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deepmodeling / dpgen

The deep potential generator to generate a deep-learning based model of interatomic potential energy and force field
https://docs.deepmodeling.com/projects/dpgen/
GNU Lesser General Public License v3.0
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IndexError: list index out of range in dpgen init_bulk #647

Closed PKUfjh closed 2 years ago

PKUfjh commented 2 years ago

When I run dpgen init_bulk, I found out the following IndexError:

File "/rhome/dhileept/.local/lib/python3.9/site-packages/dpgen/data/gen.py", line 176, in poscar_scale if 'D' == lines[7][0] or 'd' == lines[7][0]: IndexError: list index out of range

DPGEN 0.10.3 Platform: Lebesgue DPGEN image

INCAR_fullerene.rlx PREC=A ENCUT=400 ISYM=0 ALGO=Fast EDIFF=1.000000e-06 LREAL=False NPAR=4 KPAR=1 NELM=120 NELMIN=4 ISIF=2 ISMEAR=0 SIGMA=0.20000 IBRION=2 NSW=50 LWAVE=F LCHARG=F PSTRESS=0 KSPACING=0.500000 KGAMMA=.FALSE.

INCAR_fullerene.md PREC=A ENCUT=400 ISYM=0 ALGO=Fast EDIFF=1.000000e-06 LREAL=False NPAR=4 KPAR=1 NELM=120 NELMIN=4 ISIF=2 ISMEAR=0 SIGMA=0.20000 IBRION=0 POTIM=0.5 NSW=10 LWAVE=F LCHARG=F PSTRESS=0 KSPACING=0.500000 KGAMMA=.FALSE.

C60.POSCAR C240 1.0 14.023496 0.000000 0.000000 0.000000 14.023496 0.000000 0.000000 0.000000 14.023496 C 240 direct 0.551807 0.185443 0.164208 C 0.551807 0.185443 0.835793 C 0.783635 0.416276 0.101528 C 0.164208 0.448193 0.814558 C 0.164208 0.448193 0.185443 C 0.283635 0.083724 0.101528 C 0.814558 0.335792 0.051807 C 0.416276 0.101528 0.216365 C 0.500000 0.050028 0.249030 C 0.398472 0.216365 0.083724 C 0.814558 0.335792 0.948193 C 0.101528 0.283635 0.916276 C 0.250970 0.000000 0.050028 C 0.835793 0.448193 0.814558 C 0.314557 0.164208 0.948193 C 0.685442 0.164208 0.948193 C 0.916276 0.398472 0.783635 C 0.185443 0.335792 0.948193 C 0.314557 0.164208 0.051807 C 0.448193 0.185443 0.164208 C 0.398472 0.216365 0.916276 C 0.664207 0.051807 0.814558 C 0.749031 0.000000 0.949971 C 0.601528 0.216365 0.916276 C 0.216365 0.416276 0.898472 C 0.685442 0.164208 0.051807 C 0.948193 0.314557 0.164208 C 0.000000 0.449972 0.750969 C 0.083724 0.398472 0.783635 C 0.185443 0.335792 0.051807 C 0.416276 0.101528 0.783635 C 0.716365 0.083724 0.101528 C 0.583724 0.101528 0.783635 C 0.500000 0.050028 0.750969 C 0.216365 0.416276 0.101528 C 0.948193 0.314557 0.835793 C 0.449972 0.249030 0.000000 C 0.583724 0.101528 0.216365 C 0.083724 0.398472 0.216365 C 0.601528 0.216365 0.083724 C 0.448193 0.185443 0.835793 C 0.916276 0.398472 0.216365 C 0.000000 0.449972 0.249030 C 0.783635 0.416276 0.898472 C 0.749031 0.000000 0.050028 C 0.898472 0.283635 0.916276 C 0.835793 0.448193 0.185443 C 0.664207 0.051807 0.185443 C 0.101528 0.283635 0.083724 C 0.250970 0.000000 0.949971 C 0.949971 0.250970 0.000000 C 0.051807 0.314557 0.164208 C 0.335792 0.051807 0.185443 C 0.283635 0.083724 0.898472 C 0.898472 0.283635 0.083724 C 0.335792 0.051807 0.814558 C 0.716365 0.083724 0.898472 C 0.050028 0.250970 0.000000 C 0.051807 0.314557 0.835793 C 0.550029 0.249030 0.000000 C 0.551807 0.685442 0.664207 C 0.551807 0.685442 0.335792 C 0.783635 0.916276 0.601528 C 0.164208 0.948193 0.314557 C 0.164208 0.948193 0.685442 C 0.283635 0.583724 0.601528 C 0.814558 0.835793 0.551807 C 0.416276 0.601528 0.716365 C 0.500000 0.550029 0.749031 C 0.398472 0.716365 0.583724 C 0.814558 0.835793 0.448193 C 0.101528 0.783635 0.416276 C 0.250970 0.500000 0.550029 C 0.835793 0.948193 0.314557 C 0.314557 0.664207 0.448193 C 0.685442 0.664207 0.448193 C 0.916276 0.898472 0.283635 C 0.185443 0.835793 0.448193 C 0.314557 0.664207 0.551807 C 0.448193 0.685442 0.664207 C 0.398472 0.716365 0.416276 C 0.664207 0.551807 0.314557 C 0.749031 0.500000 0.449972 C 0.601528 0.716365 0.416276 C 0.216365 0.916276 0.398472 C 0.685442 0.664207 0.551807 C 0.948193 0.814558 0.664207 C 0.000000 0.949971 0.250970 C 0.083724 0.898472 0.283635 C 0.185443 0.835793 0.551807 C 0.416276 0.601528 0.283635 C 0.716365 0.583724 0.601528 C 0.583724 0.601528 0.283635 C 0.500000 0.550029 0.250970 C 0.216365 0.916276 0.601528 C 0.948193 0.814558 0.335792 C 0.449972 0.749031 0.500000 C 0.583724 0.601528 0.716365 C 0.083724 0.898472 0.716365 C 0.601528 0.716365 0.583724 C 0.448193 0.685442 0.335792 C 0.916276 0.898472 0.716365 C 0.000000 0.949971 0.749031 C 0.783635 0.916276 0.398472 C 0.749031 0.500000 0.550029 C 0.898472 0.783635 0.416276 C 0.835793 0.948193 0.685442 C 0.664207 0.551807 0.685442 C 0.101528 0.783635 0.583724 C 0.250970 0.500000 0.449972 C 0.949971 0.750969 0.500000 C 0.051807 0.814558 0.664207 C 0.335792 0.551807 0.685442 C 0.283635 0.583724 0.398472 C 0.898472 0.783635 0.583724 C 0.335792 0.551807 0.314557 C 0.716365 0.583724 0.398472 C 0.050028 0.750969 0.500000 C 0.051807 0.814558 0.335792 C 0.550029 0.749031 0.500000 C 0.051807 0.185443 0.664207 C 0.051807 0.185443 0.335792 C 0.283635 0.416276 0.601528 C 0.664207 0.448193 0.314557 C 0.664207 0.448193 0.685442 C 0.783635 0.083724 0.601528 C 0.314557 0.335792 0.551807 C 0.916276 0.101528 0.716365 C 0.000000 0.050028 0.749031 C 0.898472 0.216365 0.583724 C 0.314557 0.335792 0.448193 C 0.601528 0.283635 0.416276 C 0.750969 0.000000 0.550029 C 0.335792 0.448193 0.314557 C 0.814558 0.164208 0.448193 C 0.185443 0.164208 0.448193 C 0.416276 0.398472 0.283635 C 0.685442 0.335792 0.448193 C 0.814558 0.164208 0.551807 C 0.948193 0.185443 0.664207 C 0.898472 0.216365 0.416276 C 0.164208 0.051807 0.314557 C 0.249030 0.000000 0.449972 C 0.101528 0.216365 0.416276 C 0.716365 0.416276 0.398472 C 0.185443 0.164208 0.551807 C 0.448193 0.314557 0.664207 C 0.500000 0.449972 0.250970 C 0.583724 0.398472 0.283635 C 0.685442 0.335792 0.551807 C 0.916276 0.101528 0.283635 C 0.216365 0.083724 0.601528 C 0.083724 0.101528 0.283635 C 0.000000 0.050028 0.250970 C 0.716365 0.416276 0.601528 C 0.448193 0.314557 0.335792 C 0.949971 0.249030 0.500000 C 0.083724 0.101528 0.716365 C 0.583724 0.398472 0.716365 C 0.101528 0.216365 0.583724 C 0.948193 0.185443 0.335792 C 0.416276 0.398472 0.716365 C 0.500000 0.449972 0.749031 C 0.283635 0.416276 0.398472 C 0.249030 0.000000 0.550029 C 0.398472 0.283635 0.416276 C 0.335792 0.448193 0.685442 C 0.164208 0.051807 0.685442 C 0.601528 0.283635 0.583724 C 0.750969 0.000000 0.449972 C 0.449972 0.250970 0.500000 C 0.551807 0.314557 0.664207 C 0.835793 0.051807 0.685442 C 0.783635 0.083724 0.398472 C 0.398472 0.283635 0.583724 C 0.835793 0.051807 0.314557 C 0.216365 0.083724 0.398472 C 0.550029 0.250970 0.500000 C 0.551807 0.314557 0.335792 C 0.050028 0.249030 0.500000 C 0.051807 0.685442 0.164208 C 0.051807 0.685442 0.835793 C 0.283635 0.916276 0.101528 C 0.664207 0.948193 0.814558 C 0.664207 0.948193 0.185443 C 0.783635 0.583724 0.101528 C 0.314557 0.835793 0.051807 C 0.916276 0.601528 0.216365 C 0.000000 0.550029 0.249030 C 0.898472 0.716365 0.083724 C 0.314557 0.835793 0.948193 C 0.601528 0.783635 0.916276 C 0.750969 0.500000 0.050028 C 0.335792 0.948193 0.814558 C 0.814558 0.664207 0.948193 C 0.185443 0.664207 0.948193 C 0.416276 0.898472 0.783635 C 0.685442 0.835793 0.948193 C 0.814558 0.664207 0.051807 C 0.948193 0.685442 0.164208 C 0.898472 0.716365 0.916276 C 0.164208 0.551807 0.814558 C 0.249030 0.500000 0.949971 C 0.101528 0.716365 0.916276 C 0.716365 0.916276 0.898472 C 0.185443 0.664207 0.051807 C 0.448193 0.814558 0.164208 C 0.500000 0.949971 0.750969 C 0.583724 0.898472 0.783635 C 0.685442 0.835793 0.051807 C 0.916276 0.601528 0.783635 C 0.216365 0.583724 0.101528 C 0.083724 0.601528 0.783635 C 0.000000 0.550029 0.750969 C 0.716365 0.916276 0.101528 C 0.448193 0.814558 0.835793 C 0.949971 0.749031 0.000000 C 0.083724 0.601528 0.216365 C 0.583724 0.898472 0.216365 C 0.101528 0.716365 0.083724 C 0.948193 0.685442 0.835793 C 0.416276 0.898472 0.216365 C 0.500000 0.949971 0.249030 C 0.283635 0.916276 0.898472 C 0.249030 0.500000 0.050028 C 0.398472 0.783635 0.916276 C 0.335792 0.948193 0.185443 C 0.164208 0.551807 0.185443 C 0.601528 0.783635 0.083724 C 0.750969 0.500000 0.949971 C 0.449972 0.750969 0.000000 C 0.551807 0.814558 0.164208 C 0.835793 0.551807 0.185443 C 0.783635 0.583724 0.898472 C 0.398472 0.783635 0.083724 C 0.835793 0.551807 0.814558 C 0.216365 0.583724 0.898472 C 0.550029 0.750969 0.000000 C 0.551807 0.814558 0.835793 C 0.050028 0.749031 0.000000 C

POTCAR_C download from official website

init.json file { "stages": [1,2,3,4], "cell_type": "fcc", "super_cell": [1, 1, 1], "elements": ["C"], "from_poscar": true, "from_poscar_path": "./C60.POSCAR", "potcars": ["./POTCAR_C"], "relax_incar": "./INCAR_fullerene.rlx", "md_incar" : "./INCAR_fullerene.md", "scale": [1.00], "skip_relax": false, "pert_numb": 30, "md_nstep" : 10, "pert_box": 0.03, "pert_atom": 0.01, "deepgen_templ": "../generator/template/", "coll_ndata": 5000, "_comment": "that's all" }

machine.json file (neglect the train and model_devi section) { "api_version": "1.0", "deepmd_version": "2.0.1", "fp": [{ "command": "mpirun -n 16 vasp_std", "machine": { "batch_type": "Lebesgue", "context_type": "LebesgueContext", "local_root" : "./", "remote_profile":{ "email": "***", "password": "****", "program_id": 717, "keep_backup":true, "input_data":{ "job_type": "indicate", "log_file": "task*/fp.log", "grouped":true, "job_name": "dpgen_fp_job", "disk_size": 300, "checkpoint_files": "sync_files", "checkpoint_time":15, "scass_type":"c32_m128_cpu", "platform": "ali", "image_name":"LBG_vasp-vtst-5-4-4_v1", "on_demand":1 } } }, "resources": { "group_size": 50, "local_root":"./", "source_list": ["/opt/intel/oneapi/setvars.sh"] } } ] }

Expected Behavior

Actual Behavior In 00.place_ele directory, POSCAR is generated the same with the original C60.POSCAR. But CONTCAR is empty. The submitted job is terminated and generate this IndexError.

Steps to Reproduce dpgen init_bulk init.json machine.json

Additional information the system to use running dpgen has 240 atoms, it has this error. When I use the same INCAR and POTCAR, but change the number of atoms to less than 120, it does not has this error.

AnguseZhang commented 2 years ago

Can you post your original POSCAR, and CONTCAR generated in 00.place_ele?

PKUfjh commented 2 years ago

Found the problem, it is the memory issue. One should set unlimit -s unlimited in the source lists.