===== Periodic QMMM embedding of KCl =====
Here is the example file for KCl from the lecture
A full tar ball is here {{exercises:2016_summer_school:qmmm_island.tar.gz | qmmmm_island.tar.gz}}
@SET METHOD = QMMM # FIST all classical treatment # QS all quantum treatment
&GLOBAL
FLUSH_SHOULD_FLUSH
PRINT_LEVEL LOW
PROJECT KCl
RUN_TYPE GEO_OPT
&END GLOBAL
&FORCE_EVAL
METHOD $METHOD
@include QS.inc
@include MM.inc
&QMMM
#this defines the QS cell in the QMMM calc
&CELL
ABC 12.6 15.0 12.6
PERIODIC XZ
&END CELL
ECOUPL GAUSS # use GEEP method
NOCOMPATIBILITY
USE_GEEP_LIB 6 # use GEEP method
&PERIODIC # apply periodic potential
#in this case QM box = MM box in XZ so turn
#off coupling/recoupling of the QM multipole
&MULTIPOLE OFF
&END
&END PERIODIC
#these are just the ionic radii of K Cl
#but should be treated as parameters in general
#fit to some physical property
&MM_KIND K
RADIUS 1.52
&END MM_KIND
&MM_KIND Cl
RADIUS 1.67
&END MM_KIND
#define the model
&QM_KIND K
MM_INDEX 25..32 41..48
&END QM_KIND
&MM_KIND Cl
RADIUS 1.67
&END MM_KIND
#define the model
&QM_KIND K
MM_INDEX 25..32 41..48
&END QM_KIND
&QM_KIND Cl
MM_INDEX 17..24 33..40
&END QM_KIND
&END QMMM
&SUBSYS
#this defines the cell of the whole system
#must be orthorhombic, I think
&CELL
ABC 12.6 100.0 12.6
&END CELL
&TOPOLOGY
COORD_FILE_NAME kcl.xyz
COORD_FILE_FORMAT XYZ
&GENERATE
&ISOLATED_ATOMS
#ignores bonds dihedrals etc in classical part
LIST 1..48
&END
&END
&END
&KIND K
ELEMENT K
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE-q9
&END KIND
&KIND Cl
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE-q7
&END
&END SUBSYS
&END FORCE_EVAL
#should be able to use most motion sections
#analytic stress tensor not available, I think
@include motion.inc
and includes as separate files, using the @include macro, for the QS, MM and motion sections
&DFT
BASIS_SET_FILE_NAME BASIS_MOLOPT
POTENTIAL_FILE_NAME GTH_POTENTIALS
&MGRID
COMMENSURATE
CUTOFF 150
&END MGRID
&QS
EPS_DEFAULT 1.0E-12
&END QS
&SCF
EPS_SCF 1.0E-06
MAX_SCF 26
SCF_GUESS RESTART
&OT
MINIMIZER CG
PRECONDITIONER FULL_SINGLE_INVERSE
ENERGY_GAP 0.001
&END OT
&OUTER_SCF
EPS_SCF 1.0E-05
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&END XC
&PRINT
&MO_CUBES
NLUMO 10
WRITE_CUBE T
&END MO_CUBES
&V_HARTREE_CUBE
STRIDE 2 2 2
&END
&END PRINT
&END DFT
&MM
&FORCEFIELD
&CHARGE
ATOM K
CHARGE 1.0
&END CHARGE
&CHARGE
ATOM Cl
CHARGE -1.0
&END CHARGE
&NONBONDED
&WILLIAMS
atoms K Cl
A [eV] 4117.9
B [angstrom^-1] 3.2808
C [eV*angstrom^6] 0.0
RCUT [angstrom] 3.0
&END WILLIAMS
&WILLIAMS
atoms Cl Cl
A [eV] 1227.2
B [angstrom^-1] 3.1114
C [eV*angstrom^6] 124.0
RCUT [angstrom] 3.0
&END WILLIAMS
&WILLIAMS
atoms K K
A [eV] 3796.9
B [angstrom^-1] 3.84172
C [eV*angstrom^6] 124.0
RCUT [angstrom] 3.0
&END WILLIAMS
&END NONBONDED
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE spme
ALPHA .44
GMAX 40
&END EWALD
&END POISSON
&END MM
&MOTION
&GEO_OPT
OPTIMIZER LBFGS
&END
&CONSTRAINT
&FIXED_ATOMS
LIST 1..16
EXCLUDE_MM .FALSE.
EXCLUDE_QM .TRUE.
&END FIXED_ATOMS
&END CONSTRAINT
&END MOTION
48
Cl 0.00000 15.00000 0.00000
Cl 3.15000 15.00000 3.15000
Cl 0.00000 15.00000 6.30000
Cl 3.15000 15.00000 9.45000
Cl 6.30000 15.00000 0.00000
Cl 9.45000 15.00000 3.15000
Cl 6.30000 15.00000 6.30000
Cl 9.45000 15.00000 9.45000
K 3.15000 15.00000 0.00000
K 0.00000 15.00000 3.15000
K 3.15000 15.00000 6.30000
K 0.00000 15.00000 9.45000
K 9.45000 15.00000 0.00000
K 6.30000 15.00000 3.15000
K 9.45000 15.00000 6.30000
K 6.30000 15.00000 9.45000
Cl 3.15000 18.15000 0.00000
Cl 0.00000 18.15000 3.15000
Cl 3.15000 18.15000 6.30000
Cl 0.00000 18.15000 9.45000
Cl 9.45000 18.15000 0.00000
Cl 6.30000 18.15000 3.15000
Cl 9.45000 18.15000 6.30000
Cl 6.30000 18.15000 9.45000
K 0.00000 18.15000 0.00000
K 3.15000 18.15000 3.15000
K 0.00000 18.15000 6.30000
K 3.15000 18.15000 9.45000
K 6.30000 18.15000 0.00000
K 9.45000 18.15000 3.15000
K 6.30000 18.15000 6.30000
K 9.45000 18.15000 9.45000
Cl 0.00000 21.30000 0.00000
Cl 3.15000 21.30000 3.15000
Cl 0.00000 21.30000 6.30000
Cl 3.15000 21.30000 9.45000
Cl 6.30000 21.30000 0.00000
Cl 9.45000 21.30000 3.15000
Cl 6.30000 21.30000 6.30000
Cl 9.45000 21.30000 9.45000
K 3.15000 21.30000 0.00000
K 0.00000 21.30000 3.15000
K 3.15000 21.30000 6.30000
K 0.00000 21.30000 9.45000
K 9.45000 21.30000 0.00000
K 6.30000 21.30000 3.15000
K 9.45000 21.30000 6.30000
K 6.30000 21.30000 9.45000