QMMM setting up
Geng Sun
sungen... at gmail.com
Fri Aug 28 13:04:12 UTC 2015
Matt,
Thanks for the specification.
But I still have several other questions.
1) In the part of FORCE_EVAL
<http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html> / SUBSYS
<http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS.html>
/ KIND
<http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/KIND.html> section,
should I set all the types of atoms in both QM_KINDS and MM_KINDS, or just
in QM_KINDS ?
2) And, The section of FORCE_EVAL
<http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html> / QMMM
<http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM.html> /
FORCE_MIXING
<http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM/FORCE_MIXING.html>,
which uses the method of [Bernstein2012
<http://manual.cp2k.org/cp2k-2_6-branch/references.html#reference_106>] is
the place to set the adaptive QMMM method. If I don't want to use that
method,
I could just leave this section not been used. At this momenta, the
numbers of atoms in QM and MM parts do not change during simulation. Am I
right ?.
If I do not use the force_mixing scheme, the total energy
E=E(qm)+E(mm)+E(qm-mm). The forces are the derivatives of the energy, so
the energy should be conservative in principle rather than in the
force_mixing scheme. Do I understand correctly ?
Thanks in advance
Geng Sun
在 2015年8月28日星期五 UTC+8下午8:01:46，Matt W写道：
>
> Hi,
>
> the MM_index is just the number of the atom in the coordinate file (by
> default), so you give
>
> $QM_KIND Pt
> LIST 104 105 106
> &END
>
> in your example.
>
> The need for a topology depends on the classical part of the calculation.
> So in your case, if Al2O3 is just charges and non bonding parameters then
> no topology is needed. If you had a forcefield with say Al-O-Al bend
> parameters you would need a topology that specified those.
>
> Matt
>
>
>
> On Friday, August 28, 2015 at 9:40:36 AM UTC+1, Geng Sun wrote:
>>
>> Hello CP2K users,
>>
>> I am trying to study the Pt6 clusters adsorption on the Al2O3
>> surface, using the QMMM method in CP2K.
>> In this study, I want to simulate the Al2O3 surface by classical
>> forcefield assuming that the Al2O3 interacts with Pt clusters only by
>> electrostatic interaction and Van der Waals' source.
>> The Pt cluster is studied by GPW method. In the structure
>> optimization, all the Al and O atoms are fixed.
>>
>> And assuming that, Al are all the atoms whose ID from 1 to 40
>> O are all the atoms whose ID from
>> 41 to 100
>> Pt are all the atoms whose ID from
>> 101 to 106
>>
>> So, there is something which is not clear for me:
>>
>> 1) How to appoint the QM atoms and MM atoms? There are two
>> subsections, QM_KIND and MM_KIND, in the FORCE_EVAL
>> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html> /
>> QMMM
>> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/QMMM.html>
>> section. But I don't know what are the MM_indexs in QM_KIND section ?
>> Are they the atoms ID in the FORCE_EVAL
>> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL.html> /
>> SUBSYS
>> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS.html>
>> / COORD
>> <http://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/COORD.html> section
>> ? And why there are no keyword for assign the Index for MM_KIND ?
>> 2 ) I think I don't need to specify the topology structure for
>> my systems, so could I just leave this section empty ?
>>
>>
>> A trial input is shown below which is written according to my
>> understanding and the examples in test folders.
>>
>> I know my questions are quite silly for my poor understanding of the
>> philosophy in QMMM settings in CP2K. So any suggestions and advices would
>> be much appreciated.
>>
>> Geng Sun
>>
>> &FORCE_EVAL
>> METHOD QMMM
>> &DFT
>> BASIS_SET_FILE_NAME BASIS_SET
>> POTENTIAL_FILE_NAME GTH_POTENTIALS
>> &MGRID
>> COMMENSURATE
>> CUTOFF 20
>> &END MGRID
>> &QS
>> &END QS
>> &SCF
>> SCF_GUESS atomic
>> &END SCF
>> &XC
>> &XC_FUNCTIONAL PADE
>> &END XC_FUNCTIONAL
>> &END XC
>> &END DFT
>> &MM
>> &FORCEFIELD
>> IGNORE_MISSING_CRITICAL_PARAMS T
>> &CHARGE
>> ATOM Al
>> CHARGE 1.4175
>> &END CHARGE
>> &CHARGE
>> ATOM O
>> CHARGE -0.9450
>> &END CHARGE
>> &END FORCEFIELD
>> &POISSON
>> &EWALD
>> EWALD_TYPE ewald
>> ALPHA .44
>> GMAX 21
>> &END EWALD
>> &END POISSON
>> &END MM
>> &QMMM
>> USE_GEEP_LIB 10
>> CENTER NEVER
>> &CELL
>> ABC 16.8260 16.1360 25.0003
>> &END CELL
>> ECOUPL GAUSS
>> NOCOMPATIBILITY
>> &INTERPOLATOR
>> EPS_R 1.0e-14
>> EPS_X 1.0e-14
>> MAXITER 100
>> &END INTERPOLATOR
>> &QM_KIND Pt
>> MM_INDEX 101..106
>> &END QM_KIND
>> &MM_KIND Al
>> &END MM_KIND
>> &MM_KIND O
>> &END MM_KIND
>> &END QMMM
>> &SUBSYS
>> &CELL
>> ABC 16.8260 16.1360 25.0003
>> &END CELL
>> &COORD
>> .................many O and Al positions, not shown here.
>> O 16.24701734 14.39169840 5.63706764
>> O 16.24701734 14.31456832 2.94428533
>> O 16.24701734 14.25696280 8.53085237
>> Al 12.04034908 13.30606832 2.94428533
>> Al 12.04034908 13.24846280 8.53085237
>> O 12.04034908 12.14588992 4.36330236
>> O 12.04034908 12.08828440 9.94986940
>> O 12.04034908 12.28046416 1.46926763
>> O 12.04034908 12.22285864 7.05608467
>> Pt 8.14041880 4.95391336 12.72190266
>> Pt 10.22314108 4.88420584 12.97940575
>> Pt 6.98161218 7.10855344 12.92565511
>> Pt 8.98171880 7.10855344 12.92565511
>> Pt 11.31195154 7.17826096 12.66815202
>> Pt 5.81018606 4.88420584 12.97940575
>> &END COORD
>> &KIND Pt
>> BASIS_SET DZV-GTH-PADE
>> POTENTIAL GTH-PADE-q10
>> &END KIND
>> &TOPOLOGY
>> &END TOPOLOGY
>> &END SUBSYS
>> &END FORCE_EVAL
>> &GLOBAL
>> PROJECT qmmm_test
>> PRINT_LEVEL MEDIUM
>> RUN_TYPE ENERGY
>> &END GLOBAL
>>
>>
>>
>>
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