[Pw_forum] graphene with Li input problem

Mike Marchywka marchywka at hotmail.com
Sat Jun 15 18:29:27 CEST 2013

> Date: Sat, 15 Jun 2013 13:10:03 +0200
> From: akohlmey at gmail.com
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] graphene with Li input problem
> On Sat, Jun 15, 2013 at 12:48 PM, Mike Marchywka <marchywka at hotmail.com> wrote:
>> ----------------------------------------
>>> Date: Sat, 15 Jun 2013 10:40:21 +0200
>>> From: akohlmey at gmail.com
>>> To: pw_forum at pwscf.org
>>> Subject: Re: [Pw_forum] graphene with Li input problem
>>>> If you have potentials and wavefunctions, how would you define bonds?
>>> that is what the DFT calculation is for. remember that bonds exist
>> Yes but what techniques may you want to use to present these in
>> an artists conception that may be useful for either understanding the molecule or
>> debugging code and algorithm?
> this is why paolo commented, that you can make a career out of it.
> there *is* no unique and easy definition. if you want to have some

Yeah, I wasn't sure if there were libraries for this like there are for exchange-correlation
functionals. The link you give below
looks like it will help me look into some of these things when I have
something to visualize :)  I'll check google scholar as I wait for my other code
to compile or run, just thought it was relevant to add to this thread. Thanks. 

> fun, get hold of a large group of organic chemists and start a
> discussion about aromaticity and how you can define and identify it,
> and particularly how you should draw the resulting structure. you
> probably need to run away quickly, because of the riot that will
> begin.
> if you look at this less religiously, there are some rather simplistic
> ways, that often work very well. e.g. you define an effective atom
> radius and then use a purely geometric criterion. that is how most
> molecular viz programs work. if they get things wrong, they often
> misidentify the element, or make assumptions about its oxidation
> state, that don't hold. remember, that bonds are typically important
> for organic molecules, where you have mostly the elements H, C, N, O
> where the simple geometric approach works quite well.
> beyond that, you can do (empirical) increment systems or charge
> equilibration and use that to assign "a bond order" based on the
> number of available valences. again, this is working ok, for as long
> as you have only s- and p- electrons to deal with.
> there also are electron density based methods like "atoms in
> molecules" and "ELF" that partition the electron density and allow to
> do some analysis based on that which can be used to assign (and
> compare) bonds. but those are not perfect either.
>> I guess if you were going to use some set of definitions you could write
>> a program to take dft output analyze it and output some bond or graphical
>> information to display in pymol or whatever. Not sure what formats
>> for input or output or how to contemplate a library of analysis methods to
>> find "bonds."
> see above. in my personal opinion, there are two choices: 1) you get
> religious about this and will either be never satisfied yourself or
> not be able to satisfy everybody or both or option 2) tell yourself
> that it is not that important and learn how to "futz it up", in case
> the simpleminded guess doesn't work.
> i have opted for the second option and spent my time rather to make
> the futzing simpler and wrote a VMD plugin for it (and for setting up
> topologies for classical MD)
> https://sites.google.com/site/akohlmey/software/topotools
> axel.
>> note new address
>> Mike Marchywka 2295 Collinworth Drive Marietta GA 30062.
>> formerly 487 Salem Woods Drive Marietta GA 30067 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency
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> --
> Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
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