V1

py/make_sh.py

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+import os
+
+
+def creat_sh(input_folder, anion, sh_file_path='analyze.sh'):
+    """
+    创建shell脚本，只处理两类CIF文件：
+    1. 纯数字命名的CIF文件 (例如: 123.cif)
+    2. 数字-坐标格式的CIF文件 (例如: 123-x1y2z3.cif)
+
+    参数:
+    input_folder: 输入文件夹路径
+    anion: 阴离子类型
+    sh_file_path: 生成的shell脚本路径
+    """
+    # 文件夹路径
+    folder_path = input_folder
+
+    import re
+
+    # 定义两种文件名模式的正则表达式
+    pattern1 = re.compile(r'^\d+\.cif$')  # 纯数字.cif
+    pattern2 = re.compile(r'^\d+-x\d+y\d+z\d+\.cif$')  # 数字-x数字y数字z数字.cif
+
+    # 打开SH脚本文件用于写入
+    with open(sh_file_path, 'w') as sh_file:
+        # 写入脚本头部
+        sh_file.write('#!/bin/bash\n')
+
+        # 遍历文件夹中的所有文件
+        for filename in os.listdir(folder_path):
+            file_path = os.path.join(folder_path, filename)
+
+            # 只处理文件(不处理文件夹)
+            if os.path.isfile(file_path):
+                # 检查文件名是否匹配两种模式之一
+                if pattern1.match(filename) or pattern2.match(filename):
+                    # 生成对应的命令
+                    command = f"python ../../../tool/analyze_voronoi_nodes.py {filename} -i ../../../tool/{anion}.yaml > {filename}.txt\n"
+                    # 将命令写入SH脚本文件
+                    sh_file.write(command)
+
+    print(f"SH脚本已生成：{sh_file_path}")
+
+
+import os
+
+
+def create_sh_recursive(base_folder, tool_path="tool", relative_depth=2):
+    """
+    递归遍历文件夹，为每个包含.cif文件的文件夹生成analyze.sh脚本，
+    并在基础文件夹下创建一个sh_all.sh来执行所有脚本。
+
+    参数:
+        base_folder: 起始文件夹路径
+        tool_path: 工具目录的基本路径
+        relative_depth: 基础相对深度，用于计算正确的相对路径
+    """
+    # 用于收集所有生成的analyze.sh脚本的相对路径
+    analyze_sh_paths = []
+    base_folder_name = os.path.basename(base_folder)
+
+    def process_folder(folder_path, current_depth=0):
+        print(f"处理文件夹: {folder_path}")
+
+        # 获取当前文件夹名称
+        folder_name = os.path.basename(folder_path)
+
+        # 检查当前文件夹是否包含.cif文件
+        has_cif_files = any(
+            f.endswith('.cif') for f in os.listdir(folder_path) if os.path.isfile(os.path.join(folder_path, f)))
+
+        # 如果当前文件夹包含.cif文件，生成脚本
+        if has_cif_files:
+            # 计算正确的工具路径（根据深度增加../）
+            dots = "../" * (relative_depth + current_depth)
+            tool_relative_path = f"{dots}{tool_path}"
+
+            # 确定anion参数（使用文件夹名）
+            anion = folder_name
+
+            # 生成脚本文件路径
+            sh_file_path = os.path.join(folder_path, "analyze.sh")
+
+            # 创建脚本
+            with open(sh_file_path, 'w') as sh_file:
+                sh_file.write('#!/bin/bash\n')
+                for filename in os.listdir(folder_path):
+                    file_path = os.path.join(folder_path, filename)
+                    if os.path.isfile(file_path) and filename.endswith('.cif'):
+                        command = f"python {tool_relative_path}/analyze_voronoi_nodes.py {filename} -i {tool_relative_path}/{anion}.yaml > {filename}.txt\n"
+                        sh_file.write(command)
+
+            # 将此脚本添加到收集器中
+            # 计算相对于基础文件夹的路径
+            rel_path = os.path.relpath(folder_path, base_folder)
+            analyze_sh_paths.append(rel_path)
+
+            print(f"生成脚本: {sh_file_path} (工具路径: {tool_relative_path})")
+
+        # 获取子文件夹列表
+        subdirs = [d for d in os.listdir(folder_path) if os.path.isdir(os.path.join(folder_path, d))]
+
+        # 处理复合阴离子文件夹的特殊情况
+        if "+" in folder_name:
+            elements = folder_name.split("+")
+            for element in elements:
+                element_dir = os.path.join(folder_path, element)
+                # 如果对应元素的子文件夹不存在，创建它
+                if not os.path.exists(element_dir):
+                    os.makedirs(element_dir)
+                    print(f"创建子文件夹: {element_dir}")
+                # 确保这个子文件夹被包含在递归处理列表中
+                if element not in subdirs:
+                    subdirs.append(element)
+
+        # 递归处理所有子文件夹
+        for subdir in subdirs:
+            subdir_path = os.path.join(folder_path, subdir)
+            process_folder(subdir_path, current_depth + 1)
+
+    # 开始递归处理
+    process_folder(base_folder)
+
+    # 创建sh_all.sh脚本
+    sh_all_path = os.path.join(base_folder, "sh_all.sh")
+    with open(sh_all_path, 'w') as sh_all:
+        sh_all.write('#!/bin/bash\n\n')
+        sh_all.write(f'# process all analyze.sh\n\n')
+
+        # 记录初始目录
+        sh_all.write('# remember current dir\n')
+        sh_all.write('INITIAL_DIR=$(pwd)\n\n')
+
+        # 为每个包含analyze.sh的目录添加命令
+        for path in analyze_sh_paths:
+            sh_all.write(f'echo "process {path}/analyze.sh"\n')
+            sh_all.write(f'cd "{path}"\n')
+            sh_all.write('bash analyze.sh\n')
+            sh_all.write(f'cd "$INITIAL_DIR"\n\n')
+
+        # 添加完成消息
+        sh_all.write('echo "done!"\n')
+
+    # 修改权限使脚本可执行
+    os.chmod(sh_all_path, 0o755)
+    print(f"生成总执行脚本: {sh_all_path}")
+    print("所有脚本生成完成！")
+# 示例调用
+# create_sh_recursive("../data/after_step1")
+
+if __name__ == '__main__':
+    # creat_sh("../data/after_step1/O","O","../data/after_step1/O/analyze.sh")
+    # creat_sh("../data/after_step1/S","S","../data/after_step1/S/analyze.sh")
+    # creat_sh("../data/after_step1/Cl","Cl","../data/after_step1/Cl/analyze.sh")
+    # creat_sh("../data/after_step1/Br","Br","../data/after_step1/Br/analyze.sh")
+    create_sh_recursive("../data/after_step1")