在ubuntu shell脚本中，在while循环中使用EOM时出现语法错误

Question

我有一个包含命令的代码，其中提示用户从菜单中显示的选项中选择一个选项。这需要重复执行几次，因此我使用了while循环。现在，我已经使用EOM (End of message)方法在提示时提供输入。在使用过程中，我注意到该方法在执行时会出现折叠错误。我已经将错误缩小到代码的这一部分(第80行到第83行)，并且无法传递这个错误。

请帮我解决这个问题。

错误所在的行：

TEMP="q"
gmx_mpi make_ndx -f pull_sim.gro -o index.ndx <

错误：

./Run_Pull_Code.sh: 105: Syntax error: end of file unexpected (expecting "done")

请查找以下完整代码(请参阅此处第80至83行)：

#!/bin/sh
# The above comment sets the sh file to execute as an interpreter (Line by line)

# Finding the current working directory
BASEDIR=$(pwd)
echo "I am currently in the following directory:"
echo "$BASEDIR"
echo " "


##########################################################################################
# Setting the pulling code positions and decrements (All in nm)
##########################################################################################
DECREMENT=0.5      #Steps in nm
RANGE=1            #From the highest to the lowest position
MID_POS=9.327      #Observing the highest water molecule (O atom) of the water surface
INIT_POS=$( echo "$MID_POS + $RANGE" | bc -l)  # Initial position
LAST_POS=$( echo "$MID_POS - $RANGE" | bc -l)  # Final position
CURR_POS=$INIT_POS # Assigning the Initial position as the current position


LOOP_CNT=0
while [ 1 -eq "$(echo "${LAST_POS} <= ${CURR_POS}" | bc)" ]
do 
    # increment the value
    LOOP_CNT=$( echo "$LOOP_CNT + 1" | bc -l)
    DISTANCE=$CURR_POS

    # Setting the loop number (X) as the pull code number for simulation (X)
    SIM_CNT=$LOOP_CNT

    # Making the directories (1) X_Pull (2) X_Pull/Making
    DIR_NAME_MAIN=$SIM_CNT"_Pull"
    mkdir $DIR_NAME_MAIN
    DIR_NAME_MAKING=$SIM_CNT"_Pull/Making"
    mkdir $DIR_NAME_MAKING
    
    echo " "
    echo "I have made the directories."
    echo " "

    # Copying the files from prerequisites folder to the newly created folder
    cp Prerequisites/Avo_decanol.pdb Prerequisites/water_box.pdb $DIR_NAME_MAKING
    cp Prerequisites/simulation_file.mdp Prerequisites/topol.top $DIR_NAME_MAIN
    
    ##########################################################################################
    # Making the simulation box "pull_sim.gro"
    ##########################################################################################
    cd $DIR_NAME_MAKING
    #(1) Fix the distance of the decanol from the water surface and make the only decanol box with the same dimension as that of the water box
    DISTANCE=9.5 
    gmx_mpi editconf -f Avo_decanol.pdb -o Dec_box.pdb -center 2.5 2.5 $DISTANCE -box 5 5 12
    #(2) CREATING CONSTANT HEADER AND ENDER cat files in PDB format
    #The first 4 lines of any PDB file contains the information of the box size and the name, etc.
    #Just copy the four lines into a separate HEADER PDB file by the following command.
    sed -n '1,4p' Dec_box.pdb > HEADER.pdb
    #The last 2 lines are also common to all PDB files, hence copy these to a ENDER PDB file by the following command.
    sed -n '38,39p' Dec_box.pdb > ENDER.pdb
    #(3) Separate the decanol atom properties from its PDB file (line 5 to 37) by the follwing command
    sed -n '5,37p' Dec_box.pdb > file_1.pdb
    #(4) Separate the water atom properties from its PDB file (line 5 to 15004) by the follwing command
    sed -n '5,15004p' water_box.pdb > file_2.pdb
    #(5) Now connect all the above files with the water surface PDB file in the following sequence:
    cat HEADER.pdb file_1.pdb file_2.pdb ENDER.pdb > pull_sim.pdb
    #(6) Rearrange all the number of atoms in the pull_sim.pdb and convert it into a GRO file, pull_sim.gro file.
    gmx_mpi editconf -f pull_sim.pdb -o pull_sim.gro -center 2.5 2.5 6.0 -box 5.0 5.0 12.0 -resnr 1

    # Copying the recently made pull_sim.gro file from making folder to the previous folder
    cd ../
    cp Making/pull_sim.gro ./
        
    echo " "
    echo "The pull box has been created."
    echo " "
    
    ##########################################################################################
    # Starting the simulation
    ##########################################################################################
    # (1) Making index file
    TEMP="q"
    gmx_mpi make_ndx -f pull_sim.gro -o index.ndx <

Answer 1

Heredocs不能像脚本的其他部分那样缩进(除非您使用-EOM，但随后只能缩进选项卡)。毕竟，本文档的目的是允许您编写将以原样出现的东西。这意味着EOM不能这样：

while something; 
do
    command <

相反，EOM (或您使用的任何其他标记)需要是行中唯一的东西，因此在行之前或之后没有空白或其他任何内容。如下所示：

while something; 
do
    command <

另外，请注意，由于上述原因，还将包括前面的空格，以便：

c=0;
while [ $c -eq 0 ]; 
do
    cat <

将印刷：

$ foo.sh
    Hello!

而这一点：

c=0;
while [ $c -eq 0 ]; 
do
    cat <

将印刷：

$ foo.sh
Hello!

最后，在运行脚本时，我得到了一个不同的错误：

$ foo.sh
I am currently in the following directory:
/home/terdon/foo
 
/home/terdon/scripts/foo.sh: line 108: warning: here-document at line 84 delimited by end-of-file (wanted `EOM')
/home/terdon/scripts/foo.sh: line 109: syntax error: unexpected end of file

这将是因为我没有提供相同的输入数据，而且，由于您没有正确结束EOM，您的数据可能正在由脚本处理，这就是为什么您看到了不同的错误。我希望我的修复会摆脱它，因为它允许我在我的机器上运行您的脚本直到结束。