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

Source: Codex global repository scan of deepmodeling/dpti at commit b719828e7eeb571bd26411430197cd74ea78e38c.
Project: https://github.com/orgs/deepmodeling/projects/27

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
https://github.com/deepmodeling/dpti/blob/b719828e7eeb571bd26411430197cd74ea78e38c/examples/gdi/command.sh#L1
https://github.com/deepmodeling/dpti/blob/b719828e7eeb571bd26411430197cd74ea78e38c/examples/gdi/pb.json#L4
https://github.com/deepmodeling/dpti/blob/b719828e7eeb571bd26411430197cd74ea78e38c/examples/gdi/pb.json#L12

Reproduction
Run:

```bash
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.

Start with examples/gdi/command.sh and inspect the referenced entries in examples/gdi/pb.json, especially lines 4 and 12. From examples/gdi/, verify the documented command, script name, input paths, and fixture references against the files present there. Done means the example command is copy-paste runnable from its documented directory with the available inputs.

Written by the indexing model from the issue text.