Question about dpgen init_bulk

[Zhengyan-Jiang]

Here is my log.out:
INFO:dpgen:Current stage is 4, collect data
/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/vasp/outcar.py:102: UserWarning: The following structures were unconverged: [1]; so they are not collected.
warnings.warn(
Traceback (most recent call last):
File "/home/n12503304/deepmd-kit/bin/dpgen", line 8, in
sys.exit(main())
^^^^^^
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpgen/main.py", line 255, in main
args.func(args)
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpgen/data/gen.py", line 1568, in gen_init_bulk
coll_vasp_md(jdata)
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpgen/data/gen.py", line 1106, in coll_vasp_md
_sys = dpdata.LabeledSystem(oo, type_map=type_map)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/system.py", line 197, in init
self.from_fmt(
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/system.py", line 234, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/system.py", line 1224, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/plugins/vasp.py", line 117, in from_labeled_system
data = uniq_atom_names(data)
^^^^^^^^^^^^^^^^^^^^^
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/utils.py", line 120, in uniq_atom_names
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/n12503304/deepmd-kit/lib/python3.11/site-packages/dpdata/utils.py", line 120, in
data["atom_types"] = np.array([uidxmap[jj] for jj in tmp_type], dtype=int)
~~~~~~~^^^^
IndexError: list index out of range

This is my param.json: (MD step was set 1 for testing)
{
"stages": [1, 2, 3, 4],
"elements": ["C", "N", "Co", "H"],
"cell_type": "",
"latt": 12.0,
"super_cell": [1, 1, 1],
"from_poscar": true,
"from_poscar_path": "/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/POSCAR",
"potcars": [
"/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/POTCAR_C",
"/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/POTCAR_N",
"/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/POTCAR_Co",
"/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/POTCAR_H"
],
"relax_incar": "/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/INCAR-opt",
"md_incar": "/home/n12503304/her-pes/dpgen-test-64cpu/init_structures/INCAR-md",
"skip_relax": false,
"scale": [1.00],
"pert_numb": 4,
"pert_box": 0.02,
"pert_atom": 0.01,
"md_nstep": 1,
"coll_ndata": 5000,
"type_map": ["C", "N", "Co", "H"],
"_comment": "that's all"
}

This is my machine.json:

machine.json

This is my POSCAR:

POSCAR
1.0000000000000000
9.8400001526000000 0.0000000000000000 0.0000000000000000
-4.9200000763000000 8.5216901053999994 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C N Co H
26 4 1 1
Direct
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0.1554354015681576 0.1085014508963299 0.4687717758714467
0.2418672285075842 0.0267118208110159 0.4690370314461365
0.4100376454926568 0.1085337650731427 0.4687706461913922
0.4868557879999709 0.0157413335488300 0.4683255016915739
0.6523884272514190 0.0936908239652958 0.4681261264967694
0.7312957850283893 0.0056212648926450 0.4685186760891326
0.8982397323062367 0.0936820243413432 0.4680762941329361
0.9814923200400585 0.2618798436059844 0.4674574976269477
0.1460208801152169 0.3466209394936502 0.4674686413109229
0.6574698522908026 0.3466217259462563 0.4674907409980925
0.7372385382756642 0.2618585241753336 0.4675116008040225
0.9022248827417177 0.3476350109779835 0.4672723856237063
0.9856583038876889 0.5144954518000863 0.4672858736907984
0.1506758068926796 0.6001935737791042 0.4674731729558844
0.2304272684243690 0.5153849289392142 0.4674797923697324
0.7418407197779568 0.5153618728715414 0.4675182851466897
0.9063902561434750 0.6002006289266761 0.4675300468631145
0.9896926130631856 0.7683608154369886 0.4681106823843654
0.1566938217411077 0.8564034434097035 0.4685009230085749
0.2355934238876832 0.7683659192993401 0.4680970175950054
0.4011444060634187 0.8463043976618527 0.4683187189778881
0.4779143596402720 0.7534807564298777 0.4687826238809870
0.6461302933528043 0.8352914287759873 0.4690638653828673
0.7324393188552003 0.7534287829417032 0.4688043061101995
0.9020422233697217 0.8462376672922897 0.4683304376398007
0.2318470871144042 0.2717963415121643 0.4681739787617530
0.4968307190290839 0.2718128238536128 0.4681787887381880
0.3910623266998756 0.5901900022599891 0.4681863699824853
0.6559766919885629 0.5901400110537688 0.4682188345305093
0.4439140201255247 0.4309644287776785 0.4746623913481502
0.4438097404029228 0.4308713923507435 0.5708889031667981

0.00000000E+00 0.00000000E+00 0.00000000E+00
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