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Extending EXCLUDE_QM and EXCLUDE_MM to all type of constraints. Adding warning

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when molname is not defined. Adding warning if temperature_tolerance is ON .
Adding 8 more regtests for all constraints and both exclude possibilities.


svn-origin-rev: 6322
This commit is contained in:
Teodoro Laino 2007-08-31 17:25:52 +00:00
parent 650683afdd
commit fe9fb5ac5d
18 changed files with 1096 additions and 113 deletions
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63
src/input_cp2k_motion.F
View file

@ -900,6 +900,20 @@ CONTAINS
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="EXCLUDE_QM",&
description="Does not apply the constraint to the QM region within a QM/MM calculation",&
usage="EXCLUDE_QM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="EXCLUDE_MM",&
description="Does not apply the constraint to the MM region within a QM/MM calculation",&
usage="EXCLUDE_MM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
END IF
END SUBROUTINE create_collective_section
@ -993,6 +1007,22 @@ CONTAINS
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="EXCLUDE_QM",&
description="Does not apply the constraint to the QM region within a QM/MM calculation."//&
" This keyword is active only together with MOLNAME",&
usage="EXCLUDE_QM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="EXCLUDE_MM",&
description="Does not apply the constraint to the MM region within a QM/MM calculation."//&
" This keyword is active only together with MOLNAME",&
usage="EXCLUDE_MM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
END IF
END SUBROUTINE create_fixed_atom_section
@ -1070,10 +1100,25 @@ CONTAINS
! Real
CALL keyword_create(keyword, name="DISTANCES",&
description="The constrained distances' values.",&
usage="DISTANCES {real} {real} {real}", type_of_var=real_t, n_var=-1,error=error)
usage="DISTANCES {real} {real} {real}", type_of_var=real_t,&
unit_str="internal_cp2k",n_var=-1,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
! Logical
CALL keyword_create(keyword, name="EXCLUDE_QM",&
description="Does not apply the constraint to the QM region within a QM/MM calculation",&
usage="EXCLUDE_QM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="EXCLUDE_MM",&
description="Does not apply the constraint to the MM region within a QM/MM calculation",&
usage="EXCLUDE_MM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
END IF
END SUBROUTINE create_g3x3_section
@ -1244,10 +1289,24 @@ CONTAINS
CALL keyword_create(keyword, name="DISTANCES",&
description="The constrained distances' values.",&
usage="DISTANCES {real} {real} {real} {real} {real} {real}",&
type_of_var=real_t, n_var=6,error=error)
type_of_var=real_t, n_var=6,unit_str="internal_cp2k",error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
! Logical
CALL keyword_create(keyword, name="EXCLUDE_QM",&
description="Does not apply the constraint to the QM region within a QM/MM calculation",&
usage="EXCLUDE_QM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
CALL keyword_create(keyword, name="EXCLUDE_MM",&
description="Does not apply the constraint to the MM region within a QM/MM calculation",&
usage="EXCLUDE_MM <LOGICAL>",&
default_l_val=.FALSE.,lone_keyword_l_val=.TRUE.,error=error)
CALL section_add_keyword(section,keyword,error=error)
CALL keyword_release(keyword,error=error)
END IF
END SUBROUTINE create_g4x6_section

11
src/md.F
View file

@ -159,6 +159,9 @@ CONTAINS
TYPE(section_vals_type), POINTER :: root_section
TYPE(cp_error_type), INTENT(inout) :: error
CHARACTER(len=*), PARAMETER :: routineN = 'read_md_section', &
routineP = moduleN//':'//routineN
CHARACTER(LEN=default_path_length) :: filename
INTEGER :: iw
INTEGER, DIMENSION(:), POINTER :: iprint
@ -313,6 +316,14 @@ CONTAINS
' SHOCK| Barostat Mass [', 'au', '] ', &
simpar % cmass
END IF
! Print warning for temp_tol
IF (simpar % temp_tol > 0.0_dp) THEN
CALL cp_assert(.FALSE.,cp_warning_level,cp_assertion_failed,routineP,&
"A temperature tolerance (TEMP_TOL) is used during the MD. "//&
"Due to the velocity rescaling algorithm jumps may appear in the conserved quantity. "//&
CPSourceFileRef,&
only_ionode=.TRUE.)
END IF
END IF
CALL cp_print_key_finished_output(iw,logger,md_section,&

285
src/topology_constraint_util.F
View file

@ -132,8 +132,9 @@ CONTAINS
INTEGER, DIMENSION(:), POINTER :: constr_x_glob, inds, &
molecule_list
LOGICAL :: exclude_mm, exclude_qm, failure, fix_atom_mm, &
fix_atom_molname, fix_atom_qm, fix_atom_qmmm, fix_fixed_atom, ionode, &
is_qm, ishbond, ldummy, restart_restraint_clv, restart_restraint_pos
fix_atom_molname, fix_atom_qm, fix_atom_qmmm, fix_fixed_atom, &
found_molname, ionode, is_qm, ishbond, ldummy, restart_restraint_clv, &
restart_restraint_pos
LOGICAL, ALLOCATABLE, DIMENSION(:) :: missed_molname
REAL(KIND=dp) :: rmod, rvec(3)
REAL(KIND=dp), DIMENSION(:), POINTER :: hdist, r
@ -252,12 +253,17 @@ CONTAINS
END DO
CALL section_vals_val_get(hbonds_section,"MOLNAME",c_vals=cnds,error=error)
DO i = 1, SIZE(cnds)
found_molname = .FALSE.
DO k = 1, SIZE(molecule_kind_set)
molecule_kind => molecule_kind_set(k)
name = molecule_kind%name
ldummy = qmmm_ff_precond_only_qm(id1=name)
IF (cnds(i) == name) constr_x_mol(k)%constr(1) = 1
IF (cnds(i) == name) THEN
constr_x_mol(k)%constr(1) = 1
found_molname = .TRUE.
END IF
END DO
CALL print_warning_molname(found_molname, cnds(i), error)
END DO
END IF
END IF
@ -321,8 +327,12 @@ CONTAINS
CALL reallocate(cons_info%colv_intermolecular,1,cons_info%nconst_colv)
CALL reallocate(cons_info%colv_restraint,1,cons_info%nconst_colv)
CALL reallocate(cons_info%colv_k0,1,cons_info%nconst_colv)
CALL reallocate(cons_info%colv_exclude_qm,1,cons_info%nconst_colv)
CALL reallocate(cons_info%colv_exclude_mm,1,cons_info%nconst_colv)
! Bonds involving hydrogens are by their nature only intramolecular
cons_info%colv_intermolecular(n_start_colv+1:cons_info%nconst_colv) = .FALSE.
cons_info%colv_exclude_qm(n_start_colv+1:cons_info%nconst_colv) = .FALSE.
cons_info%colv_exclude_mm(n_start_colv+1:cons_info%nconst_colv) = .FALSE.
cons_info%colv_restraint(n_start_colv+1:cons_info%nconst_colv) = cons_info%hbonds_restraint
cons_info%colv_k0(n_start_colv+1:cons_info%nconst_colv) = cons_info%hbonds_k0
!
@ -414,6 +424,8 @@ CONTAINS
constr_x_mol,&
constr_x_glob,&
molecule_kind_set,&
cons_info%colv_exclude_qm,&
cons_info%colv_exclude_mm,&
error)
! Intramolecular constraints
gind = 0
@ -485,6 +497,8 @@ CONTAINS
constr_x_mol,&
constr_x_glob,&
molecule_kind_set,&
cons_info%g33_exclude_qm,&
cons_info%g33_exclude_mm,&
error)
! Intramolecular constraints
DO ii = 1, SIZE(molecule_kind_set)
@ -542,6 +556,8 @@ CONTAINS
constr_x_mol,&
constr_x_glob,&
molecule_kind_set,&
cons_info%g46_exclude_qm,&
cons_info%g46_exclude_mm,&
error)
! Intramolecular constraints
DO ii = 1, SIZE(molecule_kind_set)
@ -604,7 +620,7 @@ CONTAINS
molecule_kind => molecule_kind_set(i)
CALL get_molecule_kind(molecule_kind=molecule_kind,&
nmolecule=nmolecule,molecule_list=molecule_list, name=molname)
ldummy = qmmm_ff_precond_only_qm(id1=molname)
is_qm = qmmm_ff_precond_only_qm(id1=molname)
WHERE(molname.EQ.cons_info%fixed_molnames)
missed_molname=.FALSE.
END WHERE
@ -615,7 +631,13 @@ CONTAINS
CALL get_molecule ( molecule, first_atom = first, last_atom = last )
fix_atom_molname=.FALSE.
IF (ASSOCIATED(cons_info%fixed_molnames)) THEN
IF (ANY(cons_info%fixed_molnames.EQ.molname)) fix_atom_molname=.TRUE.
DO k = 1, SIZE(cons_info%fixed_molnames)
IF (cons_info%fixed_molnames(k).EQ.molname) THEN
fix_atom_molname=.TRUE.
IF (is_qm.AND.cons_info%fixed_exclude_qm(k)) fix_atom_molname=.FALSE.
IF ((.NOT.is_qm).AND.cons_info%fixed_exclude_mm(k)) fix_atom_molname=.FALSE.
END IF
END DO
ENDIF
DO k = first, last
fix_atom_qmmm=.FALSE.
@ -642,111 +664,113 @@ CONTAINS
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
kk = 0
nfixd_restraint = 0
DO j=1,nmolecule
molecule => molecule_set(molecule_list(j))
CALL get_molecule ( molecule, first_atom = first, last_atom = last )
fix_atom_molname=.FALSE.
IF (ASSOCIATED(cons_info%fixed_molnames)) THEN
DO k1loc = 1, SIZE(cons_info%fixed_molnames)
IF (cons_info%fixed_molnames(k1loc).EQ.molname) THEN
fix_atom_molname=.TRUE.
EXIT
IF (nfixed_atoms/=0) THEN
DO j=1,nmolecule
molecule => molecule_set(molecule_list(j))
CALL get_molecule ( molecule, first_atom = first, last_atom = last )
fix_atom_molname=.FALSE.
IF (ASSOCIATED(cons_info%fixed_molnames)) THEN
DO k1loc = 1, SIZE(cons_info%fixed_molnames)
IF (cons_info%fixed_molnames(k1loc).EQ.molname) THEN
fix_atom_molname=.TRUE.
EXIT
END IF
END DO
ENDIF
DO k=first,last
! FIXED LIST ATOMS
fix_fixed_atom = .FALSE.
DO k2loc=1,SIZE(cons_info%fixed_atoms)
IF (cons_info%fixed_atoms(k2loc) == k) THEN
fix_fixed_atom = .TRUE.
EXIT
END IF
END DO
! QMMM FIXED ATOMS (QM OR MM)
fix_atom_qmmm=.FALSE.
fix_atom_mm =.FALSE.
fix_atom_qm =.FALSE.
IF (PRESENT(qmmm_env)) THEN
SELECT CASE(cons_info%freeze_qm)
CASE(do_constr_atomic)
IF (ANY(qmmm_env%qm_atom_index==k)) THEN
fix_atom_qmmm=.TRUE.
fix_atom_qm = .TRUE.
END IF
CASE(do_constr_molec)
IF (ANY(qmmm_env%qm_molecule_index == molecule_list(j))) THEN
fix_atom_qmmm = .TRUE.
fix_atom_qm = .TRUE.
END IF
END SELECT
SELECT CASE(cons_info%freeze_mm)
CASE(do_constr_atomic)
IF (ALL(qmmm_env%qm_atom_index/=k)) THEN
fix_atom_qmmm=.TRUE.
fix_atom_mm = .TRUE.
END IF
CASE(do_constr_molec)
IF (ALL(qmmm_env%qm_molecule_index /= molecule_list(j))) THEN
fix_atom_qmmm = .TRUE.
fix_atom_mm = .TRUE.
END IF
END SELECT
! We should never reach this point but let's check it anyway
IF (fix_atom_qm.AND.fix_atom_mm) THEN
CALL stop_program(TRIM(routineN),"Atom number: "//cp_to_string(k)//&
" has been defined both QM and MM. General Error!")
END IF
END IF
END DO
ENDIF
DO k=first,last
! FIXED LIST ATOMS
fix_fixed_atom = .FALSE.
DO k2loc=1,SIZE(cons_info%fixed_atoms)
IF (cons_info%fixed_atoms(k2loc) == k) THEN
fix_fixed_atom = .TRUE.
EXIT
END IF
END DO
! QMMM FIXED ATOMS (QM OR MM)
fix_atom_qmmm=.FALSE.
fix_atom_mm =.FALSE.
fix_atom_qm =.FALSE.
IF (PRESENT(qmmm_env)) THEN
SELECT CASE(cons_info%freeze_qm)
CASE(do_constr_atomic)
IF (ANY(qmmm_env%qm_atom_index==k)) THEN
fix_atom_qmmm=.TRUE.
fix_atom_qm = .TRUE.
END IF
CASE(do_constr_molec)
IF (ANY(qmmm_env%qm_molecule_index == molecule_list(j))) THEN
fix_atom_qmmm = .TRUE.
fix_atom_qm = .TRUE.
END IF
END SELECT
SELECT CASE(cons_info%freeze_mm)
CASE(do_constr_atomic)
IF (ALL(qmmm_env%qm_atom_index/=k)) THEN
fix_atom_qmmm=.TRUE.
fix_atom_mm = .TRUE.
END IF
CASE(do_constr_molec)
IF (ALL(qmmm_env%qm_molecule_index /= molecule_list(j))) THEN
fix_atom_qmmm = .TRUE.
fix_atom_mm = .TRUE.
END IF
END SELECT
! We should never reach this point but let's check it anyway
IF (fix_atom_qm.AND.fix_atom_mm) THEN
! Check that the fixed atom constraint/restraint is unique
IF ((fix_fixed_atom.AND.fix_atom_qmmm).OR.(fix_fixed_atom.AND.fix_atom_molname)&
.OR.(fix_atom_qmmm.AND.fix_atom_molname)) THEN
CALL stop_program(TRIM(routineN),"Atom number: "//cp_to_string(k)//&
" has been defined both QM and MM. General Error!")
" has been constrained/restrained to be fixed in more than one"//&
" input section. Check and correct your input file!")
END IF
END IF
! Check that the fixed atom constraint/restraint is unique
IF ((fix_fixed_atom.AND.fix_atom_qmmm).OR.(fix_fixed_atom.AND.fix_atom_molname)&
.OR.(fix_atom_qmmm.AND.fix_atom_molname)) THEN
CALL stop_program(TRIM(routineN),"Atom number: "//cp_to_string(k)//&
" has been constrained/restrained to be fixed in more than one"//&
" input section. Check and correct your input file!")
END IF
! Let's store the atom index
IF (fix_fixed_atom.OR.fix_atom_qmmm.OR.fix_atom_molname) THEN
kk = kk + 1
fixd_list(kk)%fixd = k
fixd_list(kk)%coord = particle_set(k)%r
! Possibly Restraint
IF (fix_fixed_atom) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_restraint(k2loc)
fixd_list(kk)%restraint%k0 = cons_info%fixed_k0(k2loc)
ELSEIF (fix_atom_qm) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_qm_restraint
fixd_list(kk)%restraint%k0 = cons_info%fixed_qm_k0
ELSEIF (fix_atom_mm) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_mm_restraint
fixd_list(kk)%restraint%k0 = cons_info%fixed_mm_k0
ELSEIF (fix_atom_molname) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_mol_restraint(k1loc)
fixd_list(kk)%restraint%k0 = cons_info%fixed_mol_k0(k1loc)
ELSE
! Should never reach this point
CPPostcondition(.FALSE.,cp_failure_level,routineP,error,failure)
END IF
IF (fixd_list(kk)%restraint%active) THEN
nfixd_restraint = nfixd_restraint+ 1
nfixd_restart = nfixd_restart + 1
IF (restart_restraint_pos) THEN
! Read coord0 value for restraint
CALL section_vals_val_get(fixd_restr_rest,"_DEFAULT_KEYWORD_",&
i_rep_val=nfixd_restart, r_vals=r, error=error)
fixd_list(kk)%coord = r
! Let's store the atom index
IF (fix_fixed_atom.OR.fix_atom_qmmm.OR.fix_atom_molname) THEN
kk = kk + 1
fixd_list(kk)%fixd = k
fixd_list(kk)%coord = particle_set(k)%r
! Possibly Restraint
IF (fix_fixed_atom) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_restraint(k2loc)
fixd_list(kk)%restraint%k0 = cons_info%fixed_k0(k2loc)
ELSEIF (fix_atom_qm) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_qm_restraint
fixd_list(kk)%restraint%k0 = cons_info%fixed_qm_k0
ELSEIF (fix_atom_mm) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_mm_restraint
fixd_list(kk)%restraint%k0 = cons_info%fixed_mm_k0
ELSEIF (fix_atom_molname) THEN
fixd_list(kk)%restraint%active = cons_info%fixed_mol_restraint(k1loc)
fixd_list(kk)%restraint%k0 = cons_info%fixed_mol_k0(k1loc)
ELSE
! Write coord0 value for restraint
ALLOCATE(r(3),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
r = fixd_list(kk)%coord
CALL section_vals_val_set(fixd_restr_rest,"_DEFAULT_KEYWORD_",&
i_rep_val=nfixd_restart, r_vals_ptr=r, error=error)
! Should never reach this point
CPPostcondition(.FALSE.,cp_failure_level,routineP,error,failure)
END IF
IF (fixd_list(kk)%restraint%active) THEN
nfixd_restraint = nfixd_restraint+ 1
nfixd_restart = nfixd_restart + 1
IF (restart_restraint_pos) THEN
! Read coord0 value for restraint
CALL section_vals_val_get(fixd_restr_rest,"_DEFAULT_KEYWORD_",&
i_rep_val=nfixd_restart, r_vals=r, error=error)
fixd_list(kk)%coord = r
ELSE
! Write coord0 value for restraint
ALLOCATE(r(3),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
r = fixd_list(kk)%coord
CALL section_vals_val_set(fixd_restr_rest,"_DEFAULT_KEYWORD_",&
i_rep_val=nfixd_restart, r_vals_ptr=r, error=error)
END IF
END IF
END IF
END IF
END DO
END DO
END DO
END IF
IF (iw>0) THEN
WRITE(iw,*)"MOLECULE KIND:",i," NR. FIXED ATOMS:",SIZE(fixd_list(:)%fixd)," LIST::",fixd_list(:)%fixd
END IF
@ -1225,7 +1249,7 @@ END SUBROUTINE setup_lg4x6
!! INPUTS
!!*** *************************************************************************
SUBROUTINE give_constraint_array(const_mol, const_molname, const_intermolecular,&
constr_x_mol, constr_x_glob, molecule_kind_set, error)
constr_x_mol, constr_x_glob, molecule_kind_set, exclude_qm, exclude_mm, error)
INTEGER, DIMENSION(:), POINTER :: const_mol
CHARACTER(LEN=default_string_length), &
@ -1236,6 +1260,7 @@ END SUBROUTINE setup_lg4x6
INTEGER, DIMENSION(:), POINTER :: constr_x_glob
TYPE(molecule_kind_type), DIMENSION(:), &
POINTER :: molecule_kind_set
LOGICAL, DIMENSION(:), POINTER :: exclude_qm, exclude_mm
TYPE(cp_error_type), INTENT(inout) :: error
CHARACTER(len=*), PARAMETER :: routineN = 'give_constraint_array', &
@ -1244,7 +1269,7 @@ END SUBROUTINE setup_lg4x6
CHARACTER(LEN=default_string_length) :: myname, name
INTEGER :: handle, i, iglob, isize, k, &
stat
LOGICAL :: failure, ldummy
LOGICAL :: failure, found_molname, is_qm
TYPE(molecule_kind_type), POINTER :: molecule_kind
failure = .FALSE.
@ -1275,16 +1300,21 @@ END SUBROUTINE setup_lg4x6
constr_x_mol(k)%constr(isize+1) = i
ELSE
myname = const_molname(i)
found_molname = .FALSE.
DO k = 1, SIZE(molecule_kind_set)
molecule_kind => molecule_kind_set(k)
name = molecule_kind%name
ldummy = qmmm_ff_precond_only_qm(id1=name)
is_qm = qmmm_ff_precond_only_qm(id1=name)
IF (is_qm.AND.exclude_qm(i)) CYCLE
IF (.NOT.is_qm.AND.exclude_mm(i)) CYCLE
IF (name==myname) THEN
isize = SIZE(constr_x_mol(k)%constr)
CALL reallocate(constr_x_mol(k)%constr, 1, isize+1)
constr_x_mol(k)%constr(isize+1) = i
found_molname = .TRUE.
END IF
END DO
CALL print_warning_molname(found_molname, myname, error)
END IF
END IF
END DO
@ -1292,4 +1322,47 @@ END SUBROUTINE setup_lg4x6
CALL timestop(0.0_dp,handle)
END SUBROUTINE give_constraint_array
!******************************************************************************
!!****** topology_constraint_util/print_warning_molname [1.0] *
!!
!! NAME
!! print_warning_molname
!!
!! SYNOPSIS
!!
!! FUNCTION
!! Prints a warning message if undefined molnames are used to define constraints
!!
!! AUTHOR
!! Teodoro Laino [2007] - Zurich University
!!
!! MODIFICATION HISTORY
!!
!!
!! OPTIONS
!!
!! INPUTS
!!*** *************************************************************************
SUBROUTINE print_warning_molname(found, name, error)
LOGICAL, INTENT(IN) :: found
CHARACTER(LEN=*), INTENT(IN) :: name
TYPE(cp_error_type), INTENT(inout) :: error
CHARACTER(len=*), PARAMETER :: routineN = 'print_warning_molname', &
routineP = moduleN//':'//routineN
LOGICAL :: failure
failure = .FALSE.
CALL cp_assert(found,cp_warning_level,cp_assertion_failed,routineP,&
" MOLNAME ("//TRIM(name)//") was defined for constraints, but this molecule name "//&
"is not defined. Please check carefully your PDB, PSF (has priority over PDB) or "//&
"input driven CP2K coordinates. In case you may not find the reason for this warning "//&
"it may be a good idea to print all molecule information (including kind name) activating "//&
"the print_key MOLECULES specific of the SUBSYS%PRINT section. "//&
CPSourceFileRef,&
only_ionode=.TRUE.)
END SUBROUTINE print_warning_molname
END MODULE topology_constraint_util

40
src/topology_input.F
View file

@ -230,6 +230,10 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%g33_k0(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%g33_exclude_qm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%g33_exclude_mm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
DO ig = 1, ncons
CALL check_restraint(g3x3_section,&
is_restraint=cons_info%g33_restraint(ig), &
@ -239,6 +243,11 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
error=error)
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),error=error)
CALL section_vals_val_get(g3x3_section,"EXCLUDE_MM",i_rep_section=ig,&
l_val=cons_info%g33_exclude_mm(ig),error=error)
! Intramolecular restraint
CALL section_vals_val_get(g3x3_section,"INTERMOLECULAR",i_rep_section=ig,&
l_val=cons_info%g33_intermolecular(ig),error=error)
@ -317,6 +326,10 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%g46_k0(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%g46_exclude_qm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%g46_exclude_mm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
DO ig = 1, ncons
CALL check_restraint(g4x6_section,&
is_restraint=cons_info%g46_restraint(ig), &
@ -326,6 +339,11 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
error=error)
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),error=error)
CALL section_vals_val_get(g4x6_section,"EXCLUDE_MM",i_rep_section=ig,&
l_val=cons_info%g46_exclude_mm(ig),error=error)
! Intramolecular restraint
CALL section_vals_val_get(g4x6_section,"INTERMOLECULAR",i_rep_section=ig,&
l_val=cons_info%g46_intermolecular(ig),error=error)
@ -389,6 +407,10 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%fixed_mol_k0(msize),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%fixed_exclude_qm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%fixed_exclude_mm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
DO ig = 1, ncons
isize_old = isize
msize_old = msize
@ -439,6 +461,15 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
CALL reallocate(cons_info%fixed_mol_k0,1,msize+SIZE(tmpstringlist,1))
msize = SIZE(cons_info%fixed_molnames)
cons_info%fixed_molnames(:)=tmpstringlist(:)
! 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),error=error)
CALL section_vals_val_get(fix_atom_section,"EXCLUDE_MM",i_rep_section=ig,&
l_val=cons_info%fixed_exclude_mm(msize_old+1),error=error)
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
@ -513,6 +544,10 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%colv_k0(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%colv_exclude_qm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
ALLOCATE(cons_info%colv_exclude_mm(ncons),stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
DO ig = 1, ncons
CALL check_restraint(collective_section,&
is_restraint=cons_info%colv_restraint(ig), &
@ -522,6 +557,11 @@ SUBROUTINE read_constraints_section(topology, colvar_p, constraint_section, erro
error=error)
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),error=error)
CALL section_vals_val_get(collective_section,"EXCLUDE_MM",i_rep_section=ig,&
l_val=cons_info%colv_exclude_mm(ig),error=error)
! Intramolecular restraint
CALL section_vals_val_get(collective_section,"INTERMOLECULAR",i_rep_section=ig,&
l_val=cons_info%colv_intermolecular(ig),error=error)

50
src/topology_types.F
View file

@ -85,6 +85,7 @@ MODULE topology_types
LOGICAL, POINTER :: fixed_mol_restraint(:) ! Restraints control
REAL(KIND=dp), POINTER :: fixed_mol_k0(:) ! Restraints control
CHARACTER(LEN=default_string_length), POINTER :: fixed_molnames(:)
LOGICAL, POINTER, DIMENSION(:) :: fixed_exclude_qm, fixed_exclude_mm
! Collective constraints
INTEGER :: nconst_colv
INTEGER, POINTER :: const_colv_mol(:)
@ -94,6 +95,7 @@ MODULE topology_types
LOGICAL, POINTER :: colv_intermolecular(:)
LOGICAL, POINTER :: colv_restraint(:) ! Restraints control
REAL(KIND=dp), POINTER :: colv_k0(:) ! Restraints control
LOGICAL, POINTER, DIMENSION(:) :: colv_exclude_qm, colv_exclude_mm
! G3x3
INTEGER :: nconst_g33
INTEGER, POINTER :: const_g33_mol(:)
@ -107,6 +109,7 @@ MODULE topology_types
LOGICAL, POINTER :: g33_intermolecular(:)
LOGICAL, POINTER :: g33_restraint(:) ! Restraints control
REAL(KIND=dp), POINTER :: g33_k0(:) ! Restraints control
LOGICAL, POINTER, DIMENSION(:) :: g33_exclude_qm, g33_exclude_mm
! G4x6
INTEGER :: nconst_g46
INTEGER, POINTER :: const_g46_mol(:)
@ -124,6 +127,7 @@ MODULE topology_types
LOGICAL, POINTER :: g46_intermolecular(:)
LOGICAL, POINTER :: g46_restraint(:) ! Restraints control
REAL(KIND=dp), POINTER :: g46_k0(:) ! Restraints control
LOGICAL, POINTER, DIMENSION(:) :: g46_exclude_qm, g46_exclude_mm
END TYPE constraint_info_type
TYPE topology_parameters_type
@ -165,13 +169,13 @@ MODULE topology_types
END TYPE constr_list_type
PUBLIC :: atom_info_type,&
connectivity_info_type,&
constraint_info_type,&
topology_parameters_type,&
constr_list_type
connectivity_info_type,&
constraint_info_type,&
topology_parameters_type,&
constr_list_type
PUBLIC :: init_topology,&
deallocate_topology
deallocate_topology
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_types'
PRIVATE
@ -312,6 +316,7 @@ CONTAINS
NULLIFY(constraint_info%fixed_k0)
NULLIFY(constraint_info%fixed_mol_restraint)
NULLIFY(constraint_info%fixed_mol_k0)
NULLIFY(constraint_info%fixed_exclude_qm, constraint_info%fixed_exclude_mm)
! Collective Constraints
constraint_info%nconst_colv = 0
NULLIFY(constraint_info%colvar_set)
@ -321,6 +326,7 @@ CONTAINS
NULLIFY(constraint_info%colv_intermolecular)
NULLIFY(constraint_info%colv_restraint)
NULLIFY(constraint_info%colv_k0)
NULLIFY(constraint_info%colv_exclude_qm, constraint_info%colv_exclude_mm)
! G3x3
constraint_info%nconst_g33 = 0
NULLIFY(constraint_info%const_g33_mol)
@ -334,6 +340,7 @@ CONTAINS
NULLIFY(constraint_info%g33_intermolecular)
NULLIFY(constraint_info%g33_restraint)
NULLIFY(constraint_info%g33_k0)
NULLIFY(constraint_info%g33_exclude_qm, constraint_info%g33_exclude_mm)
! G4x6
constraint_info%nconst_g46 = 0
NULLIFY(constraint_info%const_g46_mol)
@ -351,6 +358,7 @@ CONTAINS
NULLIFY(constraint_info%g46_intermolecular)
NULLIFY(constraint_info%g46_restraint)
NULLIFY(constraint_info%g46_k0)
NULLIFY(constraint_info%g46_exclude_qm, constraint_info%g46_exclude_mm)
END SUBROUTINE init_constraint
@ -608,6 +616,14 @@ CONTAINS
DEALLOCATE(constraint_info%fixed_mol_k0, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%fixed_exclude_qm)) THEN
DEALLOCATE(constraint_info%fixed_exclude_qm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%fixed_exclude_mm)) THEN
DEALLOCATE(constraint_info%fixed_exclude_mm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
! Collective Constraint
IF (ASSOCIATED(constraint_info%colvar_set)) THEN
DO i = 1, SIZE(constraint_info%colvar_set)
@ -643,6 +659,14 @@ CONTAINS
DEALLOCATE(constraint_info%colv_k0,STAT=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%colv_exclude_qm)) THEN
DEALLOCATE(constraint_info%colv_exclude_qm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%colv_exclude_mm)) THEN
DEALLOCATE(constraint_info%colv_exclude_mm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
! G3x3
IF(ASSOCIATED(constraint_info%const_g33_mol)) THEN
DEALLOCATE(constraint_info%const_g33_mol,STAT=stat)
@ -688,6 +712,14 @@ CONTAINS
DEALLOCATE(constraint_info%g33_k0,STAT=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%g33_exclude_qm)) THEN
DEALLOCATE(constraint_info%g33_exclude_qm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%g33_exclude_mm)) THEN
DEALLOCATE(constraint_info%g33_exclude_mm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
! G4x6
IF(ASSOCIATED(constraint_info%const_g46_mol)) THEN
DEALLOCATE(constraint_info%const_g46_mol,STAT=stat)
@ -749,6 +781,14 @@ CONTAINS
DEALLOCATE(constraint_info%g46_k0,STAT=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%g46_exclude_qm)) THEN
DEALLOCATE(constraint_info%g46_exclude_qm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
IF(ASSOCIATED(constraint_info%g46_exclude_mm)) THEN
DEALLOCATE(constraint_info%g46_exclude_mm, stat=stat)
CPPostcondition(stat==0,cp_failure_level,routineP,error,failure)
END IF
END IF
END SUBROUTINE deallocate_constraint

14
tests/QMMM/SE/regtest_2/TEST_FILES Normal file
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@ -0,0 +1,14 @@
# runs are executed in the same order as in this file
# the second field tells which test should be run in order to compare with the last available output
# e.g. 0 means do not compare anything, running is enough
# 1 compares the last total energy in the file
# for details see cp2k/tools/do_regtest
# QM/MM
nh3_g4x6_excl_mm.inp 2
nh3_g4x6_excl_qm.inp 2
water_colv_excl_mm.inp 2
water_colv_excl_qm.inp 2
water_fixd_excl_mm.inp 2
water_fixd_excl_qm.inp 2
water_g3x3_excl_mm.inp 2
water_g3x3_excl_qm.inp 2

1
tests/QMMM/SE/regtest_2/TEST_FILES_RESET Normal file
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@ -0,0 +1 @@
#

91
tests/QMMM/SE/regtest_2/nh3_g4x6_excl_mm.inp Normal file
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@ -0,0 +1,91 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&QMMM
NOCENTER
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3 4
&END QM_KIND
&QM_KIND N
MM_INDEX 1
&END QM_KIND
&END
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/nh3.pot
parmtype CHM
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 10.0 10.0 10.0
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../sample_pdb/NH3.pdb
COORDINATE pdb
CONNECTIVITY MOL_SET
&MOL_SET
&MOLECULE
NMOL 2
CONN_FILE_NAME ../../../Fist/sample_psf/nh3.psf
CONNECTIVITY UPSF
&END
&END
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT NH3-G46-EXMM
RUN_TYPE md
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&G4X6
DISTANCES 1.9275 1.9275 1.9275 3.1483 3.1483 3.1483
MOLNAME MOL01
ATOMS 1 2 3 4
EXCLUDE_MM
&END G4X6
&END CONSTRAINT
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

91
tests/QMMM/SE/regtest_2/nh3_g4x6_excl_qm.inp Normal file
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@ -0,0 +1,91 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&QMMM
NOCENTER
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3 4
&END QM_KIND
&QM_KIND N
MM_INDEX 1
&END QM_KIND
&END
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/nh3.pot
parmtype CHM
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
O_SPLINE 6
&END EWALD
&END POISSON
&END MM
&SUBSYS
&CELL
ABC 10.0 10.0 10.0
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../sample_pdb/NH3.pdb
COORDINATE pdb
CONNECTIVITY MOL_SET
&MOL_SET
&MOLECULE
NMOL 2
CONN_FILE_NAME ../../../Fist/sample_psf/nh3.psf
CONNECTIVITY UPSF
&END
&END
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT NH3-G46-EXQM
RUN_TYPE md
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&G4X6
DISTANCES 1.9275 1.9275 1.9275 3.1483 3.1483 3.1483
MOLNAME MOL01
ATOMS 1 2 3 4
EXCLUDE_QM
&END G4X6
&END CONSTRAINT
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

18
tests/QMMM/SE/regtest_2/tidy Normal file
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@ -0,0 +1,18 @@
#!/bin/tcsh
# Script to clean files after execution of a test
echo "This script will clean the directory" $PWD "from scratch files.."
echo
foreach file (`cvs update -A -P|grep '? '|awk '{print $2}'`)
if ( ${file:e} == 'inp' ) then
echo "This files could be a new input file you don't want to be deleted.. Do you really want it deleted?"
if ( $1 == "-int" ) then
echo "You requested to run the cleaning script interactively! Forget about complains!"
rm -f $file
else
rm -i $file
endif
else
rm -f $file
endif
end
rm -f *.bak

93
tests/QMMM/SE/regtest_2/water_colv_excl_mm.inp Normal file
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@ -0,0 +1,93 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/water.pot
parmtype CHM
&CHARGE
ATOM OT
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HT
CHARGE 0.4238
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3
&END QM_KIND
&QM_KIND O
MM_INDEX 1
&END QM_KIND
&END
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../../../Fist/sample_pdb/water_2.pdb
COORDINATE pdb
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&COLVAR
&DISTANCE
ATOMS 2 3
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT WAT-COLV-EXMM
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&COLLECTIVE
COLVAR 1
TARGET 3.0
MOLNAME WAT
EXCLUDE_MM
&END
&END
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

93
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@ -0,0 +1,93 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/water.pot
parmtype CHM
&CHARGE
ATOM OT
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HT
CHARGE 0.4238
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3
&END QM_KIND
&QM_KIND O
MM_INDEX 1
&END QM_KIND
&END
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../../../Fist/sample_pdb/water_2.pdb
COORDINATE pdb
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&COLVAR
&DISTANCE
ATOMS 2 3
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT WAT-COLV-EXQM
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&COLLECTIVE
COLVAR 1
TARGET 3.0
MOLNAME WAT
EXCLUDE_QM
&END
&END
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

87
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@ -0,0 +1,87 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/water.pot
parmtype CHM
&CHARGE
ATOM OT
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HT
CHARGE 0.4238
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
&END EWALD
&END POISSON
&END MM
&QMMM
NOCENTER
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3
&END QM_KIND
&QM_KIND O
MM_INDEX 1
&END QM_KIND
&END
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../../../Fist/sample_pdb/water_2.pdb
COORDINATE pdb
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT WAT-FXD-EXMM
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&FIXED_ATOMS
MOLNAME WAT
EXCLUDE_MM
&END
&END
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

87
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@ -0,0 +1,87 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/water.pot
parmtype CHM
&CHARGE
ATOM OT
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HT
CHARGE 0.4238
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
&END EWALD
&END POISSON
&END MM
&QMMM
NOCENTER
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3
&END QM_KIND
&QM_KIND O
MM_INDEX 1
&END QM_KIND
&END
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../../../Fist/sample_pdb/water_2.pdb
COORDINATE pdb
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT WAT-FXD-EXQM
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&FIXED_ATOMS
MOLNAME WAT
EXCLUDE_QM
&END
&END
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

88
tests/QMMM/SE/regtest_2/water_g3x3_excl_mm.inp Normal file
View file

@ -0,0 +1,88 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/water.pot
parmtype CHM
&CHARGE
ATOM OT
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HT
CHARGE 0.4238
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3
&END QM_KIND
&QM_KIND O
MM_INDEX 1
&END QM_KIND
&END
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../../../Fist/sample_pdb/water_2.pdb
COORDINATE pdb
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT WAT-G33-EXMM
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&G3X3
DISTANCES 1.8897268 1.8897268 3.0859239
MOLNAME WAT
ATOMS 1 2 3
EXCLUDE_MM
&END G3X3
&END
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

88
tests/QMMM/SE/regtest_2/water_g3x3_excl_qm.inp Normal file
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@ -0,0 +1,88 @@
&FORCE_EVAL
METHOD QMMM
&DFT
&QS
METHOD AM1
&END QS
&SCF
SCF_GUESS ATOMIC
&END SCF
&END DFT
&MM
&FORCEFIELD
parm_file_name ../../../Fist/sample_pot/water.pot
parmtype CHM
&CHARGE
ATOM OT
CHARGE -0.8476
&END CHARGE
&CHARGE
ATOM HT
CHARGE 0.4238
&END CHARGE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 30
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 6.0 6.0 6.0
UNIT ANGSTROM
&END CELL
ECOUPL NONE
&QM_KIND H
MM_INDEX 2 3
&END QM_KIND
&QM_KIND O
MM_INDEX 1
&END QM_KIND
&END
&SUBSYS
&CELL
ABC 24.955 24.955 24.955
UNIT ANGSTROM
&END CELL
&TOPOLOGY
COORD_FILE_NAME ../../../Fist/sample_pdb/water_2.pdb
COORDINATE pdb
&END TOPOLOGY
&PRINT
&MOLECULES
&END
&END
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
FFTLIB FFTSG
PROJECT WAT-G33-EXQM
RUN_TYPE MD
&END GLOBAL
&MOTION
&CONSTRAINT
CONSTRAIN_INIT T
&G3X3
DISTANCES 1.8897268 1.8897268 3.0859239
MOLNAME WAT
ATOMS 1 2 3
EXCLUDE_QM
&END G3X3
&END
&MD
ENSEMBLE NVE
STEPS 20
TIMESTEP 0.5
TEMPERATURE 298
&NOSE
LENGTH 3
YOSHIDA 3
TIMECON 1000
MTS 2
&END NOSE
&END MD
&END MOTION

8
tests/QMMM/SE/sample_pdb/NH3.pdb Normal file
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@ -0,0 +1,8 @@
ATOM 5 NH3 NH3 A 2 -5.612 0.338 1.176 1.00 -1.14 AMMO N
ATOM 6 HC NH3 A 2 -4.751 0.181 0.654 1.00 0.38 AMMO H
ATOM 7 HC NH3 A 2 -5.594 -0.259 2.043 1.00 0.38 AMMO H
ATOM 8 HC NH3 A 2 -5.450 1.320 1.518 1.00 0.38 AMMO H
ATOM 21 NH3 NH3 A 6 -5.431 -5.410 1.645 1.00 -1.14 AMMO N
ATOM 22 HC NH3 A 6 -4.538 -5.350 1.105 1.00 0.38 AMMO H
ATOM 23 HC NH3 A 6 -5.088 -6.094 2.380 1.00 0.38 AMMO H
ATOM 24 HC NH3 A 6 -6.119 -5.889 1.072 1.00 0.38 AMMO H

1
tests/TEST_DIRS
View file

@ -23,6 +23,7 @@ QS/regtest-gapw
NEB/regtest-2
QS/regtest-nmr-uks-1
QMMM/SE/regtest
QMMM/SE/regtest_2
QS/regtest-gapw-2
Fist/regtest-4
QS/regtest-nmr-1