exercises:2016_summer_school:qmmm
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===== Periodic QMMM embedding of KCl ===== | ===== Periodic QMMM embedding of KCl ===== | ||
- | * {{http://www.cp2k.org/_media/exercises: | + | Here is the example file for KCl from the lecture |
+ | |||
+ | A full tar ball is here {{exercises:2016_summer_school: | ||
+ | |||
+ | <code cp2k input.inp> | ||
+ | @SET METHOD = QMMM # FIST all classical treatment # QS all quantum treatment | ||
+ | |||
+ | & | ||
+ | FLUSH_SHOULD_FLUSH | ||
+ | PRINT_LEVEL LOW | ||
+ | PROJECT KCl | ||
+ | RUN_TYPE GEO_OPT | ||
+ | &END GLOBAL | ||
+ | |||
+ | & | ||
+ | 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 | ||
+ | & | ||
+ | #in this case QM box = MM box in XZ so turn | ||
+ | #off coupling/recoupling of the QM multipole | ||
+ | & | ||
+ | &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 | ||
+ | & | ||
+ | RADIUS 1.52 | ||
+ | &END MM_KIND | ||
+ | & | ||
+ | RADIUS 1.67 | ||
+ | &END MM_KIND | ||
+ | #define the model | ||
+ | & | ||
+ | MM_INDEX 25..32 41..48 | ||
+ | &END QM_KIND | ||
+ | & | ||
+ | RADIUS 1.67 | ||
+ | &END MM_KIND | ||
+ | #define the model | ||
+ | & | ||
+ | MM_INDEX 25..32 41..48 | ||
+ | &END QM_KIND | ||
+ | & | ||
+ | MM_INDEX 17..24 33..40 | ||
+ | &END QM_KIND | ||
+ | &END QMMM | ||
+ | |||
+ | & | ||
+ | #this defines the cell of the whole system | ||
+ | #must be orthorhombic, | ||
+ | &CELL | ||
+ | ABC 12.6 100.0 12.6 | ||
+ | &END CELL | ||
+ | & | ||
+ | COORD_FILE_NAME kcl.xyz | ||
+ | COORD_FILE_FORMAT XYZ | ||
+ | & | ||
+ | & | ||
+ | # | ||
+ | LIST 1..48 | ||
+ | & | ||
+ | &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 | ||
+ | </code> | ||
+ | |||
+ | and includes as separate files, using the @include macro, for the QS, MM and motion sections | ||
+ | |||
+ | <code cp2k QS.inc> | ||
+ | &DFT | ||
+ | BASIS_SET_FILE_NAME BASIS_MOLOPT | ||
+ | POTENTIAL_FILE_NAME GTH_POTENTIALS | ||
+ | & | ||
+ | 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 | ||
+ | & | ||
+ | EPS_SCF 1.0E-05 | ||
+ | &END OUTER_SCF | ||
+ | &END SCF | ||
+ | &XC | ||
+ | & | ||
+ | &END XC_FUNCTIONAL | ||
+ | &END XC | ||
+ | & | ||
+ | & | ||
+ | NLUMO 10 | ||
+ | | ||
+ | & | ||
+ | & | ||
+ | | ||
+ | & | ||
+ | &END PRINT | ||
+ | &END DFT | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | &MM | ||
+ | & | ||
+ | & | ||
+ | ATOM K | ||
+ | | ||
+ | &END CHARGE | ||
+ | & | ||
+ | ATOM Cl | ||
+ | | ||
+ | &END CHARGE | ||
+ | & | ||
+ | & | ||
+ | atoms K Cl | ||
+ | A [eV] 4117.9 | ||
+ | B [angstrom^-1] 3.2808 | ||
+ | C [eV*angstrom^6] 0.0 | ||
+ | RCUT [angstrom] 3.0 | ||
+ | &END 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 | ||
+ | & | ||
+ | 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 | ||
+ | & | ||
+ | & | ||
+ | EWALD_TYPE spme | ||
+ | ALPHA .44 | ||
+ | GMAX 40 | ||
+ | &END EWALD | ||
+ | &END POISSON | ||
+ | &END MM | ||
+ | </code> | ||
+ | |||
+ | <code cp2k motion.inc> | ||
+ | & | ||
+ | | ||
+ | &END | ||
+ | & | ||
+ | & | ||
+ | LIST 1..16 | ||
+ | | ||
+ | | ||
+ | & | ||
+ | &END CONSTRAINT | ||
+ | &END MOTION | ||
+ | </code> | ||
+ | |||
+ | <code xyz kcl.xyz> | ||
+ | 48 | ||
+ | |||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | K 3.15000 | ||
+ | K 0.00000 | ||
+ | K 3.15000 | ||
+ | K 0.00000 | ||
+ | K 9.45000 | ||
+ | K 6.30000 | ||
+ | K 9.45000 | ||
+ | K 6.30000 | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | K 0.00000 | ||
+ | K 3.15000 | ||
+ | K 0.00000 | ||
+ | K 3.15000 | ||
+ | K 6.30000 | ||
+ | K 9.45000 | ||
+ | K 6.30000 | ||
+ | K 9.45000 | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | Cl | ||
+ | K 3.15000 | ||
+ | K 0.00000 | ||
+ | K 3.15000 | ||
+ | K 0.00000 | ||
+ | K 9.45000 | ||
+ | K 6.30000 | ||
+ | K 9.45000 | ||
+ | K 6.30000 | ||
+ | </ |
exercises/2016_summer_school/qmmm.txt · Last modified: 2020/08/21 10:15 by 127.0.0.1