admin
1cefe184d7
Add show=False parameter to plot_wave(); when called from dynamics.py, pass show=False and set matplotlib Agg backend to avoid NonGuiException. Also print full traceback on failure for easier debugging. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
378 lines
14 KiB
Python
378 lines
14 KiB
Python
"""
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plot_wave.py
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============
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波形与能量动态图：读取 display.txt，绘制原子位移波形
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（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。
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用法：
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python plot_wave.py # 使用 dynamics 根目录下 output/
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python plot_wave.py examples/case05/output # 指定案例输出目录
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"""
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import numpy as np
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import matplotlib.pyplot as plt
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from matplotlib.animation import FuncAnimation
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import os
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import sys
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import json
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sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
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import compute
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def load_disp_data(output_dir):
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"""加载 display.npz（优先）或 display.txt。"""
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npz_path = os.path.join(output_dir, "display.npz")
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txt_path = os.path.join(output_dir, "display.txt")
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if os.path.exists(npz_path):
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return compute.load_display_npz(npz_path)
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if os.path.exists(txt_path):
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return compute.load_display_txt(txt_path)
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raise FileNotFoundError(f"找不到 display.npz 或 display.txt in {output_dir}")
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def _header_json(header_fields, key, default):
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raw = header_fields.get(key, "")
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if not raw:
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return default
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try:
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return json.loads(raw)
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except json.JSONDecodeError:
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return default
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def _load_wave_dataset(output_dir):
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"""Load wave/energy plotting data from display metadata or sibling input files."""
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disp_data = load_disp_data(output_dir)
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header = disp_data["header_fields"]
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x = disp_data["frames_x"]
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y = disp_data["frames_y"]
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z = disp_data["frames_z"]
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vx = disp_data["frames_vx"]
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vy = disp_data["frames_vy"]
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vz = disp_data["frames_vz"]
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atom_ids = np.array(disp_data["atom_ids"], dtype=np.int64)
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n_frames = x.shape[0]
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dt = float(header.get("DT", 0.001))
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nstep = int(header.get("NSTEP", 1))
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t = np.arange(n_frames, dtype=np.float64) * dt * nstep
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masses = np.array(_header_json(header, "atom_masses", []), dtype=np.float64)
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pos_0 = np.array(_header_json(header, "atom_positions", []), dtype=np.float64)
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bond_pairs = np.array(_header_json(header, "bond_pairs", []), dtype=np.int64)
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bond_stiffness = np.array(_header_json(header, "bond_stiffness", []), dtype=np.float64)
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bond_rest_lengths = np.array(_header_json(header, "bond_rest_lengths", []), dtype=np.float64)
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gravity_vec = _header_json(header, "G", [0.0, 0.0, 0.0])
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# Backward-compatible fallback for older display.txt outputs.
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if masses.size == 0 or pos_0.size == 0:
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input_dir = os.path.join(os.path.dirname(output_dir), "input")
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coord_path = os.path.join(input_dir, "coord.txt")
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if os.path.exists(coord_path):
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(_, masses_fb, _, positions_fb, _, _) = compute.load_coord_file(coord_path)
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masses = np.array(masses_fb, dtype=np.float64)
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pos_0 = np.array(positions_fb, dtype=np.float64)
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else:
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raise ValueError("display.txt 缺少 atom_masses/atom_positions 元数据，且未找到 input/coord.txt")
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if bond_pairs.size == 0:
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input_dir = os.path.join(os.path.dirname(output_dir), "input")
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connection_path = os.path.join(input_dir, "connection.txt")
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bond_path = os.path.join(input_dir, "bond.txt")
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if os.path.exists(connection_path) and os.path.exists(bond_path):
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bond_map = compute.load_bond_parameters(bond_path)
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pairs_fb, _, stiffness_fb, rest_lengths_fb = compute.load_bond_connections(
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connection_path, atom_ids, pos_0, bond_map)
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bond_pairs = np.array(pairs_fb, dtype=np.int64)
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bond_stiffness = np.array(stiffness_fb, dtype=np.float64)
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bond_rest_lengths = np.array(rest_lengths_fb, dtype=np.float64)
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return {
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"n_frames": n_frames,
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"t": t,
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"x": x,
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"y": y,
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"z": z,
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"vx": vx,
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"vy": vy,
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"vz": vz,
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"pos_0": pos_0,
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"masses": masses,
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"atom_ids": atom_ids,
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"bond_pairs": bond_pairs,
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"bond_stiffness": bond_stiffness,
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"bond_rest_lengths": bond_rest_lengths,
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"gravity_field": int(header.get("gravity_field", 0)),
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"gravity_interaction": int(header.get("gravity_interaction", 0)),
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"gravity_strength": float(header.get("gravity_strength", 1.0)),
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"G": gravity_vec,
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"driving_force": int(header.get("driving_force", 0)),
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}
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def compute_energy(x, y, z, vx, vy, vz, masses, mass_arr,
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bond_pairs, bond_stiffness, bond_rest_lengths,
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gravity_field, G, gravity_interaction, gravity_strength):
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"""计算系统各能量分量。
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Returns:
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ek_sys: 系统动能 (n_frames,)
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us_sys: 系统弹性势能 (n_frames,)
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ug_sys: 系统重力势能 (n_frames,)
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ugr_sys: 系统万有引力势能 (n_frames,)
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"""
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n_frames = x.shape[0]
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masses_2d = masses[np.newaxis, :] # (1, n_atoms)
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# 动能 Ek = ½ m v²
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ek = 0.5 * masses_2d * (vx**2 + vy**2 + vz**2)
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ek_sys = np.sum(ek, axis=1)
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# 弹性势能 Us = ½ k (d - d₀)²
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us_sys = np.zeros(n_frames)
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if bond_pairs is not None and len(bond_pairs) > 0:
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for b_idx in range(len(bond_pairs)):
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i, j = bond_pairs[b_idx]
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dx = x[:, j] - x[:, i]
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dy = y[:, j] - y[:, i]
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dz = z[:, j] - z[:, i]
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dist = np.sqrt(dx**2 + dy**2 + dz**2)
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stretch = dist - bond_rest_lengths[b_idx]
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us_sys += 0.5 * bond_stiffness[b_idx] * stretch**2
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# 均匀重力场势能 Ug = -m G·r
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ug_sys = np.zeros(n_frames)
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if gravity_field:
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G_vec = np.array(G)
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ug_sys = -masses_2d * (G_vec[0] * x + G_vec[1] * y + G_vec[2] * z)
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ug_sys = np.sum(ug_sys, axis=1)
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# 万有引力势能 Ug_grav = -G_grav Σ m_i m_j / r
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ugr_sys = np.zeros(n_frames)
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if gravity_interaction:
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n_atoms = len(masses)
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# 为避免巨大计算量，仅当原子数较少时计算
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if n_atoms <= 200:
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for i in range(n_atoms):
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for j in range(i + 1, n_atoms):
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dx = x[:, j] - x[:, i]
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dy = y[:, j] - y[:, i]
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dz = z[:, j] - z[:, i]
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dist = np.sqrt(dx**2 + dy**2 + dz**2)
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dist = np.maximum(dist, 1e-12)
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pair_pe = -gravity_strength * masses[i] * masses[j] / dist
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ugr_sys += pair_pe
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return ek_sys, us_sys, ug_sys, ugr_sys
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def plot_wave(output_dir, save_gif=False, save_mp4=False, show=True):
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"""主绘图函数：读取 display.txt 并生成波形+能量动画。
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Args:
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output_dir: 输出目录（含 display.txt）
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save_gif: 是否保存 GIF
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save_mp4: 是否保存 MP4
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"""
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data = _load_wave_dataset(output_dir)
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n_frames = int(data["n_frames"])
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t = np.array(data["t"])
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# 位置 / 速度
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x = np.array(data["x"])
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y = np.array(data["y"])
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z = np.array(data["z"])
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vx = np.array(data["vx"])
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vy = np.array(data["vy"])
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vz = np.array(data["vz"])
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# 原子信息
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pos_0 = np.array(data["pos_0"])
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masses = np.array(data["masses"])
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atom_ids = np.array(data["atom_ids"])
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n_atoms = len(atom_ids)
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# 成键
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bond_pairs = np.array(data.get("bond_pairs", []), dtype=np.int64)
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bond_stiffness = np.array(data.get("bond_stiffness", []), dtype=np.float64)
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bond_rest_lengths = np.array(data.get("bond_rest_lengths", []), dtype=np.float64)
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# 物理开关
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gravity_field = int(data.get("gravity_field", 0))
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gravity_interaction = int(data.get("gravity_interaction", 0))
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G = data.get("G", [0, 0, 0])
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gravity_strength = float(data.get("gravity_strength", 1.0))
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driving_force = int(data.get("driving_force", 0))
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# ── 位移（偏离初始平衡位形）──
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dx = x - pos_0[np.newaxis, :, 0] # 纵波（沿链方向 x）
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dy = y - pos_0[np.newaxis, :, 1] # 横波 1（y 方向）
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dz = z - pos_0[np.newaxis, :, 2] # 横波 2（z 方向）
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# ── 能量 ──
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ek, us, ug, ugr = compute_energy(
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x, y, z, vx, vy, vz, masses, masses,
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bond_pairs, bond_stiffness, bond_rest_lengths,
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gravity_field, G, gravity_interaction, gravity_strength)
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e_total = ek + us + ug + ugr
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power = np.gradient(e_total, t) # 输入功率 = dE/dt
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# ── 波形纵轴范围（全局统一，避免抖动）──
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def get_ylim(disp_data):
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vmax = np.max(np.abs(disp_data))
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if vmax < 1e-10:
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return -1.0, 1.0
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margin = vmax * 0.2
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return -vmax - margin, vmax + margin
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ylims = [get_ylim(dx), get_ylim(dy), get_ylim(dz)]
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e_max = max(np.max(e_total), 0.01) * 1.3
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p_abs = np.max(np.abs(power))
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p_max = max(p_abs * 1.3, 0.01)
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atom_idx = np.arange(n_atoms)
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# ── 图形设置 ──
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plt.rcParams['font.sans-serif'] = ['Microsoft YaHei', 'SimHei', 'DejaVu Sans']
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plt.rcParams['axes.unicode_minus'] = False
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fig, axes = plt.subplots(2, 2, figsize=(14, 10))
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fig.suptitle("波形与能量分析", fontsize=16)
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# ── 3 个波形子图 ──
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titles = [
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"纵波 (x 方向位移)",
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"横波 (y 方向位移)",
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"横波 (z 方向位移)",
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]
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colors = ["#2563eb", "#ea580c", "#16a34a"]
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wave_configs = list(zip(
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[axes[0, 0], axes[0, 1], axes[1, 0]],
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[dx, dy, dz], titles, colors, ylims
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))
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wave_lines = []
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time_texts = []
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for ax, disp, title, color, yl in wave_configs:
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ax.set_xlim(0, n_atoms - 1)
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ax.set_ylim(yl)
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ax.set_xlabel("原子序号")
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ax.set_ylabel("位移")
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ax.set_title(title)
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ax.grid(True, alpha=0.3)
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line, = ax.plot([], [], color=color, linewidth=1.5)
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wave_lines.append(line)
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tt = ax.text(0.02, 0.95, "", transform=ax.transAxes,
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fontsize=11, verticalalignment="top")
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time_texts.append(tt)
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# ── 能量+功率子图 ──
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ax_ep = axes[1, 1]
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ax_ep.set_xlim(t[0], t[-1])
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ep_ylow = min(-0.1 * max(e_max, p_max), -p_max * 0.1)
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ep_yhigh = max(e_max, p_max)
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ax_ep.set_ylim(ep_ylow, ep_yhigh)
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ax_ep.set_xlabel("时间 (s)")
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ax_ep.set_ylabel("能量 / 功率")
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ax_ep.set_title("系统能量与输入功率")
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ax_ep.grid(True, alpha=0.3)
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line_ek, = ax_ep.plot([], [], "b-", lw=1.5, label="动能")
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line_us, = ax_ep.plot([], [], "orange", lw=1.5, label="弹性势能")
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line_et, = ax_ep.plot([], [], "r--", lw=1.5, label="总能量")
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line_pw, = ax_ep.plot([], [], "g-", lw=1.5, alpha=0.7, label="输入功率 (dE/dt)")
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if gravity_field:
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line_ug, = ax_ep.plot([], [], "purple", lw=1.0, alpha=0.5, label="重力势能")
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else:
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line_ug = None
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if gravity_interaction and n_atoms <= 200:
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line_ugr, = ax_ep.plot([], [], "brown", lw=1.0, alpha=0.5, label="万有引力势能")
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else:
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line_ugr = None
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ax_ep.legend(loc="upper right", fontsize=9)
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plt.tight_layout(rect=[0, 0, 1, 0.95])
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# ── 动画更新 ──
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def update(frame):
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# 波形
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for i in range(3):
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wave_lines[i].set_data(atom_idx, [dx, dy, dz][i][frame])
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time_texts[i].set_text(f"t = {t[frame]:.2f} s | 帧 {frame+1}/{n_frames}")
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# 能量（累计到当前帧）
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cur_t = t[:frame + 1]
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line_ek.set_data(cur_t, ek[:frame + 1])
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line_us.set_data(cur_t, us[:frame + 1])
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line_et.set_data(cur_t, e_total[:frame + 1])
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line_pw.set_data(cur_t, power[:frame + 1])
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if line_ug:
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line_ug.set_data(cur_t, ug[:frame + 1])
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if line_ugr:
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line_ugr.set_data(cur_t, ugr[:frame + 1])
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# 能量图 x 轴动态扩展
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ax_ep.set_xlim(t[0], max(t[frame] + max(t[-1] * 0.05, 1), t[-1]))
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artists = wave_lines + time_texts + [line_ek, line_us, line_et, line_pw]
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if line_ug: artists.append(line_ug)
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if line_ugr: artists.append(line_ugr)
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return artists
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ani = FuncAnimation(fig, update, frames=n_frames, interval=50, blit=True)
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# ── 输出 GIF ──
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if save_gif:
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gif_path = os.path.join(output_dir, "wave_animation.gif")
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ani.save(gif_path, writer="pillow", fps=min(20, max(1, n_frames // 5)))
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print(f"[plot_wave] GIF 已保存: {gif_path}")
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# ── 输出 MP4（需要 ffmpeg）──
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gif_path = None
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if save_gif:
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gif_path = os.path.join(output_dir, "wave_animation.gif")
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if save_mp4:
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try:
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import matplotlib.animation as manim
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import matplotlib.pyplot as _plt
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# 尝试通过 imageio_ffmpeg 定位 ffmpeg
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ffmpeg_path = None
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try:
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import imageio_ffmpeg
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ffmpeg_path = imageio_ffmpeg.get_ffmpeg_exe()
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except Exception:
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pass
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if ffmpeg_path and os.path.exists(ffmpeg_path):
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_plt.rcParams['animation.ffmpeg_path'] = ffmpeg_path
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ffps = min(20, max(1, n_frames // 5))
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writer = manim.FFMpegWriter(fps=ffps, codec="libx264",
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extra_args=["-pix_fmt", "yuv420p"])
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mp4_path = os.path.join(output_dir, "wave_animation.mp4")
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ani.save(mp4_path, writer=writer)
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print(f"[plot_wave] MP4 已保存: {mp4_path}")
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except FileNotFoundError:
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print("[plot_wave] 警告: 未找到 ffmpeg，跳过 MP4 输出")
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except Exception as e:
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print(f"[plot_wave] 警告: MP4 输出失败 ({e})，跳过")
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# ── 最后显示动画窗口（仅直接运行时）──
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if show:
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plt.show()
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else:
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plt.close(fig)
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return gif_path
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if __name__ == "__main__":
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script_dir = os.path.dirname(os.path.abspath(__file__))
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if len(sys.argv) > 1:
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output_dir = os.path.abspath(sys.argv[1])
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else:
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output_dir = compute.get_output_dir(script_dir)
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plot_wave(output_dir)
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