=explicit, n_repetition=ncons)
IF (explicit) THEN
topology%const_vsite = .TRUE.
cons_info%nconst_vsite = ncons
!
ALLOCATE (cons_info%const_vsite_mol(ncons))
ALLOCATE (cons_info%const_vsite_molname(ncons))
ALLOCATE (cons_info%const_vsite_a(ncons))
ALLOCATE (cons_info%const_vsite_b(ncons))
ALLOCATE (cons_info%const_vsite_c(ncons))
ALLOCATE (cons_info%const_vsite_d(ncons))
ALLOCATE (cons_info%const_vsite_wbc(ncons))
ALLOCATE (cons_info%const_vsite_wdc(ncons))
ALLOCATE (cons_info%vsite_intermolecular(ncons))
ALLOCATE (cons_info%vsite_restraint(ncons))
ALLOCATE (cons_info%vsite_k0(ncons))
ALLOCATE (cons_info%vsite_exclude_qm(ncons))
ALLOCATE (cons_info%vsite_exclude_mm(ncons))
DO ig = 1, ncons
CALL check_restraint(vsite_section, &
is_restraint=cons_info%vsite_restraint(ig), &
k0=cons_info%vsite_k0(ig), &
i_rep_section=ig, &
label="Virtual_SITE")
cons_info%const_vsite_mol(ig) = 0
cons_info%const_vsite_molname(ig) = "UNDEF"
! Exclude QM or MM
CALL section_vals_val_get(vsite_section, "EXCLUDE_QM", i_rep_section=ig, &
l_val=cons_info%vsite_exclude_qm(ig))
CALL section_vals_val_get(vsite_section, "EXCLUDE_MM", i_rep_section=ig, &
l_val=cons_info%vsite_exclude_mm(ig))
! Intramolecular restraint
CALL section_vals_val_get(vsite_section, "INTERMOLECULAR", i_rep_section=ig, &
l_val=cons_info%vsite_intermolecular(ig))
! If it is intramolecular let's unset (in case user did it)
! the molecule and molname field
IF (cons_info%vsite_intermolecular(ig)) THEN
CALL section_vals_val_unset(vsite_section, "MOLECULE", i_rep_section=ig)
CALL section_vals_val_unset(vsite_section, "MOLNAME", i_rep_section=ig)
END IF
! Let's tag to which molecule we want to apply constraints
CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(vsite_section, "MOLECULE", i_rep_section=ig, &
i_val=cons_info%const_vsite_mol(ig))
END IF
CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(vsite_section, "MOLNAME", i_rep_section=ig, &
c_val=cons_info%const_vsite_molname(ig))
END IF
IF ((cons_info%const_vsite_mol(ig) /= 0) .AND. (cons_info%const_vsite_molname(ig) /= "UNDEF")) THEN
CPABORT("")
END IF
IF ((cons_info%const_vsite_mol(ig) == 0) .AND. (cons_info%const_vsite_molname(ig) == "UNDEF") .AND. &
(.NOT. cons_info%vsite_intermolecular(ig))) THEN
CPABORT("")
END IF
CALL section_vals_val_get(vsite_section, "ATOMS", i_rep_section=ig, &
i_vals=ilist)
CALL section_vals_val_get(vsite_section, "PARAMETERS", i_rep_section=ig, &
r_vals=rlist)
cons_info%const_vsite_a(ig) = ilist(1)
cons_info%const_vsite_b(ig) = ilist(2)
cons_info%const_vsite_c(ig) = ilist(3)
cons_info%const_vsite_d(ig) = ilist(4)
cons_info%const_vsite_wbc(ig) = rlist(1)
cons_info%const_vsite_wdc(ig) = rlist(2)
END DO
END IF
! FIXED ATOMS
CALL section_vals_get(fix_atom_section, explicit=explicit, n_repetition=ncons)
IF (explicit) THEN
NULLIFY (tmplist, tmpstringlist)
isize = 0
msize = 0
ALLOCATE (cons_info%fixed_atoms(isize))
ALLOCATE (cons_info%fixed_type(isize))
ALLOCATE (cons_info%fixed_restraint(isize))
ALLOCATE (cons_info%fixed_k0(isize))
ALLOCATE (cons_info%fixed_molnames(msize))
ALLOCATE (cons_info%fixed_mol_type(isize))
ALLOCATE (cons_info%fixed_mol_restraint(msize))
ALLOCATE (cons_info%fixed_mol_k0(msize))
ALLOCATE (cons_info%fixed_exclude_qm(ncons))
ALLOCATE (cons_info%fixed_exclude_mm(ncons))
DO ig = 1, ncons
isize_old = isize
msize_old = msize
CALL section_vals_val_get(fix_atom_section, "COMPONENTS_TO_FIX", i_rep_section=ig, &
i_val=itype)
CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
n_rep_val=n_rep)
DO jg = 1, n_rep
CALL section_vals_val_get(fix_atom_section, "LIST", i_rep_section=ig, &
i_rep_val=jg, i_vals=tmplist)
CALL reallocate(cons_info%fixed_atoms, 1, isize + SIZE(tmplist))
cons_info%fixed_atoms(isize + 1:isize + SIZE(tmplist)) = tmplist
CALL reallocate(cons_info%fixed_restraint, 1, isize + SIZE(tmplist))
CALL reallocate(cons_info%fixed_k0, 1, isize + SIZE(tmplist))
CALL reallocate(cons_info%fixed_type, 1, isize + SIZE(tmplist))
cons_info%fixed_type(isize + 1:isize + SIZE(tmplist)) = itype
isize = SIZE(cons_info%fixed_atoms)
END DO
!Check for restraints
IF ((isize - isize_old) > 0) THEN
CALL check_restraint(fix_atom_section, &
is_restraint=cons_info%fixed_restraint(isize_old + 1), &
k0=cons_info%fixed_k0(isize_old + 1), &
i_rep_section=ig, &
label="FIXED ATOM")
cons_info%fixed_restraint(isize_old + 1:isize) = cons_info%fixed_restraint(isize_old + 1)
cons_info%fixed_k0(isize_old + 1:isize) = cons_info%fixed_k0(isize_old + 1)
END IF
CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
n_rep_val=n_rep)
IF (n_rep /= 0) THEN
DO jg = 1, n_rep
CALL section_vals_val_get(fix_atom_section, "MOLNAME", i_rep_section=ig, &
i_rep_val=jg, c_vals=tmpstringlist)
CALL reallocate(cons_info%fixed_molnames, 1, msize + SIZE(tmpstringlist, 1))
CALL reallocate(cons_info%fixed_mol_type, 1, msize + SIZE(tmpstringlist, 1))
CALL reallocate(cons_info%fixed_mol_restraint, 1, msize + SIZE(tmpstringlist, 1))
CALL reallocate(cons_info%fixed_mol_k0, 1, msize + SIZE(tmpstringlist, 1))
cons_info%fixed_molnames(msize + 1:msize + SIZE(tmpstringlist, 1)) = tmpstringlist
cons_info%fixed_mol_type(msize + 1:msize + SIZE(tmpstringlist, 1)) = itype
msize = SIZE(cons_info%fixed_molnames)
END DO
! Exclude QM or MM work only if defined MOLNAME
CALL reallocate(cons_info%fixed_exclude_qm, 1, msize)
CALL reallocate(cons_info%fixed_exclude_mm, 1, msize)
CALL section_vals_val_get(fix_atom_section, "EXCLUDE_QM", i_rep_section=ig, &
l_val=cons_info%fixed_exclude_qm(msize_old + 1))
CALL section_vals_val_get(fix_atom_section, "EXCLUDE_MM", i_rep_section=ig, &
l_val=cons_info%fixed_exclude_mm(msize_old + 1))
cons_info%fixed_exclude_qm(msize_old + 1:msize) = cons_info%fixed_exclude_qm(msize_old + 1)
cons_info%fixed_exclude_mm(msize_old + 1:msize) = cons_info%fixed_exclude_mm(msize_old + 1)
END IF
!Check for restraints
IF (n_rep /= 0) THEN
CALL check_restraint(fix_atom_section, &
is_restraint=cons_info%fixed_mol_restraint(msize_old + 1), &
k0=cons_info%fixed_mol_k0(msize_old + 1), &
i_rep_section=ig, &
label="FIXED ATOM")
cons_info%fixed_mol_restraint(msize_old + 1:msize) = cons_info%fixed_mol_restraint(msize_old + 1)
cons_info%fixed_mol_k0(msize_old + 1:msize) = cons_info%fixed_mol_k0(msize_old + 1)
END IF
CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_rep_section=ig, &
n_rep_val=nrep, explicit=explicit)
IF (nrep == 1 .AND. explicit) THEN
CPASSERT(cons_info%freeze_mm == do_constr_none)
CALL section_vals_val_get(fix_atom_section, "MM_SUBSYS", i_val=cons_info%freeze_mm, &
i_rep_section=ig)
cons_info%freeze_mm_type = itype
END IF
CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_rep_section=ig, &
n_rep_val=nrep, explicit=explicit)
IF (nrep == 1 .AND. explicit) THEN
CPASSERT(cons_info%freeze_qm == do_constr_none)
CALL section_vals_val_get(fix_atom_section, "QM_SUBSYS", i_val=cons_info%freeze_qm, &
i_rep_section=ig)
cons_info%freeze_qm_type = itype
END IF
IF (cons_info%freeze_mm /= do_constr_none) THEN
CALL check_restraint(fix_atom_section, &
is_restraint=cons_info%fixed_mm_restraint, &
k0=cons_info%fixed_mm_k0, &
i_rep_section=ig, &
label="FIXED ATOM")
END IF
IF (cons_info%freeze_qm /= do_constr_none) THEN
CALL check_restraint(fix_atom_section, &
is_restraint=cons_info%fixed_qm_restraint, &
k0=cons_info%fixed_qm_k0, &
i_rep_section=ig, &
label="FIXED ATOM")
END IF
END DO
IF ((isize /= 0) .OR. (msize /= 0) .OR. &
(cons_info%freeze_mm /= do_constr_none) .OR. &
(cons_info%freeze_qm /= do_constr_none)) THEN
topology%const_atom = .TRUE.
END IF
END IF
! Collective Constraints
CALL section_vals_get(collective_section, explicit=explicit, n_repetition=ncons)
IF (explicit) THEN
topology%const_colv = .TRUE.
DO ig = 1, ncons
CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, i_val=icolvar)
CPASSERT(icolvar <= SIZE(colvar_p))
END DO
cons_info%nconst_colv = ncons
ALLOCATE (cons_info%const_colv_mol(ncons))
ALLOCATE (cons_info%const_colv_molname(ncons))
ALLOCATE (cons_info%const_colv_target(ncons))
ALLOCATE (cons_info%const_colv_target_growth(ncons))
ALLOCATE (cons_info%colvar_set(ncons))
ALLOCATE (cons_info%colv_intermolecular(ncons))
ALLOCATE (cons_info%colv_restraint(ncons))
ALLOCATE (cons_info%colv_k0(ncons))
ALLOCATE (cons_info%colv_exclude_qm(ncons))
ALLOCATE (cons_info%colv_exclude_mm(ncons))
DO ig = 1, ncons
CALL check_restraint(collective_section, &
is_restraint=cons_info%colv_restraint(ig), &
k0=cons_info%colv_k0(ig), &
i_rep_section=ig, &
label="COLLECTIVE")
cons_info%const_colv_mol(ig) = 0
cons_info%const_colv_molname(ig) = "UNDEF"
! Exclude QM or MM
CALL section_vals_val_get(collective_section, "EXCLUDE_QM", i_rep_section=ig, &
l_val=cons_info%colv_exclude_qm(ig))
CALL section_vals_val_get(collective_section, "EXCLUDE_MM", i_rep_section=ig, &
l_val=cons_info%colv_exclude_mm(ig))
! Intramolecular restraint
CALL section_vals_val_get(collective_section, "INTERMOLECULAR", i_rep_section=ig, &
l_val=cons_info%colv_intermolecular(ig))
! If it is intramolecular let's unset (in case user did it)
! the molecule and molname field
IF (cons_info%colv_intermolecular(ig)) THEN
CALL section_vals_val_unset(collective_section, "MOLECULE", i_rep_section=ig)
CALL section_vals_val_unset(collective_section, "MOLNAME", i_rep_section=ig)
END IF
! Let's tag to which molecule we want to apply constraints
CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(collective_section, "MOLECULE", i_rep_section=ig, &
i_val=cons_info%const_colv_mol(ig))
END IF
CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
n_rep_val=nrep)
IF (nrep /= 0) THEN
CALL section_vals_val_get(collective_section, "MOLNAME", i_rep_section=ig, &
c_val=cons_info%const_colv_molname(ig))
END IF
IF (((cons_info%const_colv_mol(ig) /= 0) .AND. (cons_info%const_colv_molname(ig) /= "UNDEF"))) THEN
CPABORT("Both MOLNAME and MOLECULE specified for CONSTRAINT section. ")
END IF
IF ((cons_info%const_colv_mol(ig) == 0) .AND. (cons_info%const_colv_molname(ig) == "UNDEF") .AND. &
(.NOT. cons_info%colv_intermolecular(ig))) THEN
CALL cp_abort(__LOCATION__, &
"Constraint section error: you have to specify at least one of the "// &
"following keywords: MOLECULE, MOLNAME or INTERMOLECULAR! ")
END IF
NULLIFY (cons_info%colvar_set(ig)%colvar)
CALL section_vals_val_get(collective_section, "COLVAR", i_rep_section=ig, &
i_val=icolvar)
CALL colvar_clone(cons_info%colvar_set(ig)%colvar, &
colvar_p(icolvar)%colvar)
CALL section_vals_val_get(collective_section, "TARGET", &
n_rep_val=n_rep, i_rep_section=ig)
IF (n_rep /= 0) THEN
CALL section_vals_val_get(collective_section, "TARGET", &
r_val=cons_info%const_colv_target(ig), i_rep_section=ig)
ELSE
cons_info%const_colv_target(ig) = -HUGE(0.0_dp)
END IF
CALL section_vals_val_get(collective_section, "TARGET_GROWTH", &
r_val=cons_info%const_colv_target_growth(ig), i_rep_section=ig)
END DO
END IF
END IF
END SUBROUTINE read_constraints_section
! **************************************************************************************************
!> \brief Reads input and decides if apply restraints instead of constraints
!> \param cons_section ...
!> \param is_restraint ...
!> \param k0 ...
!> \param i_rep_section ...
!> \param label ...
!> \author teo
! **************************************************************************************************
SUBROUTINE check_restraint(cons_section, is_restraint, k0, i_rep_section, label)
TYPE(section_vals_type), POINTER :: cons_section
LOGICAL, INTENT(OUT) :: is_restraint
REAL(KIND=dp), INTENT(OUT) :: k0
INTEGER, INTENT(IN), OPTIONAL :: i_rep_section
CHARACTER(LEN=*), INTENT(IN) :: label
CHARACTER(LEN=default_string_length) :: nlabel
INTEGER :: output_unit
LOGICAL :: explicit
TYPE(section_vals_type), POINTER :: restraint_section
is_restraint = .FALSE.
output_unit = cp_logger_get_default_io_unit()
CALL section_vals_get(cons_section, explicit=explicit)
IF (explicit) THEN
restraint_section => section_vals_get_subs_vals(cons_section, "RESTRAINT", &
i_rep_section=i_rep_section)
CALL section_vals_get(restraint_section, explicit=is_restraint)
IF (is_restraint) THEN
CALL section_vals_val_get(restraint_section, "K", r_val=k0)
IF (output_unit > 0) THEN
nlabel = cp_to_string(i_rep_section)
WRITE (output_unit, FMT='(T2,"RESTRAINT|",1X,A,F9.6)') &
"Active restraint on "//label//" section Nr."// &
TRIM(nlabel)//". K [a.u.]=", k0
END IF
END IF
END IF
END SUBROUTINE check_restraint
END MODULE topology_input