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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"""
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engines/python/main.py
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-----------------------
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独立 Python 计算引擎。
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与 main.c / main.cpp / main.f90 结构一致：
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输入: <input_dir>/coord.txt, connection.txt, bond.txt, [driver.txt]
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<param_json> (同 engines/c/param.json 格式)
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输出: <output_dir>/display.txt (+ display.npz)
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<output_dir>/trajectory.txt (若 save_trajectory=1)
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用法:
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python main.py <input_dir> <output_dir> <param_json>
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内部调用 dynamics_lib.run_dynamics()，算法与 compute.py 完全一致。
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"""
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import json
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import os
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import sys
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import time
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import numpy as np
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# 将父目录（engines/python 的上级 engines）加入 sys.path，
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# 以便在独立运行时也能找到 dynamics_lib
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_HERE = os.path.dirname(os.path.abspath(__file__))
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sys.path.insert(0, _HERE)
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from dynamics_lib import run_dynamics
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# 为读取 coord/bond/display，复用 compute.py 中的 I/O 函数
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_COMPUTE = os.path.join(_HERE, "..", "..")
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sys.path.insert(0, _COMPUTE)
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import compute as _c
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_METHOD_ID = {
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"explicit_euler": 0,
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"euler": 0,
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"implicit_euler": 1,
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"midpoint": 2,
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"leapfrog": 3,
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}
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def _load_params(param_path):
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"""读取 param.json（与 C 引擎格式相同）."""
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with open(param_path, "r", encoding="utf-8") as f:
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p = json.load(f)
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return p
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def main():
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if len(sys.argv) < 4:
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print("用法: python main.py <input_dir> <output_dir> <param_json>")
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sys.exit(1)
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input_dir = sys.argv[1]
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output_dir = sys.argv[2]
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param_path = sys.argv[3]
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os.makedirs(output_dir, exist_ok=True)
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# ── 读取参数 ─────────────────────────────────────────────
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p = _load_params(param_path)
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box_a = float(p.get("box_a", 10.0))
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NT = int(p.get("NT", 10000))
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dt = float(p.get("DT", 0.001))
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NSTEP = int(p.get("NSTEP", 100))
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warmup_steps = int(p.get("warmup_steps", 0))
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method_str = str(p.get("method", "leapfrog")).lower().replace(" ", "_")
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method_id = _METHOD_ID.get(method_str, 3)
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G = p.get("G", [0.0, 0.0, -9.8])
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B = p.get("B", [0.0, 0.0, 0.0])
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gravity_field = int(p.get("gravity_field", 1))
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elastic_force = int(p.get("elastic_force", 1))
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damping_force = int(p.get("damping_force", 0))
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gravity_strength = float(p.get("gravity_strength", 1.0))
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driving_force = int(p.get("driving_force", 0))
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save_traj = int(p.get("save_trajectory", 0))
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# ── 读取原子数据 ──────────────────────────────────────────
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coord_path = os.path.join(input_dir, "coord.txt")
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atom_ids, masses, radii, positions, velocities, fixed = _c.load_coord_file(coord_path)
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# ── 读取键数据 ────────────────────────────────────────────
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conn_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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bond_map = _c.load_bond_parameters(bond_path)
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bond_pairs, bond_names, bond_stiffness, bond_rest_lengths = \
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_c.load_bond_connections(conn_path, atom_ids, positions, bond_map)
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n_bonds = len(bond_pairs)
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# ── 读取驱动力 ────────────────────────────────────────────
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drv_list = []
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if driving_force:
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driver_path = os.path.join(input_dir, "driver.txt")
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raw_drivers = _c.load_driver_file(driver_path, atom_ids)
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if raw_drivers:
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atom_id_map = {int(aid): i for i, aid in enumerate(atom_ids)}
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for d in raw_drivers:
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aid = int(d["atom_id"])
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if aid not in atom_id_map:
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continue
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lidx = atom_id_map[aid]
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eq = positions[lidx].tolist()
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d["eq_pos"] = np.array(eq)
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pc = d.get("period_cycles")
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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({
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"local_idx": lidx,
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"amp": d["amp"].tolist(),
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"freq": d["freq"].tolist(),
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"phi": d["phi"].tolist(), # radians
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"eq": eq,
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"nc": nc,
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"hp": hp,
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})
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nd = len(drv_list)
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if nd > 0:
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drv_idx = np.array([d["local_idx"] for d in drv_list], dtype=np.int64)
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drv_amp = np.array([d["amp"] for d in drv_list], dtype=np.float64)
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drv_freq = np.array([d["freq"] for d in drv_list], dtype=np.float64)
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drv_phi = np.array([d["phi"] for d in drv_list], dtype=np.float64)
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drv_eq = np.array([d["eq"] for d in drv_list], dtype=np.float64)
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drv_nc = np.array([d["nc"] for d in drv_list], dtype=np.float64)
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drv_hp = np.array([d["hp"] for d in drv_list], dtype=np.int32)
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else:
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drv_idx = drv_amp = drv_freq = drv_phi = drv_eq = drv_nc = drv_hp = \
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np.zeros(0, dtype=np.int64)
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# ── 计算帧数 ──────────────────────────────────────────────
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record_steps = NT - warmup_steps
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n_frames = max(1, record_steps // NSTEP)
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# ── 进度回调 ──────────────────────────────────────────────
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def _progress(step, total):
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pct = step * 100 // total
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print(f"[python-engine] progress: {step}/{total} ({pct}%)", flush=True)
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# ── 运行计算 ──────────────────────────────────────────────
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t0 = time.time()
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print(f"[python-engine] NT={NT} NSTEP={NSTEP} method={method_str} "
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f"n_atoms={len(atom_ids)} n_bonds={n_bonds}")
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out_x, out_y, out_z, out_vx, out_vy, out_vz = run_dynamics(
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n_atoms=len(atom_ids),
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pos_init=positions,
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vel_init=velocities,
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masses=masses,
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fixed=fixed,
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n_bonds=n_bonds,
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bond_pairs=bond_pairs,
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bond_k=bond_stiffness,
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bond_r0=bond_rest_lengths,
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box_a=box_a,
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dt=dt,
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NT=NT,
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NSTEP=NSTEP,
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warmup_steps=warmup_steps,
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method_id=method_id,
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Gx=float(G[0]), Gy=float(G[1]), Gz=float(G[2]),
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Bx=float(B[0]), By=float(B[1]), Bz=float(B[2]),
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gravity_field=gravity_field,
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elastic_force=elastic_force,
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damping_force=damping_force,
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gravity_strength=gravity_strength,
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n_drivers=nd,
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drv_idx=drv_idx,
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drv_amp=drv_amp,
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drv_freq=drv_freq,
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drv_phi=drv_phi,
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drv_eq=drv_eq,
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drv_ncycles=drv_nc,
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drv_has_period=drv_hp,
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n_frames=n_frames,
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progress_cb=_progress,
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)
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elapsed = time.time() - t0
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print(f"[python-engine] 完成: {n_frames} 帧 {elapsed:.3f} s")
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# ── 构建 display header ───────────────────────────────────
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ball_radius = float(p.get("ball_radius", 0.5))
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ball_color = p.get("ball_color", [0.9, 0.2, 0.2])
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box_color = p.get("box_color", [0.8, 0.8, 0.85])
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use_marker = int(p.get("use_marker", 0))
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alpha_val = p.get("alpha", 0.2)
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cam_dist = float(p.get("camera_distance", 40.0))
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cam_elev = float(p.get("camera_elevation", 0.0))
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cam_azim = float(p.get("camera_azimuth", 0.0))
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cam_cx = float(p.get("camera_center_x", 0.0))
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cam_cy = float(p.get("camera_center_y", 0.0))
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cam_cz = float(p.get("camera_center_z", 0.0))
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header = {
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"DT": str(dt),
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"NSTEP": str(NSTEP),
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"method": method_str,
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"NT": str(NT),
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"warmup_steps": str(warmup_steps),
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"dynamic_steps": str(record_steps),
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"T_total": str(NT * dt),
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"box_a": str(box_a),
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"gravity_field": str(gravity_field),
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"elastic_force": str(elastic_force),
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"damping_force": str(damping_force),
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"driving_force": str(driving_force),
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"gravity_strength": str(gravity_strength),
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"G": json.dumps([float(v) for v in G]),
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"B": json.dumps([float(v) for v in B]),
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"number_of_frames": str(n_frames),
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"number_of_particles": str(len(atom_ids)),
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"use_marker": str(use_marker),
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"ball_radius": str(ball_radius),
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"ball_color_r": str(ball_color[0]),
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"ball_color_g": str(ball_color[1]),
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"ball_color_b": str(ball_color[2]),
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"box_color_r": str(box_color[0]),
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"box_color_g": str(box_color[1]),
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"box_color_b": str(box_color[2]),
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"alpha": str(alpha_val) if not isinstance(alpha_val, list)
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else ",".join(str(a) for a in alpha_val),
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"atom_radii": ",".join(str(r) for r in radii),
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"atom_masses": json.dumps([float(m) for m in masses]),
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"atom_positions": json.dumps(positions.tolist()),
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"bond_pairs": json.dumps(bond_pairs.tolist() if n_bonds else []),
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"bond_stiffness": json.dumps(bond_stiffness.tolist() if n_bonds else []),
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"bond_rest_lengths": json.dumps(bond_rest_lengths.tolist() if n_bonds else []),
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"X_MIN": str(-box_a), "X_MAX": str(box_a),
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"Y_MIN": str(-box_a), "Y_MAX": str(box_a),
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"Z_MIN": str(-box_a), "Z_MAX": str(box_a),
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"camera_distance": str(cam_dist),
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"camera_elevation": str(cam_elev),
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"camera_azimuth": str(cam_azim),
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"camera_center_x": str(cam_cx),
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"camera_center_y": str(cam_cy),
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"camera_center_z": str(cam_cz),
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"camera_keyframes": "",
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}
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# ── 保存 display.txt + display.npz ───────────────────────
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disp_txt = os.path.join(output_dir, "display.txt")
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_c.save_display_txt(
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disp_txt,
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out_x, out_y, out_z, out_vx, out_vy, out_vz,
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atom_ids, record_steps, len(atom_ids),
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header_fields=header,
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)
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print(f"[python-engine] display.txt 已保存: {disp_txt}")
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disp_npz = os.path.join(output_dir, "display.npz")
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_c.save_display_npz(
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disp_npz,
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out_x, out_y, out_z, out_vx, out_vy, out_vz,
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atom_ids, header_fields=header,
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)
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print(f"[python-engine] display.npz 已保存: {disp_npz}")
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# ── 可选：保存 trajectory.txt ─────────────────────────────
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if save_traj:
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traj_payload = {
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"traj_x": out_x, "traj_y": out_y, "traj_z": out_z,
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"traj_vx": out_vx, "traj_vy": out_vy, "traj_vz": out_vz,
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"NT": record_steps, "DT": dt, "NSTEP": NSTEP,
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"method": method_str,
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"atom_ids": atom_ids,
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"atom_masses": masses,
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"atom_radii": radii,
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"atom_positions": positions,
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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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"G": [float(v) for v in G],
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"B": [float(v) for v in B],
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}
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traj_path = os.path.join(output_dir, "trajectory.txt")
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_c.save_text_data(traj_path, traj_payload)
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print(f"[python-engine] trajectory.txt 已保存: {traj_path}")
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if __name__ == "__main__":
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main()
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