167 lines
6.5 KiB
Python
167 lines
6.5 KiB
Python
import shutil
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import subprocess
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import glob
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from pathlib import Path
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from nep_auto.modules.base_module import BaseModule
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class SCFModule(BaseModule):
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def __init__(self, driver, iter_id):
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super().__init__(driver, iter_id)
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self.template_subdir = "02_scf"
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self.work_dir = self.iter_dir / "02.scf"
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self.select_dir = self.iter_dir / "01.select"
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def get_work_dir(self):
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return self.work_dir
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def run(self):
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self.logger.info(f"⚛️ [SCF] Starting DFT Calculation Iter {self.iter_id}...")
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self.initialize()
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# ----------------------------------------
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# 1. 准备数据: selected.xyz -> 301 切分
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# ----------------------------------------
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src_xyz = self.select_dir / "selected.xyz"
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if not src_xyz.exists():
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raise FileNotFoundError("selected.xyz missing from select module")
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shutil.copy(src_xyz, self.work_dir / "selected.xyz")
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# 调用 gpumdkit.sh (301 -> prefix)
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# Prefix 使用 "task" 或者 "job"，生成 job_1, job_2...
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prefix = "task"
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input_str = f"301\n{prefix}\n"
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gpumdkit_cmd = self.machine_config['tools']['gpumdkit']['command']
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self.logger.info(" -> Splitting structures using gpumdkit...")
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try:
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subprocess.run(
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gpumdkit_cmd,
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input=input_str,
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cwd=self.work_dir,
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shell=True,
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executable="/bin/bash",
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stdout=subprocess.PIPE,
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stderr=subprocess.PIPE,
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text=True,
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check=True
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)
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except subprocess.CalledProcessError as e:
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self.logger.error(f"gpumdkit splitting failed: {e.stderr}")
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raise
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# ----------------------------------------
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# 2. 准备 DFT 输入文件 (fp 文件夹)
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# ----------------------------------------
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# gpumdkit 会生成一个 fp 文件夹，我们需要把模版放进去
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fp_dir = self.work_dir / "fp"
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if not fp_dir.exists():
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# 某些版本的脚本可能不自动创建 fp，手动建一个保险
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fp_dir.mkdir(exist_ok=True)
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self.logger.info(" -> preparing INCAR/KPOINTS/POTCAR...")
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# 从 template/02_scf 复制到 02.scf/fp
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self.copy_template("INCAR", target_name=None)
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shutil.copy(self.work_dir / "INCAR", fp_dir / "INCAR")
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self.copy_template("KPOINTS", target_name=None)
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shutil.copy(self.work_dir / "KPOINTS", fp_dir / "KPOINTS")
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self.copy_template("POTCAR", target_name=None)
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shutil.copy(self.work_dir / "POTCAR", fp_dir / "POTCAR")
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# ----------------------------------------
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# 3. 分发文件并提交任务
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# ----------------------------------------
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# 找到所有生成的文件夹 (task_1, task_2...)
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task_dirs = sorted(list(self.work_dir.glob(f"{prefix}_*")))
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if not task_dirs:
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raise RuntimeError(f"No {prefix}_* folders generated!")
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self.logger.info(f" -> Found {len(task_dirs)} tasks. Distributing input files...")
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# 将 fp 里的文件分发到每个 task 文件夹 (替代 presub.sh 的功能)
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common_files = ["INCAR", "KPOINTS", "POTCAR"]
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for t_dir in task_dirs:
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if not t_dir.is_dir(): continue
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for f in common_files:
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shutil.copy(fp_dir / f, t_dir / f)
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# 提交计算
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self.logger.info(" -> Running VASP jobs...")
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success_count = 0
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# 这里的并行策略取决于 machine.yaml
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# 如果是 Interactive GPU，我们通常是串行跑，或者一次跑 N 个
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# 这里先简单实现串行跑
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for t_dir in task_dirs:
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self.logger.info(f" -> Running {t_dir.name}...")
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try:
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# 调用 machine.yaml 里的 vasp 工具
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self.runner.run("vasp", cwd=t_dir)
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if (t_dir / "OUTCAR").exists(): # 简单判据
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success_count += 1
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except Exception as e:
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self.logger.error(f"Job {t_dir.name} failed: {e}")
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self.logger.info(f" -> Finished. Success: {success_count}/{len(task_dirs)}")
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# ----------------------------------------
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# 4. 收集结果 (OUTCARs -> NEP-dataset.xyz)
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# ----------------------------------------
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# 使用 gpumdkit 104 功能: Format Conversion -> OUTCAR to xyz (需提供路径)
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# 或者 108? 根据你的描述是 gpumdkit.sh -out2xyz .
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self.logger.info(" -> Converting OUTCARs to NEP-dataset.xyz...")
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# 方式 A: 命令行参数调用 (如果你确认支持)
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# cmd = f"{gpumdkit_cmd} -out2xyz ."
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# 方式 B: 交互式调用 (104/108) - 这里假设 -out2xyz 可用，这是最方便的
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# 如果不支持，我们需要知道交互式的代码。根据你的描述 7: "-out2xyz ."
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try:
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# 尝试直接调用 -out2xyz
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subprocess.run(
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f"{gpumdkit_cmd} -out2xyz .",
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cwd=self.work_dir,
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shell=True,
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executable="/bin/bash",
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check=True
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)
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# gpumdkit 通常生成 model.xyz 或 out.xyz，我们需要重命名为 NEP-dataset.xyz
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# 假设生成的是 model.xyz
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potential_outputs = ["model.xyz", "movie.xyz", "out.xyz"]
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found = False
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for f in potential_outputs:
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if (self.work_dir / f).exists():
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shutil.move(self.work_dir / f, self.work_dir / "NEP-dataset.xyz")
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found = True
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break
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if not found and not (self.work_dir / "NEP-dataset.xyz").exists():
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# 如果没找到，可能已经在子文件夹里？
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pass
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except subprocess.CalledProcessError:
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self.logger.warning("gpumdkit -out2xyz failed, falling back to ASE...")
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# Fallback: 使用 ASE 收集 (更稳健)
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from ase.io import read, write
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all_atoms = []
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for t_dir in task_dirs:
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try:
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all_atoms.append(read(t_dir / "OUTCAR", format="vasp-outcar"))
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except:
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pass
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if all_atoms:
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write(self.work_dir / "NEP-dataset.xyz", all_atoms, format="extxyz")
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self.check_done()
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def check_done(self):
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if (self.work_dir / "NEP-dataset.xyz").exists():
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return True
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raise RuntimeError("SCF failed: NEP-dataset.xyz not generated") |