[ase-users] trajectory format error during structure optimization

Aldo Ugolotti aldo.ugolotti at unimib.it
Mon Jul 8 14:40:08 CEST 2024 

Dear David,


thank you for the suggestion, but I don't think that's a mistake I am 
making. I get such an error message 'when' I read the file/attempt at  
getting an image.


Just to clarify, I get the same error message reported above with the 
two following pieces of code:


1) from ase.io import read

read('opt.traj',format='trajectory') -->> ERROR


2)  from ase.io.trajectory import TrajectoryReader


TrajectoryReader('opt.traj')[0] -->> ERROR


hence I think the issues should lie in the content of the file. I 
thought it could have been related to the calculator not cleanly exiting 
from the optimization step, but I get the same behavior in different 
conditions.


Aldo


On 08/07/2024 14:28, David Willock wrote:
> Dear Aldo,
>
> From the error message it looks like you are trying to read back the 
> trajectory file that the optimisers write? The trajectory file is a 
> list of the structures visited during the optimisation so should be 
> treated like a list of structures. The ASE site gives details at:
>
> Trajectory files — ASE documentation (dtu.dk) 
> <https://wiki.fysik.dtu.dk/ase/ase/io/trajectory.html>
>
> Best Wishes
> David
>
> ------------------------------------------------------------------------
> *From:* ase-users <ase-users-bounces at listserv.fysik.dtu.dk> on behalf 
> of Aldo Ugolotti via ase-users <ase-users at listserv.fysik.dtu.dk>
> *Sent:* 08 July 2024 13:10
> *To:* ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
> *Subject:* [ase-users] trajectory format error during structure 
> optimization
> External email to Cardiff University - Take care when replying/opening 
> attachments or links.
> Nid ebost mewnol o Brifysgol Caerdydd yw hwn - Cymerwch ofal wrth 
> ateb/agor atodiadau neu ddolenni.
>
>
>
> Dear users,
>
> I am optimizing a structure via different optimizers, e.g. FIRE or BFGS,
> through a calculator, however I have issues in reading the trajectory
> file that is produced.
>
> When I try to open it, I get the following error messages:
>
> Traceback (most recent call last):
>    File "<stdin>", line 1, in <module>
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/io/formats.py",
> line 800, in read
>      return next(_iread(filename, slice(index, None), format, io,
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/parallel.py",
> line 302, in new_generator
>      for result in generator(*args, **kwargs):
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/io/formats.py",
> line 866, in _iread
>      for dct in io.read(fd, *args, **kwargs):
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/io/trajectory.py",
> line 423, in read_traj
>      yield trj[i]
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/io/trajectory.py",
> line 278, in __getitem__
>      atoms = read_atoms(b, traj=self)
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/io/trajectory.py",
> line 359, in read_atoms
>      return read_atoms(backend, header, traj, False)
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/io/trajectory.py",
> line 379, in read_atoms
>      atoms = Atoms(positions=b.positions,
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/atoms.py",
> line 231, in __init__
>      self.new_array('positions', positions, float, (3,))
>    File
> "/home_most1/software/python_virtual_env/enviro_01/lib/python3.10/site-packages/ase/atoms.py",
> line 491, in new_array
>      raise ValueError('Array "%s" has wrong length: %d != %d.' %
> ValueError: Array "positions" has wrong length: 23 != 20.
>
> The structure is usually the following (in a POSCAR file):
>
> Ga O
>   1.0000000000000000
>       3.0437424088662963    0.0000000000000000 0.0000000000000000
>       0.0000031622422840   14.7017269524877570 0.0000000000000000
>       0.0000009260717257    3.4260834604639068 4.7082612932516961
>   Ga  O
>     8  12
> Cartesian
>    1.5218723357039710 15.8188718574327893  2.9079613676911555
>    0.0000059327733076 13.1052255051097770  2.8745980271043003
>   -0.0000107921034274 14.7011495642250427  0.0085871970445676
>    1.5219166606336012 10.7968514552615158  1.0658204805351676
>    3.0437429809987315  8.4679781419058902  2.9078954397593910
>    1.5218700428854757  5.7544245018196456  2.8745176343712169
>    1.5218699118892460  7.3501954535310761  0.0085254000378572
>    3.0437414219421695  3.4459684229877086  1.0657976752349458
>    0.0000120138472444  9.9397499435454684  1.6461898751266788
>    1.5218574348726146  4.2809758546542236  4.1343011562496468
>    3.0437402313938988 14.8510944838742400  1.8739821734909685
>    1.5218703192113834 14.0724457821694671  3.9088746953136773
>    1.5218709568204642 12.4588634753633229  1.8487030038014953
>    3.0437437766782129 16.4641054642267406  3.9360811195554040
>    1.5218728276782361  2.5889021769267080  1.6461839979364055
>    3.0437389902045822 11.6318087791170388  4.1343355926457086
>    1.5218694913323356  7.5002250144759159  1.8739212272855050
>    3.0437401536740056  6.7215584472524945  3.9088410244254468
>    3.0437392898354014  5.1079805611873921  1.8486885018616095
>    1.5218736571575349  9.1131861654179929  3.9359949123592188
>
>
> Can anyone give me an hint about solving this issue?
>
> Thank you in advance,
>
> --
> Aldo Ugolotti, Ph.D.
>
> Post-doc fellow
> Materials Science Dept. U5,
> Università degli Studi di Milano-Bicocca
> via Cozzi 55,
> 20125 Milano (MI)
> Italy
> e-mail: aldo.ugolotti at unimib.it
>
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-- 
Aldo Ugolotti, Ph.D.

Post-doc fellow
Materials Science Dept. U5,
Università degli Studi di Milano-Bicocca
via Cozzi 55,
20125 Milano (MI)
Italy
e-mail:aldo.ugolotti at unimib.it
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