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There are four files I am using here for this task: an input file, the file whose values I want to change, and two shell scripts. The first file, models_linearanalysis_Cep.dat is an input file that is organized as so:

1 0.020 0.700 5.4 1500 4000 2 0.020 0.700 5.4 1500 4050 3 0.020 0.700 5.4 1500 4100 4 0.020 0.700 5.4 1500 4150 5 0.020 0.700 5.4 1500 4200

The columns from 1-6 are respectively organized as directory number (d_number), Z, X, mass, L, and Teff. I want to use the 6 values from every row to change the assignments of the variables in this second file inlist_rsp_Cepheid which has the variables:

 RSP_mass = 4.165d0 RSP_Teff = 6050 RSP_L = 1438.8d0 RSP_X = 0.73d0 RSP_Z = 0.007d0 log_directory='LOGS_1' photo_directory='photos_1'

In this instance, the directory number (i.e. the number attached to LOGS_ and photos_) is 1.

In my first shell script, Inlists_Bash.sh, shown below I attempt to read values from the six columns of the file models_linearanalysis_Cep.dat here, which I intend to read into a second shell script inlist_changer.sh.

while read -ra fields; do for field in "${fields[@]}"; do bash inlist_changer.sh <<<"$field" done ./mk ./rn done < models_linearanalysis_Cep.dat

Finally, with the second shell script inlist_changer.sh, I use the inputs to finally change the lines in inlist_rsp_Cepheid such that the variables have the appropriate values.

#!/bin/bash export OMP_NUM_THREADS=12 #used for testing variables #export mass=4.165d0 #export teff=6050 #export l=1438.8d0 #export x=0.73d0 #export z=0.007d0 #export d_number=2 #read in inputs from the Inlists_Bash.sh file read -p d_number z x mass l teff #inlist directory export MESA_INLIST="/home/nick/mesa-r11701/star/test_suite/rsp_Cepheid_grid/inlist_rsp_Cepheid" #change the lines in the MESA_INLIST file sed -i \ -e "s/^\([[:blank:]]*RSP_mass\).*/\1 = $mass/i" \ -e "s/^\([[:blank:]]*RSP_Teff\).*/\1 = $teff/i" \ -e "s/^\([[:blank:]]*RSP_L\).*/\1 = $l/i" \ -e "s/^\([[:blank:]]*RSP_X\).*/\1 = $x/i" \ -e "s/^\([[:blank:]]*RSP_Z\).*/\1 = $z/i" \ -e "s/^\([[:blank:]]*log_directory\).*/\1 = 'LOGS_$d_number'/i" \ -e "s/^\([[:blank:]]*photo_directory\).*/\1 = 'photos_$d_number'/i" \ "$MESA_INLIST"

For the first row, I was expecting inlist_rsp_Cepheid to look like this:

 RSP_mass = 5.4 RSP_Teff = 4000 RSP_L = 1500 RSP_X = 0.700 RSP_Z = 0.020 log_directory='LOGS_1' photo_directory='photos_1'

However, it is clear something is wrong with how I am reading the inputs between these files as I receive this instead:

 RSP_mass = RSP_Teff = RSP_L = RSP_X = RSP_Z = 4000 log_directory='LOGS_' photo_directory='photos_'

Would someone please explain what I may be missing or doing incorrectly here?

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Change Inlists_Bash.sh to this and pass all six values of the array at once to inlist_changer.sh:

#!/bin/bash while read -ra fields; do ./inlist_changer.sh "${fields[@]}" ./mk ./rn done < models_linearanalysis_Cep.dat

Change inlist_changer.sh to use parameters $1 ... $6 instead of using read.
The -p in read is used to print a prompt string (d_number in your case) and you were only setting variable z in each of your calls.

#!/bin/bash export OMP_NUM_THREADS=12 mesa_inlist=/home/nick/mesa-r11701/star/test_suite/rsp_Cepheid_grid/inlist_rsp_Cepheid sed -i \ -e "s/^\([[:blank:]]*RSP_mass\).*/\1 = $4/i" \ -e "s/^\([[:blank:]]*RSP_Teff\).*/\1 = $6/i" \ -e "s/^\([[:blank:]]*RSP_L\).*/\1 = $5/i" \ -e "s/^\([[:blank:]]*RSP_X\).*/\1 = $3/i" \ -e "s/^\([[:blank:]]*RSP_Z\).*/\1 = $2/i" \ -e "s/^\([[:blank:]]*log_directory\).*/\1 = 'LOGS_$1'/i" \ -e "s/^\([[:blank:]]*photo_directory\).*/\1 = 'photos_$1'/i" \ "$mesa_inlist"

Note: It's not clear where you need the exported variable OMP_NUM_THREADS.

Or put everything into one script:

#!/bin/bash export OMP_NUM_THREADS=12 mesa_inlist=/home/nick/mesa-r11701/star/test_suite/rsp_Cepheid_grid/inlist_rsp_Cepheid while read -ra fields; do sed -i \ -e "s/^\([[:blank:]]*RSP_mass\).*/\1 = ${fields[3]}/i" \ -e "s/^\([[:blank:]]*RSP_Teff\).*/\1 = ${fields[5]}/i" \ -e "s/^\([[:blank:]]*RSP_L\).*/\1 = ${fields[4]}/i" \ -e "s/^\([[:blank:]]*RSP_X\).*/\1 = ${fields[2]}/i" \ -e "s/^\([[:blank:]]*RSP_Z\).*/\1 = ${fields[1]}/i" \ -e "s/^\([[:blank:]]*log_directory\).*/\1 = 'LOGS_${fields[0]}'/i" \ -e "s/^\([[:blank:]]*photo_directory\).*/\1 = 'photos_${fields[0]}'/i" \ "$mesa_inlist" ./mk ./rn done < models_linearanalysis_Cep.dat
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  • Now, say I want to put all the LOGS_ and photos_ into directories: named LOGS_A. I and photos_A. I tried to change LOGS_${fields[0])} to LOGS_A/LOGS_${fields[0])}, but the LOGS_A directory is not even created and I get the error sed: -e expression #6, char 49:unkown option to 's'. How would you modify the script to do this? Commented May 18, 2020 at 17:20
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    The / is the separator for the substitution ("s/regexp/replacement/i"), either escape it as LOGS_A\/LOGS_${fields[0]} or change the separator to a different character ("s#regexp#replacement#i"). Commented May 18, 2020 at 17:40
  • One small question. Let's say I don't want to read all the rows in models_linearanalysis_Cep.dat, perhaps for example the last 5000 rows. I know that a for loop would be appropriate for this situation, but I am naive about the syntax. Woulf you simply replace while read -ra fields with for read -ra field in fields? Commented May 22, 2020 at 1:19
  • You can read the last N lines of a file with tail -nN file and you could change the last line to done < <(tail -n5000 models_linearanalysis_Cep.dat) using a process substitution <(...). Commented May 22, 2020 at 1:38

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