[BUG] Converting from Quantum Espresso cp.x traj gives error when there is only one line in the energy output file #899
Description
Bug summary
In dpdata/qe/traj.py in load_energy function data = np.loadtxt(fname) is expected to be 2D array, but in the case when the .evp file contains a single line, it becomes a 1D array, which raises error afterwards.
Solution: add the following after loading the data
if data.ndim == 1: data = data[np.newaxis, :]
dpdata Version
dpdata v0.2.25
Input Files, Running Commands, Error Log, etc.
Input files: qe-cpx.zip
Error log:
dpdata --from_format qe/cp/traj P
Traceback (most recent call last):
File "/home/constant/miniconda3/envs/deepmd310/bin/dpdata", line 8, in
sys.exit(dpdata_cli())
^^^^^^^^^^^^
File "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/cli.py", line 56, in dpdata_cli
convert(**vars(parsed_args))
File "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/cli.py", line 96, in convert
s = LabeledSystem(from_file, fmt=from_format, type_map=type_map)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/system.py", line 197, in init
self.from_fmt(
File "/home/constant/miniconda3/envs/deepmd310/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 "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/system.py", line 1224, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/plugins/qe.py", line 31, in from_labeled_system
data["energies"], data["forces"], es = dpdata.qe.traj.to_system_label(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/qe/traj.py", line 262, in to_system_label
energy, esteps = load_energy(prefix + ".evp", begin=begin, step=step)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/constant/miniconda3/envs/deepmd310/lib/python3.12/site-packages/dpdata/qe/traj.py", line 174, in load_energy
for ii in data[begin::step, 0]:
~~~~^^^^^^^^^^^^^^^^
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed
Steps to Reproduce
Unpack zip and run dpdata --from_format qe/cp/traj P
Further Information, Files, and Links
No response