feat: 增加驱动力系统、Marker渲染模式、动画防闪退、案例文档
- 新增 driving_force 驱动力系统（driver.txt 定义，支持周期控制） - 新增 use_marker 渲染开关（GPU实例化点精灵，提升大量原子性能） - 修复动画闪退：独立控制台、错误日志、启动存活检测 - 重绘 draw.py 架构：双渲染模式 + 预分配键线缓冲区 - 修复 raw trajectory 采样时间变量遮蔽 bug - 重构 case05: 60原子一维链 + 驱动力 + 完整案例文档 - 修复所有案例 Readme.md 编码（GBK → UTF-8） - 所有 input.txt 新增 driver_file / driving_force / use_marker 参数
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@@ -69,8 +69,12 @@ GRAVITY_FIELD = 1 # 均匀重力场
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GRAVITY_INTERACTION = 0 # 原子间万有引力
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ELASTIC_FORCE = 1 # 弹簧键力
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DAMPING_FORCE = 0 # 阻尼
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DRIVING_FORCE = 0 # 驱动力
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GRAVITY_STRENGTH = 1.0
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# 驱动力数据
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DRIVER_DATA = None # 加载自 driver.txt
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# 派生边界（根据 box_a 计算）
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X_MIN = None
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X_MAX = None
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@@ -328,6 +332,135 @@ def load_bond_connections(connection_path, atom_ids, atom_positions, bond_map):
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)
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# ===========================================================================
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# 驱动力加载 & 应用
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# ===========================================================================
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def load_driver_file(driver_path, atom_ids):
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"""从 driver.txt 加载驱动力定义。
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格式：
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n amp_x amp_y amp_z freq_x freq_y freq_z phi_x phi_y phi_z period
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数值 0 0 0 0 0 10 0 0 90 all
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其中：
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position = A * cos(2π f t + φ), φ 为角度制（自动转弧度）
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period = all | 数值（周期数，结束后原子静止）
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"""
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if not os.path.exists(driver_path):
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print(f"[compute] 警告: 驱动力文件不存在: {driver_path}")
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return None
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atom_index = {int(aid): idx for idx, aid in enumerate(atom_ids)}
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drivers = []
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ncols = 11
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with open(driver_path, "r", encoding="utf-8") as f:
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header = f.readline().strip().split()
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expected = ["n", "amp_x", "amp_y", "amp_z",
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"freq_x", "freq_y", "freq_z",
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"phi_x", "phi_y", "phi_z", "period"]
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if header != expected:
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raise ValueError(
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f"driver.txt 表头应为: {' '.join(expected)}，实际为: {' '.join(header)}")
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for line_no, line in enumerate(f, start=2):
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stripped = line.strip()
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if not stripped or stripped.startswith("#"):
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continue
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parts = stripped.split()
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if len(parts) != ncols:
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raise ValueError(
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f"{driver_path}:{line_no} 应有 {ncols} 列，实际为 {len(parts)} 列")
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n = int(parts[0])
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if n not in atom_index:
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raise ValueError(f"{driver_path}:{line_no} 原子序号 {n} 不在 coord.txt 中")
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amp = np.array([float(parts[1]), float(parts[2]), float(parts[3])],
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dtype=np.float64)
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freq = np.array([float(parts[4]), float(parts[5]), float(parts[6])],
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dtype=np.float64)
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phi_deg = np.array([float(parts[7]), float(parts[8]), float(parts[9])],
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dtype=np.float64)
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phi_rad = phi_deg * np.pi / 180.0
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period_str = parts[10]
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drivers.append({
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"atom_index": atom_index[n],
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"atom_id": n,
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"amp": amp,
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"freq": freq,
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"phi": phi_rad,
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"period_str": period_str,
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"period_cycles": None if period_str == "all" else float(period_str),
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# 在模拟中动态记录：冻结步数索引、冻结位置
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"freeze_step": None,
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"freeze_pos": None,
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})
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if not drivers:
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print(f"[compute] 警告: driver.txt 中没有有效数据")
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return None
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print(f"[compute] 已加载驱动力: {len(drivers)} 条定义")
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for d in drivers:
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print(f" 原子 {d['atom_id']}: "
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f"A=({d['amp'][0]},{d['amp'][1]},{d['amp'][2]}), "
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f"f=({d['freq'][0]},{d['freq'][1]},{d['freq'][2]}), "
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f"φ=({phi_deg[d['amp'].tolist().index(max(d['amp']))]}° 等), "
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f"period={d['period_str']}")
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return drivers
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def apply_driving_force(x, y, z, vx, vy, vz, t, step, drivers, dt):
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"""对受驱原子按驱动力函数覆盖位置/速度。
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驱动力公式：pos = A * cos(2π f t + φ)
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vel = -A * 2π f * sin(2π f t + φ)
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"""
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if drivers is None:
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return x, y, z, vx, vy, vz
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for d in drivers:
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idx = d["atom_index"]
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# 确定驱动力持续到哪一步
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if d["period_cycles"] is not None:
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max_freq = np.max(np.abs(d["freq"]))
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if max_freq > 1e-12:
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period_duration = d["period_cycles"] / max_freq
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period_steps = int(period_duration / dt)
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else:
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period_steps = 0
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if step > period_steps:
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# 驱动力已结束：原子静止（保持最后位置，速度归零）
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if d["freeze_pos"] is not None:
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x[idx], y[idx], z[idx] = d["freeze_pos"]
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vx[idx] = vy[idx] = vz[idx] = 0.0
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continue
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else:
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period_steps = None # 全程驱动
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# 当前驱动力下的位置 / 速度
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t_vec = np.array([t, t, t], dtype=np.float64)
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pos_drive = d["amp"] * np.cos(2.0 * np.pi * d["freq"] * t_vec + d["phi"])
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vel_drive = -d["amp"] * 2.0 * np.pi * d["freq"] * np.sin(2.0 * np.pi * d["freq"] * t_vec + d["phi"])
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x[idx] = pos_drive[0]
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y[idx] = pos_drive[1]
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z[idx] = pos_drive[2]
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vx[idx] = vel_drive[0]
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vy[idx] = vel_drive[1]
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vz[idx] = vel_drive[2]
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# 若周期有限，记录冻结位置（驱动力最后一帧的位置）
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if period_steps is not None and step == period_steps:
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d["freeze_pos"] = (float(pos_drive[0]), float(pos_drive[1]), float(pos_drive[2]))
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return x, y, z, vx, vy, vz
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def parse_gravity_vector(value):
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"""Parse gravity into a 3D acceleration vector.
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@@ -379,6 +512,7 @@ def run_from_config(config, out_dir=None):
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global box_color_r, box_color_g, box_color_b
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global warmup_steps, sample_start, sample_end
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global GRAVITY_FIELD, GRAVITY_INTERACTION, ELASTIC_FORCE, DAMPING_FORCE, GRAVITY_STRENGTH
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global DRIVING_FORCE, DRIVER_DATA
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box_a = float(config.get("box_a", 10.0))
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raw_alpha = config.get("alpha", 0.2)
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@@ -439,11 +573,22 @@ def run_from_config(config, out_dir=None):
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# 力开关
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global GRAVITY_FIELD, GRAVITY_INTERACTION, ELASTIC_FORCE, DAMPING_FORCE, GRAVITY_STRENGTH
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global DRIVING_FORCE, DRIVER_DATA
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GRAVITY_FIELD = int(config.get("gravity_field", 1))
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GRAVITY_INTERACTION = int(config.get("gravity_interaction", 0))
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ELASTIC_FORCE = int(config.get("elastic_force", 1))
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DAMPING_FORCE = int(config.get("damping_force", 0))
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GRAVITY_STRENGTH = float(config.get("gravity_strength", 1.0))
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DRIVING_FORCE = int(config.get("driving_force", 0))
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# 加载驱动力定义
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DRIVER_DATA = None
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if DRIVING_FORCE:
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driver_rel = str(config.get("driver_file", os.path.join("input", "driver.txt")))
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driver_path = driver_rel
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if out_dir is not None and not os.path.isabs(driver_rel):
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driver_path = os.path.join(out_dir, driver_rel)
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DRIVER_DATA = load_driver_file(driver_path, ATOM_IDS)
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print(f"[compute] 使用算法: {METHOD}")
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print(f"[compute] 已加载成键信息: {len(BOND_PAIRS)} 条键")
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@@ -1062,11 +1207,14 @@ def run_simulation():
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vy = ATOM_VELOCITIES[:, 1].copy()
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vz = ATOM_VELOCITIES[:, 2].copy()
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x, y, z, vx, vy, vz = apply_fixed_constraints(x, y, z, vx, vy, vz)
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# 初始时刻驱动力（t=0 时原子 1 的位置由驱动力决定而非 coord.txt）
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x, y, z, vx, vy, vz = apply_driving_force(x, y, z, vx, vy, vz, 0.0, 0, DRIVER_DATA, DT)
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if warmup_steps is not None and warmup_steps > 0:
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print(f"[compute] 预热阶段: 前 {warmup_steps} 步不记录")
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for step in trange(warmup_steps, desc="[compute] 预热"):
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t = (step + 1) * DT
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x, y, z, vx, vy, vz = apply_driving_force(x, y, z, vx, vy, vz, t, step, DRIVER_DATA, DT)
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x, y, z, vx, vy, vz = apply_motion_update(x, y, z, vx, vy, vz, DT, ATOM_MASSES, G, B)
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x, y, z = wrap_position(x, y, z)
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x, y, z, vx, vy, vz = apply_fixed_constraints(x, y, z, vx, vy, vz)
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@@ -1086,6 +1234,10 @@ def run_simulation():
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traj_vz = np.zeros((record_steps, n_atoms), dtype=np.float64)
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for step in trange(record_steps, desc="[compute] 计算中"):
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t = (step + (warmup_steps or 0)) * DT
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# 先施加驱动力（受驱原子的位置覆盖初始/固定约束，为弹簧力提供正确参考）
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x, y, z, vx, vy, vz = apply_driving_force(x, y, z, vx, vy, vz, t, step, DRIVER_DATA, DT)
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traj_x[step] = x
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traj_y[step] = y
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traj_z[step] = z
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