[Pw_forum] Prep CI-NEB analysis for Espresso

Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
Sun Jan 13 14:25:55 CET 2008

On 1/12/08, Jack Shultz <jackygrahamez at gmail.com> wrote:
> I am attempting to simulate a H2O2 redox to O2 and H2O such as this
> 2 H2O2 --> O2 + H2O
> I'm not sure exactly what I'm doing here. I'm trying to apply example 17
> (proton transfer) to another reaction so I can understand how this works. If
> you got a better reaction for me to learn on, I'm all ears.

you are trying to 'run before you can walk', which means you are bound
to fail and not understand what went wrong.

please have a look at the tutorials for simple pw.x calculations (single point
energy, geometry optimizations) and then at the file Doc/INPUT_PW which
explains all input parameters and the structure of the input file. particularly
the entries for 'nat' and 'ntyp' warrant closer inspection. but also
'nspin', 'ecutwfc' and 'ecutrho'.  the latter two are connected to your choice
of pseudopotentials, and (again) those have to be chosen properly (e.g.
you cannot mix and match pseudopotentials generated for different
DFT functionals. finally, you'll have to look into how the size of the unit cell
affects the accuracy of your results. plane wave pseudopotential calculations
are _always_ periodic, so you have to minimize the impact of the periodic
images on the structures.

if you don't those right and a working geometry optimization, there is
no point in starting a NEB calculation. then please also have a look at
what are the prerequisites or starting points for NEB calculations.

on the quantum espresso homepage are links to collections of tutorial
material (click on 'learn') that has been tried, tested and refined over
several years and provide a good starting point into this field. as with
any first principles application, you have to have a reasonably good
understanding of what approximations you are making so that you
are getting meaningful results and are not generating expensive
random numbers. even very experienced users (hmmm... or perhaps
particularly experience users) tend to have always doubts whether
everything really went ok, or whether they have overlooked something,
that does not show immediately.

if you have seen 'home improvement' you'll know, that powerful tools
can also do the most damage. ;-)


> I tried a couple pseudo potentials for Oxygen. Here are parameters for
> Atomic species which I used
> H 1.00794 HUSPBE.RRKJ3
> O 15.9994 O.LDA.US.RRKJ3.UPF
> Then I get this error when I run it.
> Warning: card O  15.9994  O.LDA.US.RRKJ3.UPF ignored
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from read_cards : error #         1
>      wrong index in ATOMIC_POSITIONS
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
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Axel Kohlmeyer   akohlmey at cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.

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