parse_output error

[김현우]

Hello

I am trying to calculate 'defect_data.json' using command 'pycdt parse_output -d [directory name]'

but it doesn't work, i get error message in the 'pycdt_parse_output.log'

I am wondering why the error occurs.(please see below)

Also, I am curious about what files (ex: POSCAR, CONTCAR, vasprun.xml. etc...) are read by the command 'pycdt parse_output'

Regards

--------------------pycdt_parse_output.log--------------------------

2021-03-08 13:39:20,617 - root - ERROR - No Materials Project structure ID provided! (proceeding anyway)

2021-03-08 13:39:22,811 - pycdt.utils.parse_calculations - DEBUG - Parsing folder SnO_hse/inter_2_C/charge_-1

2021-03-08 13:39:24,951 - root - ERROR - ERROR in running PyCDT:

PyCDT is a script that generates vasp input files, parses vasp output files, and computes the formation energy of charged defects.

This script works based on several sub-commands with their own options. To see the options for sub-commands, type: pycdt -h

Traceback (most recent call last):

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/pycdt-2.0.5-py3.8.egg/EGG-INFO/scripts/pycdt", line 545, in main

    args.func(args)

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/pycdt-2.0.5-py3.8.egg/EGG-INFO/scripts/pycdt", line 189, in parse_output

    defect_data = PostProcess(root_fldr, mp_id, mapi_key).compile_all()

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/pycdt-2.0.5-py3.8.egg/pycdt/utils/parse_calculations.py", line 814, in compile_all

    output = self.parse_defect_calculations()

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/pycdt-2.0.5-py3.8.egg/pycdt/utils/parse_calculations.py", line 694, in parse_defect_calculations

    defect = MontyDecoder().process_decoded( defect_dict)

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/monty-4.0.0-py3.8.egg/monty/json.py", line 340, in process_decoded

    return cls_.from_dict(data)

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/monty-4.0.0-py3.8.egg/monty/json.py", line 175, in from_dict

    return cls(**decoded)

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/pymatgen-2020.9.14-py3.8-linux-x86_64.egg/pymatgen/analysis/defects/core.py", line 321, in __init__

    super().__init__(structure=structure, defect_site=defect_site, charge=charge)

  File "/home/khw/src/anaconda3/envs/pycdt_venv/lib/python3.8/site-packages/pymatgen-2020.9.14-py3.8-linux-x86_64.egg/pymatgen/analysis/defects/core.py", line 61, in __init__

    raise ValueError("defect_site lattice must be same as structure "

ValueError: defect_site lattice must be same as structure lattice.

-------------------------

[PyCDT forum]

From the error message, looks like you did a full relaxation (ISIF=3) instead of constant volume relaxation. For defect calculations, you need to do a constant volume relaxation.

Bharat