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docs: case05纵波 + case06横波一维原子链

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- case05 Readme.md 更新为纵波模拟描述
- case05 run_dynamics.py 注释更新
- case06 创建为一维原子链横波模拟
  - coord.txt: fix_x=1, fix_y=1, fix_z=0 (z方向自由)
  - driver.txt: amp_z=0.5, freq_z=0.1, phi_z=90°
  - input.txt: 横波配置 + step_plot_wave
  - Readme.md + doc/index.html + run_dynamics.py
- 模拟验证通过 (50000步/30s)
This commit is contained in:
Ying-Li Niu
2026-06-11 13:27:43 +08:00
parent 80520590d1
commit 131f52fe19
10 changed files with 119 additions and 99 deletions
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examples/case06/input/bond.txt
+2 -2
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@@ -1,2 +1,2 @@
bond_name k rest_length
k1 100.0 1.0
bond_name k rest_length
k1 1.0 1.0
examples/case06/input/coord.txt
+60 -60
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@@ -1,61 +1,61 @@
n mass radius x y z vx vy vz fix_x fix_y fix_z
1 1 0.1 0 0 1 0 0 0 0 1 1
2 1 0.1 1 0 0 0 0 0 0 1 1
3 1 0.1 2 0 0 0 0 0 0 1 1
4 1 0.1 3 0 0 0 0 0 0 1 1
5 1 0.1 4 0 0 0 0 0 0 1 1
6 1 0.1 5 0 0 0 0 0 0 1 1
7 1 0.1 6 0 0 0 0 0 0 1 1
8 1 0.1 7 0 0 0 0 0 0 1 1
9 1 0.1 8 0 0 0 0 0 0 1 1
10 1 0.1 9 0 0 0 0 0 0 1 1
11 1 0.1 10 0 0 0 0 0 0 1 1
12 1 0.1 11 0 0 0 0 0 0 1 1
13 1 0.1 12 0 0 0 0 0 0 1 1
14 1 0.1 13 0 0 0 0 0 0 1 1
15 1 0.1 14 0 0 0 0 0 0 1 1
16 1 0.1 15 0 0 0 0 0 0 1 1
17 1 0.1 16 0 0 0 0 0 0 1 1
18 1 0.1 17 0 0 0 0 0 0 1 1
19 1 0.1 18 0 0 0 0 0 0 1 1
20 1 0.1 19 0 0 0 0 0 0 1 1
21 1 0.1 20 0 0 0 0 0 0 1 1
22 1 0.1 21 0 0 0 0 0 0 1 1
23 1 0.1 22 0 0 0 0 0 0 1 1
24 1 0.1 23 0 0 0 0 0 0 1 1
25 1 0.1 24 0 0 0 0 0 0 1 1
26 1 0.1 25 0 0 0 0 0 0 1 1
27 1 0.1 26 0 0 0 0 0 0 1 1
28 1 0.1 27 0 0 0 0 0 0 1 1
29 1 0.1 28 0 0 0 0 0 0 1 1
30 1 0.1 29 0 0 0 0 0 0 1 1
31 1 0.1 30 0 0 0 0 0 0 1 1
32 1 0.1 31 0 0 0 0 0 0 1 1
33 1 0.1 32 0 0 0 0 0 0 1 1
34 1 0.1 33 0 0 0 0 0 0 1 1
35 1 0.1 34 0 0 0 0 0 0 1 1
36 1 0.1 35 0 0 0 0 0 0 1 1
37 1 0.1 36 0 0 0 0 0 0 1 1
38 1 0.1 37 0 0 0 0 0 0 1 1
39 1 0.1 38 0 0 0 0 0 0 1 1
40 1 0.1 39 0 0 0 0 0 0 1 1
41 1 0.1 40 0 0 0 0 0 0 1 1
42 1 0.1 41 0 0 0 0 0 0 1 1
43 1 0.1 42 0 0 0 0 0 0 1 1
44 1 0.1 43 0 0 0 0 0 0 1 1
45 1 0.1 44 0 0 0 0 0 0 1 1
46 1 0.1 45 0 0 0 0 0 0 1 1
47 1 0.1 46 0 0 0 0 0 0 1 1
48 1 0.1 47 0 0 0 0 0 0 1 1
49 1 0.1 48 0 0 0 0 0 0 1 1
50 1 0.1 49 0 0 0 0 0 0 1 1
51 1 0.1 50 0 0 0 0 0 0 1 1
52 1 0.1 51 0 0 0 0 0 0 1 1
53 1 0.1 52 0 0 0 0 0 0 1 1
54 1 0.1 53 0 0 0 0 0 0 1 1
55 1 0.1 54 0 0 0 0 0 0 1 1
56 1 0.1 55 0 0 0 0 0 0 1 1
57 1 0.1 56 0 0 0 0 0 0 1 1
58 1 0.1 57 0 0 0 0 0 0 1 1
59 1 0.1 58 0 0 0 0 0 0 1 1
60 1 0.1 59 0 0 0 0 0 1 1 1
1 1 0.1 0 0 0 0 0 0 1 1 0
2 1 0.1 1 0 0 0 0 0 1 1 0
3 1 0.1 2 0 0 0 0 0 1 1 0
4 1 0.1 3 0 0 0 0 0 1 1 0
5 1 0.1 4 0 0 0 0 0 1 1 0
6 1 0.1 5 0 0 0 0 0 1 1 0
7 1 0.1 6 0 0 0 0 0 1 1 0
8 1 0.1 7 0 0 0 0 0 1 1 0
9 1 0.1 8 0 0 0 0 0 1 1 0
10 1 0.1 9 0 0 0 0 0 1 1 0
11 1 0.1 10 0 0 0 0 0 1 1 0
12 1 0.1 11 0 0 0 0 0 1 1 0
13 1 0.1 12 0 0 0 0 0 1 1 0
14 1 0.1 13 0 0 0 0 0 1 1 0
15 1 0.1 14 0 0 0 0 0 1 1 0
16 1 0.1 15 0 0 0 0 0 1 1 0
17 1 0.1 16 0 0 0 0 0 1 1 0
18 1 0.1 17 0 0 0 0 0 1 1 0
19 1 0.1 18 0 0 0 0 0 1 1 0
20 1 0.1 19 0 0 0 0 0 1 1 0
21 1 0.1 20 0 0 0 0 0 1 1 0
22 1 0.1 21 0 0 0 0 0 1 1 0
23 1 0.1 22 0 0 0 0 0 1 1 0
24 1 0.1 23 0 0 0 0 0 1 1 0
25 1 0.1 24 0 0 0 0 0 1 1 0
26 1 0.1 25 0 0 0 0 0 1 1 0
27 1 0.1 26 0 0 0 0 0 1 1 0
28 1 0.1 27 0 0 0 0 0 1 1 0
29 1 0.1 28 0 0 0 0 0 1 1 0
30 1 0.1 29 0 0 0 0 0 1 1 0
31 1 0.1 30 0 0 0 0 0 1 1 0
32 1 0.1 31 0 0 0 0 0 1 1 0
33 1 0.1 32 0 0 0 0 0 1 1 0
34 1 0.1 33 0 0 0 0 0 1 1 0
35 1 0.1 34 0 0 0 0 0 1 1 0
36 1 0.1 35 0 0 0 0 0 1 1 0
37 1 0.1 36 0 0 0 0 0 1 1 0
38 1 0.1 37 0 0 0 0 0 1 1 0
39 1 0.1 38 0 0 0 0 0 1 1 0
40 1 0.1 39 0 0 0 0 0 1 1 0
41 1 0.1 40 0 0 0 0 0 1 1 0
42 1 0.1 41 0 0 0 0 0 1 1 0
43 1 0.1 42 0 0 0 0 0 1 1 0
44 1 0.1 43 0 0 0 0 0 1 1 0
45 1 0.1 44 0 0 0 0 0 1 1 0
46 1 0.1 45 0 0 0 0 0 1 1 0
47 1 0.1 46 0 0 0 0 0 1 1 0
48 1 0.1 47 0 0 0 0 0 1 1 0
49 1 0.1 48 0 0 0 0 0 1 1 0
50 1 0.1 49 0 0 0 0 0 1 1 0
51 1 0.1 50 0 0 0 0 0 1 1 0
52 1 0.1 51 0 0 0 0 0 1 1 0
53 1 0.1 52 0 0 0 0 0 1 1 0
54 1 0.1 53 0 0 0 0 0 1 1 0
55 1 0.1 54 0 0 0 0 0 1 1 0
56 1 0.1 55 0 0 0 0 0 1 1 0
57 1 0.1 56 0 0 0 0 0 1 1 0
58 1 0.1 57 0 0 0 0 0 1 1 0
59 1 0.1 58 0 0 0 0 0 1 1 0
60 1 0.1 59 0 0 0 0 0 1 1 0
examples/case06/input/driver.txt
+1 -1
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@@ -1,2 +1,2 @@
n amp_x amp_y amp_z freq_x freq_y freq_z phi_x phi_y phi_z period
1 0.5 0 0 0.1 0 0 0 0 0 all
1 0 0 0.5 0 0 0.1 0 0 90 all
examples/case06/input/input.txt
+2 -1
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@@ -8,6 +8,7 @@
step_simulate: 1 # 运行物理模拟 → output/trajectory.txt
step_sample: 1 # 抽帧 → output/display.txt
step_plot: 0 # 绘制轨迹/能量图 → output/trajectory_plots.png
step_plot_wave: 0 # 绘制波形能量动画 → output/wave_animation.gif
step_animation: 1 # 自动播放 VisPy 3D 动画窗口（需安装 vispy）
force_calc: 0 # 强制重新计算：1=跳过缓存强算，0=自动使用已有输出
@@ -63,7 +64,7 @@ warmup_steps: 0 # 默认 0（立即开始记录）
T_total: 50.0
# 抽帧间隔（每 NSTEP 步取一帧用于动画）
NSTEP: 50
NSTEP: 100
# ── 时间步长 ──────────────────────────────────
DT: 0.001 # 时间步长 (s)