----------------------------------------
> 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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