Bash for loop issue with file name

Question

I have a simple bash for loop and am trying to execute a command inside of it. The loop is so I can execute different file names.

the files are:

crystal0_cmin.pdb
crystal1_cmin.pdb
.
. 
.

the loop is:

for ((i=0;i<=10;i++))
do
cp Files/crystal$i_cmin.pdb Energy/
cp Files/crystal$i_cmin.psf Energy/
done

The problem is that I always get the following error message:

cp: cannot stat `Files/crystal.pdb': No such file or directory
cp: cannot stat `Files/crystal.psf': No such file or directory

but I never specify the files crystal.pdb and crystal.psf. It just ignores the $i extension for all i. That is, none of the files get copied.

Does anyone know how I can fix this.

Thanks!

It is easier to do: cp Files/crystal{0..10}_cmin.p{db,sf} Energy — William Pursell
– William Pursell, Commented Sep 14, 2012 at 20:56

Adam Mihalcin · Accepted Answer · 2012-09-14 20:47:02Z

6

The problem is that bash is interpreting $i_cmin as a variable. To fix it, use braces to tell bash that $i is a variable and should be interpreted as such:

cp Files/crystal${i}_cmin.pdb Energy/
cp Files/crystal${i}_cmin.psf Energy/

answered Sep 14, 2012 at 20:47

Adam Mihalcin

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Comments

chepner · Accepted Answer · 2012-09-14 21:08:08Z

The immediate fix is to use braces as suggested by Adam to limit the parameter name to i:

for ((i=0; i<=10; i++)); do
    cp Files/crystal${i}_cmin.pdb Energy/
    cp Files/crystal${i}_cmin.psf Energy/
done

The next step is to realize that you don't need to use a C-style for-loop to iterate over generated file names; you can use brace expansion to iterate over the desired files directly (this is the half-way point between your loop and William's comment:

for f in Files/crystal{0..10}_cmin.p{db,sf}; do
    cp "$f" Energy/
done

The last step is to realize you don't need a for-loop at all, because the list of files generated by the brace expansion can be used as the file list passed to cp directly (William's comment):

cp Files/crystal{0..10}_cmin.p{db,sf} Energy/

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