calc—_v1
This commit is contained in:
102
py/make_sh.py
102
py/make_sh.py
@@ -1,63 +1,13 @@
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import os
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def creat_sh(input_folder, anion, sh_file_path='analyze.sh'):
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"""
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创建shell脚本，只处理两类CIF文件：
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1. 纯数字命名的CIF文件 (例如: 123.cif)
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2. 数字-坐标格式的CIF文件 (例如: 123-x1y2z3.cif)
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参数:
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input_folder: 输入文件夹路径
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anion: 阴离子类型
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sh_file_path: 生成的shell脚本路径
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"""
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# 文件夹路径
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folder_path = input_folder
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import re
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# 定义两种文件名模式的正则表达式
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pattern1 = re.compile(r'^\d+\.cif$') # 纯数字.cif
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pattern2 = re.compile(r'^\d+-x\d+y\d+z\d+\.cif$') # 数字-x数字y数字z数字.cif
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# 打开SH脚本文件用于写入
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with open(sh_file_path, 'w') as sh_file:
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# 写入脚本头部
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sh_file.write('#!/bin/bash\n')
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# 遍历文件夹中的所有文件
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for filename in os.listdir(folder_path):
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file_path = os.path.join(folder_path, filename)
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# 只处理文件(不处理文件夹)
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if os.path.isfile(file_path):
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# 检查文件名是否匹配两种模式之一
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if pattern1.match(filename) or pattern2.match(filename):
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# 生成对应的命令
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command = f"python ../../../tool/analyze_voronoi_nodes.py {filename} -i ../../../tool/{anion}.yaml > {filename}.txt\n"
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# 将命令写入SH脚本文件
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sh_file.write(command)
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print(f"SH脚本已生成：{sh_file_path}")
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import os
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def create_sh_recursive(base_folder, tool_path="tool", relative_depth=2):
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"""
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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，
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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,
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并在基础文件夹下创建一个sh_all.sh来执行所有脚本。
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参数:
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base_folder: 起始文件夹路径
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tool_path: 工具目录的基本路径
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relative_depth: 基础相对深度，用于计算正确的相对路径
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"""
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# 用于收集所有生成的analyze.sh脚本的相对路径
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analyze_sh_paths = []
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base_folder_name = os.path.basename(base_folder)
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def process_folder(folder_path, current_depth=0):
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print(f"处理文件夹: {folder_path}")
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@@ -66,17 +16,31 @@ def create_sh_recursive(base_folder, tool_path="tool", relative_depth=2):
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folder_name = os.path.basename(folder_path)
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# 检查当前文件夹是否包含.cif文件
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has_cif_files = any(
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f.endswith('.cif') for f in os.listdir(folder_path) if os.path.isfile(os.path.join(folder_path, f)))
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# 注意：这里我们只关心当前层级下的cif文件
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cif_files = [f for f in os.listdir(folder_path) if
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f.endswith('.cif') and os.path.isfile(os.path.join(folder_path, f))]
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has_cif_files = len(cif_files) > 0
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# 如果当前文件夹包含.cif文件，生成脚本
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# 如果当前文件夹包含.cif文件,生成脚本
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if has_cif_files:
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# 计算正确的工具路径（根据深度增加../）
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# 计算正确的工具路径(根据深度增加../)
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dots = "../" * (relative_depth + current_depth)
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tool_relative_path = f"{dots}{tool_path}"
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# 确定anion参数（使用文件夹名）
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anion = folder_name
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# --- 修改开始: 修正Anion识别逻辑 ---
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# 如果结构是 Anion/MaterialID/file.cif，此时folder_name是MaterialID
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# 我们需要上一级目录的名字作为Anion (例如 'O', 'S', 'Cl') 来寻找对应的 .yaml 文件
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# 简单的判断逻辑：如果当前文件夹名字主要由数字组成(或者是ID格式)，且包含cif文件，我们假设其父目录是Anion类型
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# 或者更直接的逻辑：在你的新结构中，包含cif的文件夹必定是底层文件夹，其父目录必定是Anion
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parent_dir_name = os.path.basename(os.path.dirname(folder_path))
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# 这里做一个简单的保护，如果是在第一层(比如直接在O文件夹下有cif)，保持原状，否则使用父目录名
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# 在新结构下，cif总是在 '.../O/141/141.cif'，所以anion应该是 parent_dir_name ('O')
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if parent_dir_name in ['O', 'S', 'Cl', 'Br'] or folder_name not in ['O', 'S', 'Cl', 'Br']:
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anion = parent_dir_name
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else:
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anion = folder_name
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# --- 修改结束 ---
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# 生成脚本文件路径
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sh_file_path = os.path.join(folder_path, "analyze.sh")
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@@ -84,18 +48,17 @@ def create_sh_recursive(base_folder, tool_path="tool", relative_depth=2):
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# 创建脚本
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with open(sh_file_path, 'w') as sh_file:
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sh_file.write('#!/bin/bash\n')
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for filename in os.listdir(folder_path):
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file_path = os.path.join(folder_path, filename)
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if os.path.isfile(file_path) and filename.endswith('.cif'):
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command = f"python {tool_relative_path}/analyze_voronoi_nodes.py {filename} -i {tool_relative_path}/{anion}.yaml > {filename}.txt\n"
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sh_file.write(command)
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for filename in cif_files:
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# --- 修改开始: 输出重定向到 log.txt ---
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command = f"python {tool_relative_path}/analyze_voronoi_nodes.py {filename} -i {tool_relative_path}/{anion}.yaml > log.txt\n"
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# --- 修改结束 ---
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sh_file.write(command)
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# 将此脚本添加到收集器中
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# 计算相对于基础文件夹的路径
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rel_path = os.path.relpath(folder_path, base_folder)
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analyze_sh_paths.append(rel_path)
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print(f"生成脚本: {sh_file_path} (工具路径: {tool_relative_path})")
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print(f"生成脚本: {sh_file_path} (工具路径: {tool_relative_path}, Anion: {anion})")
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# 获取子文件夹列表
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subdirs = [d for d in os.listdir(folder_path) if os.path.isdir(os.path.join(folder_path, d))]
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@@ -105,7 +68,7 @@ def create_sh_recursive(base_folder, tool_path="tool", relative_depth=2):
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elements = folder_name.split("+")
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for element in elements:
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element_dir = os.path.join(folder_path, element)
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# 如果对应元素的子文件夹不存在，创建它
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# 如果对应元素的子文件夹不存在,创建它
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if not os.path.exists(element_dir):
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os.makedirs(element_dir)
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print(f"创建子文件夹: {element_dir}")
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@@ -144,13 +107,8 @@ def create_sh_recursive(base_folder, tool_path="tool", relative_depth=2):
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# 修改权限使脚本可执行
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os.chmod(sh_all_path, 0o755)
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print(f"生成总执行脚本: {sh_all_path}")
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print("所有脚本生成完成！")
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# 示例调用
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# create_sh_recursive("../data/after_step1")
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print("所有脚本生成完成!")
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if __name__ == '__main__':
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# creat_sh("../data/after_step1/O","O","../data/after_step1/O/analyze.sh")
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# creat_sh("../data/after_step1/S","S","../data/after_step1/S/analyze.sh")
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# creat_sh("../data/after_step1/Cl","Cl","../data/after_step1/Cl/analyze.sh")
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# creat_sh("../data/after_step1/Br","Br","../data/after_step1/Br/analyze.sh")
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create_sh_recursive("../data/after_step1")
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