85 lines
2.5 KiB
Bash
85 lines
2.5 KiB
Bash
#!/bin/bash
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# ==========================================
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# 全流程自动化脚本 (直通筛选版)
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# ==========================================
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# 1. 环境初始化
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echo "============ Stage 0: Initialization ============"
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chmod -R u+w ../Screen
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source $(conda info --base)/etc/profile.d/conda.sh
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# 激活 screen 环境
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conda activate ~/anaconda3/envs/screen
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cd py/
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export PYTHONPATH=$(pwd):$PYTHONPATH
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# 2. 预处理与文件整理 (替代原 Step 1)
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echo "============ Stage 1: File Organization (Direct Pass) ============"
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# 运行预处理 (可选，确保 input 文件夹就绪)
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python pre_process.py
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# 运行直通版整理脚本
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# 功能: 读取 input, 识别阴离子, 按结构复制到 after_step1/Anion/ID/ID.cif
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# 跳过 check_basic 等耗时检查
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python step1_direct.py
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# 生成 Zeo++ 运行脚本
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# 功能: 遍历 after_step1, 生成 analyze.sh 和 sh_all.sh
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python make_sh.py
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# 3. 运行 Zeo++ 计算
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echo "============ Stage 2: Zeo++ Calculations ============"
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conda deactivate
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conda activate ~/anaconda3/envs/zeo
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# 进入数据目录
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cd ../data/after_step1
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if [ -f "sh_all.sh" ]; then
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# 执行所有计算
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source sh_all.sh
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# 清理总脚本 (可选)
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# rm sh_all.sh
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else
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echo "Error: sh_all.sh not found! Please check Stage 1."
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exit 1
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fi
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# 4. 数据提取与高级分析
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echo "============ Stage 3: Data Extraction & Analysis ============"
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# 切回 screen 环境
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conda deactivate
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conda activate ~/anaconda3/envs/screen
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cd ../../py
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# 3.1 提取 Zeo++ 基础数据
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# 输出: ../output/Anion/Anion.csv (含 Perc, Min_d, Max_node)
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python extract_data.py
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# 3.2 计算角共享 (Corner Sharing)
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# 输出: 更新 CSV, 增加 Is_Only_Corner_Sharing 列
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echo "Running Corner Sharing Analysis..."
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python analyze_cs.py
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# 3.3 联合筛选
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# 功能: 读取 CSV, 根据阈值筛选, 生成 ../data/after_screening 软链接/文件
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python step2_4_combined.py
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# 3.4 CSM 分析 (仅针对筛选后的材料)
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# 输出: ../output/CSM/Anion/ID.dat
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echo "Running CSM Analysis..."
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python analyze_csm.py
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# 3.5 统计四面体占据率
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# 输出: 读取 .dat, 更新 CSV, 增加 Tet_Li_Ratio 列
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echo "Updating Tetrahedral Li Ratio..."
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python update_tet_occupancy.py
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# 5. 结束
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echo "========================================================"
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echo "All tasks completed!"
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echo "Results stored in:"
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echo " - CSV Data: ../output/"
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echo " - Screened: ../data/after_screening/"
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echo " - CSM Details: ../output/CSM/"
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echo "========================================================" |