modified: CMakeLists.txt

modified:   INSTALL.md
	modified:   README.md
	modified:   build_release_zip.py
	modified:   compute.py
	new file:   doc/index.html
	modified:   dynamics.py
	modified:   engines/c/main.c
	modified:   engines/cpp/main.cpp
	modified:   engines/fortran/main.f90
	modified:   examples/case01/input/coord.txt
	renamed:    examples/case01/input/parameters.yaml -> examples/case01/input/input.txt
	modified:   examples/case01/run_dynamics.py
	new file:   examples/case02/input/bond.txt
	new file:   examples/case02/input/connection.txt
	new file:   examples/case02/input/coord.txt
	new file:   examples/case02/input/input.txt
	new file:   examples/case02/run_dynamics.py

INSTALL.md

@@ -461,7 +461,7 @@ py -3 examples/case01/run_dynamics.py
 ### C 引擎验证
 
 ```bash
-# 修改 parameters.yaml 中 engine: python → engine: c
+# 修改 input.txt 中 engine: python → engine: c
 # 或用命令行指定
 py -3 examples/case01/run_dynamics.py
 ```
@@ -543,7 +543,7 @@ pip install -i https://pypi.tuna.tsinghua.edu.cn/simple numpy pyyaml tqdm matplo
 ### Q: 如何使用 C 引擎？
 
 ```yaml
-# 1. 修改 examples/case01/input/parameters.yaml
+# 1. 修改 examples/case01/input/input.txt
 engine: c
 
 # 2. 先编译