[BUG] dpgen init_bulk failed: ValueError(f"Can't parse Element or Species from {type(obj).__name__}: {obj}.")

[denghuilu]

Bug summary

While executing the init_bulk command as outlined in the documentation at https://bohrium-doc.dp.tech/docs/software/DP-GEN_init/, an unexpected error occurred:

DeepModeling
------------
Version: 0.12.0
Path:    /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/dpgen

Dependency
------------
     numpy     1.26.4   /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/numpy
    dpdata     0.2.18   /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/dpdata
  pymatgen            unknown version or path
     monty  2024.3.31   /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/monty
       ase     3.22.1   /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/ase
  paramiko      3.4.0   /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/paramiko
 custodian  2024.3.12   /home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/custodian

Reference
------------
Please cite:
Yuzhi Zhang, Haidi Wang, Weijie Chen, Jinzhe Zeng, Linfeng Zhang, Han Wang, and Weinan E,
DP-GEN: A concurrent learning platform for the generation of reliable deep learning
based potential energy models, Computer Physics Communications, 2020, 107206.
------------

Description
------------
Traceback (most recent call last):
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/periodic_table.py", line 1466, in get_el_sp
    return DummySpecies.from_str(obj)  # type: ignore
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/periodic_table.py", line 1372, in from_str
    return cls(sym, oxi, **properties)
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/periodic_table.py", line 1280, in __init__
    raise ValueError(f"{symbol} contains {symbol[:idx]}, which is a valid element symbol")
ValueError: Type contains T, which is a valid element symbol

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/denghui/deepmd-kit/venv/bin/dpgen", line 8, in <module>
    sys.exit(main())
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/dpgen/main.py", line 255, in main
    args.func(args)
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/dpgen/data/gen.py", line 1537, in gen_init_bulk
    make_super_cell(jdata)
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/dpgen/data/gen.py", line 318, in make_super_cell
    from_struct = Structure.from_file(from_file)
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/structure.py", line 2939, in from_file
    struct = cls.from_str(contents, fmt="poscar", primitive=primitive, sort=sort, merge_tol=merge_tol, **kwargs)
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/structure.py", line 2851, in from_str
    struct = Poscar.from_str(input_string, default_names=False, read_velocities=False, **kwargs).structure
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/io/vasp/inputs.py", line 442, in from_str
    struct = Structure(
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/structure.py", line 3751, in __init__
    super().__init__(
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/structure.py", line 986, in __init__
    site = PeriodicSite(
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/sites.py", line 334, in __init__
    species = Composition({get_el_sp(species): 1})  # type: ignore
  File "/home/denghui/deepmd-kit/venv/lib/python3.10/site-packages/pymatgen/core/periodic_table.py", line 1468, in get_el_sp
    raise ValueError(f"Can't parse Element or Species from {type(obj).__name__}: {obj}.")
ValueError: Can't parse Element or Species from str: Type.

DP-GEN Version

0.12.0

Platform, Python Version, Remote Platform, etc

No response

Input Files, Running Commands, Error Log, etc.

Arxiv.zip

Steps to Reproduce

Run

dpgen init_bulk param.json machine.json.

Further Information, Files, and Links

No response

[njzjz]

Have been fixed in #1471

[njzjz]

@wanghan-iapcm perhaps release a new version?

[njzjz]

v0.12.1 has been released.