feat: 外部引擎实时进度条 + C引擎read_bonds rewind修复

1. 引擎端：C/C++/Fortran 主循环每 1% 输出 progress 到 stdout
2. compute.py：读取 "[xxx] progress: N/total" 行更新 tqdm
3. 移除不准的时间估算逻辑，改用真实引擎进度
4. C引擎 read_bonds：rewind 后补 fgets 跳表头
5. gitignore 添加 output_test/

compute.py

@@ -10,6 +10,7 @@ compute.py
 """
 
 import json
+import re
 import numpy as np
 import os
 import platform
@@ -760,6 +761,14 @@ def run_engine(engine, input_dir, output_dir, config):
                 _line = _line.strip()
                 if _line:
                     _engine_lines.append(_line)
+                    # 读取外部引擎真实进度：格式 "[xxx-engine] progress: N/total"
+                    _prog_match = re.search(r'progress:\s*(\d+)/(\d+)', _line)
+                    if _pbar is not None and _prog_match:
+                        _prog_done = int(_prog_match.group(1))
+                        _prog_total = int(_prog_match.group(2))
+                        if _prog_total > 0:
+                            _pbar.n = min(_prog_done, total_steps)
+                            _pbar.refresh()
             if _p.poll() is not None:
                 if _p.stdout:
                     for _r in _p.stdout:
@@ -767,9 +776,6 @@ def run_engine(engine, input_dir, output_dir, config):
                         if _r:
                             _engine_lines.append(_r)
                 break
-            if _pbar is not None and _est_total > 0:
-                _pbar.n = int(min((time.time() - t_start) / _est_total, 0.99) * total_steps)
-                _pbar.refresh()
             time.sleep(0.2)
     finally:
         if _pbar is not None: