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

Fri Jun 30 21:35:14 CEST 2017

Hi Ask,

I don't see any energy store in the traj file.
$ ase info A2B_gpaw.traj -v
A2B_gpaw.traj: ASE trajectory (traj)
A2B_gpaw.traj  (tag: "ASE-Trajectory", 5 items)
item #0:
{
     ase_version: 3.14.0b1,
     cell: [[ 30.   0.   0.]
            [  0.  30.   0.]
            [  0.   0.  30.]],
     description: {u'type': u'optimization', u'interval': 1, 
u'optimizer': u'MDMin'},
     numbers: <ndarray shape=(8,) dtype=int64>,
     pbc: [False False False],
     positions: <ndarray shape=(8, 3) dtype=float64>,
     version: 1}

As you can see I'm using 3.14.0b1.

I will update and try again.

Best regards,
Marc

On 06/30/2017 06:05 PM, Ask Hjorth Larsen wrote:
> 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):
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> ase-users mailing list
>>>>> ase-users at listserv.fysik.dtu.dk
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>>>>>
>>>>>
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>>>>>
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>>>>>
>>>>>
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[ase-users] ***SPAM*** Re: info NEB+Siesta

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