docs: 更新 examples/Readme.md 并新增 Readme.html
- 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
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@@ -947,6 +947,179 @@ def run_from_config(config, out_dir=None):
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return traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz
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def run_engine_dll(engine, output_dir, config):
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"""通过 DLL（ctypes）调用计算引擎，不经过文件 I/O，直接返回轨迹数组。
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Args:
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engine: 引擎名称 "c", "cpp", 或 "fortran"
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output_dir: 输出目录（用于保存 display.npz）
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config: YAML 配置字典
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Returns:
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None（结果直接写入 output_dir/display.npz）
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Raises:
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FileNotFoundError: DLL 尚未编译
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RuntimeError: DLL 运算出错
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"""
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import sys as _sys
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import datetime as _datetime
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_eng_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "engines")
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if _eng_dir not in _sys.path:
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_sys.path.insert(0, _eng_dir)
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from engine_dll import load_dll, run_dynamics_dll, is_dll_available
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if not is_dll_available(engine):
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raise FileNotFoundError(
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f"DLL 未找到（引擎 {engine}）。"
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f"请先编译：cd engines/{engine} && make dll")
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lib = load_dll(engine)
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# ── 构造原子数据 ──────────────────────────────────────────
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if ATOM_POSITIONS is None:
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raise RuntimeError("run_engine_dll: 请先调用 load_parameters() 加载配置")
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pos = np.asarray(ATOM_POSITIONS, dtype=np.float64) # (n, 3)
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vel = np.asarray(ATOM_VELOCITIES, dtype=np.float64)
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mass = np.asarray(ATOM_MASSES, dtype=np.float64)
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fixed= np.asarray(ATOM_FIXED, dtype=np.int32) # (n, 3)
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# ── 键数据 ────────────────────────────────────────────────
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n_bonds = len(BOND_PAIRS) if BOND_PAIRS is not None else 0
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bp = np.asarray(BOND_PAIRS, dtype=np.int32) if n_bonds else np.zeros((0,2), dtype=np.int32)
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bk = np.asarray(BOND_STIFFNESS, dtype=np.float64) if n_bonds else np.zeros(0)
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br0 = np.asarray(BOND_REST_LENGTHS,dtype=np.float64) if n_bonds else np.zeros(0)
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# ── 驱动数据 ──────────────────────────────────────────────
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drv_list = []
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if int(config.get("driving_force", 0)) and DRIVER_DATA:
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atom_id_to_local = {int(aid): i for i, aid in enumerate(ATOM_IDS)}
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for d in DRIVER_DATA:
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aid = int(d.get("atom_id", -1))
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if aid not in atom_id_to_local:
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continue
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local_idx = atom_id_to_local[aid]
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# d["amp"], d["freq"], d["phi"] are numpy arrays; d["phi"] is already in radians
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amp = [float(v) for v in d["amp"]]
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freq = [float(v) for v in d["freq"]]
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phi = [float(v) for v in d["phi"]] # radians
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# eq_pos is set by run_from_config; fall back to initial position
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eq_pos = d.get("eq_pos")
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eq = ([float(v) for v in eq_pos] if eq_pos is not None
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else [float(pos[local_idx, 0]), float(pos[local_idx, 1]), float(pos[local_idx, 2])])
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pc = d.get("period_cycles") # None → unlimited, float → finite
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nc = float(pc) if pc is not None else 0.0
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hp = 1 if nc > 0 else 0
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drv_list.append({"local_idx": local_idx, "amp": amp, "freq": freq,
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"phi": phi, "eq_pos": eq, "n_cycles": nc, "has_period": hp})
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# ── 进度回调 ──────────────────────────────────────────────
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total_steps = int(config["NT"]) - int(config.get("warmup_steps", 0))
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try:
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from tqdm import tqdm as _tqdm
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_pbar = _tqdm(total=total_steps, desc=f"[compute] DLL {engine}",
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unit="步", bar_format='{l_bar}{bar}| {n_fmt}/{total_fmt} [{elapsed}<{remaining}]')
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def _cb(step, total):
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_pbar.n = step
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_pbar.refresh()
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except ImportError:
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_pbar = None
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_cb = None
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_t0 = time.time()
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try:
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result = run_dynamics_dll(
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lib, config,
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pos, vel, mass, fixed,
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bp, bk, br0,
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drv_list, np.asarray(ATOM_IDS),
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progress_cb=_cb,
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)
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finally:
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if _pbar is not None:
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_pbar.n = total_steps
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_pbar.close()
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elapsed = time.time() - _t0
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n_frames, n_atoms = result["x"].shape
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print(f"[compute] DLL 完成: {n_frames} 帧 {n_atoms} 原子 {elapsed:.3f} s")
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# ── 构建 header 并保存 display.npz ────────────────────────
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# 与 run_simulation 写入的 header 保持字段完全一致，
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# 确保 draw.py / plot_wave.py 读到所有必要参数。
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G_vec = parse_gravity_vector(config.get("G", [0, 0, 0]))
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B_vec = parse_damping_vector(config.get("B", [0, 0, 0]))
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record_steps_hdr = int(config["NT"]) - int(config.get("warmup_steps", 0))
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header = {
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"DT": str(config["DT"]),
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"NSTEP": str(config.get("NSTEP", 1)),
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"method": str(config.get("method", "leapfrog")),
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"NT": str(config["NT"]),
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"warmup_steps": str(config.get("warmup_steps", 0)),
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"dynamic_steps": str(record_steps_hdr),
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"T_total": str(int(config["NT"]) * float(config["DT"])),
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"box_a": str(config.get("box_a", 300.0)),
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"gravity_field": str(config.get("gravity_field", 0)),
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"gravity_interaction": str(config.get("gravity_interaction", 0)),
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"elastic_force": str(config.get("elastic_force", 1)),
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"damping_force": str(config.get("damping_force", 0)),
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"driving_force": str(config.get("driving_force", 0)),
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"gravity_strength": str(config.get("gravity_strength", 1.0)),
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"G": json.dumps(G_vec.tolist()),
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"B": json.dumps(B_vec.tolist()),
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"number_of_frames": str(n_frames),
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"number_of_particles": str(n_atoms),
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# draw.py 需要的渲染参数
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"use_marker": str(use_marker),
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"ball_radius": str(config.get("ball_radius", float(ATOM_RADII[0]) if ATOM_RADII is not None else 0.5)),
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"ball_color_r": str(config.get("ball_color_r", 0.9)),
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"ball_color_g": str(config.get("ball_color_g", 0.2)),
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"ball_color_b": str(config.get("ball_color_b", 0.2)),
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"box_color_r": str(config.get("box_color_r", 0.8)),
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"box_color_g": str(config.get("box_color_g", 0.8)),
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"box_color_b": str(config.get("box_color_b", 0.85)),
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"alpha": ",".join(str(a) for a in (alpha if isinstance(alpha, list) else [alpha])),
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# draw.py / plot_wave.py 需要的原子、键数据
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"atom_radii": ",".join(str(r) for r in ATOM_RADII),
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"atom_masses": json.dumps([float(v) for v in ATOM_MASSES]),
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"atom_positions": json.dumps(ATOM_POSITIONS.tolist()),
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"bond_pairs": json.dumps(BOND_PAIRS.tolist() if BOND_PAIRS is not None else []),
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"bond_stiffness": json.dumps(BOND_STIFFNESS.tolist() if BOND_STIFFNESS is not None else []),
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"bond_rest_lengths": json.dumps(BOND_REST_LENGTHS.tolist() if BOND_REST_LENGTHS is not None else []),
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# 边界（draw.py 用于场景缩放）
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"X_MIN": str(-float(config.get("box_a", 300.0))),
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"X_MAX": str( float(config.get("box_a", 300.0))),
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"Y_MIN": str(-float(config.get("box_a", 300.0))),
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"Y_MAX": str( float(config.get("box_a", 300.0))),
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"Z_MIN": str(-float(config.get("box_a", 300.0))),
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"Z_MAX": str( float(config.get("box_a", 300.0))),
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# 相机参数
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"camera_distance": str(camera_distance),
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"camera_elevation": str(camera_elevation),
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"camera_azimuth": str(camera_azimuth),
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"camera_center_x": str(camera_center_x),
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"camera_center_y": str(camera_center_y),
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"camera_center_z": str(camera_center_z),
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"camera_keyframes": str(camera_keyframes_raw),
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}
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if display_amp_str:
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header["display_amp"] = display_amp_str
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if camera_pos_x is not None:
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header["camera_pos_x"] = str(camera_pos_x)
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header["camera_pos_y"] = str(camera_pos_y)
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header["camera_pos_z"] = str(camera_pos_z)
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os.makedirs(output_dir, exist_ok=True)
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npz_path = os.path.join(output_dir, "display.npz")
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save_display_npz(
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npz_path,
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result["x"], result["y"], result["z"],
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result["vx"], result["vy"], result["vz"],
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np.asarray(ATOM_IDS),
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header_fields=header,
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)
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print(f"[compute] display.npz 已生成: {npz_path}")
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def run_engine(engine, input_dir, output_dir, config):
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"""调用外部计算引擎（C/C++/Fortran），生成 trajectory.txt。
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@@ -961,32 +1134,43 @@ def run_engine(engine, input_dir, output_dir, config):
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script_dir = os.path.dirname(os.path.abspath(__file__))
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system = platform.system().lower()
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engine_map = {
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"c": "engines/c/build/dynamics_c",
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"cpp": "engines/cpp/build/dynamics_cpp",
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"c": "engines/c/build/dynamics_c",
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"cpp": "engines/cpp/build/dynamics_cpp",
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"c++": "engines/cpp/build/dynamics_cpp",
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"fortran": "engines/fortran/build/dynamics_f90",
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"f90": "engines/fortran/build/dynamics_f90",
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"python": None, # 特殊处理：用 sys.executable 调用 main.py
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}
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if engine not in engine_map:
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raise ValueError(f"不支持的引擎: {engine}，可选: {list(engine_map.keys())}")
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raise ValueError(f"不支持的引擎: {engine}，可选: c, cpp, fortran, python")
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engine_rel = engine_map[engine]
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engine_path = os.path.join(script_dir, engine_rel)
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if engine == "python":
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# Python 引擎：用当前解释器运行 engines/python/main.py
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py_main = os.path.join(script_dir, "engines", "python", "main.py")
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if not os.path.exists(py_main):
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raise FileNotFoundError(f"Python 引擎脚本不存在: {py_main}")
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found = py_main
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engine_path = sys.executable
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else:
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engine_rel = engine_map[engine]
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engine_path = os.path.join(script_dir, engine_rel)
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# 自动检测可执行文件后缀和平台专用版本
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candidates = [
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engine_path, # 无后缀
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engine_path + ".exe", # Windows .exe
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engine_path + f"_{system}.exe", # 平台专用 (c_linux.exe, c_darwin.exe)
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]
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found = None
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for p in candidates:
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if os.path.exists(p):
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found = p
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break
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if found is None:
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raise FileNotFoundError(
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f"引擎可执行文件不存在: 尝试了 {candidates}\n"
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f"请先编译: cd engines/{engine} && make\n"
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f"或安装交叉编译器后: cd engines/{engine} && make {system}")
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# 自动检测可执行文件后缀和平台专用版本
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candidates = [
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engine_path,
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engine_path + ".exe",
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engine_path + f"_{system}.exe",
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]
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found = None
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for p in candidates:
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if os.path.exists(p):
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found = p
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break
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if found is None:
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raise FileNotFoundError(
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f"引擎可执行文件不存在: 尝试了 {candidates}\n"
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f"请先编译: cd engines/{engine} && make\n"
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f"或安装交叉编译器后: cd engines/{engine} && make {system}")
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# 构造 param.json（数值参数）
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G = parse_gravity_vector(config.get("G", [0, 0, -9.8]))
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@@ -1089,8 +1273,11 @@ def run_engine(engine, input_dir, output_dir, config):
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t_start = time.time()
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t_start_str = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
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# Python 引擎：[python, main.py, args]；其他引擎：[exe, args]
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_cmd = ([engine_path, found] if engine == "python" else [engine_path]) + \
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[os.path.abspath(input_dir), os.path.abspath(output_dir), param_path]
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_p = subprocess.Popen(
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[engine_path, os.path.abspath(input_dir), os.path.abspath(output_dir), param_path],
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_cmd,
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stdout=subprocess.PIPE, stderr=subprocess.PIPE,
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text=True, encoding='utf-8', errors='replace')
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_engine_lines = []
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