exercises:2016_summer_school:qmmm
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Periodic QMMM embedding of KCl
Here is the example file for KCl from the lecture
@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
&GEO_OPT OPTIMIZER LBFGS &END &CONSTRAINT &FIXED_ATOMS LIST 1..16 EXCLUDE_MM .FALSE. EXCLUDE_QM .TRUE. &END FIXED_ATOMS &END CONSTRAINT &END MOTION
exercises/2016_summer_school/qmmm.1472113740.txt.gz · Last modified: 2020/08/21 10:15 (external edit)