From 13d9ce4385fbaba9c0a4a221659e4a6442cd1061 Mon Sep 17 00:00:00 2001 From: koko <1429659362@qq.com> Date: Tue, 9 Dec 2025 10:46:24 +0800 Subject: [PATCH] =?UTF-8?q?NEP=E6=A1=86=E6=9E=B6=E9=87=8D=E6=9E=84?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/workflow.py | 121 +++++++++++++++++++++++++++--------------------- 1 file changed, 69 insertions(+), 52 deletions(-) diff --git a/src/workflow.py b/src/workflow.py index 56617fa..163930c 100644 --- a/src/workflow.py +++ b/src/workflow.py @@ -50,75 +50,92 @@ class Workflow: if step_name == "00.md": step_dir = os.path.join(iter_path, "00.md") - # --- A. 第一轮初始化：POSCAR -> model.xyz --- + # 1. 第一轮初始化：POSCAR -> model.xyz (保持不变) if iter_id == 0: os.makedirs(step_dir, exist_ok=True) poscar_name = self.param['files']['poscar'] poscar_src = os.path.join(self.data_dir, poscar_name) - if os.path.exists(poscar_src): shutil.copy(poscar_src, os.path.join(step_dir, poscar_name)) - atom_labels = self.param['files'].get('label', '') kit_path = self.machine.config['paths'].get('gpumdkit', 'gpumdkit.sh') - cmd = f"{kit_path} -addlabel {poscar_name} {atom_labels}" self.logger.info(f"Initializing model.xyz: {cmd}") subprocess.check_call(cmd, shell=True, cwd=step_dir) else: self.logger.error(f"POSCAR missing: {poscar_src}") - continue # 跳过这一步 - - # 检查 model.xyz 是否存在 (无论是刚生成的，还是上一轮传过来的) - # 注意：如果是 Iter > 0，这里需要逻辑从上一轮获取，目前先保证 Iter 0 - current_model_xyz = os.path.join(step_dir, "model.xyz") - if not os.path.exists(current_model_xyz): - self.logger.error(f"Critical: model.xyz not found in {step_dir}") - continue - - # --- B. 执行子任务 (Preheat / Production) --- - sub_tasks = step_conf.get('sub_tasks', []) - if not sub_tasks: - self.logger.warning("No sub_tasks defined for 00.md in param.yaml!") - - for sub in sub_tasks: - template_sub_name = sub.get('template_sub') - if not template_sub_name: continue - - # 1. 定义子目录 (e.g., iter_00/00.md/preheat) - sub_work_dir = os.path.join(step_dir, template_sub_name) - os.makedirs(sub_work_dir, exist_ok=True) - - self.logger.info(f"--> Setup Sub-task: {template_sub_name}") - - # 2. 【关键】将 model.xyz 分发到子目录 - shutil.copy(current_model_xyz, os.path.join(sub_work_dir, "model.xyz")) - - # 3. 准备 Template (run.in) - # 路径: template/00.md/preheat/ - template_path = os.path.join(self.template_dir, "00.md", template_sub_name) - if not os.path.exists(template_path): - self.logger.error(f"Template not found: {template_path}") continue - # 4. 实例化 MD 任务 - # 这里的 name 仅仅是日志用的标识 - md_task = MDStep(f"MD-{template_sub_name}", sub_work_dir, self.machine, self.config) + # 确保 gpumdkit 路径可用 + kit_path = self.machine.config['paths'].get('gpumdkit', 'gpumdkit.sh') - # 5. 运行 (传入势函数路径 和 模板路径) - # run() 方法内部会处理 nep.txt 的复制和 run.in 的复制 - success = md_task.run(self.current_nep_pot, template_path) + # ---------------------------------------------------- + # 2. 核心修改：分别处理 preheat 和 production + # ---------------------------------------------------- - if success: - # 记录最新的 dump.xyz 位置，供下一步 Select 使用 - self.last_dump_path = os.path.join(sub_work_dir, "dump.xyz") - # 同时也把最新的 model.xyz (如果MD改变了结构) 或 dump 更新为下一次的起点？ - # 目前逻辑：Select 步会用 self.last_dump_path - else: - self.logger.error(f"MD Sub-task {template_sub_name} Failed.") - # 根据策略决定是否中断，这里暂时中断 - break - # ========================== + # === Sub-task 1: Preheat (预热) === + # 逻辑：复制model.xyz -> 跑MD -> 跑201采样 -> 生成 sampled_structures.xyz + preheat_dir = os.path.join(step_dir, "preheat") + os.makedirs(preheat_dir, exist_ok=True) + + # 准备文件 + current_model_xyz = os.path.join(step_dir, "model.xyz") + shutil.copy(current_model_xyz, os.path.join(preheat_dir, "model.xyz")) + shutil.copy(self.current_nep_pot, os.path.join(preheat_dir, "nep.txt")) + shutil.copy(os.path.join(self.template_dir, "00.md", "preheat", "run.in"), + os.path.join(preheat_dir, "run.in")) + + self.logger.info(">>> Running Preheat MD...") + # 使用 Machine 运行 GPUMD (假设 machine.yaml 里 gpumd 是基础命令) + self.machine.execute("gpumd", preheat_dir) + + # [关键] Preheat 后处理：采样 + if os.path.exists(os.path.join(preheat_dir, "dump.xyz")): + self.logger.info(">>> Running Sampling (201)...") + # 构造命令: echo -e "201\ndump.xyz\nuniform\n4" | gpumdkit.sh + # 注意：根据你的描述 "dump.xyz uniform 4"，我这里构造输入流 + # 如果你的脚本交互顺序不同，请调整这里的字符串 + # 这里的 \n 代表回车 + input_str = "201\ndump.xyz\nuniform\n4" + + try: + # 调用 gpumdkit + process = subprocess.Popen( + kit_path, + shell=True, + cwd=preheat_dir, + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + text=True + ) + stdout, stderr = process.communicate(input=input_str) + + if os.path.exists(os.path.join(preheat_dir, "sampled_structures.xyz")): + self.logger.info("Sampled structures generated successfully.") + else: + self.logger.error(f"Sampling failed. Output: {stdout} Error: {stderr}") + continue # 如果没生成采样文件，后续Production没法做 + except Exception as e: + self.logger.error(f"Error executing sampling: {e}") + continue + else: + self.logger.error("Preheat dump.xyz missing.") + continue + + # === Sub-task 2: Production (加工/正式采样) === + # 逻辑：链接 sampled_structures -> 跑302 -> 跑presub.sh + prod_dir = os.path.join(step_dir, "production") + os.makedirs(prod_dir, exist_ok=True) + + # 1. 建立软链接 (sampled_structures.xyz) + src_sample = os.path.abspath(os.path.join(preheat_dir, "sampled_structures.xyz")) + dst_sample = os.path.join(prod_dir, "sampled_structures.xyz") + if os.path.exists(dst_sample): os.remove(dst_sample) # 清理旧的 + os.symlink(src_sample, dst_sample) + + # 2. 准备基础文件 + self.logger.error(f"presub.sh execution failed: {e}") # Step: 01.select # ========================== elif step_name == "01.select":