feat: 真蛙跳法重构（Python/C/C++/Fortran 四引擎统一）

- 新增 compute_accel_conservative / accel_conservative：保守力加速度（弹簧+重力+原子间引力），不含阻尼，供蛙跳专用 - 重写 leapfrog_step / leapfrog_full： - 无阻尼：纯辛积分器，每步 1 次力计算（原 Velocity-Verlet 需 2 次） - 有阻尼：半隐式处理 v(t+dt/2)=[v(t-dt/2)*(1-α)+a_c*dt]/(1+α)，无条件稳定 - 主循环加初始化反向半步 v(-dt/2)=v(0)-0.5*a_c(0)*dt - 修复 C/C++ number of frames 字段写采样帧数而非总积分步数的 bug - Python 引擎：新增 display.npz 二进制格式，draw.py/plot_wave.py 优先读取 - 编译参数统一为 -O3 -march=native -ffast-math
2026-06-12 18:36:37 +08:00
parent e1ade53fff
commit e62e536cee
12 changed files with 627 additions and 355 deletions
@@ -14,17 +14,101 @@ import matplotlib.pyplot as plt
 from matplotlib.animation import FuncAnimation
 import os
 import sys
+import json

 sys.path.insert(0, os.path.dirname(os.path.abspath(__file__)))
 import compute


 def load_disp_data(output_dir):
-    """加载 display.txt"""
-    disp_path = os.path.join(output_dir, "display.txt")
-    if not os.path.exists(disp_path):
-        raise FileNotFoundError(f"找不到 {disp_path}")
-    return compute.load_text_data(disp_path)
+    """加载 display.npz（优先）或 display.txt。"""
+    npz_path = os.path.join(output_dir, "display.npz")
+    txt_path = os.path.join(output_dir, "display.txt")
+    if os.path.exists(npz_path):
+        return compute.load_display_npz(npz_path)
+    if os.path.exists(txt_path):
+        return compute.load_display_txt(txt_path)
+    raise FileNotFoundError(f"找不到 display.npz 或 display.txt in {output_dir}")
+
+
+def _header_json(header_fields, key, default):
+    raw = header_fields.get(key, "")
+    if not raw:
+        return default
+    try:
+        return json.loads(raw)
+    except json.JSONDecodeError:
+        return default
+
+
+def _load_wave_dataset(output_dir):
+    """Load wave/energy plotting data from display metadata or sibling input files."""
+    disp_data = load_disp_data(output_dir)
+    header = disp_data["header_fields"]
+
+    x = disp_data["frames_x"]
+    y = disp_data["frames_y"]
+    z = disp_data["frames_z"]
+    vx = disp_data["frames_vx"]
+    vy = disp_data["frames_vy"]
+    vz = disp_data["frames_vz"]
+    atom_ids = np.array(disp_data["atom_ids"], dtype=np.int64)
+    n_frames = x.shape[0]
+    dt = float(header.get("DT", 0.001))
+    nstep = int(header.get("NSTEP", 1))
+    t = np.arange(n_frames, dtype=np.float64) * dt * nstep
+
+    masses = np.array(_header_json(header, "atom_masses", []), dtype=np.float64)
+    pos_0 = np.array(_header_json(header, "atom_positions", []), dtype=np.float64)
+    bond_pairs = np.array(_header_json(header, "bond_pairs", []), dtype=np.int64)
+    bond_stiffness = np.array(_header_json(header, "bond_stiffness", []), dtype=np.float64)
+    bond_rest_lengths = np.array(_header_json(header, "bond_rest_lengths", []), dtype=np.float64)
+    gravity_vec = _header_json(header, "G", [0.0, 0.0, 0.0])
+
+    # Backward-compatible fallback for older display.txt outputs.
+    if masses.size == 0 or pos_0.size == 0:
+        input_dir = os.path.join(os.path.dirname(output_dir), "input")
+        coord_path = os.path.join(input_dir, "coord.txt")
+        if os.path.exists(coord_path):
+            (_, masses_fb, _, positions_fb, _, _) = compute.load_coord_file(coord_path)
+            masses = np.array(masses_fb, dtype=np.float64)
+            pos_0 = np.array(positions_fb, dtype=np.float64)
+        else:
+            raise ValueError("display.txt 缺少 atom_masses/atom_positions 元数据，且未找到 input/coord.txt")
+
+    if bond_pairs.size == 0:
+        input_dir = os.path.join(os.path.dirname(output_dir), "input")
+        connection_path = os.path.join(input_dir, "connection.txt")
+        bond_path = os.path.join(input_dir, "bond.txt")
+        if os.path.exists(connection_path) and os.path.exists(bond_path):
+            bond_map = compute.load_bond_parameters(bond_path)
+            pairs_fb, _, stiffness_fb, rest_lengths_fb = compute.load_bond_connections(
+                connection_path, atom_ids, pos_0, bond_map)
+            bond_pairs = np.array(pairs_fb, dtype=np.int64)
+            bond_stiffness = np.array(stiffness_fb, dtype=np.float64)
+            bond_rest_lengths = np.array(rest_lengths_fb, dtype=np.float64)
+
+    return {
+        "n_frames": n_frames,
+        "t": t,
+        "x": x,
+        "y": y,
+        "z": z,
+        "vx": vx,
+        "vy": vy,
+        "vz": vz,
+        "pos_0": pos_0,
+        "masses": masses,
+        "atom_ids": atom_ids,
+        "bond_pairs": bond_pairs,
+        "bond_stiffness": bond_stiffness,
+        "bond_rest_lengths": bond_rest_lengths,
+        "gravity_field": int(header.get("gravity_field", 0)),
+        "gravity_interaction": int(header.get("gravity_interaction", 0)),
+        "gravity_strength": float(header.get("gravity_strength", 1.0)),
+        "G": gravity_vec,
+        "driving_force": int(header.get("driving_force", 0)),
+    }


 def compute_energy(x, y, z, vx, vy, vz, masses, mass_arr,
@@ -91,36 +175,36 @@ def plot_wave(output_dir, save_gif=False, save_mp4=False):
        save_gif:   是否保存 GIF
        save_mp4:   是否保存 MP4
    """
-    data = load_disp_data(output_dir)
+    data = _load_wave_dataset(output_dir)

    n_frames = int(data["n_frames"])
-    t = np.array(data["disp_t"])
+    t = np.array(data["t"])

    # 位置 / 速度
-    x  = np.array(data["disp_all_x"])
-    y  = np.array(data["disp_all_y"])
-    z  = np.array(data["disp_all_z"])
-    vx = np.array(data["disp_all_vx"])
-    vy = np.array(data["disp_all_vy"])
-    vz = np.array(data["disp_all_vz"])
+    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"])

    # 原子信息
-    pos_0    = np.array(data["atom_positions"])  # (n_atoms, 3)
-    masses   = np.array(data["atom_masses"])
+    pos_0 = np.array(data["pos_0"])
+    masses = np.array(data["masses"])
    atom_ids = np.array(data["atom_ids"])
-    n_atoms  = len(atom_ids)
+    n_atoms = len(atom_ids)

    # 成键
-    bond_pairs        = data.get("bond_pairs", [])
-    bond_stiffness    = np.array(data.get("bond_stiffness", []))
-    bond_rest_lengths = np.array(data.get("bond_rest_lengths", []))
+    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)

    # 物理开关
-    gravity_field       = int(data.get("gravity_field", 0))
+    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))
+    G = data.get("G", [0, 0, 0])
+    gravity_strength = float(data.get("gravity_strength", 1.0))
+    driving_force = int(data.get("driving_force", 0))

    # ── 位移（偏离初始平衡位形）──
    dx = x - pos_0[np.newaxis, :, 0]   # 纵波（沿链方向 x）