mcp
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19
softBV/out/Br.csv
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19
softBV/out/Br.csv
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@@ -0,0 +1,19 @@
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filename,formula,conductivity(e-3S/m)
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1080005.cif,Cs3Li2Br5,21.23
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1147619.cif,Li3YBr6,20.00
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1147621.cif,Li3InBr6,7.23
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1211043.cif,LiFeBr4,11.60
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1222492.cif,Li3ErBr6,29.61
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1222679.cif,Li2MnBr4,9.68
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2033990.cif,CsLi2Br3,9.71
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22967.cif,Li2FeBr4,11.21
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23057.cif,CsLiBr2,5.12
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2763849.cif,Cs3Li2Br5,121.34
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28237.cif,RbLiBr2,3.46
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28250.cif,Li2MnBr4,12.25
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28326.cif,LiGaBr4,1.56
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28327.cif,LiGaBr3,8.32
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28829.cif,Li2ZnBr4,15.71
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37873.cif,Li3ErBr6,10.90
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580554.cif,CsLi3Br4,38.40
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606680.cif,CsLi2Br3,20.63
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@@ -3,17 +3,16 @@ import sys
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import subprocess
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import re
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import csv
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import argparse
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from pathlib import Path
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# --- 配置区 ---
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# softBV.x 可执行文件的路径，请根据你的实际情况修改
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# 使用 Path.home() 来自动获取用户家目录，比 '~' 更可靠
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SOFTBV_EXECUTABLE = Path.home() / "tool/softBV-GUI_linux/bin/softBV.x"
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# 固定的命令参数
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MOBILE_ION = "Li"
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ION_VALENCE = "1"
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SF_VALUE = "1000"
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# 输出CSV文件的名称
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OUTPUT_CSV_FILE = "conductivity_results.csv"
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@@ -33,47 +32,73 @@ def check_executable():
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sys.exit(1)
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def get_formula_from_cif_line2(cif_path):
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"""
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通过读取CIF文件的第二行来提取化学式。
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期望的格式是 'data_FORMULA'。
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"""
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try:
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with open(cif_path, 'r', encoding='utf-8') as f:
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lines = f.readlines()
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if len(lines) > 1:
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second_line = lines[1].strip() # .strip() 去除首尾空白和换行符
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if second_line.lower().startswith('data_'):
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# 提取 'data_' 之后的内容作为化学式
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return second_line[5:]
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else:
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print(f"\n警告: 文件 {cif_path.name} 的第二行格式不正确 (不是以'data_'开头)。", file=sys.stderr)
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return "FormatError"
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else:
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print(f"\n警告: 文件 {cif_path.name} 行数不足2行。", file=sys.stderr)
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return "FileTooShort"
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except Exception as e:
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print(f"\n警告: 读取文件 {cif_path.name} 时发生错误: {e}", file=sys.stderr)
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return "ReadError"
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def parse_conductivity(output_text):
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"""
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从 softBV.x 的输出文本中解析电导率(conductivity)。
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使用正则表达式来匹配 'MD: conductivity = <value>' 格式的行。
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"""
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# 正则表达式解释:
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# ^ - 匹配行首
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# \s* - 匹配任意数量的空白字符
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# MD: conductivity - 匹配字面字符串
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# \s*=\s* - 匹配等号，前后可以有任意空白
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# ([-\d.eE+]+) - 捕获组1: 匹配并捕获一个或多个数字、点、'e'/'E'、'+'/'-' (科学计数法)
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"""从 softBV.x 的输出文本中解析并格式化电导率"""
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pattern = re.compile(r"^\s*MD: conductivity\s*=\s*([-\d.eE+]+)", re.MULTILINE)
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match = pattern.search(output_text)
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if match:
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# 返回捕获到的第一个组 (也就是数值部分)
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return match.group(1)
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conductivity_str = match.group(1)
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try:
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conductivity_val = float(conductivity_str)
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# 将单位从 S/m 转换为 1e-3 S/m (mS/m), 需要乘以 1000
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conductivity_ms_m = conductivity_val * 1000
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# 格式化为两位小数的字符串
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return f"{conductivity_ms_m:.2f}"
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except ValueError:
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return "ValueError"
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else:
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# 如果没有找到匹配的行，返回 None
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return None
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def main():
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"""主函数"""
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# 1. 检查命令行参数
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if len(sys.argv) != 2:
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print(f"用法: python {sys.argv[0]} <cif_folder_name>")
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print(f"例如: python {sys.argv[0]} Br")
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sys.exit(1)
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parser = argparse.ArgumentParser(
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description="运行 softBV.x 计算电导率并汇总到CSV文件。",
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formatter_class=argparse.RawTextHelpFormatter
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)
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parser.add_argument("folder", type=str, help="包含CIF文件的目标文件夹路径。")
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parser.add_argument(
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"-t", "--temperature",
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type=int,
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default=1000,
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help="模拟温度 (K)，对应 softBV.x 的最后一个参数。\n默认值: 1000"
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)
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args = parser.parse_args()
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target_folder = Path(sys.argv[1])
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target_folder = Path(args.folder)
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temperature = str(args.temperature)
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# 检查目标文件夹是否存在
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if not target_folder.is_dir():
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print(f"错误: 文件夹 '{target_folder}' 不存在。")
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sys.exit(1)
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# 检查 softBV.x 是否配置正确
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check_executable()
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# 2. 查找所有 .cif 文件
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cif_files = sorted(list(target_folder.glob("*.cif")))
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if not cif_files:
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@@ -81,61 +106,45 @@ def main():
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return
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print(f"在 '{target_folder}' 中找到 {len(cif_files)} 个 .cif 文件，开始处理...")
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print(f"模拟温度设置为: {temperature} K")
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results = [] # 用于存储 (文件名, 电导率)
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results = []
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# 3. 遍历文件，执行命令并提取数据
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for cif_file in cif_files:
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print(f" -> 正在处理: {cif_file} ...", end="", flush=True)
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# 构建命令
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# 使用新的函数获取化学式
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formula = get_formula_from_cif_line2(cif_file)
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command = [
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str(SOFTBV_EXECUTABLE),
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"--md",
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str(cif_file),
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MOBILE_ION,
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ION_VALENCE,
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SF_VALUE
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str(SOFTBV_EXECUTABLE), "--md", str(cif_file),
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MOBILE_ION, ION_VALENCE, temperature
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]
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try:
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# 执行命令并捕获输出
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# capture_output=True 将 stdout 和 stderr 分别捕获
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# text=True (或 encoding='utf-8') 将输出解码为字符串
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# check=True 如果命令返回非零退出码 (表示错误)，则会抛出异常
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process_result = subprocess.run(
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command,
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capture_output=True,
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text=True,
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check=True,
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timeout=300 # 设置一个超时时间（例如300秒），防止程序卡死
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command, capture_output=True, text=True, check=True, timeout=300
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)
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# 从标准输出中解析数据
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conductivity = parse_conductivity(process_result.stdout)
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if conductivity is not None:
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results.append((cif_file.name, conductivity))
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print(f" 成功, conductivity = {conductivity}")
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results.append([cif_file.name, formula, conductivity])
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print(f" 成功, Formula: {formula}, Conductivity: {conductivity} (x10^-3 S/m)")
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else:
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print(" 失败 (无法在输出中找到conductivity)")
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# 你也可以选择将错误信息记录下来
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# results.append((cif_file.name, "Error: Not Found"))
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results.append([cif_file.name, formula, "NotFound"])
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except subprocess.CalledProcessError as e:
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# 命令执行失败
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print(f" 失败 (命令执行错误)")
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print(f" 错误信息: {e.stderr.strip()}")
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# results.append((cif_file.name, "Error: Execution Failed"))
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print(f" 错误信息: {e.stderr.strip()}", file=sys.stderr)
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results.append([cif_file.name, formula, "ExecError"])
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except subprocess.TimeoutExpired:
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print(f" 失败 (命令执行超时)")
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# results.append((cif_file.name, "Error: Timeout"))
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results.append([cif_file.name, formula, "Timeout"])
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except Exception as e:
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# 其他未知错误
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print(f" 失败 (发生未知错误: {e})")
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# results.append((cif_file.name, f"Error: {e}"))
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print(f" 失败 (发生未知错误: {e})", file=sys.stderr)
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results.append([cif_file.name, formula, "UnknownError"])
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# 4. 将结果写入CSV文件
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if not results:
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print("没有成功处理任何文件，不生成CSV。")
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return
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@@ -145,9 +154,7 @@ def main():
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try:
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with open(OUTPUT_CSV_FILE, 'w', newline='', encoding='utf-8') as csvfile:
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writer = csv.writer(csvfile)
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# 写入表头
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writer.writerow(['filename', 'conductivity'])
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# 写入数据
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writer.writerow(['filename', 'formula', 'conductivity(e-3S/m)'])
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writer.writerows(results)
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print("CSV文件已成功生成！")
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except IOError as e:
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