[CP2K:5514] Some newbie questions about CP2K

[C Mason]

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