[ase-users] neb documentation hard to understand

[Ask Hjorth Larsen]

2016-12-05 15:40 GMT+01:00 Ask Hjorth Larsen <asklarsen at gmail.com>:
> Dear Markus
>
> 2016-12-05 9:15 GMT+01:00 Markus Kaukonen via ase-users
> <ase-users at listserv.fysik.dtu.dk>:
>> Dear All,
>>
>> I'm trying to understand the traj file in connection with neb calculations.
>>
>> In
>> https://wiki.fysik.dtu.dk/ase/ase/neb.html#the-neb-class
>>
>> there are lines:
>>
>> """
>>
>> For the example above, you can write the images to individual trajectory
>> files like this:
>>
>> for i in range(1, 4):
>>     qn.attach(io.Trajectory('A2B-%d.traj' % i, 'w', images[i]))
>>
>> """
>>
>> but I cannot find anything related to 'qn'
>
> qn is the 'optimizer' variable a few lines above.  I just committed a
> fix; now it will be called 'opt' consistently.
>
>>
>>
>> Another thing:
>> How does one get the energy related to a traj structure file?
>> Is the easiest way:
>> """
>> atoms = read('A.traj')
>> print(atoms.get_calculator().get_potential_energy(image))
>> """
>>
>> Terveisin, Markus
>
> read('md.anneal.jun7.Au.traj@:')

I should add that this will give you a list of Atoms objects.

>
> The part after @ can also be things like 5:10, -1, etc.
>
> Best regards
> Ask
>
>>
>> --
>> --www=http://www.iki.fi/markus.kaukonen
>> --Markus.Kaukonen at iki.fi
>> --office: www.helsinki.fi/kemia/svenskakemen/index_eng.html
>> --home: Viinirinne 3 F 12, 02630 Espoo, FIN
>> --tel: h 045-1242068
>>
>>
>>
>>
>>
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