[ase-users] info NEB+Siesta

[Ask Hjorth Larsen]

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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