[Pw_forum] graphene with Li input problem

Sat Jun 15 12:48:15 CEST 2013

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> 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?  

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."

> 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.
>

Thanks, I'll take a look at xsf but for some reason I seem to recall it was
easier to use xplor after looking at pymol source code. I  dug though the pymol source code and took a few days
and converted my corrent version to be essentially al c++ files except I did not bother making
it link with the plugins or some group of code that IIRC already was c++ LOL. I was actually
going to write code to assemble something from a set of jdftx output files that could be generalized
to take binary grid data and short ascii parameters like grid dimensions but I wanted to understand
the dft code first :)
. 

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