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:

engines/c/main.c

@@ -926,7 +926,13 @@ int main(int argc, char **argv) {
     }
 
     /* 记录 */
+    int _prog_interval = record_steps / 100;
+    if (_prog_interval < 1) _prog_interval = 1;
     for (int s = 0; s < record_steps; s++) {
+        if (s % _prog_interval == 0 && s > 0) {
+            printf("[C-engine] progress: %d/%d\n", s, record_steps);
+            fflush(stdout);
+        }
         double t = (s + params.warmup_steps) * params.DT;
         if (params.driving_force) apply_driving_force(n, x, y, z, vx, vy, vz, t, s, params.DT, &drivers);
         for (int i = 0; i < n; i++) {

engines/cpp/main.cpp

@@ -843,7 +843,12 @@ int main(int argc, char **argv) {
     }
 
     // 记录
+    int _prog_int = record_steps / 100;
+    if (_prog_int < 1) _prog_int = 1;
     for (int s = 0; s < record_steps; s++) {
+        if (s % _prog_int == 0 && s > 0) {
+            std::cout << "[Cpp-engine] progress: " << s << "/" << record_steps << std::endl;
+        }
         double t = (s + params.warmup_steps) * params.DT;
         if (params.driving_force)
             apply_driving_force(n, x.data(), y.data(), z.data(), vx.data(), vy.data(), vz.data(), t, s, params.DT, drivers);

engines/fortran/main.f90

@@ -34,7 +34,7 @@ program dynamics_f90
     double precision, allocatable :: bond_stiffness(:), bond_rest_lengths(:)
 
     ! 驱动力数据
-    integer :: n_drivers
+    integer :: n_drivers, prog_step
     integer, allocatable :: drv_atom_idx(:)
     double precision, allocatable :: drv_amp_x(:), drv_amp_y(:), drv_amp_z(:)
     double precision, allocatable :: drv_freq_x(:), drv_freq_y(:), drv_freq_z(:)
@@ -139,7 +139,12 @@ program dynamics_f90
     end do
 
     ! 记录
+    prog_step = record_steps / 100
+    if (prog_step < 1) prog_step = 1
     do s = 1, record_steps
+        if (mod(s, prog_step) == 0 .and. s > 0) then
+            write(*, '("[Fortran-engine] progress: ", i0, "/", i0)') s, record_steps
+        end if
         if (driving_force /= 0 .and. n_drivers > 0) then
             tw = ((s-1 + warmup_steps) * 1.0d0) * DT
             call apply_driving(n, x, y, z, vx, vy, vz, tw, s-1, DT, &

examples/case06/input/input.txt

@@ -63,7 +63,7 @@ warmup_steps: 0           # 默认 0（立即开始记录）
 
 # 总模拟时间（秒），程序自动计算 NT = T_total / DT
 # 如果同时指定了 NT，以 NT 为准
-T_total:  10.0
+T_total:  50.0
 
 # 抽帧间隔（每 NSTEP 步取一帧用于动画）
 NSTEP: 100