Linux实用脚本以及bashrc配置收集 - 计算化学公社

#!/bin/bash
export MOL=$1
export FCHK=$2
export SUBDIR=~+
export GAUSS_SCRDIR=~/tmp/gaussian/$
export GAUSS_EXEDIR=xxxxxxxxxxxxxxxx #写自己的gaussian路径
export USERNAME=`whoami`
if [ null$MOL == null ]; then
echo -e "\n\033[31m ************************************* \033[0m"
echo -e "\033[31m Please input the name of a .com file! \033[0m"
echo -e "\033[31m ************************************* \033[0m"
exit
fi
full=`date --rfc-2822` #时间这儿，这样写，适合中文系统的同学想获得英文缩写。
week=${full%,*}
submit=`date "+%Y-%m-%d, $week, %T"`
start=`date +%s`
if [ -e $SUBDIR/$MOL.com ] ; then
echo -e "\n *******************************************************"
echo " Gaussian Task:"
echo " Now calculating $SUBDIR/$MOL.com!"
echo " *******************************************************"
mkdir -p $GAUSS_SCRDIR
cd $GAUSS_SCRDIR
echo -e "\033[31m Now $SUBDIR/$MOL.com is still calculated in the background~ \033[0m" >> ~/tmp/now.log
$GAUSS_EXEDIR/g09 $SUBDIR/$MOL.com $SUBDIR/$MOL.log
else
echo -e "\n\033[31m ************************************************************************* \033[0m"
echo -e "\033[31m Cannot find $SUBDIR/$MOL.com! Please check your PATH! \033[0m"
echo -e "\033[31m ************************************************************************* \033[0m"
exit
fi
if grep -i '%chk=' $SUBDIR/$MOL.com ; then
if [ -e *.chk ] ; then
mv -f *.chk $SUBDIR/$MOL.chk
fi
else
echo -e "\nYou didn't request the .chk file!"
fi
if [ -e *.wfx ] ; then
mv -f *.wfx $SUBDIR/$MOL.wfx
fi
if [ -e *.wfn ] ; then #这部分自己想要啥文件自己加就好
mv -f *.wfn $SUBDIR/$MOL.wfn
fi
for ((k=31; k<=41; k++))
do
if [ -e *.$k ] ; then
mv -f *.$k $SUBDIR/$MOL.$k
fi
done
if [ $FCHK !="fchk" ] || [ null$2 == null ] ; then > /dev/null
echo "You didn't request to produce the .fchk file!"
else
if [ -e $SUBDIR/$MOL.chk ] ; then
formchk $SUBDIR/$MOL.chk $SUBDIR/$MOL.fchk
echo ".fchk file formed sucessfully"
else
echo "So cannot form .fchk file!"
fi
fi
rm -rf $GAUSS_SCRDIR
echo -e "\n=========================================================================="
echo "The temporary folder $GAUSS_SCRDIR of calculation was deleted"
stop=`date +%s`
time=`expr "$stop" - "$start"`
end=`date "+%Y-%m-%d, $week, %T"`
echo "**************************************************************************" >> $SUBDIR/$MOL.log
echo File: $SUBDIR/$MOL.com >> $SUBDIR/$MOL.log
if [ $time -le 60 ] ; then
echo Time consuming: $time seconds >> $SUBDIR/$MOL.log
elif [ $time -gt 60 -a $time -le 3600 ] ; then
echo "Time consuming: `echo "scale=2;$time/60"|bc` minutes" >> $SUBDIR/$MOL.log
elif [ $time -gt 3600 -a $time -le 86400 ] ; then
echo "Time consuming: `echo "scale=2;$time/3600"|bc` hours" >> $SUBDIR/$MOL.log
elif [ $time -gt 86400 ] ; then
echo "Time consuming: `echo "scale=2;$time/86400"|bc` days" >> $SUBDIR/$MOL.log
fi
echo Submission time: $submit >> $SUBDIR/$MOL.log
echo Ending time: $end >> $SUBDIR/$MOL.log
echo "**************************************************************************" >> $SUBDIR/$MOL.log
echo Temporary folder is $GAUSS_SCRDIR >> $SUBDIR/$MOL.log
echo "=========================================================================="
tail -25 $SUBDIR/$MOL.log
echo "These last 25 lines are from file: $SUBDIR/$MOL.log"
echo "=========================================================================="
echo -e "\n\033[31m ************************************************************************************** \033[0m" >> ~/tmp/results.log
echo -e "\033[31m Gaussian Task：\033[0m" >> ~/tmp/results.log
grep -q "Normal termination" $SUBDIR/$MOL.log
if [ $? -eq 1 ] ; then
echo -e "\033[31m $SUBDIR/$MOL.com !!!ERROR TERMINATED!!! at $end \033[0m" >> ~/tmp/results.log
else
echo -e "\033[31m $SUBDIR/$MOL.com !!!NORMAL TERMINATED!!! at $end \033[0m" >> ~/tmp/results.log
fi
echo -e "\033[31m ************************************************************************************** \033[0m" >> ~/tmp/results.log
w|grep "$USERNAME"|head -n 1|sed 's/ //g' > /dev/null
if [ $? -eq 0 ] ; then
rm -f ~/tmp/results.log
fi
sed -i '/'$MOL.com'/d' ~/tmp/now.log

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if [ -e ~/tmp/results.log ] ; then
echo -e "\n\033[33m Tasks that have been already done:\033[0m"
/bin/cat ~/tmp/results.log
fi
rm -f ~/tmp/results.log > /dev/null
if [ -s ~/tmp/now.log ] ; then
echo -e "\n\033[33m Tasks that are still going on:\033[0m"
/bin/cat -n ~/tmp/now.log
else
rm -f ~/tmp/now.log > /dev/null
fi

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#!/bin/bash
export MOL=$1
export NCPUS=$2 #gamess还得自己在外部指定核数，挺讨厌。
export SUBDIR=~+
export GMS_SCRDIR=~/tmp/gamess/$
export GMS_EXEDIR=xxxxxxxxxxxxxxxxx #写你的gamess路径
export VERNO=00
if [ null$MOL == null ]; then
echo -e "\n\033[31m ************************************* \033[0m"
echo -e "\033[31m Please input the name of a .inp file! \033[0m"
echo -e "\033[31m ************************************* \033[0m"
exit
fi
if [ null"$NCPUS" == null ] ; then
export NCPUS=1
fi
if [ -e $MOL.inp ] ; then #这儿自动创建路径的地方您要是不喜欢自己可以改改。
dir=$(dirname `find $PWD -name $MOL.inp`)
dirpart=${dir#*gamess}
if [ -e $SUBDIR/$MOL.dat ] ; then #这个地方主要是删除同一任务上次的dat等文件，以确保运算进行。
rm -f $SUBDIR/$MOL.dat
echo -e "\n Files that produced by last calculation has been deleted, calculation is going on~"
else
echo -e "\n There is no files that produced by last calculation, calculation is just going on~"
fi
echo -e "\n *******************************************************"
echo " Gamess Task:"
echo " Now calculating $SUBDIR/$MOL.inp!"
echo " *******************************************************"
mkdir -p ~/gamess/scratch/$dirpart/$MOL
export INTGLDIR=~/gamess/scratch/$dirpart/$MOL
mkdir -p $GMS_SCRDIR
echo -e "\033[31m Now $SUBDIR/$MOL.inp is still calculated in the background~ \033[0m" >> ~/tmp/now.log
$GMS_EXEDIR/rungms $MOL $VERNO $NCPUS $GMS_SCRDIR $SUBDIR $GMS_EXEDIR >& $SUBDIR/$MOL.log
else
echo -e "\n\033[31m ************************************************************************* \033[0m"
echo -e "\033[31m Cannot find $SUBDIR/$MOL.inp! Please check your PATH! \033[0m"
echo -e "\033[31m ************************************************************************* \033[0m"
exit
剩下的和gaussian大同小异。

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#!/bin/bash
export LOG=$1
export PATH=~+
exten=${LOG#*.}
if [ $exten == "log" ] ; then
if [ `/usr/bin/grep 'Converged' $PATH/$LOG|/usr/bin/head -n 1|/usr/bin/sed 's/ //g'` ] ; then
echo -e "\n Now Shows the CONVERGED condition of this calculation:\n"
/usr/bin/grep 'Converged' $PATH/$LOG -A4
times=`/usr/bin/grep 'Converged' $PATH/$LOG -c`
/usr/bin/grep -q "Normal termination" $PATH/$LOG
if [ $? -eq 0 ] ; then
echo -e "\n The molecule experienced \033[31m$times\033[0m times iteration during this calculation~\n"
else
echo -e "\n This molecule is ERROR terminated or the calculation is still going on with the \033[31m$times\033[0m th iteration~\n"
fi
else
echo -e "\n There exists no CONVERGED information during this calculation~\n"
fi
else
echo -e "\n Please input the right logfile name or make sure that you are inputting a logfile!\n"
fi

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#!/bin/bash
log=$1
state=$( (grep -q 'Error termination' $log && echo Error) || (grep -q 'Normal termination' $log && echo Normal) || echo Processing )
time=$(grep -c 'Conver' $log)
echo -e "The state of this job:$state\nOpt converged $time times\n$(grep -E '\ *(Displace|Force\ )' $log | tail -n 8)"

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