[ase-users] ***SPAM*** Re: info NEB+Siesta
marc
marc.barbry at mailoo.org
Sat Jul 1 14:17:42 CEST 2017
Hi ask,
I updated ase, I'm now in version 3.14.1 but I still don't get energy in
the traj file. Maybe a problem with the script that I use? Did you use
the one that I send?
ase info A2B_gpaw.traj -v
A2B_gpaw.traj: ASE trajectory (traj)
A2B_gpaw.traj (tag: "ASE-Trajectory", 5 items)
item #0:
{
ase_version: 3.15.0b1,
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}
Weirdly ase info tell me that the ase version is 3.15 (git was giving me
3.14.1).
Best regards,
Marc
On 06/30/2017 09:35 PM, marc via ase-users wrote:
> 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):
>>>>>>
>>>>>>
>>>>>>
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>>>>>>
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>>>
>
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