---------------------------------------- > 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 >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0 > International Centre for Theoretical Physics, Trieste. Italy. > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum >
