[Code scan] GDI example command and fixture paths are stale

[njzjz]

Source: Codex global repository scan of deepmodeling/dpti at commit b719828.
Project: DeepModeling Agent Code Scan

Problem
The GDI example command cannot run as written. It uses pb.josn instead of pb.json, calls python gdi.py from examples/gdi/ where no gdi.py exists, references machine.json that is not present in that directory, and pb.json points phase_i.equi_conf to beta.lmp while only alpha.lmp and bct.lmp are present locally.

Code references

dpti/examples/gdi/command.sh

Line 1 in b719828

python gdi.py pb.josn machine.json -g gdidata.json

dpti/examples/gdi/pb.json

Line 4 in b719828

"equi_conf": "beta.lmp",

dpti/examples/gdi/pb.json

Line 12 in b719828

"model": "../graph.pb",

Reproduction
Run:

cd examples/gdi
python gdi.py pb.josn machine.json -g gdidata.json

Expected result
Example commands should be copy-paste runnable from their documented directory, or clearly specify the required working directory and input files.