From 081540c27493033de9dd5a340c3f3c26f99d3bc1 Mon Sep 17 00:00:00 2001
From: koko <1429659362@qq.com>
Date: Tue, 9 Dec 2025 11:30:26 +0800
Subject: [PATCH] =?UTF-8?q?NEP=E6=A1=86=E6=9E=B6=E9=87=8D=E6=9E=8400?=
 =?UTF-8?q?=E9=98=B6=E6=AE=B5?=
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---
 src/workflow.py | 24 +++++++++++++++++++-----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/src/workflow.py b/src/workflow.py
index 2c018e7..4c94c29 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -125,7 +125,7 @@ class Workflow:
                         self.logger.info(">>> Starting Production...")
                         os.makedirs(prod_dir, exist_ok=True)
 
-                        # 软链接
+                        # 1. 准备基础文件到 production 根目录
                         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)
@@ -135,7 +135,8 @@ class Workflow:
                         shutil.copy(os.path.join(self.template_dir, "00.md", "production", "run.in"),
                                     os.path.join(prod_dir, "run.in"))
 
-                        # A. 运行 302 生成 presub.sh
+                        # 2. 运行 302 (生成 md 文件夹, sample_* 文件夹, presub.sh)
+                        # 302 通常会读取当前目录的 run.in 并在 md/ 下生成拆分后的 run_x.in
                         input_str_302 = "302"
                         if not run_cmd_with_log(kit_path, prod_dir, "step_exec.log", input_str=input_str_302):
                             self.logger.error("302 command failed.")
@@ -145,7 +146,20 @@ class Workflow:
                             self.logger.error("presub.sh not found.")
                             return
 
-                        # B. 运行 presub.sh
+                        # ---------------------------------------------------------
+                        # [新增] 3. 补全文件：将 nep.txt 和 run.in 复制到 md 文件夹
+                        # ---------------------------------------------------------
+                        md_subdir = os.path.join(prod_dir, "md")
+                        if os.path.exists(md_subdir):
+                            self.logger.info("Copying nep.txt and run.in to 'md' folder...")
+                            shutil.copy(os.path.join(prod_dir, "nep.txt"), os.path.join(md_subdir, "nep.txt"))
+                            # 复制 run.in，虽然 302 可能已经生成了 run_1.in 等，但为了保险或用户习惯，我们也拷进去
+                            shutil.copy(os.path.join(prod_dir, "run.in"), os.path.join(md_subdir, "run.in"))
+                        else:
+                            self.logger.error("'md' folder was not created by 302 command.")
+                            return
+
+                        # 4. 运行 presub.sh
                         os.chmod(os.path.join(prod_dir, "presub.sh"), 0o755)
                         self.logger.info(">>> Executing presub.sh...")
 
@@ -153,14 +167,14 @@ class Workflow:
                             self.logger.error("presub.sh execution failed.")
                             return
 
-                        # C. 合并 dump
+                        # 5. 合并 dump
+                        self.logger.info("Merging dump files...")
                         run_cmd_with_log("cat sample_*/dump.xyz > dump.xyz", prod_dir, "step_exec.log")
 
                         self.last_dump_path = os.path.join(prod_dir, "dump.xyz")
                         self.tracker.mark_done(task_id_prod)
                     else:
                         self.logger.info("Skipping Production (Already Done).")
-                        # 即使跳过，也要更新变量给下一步用
                         self.last_dump_path = os.path.join(prod_dir, "dump.xyz")
 
                 # ==========================