Bend potential having no effect & excluding specific electrostatic interactions
Christopher Mauney
christop... at gmail.com
Mon Feb 16 23:40:28 UTC 2015
Thanks for viewing, but I have figured out how to solve the issue using
&TOPOLOGY
...
CONNECTIVITY GENERATE
&GENERATE
CREATE_MOLECULES
REORDER
&END GENERATE
....
On Monday, February 16, 2015 at 2:14:03 PM UTC-8, Christopher Mauney wrote:
>
> I am attempting to run a geometry optimization on MgSi2O3 using a
> Buckingham potential. I attempted to include a three-body interaction
> among the Si-O, but it does not appear to have any effect at all on the
> outcome. I've attempted to adjust the force constant, but no difference in
> final result. Am I missing the meaning of this section?
>
> Furthermore, I would like to (for testing purposes) eliminate the Mg-Si
> electrostatic interaction, but am unsure how to do this. Is there a way to
> exclude this interaction?
>
> Thanks.
>
> -Christopher Mauney
>
> input file:
>
>> &GLOBAL
>> BLACS_GRID SQUARE
>> BLACS_REPEATABLE F
>> PREFERRED_DIAG_LIBRARY SL
>> PREFERRED_FFT_LIBRARY FFTW3
>> FFTW_WISDOM_FILE_NAME /etc/fftw/wisdom
>> FFTW_PLAN_TYPE ESTIMATE
>> EXTENDED_FFT_LENGTHS F
>> FFT_POOL_SCRATCH_LIMIT 15
>> ALLTOALL_SGL F
>> PRINT_LEVEL LOW
>> PROGRAM_NAME CP2K
>> PROJECT_NAME sigen-test
>> OUTPUT_FILE_NAME
>> RUN_TYPE GEO_OPT
>> WALLTIME
>> ECHO_INPUT F
>> ECHO_ALL_HOSTS F
>> TRACE F
>> TRACE_MASTER T
>> TRACE_MAX 2147483647
>> FLUSH_SHOULD_FLUSH T
>> CALLGRAPH NONE
>> CALLGRAPH_FILE_NAME
>> SEED 2000
>> SAVE_MEM F
>> ENABLE_UNSUPPORTED_FEATURES F
>> &END GLOBAL
>> &MOTION
>> &GEO_OPT
>> TYPE MINIMIZATION
>> OPTIMIZER BFGS
>> MAX_ITER 100
>> MAX_DR 1.0000000000000000E-04
>> MAX_FORCE 1.0000000000000001E-05
>> RMS_DR 1.5000000000000000E-03
>> RMS_FORCE 2.9999999999999997E-04
>> STEP_START_VAL 0
>> &BFGS
>> TRUST_RADIUS 2.5000000000000000E-01
>> USE_MODEL_HESSIAN T
>> USE_RAT_FUN_OPT F
>> RESTART_HESSIAN F
>> RESTART_FILE_NAME
>> &RESTART OFF
>> ADD_LAST NUMERIC
>> COMMON_ITERATION_LEVELS 2
>> FILENAME BFGS
>> LOG_PRINT_KEY F
>> &END RESTART
>> &END BFGS
>> &END GEO_OPT
>> &PRINT
>> &TRAJECTORY SILENT
>> ADD_LAST NUMERIC
>> COMMON_ITERATION_LEVELS 1
>> FILENAME
>> LOG_PRINT_KEY F
>> UNIT angstrom
>> FORMAT XMOL
>> CHARGE_OCCUP F
>> CHARGE_BETA F
>> CHARGE_EXTENDED F
>> &EACH
>> JUST_ENERGY 1
>> POWELL_OPT 1
>> QS_SCF 1
>> XAS_SCF 1
>> MD 1
>> METADYNAMICS 1
>> GEO_OPT 1
>> ROT_OPT 1
>> CELL_OPT 1
>> BAND 1
>> EP_LIN_SOLVER 1
>> SPLINE_FIND_COEFFS 1
>> REPLICA_EVAL 1
>> BSSE 1
>> SHELL_OPT 1
>> &END EACH
>> &END TRAJECTORY
>> &RESTART OFF
>> ADD_LAST NUMERIC
>> COMMON_ITERATION_LEVELS 1
>> FILENAME
>> LOG_PRINT_KEY F
>> BACKUP_COPIES 3
>> SPLIT_RESTART_FILE F
>> &END RESTART
>> &RESTART_HISTORY OFF
>> ADD_LAST NO
>> COMMON_ITERATION_LEVELS 0
>> FILENAME
>> LOG_PRINT_KEY F
>> &END RESTART_HISTORY
>> &END PRINT
>> &END MOTION
>> &FORCE_EVAL
>> METHOD FIST
>> STRESS_TENSOR NONE
>> &MM
>> &FORCEFIELD
>> PARMTYPE OFF
>> VDW_SCALE14 1.0000000000000000E+00
>> EI_SCALE14 0.0000000000000000E+00
>> SHIFT_CUTOFF T
>> DO_NONBONDED T
>> IGNORE_MISSING_CRITICAL_PARAMS F
>> MULTIPLE_POTENTIAL F
>> ZBL_SCATTERING F
>> &SPLINE
>> R0_NB 1.0000000000000001E-01
>> RCUT_NB -1.0000000000000000E+00
>> EMAX_SPLINE 1.0000000000000000E+02
>> EMAX_ACCURACY 2.0000000000000000E-02
>> EPS_SPLINE 9.9999999999999995E-08
>> NPOINTS -1
>> UNIQUE_SPLINE F
>> &END SPLINE
>> &NONBONDED
>> &WILLIAMS
>> ATOMS O O
>> A 2.6416495841429514E+08
>> B 6.7114093959731544E+00
>> C 3.2353360747630242E+05
>> RCUT 1.0000000000000002E+01
>> &END WILLIAMS
>> &WILLIAMS
>> ATOMS Si O
>> A 1.4899105572958285E+07
>> B 3.1199301135654558E+00
>> C 1.2372236150635568E+05
>> RCUT 1.0000000000000002E+01
>> &END WILLIAMS
>> &WILLIAMS
>> ATOMS Si Si
>> A 9.2258269084930563E+08
>> B 4.9751243781094523E+00
>> C 5.1846608733236147E+06
>> RCUT 1.0000000000000002E+01
>> &END WILLIAMS
>> &WILLIAMS
>> ATOMS Mg O
>> A 9.5342615460017957E+06
>> B 3.0845157310302285E+00
>> C 0.0000000000000000E+00
>> RCUT 1.0000000000000002E+01
>> &END WILLIAMS
>> &WILLIAMS
>> ATOMS Mg Si
>> A 0.0000000000000000E+00
>> B 0.0000000000000000E+00
>> C 0.0000000000000000E+00
>> RCUT 1.0000000000000002E+01
>> &END WILLIAMS
>> &WILLIAMS
>> ATOMS Mg Mg
>> A 0.0000000000000000E+00
>> B 0.0000000000000000E+00
>> C 0.0000000000000000E+00
>> RCUT 1.0000000000000002E+01
>> &END WILLIAMS
>> &END NONBONDED
>> &CHARGE
>> ATOM O
>> CHARGE -2.0000000000000000E+00
>> &END CHARGE
>> &CHARGE
>> ATOM SI
>> CHARGE 4.0000000000000000E+00
>> &END CHARGE
>> &CHARGE
>> ATOM MG
>> CHARGE 2.0000000000000000E+00
>> &END CHARGE
>> &BEND
>> ATOMS O SI O
>> KIND HARMONIC
>> K 2.0972000000000000E+00
>> CB 0.0000000000000000E+00
>> R012 0.0000000000000000E+00
>> R032 0.0000000000000000E+00
>> KBS12 0.0000000000000000E+00
>> KBS32 0.0000000000000000E+00
>> KSS 0.0000000000000000E+00
>> THETA0 1.9106119321581925E+00
>> &END BEND
>> &BEND
>> ATOMS O MG O
>> KIND HARMONIC
>> K 2.0972000000000000E+00
>> CB 0.0000000000000000E+00
>> R012 0.0000000000000000E+00
>> R032 0.0000000000000000E+00
>> KBS12 0.0000000000000000E+00
>> KBS32 0.0000000000000000E+00
>> KSS 0.0000000000000000E+00
>> THETA0 1.5707963267948966E+00
>> &END BEND
>> &END FORCEFIELD
>> &POISSON
>> POISSON_SOLVER ANALYTIC
>> PERIODIC NONE
>> &EWALD
>> EWALD_TYPE NONE
>> EWALD_ACCURACY 9.9999999999999995E-07
>> ALPHA 3.4999999999999998E-01
>> NS_MAX 11
>> O_SPLINE 6
>> EPSILON 9.9999999999999995E-07
>> &END EWALD
>> &END POISSON
>> &END MM
>> &SUBSYS
>> &CELL
>> ABC 2.0000000000000004E+01 2.0000000000000004E+01
>> 2.0000000000000004E+01
>> ALPHA_BETA_GAMMA 9.0000000000000000E+01
>> 9.0000000000000000E+01 9.0000000000000000E+01
>> CELL_FILE_FORMAT CP2K
>> PERIODIC NONE
>> MULTIPLE_UNIT_CELL 1 1 1
>> SYMMETRY NONE
>> &END CELL
>> &TOPOLOGY
>> CHARGE_OCCUP F
>> CHARGE_BETA F
>> CHARGE_EXTENDED F
>> PARA_RES T
>> MOL_CHECK T
>> USE_G96_VELOCITY F
>> COORD_FILE_NAME mgsi-test.xyz
>> COORD_FILE_FORMAT XYZ
>> NUMBER_OF_ATOMS -1
>> CONN_FILE_FORMAT GENERATE
>> DISABLE_EXCLUSION_LISTS F
>> EXCLUDE_VDW 1-3
>> EXCLUDE_EI 1-3
>> AUTOGEN_EXCLUDE_LISTS F
>> MULTIPLE_UNIT_CELL 1 1 1
>> MEMORY_PROGRESSION_FACTOR 1.2000000000000000E+00
>> &END TOPOLOGY
>> &END SUBSYS
>> &END FORCE_EVAL
>
>
> mgsi-test.xyz:
>
>> 6
>
>
>
> Si 5.100733801 7.021427036 5.000000000
>> Si 8.599266199 7.021427036 5.000000000
>> O 6.850000000 7.149878576 5.000000000
>> O 5.000213137 5.388401447 5.000000000
>> O 8.699786863 5.388401447 5.000000000
>> Mg 6.850000000 5.000464458 5.000000000
>
>
>
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