[ase-users] ***SPAM*** Re: info NEB+Siesta

[Ask Hjorth Larsen]

Hi Marc

I cannot reproduce the issue.  It appears to me that energies are
correctly stored in trajectories when running NEB with GPAW.  Which
version of ASE are you using?

Best regards
Ask

2017-06-30 12:32 GMT+02:00 marc <marc.barbry at mailoo.org>:
> Hi Ask,
>
> I attached the input file than Tommy sends and the output A2B_siesta.traj
> and A2B_gpaw.traj. The gui is giving in the both case similar results. The
> problem is probably at the writing of the files.
>
> Best regards,
> Marc
>
> On 06/29/2017 05:17 PM, Ask Hjorth Larsen wrote:
>>
>> Actually wait - if it affects GPAW too, it must be something else.
>> Might it be because the end points are part of the trajectory but do
>> not have energies?  Anyway running the same command and posting the
>> output would help.
>>
>> Best regards
>> Ask
>>
>> 2017-06-29 17:10 GMT+02:00 Ask Hjorth Larsen <asklarsen at gmail.com>:
>>>
>>> Hi
>>>
>>> 2017-06-28 14:03 GMT+02:00 marc via ase-users
>>> <ase-users at listserv.fysik.dtu.dk>:
>>>>
>>>> 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
>>>
>>> There could be some irregularity of how the Siesta calculator handles
>>> its results, so energies are not recorded in trajectories.  I seem to
>>> remember something related happening.  Can someone who has Siesta
>>> installed perform a quick relaxation of a small molecule and check (or
>>> send) the trajectory file?
>>>
>>> e.g.: ase info mytrajectoryfile.traj -v
>>>
>>> And also check the NEB trajectories similarly, in case there's a
>>> difference.
>>>
>>> The question is whether the "energy" entry is there.
>>>
>>> Here's an excerpt from one of my trajectry files:
>>>
>>> askhl at jormungandr:~$ ase info opt.traj -v
>>> opt.traj: ASE trajectory (traj)
>>> opt.traj  (tag: "ASE-Trajectory", 3 items)
>>> item #0:
>>> {
>>>      ase_version: 3.14.0b1,
>>>      calculator: {
>>>          dipole: [ -1.08619140e-13  -2.88470856e-16   8.72627641e-14],
>>>          energy: -6.74028940919,
>>>          forces: <ndarray shape=(2, 3) dtype=float64>,
>>>          name: gpaw,
>>>          parameters: {u'xc': {u'name': u'vdW-DF-CX', u'libvdwxc_name':
>>> u'vdW-DF-CX', u'vdwcoef': 1.0, u'setup_name': u'revPBE', u'pfft_grid':
>>> None, u'mode': u'auto', u'type': u'libvdwxc', u'semilocal_xc':
>>> u'GGA_X_LV_RPW86+LDA_C_PW'}, u'mode': u'pw'}},
>>>      cell: [[ 4.1       0.        0.      ]
>>>             [ 0.        4.        0.      ]
>>>             [ 0.        0.        4.737166]],
>>>      description: {u'type': u'optimization', u'maxstep': 0.04,
>>> u'optimizer': u'BFGS', u'interval': 1},
>>>      numbers: <ndarray shape=(2,) dtype=int64>,
>>>      pbc: [False False False],
>>>      positions: <ndarray shape=(2, 3) dtype=float64>,
>>>      version: 1}
>>> (....)
>>>
>>> Best regards
>>> Ask
>>>
>>>> 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> 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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