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

[marc]

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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