inference/run_molecular_md.py

from ase import units
from ase.io import write, Trajectory, read
from ase.md.langevin import Langevin
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution, Stationary, ZeroRotation
from ase.build import molecule
from ase.md import MDLogger
import numpy as np

# 自动定位 UMA 旋转基文件 Jd.pt
import os
_REPO_ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
_JD_PATH = os.path.join(_REPO_ROOT, "weight", "Jd.pt")
if os.path.isfile(_JD_PATH):
    os.environ.setdefault("ONESCIENCE_UMA_JD_PATH", _JD_PATH)

from onescience.utils.uma.units.mlip_unit import load_predict_unit
from onescience.utils.uma.calculate.ase_calculator import FAIRChemCalculator

# === 本地检查点路径（改成你的实际路径）===
ckpt = "../weight/uma-s-1p1_converted.pt"

# === 加载预测器与计算器 ===
predictor = load_predict_unit(ckpt, device="cuda")     # GPU加速
calc = FAIRChemCalculator(predictor, task_name="omol") # 分子任务

# === 构建体系 ===
atoms = molecule("H2O")  # 可替换为其它分子
atoms.calc = calc

# === 速度初始化（400 K），去线动量/角动量 ===
T0 = 400  # K
MaxwellBoltzmannDistribution(atoms, temperature_K=T0)
Stationary(atoms)       # 去整体平动
ZeroRotation(atoms)     # 去整体转动

# === 动力学设置：Langevin ===
dt = 0.1 * units.fs
gamma = 0.001 / units.fs
dyn = Langevin(atoms, timestep=dt, temperature_K=T0, friction=gamma)

# === 轨迹与日志 ===
traj = Trajectory("my_md.traj", "w", atoms)            # ASE 原生轨迹
dyn.attach(traj.write, interval=1)                     # 每步写一帧
logger = MDLogger(dyn, atoms, "md.log", header=True, stress=False, peratom=False)
dyn.attach(logger, interval=10)                        # 每10步记录一次

# 也打印到屏幕（可选）
def printer():
    epot = atoms.get_potential_energy()
    ekin = atoms.get_kinetic_energy()
    Tinst = 2.0 * ekin / (3 * len(atoms) * units.kB)
    print(f"Step {dyn.nsteps:5d}  Epot={epot: .6f} eV  Ekin={ekin: .6f} eV  T={Tinst: .1f} K")
dyn.attach(printer, interval=50)

# === 运行MD ===
steps = 1000
dyn.run(steps=steps)

# === 结束后输出关键信息与保存 ===
Epot = atoms.get_potential_energy()
Ekin = atoms.get_kinetic_energy()
Tfinal = 2.0 * Ekin / (3 * len(atoms) * units.kB)
print("\n== MD Finished ==")
print(f"Final Epot = {Epot:.6f} eV,  Ekin = {Ekin:.6f} eV,  T = {Tfinal:.2f} K")
print("COM =", atoms.get_center_of_mass())

# 保存最终结构（xyz 与 cif）
write("final.xyz", atoms)
try:
    write("final.cif", atoms)  # 分子一般无PBC，cif可有可无
except Exception as e:
    print("Save CIF skipped:", e)

# 如需导出整段轨迹为 .xyz（多帧），取消注释以下两行
# frames = read("my_md.traj", ":")
# write("my_md_all.xyz", frames)