[CP2K:5517] Some newbie questions about CP2K

[Carlos Campana]

Just pick your favorite chemistry database and search for those keywords.
Not my work topic.
Carlos


On Tue, Jul 15, 2014 at 2:40 PM, C Mason <bono... at gmail.com> wrote:

> Thank you so much! Is there any other suggestion on cp2k? Such as some
> property research on asphalt using ab-initio method?
>
> Really appreciate it
> Mason
>
> 在 2014年7月15日星期二UTC-5下午12时55分04秒，ccampana写道：
>>
>> 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 <bon... 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
>>>
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>>
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