add README in calc utils

calc_utils/bin/gsub_wait

@@ -0,0 +1,116 @@
+#!/bin/bash
+set -u
+
+# Usage: gsub_wait <jobname>
+
+job=${1:-}
+if [[ -z "$job" ]]; then
+  echo "Usage: $0 <jobname-without-extension>"
+  exit 1
+fi
+
+# ==========================================
+# 1. 提交任务 (Submit Job)
+# ==========================================
+
+# 确定 gsub 命令位置
+# 优先查找当前目录下的 gsub，否则查找 PATH
+if [[ -x "./gsub" ]]; then
+    GSUB_CMD="./gsub"
+else
+    GSUB_CMD="gsub"
+fi
+
+# 调用 gsub 并捕获输出
+# 注意：gsub 内部可能通过 SSH 在远程执行，最终返回 qsub 的输出
+output=$($GSUB_CMD "$job")
+echo "$output"
+
+# ==========================================
+# 2. 检查是否需要等待 (Check Silent Mode)
+# ==========================================
+# 如果 GSUB_SILENT 为 1，则不进行监控，直接退出
+if [[ "${GSUB_SILENT:-0}" == "1" ]]; then
+  exit 0
+fi
+
+# ==========================================
+# 3. 监控任务进度 (Monitor Progress)
+# ==========================================
+
+# 尝试提取 Job ID (例如: 67147.cluster -> 67147)
+jobid_full=$(echo "$output" | grep -oE '[0-9]+\.cluster|[0-9]+' | head -n 1 || true)
+
+if [[ -n "$jobid_full" ]]; then
+  jobid=${jobid_full%%.*}
+  
+  # 准备参数
+  out_file="$job.out"
+  gin_file="$job.gin"
+  end_file="$job.job.o$jobid"
+  
+  if [[ ! -f "$gin_file" ]]; then
+      # 如果 gin 文件找不到（可能是远程路径问题？），跳过监控
+      echo "Warning: $gin_file not found nearby. Skipping monitor."
+      exit 0
+  fi
+  
+  # 计算 Total Steps: (--link1-- 数量) + 1
+  link_count=$(grep -c -- "--link1--" "$gin_file" || true)
+  total=$((link_count + 1))
+  cntDone=0
+  cntSCF=0
+  
+  last_lines=0
+  
+  echo "Monitoring Job $jobid..."
+
+  while true; do
+    # A. 检查 PBS 结束文件 (Job 完成标志)
+    if [[ -f "$end_file" ]]; then
+      echo "Job finished (found $end_file)."
+      break
+    fi
+    
+    # B. 检查并读取 .out 输出文件
+    if [[ -f "$out_file" ]]; then
+      curr_lines=$(wc -l < "$out_file" 2>/dev/null || echo 0)
+      
+      # 如果文件变小（被截断或重新生成），重置读取位置
+      if (( curr_lines < last_lines )); then last_lines=0; fi
+      
+      if (( curr_lines > last_lines )); then
+        # 逐行处理新增内容
+        # 使用进程替换 < <(...) 避免管道导致的子shell变量丢失问题
+        while IFS= read -r line; do
+          
+          # 检查 SCF Done
+          # 正则匹配: SCF Done: ... E ... = (数值) A.U.
+          if [[ "$line" =~ SCF[[:space:]]Done:.*E.*=[[:space:]]*([-0-9.]+)[[:space:]]*A\.U\. ]]; then
+             energy="${BASH_REMATCH[1]}"
+             cntSCF=$((cntSCF + 1))
+             echo "$job: SCF Done: $energy [$cntSCF] ($cntDone/$total)"
+          fi
+          
+          # 检查 Termination
+          if [[ "$line" == *"termination of Gaussian"* ]]; then
+             cntDone=$((cntDone + 1))
+             echo "$job: task done ($cntDone/$total)"
+          fi
+          
+        done < <(tail -n "+$((last_lines + 1))" "$out_file")
+        
+        last_lines=$curr_lines
+      fi
+    fi
+    
+    sleep 2
+  done
+  
+  # C. 最终校验
+  if (( cntDone != total )); then
+    echo "Warning: cntDone ($cntDone) != total ($total)"
+  fi
+else
+  echo "Could not parse Job ID from output. Monitor skipped."
+fi