[Pw_forum] graphene with Li input problem

[Axel Kohlmeyer]

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
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.


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--
Dr. Axel Kohlmeyer  akohlmey at gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.