[Pw_forum] graphene with Li input problem

[Axel Kohlmeyer]

> If you have potentials and wavefunctions, how would you define bonds?

that is what the DFT calculation is for. remember that bonds exist
only in our imagination. they are a model that humans have made to
describe the behavior of atoms (or rather point charges and electrons,
or pseudopotentials and electrons) that follow the laws of quantum
mechanics with a simple phenomenological model (balls and springs).
the problem is, those models are not fully equivalent, but only the
classical, simplified model is what we can properly visualize. most of
the time, this is instructive and "good enough". but if you reduce the
information even more and only provide the coordinates and some labels
(atom names), then things are likely to be inaccurate for anything
that is not dead obvious.

> Hydrogen bonds? etc. Is there something that could generate this?

hydrogen bonds is an even more heated and argued about topic. there
are a large number of papers with scientists arguing over who is
counting/defining them correctly.

that aside, if you look at a tool to generate assemblies of molecules
from templates with a "shape" description input, have a look at the
packmol program, and if you look at some tool to define bonds in a
smarter way, you can do some scripting, e.g. in VMD or pymol and then
record *your* bond assignment in a suitable file format that contains
explicit bond information, e.g. one of the classical MD software
formats like .psf or .mol2

> 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 :)

generate .xsf files. AFAIK, pymol uses the molfile plugin library from
VMD and a loong time ago, i wrote an (a)xsf plugin for VMD, that
should be still good, if the format hasn't changed since.

axel.

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