Index error and work flow questions

[Ziqi Cui]

Dear all,

I've just started to use PyCDT to calculate the correction term for my charged defect system. 

My system has 215 atoms and 1 vacancy. I have finished relaxing the bulk structure and defect structure and obtained the values of chemical potential and dielectric constant. Now I only want to calculate the correction term. Do I have to follow the workflow step by step? Can I only run the coding for correction term and how should I do this?

I tried running only the computation of correction term, but I got the error:

Will remove DefectsAnalyzer with Version 2.5 of PyCDT.
  warnings.warn("Replaced PyCDT usage of DefectsAnalyzer objects with "
No transformation file exists at /scratch/ziqicui/Ti8V4N10validate/VN1vac_benchmark/+1/transformation.json.
Calculating defect index manually (proceed with caution)
Traceback (most recent call last):
  File "/scratch/ziqicui/Ti8V4N10validate/VN1vac_benchmark/corr.py", line 10, in <module>
    kc = kumagai_correction_from_paths( defect_file_path, bulk_file_path,
  File "/home/ziqicui/pymatgen/lib/python3.10/site-packages/pycdt/core/defects_analyzer.py", line 76, in kumagai_correction_from_paths
    sdp = SingleDefectParser.from_paths( defect_file_path, bulk_file_path, dielectric, defect_charge)
  File "/home/ziqicui/pymatgen/lib/python3.10/site-packages/pycdt/utils/parse_calculations.py", line 217, in from_paths
    defect_index_sc_coords = poss_defect[0][0]
IndexError: list index out of range

How should I do in this case?

Thank you so much.