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/

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, &