admin
b584c4489c
- Plot 1: x/y/z displacements overlaid on one axes - Plot 2: per-atom KE/PE/total energy overlaid on one axes - Plot 3: system energy vs time (unchanged) All three stacked vertically. Shared y-axis scale within each panel. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
494 lines
19 KiB
Python
494 lines
19 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 _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 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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布局（3行×1列，纵向排列）：
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行0：x/y/z 位移波形叠加在同一子图（vs 原子序号）
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行1：每粒子动能、势能、总能叠加在同一子图
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行2：系统总能量随时间变化
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Args:
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output_dir: 输出目录（含 display.npz 或 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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show: 是否弹出交互窗口
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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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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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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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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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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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# 驱动原子信息（用于势能计算）
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driver_info = _load_driver_info(output_dir) if driving_force else {}
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# ── 位移 ──
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dx = x - pos_0[np.newaxis, :, 0]
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dy = y - pos_0[np.newaxis, :, 1]
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dz = z - pos_0[np.newaxis, :, 2]
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# ── 系统总能量（用于右下时间图）──
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ek_sys, us_sys, ug_sys, ugr_sys = 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_sys + us_sys + ug_sys + ugr_sys
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power = np.gradient(e_total, t)
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# ── 每粒子能量 ──
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ek_atom, pe_atom, et_atom = compute_per_atom_energy(
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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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# ── y 轴范围 ──
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def get_ylim(arr):
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vmax = np.max(np.abs(arr))
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if vmax < 1e-10:
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return -1.0, 1.0
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m = vmax * 0.2
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return -vmax - m, vmax + m
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def get_ylim_pos(arr):
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vmax = np.max(arr)
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if vmax < 1e-12:
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return 0.0, 1.0
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return 0.0, vmax * 1.2
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# 共用 y 轴范围：位移图取三个方向最大值统一
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disp_vmax = max(np.max(np.abs(dx)), np.max(np.abs(dy)), np.max(np.abs(dz)))
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disp_vmax = disp_vmax if disp_vmax > 1e-10 else 1.0
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disp_ylim = (-disp_vmax * 1.2, disp_vmax * 1.2)
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# 每粒子能量：取三者最大值统一 y 轴
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energy_vmax = max(np.max(ek_atom), np.max(pe_atom), np.max(et_atom))
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energy_vmax = energy_vmax if energy_vmax > 1e-12 else 1.0
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energy_ylim = (0.0, energy_vmax * 1.2)
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e_max = max(np.max(e_total), 0.01) * 1.3
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p_max = max(np.max(np.abs(power)) * 1.3, 0.01)
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atom_idx = np.arange(n_atoms)
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# ── 图形布局：3 行 × 1 列，纵向排列 ──
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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, (ax_wave, ax_energy, ax_ep) = plt.subplots(3, 1, figsize=(12, 14))
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fig.suptitle("波形与能量分析", fontsize=16)
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fig.subplots_adjust(hspace=0.40, top=0.94)
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# ── 图1：x/y/z 位移波形叠加 ──
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ax_wave.set_xlim(0, n_atoms - 1)
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ax_wave.set_ylim(disp_ylim)
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ax_wave.set_xlabel("原子序号")
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ax_wave.set_ylabel("位移")
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ax_wave.set_title("粒子位移（x / y / z 方向）")
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ax_wave.grid(True, alpha=0.3)
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wave_disps = [dx, dy, dz]
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wave_labels = ["x 方向（纵波）", "y 方向（横波）", "z 方向（横波）"]
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wave_colors = ["#2563eb", "#ea580c", "#16a34a"]
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wave_lines = []
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for label, color in zip(wave_labels, wave_colors):
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ln, = ax_wave.plot([], [], color=color, linewidth=1.5, label=label)
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wave_lines.append(ln)
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ax_wave.legend(loc="upper right", fontsize=9)
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time_text = ax_wave.text(0.02, 0.95, "", transform=ax_wave.transAxes,
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fontsize=10, verticalalignment="top")
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# ── 图2：每粒子动能、势能、总能叠加 ──
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ax_energy.set_xlim(0, n_atoms - 1)
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ax_energy.set_ylim(energy_ylim)
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ax_energy.set_xlabel("原子序号")
|
||
ax_energy.set_ylabel("能量")
|
||
ax_energy.set_title("每粒子能量（动能 / 势能 / 总能）")
|
||
ax_energy.grid(True, alpha=0.3)
|
||
|
||
energy_arrays = [ek_atom, pe_atom, et_atom]
|
||
energy_labels = ["动能", "势能", "总能"]
|
||
energy_colors = ["#1d4ed8", "#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_energy.legend(loc="upper right", fontsize=9)
|
||
|
||
# ── 图3：系统总能量随时间 ──
|
||
ax_ep.set_xlim(t[0], t[-1])
|
||
ep_yhigh = max(e_max, p_max)
|
||
ep_ylow = min(-p_max * 0.1, 0.0)
|
||
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)
|
||
|
||
ln_ek, = ax_ep.plot([], [], "b-", lw=1.5, label="动能")
|
||
ln_us, = ax_ep.plot([], [], "orange", lw=1.5, label="弹性势能")
|
||
ln_et, = ax_ep.plot([], [], "r--", lw=1.5, label="总能量")
|
||
ln_pw, = ax_ep.plot([], [], "g-", lw=1.5, alpha=0.7, label="输入功率 (dE/dt)")
|
||
ln_ug = None
|
||
ln_ugr = None
|
||
if gravity_field:
|
||
ln_ug, = ax_ep.plot([], [], "purple", lw=1.0, alpha=0.5, label="重力势能")
|
||
if gravity_interaction and n_atoms <= 200:
|
||
ln_ugr, = ax_ep.plot([], [], "brown", lw=1.0, alpha=0.5, label="万有引力势能")
|
||
ax_ep.legend(loc="upper left", fontsize=9)
|
||
|
||
# ── 动画更新 ──
|
||
def update(frame):
|
||
# 图1：位移波形
|
||
for i, ln in enumerate(wave_lines):
|
||
ln.set_data(atom_idx, wave_disps[i][frame])
|
||
time_text.set_text(f"t = {t[frame]:.2f} s | 帧 {frame+1}/{n_frames}")
|
||
|
||
# 图2：每粒子能量
|
||
for i, ln in enumerate(energy_lines):
|
||
ln.set_data(atom_idx, energy_arrays[i][frame])
|
||
|
||
# 图3：系统能量（累计到当前帧）
|
||
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])
|
||
ax_ep.set_xlim(t[0], max(t[frame] + max(t[-1] * 0.05, 1), t[-1]))
|
||
|
||
artists = wave_lines + [time_text] + energy_lines + \
|
||
[ln_ek, ln_us, ln_et, ln_pw]
|
||
if ln_ug: artists.append(ln_ug)
|
||
if ln_ugr: artists.append(ln_ugr)
|
||
return artists
|
||
|
||
ani = FuncAnimation(fig, update, frames=n_frames, interval=50, blit=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)
|