[ase-users] trajectory format error during structure optimization
Adam Jackson
a.j.jackson at physics.org
Mon Jul 8 15:54:30 CEST 2024
Hmm, there are 20 atoms in the structure but 23 positions in the trajectory information… I wonder if this is something to do with using a filter on the optimiser that exposes some extra degrees of freedom. I would expect that to add more than 3 values, though. Maybe some were removed with constraints?
Can you show us the code that created the optimiser/trajectory? Or make a small reproducible example using the EMT calculator?
Cheers,
Adam
From: ase-users <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of ase-users-request at listserv.fysik.dtu.dk <ase-users-request at listserv.fysik.dtu.dk>
Date: Monday, 8 July 2024 at 14:37
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Subject: ase-users Digest, Vol 193, Issue 2
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Today's Topics:
1. Re: trajectory format error during structure optimization
(Aldo Ugolotti)
2. Re: trajectory format error during structure optimization
(David Willock)
----------------------------------------------------------------------
Message: 1
Date: Mon, 8 Jul 2024 14:40:08 +0200
From: Aldo Ugolotti <aldo.ugolotti at unimib.it>
To: David Willock <WillockDJ at cardiff.ac.uk>,
"ase-users at listserv.fysik.dtu.dk" <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] trajectory format error during structure
optimization
Message-ID: <c55d33ce-852e-4815-9044-a66c80d99f0e at unimib.it>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
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<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,
> Universit? degli Studi di Milano-Bicocca
> via Cozzi 55,
> 20125 Milano (MI)
> Italy
> e-mail: aldo.ugolotti at unimib.it
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users<https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users>
> <https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users<https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users>>
--
Aldo Ugolotti, Ph.D.
Post-doc fellow
Materials Science Dept. U5,
Universit? degli Studi di Milano-Bicocca
via Cozzi 55,
20125 Milano (MI)
Italy
e-mail:aldo.ugolotti at unimib.it
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Message: 2
Date: Mon, 8 Jul 2024 13:36:12 +0000
From: David Willock <WillockDJ at cardiff.ac.uk>
To: Aldo Ugolotti <aldo.ugolotti at unimib.it>,
"ase-users at listserv.fysik.dtu.dk" <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] trajectory format error during structure
optimization
Message-ID:
<LO2P265MB5789CA2381C29D3F60D9EEA4ECDA2 at LO2P265MB5789.GBRP265.PROD.OUTLOOK.COM>
Content-Type: text/plain; charset="windows-1252"
Dear Aldo,
Does your opt.traj file have any size, i.e. check it is not zero length in case nothing has been written.
We would usually use the code on the page I sent the link to:
from ase.io.trajectory import Trajectory
traj = Trajectory('example.traj')
atoms = traj[-1]
It is difficult to look at this more unless you share the opt.traj file.
Best Wishes
David
________________________________
From: Aldo Ugolotti <aldo.ugolotti at unimib.it>
Sent: 08 July 2024 13:40
To: David Willock <WillockDJ at cardiff.ac.uk>; ase-users at listserv.fysik.dtu.dk <ase-users at listserv.fysik.dtu.dk>
Subject: Re: [ase-users] trajectory format error during structure optimization
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><mailto:ase-users-bounces at listserv.fysik.dtu.dk> on behalf of Aldo Ugolotti via ase-users <ase-users at listserv.fysik.dtu.dk><mailto:ase-users at listserv.fysik.dtu.dk>
Sent: 08 July 2024 13:10
To: ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk> <ase-users at listserv.fysik.dtu.dk><mailto: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,
Universit? degli Studi di Milano-Bicocca
via Cozzi 55,
20125 Milano (MI)
Italy
e-mail: aldo.ugolotti at unimib.it<mailto:aldo.ugolotti at unimib.it>
_______________________________________________
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--
Aldo Ugolotti, Ph.D.
Post-doc fellow
Materials Science Dept. U5,
Universit? degli Studi di Milano-Bicocca
via Cozzi 55,
20125 Milano (MI)
Italy
e-mail: aldo.ugolotti at unimib.it<mailto:aldo.ugolotti at unimib.it>
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