[Pw_forum] graphene with Li input problem

[Mike Marchywka]

----------------------------------------
> From: paolo.giannozzi at uniud.it
> To: pw_forum at pwscf.org
> Date: Fri, 14 Jun 2013 18:06:37 +0200
> Subject: Re: [Pw_forum] graphene with Li input problem
>
> On Fri, 2013-06-14 at 16:55 +0200, yelena wrote:
>
>> So I have graphene
>
> or so you think (I don't, see below)
>
>> I don’t understand why all C atoms are connected
>> with every other C?
>
> because xcrysden, like most visualization tools, assumes
> that two atoms have a bond when they are closer than a
> typical bond length.

If you have potentials and wavefunctions, how would you define bonds?
Hydrogen bonds? etc. Is there something that could generate this?
And, using jdftx I had to write some code to translate binary potentials and
densities into xplor format to view. What is the eaisest way to get to pymol
from QE?  I can probably look all of this up when I need to know but thought
it may help this thread :) 


>
> Many years ago I wrote a small code calculating interatomic
> distances from PWscf input data: PW/tools/dist.f . It reads
> the following input data, as explained in the file header:

I started to write code to generate polymers into xya files by specifying things
like a normal direction for a planar molecule  and bond lengths and angles relative to last bond ,
presumably this could be extened to generate helicies etc.
I was debating about writing something to try to analyze a molecule collection
and regenerate from specifications like this but I was never sure
it was worth the effort or that I could specifiy the problem well engough to code :)

>
> 7 0 4.66 0.0 0.0 0.0 0.0 0.0 ! nat, ibrav, celldm(1-6)
> CELL_PARAMETERS (alat=4.66000000){hexagonal}
> 0.999984012 0.000000000 0.000000000
> -0.499992006 0.866011558 0.000000000
> 0.000000000 0.000000000 12.188495864
> ATOMIC_POSITIONS (crystal)
> C 0.333333000 -0.000000730 -0.024511570
> C 0.666665270 -0.000000730 -0.024511570
> C 0.000000730 0.333333730 -0.024511570
> C 0.000000730 0.666666000 -0.024511570
> C 0.333333000 0.333333730 -0.024511570
> C 0.666665270 0.666666000 -0.024511570
> Li 0.333333000 0.666666000 0.197069420
>
> and this is what you get (* = in another cell):
>
> species: C - C 0.00 < D < 1.00
> atoms: 1 2 distance = 0.82197 A
> atoms: 3 5 distance = 0.82197 A
> atoms: 3 4 distance = 0.82197 A
> atoms: 5 6 distance = 0.82197 A
> atoms: 1 4* distance = 0.82197 A
> atoms: 2 6* distance = 0.82197 A
> atoms: 1 5 distance = 0.82198 A
> atoms: 2 3* distance = 0.82198 A
> atoms: 4 6* distance = 0.82198 A
> C 1: neighbors at 0.822 0.822 0.822
> d(center): 1.104 A angles : 120.0 120.0 120.0
> C 2: neighbors at 0.822 0.822 0.822
> d(center): 1.801 A angles : 120.0 120.0 120.0
> C 3: neighbors at 0.822 0.822 0.822
> d(center): 1.104 A angles : 120.0 120.0 120.0
> C 4: neighbors at 0.822 0.822 0.822
> d(center): 1.801 A angles : 120.0 120.0 120.0
> C 5: neighbors at 0.822 0.822 0.822
> d(center): 1.104 A angles : 120.0 120.0 120.0
> C 6: neighbors at 0.822 0.822 0.822
> d(center): 1.801 A angles : 120.0 120.0 120.0
> Li 7: neighbors at 2.466 2.466 2.466
> d(center): 6.092 A angles : 180.0 120.0 60.0
>
> P.
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
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