modified: CMakeLists.txt
modified: INSTALL.md modified: README.md modified: build_release_zip.py modified: compute.py new file: doc/index.html modified: dynamics.py modified: engines/c/main.c modified: engines/cpp/main.cpp modified: engines/fortran/main.f90 modified: examples/case01/input/coord.txt renamed: examples/case01/input/parameters.yaml -> examples/case01/input/input.txt modified: examples/case01/run_dynamics.py new file: examples/case02/input/bond.txt new file: examples/case02/input/connection.txt new file: examples/case02/input/coord.txt new file: examples/case02/input/input.txt new file: examples/case02/run_dynamics.py
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@@ -4,9 +4,9 @@ dynamics.py
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统一入口：读取 YAML 配置文件 → 运行模拟 → 抽帧 → 绘图（可选）
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用法：
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python dynamics.py # 使用 input/parameters.yaml
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python dynamics.py input/parameters.yaml # 指定配置文件
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python dynamics.py --config input/parameters.yaml --no-plot
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python dynamics.py # 使用 input/input.txt
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python dynamics.py input/input.txt # 指定配置文件（YAML 格式）
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python dynamics.py --config input/input.txt --no-plot
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"""
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import os
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@@ -115,6 +115,14 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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config = load_yaml_config(config_path)
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print(f"[run] 已加载配置: {config_path}")
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# ── T_total → NT 自动转换 ──────────────────────
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if "T_total" in config and "NT" not in config:
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dt = float(config["DT"])
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config["NT"] = int(float(config["T_total"]) / dt)
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print(f"[run] T_total={config['T_total']} → NT={config['NT']} (DT={dt})")
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elif "T_total" in config and "NT" in config:
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print(f"[run] 同时指定了 T_total 和 NT，使用 NT={config['NT']}")
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# 显示步骤控制信息
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steps_info = {k: config.get(k, 1) for k in ["step_simulate", "step_sample", "step_plot", "step_animation"]}
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step_flags = ", ".join(f"{k}={v}" for k, v in steps_info.items())
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@@ -136,27 +144,42 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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disp_path = os.path.join(output_dir_abs, "display.txt")
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# ── 自动缓存检测 ───────────────────────────────────────
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# 若 output/ 中 trajectory.txt 和 display.txt 均已存在，
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# 自动跳过模拟和抽帧，直接使用已有结果。
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# 如需强制重新计算，删除 output/ 目录或设 step_simulate: 1 即可。
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output_exists = (
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os.path.isdir(output_dir_abs)
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and os.path.exists(traj_path)
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and os.path.exists(disp_path)
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)
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if output_exists:
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if config.get("step_simulate", 1):
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print(f"[run] 检测到已有输出（{traj_path}），自动跳过模拟与抽帧，直接进入后续步骤")
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config["step_simulate"] = 0
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config["step_sample"] = 0
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else:
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print(f"[run] 已有输出，步骤已被跳过")
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# force_calc=1: 强制重新计算，忽略缓存
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# force_calc=0: 尊重 step_simulate 设置，不自动覆盖
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force_calc = int(config.get("force_calc", 0))
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if force_calc:
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print(f"[run] force_calc=1，跳过缓存，强制重新计算")
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config["step_simulate"] = 1
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config["step_sample"] = 1
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elif config.get("step_simulate", 1):
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# step_simulate=1 且 force_calc=0 → 按用户要求执行计算
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# 但检测一下参数是否已变更（NT），如果变了则自动更新 step_sample
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if os.path.isdir(output_dir_abs) and os.path.exists(traj_path) and os.path.exists(disp_path):
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cached_nt = None
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try:
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with open(traj_path, 'rb') as _f:
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_f.seek(-4096, 2)
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_tail = _f.read().decode('utf-8', errors='replace')
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import re as _re
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_m = _re.search(r'"NT":\s*(\d+)', _tail)
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if _m:
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cached_nt = int(_m.group(1))
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except Exception:
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pass
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config_nt = int(config.get("NT", 0))
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if cached_nt is not None and cached_nt != config_nt:
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print(f"[run] 参数已变更（缓存 NT={cached_nt}，配置 NT={config_nt}），"
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f"将重新计算")
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config["step_sample"] = 1
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else:
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# 参数一致，按 step_simulate=1 执行，step_sample 由用户设置决定
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pass
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else:
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# 目录存在但文件不全 → 强制重新计算
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if os.path.isdir(output_dir_abs):
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print(f"[run] output/ 目录存在但文件不完整，将重新计算")
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# step_simulate=0 → 检测缓存是否存在并提示
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if os.path.isdir(output_dir_abs) and os.path.exists(traj_path) and os.path.exists(disp_path):
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print(f"[run] 已有输出，步骤已被跳过")
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else:
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print(f"[run] output/ 目录不存在，将执行完整流程")
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print(f"[run] 没有可用的缓存输出，但 step_simulate=0，将跳过模拟")
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# 2. 运行物理模拟 → output/trajectory.txt
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if config.get("step_simulate", 1):
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@@ -164,9 +187,12 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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total_steps = config["NT"]
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record_steps = total_steps - (config.get("warmup_steps") or 0)
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print(f"[run] 开始计算 总步数={total_steps} 记录步数={record_steps} DT={config['DT']}")
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import time as _time
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_t0 = _time.time()
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if engine == "python":
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traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz = compute.run_from_config(config, str(runtime_base))
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print(f"[run] 计算完成，记录 {record_steps} 步")
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compute.save_trajectory_txt(traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz, str(runtime_base))
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else:
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# 外部引擎：先加载配置到全局变量，再运行引擎，再用 save_trajectory_txt 补全 metadata
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@@ -178,6 +204,9 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz = compute.run_engine(
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engine, input_dir_abs, output_dir_abs, config)
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compute.save_trajectory_txt(traj_x, traj_y, traj_z, traj_vx, traj_vy, traj_vz, str(runtime_base))
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_elapsed = _time.time() - _t0
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print(f"[run] 引擎: {engine} 计算完成: {record_steps} 步 {_elapsed:.3f} s")
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else:
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print("[run] 步骤 [模拟] 已跳过，直接加载已有轨迹")
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if not os.path.exists(traj_path):
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@@ -282,6 +311,11 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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"box_color_r": float(data["box_color_r"]),
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"box_color_g": float(data["box_color_g"]),
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"box_color_b": float(data["box_color_b"]),
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"gravity_field": int(data.get("gravity_field", 1)),
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"gravity_interaction": int(data.get("gravity_interaction", 0)),
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"elastic_force": int(data.get("elastic_force", 1)),
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"damping_force": int(data.get("damping_force", 0)),
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"gravity_strength": float(data.get("gravity_strength", 1.0)),
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}
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save_display_txt(disp_data, str(runtime_base))
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print(f"[run] 抽帧完成: {sample_end - sample_start} 步 -> {n_frames} 帧")
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@@ -328,21 +362,28 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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# ── 能量计算 ─────────────────────────────────────
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masses = np.array(data["atom_masses"]) # (n_atoms,)
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G_vec = np.array(data.get("G", [0.0, 0.0, -9.8])) # [gx, gy, gz]
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gravity_field_enabled = int(data.get("gravity_field", 1))
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gravity_interaction_enabled = int(data.get("gravity_interaction", 0))
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gravity_strength = float(data.get("gravity_strength", 1.0))
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elastic_force_enabled = int(data.get("elastic_force", 1))
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damping_force_enabled = int(data.get("damping_force", 0))
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# 动能 Ek = ½ m v²
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ek = 0.5 * masses[np.newaxis, :] * (all_vx**2 + all_vy**2 + all_vz**2)
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# 重力势能 Ug = -m G·r
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ug = -masses[np.newaxis, :] * (
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G_vec[0] * all_x + G_vec[1] * all_y + G_vec[2] * all_z
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)
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# 均匀重力场势能 Ug = -m G·r
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ug = np.zeros_like(ek)
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if gravity_field_enabled:
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ug = -masses[np.newaxis, :] * (
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G_vec[0] * all_x + G_vec[1] * all_y + G_vec[2] * all_z
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)
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# 弹性势能 Us = ½ k (d - d₀)²
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us = np.zeros_like(ek)
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bond_pairs = data.get("bond_pairs")
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bond_stiffness = data.get("bond_stiffness")
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bond_rest_lengths = data.get("bond_rest_lengths")
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if bond_pairs is not None and len(bond_pairs) > 0:
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if elastic_force_enabled and 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 = all_x[:, j] - all_x[:, i]
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@@ -350,17 +391,33 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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dz = all_z[:, j] - all_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[:, i] += 0.5 * bond_stiffness[b_idx] * stretch**2
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us[:, j] += 0.5 * bond_stiffness[b_idx] * stretch**2
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us_each = 0.5 * bond_stiffness[b_idx] * stretch**2
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us[:, i] += us_each # 将整根键的势能记给 i
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# 万有引力势能 Ug_grav = -G_grav * m_i * m_j / r
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ug_grav = np.zeros_like(ek)
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if gravity_interaction_enabled:
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n_atoms_en = len(masses)
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for i in range(n_atoms_en):
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for j in range(i + 1, n_atoms_en):
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dx = all_x[:, j] - all_x[:, i]
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dy = all_y[:, j] - all_y[:, i]
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dz = all_z[:, j] - all_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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ug_grav[:, i] += 0.5 * pair_pe
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ug_grav[:, j] += 0.5 * pair_pe
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# 各原子总能量
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e_total = ek + ug + us # (NT, n_atoms)
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e_total = ek + ug + us + ug_grav # (NT, n_atoms)
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# 系统能量分量
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ek_sys = np.sum(ek, axis=1)
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ug_sys = np.sum(ug, axis=1)
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us_sys = np.sum(us, axis=1)
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e_sys = ek_sys + ug_sys + us_sys
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ug_grav_sys = np.sum(ug_grav, axis=1)
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e_sys = ek_sys + ug_sys + us_sys + ug_grav_sys
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# ── 第 3 行左：各原子总能量 ──
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ax_e = axes[2, 0]
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@@ -376,9 +433,11 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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# ── 第 3 行右：系统总能量 ──
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ax_sys = axes[2, 1]
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ax_sys.plot(time, ek_sys, 'b-', linewidth=1.5, label="系统动能")
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ax_sys.plot(time, ug_sys, 'g-', linewidth=1.5, label="系统重力势能")
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if bond_pairs is not None and len(bond_pairs) > 0:
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ax_sys.plot(time, ug_sys, 'g-', linewidth=1.5, label="均匀重力势能")
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if elastic_force_enabled and bond_pairs is not None and len(bond_pairs) > 0:
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ax_sys.plot(time, us_sys, color='orange', linewidth=1.5, label="系统弹性势能")
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if gravity_interaction_enabled:
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ax_sys.plot(time, ug_grav_sys, color='purple', linewidth=1.5, label="万有引力势能")
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ax_sys.plot(time, e_sys, 'r--', linewidth=1.5, label="系统总能量")
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ax_sys.set_title("系统总能量")
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ax_sys.set_xlabel("时间 (s)")
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@@ -421,8 +480,8 @@ def run_case(config_path, runtime_base, input_dir="input", output_dir="output",
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def main():
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parser = argparse.ArgumentParser(description="物理模拟统一入口")
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parser.add_argument("config_file", nargs="?", default=os.path.join("input", "parameters.yaml"),
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help="YAML 配置文件路径（默认: input/parameters.yaml）")
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parser.add_argument("config_file", nargs="?", default=os.path.join("input", "input.txt"),
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help="YAML 配置文件路径（默认: input/input.txt，虽然是 .txt 后缀但使用 YAML 格式）")
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parser.add_argument("--config", dest="config_override",
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help="YAML 配置文件路径（可选，优先于位置参数）")
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parser.add_argument("--input-dir", default="input",
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