exercises:2016_summer_school:qmmm
Periodic QMMM embedding of KCl
Here is the example file for KCl from the lecture
A full tar ball is here qmmmm_island.tar.gz
- input.inp
@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
- QS.inc
&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.inc
&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.inc
&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
- kcl.xyz
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
exercises/2016_summer_school/qmmm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1