nep框架搭建

.idea/NEP-auto.iml

@@ -2,7 +2,7 @@
 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
     <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
+    <orderEntry type="jdk" jdkName="Python 3.12" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
 </module>

config/machine.yaml

@@ -25,7 +25,12 @@ systems:
         command: "nep"
         env_setup: ""
         gpu_id: 0
-
+      gpumdkit:
+        # 假设是 GPU 版本，可能不需要 mpirun 或者只需要少量核
+        command: "gpumdkit.sh"
+        env_setup: ""
+        # 即使是 local 模式，有时也需要指定并行度
+        n_procs: 1
       # 3. VASP (GPU 版) 配置
       vasp:
         # 假设是 GPU 版本，可能不需要 mpirun 或者只需要少量核

config/param.yaml

@@ -32,9 +32,7 @@ notification:
 # --- 3. 各模块具体的物理/算法参数 ---
 params:
   preheat:
-    temp: 300
-    steps: 10000
-    # 这里不需要指定 gpumd 路径，只需要指定物理量
+    template_file: "run_ramp.in"
 
   select:
     target_min: 60

nep_auto/modules/m0_preheat.py

@@ -0,0 +1,113 @@
+import shutil
+import logging
+from pathlib import Path
+from .base_module import BaseModule
+
+
+class PreheatModule(BaseModule):
+    def __init__(self, driver, iter_id):
+        super().__init__(driver, iter_id)
+        self.template_subdir = "00_md"
+
+    def get_work_dir(self):
+        return self.iter_dir / "00.md" / "preheat"
+
+    def initialize(self):
+        super().initialize()  # 创建目录
+        work_dir = self.get_work_dir()
+
+        # 1. 准备 run.in (从配置读取模板名)
+        template_name = self.config_param['params']['preheat'].get('template_file', 'run.in')
+        self.copy_template(template_name, "run.in")
+
+        # 2. 准备 nep.in (GPUMD 运行必需，虽然内容可能很简单)
+        self.copy_template("nep.in")
+
+        # 3. 准备 nep.txt (势函数)
+        self._prepare_potential()
+
+        # 4. 准备 model.xyz (结构)
+        self._prepare_structure()
+
+    def _prepare_potential(self):
+        """准备势函数文件 nep.txt"""
+        dst = self.get_work_dir() / "nep.txt"
+
+        if self.iter_id == 1:
+            # 第一轮：使用 system.yaml 里定义的初始势
+            init_pot = Path(self.config_sys['system']['initial_potential'])
+            if not init_pot.exists():
+                raise FileNotFoundError(f"Initial potential not found: {init_pot}")
+            shutil.copy(init_pot, dst)
+            self.logger.info(f"   -> Copied initial potential: {init_pot.name}")
+        else:
+            # 后续轮次：使用上一轮训练结果
+            prev_iter = f"iter_{self.iter_id - 1:03d}"
+            prev_train_dir = self.root / prev_iter / "03.train"
+            src = prev_train_dir / "nep.txt"
+
+            if not src.exists():
+                raise FileNotFoundError(f"Previous potential not found: {src}")
+            shutil.copy(src, dst)
+            self.logger.info(f"   -> Copied potential from {prev_iter}")
+
+    def _prepare_structure(self):
+        """准备 model.xyz"""
+        work_dir = self.get_work_dir()
+
+        # 目前逻辑：Preheat 总是从初始结构开始（或者你可以改为从上一轮的 dump 中取）
+        # 这里演示从 VASP 文件转换
+        vasp_path = Path(self.config_sys['system']['initial_structure'])
+        if not vasp_path.exists():
+            raise FileNotFoundError(f"Structure file not found: {vasp_path}")
+
+        # 复制到工作目录
+        local_vasp = work_dir / vasp_path.name
+        shutil.copy(vasp_path, local_vasp)
+
+        # 调用 gpumdkit.sh -addlabel 进行转换
+        # 命令格式: gpumdkit.sh -addlabel file.vasp Li Y Cl
+        elements = " ".join(self.config_sys['system']['elements'])
+
+        self.logger.info("   -> Converting VASP to model.xyz...")
+
+        # 使用 runner 调用 gpumdkit (必须在 machine.yaml 里定义了 'gpumdkit')
+        # 注意：gpumdkit.sh 可能不输出 model.xyz 而是输出 file.xyz，需要确认
+        # 假设输出为 model.xyz
+        cmd_args = f"-addlabel {local_vasp.name} {elements}"
+
+        self.runner.run("gpumdkit", cwd=work_dir, extra_args=cmd_args)
+
+        # 检查是否生成成功
+        if not (work_dir / "model.xyz").exists():
+            # 有时候 gpumdkit 生成的文件名可能是 LiYCl.xyz，需要重命名为 model.xyz
+            # 这里做一个容错检查
+            expected_name = local_vasp.stem + ".xyz"  # e.g., LiYCl.xyz
+            if (work_dir / expected_name).exists():
+                shutil.move(work_dir / expected_name, work_dir / "model.xyz")
+            else:
+                raise RuntimeError("Failed to generate model.xyz from gpumdkit")
+
+    def run(self):
+        """执行 GPUMD"""
+        work_dir = self.get_work_dir()
+
+        # 检查是否已经跑完 (简单的锁文件机制)
+        if (work_dir / "thermo.out").exists():
+            self.logger.info(f"   -> Pre-check: thermo.out exists, skipping preheat.")
+            # 这里可以加更复杂的检查，比如步数是否足够
+            return
+
+        self.logger.info(f"🔥 Running Preheat in {self.iter_name}")
+        self.initialize()
+
+        # 调用 GPUMD
+        # GPUMD 没有参数，直接运行
+        self.runner.run("gpumd", cwd=work_dir)
+
+        self.logger.info("   -> Preheat finished.")
+
+    def check_done(self):
+        # 简单检查 thermo.out 是否存在且非空
+        f = self.get_work_dir() / "thermo.out"
+        return f.exists() and f.stat().st_size > 0

nep_auto/modules/m1_md.py

@@ -0,0 +1,116 @@
+import shutil
+import glob
+from pathlib import Path
+from nep_auto.modules.base_module import BaseModule
+
+
+class MDModule(BaseModule):
+    def __init__(self, driver, iter_id):
+        super().__init__(driver, iter_id)
+        self.template_subdir = "00_md"
+        # 预热目录 (输入源)
+        self.preheat_dir = self.iter_dir / "00.md" / "preheat"
+        # MD 目录 (工作区)
+        self.work_dir = self.iter_dir / "00.md" / "md"
+
+    def get_work_dir(self):
+        return self.work_dir
+
+    def run(self):
+        self.logger.info(f"🌪️ [MD] Starting Sampling Phase Iter {self.iter_id}...")
+        self.initialize()
+
+        # ----------------------------------------
+        # 1. 从预热轨迹中采样 (dump.xyz -> sampled_structures.xyz)
+        # ----------------------------------------
+        preheat_dump = self.preheat_dir / "dump.xyz"
+        if not preheat_dump.exists():
+            raise FileNotFoundError(f"Preheat dump not found: {preheat_dump}")
+
+        # 调用 sample_structures.py
+        # 假设参数: input_file method number
+        kit_root = self.driver.config_param['env']['gpumdkit_root']
+        script = f"{kit_root}/Scripts/sample_structures/sample_structures.py"
+
+        # 复制 dump 到当前目录以便处理
+        local_dump = self.work_dir / "preheat_dump.xyz"
+        shutil.copy(preheat_dump, local_dump)
+
+        self.logger.info("   -> Sampling structures from preheat trajectory...")
+        # 按照你的描述: sample_structures.py dump.xyz uniform 4
+        # 这里 "4" 可以放到 param.yaml 里配置，暂时写死或读取默认
+        self.runner.run(
+            "python_script",  # 这里可以用 local runner 直接跑 python
+            cwd=self.work_dir,
+            extra_args=f"{script} preheat_dump.xyz uniform 4"
+        )
+
+        # 产物通常叫 sampled_structures.xyz，我们需要把它作为后续 MD 的起始结构
+        # 但注意：GPUMD MD 通常读取 model.xyz 或者 restart。
+        # 如果你的 run.in 里写的是 load_xyz sampled_structures.xyz，那就没问题。
+        # 如果不是，通常做法是把 sampled_structures.xyz 切分成多个文件夹。
+
+        # --- 修正逻辑：根据你的描述 "生成 sample_1-4 文件夹" ---
+        # 我们遍历 template/00_md/md_run_*.in
+        tpl_path = Path("template") / self.template_subdir
+        run_templates = sorted(list(tpl_path.glob("md_run_*.in")))
+
+        if not run_templates:
+            self.logger.warning(f"⚠️ No 'md_run_*.in' found in {tpl_path}, looking for 'run.in'...")
+            run_templates = list(tpl_path.glob("run.in"))
+
+        sub_tasks = []
+        nep_source = self.preheat_dir / "nep.txt"  # 沿用预热阶段的势函数
+
+        for idx, tpl in enumerate(run_templates, start=1):
+            task_name = f"sample_{idx}"
+            task_dir = self.work_dir / task_name
+            task_dir.mkdir(exist_ok=True)
+            sub_tasks.append(task_dir)
+
+            # 1. 复制 run.in
+            shutil.copy(tpl, task_dir / "run.in")
+
+            # 2. 复制 nep.txt
+            shutil.copy(nep_source, task_dir / "nep.txt")
+
+            # 3. 复制结构 (假设所有 sample 都从预热的最后一帧或 sampled_structures 开始)
+            # 这里简化处理：复制 model.xyz (初始结构) 或者 使用 preheat 的最后状态
+            # 根据你的流程，通常需要把 sampled_structures.xyz 里的某一帧放进去
+            # 或者 GPUMD 支持直接读取 exyz。
+            # 这里我们假设 run.in 里配置好了读取方式，我们只负责给文件。
+            if (self.preheat_dir / "model.xyz").exists():
+                shutil.copy(self.preheat_dir / "model.xyz", task_dir / "model.xyz")
+
+        # ----------------------------------------
+        # 2. 执行所有 Sample 任务
+        # ----------------------------------------
+        self.logger.info(f"   -> Submitting {len(sub_tasks)} MD tasks...")
+
+        for task_dir in sub_tasks:
+            self.logger.info(f"      -> Running {task_dir.name}...")
+            self.runner.run("gpumd", cwd=task_dir)
+
+        # ----------------------------------------
+        # 3. 合并结果
+        # ----------------------------------------
+        self.logger.info("   -> Merging dump files...")
+        # cat sample_*/dump.xyz >> dump.xyz
+        # 使用 python 实现 cat 以跨平台安全
+        target_dump = self.work_dir / "dump.xyz"
+        with open(target_dump, 'wb') as outfile:
+            for task_dir in sub_tasks:
+                src = task_dir / "dump.xyz"
+                if src.exists():
+                    with open(src, 'rb') as infile:
+                        shutil.copyfileobj(infile, outfile)
+                else:
+                    self.logger.warning(f"⚠️ {task_dir.name} generated no dump.xyz")
+
+        self.check_done()
+
+    def check_done(self):
+        if (self.work_dir / "dump.xyz").exists():
+            self.logger.info("✅ MD Sampling finished.")
+            return True
+        raise RuntimeError("MD failed: dump.xyz not created.")

nep_auto/modules/m2_select.py

@@ -0,0 +1,105 @@
+import shutil
+import re
+from pathlib import Path
+from nep_auto.modules.base_module import BaseModule
+
+
+class SelectModule(BaseModule):
+    def __init__(self, driver, iter_id):
+        super().__init__(driver, iter_id)
+        self.work_dir = self.iter_dir / "01.select"
+        self.md_dir = self.iter_dir / "00.md" / "md"
+
+    def get_work_dir(self):
+        return self.work_dir
+
+    def get_frame_count(self, xyz_file):
+        """读取 xyz 文件帧数 (简单通过 grep 'Lattice' 计数，或用 ASE)"""
+        if not xyz_file.exists():
+            return 0
+        # 简单方法：读取文件统计 Lattice 出现的次数 (ExtXYZ 格式)
+        try:
+            with open(xyz_file, 'r') as f:
+                content = f.read()
+                return content.count("Lattice=")
+        except:
+            return 0
+
+    def run(self):
+        self.logger.info(f"🔍 [Select] Starting Active Learning Selection Iter {self.iter_id}...")
+        self.initialize()
+
+        # 准备数据
+        src_dump = self.md_dir / "dump.xyz"
+        train_xyz_prev = self.root / "00.data" / "train.xyz"  # 或者是上一轮的 train
+        # 如果是 iter > 1，train.xyz 应该是累积的。这里简化，先假设有一个参考的 train.xyz
+
+        # 必须文件：dump.xyz, train.xyz, nep.txt
+        shutil.copy(src_dump, self.work_dir / "dump.xyz")
+
+        # 这里的 train.xyz 是给 neptrain_select_structs.py 用作参考的
+        if self.iter_id == 1:
+            # 第一轮可以用 data 里的初始文件，或者做一个空的
+            pass
+        else:
+            # 复制上一轮的 train.xyz
+            pass
+
+        # 复制 nep.txt
+        shutil.copy(self.md_dir / "nep.txt", self.work_dir / "nep.txt")
+
+        # 读取参数
+        cfg = self.config_param['params']['select']
+        target_min = cfg.get('target_min', 60)
+        target_max = cfg.get('target_max', 120)
+        threshold = cfg.get('init_threshold', 0.01)
+
+        kit_root = self.driver.config_param['env']['gpumdkit_root']
+        script = f"{kit_root}/Scripts/sample_structures/neptrain_select_structs.py"
+
+        # 循环筛选
+        max_attempts = 10
+        attempt = 0
+
+        while attempt < max_attempts:
+            self.logger.info(f"   -> Attempt {attempt + 1}: Threshold = {threshold}")
+
+            # 构造命令: python script dump.xyz train.xyz nep.txt [options]
+            # 注意：如果你的脚本不支持命令行传参阈值，需要修改脚本或用 sed 修改
+            # 假设脚本已经被修改支持 --distance {threshold}，或者我们用一种 hack 方式
+            # 既然原流程是交互式的，这里强烈建议你修改 neptrain_select_structs.py
+            # 让它支持命令行参数：parser.add_argument('--distance', ...)
+
+            cmd_args = f"{script} dump.xyz train.xyz nep.txt --distance {threshold} --auto_confirm"
+
+            try:
+                self.runner.run("python_script", cwd=self.work_dir, extra_args=cmd_args)
+            except Exception as e:
+                self.logger.warning(f"Select script warning: {e}")
+
+            # 检查结果
+            selected_file = self.work_dir / "selected.xyz"
+            count = self.get_frame_count(selected_file)
+            self.logger.info(f"      -> Selected {count} structures.")
+
+            if target_min <= count <= target_max:
+                self.logger.info("✅ Selection criteria met!")
+                break
+            elif count < target_min:
+                self.logger.info("      -> Too few, lowering threshold (-0.01)...")
+                threshold = threshold - 0.01
+            else:
+                self.logger.info("      -> Too many, raising threshold (+0.01)...")
+                threshold = threshold + 0.01
+
+            attempt += 1
+
+        if attempt >= max_attempts:
+            self.logger.warning("⚠️ Max attempts reached in selection. Proceeding with current best.")
+
+        self.check_done()
+
+    def check_done(self):
+        if (self.work_dir / "selected.xyz").exists():
+            return True
+        raise RuntimeError("Selection failed: selected.xyz not found")

nep_auto/modules/m3_scf.py

@@ -0,0 +1,91 @@
+import shutil
+from pathlib import Path
+from ase.io import read, write
+from nep_auto.modules.base_module import BaseModule
+
+
+class SCFModule(BaseModule):
+    def __init__(self, driver, iter_id):
+        super().__init__(driver, iter_id)
+        self.template_subdir = "02_scf"
+        self.work_dir = self.iter_dir / "02.scf"
+        self.select_dir = self.iter_dir / "01.select"
+
+    def get_work_dir(self):
+        return self.work_dir
+
+    def run(self):
+        self.logger.info(f"⚛️ [SCF] Starting DFT Calculation Iter {self.iter_id}...")
+        self.initialize()
+
+        # 1. 读取 selected.xyz
+        selected_xyz = self.select_dir / "selected.xyz"
+        if not selected_xyz.exists():
+            raise FileNotFoundError("selected.xyz missing")
+
+        self.logger.info("   -> Reading structures using ASE...")
+        atoms_list = read(selected_xyz, index=':')
+        self.logger.info(f"   -> Found {len(atoms_list)} structures.")
+
+        # 2. 准备任务文件夹
+        task_dirs = []
+        for i, atoms in enumerate(atoms_list):
+            task_name = f"task.{i:03d}"
+            task_dir = self.work_dir / task_name
+            task_dir.mkdir(exist_ok=True)
+            task_dirs.append(task_dir)
+
+            # 写 POSCAR
+            write(task_dir / "POSCAR", atoms, format='vasp')
+
+            # 复制模版 INCAR, KPOINTS, POTCAR
+            self.copy_template("INCAR", target_name=None)  # 复制到 self.work_dir
+            shutil.copy(self.work_dir / "INCAR", task_dir / "INCAR")  # 再分发
+            self.copy_template("KPOINTS", target_name=None)
+            shutil.copy(self.work_dir / "KPOINTS", task_dir / "KPOINTS")
+            self.copy_template("POTCAR", target_name=None)
+            shutil.copy(self.work_dir / "POTCAR", task_dir / "POTCAR")
+
+        # 3. 提交任务
+        # 这里区分 local 模式和 slurm 模式
+        # 既然你目前是 interactive gpu，我们假设是串行或者简单的并行
+        self.logger.info("   -> Running VASP jobs...")
+
+        success_count = 0
+        for task_dir in task_dirs:
+            self.logger.info(f"      -> Running {task_dir.name}...")
+            try:
+                # 调用 machine.yaml 里定义的 vasp
+                # 注意：如果 task 很多，这里最好写成多进程并发
+                self.runner.run("vasp", cwd=task_dir)
+
+                # 简单检查
+                if (task_dir / "OUTCAR").exists():
+                    success_count += 1
+            except Exception as e:
+                self.logger.error(f"Task {task_dir.name} failed: {e}")
+
+        self.logger.info(f"   -> Finished. Success: {success_count}/{len(task_dirs)}")
+
+        # 4. 收集数据 (OUTCAR -> NEP-dataset.xyz)
+        self.logger.info("   -> Collecting data...")
+        valid_atoms = []
+        for task_dir in task_dirs:
+            try:
+                # 读取 OUTCAR
+                atoms = read(task_dir / "OUTCAR", format='vasp-outcar')
+                valid_atoms.append(atoms)
+            except:
+                pass
+
+        if valid_atoms:
+            write(self.work_dir / "NEP-dataset.xyz", valid_atoms, format='extxyz')
+        else:
+            raise RuntimeError("No valid OUTCARs found!")
+
+        self.check_done()
+
+    def check_done(self):
+        if (self.work_dir / "NEP-dataset.xyz").exists():
+            return True
+        raise RuntimeError("SCF failed: NEP-dataset.xyz not generated")

nep_auto/modules/m4_train.py

@@ -0,0 +1,57 @@
+import shutil
+from nep_auto.modules.base_module import BaseModule
+
+
+class TrainModule(BaseModule):
+    def __init__(self, driver, iter_id):
+        super().__init__(driver, iter_id)
+        self.template_subdir = "03_train"
+        self.work_dir = self.iter_dir / "03.train"
+
+    def get_work_dir(self):
+        return self.work_dir
+
+    def run(self):
+        self.logger.info(f"🧠 [Train] Starting Training Iter {self.iter_id}...")
+        self.initialize()
+
+        # 1. 准备 train.xyz
+        # 逻辑：当前 train.xyz = 上一轮 train.xyz + 本轮 scf/NEP-dataset.xyz
+        current_train_xyz = self.work_dir / "train.xyz"
+
+        # 打开输出文件
+        with open(current_train_xyz, 'wb') as outfile:
+            # A. 写入上一轮数据 (或初始数据)
+            if self.iter_id == 1:
+                # 第一轮，看是否有初始训练集，如果没有则只用本轮的 SCF 数据
+                # 这里假设 iter_000 是个虚拟的，或者直接去 00.data 里找
+                init_data = self.root / "00.data" / "train.xyz"  # 预留位置
+                pass
+            else:
+                prev_train = self.root / f"iter_{self.iter_id - 1:03d}" / "03.train" / "train.xyz"
+                if prev_train.exists():
+                    with open(prev_train, 'rb') as infile:
+                        shutil.copyfileobj(infile, outfile)
+
+            # B. 写入本轮新数据
+            new_data = self.iter_dir / "02.scf" / "NEP-dataset.xyz"
+            if new_data.exists():
+                with open(new_data, 'rb') as infile:
+                    shutil.copyfileobj(infile, outfile)
+            else:
+                raise FileNotFoundError("New training data (NEP-dataset.xyz) missing!")
+
+        # 2. 准备 nep.in
+        self.copy_template("nep.in")
+
+        # 3. 运行训练
+        self.logger.info("   -> Running NEP training...")
+        self.runner.run("nep", cwd=self.work_dir)
+
+        self.check_done()
+
+    def check_done(self):
+        if (self.work_dir / "nep.txt").exists():
+            self.logger.info("✅ Training finished.")
+            return True
+        raise RuntimeError("Training failed: nep.txt not generated")

template/00_md/run_rump.in

@@ -0,0 +1,8 @@
+potential ./nep.txt
+velocity 100
+ensemble npt_mttk temp 100 400 aniso 0 0
+run 100000
+ensemble npt_mttk temp 400 1200 aniso 0 0
+dump_thermo 10
+dump_exyz 10000
+run 100000