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- 覆盖全部 10 个案例（原 Readme 只到 case06） - 新增案例选择指南表格 - Readme.html 为深色主题独立 HTML 页面 （含卡片布局、标签分类、代码高亮、响应式设计） - 各案例详情对齐最新配置参数
940 lines
38 KiB
Python
940 lines
38 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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"display_amp": _parse_display_amp(header.get("display_amp", "")),
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}
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def _parse_display_amp(raw):
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if not raw or not str(raw).strip():
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return np.ones(3)
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try:
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import ast as _ast
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v = np.array(_ast.literal_eval(str(raw).strip()), dtype=np.float64)
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return v if v.shape == (3,) else np.ones(3)
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except Exception:
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return np.ones(3)
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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 _load_driver_info(output_dir):
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"""从 input/driver.txt 读取驱动原子的 atom_id, amp, freq（仅用于能量计算）。
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返回 dict: {atom_id: {'amp': [ax,ay,az], 'freq': [fx,fy,fz]}}，失败返回 {}。
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"""
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input_dir = os.path.join(os.path.dirname(output_dir), "input")
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path = os.path.join(input_dir, "driver.txt")
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if not os.path.exists(path):
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return {}
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drivers = {}
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try:
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with open(path, encoding="utf-8") as f:
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f.readline() # skip header
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for line in f:
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line = line.strip()
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if not line or line.startswith("#"):
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continue
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parts = line.split()
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if len(parts) < 10:
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continue
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n = int(parts[0])
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amp = np.array([float(parts[1]), float(parts[2]), float(parts[3])])
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freq = np.array([float(parts[4]), float(parts[5]), float(parts[6])])
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drivers[n] = {"amp": amp, "freq": freq}
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except Exception:
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pass
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return drivers
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def compute_per_atom_energy(x, y, z, vx, vy, vz, masses,
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bond_pairs, bond_stiffness, bond_rest_lengths,
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atom_ids, driver_info):
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"""计算每帧每个粒子的动能、势能、总能。
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势能分配规则：
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- 非驱动粒子之间的键：势能各分一半
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- 键的一端是驱动粒子：势能全部归非驱动端
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- 驱动粒子自身：按简谐振子 PE = ½ m (2πf)² A² cos²(2πft+φ) 计算
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（此处用 KE_driven = ½m·v² 的互补式：PE_driven = E_total_sho - KE_driven）
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Returns:
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ek_atom: (n_frames, n_atoms) 每原子动能
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pe_atom: (n_frames, n_atoms) 每原子势能
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et_atom: (n_frames, n_atoms) 每原子总能
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"""
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n_frames, n_atoms = x.shape
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# 动能 per atom
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masses_2d = masses[np.newaxis, :]
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ek_atom = 0.5 * masses_2d * (vx**2 + vy**2 + vz**2) # (n_frames, n_atoms)
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# 构建 atom_id → index 映射，以及驱动原子 index 集合
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id_to_idx = {int(aid): i for i, aid in enumerate(atom_ids)}
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driven_idx = set()
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for aid in driver_info:
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if aid in id_to_idx:
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driven_idx.add(id_to_idx[aid])
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# 势能 per atom（弹簧键）
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pe_atom = np.zeros((n_frames, n_atoms))
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if bond_pairs is not None and len(bond_pairs) > 0:
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for b in range(len(bond_pairs)):
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i, j = int(bond_pairs[b, 0]), int(bond_pairs[b, 1])
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ddx = x[:, j] - x[:, i]
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ddy = y[:, j] - y[:, i]
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ddz = z[:, j] - z[:, i]
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dist = np.sqrt(ddx**2 + ddy**2 + ddz**2)
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bond_pe = 0.5 * bond_stiffness[b] * (dist - bond_rest_lengths[b])**2
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i_driven = i in driven_idx
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j_driven = j in driven_idx
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if i_driven and not j_driven:
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pe_atom[:, j] += bond_pe # 全归非驱动端
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elif j_driven and not i_driven:
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pe_atom[:, i] += bond_pe # 全归非驱动端
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else:
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pe_atom[:, i] += bond_pe * 0.5
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pe_atom[:, j] += bond_pe * 0.5
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# 驱动粒子：用简谐振子总能 E_sho = ½m(2πf)²A²，PE_sho = E_sho - KE
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TWO_PI = 2.0 * np.pi
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for aid, info in driver_info.items():
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if aid not in id_to_idx:
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continue
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idx = id_to_idx[aid]
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m = masses[idx]
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amp = info["amp"]
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freq = info["freq"]
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e_sho = 0.5 * m * np.sum((TWO_PI * freq)**2 * amp**2)
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pe_sho = e_sho - ek_atom[:, idx]
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pe_atom[:, idx] = np.maximum(pe_sho, 0.0) # SHO 势能非负
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et_atom = ek_atom + pe_atom
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return ek_atom, pe_atom, et_atom
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def compute_energy_flux(x, y, z, vx, vy, vz,
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bond_pairs, bond_stiffness, bond_rest_lengths):
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"""计算每帧每根键的能流密度（Hardy 公式）。
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对键 b 连接原子 i, j（j > i，方向 i→j）：
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J_b = ½ · F_{b,i} · (v_i + v_j)
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其中 F_{b,i} = k(d - r₀) * (r_j - r_i)/d 是键对原子 i 的弹力矢量，
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点乘取两端速度均值。
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- J > 0：能量从 i 流向 j（沿键方向正流）
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- J = 0：驻波，能量不流动
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- 沿链从左到右，J 的分布揭示能量传播方向
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Returns:
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flux: (n_frames, n_bonds) 每帧每键的能流（标量）
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bond_xpos: (n_bonds,) 各键中点的初始 x 坐标（用于绘图横轴）
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"""
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if bond_pairs is None or len(bond_pairs) == 0:
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n_frames = x.shape[0]
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return np.zeros((n_frames, 0)), np.zeros(0)
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n_bonds = len(bond_pairs)
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n_frames = x.shape[0]
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flux = np.zeros((n_frames, n_bonds))
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# 键中点初始 x 坐标（用于横轴定位）
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bond_xpos = np.array([
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0.5 * (x[0, bond_pairs[b, 0]] + x[0, bond_pairs[b, 1]])
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for b in range(n_bonds)
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])
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for b in range(n_bonds):
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i, j = int(bond_pairs[b, 0]), int(bond_pairs[b, 1])
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k = bond_stiffness[b]
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r0 = bond_rest_lengths[b]
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# 键矢量与长度
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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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d = np.sqrt(dx_**2 + dy_**2 + dz_**2)
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d = np.maximum(d, 1e-12)
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# 弹力矢量（作用于原子 i，指向 j 方向）
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fac = k * (d - r0) / d # 标量因子
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fx = fac * dx_
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fy = fac * dy_
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fz = fac * dz_
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# 能流 = F_i · (v_i + v_j) / 2
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flux[:, b] = 0.5 * (fx * (vx[:, i] + vx[:, j])
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+ fy * (vy[:, i] + vy[:, j])
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+ fz * (vz[:, i] + vz[:, j]))
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return flux, bond_xpos
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def compute_driver_work_power(x, y, z, vx, vy, vz,
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bond_pairs, bond_stiffness, bond_rest_lengths,
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atom_ids, driver_info):
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"""计算每个驱动原子通过键对系统（非驱动原子）做功的功率。
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对于驱动原子 d 与系统原子 j 之间的键：
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P_{d→j} = F_{d→j} · v_j
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其中 F_{d→j} 是键对系统原子 j 的弹簧力。
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Returns:
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drv_powers: dict {atom_id: (n_frames,)} 每个驱动原子的瞬时功率
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total_power: (n_frames,) 所有驱动原子功率之和
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"""
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if bond_pairs is None or len(bond_pairs) == 0:
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n_frames = x.shape[0]
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return {}, np.zeros(n_frames)
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id_to_idx = {int(aid): i for i, aid in enumerate(atom_ids)}
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driven_idx = {id_to_idx[aid] for aid in driver_info if aid in id_to_idx}
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n_frames = x.shape[0]
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drv_powers = {}
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for b in range(len(bond_pairs)):
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ii, jj = int(bond_pairs[b, 0]), int(bond_pairs[b, 1])
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i_drv = ii in driven_idx
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j_drv = jj in driven_idx
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if i_drv == j_drv: # 两端同为驱动或同为自由，跳过
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continue
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drv_loc = ii if i_drv else jj # 驱动端 index
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sys_loc = jj if i_drv else ii # 系统端 index
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drv_aid = int(atom_ids[drv_loc])
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dx_ = x[:, jj] - x[:, ii]
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dy_ = y[:, jj] - y[:, ii]
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dz_ = z[:, jj] - z[:, ii]
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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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k = bond_stiffness[b]
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r0 = bond_rest_lengths[b]
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fac = k * (dist - r0) / dist # 标量弹力因子
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# 作用于系统原子的弹簧力：指向驱动原子方向
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if i_drv: # drv=i, sys=j: 力方向 j→i，即 -(dx_, dy_, dz_)
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fx = -fac * dx_
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fy = -fac * dy_
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fz = -fac * dz_
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else: # drv=j, sys=i: 力方向 i→j，即 +(dx_, dy_, dz_)
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fx = fac * dx_
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fy = fac * dy_
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fz = fac * dz_
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power = fx * vx[:, sys_loc] + fy * vy[:, sys_loc] + fz * vz[:, sys_loc]
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if drv_aid not in drv_powers:
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drv_powers[drv_aid] = np.zeros(n_frames)
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drv_powers[drv_aid] += power
|
||
|
||
total_power = sum(drv_powers.values()) if drv_powers else np.zeros(n_frames)
|
||
return drv_powers, total_power
|
||
|
||
|
||
def plot_wave(output_dir, save_gif=False, save_mp4=False, show=True):
|
||
"""主绘图函数：读取 display.txt 并生成波形+能量动画。
|
||
|
||
布局（4行×1列，纵向排列）：
|
||
行0：x/y/z 位移波形叠加在同一子图（vs 原子序号）
|
||
行1：每粒子动能、势能、总能叠加在同一子图
|
||
行2：键能流密度 J（Hardy 公式，vs 键中点位置）
|
||
行3：系统总能量随时间变化
|
||
|
||
Args:
|
||
output_dir: 输出目录（含 display.npz 或 display.txt）
|
||
save_gif: 是否保存 GIF
|
||
save_mp4: 是否保存 MP4
|
||
show: 是否弹出交互窗口
|
||
"""
|
||
data = _load_wave_dataset(output_dir)
|
||
|
||
n_frames = int(data["n_frames"])
|
||
t = np.array(data["t"])
|
||
|
||
x = np.array(data["x"])
|
||
y = np.array(data["y"])
|
||
z = np.array(data["z"])
|
||
vx = np.array(data["vx"])
|
||
vy = np.array(data["vy"])
|
||
vz = np.array(data["vz"])
|
||
|
||
pos_0 = np.array(data["pos_0"])
|
||
masses = np.array(data["masses"])
|
||
atom_ids = np.array(data["atom_ids"])
|
||
n_atoms = len(atom_ids)
|
||
|
||
bond_pairs = np.array(data.get("bond_pairs", []), dtype=np.int64)
|
||
bond_stiffness = np.array(data.get("bond_stiffness", []), dtype=np.float64)
|
||
bond_rest_lengths= np.array(data.get("bond_rest_lengths",[]), dtype=np.float64)
|
||
|
||
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))
|
||
|
||
# 驱动原子信息（用于势能计算）
|
||
driver_info = _load_driver_info(output_dir) if driving_force else {}
|
||
|
||
# ── 位移 ──
|
||
dx = x - pos_0[np.newaxis, :, 0]
|
||
dy = y - pos_0[np.newaxis, :, 1]
|
||
dz = z - pos_0[np.newaxis, :, 2]
|
||
|
||
# ── 每粒子能量（图2 与图3 共用同一套计算）──
|
||
ek_atom, pe_atom, et_atom = compute_per_atom_energy(
|
||
x, y, z, vx, vy, vz, masses,
|
||
bond_pairs, bond_stiffness, bond_rest_lengths,
|
||
atom_ids, driver_info)
|
||
|
||
# ── 系统总能量 = 各粒子求和（与图2 完全一致）──
|
||
ek_sys = np.sum(ek_atom, axis=1)
|
||
us_sys = np.sum(pe_atom, axis=1)
|
||
e_total = np.sum(et_atom, axis=1)
|
||
power = np.gradient(e_total, t)
|
||
# 重力势能：仍用原有函数提供（若启用重力场）
|
||
_, _, ug_sys, ugr_sys = compute_energy(
|
||
x, y, z, vx, vy, vz, masses, masses,
|
||
bond_pairs, bond_stiffness, bond_rest_lengths,
|
||
gravity_field, G, gravity_interaction, gravity_strength)
|
||
if gravity_field or gravity_interaction:
|
||
e_total = e_total + ug_sys + ugr_sys
|
||
power = np.gradient(e_total, t)
|
||
|
||
# ── 能流密度 ──
|
||
flux, bond_xpos = compute_energy_flux(
|
||
x, y, z, vx, vy, vz,
|
||
bond_pairs, bond_stiffness, bond_rest_lengths)
|
||
|
||
# ── 驱动做功功率 ──
|
||
drv_powers, total_drv_power = compute_driver_work_power(
|
||
x, y, z, vx, vy, vz,
|
||
bond_pairs, bond_stiffness, bond_rest_lengths,
|
||
atom_ids, driver_info)
|
||
|
||
# ── 原子可视化预计算 ──
|
||
display_amp = np.array(data.get("display_amp", [1.0, 1.0, 1.0]), dtype=np.float64)
|
||
eq_x_vis = pos_0[:, 0]
|
||
eq_z_vis = pos_0[:, 2]
|
||
# 视觉坐标 = 平衡位置 + 放大的位移
|
||
x_vis = eq_x_vis + (x - eq_x_vis) * display_amp[0] # (n_frames, n_atoms)
|
||
z_vis = eq_z_vis + (z - eq_z_vis) * display_amp[2]
|
||
|
||
# 找边界原子（与驱动原子成键的系统原子）及对应键
|
||
id_to_idx_vis = {int(aid): i for i, aid in enumerate(atom_ids)}
|
||
driven_set_vis = {id_to_idx_vis[aid] for aid in driver_info if aid in id_to_idx_vis}
|
||
bond_boundary_list = [] # (drv_idx, sys_idx, bond_b)
|
||
for _b in range(len(bond_pairs)):
|
||
_ii, _jj = int(bond_pairs[_b, 0]), int(bond_pairs[_b, 1])
|
||
if (_ii in driven_set_vis) ^ (_jj in driven_set_vis):
|
||
_drv = _ii if _ii in driven_set_vis else _jj
|
||
_sys = _jj if _ii in driven_set_vis else _ii
|
||
bond_boundary_list.append((_drv, _sys, _b))
|
||
|
||
# 唯一边界原子索引列表
|
||
_bnd_set = {}
|
||
for _drv, _sys, _b in bond_boundary_list:
|
||
if _sys not in _bnd_set:
|
||
_bnd_set[_sys] = len(_bnd_set)
|
||
boundary_atom_idx = np.array(list(_bnd_set.keys()), dtype=int)
|
||
n_boundary = len(boundary_atom_idx)
|
||
|
||
_lat = (eq_x_vis[-1] - eq_x_vis[0]) / max(n_atoms - 1, 1)
|
||
_z_all = z_vis.reshape(-1)
|
||
_z_min, _z_max = np.min(_z_all), np.max(_z_all)
|
||
_z_mg = max((_z_max - _z_min) * 0.2, _lat * 2)
|
||
_z_range = max((_z_max - _z_min) + 2 * _z_mg, _lat * 4)
|
||
_arrow_len = _z_range * 0.50 # 箭头最大显示长度 = 纵坐标范围的 50%
|
||
|
||
# 预计算边界原子受到的驱动力
|
||
# 方向：沿显示坐标下的键方向（消除坐标轴比例失真）；大小：胡克力模 k|d-r0|
|
||
bnd_fx_scaled = np.zeros((n_frames, max(n_boundary, 1)))
|
||
bnd_fz_scaled = np.zeros((n_frames, max(n_boundary, 1)))
|
||
_f_mag_all = []
|
||
for _drv, _sys, _b in bond_boundary_list:
|
||
_bi = _bnd_set[_sys]
|
||
# 物理键长
|
||
_dx3 = x[:, _drv] - x[:, _sys]
|
||
_dy3 = y[:, _drv] - y[:, _sys]
|
||
_dz3 = z[:, _drv] - z[:, _sys]
|
||
_dist = np.maximum(np.sqrt(_dx3**2 + _dy3**2 + _dz3**2), 1e-12)
|
||
# 有符号力大小（正 = 拉向驱动原子，负 = 推离）
|
||
_f_signed = bond_stiffness[_b] * (_dist - bond_rest_lengths[_b])
|
||
# 显示坐标下的键方向（x-z 平面）
|
||
_dx_d = x_vis[:, _drv] - x_vis[:, _sys]
|
||
_dz_d = z_vis[:, _drv] - z_vis[:, _sys]
|
||
_disp_len = np.maximum(np.sqrt(_dx_d**2 + _dz_d**2), 1e-12)
|
||
bnd_fx_scaled[:, _bi] += _f_signed * _dx_d / _disp_len
|
||
bnd_fz_scaled[:, _bi] += _f_signed * _dz_d / _disp_len
|
||
_f_mag_all.append(np.abs(_f_signed))
|
||
_f_max = np.max(_f_mag_all) if _f_mag_all else 1.0
|
||
_f_max = _f_max if _f_max > 1e-20 else 1.0
|
||
bnd_fx_scaled = bnd_fx_scaled / _f_max * _arrow_len
|
||
bnd_fz_scaled = bnd_fz_scaled / _f_max * _arrow_len
|
||
|
||
# 边界原子速度（方向沿实际速度，大小归一化）
|
||
bnd_vx_raw = vx[:, boundary_atom_idx] if n_boundary > 0 else np.zeros((n_frames, 1))
|
||
bnd_vz_raw = vz[:, boundary_atom_idx] if n_boundary > 0 else np.zeros((n_frames, 1))
|
||
_v_max = np.max(np.sqrt(bnd_vx_raw**2 + bnd_vz_raw**2)) if n_boundary > 0 else 1.0
|
||
_v_max = _v_max if _v_max > 1e-20 else 1.0
|
||
bnd_vx_scaled = bnd_vx_raw / _v_max * _arrow_len
|
||
bnd_vz_scaled = bnd_vz_raw / _v_max * _arrow_len
|
||
|
||
# y 轴范围 ──
|
||
def get_ylim(arr):
|
||
vmax = np.max(np.abs(arr))
|
||
if vmax < 1e-10:
|
||
return -1.0, 1.0
|
||
m = vmax * 0.2
|
||
return -vmax - m, vmax + m
|
||
|
||
def get_ylim_pos(arr):
|
||
vmax = np.max(arr)
|
||
if vmax < 1e-12:
|
||
return 0.0, 1.0
|
||
return 0.0, vmax * 1.2
|
||
|
||
# 共用 y 轴范围：位移图取三个方向最大值统一
|
||
disp_vmax = max(np.max(np.abs(dx)), np.max(np.abs(dy)), np.max(np.abs(dz)))
|
||
disp_vmax = disp_vmax if disp_vmax > 1e-10 else 1.0
|
||
disp_ylim = (-disp_vmax * 1.2, disp_vmax * 1.2)
|
||
|
||
# 每粒子能量：取三者最大值统一 y 轴
|
||
energy_vmax = max(np.max(ek_atom), np.max(pe_atom), np.max(et_atom))
|
||
energy_vmax = energy_vmax if energy_vmax > 1e-12 else 1.0
|
||
energy_ylim = (0.0, energy_vmax * 1.2)
|
||
|
||
e_max = max(np.max(e_total), 1e-12)
|
||
e_min = min(np.min(e_total), 0.0)
|
||
p_max = max(np.percentile(np.abs(power), 95) if len(power) > 0 else 0.0, 0.0)
|
||
|
||
# 能流 y 轴范围（对称，正负各半）
|
||
if flux.size > 0:
|
||
flux_vmax = np.max(np.abs(flux))
|
||
flux_vmax = flux_vmax if flux_vmax > 1e-12 else 1.0
|
||
flux_ylim = (-flux_vmax * 1.2, flux_vmax * 1.2)
|
||
else:
|
||
flux_ylim = (-1.0, 1.0)
|
||
|
||
atom_idx = np.arange(n_atoms)
|
||
|
||
# ── 驱动/非驱动粒子能量（右下图）──
|
||
id_to_idx = {int(aid): i for i, aid in enumerate(atom_ids)}
|
||
driven_idx = np.array([id_to_idx[aid] for aid in driver_info if aid in id_to_idx], dtype=int)
|
||
free_idx = np.setdiff1d(np.arange(n_atoms), driven_idx)
|
||
has_driver = len(driven_idx) > 0
|
||
|
||
if has_driver:
|
||
ek_drv = np.sum(ek_atom[:, driven_idx], axis=1)
|
||
ep_drv = np.sum(pe_atom[:, driven_idx], axis=1)
|
||
ek_free = np.sum(ek_atom[:, free_idx], axis=1)
|
||
ep_free = np.sum(pe_atom[:, free_idx], axis=1)
|
||
|
||
# ── 图形布局：左3行、右3行（subplot_mosaic）──
|
||
plt.rcParams['font.sans-serif'] = ['Microsoft YaHei', 'SimHei', 'DejaVu Sans']
|
||
plt.rcParams['axes.unicode_minus'] = False
|
||
|
||
from matplotlib.collections import LineCollection as _LC
|
||
|
||
fig, axes = plt.subplot_mosaic(
|
||
[['atoms', 'ep'],
|
||
['wave', 'drv'],
|
||
['energy', 'pwr']],
|
||
figsize=(20, 15))
|
||
ax_atoms = axes['atoms']
|
||
ax_wave = axes['wave']
|
||
ax_ep = axes['ep']
|
||
ax_energy = axes['energy']
|
||
ax_drv = axes['drv']
|
||
ax_pwr = axes['pwr']
|
||
fig.subplots_adjust(hspace=0.45, wspace=0.32, top=0.97)
|
||
|
||
# ── 左上：原子位置 + 键 + 力/速度箭头 ──
|
||
_x_min, _x_max = eq_x_vis[0], eq_x_vis[-1]
|
||
ax_atoms.set_xlim(_x_min - _lat, _x_max + _lat)
|
||
ax_atoms.set_ylim(_z_min - _z_mg, _z_max + _z_mg)
|
||
ax_atoms.set_xlabel("位置 $x$")
|
||
ax_atoms.set_ylabel("位移 $z$（放大 {:.0f}×）".format(display_amp[2]))
|
||
ax_atoms.set_title("原子运动（红=驱动，箭头：红=驱动力，蓝=边界速度）")
|
||
ax_atoms.set_aspect('auto')
|
||
ax_atoms.grid(True, alpha=0.2)
|
||
|
||
# 键线段（LineCollection，初始帧）
|
||
def _make_bond_segs(frame_idx):
|
||
segs = []
|
||
for _b in range(len(bond_pairs)):
|
||
_ii, _jj = int(bond_pairs[_b, 0]), int(bond_pairs[_b, 1])
|
||
segs.append([(x_vis[frame_idx, _ii], z_vis[frame_idx, _ii]),
|
||
(x_vis[frame_idx, _jj], z_vis[frame_idx, _jj])])
|
||
return segs
|
||
|
||
_bond_lc = _LC(_make_bond_segs(0), colors='#888888', linewidths=0.8, zorder=1)
|
||
ax_atoms.add_collection(_bond_lc)
|
||
|
||
# 散点：自由原子（黑）
|
||
_free_mask = np.array([i not in driven_set_vis for i in range(n_atoms)])
|
||
_scat_free, = ax_atoms.plot(
|
||
x_vis[0, _free_mask], z_vis[0, _free_mask],
|
||
'o', color='black', ms=4, zorder=3)
|
||
|
||
# 散点：驱动原子（红）
|
||
_drv_mask = ~_free_mask
|
||
_scat_drv, = ax_atoms.plot(
|
||
x_vis[0, _drv_mask], z_vis[0, _drv_mask],
|
||
'o', color='red', ms=6, zorder=4)
|
||
|
||
# 力箭头（红，边界原子）
|
||
_q_force = ax_atoms.quiver(
|
||
x_vis[0, boundary_atom_idx] if n_boundary > 0 else [],
|
||
z_vis[0, boundary_atom_idx] if n_boundary > 0 else [],
|
||
bnd_fx_scaled[0] if n_boundary > 0 else [],
|
||
bnd_fz_scaled[0] if n_boundary > 0 else [],
|
||
color='red', angles='xy', scale_units='xy', scale=1,
|
||
width=0.007, headwidth=5, headlength=5, zorder=5)
|
||
|
||
# 速度箭头（蓝，边界原子）
|
||
_q_vel = ax_atoms.quiver(
|
||
x_vis[0, boundary_atom_idx] if n_boundary > 0 else [],
|
||
z_vis[0, boundary_atom_idx] if n_boundary > 0 else [],
|
||
bnd_vx_scaled[0] if n_boundary > 0 else [],
|
||
bnd_vz_scaled[0] if n_boundary > 0 else [],
|
||
color='blue', angles='xy', scale_units='xy', scale=1,
|
||
width=0.007, headwidth=5, headlength=5, zorder=5)
|
||
|
||
# ── 左上：x/y/z 位移波形 ──
|
||
ax_wave.set_xlim(0, n_atoms - 1)
|
||
ax_wave.set_ylim(disp_ylim)
|
||
ax_wave.set_xlabel("原子序号")
|
||
ax_wave.set_ylabel("位移 $u$")
|
||
ax_wave.set_title("粒子位移（$x$ / $y$ / $z$ 方向）")
|
||
ax_wave.grid(True, alpha=0.3)
|
||
|
||
wave_disps = [dx, dy, dz]
|
||
wave_labels = ["$u_x$（纵波）", "$u_y$（横波）", "$u_z$（横波）"]
|
||
wave_colors = ["#2563eb", "#ea580c", "#16a34a"]
|
||
wave_lines = []
|
||
for label, color in zip(wave_labels, wave_colors):
|
||
ln, = ax_wave.plot([], [], color=color, linewidth=1.5, label=label)
|
||
wave_lines.append(ln)
|
||
ax_wave.legend(loc="upper right", fontsize=9)
|
||
_dt_frame = (t[1] - t[0]) if len(t) > 1 else 0.0
|
||
_t_total_str = f"{t[-1] + _dt_frame:.2f} s"
|
||
_time_axes = [ax_atoms, ax_wave, ax_energy, ax_ep, ax_drv, ax_pwr]
|
||
time_texts = [
|
||
ax.text(0.02, 0.97, "", transform=ax.transAxes,
|
||
fontsize=9, verticalalignment="top",
|
||
bbox=dict(boxstyle="round,pad=0.2", fc="white", alpha=0.7))
|
||
for ax in _time_axes
|
||
]
|
||
time_text = time_texts[1] # 保留旧名兼容下面的代码
|
||
|
||
# ── 左下：每粒子能量（左轴）+ 能流密度（右轴）──
|
||
ax_energy.set_xlim(0, n_atoms - 1)
|
||
ax_energy.set_ylim(energy_ylim)
|
||
ax_energy.set_xlabel("原子序号 / 键位置")
|
||
ax_energy.set_ylabel("能量 $E$")
|
||
ax_energy.set_title(
|
||
r"每粒子能量（$E_k$/$E_p$/$E_{tot}$）与能流密度 $J$"
|
||
)
|
||
ax_energy.grid(True, alpha=0.3)
|
||
|
||
energy_arrays = [ek_atom, pe_atom, et_atom]
|
||
energy_labels = ["$E_k$（动能）", "$E_p$（势能）", "$E_{tot}$（总能）"]
|
||
energy_colors = ["#16a34a", "#b45309", "#7c3aed"]
|
||
energy_lines = []
|
||
for label, color in zip(energy_labels, energy_colors):
|
||
ln, = ax_energy.plot([], [], color=color, linewidth=1.5, label=label)
|
||
energy_lines.append(ln)
|
||
|
||
ax_flux = ax_energy.twinx()
|
||
ax_flux.set_ylim(flux_ylim)
|
||
ax_flux.set_ylabel("能流密度 $J$", color="#dc2626")
|
||
ax_flux.tick_params(axis='y', labelcolor="#dc2626")
|
||
ax_flux.axhline(0, color="gray", linewidth=0.8, linestyle="--")
|
||
flux_line, = ax_flux.plot([], [], color="#dc2626", linewidth=1.5,
|
||
label="$J$（能流密度）")
|
||
handles_e, labels_e = ax_energy.get_legend_handles_labels()
|
||
handles_f, labels_f = ax_flux.get_legend_handles_labels()
|
||
ax_energy.legend(handles_e + handles_f, labels_e + labels_f,
|
||
loc="upper right", fontsize=9)
|
||
|
||
# ── 右上：系统总能量随时间 ──
|
||
ax_ep.set_xlim(t[0], t[-1])
|
||
ep_margin = (e_max - e_min) * 0.15 if e_max > e_min else e_max * 0.15
|
||
ax_ep.set_ylim(e_min - ep_margin, e_max + ep_margin)
|
||
ax_ep.set_clip_on(True)
|
||
ax_ep.set_xlabel("时间 $t$ (s)")
|
||
ax_ep.set_ylabel("能量 $E$ / 功率 $P$")
|
||
ax_ep.set_title("系统能量与输入功率")
|
||
ax_ep.grid(True, alpha=0.3)
|
||
|
||
ln_ek, = ax_ep.plot([], [], "b-", lw=1.5, label="$E_k$（动能）")
|
||
ln_us, = ax_ep.plot([], [], "orange", lw=1.5, label="$E_s$（弹性势能）")
|
||
ln_et, = ax_ep.plot([], [], "r--", lw=1.5, label="$E_{tot}$（总能量）")
|
||
ln_pw, = ax_ep.plot([], [], "g-", lw=1.5, alpha=0.7, label=r"$P_{in}=dE/dt$")
|
||
ln_ug = None
|
||
ln_ugr = None
|
||
if gravity_field:
|
||
ln_ug, = ax_ep.plot([], [], "purple", lw=1.0, alpha=0.5, label="$E_g$（重力势能）")
|
||
if gravity_interaction and n_atoms <= 200:
|
||
ln_ugr, = ax_ep.plot([], [], "brown", lw=1.0, alpha=0.5, label="$E_{gr}$（万有引力势能）")
|
||
ax_ep.legend(loc="upper right", fontsize=9)
|
||
|
||
# ── 右下：驱动/非驱动粒子能量随时间 ──
|
||
ax_drv.set_xlim(t[0], t[-1])
|
||
ax_drv.set_xlabel("时间 $t$ (s)")
|
||
ax_drv.set_ylabel("能量 $E$")
|
||
ax_drv.grid(True, alpha=0.3)
|
||
ln_ek_drv = ln_ep_drv = ln_ek_free = ln_ep_free = None
|
||
ln_et_drv = ln_et_free = None
|
||
if has_driver:
|
||
et_drv = ek_drv + ep_drv
|
||
et_free = ek_free + ep_free
|
||
drv_ids = sorted(driver_info.keys())
|
||
ax_drv.set_title(f"驱动粒子（序号 {drv_ids}）向系统做功")
|
||
ln_ek_drv, = ax_drv.plot([], [], color="#dc2626", lw=1.2, linestyle="--",
|
||
label=r"$E_k^{drv}$（驱动动能）")
|
||
ln_ep_drv, = ax_drv.plot([], [], color="#f97316", lw=1.2, linestyle="--",
|
||
label=r"$E_p^{drv}$（驱动势能）")
|
||
ln_et_drv, = ax_drv.plot([], [], color="#7f1d1d", lw=2.0,
|
||
label=r"$E_{tot}^{drv}$（驱动总能）")
|
||
ln_ek_free, = ax_drv.plot([], [], color="#2563eb", lw=1.2, linestyle="--",
|
||
label=r"$E_k^{sys}$（系统动能）")
|
||
ln_ep_free, = ax_drv.plot([], [], color="#16a34a", lw=1.2, linestyle="--",
|
||
label=r"$E_p^{sys}$（系统势能）")
|
||
ln_et_free, = ax_drv.plot([], [], color="#1e3a5f", lw=2.0,
|
||
label=r"$E_{tot}^{sys}$（系统总能）")
|
||
ax_drv.legend(loc="upper right", fontsize=8)
|
||
# y 轴一次定好
|
||
_drv_all = np.concatenate([ek_drv, ep_drv, et_drv, ek_free, ep_free, et_free])
|
||
_dy_max = np.max(_drv_all)
|
||
_dy_min = np.min(_drv_all)
|
||
_dy_mg = (_dy_max - _dy_min) * 0.15 if _dy_max > _dy_min else abs(_dy_max) * 0.15 + 1e-12
|
||
ax_drv.set_ylim(_dy_min - _dy_mg, _dy_max + _dy_mg)
|
||
else:
|
||
ax_drv.set_title("驱动粒子能量（无驱动力）")
|
||
ax_drv.text(0.5, 0.5, "无驱动力", transform=ax_drv.transAxes,
|
||
ha="center", va="center", fontsize=12, color="gray")
|
||
|
||
# ── 右下：驱动做功功率 ──
|
||
ax_pwr.set_xlim(t[0], t[-1])
|
||
ax_pwr.set_xlabel("时间 $t$ (s)")
|
||
ax_pwr.set_ylabel("功率 $P$")
|
||
ax_pwr.set_title("驱动原子对系统做功的功率 $P = \\mathbf{F}_{bond}\\cdot\\mathbf{v}_{sys}$")
|
||
ax_pwr.axhline(0, color="gray", linewidth=0.8, linestyle="--")
|
||
ax_pwr.grid(True, alpha=0.3)
|
||
|
||
pwr_colors = ["#dc2626", "#2563eb", "#16a34a", "#f97316", "#7c3aed"]
|
||
ln_pwr_each = {} # aid -> Line2D
|
||
if drv_powers:
|
||
for idx_d, (aid, _) in enumerate(sorted(drv_powers.items())):
|
||
color = pwr_colors[idx_d % len(pwr_colors)]
|
||
ln, = ax_pwr.plot([], [], color=color, lw=1.2, linestyle="--",
|
||
label=f"$P_{{drv,{aid}}}$（原子 {aid}）")
|
||
ln_pwr_each[aid] = ln
|
||
ln_pwr_total, = ax_pwr.plot([], [], color="black", lw=2.0,
|
||
label=r"$P_{total}$（总功率）")
|
||
ax_pwr.legend(loc="upper right", fontsize=9)
|
||
|
||
# y 轴一次定好
|
||
if drv_powers:
|
||
_pw_all = np.concatenate(list(drv_powers.values()) + [total_drv_power])
|
||
_pw_max = np.max(_pw_all)
|
||
_pw_min = np.min(_pw_all)
|
||
_pw_mg = (_pw_max - _pw_min) * 0.15 if _pw_max > _pw_min else abs(_pw_max) * 0.15 + 1e-12
|
||
ax_pwr.set_ylim(_pw_min - _pw_mg, _pw_max + _pw_mg)
|
||
|
||
# ── 动画更新 ──
|
||
def update(frame):
|
||
# 每轮开始时清屏
|
||
# 左上：原子位置动画
|
||
_bond_lc.set_segments(_make_bond_segs(frame))
|
||
_scat_free.set_xdata(x_vis[frame, _free_mask])
|
||
_scat_free.set_ydata(z_vis[frame, _free_mask])
|
||
_scat_drv.set_xdata(x_vis[frame, _drv_mask])
|
||
_scat_drv.set_ydata(z_vis[frame, _drv_mask])
|
||
if n_boundary > 0:
|
||
_q_force.set_offsets(
|
||
np.column_stack([x_vis[frame, boundary_atom_idx],
|
||
z_vis[frame, boundary_atom_idx]]))
|
||
_q_force.set_UVC(bnd_fx_scaled[frame], bnd_fz_scaled[frame])
|
||
_q_vel.set_offsets(
|
||
np.column_stack([x_vis[frame, boundary_atom_idx],
|
||
z_vis[frame, boundary_atom_idx]]))
|
||
_q_vel.set_UVC(bnd_vx_scaled[frame], bnd_vz_scaled[frame])
|
||
|
||
if frame == 0:
|
||
all_clear = list(wave_lines) + list(energy_lines) + [flux_line]
|
||
all_clear += [ln for ln in [ln_ek, ln_us, ln_et, ln_pw, ln_ug, ln_ugr]
|
||
if ln is not None]
|
||
if has_driver:
|
||
all_clear += [ln for ln in [ln_ek_drv, ln_ep_drv, ln_et_drv,
|
||
ln_ek_free, ln_ep_free, ln_et_free]
|
||
if ln is not None]
|
||
all_clear += list(ln_pwr_each.values()) + [ln_pwr_total]
|
||
for ln in all_clear:
|
||
ln.set_data([], [])
|
||
_tstr0 = f"t = {t[0]:.2f} s / {_t_total_str} | 帧 1/{n_frames}"
|
||
for _tt in time_texts:
|
||
_tt.set_text(_tstr0)
|
||
return all_clear + time_texts + [_bond_lc, _scat_free, _scat_drv,
|
||
_q_force, _q_vel]
|
||
|
||
# 左中：位移波形
|
||
for i, ln in enumerate(wave_lines):
|
||
ln.set_data(atom_idx, wave_disps[i][frame])
|
||
_tstr = f"t = {t[frame]:.2f} s / {_t_total_str} | 帧 {frame+1}/{n_frames}"
|
||
for _tt in time_texts:
|
||
_tt.set_text(_tstr)
|
||
|
||
# 左下：每粒子能量 + 能流密度
|
||
for i, ln in enumerate(energy_lines):
|
||
ln.set_data(atom_idx, energy_arrays[i][frame])
|
||
if flux.shape[1] > 0:
|
||
flux_line.set_data(bond_xpos, flux[frame])
|
||
|
||
# 右上：系统能量（累计）
|
||
cur_t = t[:frame + 1]
|
||
ln_ek.set_data(cur_t, ek_sys[:frame + 1])
|
||
ln_us.set_data(cur_t, us_sys[:frame + 1])
|
||
ln_et.set_data(cur_t, e_total[:frame + 1])
|
||
ln_pw.set_data(cur_t, power[:frame + 1])
|
||
if ln_ug: ln_ug.set_data(cur_t, ug_sys[:frame + 1])
|
||
if ln_ugr: ln_ugr.set_data(cur_t, ugr_sys[:frame + 1])
|
||
|
||
# 右中：驱动/系统粒子能量（累计）
|
||
if has_driver:
|
||
ln_ek_drv.set_data( cur_t, ek_drv[:frame + 1])
|
||
ln_ep_drv.set_data( cur_t, ep_drv[:frame + 1])
|
||
ln_et_drv.set_data( cur_t, et_drv[:frame + 1])
|
||
ln_ek_free.set_data(cur_t, ek_free[:frame + 1])
|
||
ln_ep_free.set_data(cur_t, ep_free[:frame + 1])
|
||
ln_et_free.set_data(cur_t, et_free[:frame + 1])
|
||
|
||
# 右下：驱动做功功率（累计）
|
||
for aid, ln in ln_pwr_each.items():
|
||
ln.set_data(cur_t, drv_powers[aid][:frame + 1])
|
||
ln_pwr_total.set_data(cur_t, total_drv_power[:frame + 1])
|
||
|
||
artists = (wave_lines + time_texts + energy_lines +
|
||
[flux_line, ln_ek, ln_us, ln_et, ln_pw])
|
||
if ln_ug: artists.append(ln_ug)
|
||
if ln_ugr: artists.append(ln_ugr)
|
||
if has_driver:
|
||
artists += [ln_ek_drv, ln_ep_drv, ln_et_drv,
|
||
ln_ek_free, ln_ep_free, ln_et_free]
|
||
artists += list(ln_pwr_each.values()) + [ln_pwr_total]
|
||
artists += [_bond_lc, _scat_free, _scat_drv, _q_force, _q_vel]
|
||
return artists
|
||
|
||
ani = FuncAnimation(fig, update, frames=n_frames, interval=50, blit=True, repeat=True)
|
||
|
||
# ── 输出文件 ──
|
||
gif_path = None
|
||
if save_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}")
|
||
|
||
if save_mp4:
|
||
try:
|
||
import matplotlib.animation as manim
|
||
ffmpeg_path = None
|
||
try:
|
||
import imageio_ffmpeg
|
||
ffmpeg_path = imageio_ffmpeg.get_ffmpeg_exe()
|
||
except Exception:
|
||
pass
|
||
if ffmpeg_path and os.path.exists(ffmpeg_path):
|
||
plt.rcParams['animation.ffmpeg_path'] = ffmpeg_path
|
||
ffps = min(20, max(1, n_frames // 5))
|
||
writer = manim.FFMpegWriter(fps=ffps, codec="libx264",
|
||
extra_args=["-pix_fmt", "yuv420p"])
|
||
mp4_path = os.path.join(output_dir, "wave_animation.mp4")
|
||
ani.save(mp4_path, writer=writer)
|
||
print(f"[plot_wave] MP4 已保存: {mp4_path}")
|
||
except FileNotFoundError:
|
||
print("[plot_wave] 警告: 未找到 ffmpeg，跳过 MP4 输出")
|
||
except Exception as e:
|
||
print(f"[plot_wave] 警告: MP4 输出失败 ({e})，跳过")
|
||
|
||
if show:
|
||
plt.show()
|
||
else:
|
||
plt.close(fig)
|
||
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)
|