[ase-users] info NEB+Siesta

[marc]

Hi Tommy,

I have been looking a bit around and I tried to run the calculations 
with gpaw and the results are similar than with siesta. No data are 
showing when running the ase gui command, but the second plot button in 
one of the windows give some graphic, I'm not sure that it is what you 
want. So the problem seems to be more related to the gui than with 
siesta from what I can see.

Marc

On 06/28/2017 02:03 PM, marc via ase-users wrote:
> It may be a bug in the siesta calculator. its seems that the different 
> field necessary for neb calculations are not written in the traj file. 
> I will have a look.
>
> Maybe someone that knows well neb calculations could help me with this?
>
> Marc
>
> On 06/28/2017 01:25 PM, Tommaso Francese wrote:
>> Hi Marc!
>> First of all thanks a lot for testing my system.
>>
>> The movie is only a part of what I would like to have in the end of 
>> the day. The most important thing it would be the obtaining of the 
>> energy profile computed by siesta through the Neb module. In simple 
>> terms, I would like to visualize with the ASE-gui/NEB utility the 
>> energy profile, see this example for clarity:
>> https://wiki.fysik.dtu.dk/ase/tutorials/neb/diffusion.html
>>
>> The point is the examples works fine, with the EMT algorithm, that it 
>> implemented into the ASE, but it looks like to fail while coupled 
>> with Siesta, in this case. It looks like it is not able to read the 
>> energies, or to extract them from the final file generated.
>>
>> Thanks for the help,
>> Best,
>> Tommy
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>> Il giorno 28 giu 2017, alle ore 13:13, marc via ase-users 
>>> <ase-users at listserv.fysik.dtu.dk 
>>> <mailto:ase-users at listserv.fysik.dtu.dk>> ha scritto:
>>>
>>> Hello Tommy,
>>>
>>> I have never used NEB calculation before so I'm not sure what you 
>>> want to get.
>>> I started to run the calculations and the neb.traj file is written. 
>>> Opening it with the ase -T gui command gives me a movie with the 
>>> molecule moving. Is it what you want to get?
>>>
>>> Best,
>>> Marc
>>>
>>> On 06/28/2017 11:16 AM, Tommaso Francese via ase-users wrote:
>>>> Dear all Asusers,
>>>>
>>>> I am pretty newbie in the Ase world. I was trying to run a NEB calculation making use of the Siesta code. I made use of a template for the Orca code, properly modified. The code runs fine, but when I try to visualize the output via ASE-gui with the NEB module, nothing is reported.
>>>>
>>>> I don’t know where the error lies, can you kindly help me fix this problem?
>>>>
>>>> Here I provide the script for the running the NEB coupled with Siesta, and the two input files (react.traj and prod.traj) that are interpolated for creating the NEB path. They latter contains the toy model I am testing.
>>>>
>>>> Thanks a lot for the help,
>>>> It ’s extremely important.
>>>>
>>>> Best,
>>>> Tommy
>>>>
>>>>
>>>>
>>>>
>>>> Here also the pseudos for the Siesta (they are in testing mode):
>>>>
>>>>
>>>>
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>>>
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>>
>
>
>
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