[CP2K:3448] MD doesn't run

Nikita Vakula vakul... at gmail.com
Tue Aug 23 19:03:28 CEST 2011


Thank you for your reply! Just for clarity: in order to do calculations on
periodic systems with PBC I should make connection (by declaring bonds,
angles, and so on) between atoms that are located in the supercell and atoms
that are in the image of this supercell. Am I right?
Thanks in advance,
Nikita

2011/8/23 Teodoro Laino <teodor... at gmail.com>

> the bond must be in the PSF (just fix it by hand). CP2K evaluates the bond
> directly within minimum image convention.
> Teo
>
> On Aug 23, 2011, at 12:04 PM, Nikita Vakula wrote:
>
> Hello Teo!
> Thank you very much for your prompt reply! Yes there should be a bond
> between them but it is formed only when the unit cell is replicated. And
> then the thing is: how to set this bond between two atoms which are located
> in different unit cells? I couldn't find any useful suggestions or variants
> to realise it? Could you please tell me how to set connection between these
> atoms?
> Thank you very much in advance,
> Nikita
>
> 2011/8/23 Teodoro Laino <teodor... at gmail.com>
>
>> Particles 72 and 36 are at approx 1.63 angstrom.
>> They must be bond-connected and your PSF does not include this bond. Check
>> it!
>> If there is no bond between them then there are all good reasons to abort
>> the calculation: they would fly in opposite directions in few fs.. (too
>> close!)
>>
>> Teo
>>
>> On Aug 23, 2011, at 11:43 AM, Nikita wrote:
>>
>> > Dear CP2K users and developers,
>> > I'm trying to do some MD calculations but all my attempts have
>> > finished with the following error:
>> > ****************
>> > WARNING| Particles:      72     36 at distance [au]:     3.08384421
>> > less than:      4.43366249; increase EMAX_SPLINE.
>> > *
>> > *** ERROR in build_neighbor_lists  ***
>> > *
>> > *** GEOMETRY wrong or EMAX_SPLINE too small!  ***
>> > ****************
>> > I've checked my pdb and it seems to be ok. Particles that were pointed
>> > out by the program are at the opposite sides of the unit cell. After
>> > replication this unit cell the distance between these two atoms is
>> > also ok. This geometry was taken from the dft calculation that had
>> > ended up normally. Could anybody tell me what's wrong? Input is below.
>> >
>> > Thank you in advance,
>> > Nikita
>> >
>> > &FORCE_EVAL
>> >  METHOD FIST
>> >  &MM
>> >    &FORCEFIELD
>> >      PARMTYPE CHM
>> >      PARM_FILE_NAME ./par_silicates.inp
>> >      IGNORE_MISSING_CRITICAL_PARAMS .true.
>> >    &END FORCEFIELD
>> >    &POISSON
>> >      &EWALD
>> >        EWALD_TYPE SPME
>> > #        ALPHA .44
>> >        GMAX 60 60 60
>> >      &END EWALD
>> >    &END POISSON
>> >  &END MM
>> >  &SUBSYS
>> >    &CELL
>> >      A   19.65120000    0.00000000    0.00000000
>> >      B    0.00000000   17.04684000    0.00000000
>> >      C    0.00000000    0.00000000   30.00000000
>> >      ALPHA_BETA_GAMMA 90.0 90.0 90.0
>> >      PERIODIC XY
>> >    &END CELL
>> >    &TOPOLOGY
>> >      CONN_FILE_NAME ./surf1.psf
>> >      CONNECTIVITY UPSF
>> >      COORD_FILE_NAME ./surf1.pdb
>> >      COORDINATE PDB
>> >    &END TOPOLOGY
>> >  &END SUBSYS
>> > &END FORCE_EVAL
>> > &GLOBAL
>> >  PRINT_LEVEL medium
>> >  PROJECT surf_MD
>> >  RUN_TYPE MD
>> > &END GLOBAL
>> > &MOTION
>> >    &MD
>> >        ENSEMBLE NVT
>> >        TEMPERATURE 573.15
>> >        STEPS 20000
>> >        TIMESTEP 0.5
>> >        &THERMOSTAT
>> >          &NOSE
>> > #         LENGTH 3
>> > #         YOSHIDA 3
>> > #         TIMECON 100.0
>> > #         MTS 2
>> >                  &END NOSE
>> >        &END
>> >    &END MD
>> > &END MOTION
>> >
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