docs: remove set_prefix

[njzjz]

See:

• [BUG] set_prefix doesn't work for both TF and PT deepmd-kit#3477
• breaking: deprecate set_prefix deepmd-kit#3753

Summary by CodeRabbit

• Refactor
  • Removed the "set_prefix": "set" attribute across various JSON and YAML configuration files, streamlining data handling and batch processing setups.

[coderabbitai]

Walkthrough

The recent updates involve the systematic removal of the "set_prefix": "set" attribute from the training_data section in various JSON and YAML configuration files. This change indicates a shift in how training data prefixes are managed, potentially streamlining configuration processes or adapting to new standards in data handling.

Changes

Files Affected	Change Summary
Various param.json, param.yaml files in examples/run/..., tests/generator/...	Removed "set_prefix": "set" from training_data.
param_CH4_deepmd-kit-2.0.1.json, param_C4H16N4_deepmd-kit-2.0.1.json in examples/run/dp2.x-lammps-gaussian/	Removed _set_prefix attribute from the training section.
doc/simplify/simplify.md, examples/simplify/qm7.json	Removed "set_prefix": "set" declaration under training_data.
tests/tools/run_report_test_output/param.json	Removal of "set_prefix": "set" under "training_data".

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[coderabbitai]

Actionable comments posted: 0

Out of diff range and nitpick comments (3)

doc/simplify/simplify.md (3)

Line range hint 1-119: Ensure that headings are surrounded by blank lines for better readability and adherence to Markdown formatting standards.

+ 
## Simplify
+ 
When you have a dataset containing lots of repeated data, this step will help you simplify your dataset.

---

Line range hint 119-119: Add a comma after "simplify" to improve the readability of the sentence.

- ...pick_data>` is the directory to data to simplify where the program recursively detects systems...
+ ...pick_data>` is the directory to data to simplify, where the program recursively detects systems...

---

Line range hint 1-119: Ensure that fenced code blocks are surrounded by blank lines to comply with Markdown best practices.

+ 
```bash
dpgen simplify param.json machine.json

Here is an example of param.json for QM7 dataset:
+

</blockquote></details></blockquote></details>



<!-- This is an auto-generated comment by CodeRabbit for review status -->

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 49.49%. Comparing base (f240e8b) to head (22c0aa6).

Additional details and impacted files

@@           Coverage Diff           @@
##            devel    #1537   +/-   ##
=======================================
  Coverage   49.49%   49.49%           
=======================================
  Files          83       83           
  Lines       14816    14816           
=======================================
  Hits         7333     7333           
  Misses       7483     7483           

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