How to deal with this error [dpgen autotest make ... self.data['atom_types'] = np.argsort(idx)[self.data['atom_types']] IndexError: index 2 is out of bounds for axis 0 with size 2]

[baoqinfu]

Summary

I am run “dpgen autotest make ...”
but I get the below information in my screen:

(base) [bqfu@node01 ea05]$ /home/share/dp/bin/dpgen autotest make property3c.json
DeepModeling

Version: 0.9.1.dev0+g769ccf4.d20210311
Date: Mar-11-2021
Path: /home/bqfu/.local/lib/python3.7/site-packages/dpgen

Dependency

 numpy     1.16.3   /home/bqfu/anaconda3/lib/python3.7/site-packages/numpy
dpdata     0.1.19   /home/bqfu/.local/lib/python3.7/site-packages/dpdata

pymatgen 2019.4.11 /home/bqfu/anaconda3/lib/python3.7/site-packages/pymatgen
monty 2021.3.3 /home/bqfu/.local/lib/python3.7/site-packages/monty
ase 3.21.1 /home/bqfu/.local/lib/python3.7/site-packages/ase
paramiko 2.7.2 /home/bqfu/.local/lib/python3.7/site-packages/paramiko
custodian 2021.2.8 /home/bqfu/.local/lib/python3.7/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

----------------------------------3c----------------------------------
gen eos from 0.85 to 1.15 by every 0.01
gen with norm [-0.002, -0.001, 0.001, 0.002]
gen with shear [-0.005, -0.0025, 0.0025, 0.005]
gen vacancy with supercell [3, 3, 3]
gen interstitial with supercell [6, 6, 6] with element ['Si', 'C']
Traceback (most recent call last):
File "/home/share/dp/bin/dpgen", line 11, in
sys.exit(main())
File "/home/bqfu/.local/lib/python3.7/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpgen/auto_test/run.py", line 57, in gen_test
run_task(args.TASK, args.PARAM, args.MACHINE)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpgen/auto_test/run.py", line 28, in run_task
make_property(confs, inter_parameter, property_list)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpgen/auto_test/common_prop.py", line 91, in make_property
inter.make_input_file(kk, prop.task_type(), prop.task_param())
File "/home/bqfu/.local/lib/python3.7/site-packages/dpgen/auto_test/Lammps.py", line 119, in make_input_file
lammps.cvt_lammps_conf(os.path.join(output_dir, 'POSCAR'), os.path.join(output_dir, 'conf.lmp'), lammps.element_list(self.type_map))
File "/home/bqfu/.local/lib/python3.7/site-packages/dpgen/auto_test/lib/lammps.py", line 29, in cvt_lammps_conf
d_poscar = dpdata.System(fin, fmt='vasp/poscar', type_map=type_map)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpdata/system.py", line 123, in init
self.apply_type_map(type_map)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpdata/system.py", line 405, in apply_type_map
self.check_type_map(type_map)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpdata/system.py", line 401, in check_type_map
self.sort_atom_names(type_map=type_map)
File "/home/bqfu/.local/lib/python3.7/site-packages/dpdata/system.py", line 388, in sort_atom_names
self.data['atom_types'] = np.argsort(idx)[self.data['atom_types']]
IndexError: index 2 is out of bounds for axis 0 with size 2

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[AnguseZhang]

Please provide your input files to help locate and reproduce the problem.

[njzjz]

It is probably fixed by deepmodeling/dpdata#250