[CP2K:5514] Some newbie questions about CP2K

[Carlos Campana]

Your Q is not so much about CP2K but about reaction chemistry. Reactions
are, in principle, rare events thus the likelihood of "seeing" a reaction
occurring during an MD run can be null. Due to its stochastic nature, MD is
not a great tool to study reaction chemistry. There are cases where MD can
be employed to simulate reactions but those are typically systems with a
high degree of confinement (relatively dense), highly symmetric or with
additional constraints that inhibit certain atomic motions. How to proceed
in your case really depends on what you are after but for sure you should
be consulting the appropriate textbooks to improve your understanding on
the topic. Finding "all the possible products of asphalt oxidation" sounds
like a mad quest. If you think all it takes is to drop molecules into a
simulation box and "cook" via MD just forget about it. Said this, you may
want to check works done with the classical reactive forcefield (reaxff)
which has already been used to simulate certain cases of hydrocarbon
combustion/oxidation via high temperature MD and/or accelerated MD (
http://pubs.acs.org/doi/abs/10.1021/jp709896w). Engineers also use reaction
kinetic models that solve sets of PDEs to predict reactions species under
certain conditions (http://rmg.mit.edu/). Keep in mind the aforementioned
models rely on many approximations and lack the accuracy of first-principle
methods. Yet, they are much faster that the ab-initio ones and sometimes
are the only tools to tackle certain problems. As already said, it very
much depends on what you are trying to study. I call it a day now.
Carlos









On Tue, Jul 15, 2014 at 1:00 PM, C Mason <bono... at gmail.com> wrote:

> Dear all researchers using cp2k,
>
>     I'm a pretty new user of cp2k, and still learning functions of this
> program. I got some questions right now and really need help.
>     The purpose of my research is to find all the possible products of
> asphalt oxidation. To begin with, I tried to learn if MD function in cp2k
> can do simulation of some reactions, and built a simple system containing 2
> methanol and 3 oxygen molecules in a 10X10X10 cell. Here's my input file:
>
> Reactions are not observed in 1000 steps. Can someone help me figure out
> where the problem is?
>
> &FORCE_EVAL
>   METHOD QS
>   &DFT
>     BASIS_SET_FILE_NAME /usr/share/cp2k/BASIS_MOLOPT
>     POTENTIAL_FILE_NAME /usr/share/cp2k/GTH_POTENTIALS
>     &MGRID
>       CUTOFF 200
>       NGRIDS 4
>     &END MGRID
>     &QS
>       METHOD GAPW
>     &END QS
>     &SCF
>       SCF_GUESS RESTART
>       MAX_SCF 100
>       EPS_SCF 1.0e-6
>         &OUTER_SCF
>         MAX_SCF 5
>         EPS_SCF 1.0E-6
>         &END
>        &OT TRUE
>          PRECONDITIONER FULL_ALL
>          MINIMIZER CG
>          ENERGY_GAP 0.001
>        &END OT
>     &END SCF
>     &XC
>       &XC_FUNCTIONAL PBE
>       &END XC_FUNCTIONAL
>     &END XC
>   &END DFT
>   &SUBSYS
>     &CELL
>       ABC 10.0 10.0 10.0
>     &END CELL
> &COORD
> O       5.83970000       2.50019000       2.50074000
> O       4.73464200       2.52884200       2.59250500
> O       5.55838800       3.09963100       7.32479800
> O       4.53647400       3.49381100       7.50004500
> O       6.39174700       7.49938300       4.80196400
> O       7.49930100       7.46722100       4.85377500
> C       6.90902000       4.30670800       4.62181700
> O       5.64215600       4.88509800       4.49462900
> H       5.20622900       4.78592700       5.38062100
> H       6.81478300       3.23143200       4.88781800
> H       7.49613100       4.83704900       5.40277500
> H       7.44563600       4.38928400       3.65434100
> C       3.27312300       5.91737700       3.17814600
> O       4.20868900       6.89713900       3.52519000
> H       4.62313400       7.19318900       2.67346300
> H       3.77955300       5.06361100       2.67767800
> H       2.50196900       6.34589000       2.50171900
> H       2.77520500       5.54750300       4.09795900
> &END COORD
>   &KIND H
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q1
>       POTENTIAL GTH-PBE-q1
>     &END KIND
>   &KIND O
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q6
>       POTENTIAL GTH-PBE-q6
>     &END KIND
>   &KIND C
>       BASIS_SET DZVP-MOLOPT-SR-GTH-q4
>       POTENTIAL GTH-PBE-q4
>     &END KIND
> &END SUBSYS
> &END FORCE_EVAL
> &GLOBAL
> PROJECT methanol_try2
>   RUN_TYPE MD
> &END GLOBAL
> &MOTION
>   &MD
>     ENSEMBLE NVT
>     STEPS 1000
>     TIMESTEP 1.0
>     TEMPERATURE 800
>     TEMP_TOL 100
>     &BAROSTAT
>       PRESSURE 1000
>     &END BAROSTAT
>     &THERMOSTAT
>       TYPE CSVR
>       &CSVR
>         TIMECON 200
>       &END CSVR
>     &END THERMOSTAT
>   &END MD
> &PRINT
>   &TRAJECTORY
>       LOG_PRINT_KEY T
>       FORMAT XYZ
>       &EACH
>         MD 5
>       &END EACH
>       ADD_LAST NUMERIC
>     &END TRAJECTORY
> &END PRINT
> &END MOTION
> &END
>
> Many thanks!
> Mason
>
> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at http://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20140715/d99705a7/attachment.htm>