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[feature request] dpdata Fails to Convert QE AIMD Output to npy Files

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
45/100
Issue type
Bug
Clarity
Mostly clear
Activity status
Stale
Tech stack
python
Domain
data

Research direction

Read dpdata/qe/scf.py, especially get_coords, and then the call from dpdata/plugins/qe.py shown in the traceback. Reproduce the reported QE MD trajectory failure with a suitable scf.out file or a reduced case. Done means qe/pw/scf conversion no longer raises the reported AttributeError and produces DeepMD/npy output.

Written by the indexing model from the issue text.

Description

feature request qe
Bug summary

I'm new to DeepMD and trying to convert a QE scf.out file into the DeepMD/npy format, but dpdata keeps failing.
qe/pw/scf parser raises AttributeError: 'numpy.ndarray' object has no attribute 'append' on QE MD trajectory

dpdata Version

0.2.24

Input Files, Running Commands, Error Log, etc.

Input files:

Error log:
Traceback (most recent call last):
File "/opt/ohpc/home/zzr/TeO/00.data/trans.py", line 15, in
system = dpdata.LabeledSystem(qe_out_file, fmt='qe/pw/scf')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/ohpc/home/zzr/.local/lib/python3.12/site-packages/dpdata/system.py", line 197, in init
self.from_fmt(
File "/opt/ohpc/home/zzr/.local/lib/python3.12/site-packages/dpdata/system.py", line 234, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/ohpc/home/zzr/.local/lib/python3.12/site-packages/dpdata/system.py", line 1224, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/ohpc/home/zzr/.local/lib/python3.12/site-packages/dpdata/plugins/qe.py", line 52, in from_labeled_system
) = dpdata.qe.scf.get_frame(file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/ohpc/home/zzr/.local/lib/python3.12/site-packages/dpdata/qe/scf.py", line 173, in get_frame
atom_names, natoms, types, coords = get_coords(inlines, cell)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/ohpc/home/zzr/.local/lib/python3.12/site-packages/dpdata/qe/scf.py", line 104, in get_coords
coord.append([float(jj) for jj in ii.split()[1:4]])
^^^^^^^^^^^^
AttributeError: 'numpy.ndarray' object has no attribute 'append'

Steps to Reproduce

Due to the large size of my input file, I am unable to upload it here. Are there any alternative methods for sharing it?

Further Information, Files, and Links

No response

Dominant language
Python
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Forks
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Avg merge
8d 3h
Merged PRs (30d)
1

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