feat: 新增波形能量动画系统 plot_wave.py
- 创建 plot_wave.py: 从 display.txt 读取原子位移数据 绘制纵波(x) + 横波(y) + 横波(z) 波形随时间的动画 同时绘制系统动能/弹性势能/总能量/输入功率(dE/dt)时变曲线 输出 wave_animation.gif - 所有 input.txt 新增 step_plot_wave: 0 开关 - case05 开启 step_plot_wave: 1 - dynamics.py disp_data 新增 bond_stiffness/bond_rest_lengths - 更新案例文档
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bond_name k rest_length
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k1 50.0 1.0
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k1 100.0 1.0
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n mass radius x y z vx vy vz fix_x fix_y fix_z
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1 1 0.1 0 0 1 0 0 0 1 1 0
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2 1 0.1 1 0 0 0 0 0 1 1 0
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1 1 0.1 0 0 1 0 0 0 0 1 1
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n amp_x amp_y amp_z freq_x freq_y freq_z phi_x phi_y phi_z period
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1 0 0 1 0 0 0.1 0 0 90 all
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1 0.5 0 0 1 0 0 0 0 0 all
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@@ -5,15 +5,16 @@
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# ── 流程控制 ──────────────────────────────────
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# 每步用 0/1 单独开关，1=执行，0=跳过
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# 依赖关系：抽帧依赖模拟结果，绘图依赖模拟+抽帧
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step_simulate: 1 # 运行物理模拟 → output/trajectory.txt
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step_sample: 1 # 抽帧 → output/display.txt
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step_simulate: 0 # 运行物理模拟 → output/trajectory.txt
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step_sample: 0 # 抽帧 → output/display.txt
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step_plot: 0 # 绘制轨迹/能量图 → output/trajectory_plots.png
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step_animation: 1 # 自动播放 VisPy 3D 动画窗口（需安装 vispy）
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step_animation: 0 # 自动播放 VisPy 3D 动画窗口（需安装 vispy）
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step_plot_wave: 1 # 绘制波形图
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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
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# ── 计算引擎 ──────────────────────────────────
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# 可选: python, c, cpp, fortran, java
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engine: python # 默认使用 Python 引擎
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engine: python # 默认使用 python 引擎
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# ── 盒子 ──────────────────────────────────────
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box_a: 80.0 # 立方体半边长，粒子被限制在 [-box_a, box_a]³ 内
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@@ -60,7 +61,7 @@ warmup_steps: 0 # 默认 0（立即开始记录）
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# 总模拟时间（秒），程序自动计算 NT = T_total / DT
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# 如果同时指定了 NT，以 NT 为准
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T_total: 100.0
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T_total: 10.0
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# 抽帧间隔（每 NSTEP 步取一帧用于动画）
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NSTEP: 50
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