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qm2_read_nm_and_alloc.F90
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! <compile=optimized>
#include "copyright.h"
#include "../include/assert.fh"
#include "../include/dprec.fh"
#ifdef SQM
module sqm_qmmm_read_and_alloc
#else
module qmmm_read_and_alloc
#endif
!+++++++++++++++++++++++++++++++++++++++++++++
!This subroutine reads the QMMM namelist
!and also calls allocation routines
!for QMMM based on natom.
!
!Author:
! Ross Walker (SDSC)
!+++++++++++++++++++++++++++++++++++++++++++++
private
public :: read_qmmm_nm_and_alloc
contains
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!+ Reads the qmmm namelist and calls the qmmm memory allocation routines
#ifdef SQM
subroutine read_qmmm_nm_and_alloc( natom_inout, igb, atnum, maxcyc, &
grms_tol, ntpr, ncharge_in, excharge, chgatnum )
#else
subroutine read_qmmm_nm_and_alloc( igb, ih, ix, x, cut, use_pme, ntb, qmstep, &
isabfqm, abfqmcharge, read_file, options)
#endif
use findmask
use constants, only : RETIRED_INPUT_OPTION, MAX_QUANTUM_ATOMS
#ifdef SQM
#ifdef OPENMP
use qmmm_module, only : qmmm_struct, qm2_struct, qmmm_nml, &
validate_qm_atoms, qmsort, &
allocate_qmmm, get_atomic_number, &
qmmm_opnq, qmmm_input_options, qmmm_omp
#else
use qmmm_module, only : qmmm_struct, qm2_struct, qmmm_nml, &
validate_qm_atoms, qmsort, &
allocate_qmmm, get_atomic_number, &
qmmm_opnq, qmmm_input_options
#endif
#else
#ifdef OPENMP
use qmmm_module, only : qmmm_struct, qm2_struct, qmmm_nml, &
validate_qm_atoms, qmsort, &
allocate_qmmm, get_atomic_number, qmmm_div, &
qmmm_opnq, qmmm_vsolv, qmmm_input_options, &
qmmm_omp
#else
use qmmm_module, only : qmmm_struct, qm2_struct, qmmm_nml, &
validate_qm_atoms, qmsort, &
allocate_qmmm, get_atomic_number, qmmm_div, &
qmmm_opnq, qmmm_vsolv, qmmm_input_options
#endif
use qmmm_vsolv_module, only : read_vsolv_nml
#endif
use qmmm_qmtheorymodule
use ElementOrbitalIndex, only : numberElements
use ParameterReader, only : ReadParameterFile
implicit none
!Passed in
integer :: igb !Value of igb from cntrl namelist
#ifdef SQM
integer use_pme, ntb
integer, intent(inout) :: natom_inout
integer, intent(in) :: atnum(*)
integer, intent(out) :: maxcyc, ntpr
_REAL_, intent(out) :: grms_tol
_REAL_, intent(in) :: excharge(*)
integer, intent(in) :: chgatnum(*)
integer, intent(in) :: ncharge_in
#else
character(len=4) ih(*)
integer, intent(in) :: ix(*)
_REAL_, intent(in) :: x(*)
_REAL_, intent(in) :: cut !MM-MM cutoff in angstroms
integer, intent(in) :: use_pme, ntb
integer, intent(in) :: qmstep
integer, intent(in) :: isabfqm(*)
integer, intent(in) :: abfqmcharge
logical, intent(in) :: read_file ! because the present intrinsic on "options" does not seem to work
type(qmmm_input_options), intent(in), optional :: options
#endif
!local
_REAL_ :: qmcut ! local copied to qmmm_nml%qmcut - specified cutoff to use for QM-MM electrostatics.
! Default = same as regular MM cutoff.
_REAL_ :: lnk_dis ! Distance from the QM atom to place link atom.
!A value of <0.0 means the link atom gets placed on the MM link pair atom's coordinates
!on every MD step.
_REAL_ :: scfconv ! local copied to qmmm_nml%scfconv - Convergence criteria for SCF routine. Default = 1.0D-8.
! Minimum (tightest criteria) = 1.0D-16
!+TJG 01/26/2010
_REAL_ :: errconv ! Convergence criteria for maximum value in the error matrix FP-PF
integer :: ndiis_matrices ! Maximum number of matrices used in a diis extrapolation
integer :: ndiis_attempts ! The initial number of diis tokens... the number of iterations
! that diis extrapolations will be attempted before giving up on diis
!-TJG 01/26/2010
_REAL_ :: pseudo_diag_criteria !Criteria - maximum change in density matrix between successive SCF iterations
!in which to allow pseudo diagonalisation. Default = 0.05.
integer :: lnk_atomic_no !Atomic number of link atom
integer :: lnk_method !controls how QM-MM valence terms are dealt with.
integer :: qmgb ! local copied to qmmm_nml%qmgb - flag for type of GB do with QM region
integer :: qmtheory ! deprecated flag for level of theory to use for QM region
integer :: qmcharge ! local copied to qmmm_nml%qmcharge - value of charge on QM system
integer :: corecharge
integer :: buffercharge
integer :: spin ! local copied to qmmm_nml%spin - spin state of system
integer :: i,j ! temporary counter for local loops
integer :: ifind
integer :: qmqmdx ! local copied to qmmm_nml%qmqm_analyt - 1 = analytical, 2 = numerical QM-QM derivatives in qm2
integer :: verbosity ! local copied to qmmm_nml%verbosity - Controls amount of info about QM part of calc that is printed (0=Def)
integer :: tight_p_conv ! local copied to qmmm_nml%tight_p_conv - Controls convergence of density matrix. 0 (Def) = 0.05*sqrt(SCFCRT)
! 1 = Converged both Energy and Density to SCFCONV
integer :: printcharges !Local copied to qmmm_nml%printcharges as a logical. 1 = true - print mulliken and cm1a and cm2a charges
!on every step. 0 = false = don't print charges. Default = 0 (.false.)
integer :: printdipole !Local copied to qmmm_nml%printdipole as an integer 1 = QM dipole moment, 2 = QM + MM dipole moment, (0=Def)
integer :: print_eigenvalues !Local copied to qmmm_nml%print_eigenvalues, 0 = no printing, 1 = at end of run (default), 2 = each SCF cycle, 3 = each SCF iteration
integer :: peptide_corr !Local copied to the logical qmmm_nml%peptide_corr
!Add MM correction to peptide linkages 0 = No (Default), 1 = Yes.
integer :: itrmax !Local copied to qmmm_nml%itrmax - Maximum number of scf cycles to run
!before assuming convergence has failed (default = 1000)
integer :: printbondorders !Local copied to qmmm_nml%printbondorders as a logical.
! 1 = true - print bondorders at the end of the
! calculation. 0 = false = dont print bondorders. Default = 0 (.false.)
integer :: qmshake !Local copied to qmmm_nml%qmshake - shake QM atoms if ntc>1?
integer :: qmmmrij_incore !Flag to store rij between qm-mm pairs and related equations in memory.
!1 (default) = store in memory. 0 = calc on fly.
integer :: qmqm_erep_incore !Flag to store QM-QM 1 electron repulsion integrals in memory or to calculate
!them on the fly. Only available with QM-QM analytical derivatives.
!1 (default) = store in memory. 0 = calc on fly.
integer :: pseudo_diag !Whether to allow pseudo diagonalisations to be done when possible in SCF.
!0 (default) = Always do full diagonalisations.
!1 = do pseudo diagonalisations when possible.
integer :: qm_ewald !0 (default) do only regular QM-MM interaction in periodic calculations.
!1 do ewald based periodic QM-MM interactions.
!2 do ewald based periodic QM-MM but with the QM image charges
! fixed at the previous steps mulliken charges during the SCF.
integer :: qm_pme !0 use regular Ewald for doing QM-MM interactions when qm_ewald>0.
!1 (default) use PME to do the reciprocal sum.
integer :: kmaxqx, kmaxqy, kmaxqz !Maximum K space vectors
integer :: ksqmaxq !Maximum K squared values for spherical cutoff in k space.
_REAL_ :: kappa ! the ewald coefficient for QM region ewald calculations
integer :: writepdb
integer :: qmmm_int !QM-MM interaction method
integer :: adjust_q
integer :: diag_routine !Controls diagonalization routine to use in SCF.
#ifdef OPENMP
integer :: qmmm_omp_max_threads !Maximum number of openmp threads to use for parallel QMMM routines
#endif
integer :: density_predict !Controls prediction of density matrix for next SCF step.
integer :: fock_predict !Controls prediction of Fock matrix for next SCF step.
integer :: vsolv ! = 0 by default, = 1 for simple vsolv QM/MM, = 2 for adaptive QM/MM with vsolv
_REAL_ :: fockp_d1 !prefactor for fock matrix prediction.
_REAL_ :: fockp_d2 !prefactor for fock matrix prediction.
_REAL_ :: fockp_d3 !prefactor for fock matrix prediction.
_REAL_ :: fockp_d4 !prefactor for fock matrix prediction.
_REAL_ :: damp ! AWG SCF damping
_REAL_ :: vshift ! AWG SCF level shift parameter
logical :: mdin_qmmm=.false.
logical :: do_not_print
integer :: idc
integer :: divpb
!! (GMS)
_REAL_ :: chg_lambda ! Charge scaling factor for free energy calculation
!! DFTB options
integer :: dftb_maxiter ! Max # of iterations before resetting Broyden (default: 70 ) ==> qmmm_nml%dftb_maxiter
integer :: dftb_disper ! Use dispersion? (default: 0 = false) ==> qmmm_nml%dftb_disper
integer :: dftb_chg ! DFTB CM3 charges (default: 0 = Mulliken, 1 = CM3) ==> qmmm_nml%dftb_chg
_REAL_ :: dftb_telec ! Electronic temperature, in Kelvins. (Default = 0.0K) ==> qmmm_nml%dftb_telec
_REAL_ :: dftb_telec_step ! Telec step size for convergence accelerator (Default = 0.0K) ==> qmmm_nml%dftb_telec_step
character(Len=256) :: dftb_3rd_order ! 3rd order SCC-DFTB (default: 'NONE'== No third order)
! 'PA' == Do 3rd order, Proton Affinities parameterization
! 'PR' == Phosphate reactions parameterization
! 'READ' == read the parameters from a user-specified file (TO IMPLEMENT)
character(len=256) :: dftb_slko_path
_REAL_ :: r_switch_lo !Lower bound of the QM/MM switching function
_REAL_ :: r_switch_hi !Upper bound of the QM/MM switching function
integer :: qmmm_switch !0 Turn off QM/MM switching function
!1 Turn on QM/MM switching function
integer :: abfqmmm
integer :: hot_spot
_REAL_ :: r_core_in
_REAL_ :: r_core_out
_REAL_ :: r_qm_in
_REAL_ :: r_qm_out
_REAL_ :: r_buffer_in
_REAL_ :: r_buffer_out
character(len=256) :: cut_bond_list_file
character(len=256) :: oxidation_number_list_file
integer :: mom_cons_type
integer :: mom_cons_region
integer :: fix_atom_list
integer :: solvent_atom_number
integer :: selection_type
integer :: center_type
integer :: initial_selection_type
integer :: max_bonds_per_atom
integer :: n_max_recursive
_REAL_ :: min_heavy_mass
_REAL_ :: gamma_ln_qm
character(len=256) :: read_idrst_file
character(len=256) :: write_idrst_file
integer :: ntwidrst
character(len=256) :: pdb_file
integer :: ntwpdb
#include "../include/memory.h"
!Apparently you can't use a pointer in a namelist :-( Therefore
!we need a local scratch array that will be big enough that
!the iqmatoms list never exceeds it
integer :: iqmatoms( MAX_QUANTUM_ATOMS )
integer :: core_iqmatoms( MAX_QUANTUM_ATOMS )
integer :: buffer_iqmatoms( MAX_QUANTUM_ATOMS )
character(len=8192) :: qmmask
character(len=8192) :: coremask
character(len=8192) :: buffermask
integer :: qm_subsetatoms( natom )
integer :: core_subsetatoms( natom )
integer :: buffer_subsetatoms( natom )
integer :: center_subsetatoms( natom )
character(len=8192) :: ext_qmmask_subset
character(len=8192) :: ext_coremask_subset
character(len=8192) :: ext_buffermask_subset
character(len=8192) :: centermask
character(len=12) :: qm_theory
!Options=PM3,AM1,MNDO,PDDG-PM3,PM3PDDG,PDDG-MNDO,PDDGMNDO,
! PM3-CARB1,PM3CARB1,DFTB,SCC-DFTB,RM1,PM6,PM3-ZnB,PM3-MAIS
! EXTERNAL (for external programs like ADF/GAMESS/TeraChem)
#ifndef SQM
integer, dimension(:), pointer :: isqm
#endif
integer :: ier=0
character(len=80) :: parameter_file
logical :: qxd
namelist /qmmm/ qmcut, iqmatoms,qmmask,qmgb,qm_theory, qmtheory, &
qmcharge, qmqmdx, verbosity, tight_p_conv, scfconv, &
errconv,ndiis_matrices,ndiis_attempts, &
parameter_file, qxd,&
printcharges, printdipole, print_eigenvalues, peptide_corr, itrmax, qmshake, &
qmqm_erep_incore, qmmmrij_incore, &
lnk_dis, lnk_atomic_no, lnk_method, spin, pseudo_diag, &
pseudo_diag_criteria, &
qm_ewald, qm_pme, kmaxqx, kmaxqy, kmaxqz, ksqmaxq, kappa, &
writepdb, qmmm_int, adjust_q, diag_routine, &
density_predict, fock_predict, &
fockp_d1, fockp_d2, fockp_d3, fockp_d4, idc, divpb, &
dftb_maxiter, dftb_disper, dftb_3rd_order, dftb_slko_path, dftb_chg, &
dftb_telec, dftb_telec_step, printbondorders, &
qmmm_switch, r_switch_lo, r_switch_hi, damp, vshift, &
#ifdef OPENMP
qmmm_omp_max_threads, &
#endif
#ifdef SQM
maxcyc, ntpr, grms_tol, &
#endif
chg_lambda, vsolv, &
abfqmmm, r_core_in, r_core_out, r_buffer_in, r_buffer_out, &
r_qm_in, r_qm_out, coremask, buffermask, &
cut_bond_list_file, oxidation_number_list_file, &
mom_cons_type, mom_cons_region, &
fix_atom_list, solvent_atom_number, &
selection_type, center_type, initial_selection_type, &
corecharge, buffercharge, &
max_bonds_per_atom, n_max_recursive, min_heavy_mass, &
gamma_ln_qm, &
read_idrst_file, ntwidrst, write_idrst_file, ntwpdb, pdb_file, &
ext_qmmask_subset, ext_coremask_subset, ext_buffermask_subset, &
centermask, hot_spot
!Setup defaults
#ifdef SQM
qmcut = 9999.d0
use_pme = 0
ntb = 0
maxcyc = 9999
grms_tol = 0.02
ntpr=10
do_not_print = .false.
#else
do_not_print = .not. read_file
qmcut = cut
#endif
lnk_dis=1.09d0 !Methyl C-H distance
lnk_atomic_no=1 !Hydrogen
lnk_method=1 !treat MMLink as being MM atom.
qmgb = 2 !Gets set to zero if igb==6 or igb==0.
qm_theory = ''
qmtheory = RETIRED_INPUT_OPTION
qmcharge = 0
corecharge = 0
buffercharge = 0
spin = 1
qmqmdx = 1
verbosity = 0
parameter_file=''
qxd=.false.
!+TJG 01/26/2010
#ifdef SQM
! defaults for stand-alone (geom. opt.) code:
! dac: for now, just use the same values as in the non-stand-alone
! code, but these should be updated once we figure out the best
! values for geometry optimization
tight_p_conv = 0
scfconv = 1.0D-8
errconv = 1.0d-1
ndiis_matrices = 6
ndiis_attempts = 0
#else
! defaults for MD is off:
tight_p_conv = 0
scfconv = 1.0D-8
errconv = 1.0D-1
ndiis_matrices = 6
ndiis_attempts = 0
#endif
!-TJG 01/26/2010
printcharges = 0
printbondorders = 0
printdipole = 0
print_eigenvalues = 1
peptide_corr = 0
itrmax = 1000
qmshake = 1
qmmask=''
coremask=''
buffermask=''
iqmatoms(1:MAX_QUANTUM_ATOMS) = 0
core_iqmatoms(1:MAX_QUANTUM_ATOMS) = 0
buffer_iqmatoms(1:MAX_QUANTUM_ATOMS) = 0
ext_qmmask_subset=''
ext_coremask_subset=''
ext_buffermask_subset=''
centermask=''
qm_subsetatoms(1:natom) = 0
core_subsetatoms(1:natom) = 0
buffer_subsetatoms(1:natom) = 0
center_subsetatoms(1:natom) = 0
qmmmrij_incore = 1
qmqm_erep_incore = 1
pseudo_diag = 1
pseudo_diag_criteria = 0.05d0
qm_ewald=1 !Default is to do QMEwald, with varying charges, if ntb=0 or use_pme=0 then this will get turned off
qm_pme = 1 !use pme for QM-MM
kmaxqx=8; kmaxqy=8; kmaxqz=8 !Maximum K space vectors
kappa=-1.0
ksqmaxq=100 !Maximum K squared values for spherical cutoff in k space.
writepdb = 0 !Set to 1 to write a pdb on the first step with just the QM region in it.
qmmm_int = 1 !Default, do full interaction without extra Gaussian terms for PM3 / AM1 etc.
adjust_q = 2 !Default adjust q over all atoms.
diag_routine = 0 !Select optimum diag routine based on timings
#ifdef OPENMP
qmmm_omp_max_threads = 1 !Use just 1 openmp thread by default.
#endif
density_predict = 0 !Use density matrix from previous MD step.
fock_predict = 0 !Do not attempt to predict the Fock matrix.
fockp_d1 = 2.4d0
fockp_d2 = -1.2d0
fockp_d3 = -0.8d0
fockp_d4 = 0.6d0
damp = 1.0
vshift = 0.0
idc = 0
divpb = 0
vsolv = 0 ! by default do not use simple vsolv QM/MM or adaptive QM/MM based on vsolv
qmmm_switch = 0 !Use QM/MM switching function
r_switch_hi = qmcut !Set the default value to be equal to qmcut
r_switch_lo = r_switch_hi - 2.0D0 !Set the default value to be 2 Angstrom shorter than r_switch_hi
!DFTB
dftb_maxiter = 70
dftb_disper = 0
dftb_chg = 0
dftb_telec = 0.0d0
dftb_telec_step = 0.0d0
chg_lambda = 1.0d0
dftb_3rd_order = 'NONE'
dftb_slko_path = ''
!ABFQMMM
abfqmmm = 0
hot_spot = 0
r_core_in = 0
r_core_out = 0
r_qm_in = 0
r_qm_out = 0
r_buffer_in = 0
r_buffer_out = 0
cut_bond_list_file = ''
oxidation_number_list_file = ''
mom_cons_type = 1
mom_cons_region = 1
fix_atom_list = 0
solvent_atom_number = 3
selection_type = 1
center_type = 1
initial_selection_type = 0
max_bonds_per_atom = 4
n_max_recursive = 10000
min_heavy_mass = 4.0
gamma_ln_qm = 0.0d0
read_idrst_file = ''
write_idrst_file = 'abfqmmm.idrst'
ntwidrst = 0
pdb_file = 'abfqmmm.pdb'
ntwpdb = 0
!Read qmmm namelist
#ifndef SQM
if (.not. read_file) then
! If we were passed input options, use those instead of trying to read
! them from a file
qmcut = options%qmcut
lnk_dis = options%lnk_dis
lnk_atomic_no = options%lnk_atomic_no
lnk_method = options%lnk_method
qmgb = options%qmgb
qm_theory = options%qm_theory
qmcharge = options%qmcharge
corecharge = options%corecharge
buffercharge = options%buffercharge
spin = options%spin
qmqmdx = options%qmqmdx
verbosity = options%verbosity
scfconv = options%scfconv
errconv = options%errconv
ndiis_matrices = options%ndiis_matrices
ndiis_attempts = options%ndiis_attempts
printcharges = options%printcharges
printbondorders = options%printbondorders
printdipole = options%printdipole
print_eigenvalues = options%print_eigenvalues
peptide_corr = options%peptide_corr
itrmax = options%itrmax
qmshake = options%qmshake
qmmask = options%qmmask
coremask = options%coremask
buffermask = options%buffermask
iqmatoms(1:MAX_QUANTUM_ATOMS) = options%iqmatoms(1:MAX_QUANTUM_ATOMS)
core_iqmatoms(1:MAX_QUANTUM_ATOMS) = options%core_iqmatoms(1:MAX_QUANTUM_ATOMS)
buffer_iqmatoms(1:MAX_QUANTUM_ATOMS) = options%buffer_iqmatoms(1:MAX_QUANTUM_ATOMS)
centermask = options%centermask
qmmmrij_incore = options%qmmmrij_incore
qmqm_erep_incore = options%qmqm_erep_incore
pseudo_diag = options%pseudo_diag
pseudo_diag_criteria = options%pseudo_diag_criteria
qm_ewald = options%qm_ewald
qm_pme = options%qm_pme
kmaxqx = options%kmaxqx
kmaxqy = options%kmaxqy
kmaxqz = options%kmaxqz
kappa = options%kappa
ksqmaxq = options%ksqmaxq
qmmm_int = options%qmmm_int
adjust_q = options%adjust_q
diag_routine = options%diag_routine
density_predict = options%density_predict
fock_predict = options%fock_predict
fockp_d1 = options%fockp_d1
fockp_d2 = options%fockp_d2
fockp_d3 = options%fockp_d3
fockp_d4 = options%fockp_d4
damp = options%damp
vshift = options%vshift
vsolv = options%vsolv
qmmm_switch = options%qmmm_switch
r_switch_hi = options%r_switch_hi
r_switch_lo = options%r_switch_lo
dftb_maxiter = options%dftb_maxiter
dftb_disper = options%dftb_disper
dftb_chg = options%dftb_chg
dftb_telec = options%dftb_telec
dftb_telec_step = options%dftb_telec_step
dftb_3rd_order = options%dftb_3rd_order
dftb_slko_path = options%dftb_slko_path
abfqmmm = options%abfqmmm
hot_spot = options%hot_spot
min_heavy_mass = options%min_heavy_mass
tight_p_conv = options%tight_p_conv
else
#endif
rewind 5
call nmlsrc('qmmm',5,ifind)
if (ifind /= 0) mdin_qmmm=.true.
!Read qmmm namelist
rewind 5
if ( mdin_qmmm ) then
read(5,nml=qmmm)
else
write(6, '(1x,a,/)') 'Could not find qmmm namelist'
call mexit(6,1)
endif
#ifndef SQM
end if
#endif
call CheckRetiredQmTheoryInputOption(qmtheory)
call set(qmmm_nml%qmtheory, qm_theory)
! Read-in the user-defined parameter file (TL -- Rutgers, 2011)
call ReadParameterFile(parameter_file)
! turn on OPNQ if necessary
qmmm_opnq%useOPNQ=qxd
#ifdef SQM
! Disable EXTERN in SQM since
! it does not make sense for SQM to be calling the external ADF interface.
if (qmmm_nml%qmtheory%EXTERN) then
call sander_bomb('read_qmmm_namelist','External interface is not supported in SQM.', &
'(qm_theory = ''EXTERN'')')
end if
if (qmmm_nml%qmtheory%SEBOMD) then
call sander_bomb('read_qmmm_namelist','SEBOMD interface is not supported in SQM.', &
'(qm_theory = ''SEBOMD'')')
end if
if (ncharge_in > 0) then ! we have external charge
if (maxcyc > 0) then
! external charge calculation is not supported in gradient minimization
call sander_bomb('read_qmmm_namelist','maxcyc > 0 but external charge found.', &
'external charge calculation is for single point energy calculations only.')
end if
natom = natom_inout + ncharge_in
qmmm_struct%nquant = natom_inout
qmmm_struct%nlink = 0
qmmm_struct%nquant_nlink = natom_inout
qmmm_struct%qm_mm_pairs = ncharge_in
do i=1,natom_inout
iqmatoms(i) = i
end do
!update natom_inout with the number of external charges
natom_inout = natom
else
natom = natom_inout
qmmm_struct%nquant = natom
qmmm_struct%nlink = 0
qmmm_struct%nquant_nlink = natom
do i=1,natom
iqmatoms(i) = i
end do
end if
!natom = natom_in
!qmmm_struct%nquant = natom
!qmmm_struct%nlink = 0
!qmmm_struct%nquant_nlink = natom
!do i=1,natom
! iqmatoms(i) = i
!end do
#else
if (qmmm_nml%qmtheory%SEBOMD) then
qmmm_struct%nquant = 0
else
if( (qmmask /= '') .or. (coremask /= '') ) then ! get the quantum atoms from the mask
if(abfqmmm == 1 .and. qmmm_struct%abfqmmm /= 1 &
.and. .not. do_not_print) then
write(6,'(a)') ''
write(6,'(/80("-")/" ADAPTIVE BUFFERED FORCE QM/MM",/80("-")/)')
if(hot_spot == 1) then
write(6,'(a)') ''
write(6,'(/80("-")/" HOT SPOT IS ACTIVE ",/80("-")/)')
end if
end if
if(qmmm_struct%abfqmmm /= 1 .and. .not. do_not_print) then
if(abfqmmm == 1) then
write(6,'(a)') ''
write(6,'(a)') '------------------------'
write(6,'(a)') 'Specification of regions'
write(6,'(a)') '------------------------'
write(6,'(a)') ''
write(6,'(a)') 'QM atoms:'
write(6,'(a)') '---------'
write(6,'(a)') ''
if(qmmask /= '') then
write(6,'(a)') 'INFO: loading the quantum atoms as groups'
else
write(6,'(a)') 'INFO: quantum atoms for adaptive QM/MM are not defined'
write(6,'(a)') 'INFO: core atoms will be used in reduced calculation'
end if
else
write(6,'(a)') 'LOADING THE QUANTUM ATOMS AS GROUPS'
end if
end if
allocate(isqm( natom ), stat=ier)
REQUIRE(ier==0)
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), qmmask, isqm )
if(abfqmmm == 1 .and. qmstep == 0) then
if(r_core_in == 0) then
qmmm_struct%r_core_in = r_core_out
else
qmmm_struct%r_core_in = r_core_in
end if
if(r_core_out <= r_core_in) then
qmmm_struct%r_core_out = r_core_in
else
qmmm_struct%r_core_out = r_core_out
end if
if(r_qm_in == 0) then
qmmm_struct%r_qm_in = r_qm_out
else
qmmm_struct%r_qm_in = r_qm_in
end if
if(r_qm_out <= r_qm_in) then
qmmm_struct%r_qm_out = r_qm_in
else
qmmm_struct%r_qm_out = r_qm_out
end if
if(r_buffer_in == 0) then
qmmm_struct%r_buffer_in = r_buffer_out
else
qmmm_struct%r_buffer_in = r_buffer_in
end if
if(r_buffer_out <= r_buffer_in) then
qmmm_struct%r_buffer_out = r_buffer_in
else
qmmm_struct%r_buffer_out = r_buffer_out
end if
qmmm_struct%cut_bond_list_file = cut_bond_list_file
qmmm_struct%oxidation_number_list_file = oxidation_number_list_file
qmmm_struct%mom_cons_type = mom_cons_type
qmmm_struct%mom_cons_region = mom_cons_region
qmmm_struct%fix_atom_list = fix_atom_list
qmmm_struct%solvent_atom_number = solvent_atom_number
qmmm_struct%selection_type = selection_type
qmmm_struct%center_type = center_type
qmmm_struct%initial_selection_type = initial_selection_type
qmmm_struct%max_bonds_per_atom = max_bonds_per_atom
qmmm_struct%n_max_recursive = n_max_recursive
qmmm_struct%min_heavy_mass = min_heavy_mass
qmmm_struct%gamma_ln_qm = gamma_ln_qm
qmmm_struct%read_idrst_file = read_idrst_file
qmmm_struct%write_idrst_file = write_idrst_file
qmmm_struct%ntwidrst = ntwidrst
qmmm_struct%pdb_file = pdb_file
qmmm_struct%ntwpdb = ntwpdb
end if
if (qmstep /= 0) isqm(1:natom) = isabfqm(1:natom)
qmmm_struct%nquant = sum(isqm(1:natom))
if( (qmmm_struct%abfqmmm /= 1) .and. (qmmask /= '') .and. &
.not. do_not_print) then
write(6,'(a,a,a,i5,a)') ' Mask ', qmmask(1:len_trim(qmmask)), &
' matches ',qmmm_struct%nquant,' atoms'
end if
if(abfqmmm == 1 .and. qmmm_struct%abfqmmm /= 1) then
if (.not. do_not_print) &
write(6,'(a,i2)') ' qm-charge: ', qmcharge
qmmm_nml%qmcharge = qmcharge
end if
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
iqmatoms(j) = i
end if
end do
if(abfqmmm == 1 .and. qmmm_struct%abfqmmm /= 1) then
if( ext_qmmask_subset /= '' ) then
if (.not. do_not_print) then
write(6,'(a)') 'INFO: qm subset was specified for the extended qm region'
write(6,'(a)') 'INFO: loading qm subset atoms'
end if
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), ext_qmmask_subset, isqm )
qmmm_struct%qm_nsubset = sum(isqm(1:natom))
if (.not. do_not_print) &
write(6,'(a,a,a,i5,a)') ' Mask ', trim(ext_qmmask_subset), &
' matches ',qmmm_struct%qm_nsubset,' atoms'
if(qmmm_struct%qm_nsubset == 0 .and. .not. do_not_print) then
write(6,'(a)') 'INFO: qm subset is an empty set => &
&all atoms can be in extended qm region'
end if
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
qm_subsetatoms(j) = i
end if
end do
else
if (.not. do_not_print) &
write(6,'(a)') 'INFO: qm subset was not specified for the &
&extended qm region'
qmmm_struct%qm_nsubset = 0
end if
if (.not. do_not_print) then
write(6,'(a)') ''
write(6,'(a)') 'CORE atoms:'
write(6,'(a)') '-----------'
write(6,'(a)') ''
end if
if( coremask /= '' ) then
if (.not. do_not_print) &
write(6,'(a)') 'INFO: loading the core atoms for adaptive QM/MM'
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), coremask, isqm )
qmmm_struct%core_nquant = sum(isqm(1:natom))
if (.not. do_not_print) &
write(6,'(3a,i5,a)') ' Mask ', trim(coremask), ' matches ',&
qmmm_struct%core_nquant,' atoms'
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
core_iqmatoms(j) = i
end if
end do
else
if (.not. do_not_print) then
write(6,'(a)') 'INFO: core atoms for adaptive QM/MM are not defined'
write(6,'(a)') 'INFO: reduced calculation will be full MM calculation'
write(6,'(a)') 'INFO: using FF parameters from topology file'
end if
qmmm_struct%core_nquant = 0
end if
write(6,'(a,i2)') ' core-charge: ', corecharge
qmmm_nml%corecharge = corecharge
if( ext_coremask_subset /= '' ) then
if (.not. do_not_print) then
write(6,'(a)') 'INFO: core subset was specified for the extended core region'
write(6,'(a)') 'INFO: loading core subset atoms'
end if
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), ext_coremask_subset, isqm )
qmmm_struct%core_nsubset = sum(isqm(1:natom))
if (.not. do_not_print) &
write(6,'(3a,i5,a)') ' Mask ', trim(ext_coremask_subset), &
' matches ',qmmm_struct%core_nsubset,' atoms'
if(qmmm_struct%core_nsubset == 0 .and. .not. do_not_print) then
write(6,'(a)') 'INFO: core subset is an empty set => &
&all atoms can be in extended core region'
end if
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
core_subsetatoms(j) = i
end if
end do
else
if (.not. do_not_print) &
write(6,'(a)') 'INFO: core subset was not specified for the &
&extended core region'
qmmm_struct%core_nsubset = 0
end if
if (.not. do_not_print) then
write(6,'(a)') ''
write(6,'(a)') 'BUFFER atoms:'
write(6,'(a)') '-------------'
write(6,'(a)') ''
end if
if( buffermask /= '' ) then
if (.not. do_not_print) &
write(6,'(a)')'INFO: loading the buffer atoms for adaptive QM/MM'
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), buffermask, isqm )
qmmm_struct%buffer_nquant = sum(isqm(1:natom))
if (.not. do_not_print) &
write(6,'(3a,i5,a)') ' Mask ', trim(buffermask), &
' matches ',qmmm_struct%buffer_nquant,' atoms'
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
buffer_iqmatoms(j) = i
end if
end do
else
if (.not. do_not_print) &
write(6,'(a)') 'INFO: buffer atoms for adaptive QM/MM are not defined'
if(qmmm_struct%r_buffer_out == 0 .and. .not. do_not_print) then
write(6,'(a)') 'WARNING: buffer radius was set to zero and no buffer atoms were given'
write(6,'(a)') ' this may lead to unconverged QM forces'
end if
qmmm_struct%buffer_nquant = 0
end if
if (.not. do_not_print) &
write(6,'(a,i2)') ' buffer-charge: ', buffercharge
qmmm_nml%buffercharge = buffercharge
if( ext_buffermask_subset /= '' ) then
if (.not. do_not_print) then
write(6,'(a)') 'INFO: buffer subset was specified for the &
&extended buffer region'
write(6,'(a)') 'INFO: loading buffer subset atoms'
end if
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), ext_buffermask_subset, isqm )
qmmm_struct%buffer_nsubset = sum(isqm(1:natom))
if (.not. do_not_print) &
write(6,'(3a,i5,a)') ' Mask ', trim(ext_buffermask_subset), &
' matches ',qmmm_struct%buffer_nsubset,' atoms'
if(qmmm_struct%buffer_nsubset == 0 .and. .not. do_not_print) then
write(6,'(a)') 'INFO: buffer subset is an empty set => all atoms can be in extended buffer region'
end if
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
buffer_subsetatoms(j) = i
end if
end do
else
if (.not. do_not_print) &
write(6,'(a)') 'INFO: buffer subset was not specified for &
&the extended buffer region'
qmmm_struct%buffer_nsubset = 0
end if
if (.not. do_not_print) then
write(6,'(a)') ''
write(6,'(a)') 'CENTER atoms:'
write(6,'(a)') '-------------'
write(6,'(a)') ''
end if
if(centermask /= '') then
if (.not. do_not_print) then
write(6,'(a)') 'INFO: center atom list was specified'
write(6,'(a)') 'INFO: loading the center atoms for adaptive QM/MM'
end if
call atommask(natom, nres, 0, ih(m04), ih(m06), &
ix(i02), ih(m02), x(lcrd), centermask, isqm )
qmmm_struct%center_nsubset = sum(isqm(1:natom))
if (.not. do_not_print) &
write(6,'(3a,i5,a)') ' Mask ', trim(centermask), &
' matches ',qmmm_struct%center_nsubset,' atoms'
if(qmmm_struct%center_nsubset == 0 .and. .not. do_not_print) then
if(qmmm_struct%core_nquant > 0) then
write(6,'(a)') 'INFO: center atom list is an empty set => &
¢er atom list = user defined core list'
else
write(6,'(a)') 'INFO: center atom list is an empty set => &
¢er atom list = user defined qm list'
end if
end if
j = 0
do i=1,natom
if( isqm(i)>0 ) then
j = j+1
center_subsetatoms(j) = i
end if
end do
else
if(qmmm_struct%core_nquant > 0 .and. .not. do_not_print) then
write(6,'(a)') 'INFO: center atom list is not defined => &
¢er atom list = user defined core list'
else if (.not. do_not_print) then
write(6,'(a)') 'INFO: center atom list is not defined => &
¢er atom list = user defined qm list'
end if
qmmm_struct%center_nsubset = 0
end if
end if ! (qmmask /= '' .or. (coremask /= '')
if(abfqmmm == 1) qmmm_struct%abfqmmm = 1
if(abfqmmm == 1 .and. hot_spot == 1) then
qmmm_struct%hot_spot = 1
end if
deallocate(isqm, stat=ier)
REQUIRE(ier==0)
else ! get the count from the input iqmatoms array
do i = 1,MAX_QUANTUM_ATOMS
if( iqmatoms(i) == 0 ) exit
end do
qmmm_struct%nquant = i-1
end if
end if ! (qmmm_nml%qmtheory%SEBOMD)
if(abfqmmm == 1) then
if(qmstep == 0) then
if(qmmm_struct%nquant > 0) then
call validate_qm_atoms(iqmatoms,qmmm_struct%nquant,natom)
call int_legal_range('QMMM: (number of qm atoms) ', &
qmmm_struct%nquant, 1, MAX_QUANTUM_ATOMS )
call qmsort(iqmatoms)
allocate(qmmm_struct%iqmatoms(qmmm_struct%nquant))
do i = 1, qmmm_struct%nquant
qmmm_struct%iqmatoms(i)=iqmatoms(i)
end do
end if
if(qmmm_struct%qm_nsubset > 0) then
call validate_qm_atoms(qm_subsetatoms,qmmm_struct%qm_nsubset,natom)
call int_legal_range('QMMM: (number of qm subset atoms) ', &
qmmm_struct%qm_nsubset, 1, natom )
call qmsort(qm_subsetatoms)
allocate(qmmm_struct%qm_subsetatoms(qmmm_struct%qm_nsubset))
do i = 1, qmmm_struct%qm_nsubset
qmmm_struct%qm_subsetatoms(i)=qm_subsetatoms(i)
end do
end if
if(qmmm_struct%core_nquant > 0) then
call validate_qm_atoms(core_iqmatoms,qmmm_struct%core_nquant,natom)
call int_legal_range('QMMM: (number of core atoms) ', &
qmmm_struct%core_nquant, 1, max_quantum_atoms )
allocate(qmmm_struct%core_iqmatoms(qmmm_struct%core_nquant))