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feat: 新增波形能量动画系统 plot_wave.py

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- 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
This commit is contained in:
Ying-Li Niu
2026-06-11 12:39:46 +08:00
parent 685234c84f
commit 80520590d1
20 changed files with 1231 additions and 86 deletions
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plot_wave.py
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"""
plot_wave.py
============
波形与能量动态图：读取 display.txt，绘制原子位移波形
（纵波 + 2 个横波）和系统能量/输入功率随时间变化的二维动画。
用法：
python plot_wave.py # 使用 dynamics 根目录下 output/
python plot_wave.py examples/case05/output # 指定案例输出目录
"""
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation
import os
import sys
sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
import compute
def load_disp_data(output_dir):
"""加载 display.txt"""
disp_path = os.path.join(output_dir, "display.txt")
if not os.path.exists(disp_path):
raise FileNotFoundError(f"找不到 {disp_path}")
return compute.load_text_data(disp_path)
def compute_energy(x, y, z, vx, vy, vz, masses, mass_arr,
bond_pairs, bond_stiffness, bond_rest_lengths,
gravity_field, G, gravity_interaction, gravity_strength):
"""计算系统各能量分量。
Returns:
ek_sys: 系统动能 (n_frames,)
us_sys: 系统弹性势能 (n_frames,)
ug_sys: 系统重力势能 (n_frames,)
ugr_sys: 系统万有引力势能 (n_frames,)
"""
n_frames = x.shape[0]
masses_2d = masses[np.newaxis, :] # (1, n_atoms)
# 动能 Ek = ½ m v²
ek = 0.5 * masses_2d * (vx**2 + vy**2 + vz**2)
ek_sys = np.sum(ek, axis=1)
# 弹性势能 Us = ½ k (d - d₀)²
us_sys = np.zeros(n_frames)
if bond_pairs is not None and len(bond_pairs) > 0:
for b_idx in range(len(bond_pairs)):
i, j = bond_pairs[b_idx]
dx = x[:, j] - x[:, i]
dy = y[:, j] - y[:, i]
dz = z[:, j] - z[:, i]
dist = np.sqrt(dx**2 + dy**2 + dz**2)
stretch = dist - bond_rest_lengths[b_idx]
us_sys += 0.5 * bond_stiffness[b_idx] * stretch**2
# 均匀重力场势能 Ug = -m G·r
ug_sys = np.zeros(n_frames)
if gravity_field:
G_vec = np.array(G)
ug_sys = -masses_2d * (G_vec[0] * x + G_vec[1] * y + G_vec[2] * z)
ug_sys = np.sum(ug_sys, axis=1)
# 万有引力势能 Ug_grav = -G_grav Σ m_i m_j / r
ugr_sys = np.zeros(n_frames)
if gravity_interaction:
n_atoms = len(masses)
# 为避免巨大计算量，仅当原子数较少时计算
if n_atoms <= 200:
for i in range(n_atoms):
for j in range(i + 1, n_atoms):
dx = x[:, j] - x[:, i]
dy = y[:, j] - y[:, i]
dz = z[:, j] - z[:, i]
dist = np.sqrt(dx**2 + dy**2 + dz**2)
dist = np.maximum(dist, 1e-12)
pair_pe = -gravity_strength * masses[i] * masses[j] / dist
ugr_sys += pair_pe
return ek_sys, us_sys, ug_sys, ugr_sys
def plot_wave(output_dir):
"""主绘图函数：读取 display.txt 并生成波形+能量动画。"""
data = load_disp_data(output_dir)
n_frames = int(data["n_frames"])
t = np.array(data["disp_t"])
# 位置 / 速度
x = np.array(data["disp_all_x"])
y = np.array(data["disp_all_y"])
z = np.array(data["disp_all_z"])
vx = np.array(data["disp_all_vx"])
vy = np.array(data["disp_all_vy"])
vz = np.array(data["disp_all_vz"])
# 原子信息
pos_0 = np.array(data["atom_positions"]) # (n_atoms, 3)
masses = np.array(data["atom_masses"])
atom_ids = np.array(data["atom_ids"])
n_atoms = len(atom_ids)
# 成键
bond_pairs = data.get("bond_pairs", [])
bond_stiffness = np.array(data.get("bond_stiffness", []))
bond_rest_lengths = np.array(data.get("bond_rest_lengths", []))
# 物理开关
gravity_field = int(data.get("gravity_field", 0))
gravity_interaction = int(data.get("gravity_interaction", 0))
G = data.get("G", [0, 0, 0])
gravity_strength = float(data.get("gravity_strength", 1.0))
driving_force = int(data.get("driving_force", 0))
# ── 位移（偏离初始平衡位形）──
dx = x - pos_0[np.newaxis, :, 0] # 纵波（沿链方向 x）
dy = y - pos_0[np.newaxis, :, 1] # 横波 1（y 方向）
dz = z - pos_0[np.newaxis, :, 2] # 横波 2（z 方向）
# ── 能量 ──
ek, us, ug, ugr = compute_energy(
x, y, z, vx, vy, vz, masses, masses,
bond_pairs, bond_stiffness, bond_rest_lengths,
gravity_field, G, gravity_interaction, gravity_strength)
e_total = ek + us + ug + ugr
power = np.gradient(e_total, t) # 输入功率 = dE/dt
# ── 波形纵轴范围（全局统一，避免抖动）──
def get_ylim(disp_data):
vmax = np.max(np.abs(disp_data))
if vmax < 1e-10:
return -1.0, 1.0
margin = vmax * 0.2
return -vmax - margin, vmax + margin
ylims = [get_ylim(dx), get_ylim(dy), get_ylim(dz)]
e_max = max(np.max(e_total), 0.01) * 1.3
p_abs = np.max(np.abs(power))
p_max = max(p_abs * 1.3, 0.01)
atom_idx = np.arange(n_atoms)
# ── 图形设置 ──
plt.rcParams['font.sans-serif'] = ['Microsoft YaHei', 'SimHei', 'DejaVu Sans']
plt.rcParams['axes.unicode_minus'] = False
fig, axes = plt.subplots(2, 2, figsize=(14, 10))
fig.suptitle("波形与能量分析", fontsize=16)
# ── 3 个波形子图 ──
titles = [
"纵波 (x 方向位移)",
"横波 (y 方向位移)",
"横波 (z 方向位移)",
]
colors = ["#2563eb", "#ea580c", "#16a34a"]
wave_configs = list(zip(
[axes[0, 0], axes[0, 1], axes[1, 0]],
[dx, dy, dz], titles, colors, ylims
))
wave_lines = []
time_texts = []
for ax, disp, title, color, yl in wave_configs:
ax.set_xlim(0, n_atoms - 1)
ax.set_ylim(yl)
ax.set_xlabel("原子序号")
ax.set_ylabel("位移")
ax.set_title(title)
ax.grid(True, alpha=0.3)
line, = ax.plot([], [], color=color, linewidth=1.5)
wave_lines.append(line)
tt = ax.text(0.02, 0.95, "", transform=ax.transAxes,
fontsize=11, verticalalignment="top")
time_texts.append(tt)
# ── 能量+功率子图 ──
ax_ep = axes[1, 1]
ax_ep.set_xlim(t[0], t[-1])
ep_ylow = min(-0.1 * max(e_max, p_max), -p_max * 0.1)
ep_yhigh = max(e_max, p_max)
ax_ep.set_ylim(ep_ylow, ep_yhigh)
ax_ep.set_xlabel("时间 (s)")
ax_ep.set_ylabel("能量 / 功率")
ax_ep.set_title("系统能量与输入功率")
ax_ep.grid(True, alpha=0.3)
line_ek, = ax_ep.plot([], [], "b-", lw=1.5, label="动能")
line_us, = ax_ep.plot([], [], "orange", lw=1.5, label="弹性势能")
line_et, = ax_ep.plot([], [], "r--", lw=1.5, label="总能量")
line_pw, = ax_ep.plot([], [], "g-", lw=1.5, alpha=0.7, label="输入功率 (dE/dt)")
if gravity_field:
line_ug, = ax_ep.plot([], [], "purple", lw=1.0, alpha=0.5, label="重力势能")
else:
line_ug = None
if gravity_interaction and n_atoms <= 200:
line_ugr, = ax_ep.plot([], [], "brown", lw=1.0, alpha=0.5, label="万有引力势能")
else:
line_ugr = None
ax_ep.legend(loc="upper right", fontsize=9)
plt.tight_layout(rect=[0, 0, 1, 0.95])
# ── 动画更新 ──
def update(frame):
# 波形
for i in range(3):
wave_lines[i].set_data(atom_idx, [dx, dy, dz][i][frame])
time_texts[i].set_text(f"t = {t[frame]:.2f} s | 帧 {frame+1}/{n_frames}")
# 能量（累计到当前帧）
cur_t = t[:frame + 1]
line_ek.set_data(cur_t, ek[:frame + 1])
line_us.set_data(cur_t, us[:frame + 1])
line_et.set_data(cur_t, e_total[:frame + 1])
line_pw.set_data(cur_t, power[:frame + 1])
if line_ug:
line_ug.set_data(cur_t, ug[:frame + 1])
if line_ugr:
line_ugr.set_data(cur_t, ugr[:frame + 1])
# 能量图 x 轴动态扩展
ax_ep.set_xlim(t[0], max(t[frame] + max(t[-1] * 0.05, 1), t[-1]))
artists = wave_lines + time_texts + [line_ek, line_us, line_et, line_pw]
if line_ug: artists.append(line_ug)
if line_ugr: artists.append(line_ugr)
return artists
ani = FuncAnimation(fig, update, frames=n_frames, interval=50, blit=True)
# 保存 GIF
gif_path = os.path.join(output_dir, "wave_animation.gif")
ani.save(gif_path, writer="pillow", fps=min(20, max(1, n_frames // 5)))
print(f"[plot_wave] GIF 已保存: {gif_path}")
# 尝试保存 MP4
try:
mp4_path = os.path.join(output_dir, "wave_animation.mp4")
ani.save(mp4_path, writer="ffmpeg", fps=min(20, max(1, n_frames // 5)))
print(f"[plot_wave] MP4 已保存: {mp4_path}")
except Exception:
pass
plt.show()
return gif_path
if __name__ == "__main__":
script_dir = os.path.dirname(os.path.abspath(__file__))
if len(sys.argv) > 1:
output_dir = os.path.abspath(sys.argv[1])
else:
output_dir = compute.get_output_dir(script_dir)
plot_wave(output_dir)