sed: no input files - bash

Question

I have a script where I read in columns of data from an "input file", then use those to change some variables in another file.
Here is my script, titled FA_grid_changer.sh
#!/bin/bash
# before runnning, please ensure your inlist has the following parameters: RSP_mass, RSP_Teff, RSP_L, RSP_X, RSP_Z,
# log_directory, photo_directory, RSP_alfa, photo_interval, profile_interval, history_interval, terminal_interval,
# max_num_profile_models, RSP_max_num_periods
export OMP_NUM_THREADS=8
# get current directory
dir=$PWD
data_file="$dir"/input.dat
mesa_inlist="$dir"/inlist_rsp_RR_Lyrae
# set STR to 1 for saving history and profile files BEFORE the model has reached full-amplitude pulsations
# set STR to 2 for saving history and profile files AFTER the model has reached full-amplitude pulsations
STR=1
max_num_periods=4000
max_num_periods_2=$(($max_num_periods + 4))
if [[ "$STR" = 1 ]]
then
echo Configuring inlist to save settings before full-amplitude pulsations...
sed -i \
-e "s/^\([[:blank:]]*photo_interval\).*/\1 = 1000/i" \
-e "s/^\([[:blank:]]*profile_interval\).*/\1 = 1000/i" \
-e "s/^\([[:blank:]]*history_interval\).*/\1 = 1000/i" \
-e "s/^\([[:blank:]]*terminal_interval\).*/\1 = 4000/i" \
-e "s/^\([[:blank:]]*max_num_profile_models\).*/\1 = 100/i" \
-e "s/^\([[:blank:]]*RSP_max_num_periods\).*/\1 = $max_num_periods/i" \
"$mesa_inlist"
sleep 1.5
while read -ra fields; do
echo Changing model parameters...
sleep 0.5
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\/LOGS_${fields[0]}'/i" \
-e "s/^\([[:blank:]]*photo_directory\).*/\1 = 'photos\/photos_${fields[0]}'/i" \
#-e "s/^\([[:blank:]]*RSP_alfa\).*/\1 = ${fields[6]}/i" \
"$mesa_inlist"
echo Compiling MESA...
sleep 0.5
./mk
echo Running MESA...
sleep 0.5
./rn
done < "$data_file"
elif [[ "$STR" = 2 ]]
then
echo Configuring inlist to save settings after full-amplitude pulsations...
sed -i \
-e "s/^\([[:blank:]]*photo_interval\).*/\1 = 1000/i" \
-e "s/^\([[:blank:]]*profile_interval\).*/\1 = 1/i" \
-e "s/^\([[:blank:]]*history_interval\).*/\1 = 1/i" \
-e "s/^\([[:blank:]]*terminal_interval\).*/\1 = 4000/i" \
-e "s/^\([[:blank:]]*max_num_profile_models\).*/\1 = -1/i" \
-e "s/^\([[:blank:]]*RSP_max_num_periods\).*/\1 = $max_num_periods_2/i" \
"$mesa_inlist"
sleep 1.5
else
echo STR\: Not an acceptable option. Please \set STR to 1 or 2.
fi
Here is my input file input.dat, which I am keeping in the same directory.
RRL1 0.001 0.749 0.61036165206037 48.3930329458203 6795.10018238295
RRL2 0.001 0.749 0.60627327846453 59.8125833648911 6793.11236483182
RRL3 0.001 0.749 0.606272337551755 56.5141274900899 7059.10474568471
And here is the file I am trying to change inlist_rsp_RR_Lyrae
! long-period RR Lyrae star: M=0.65Ms, L=60Ls, Teff=6500K, X=0.75, Z=0.0004
! original test case contributed by Radek Smolec.
&star_job
!pgstar_flag = .true.
/ ! end of star_job namelist
&controls
! check for retries and backups as part of test_suite
!max_number_retries = -1
!max_number_backups = 0
!max_model_number = 15000
! RSP controls
! x_integer_ctrl(1) = 10 ! which period to check
x_ctrl(1) = 0.71262d0 ! expected period (in days)
RSP_mass = 0.606272337551755
RSP_Teff = 7059.10474568471
!RSP_L = 59.3141274900899
RSP_L = 56.5141274900899
RSP_X = 0.749
RSP_Z = 0.001
RSP_max_num_periods = 4000
RSP_nmodes = 10 ! number of modes LINA will calculate for initial model
RSP_nz = 150 ! number of zones of model
log_directory = 'LOGS/LOGS_M081_second'
photo_directory = 'photos/photos_M081_second'
! output controls
!num_trace_history_values = 2
trace_history_value_name(1) = 'rel_E_err'
trace_history_value_name(2) = 'log_rel_run_E_err'
! for cases in which you have a run that has reached steady pulses
! and you want to look at plots of just a few periods to see the details,
! i suggest the following method. interrupt the run soon after
! it makes a photo. remove or delete LOGS/history.data to force
! creation of a new one when restart. edit the inlist to set
! history_interval to 1 to get maximum time resolution.
! restart the run and let it go for as many periods as desired.
do_history_file = .true.
photo_interval = 1000
profile_interval = 1000
history_interval = 1000
terminal_interval = 4000
max_num_profile_models = 100
!photo_interval = 1
!profile_interval = 1
!history_interval = 1
!terminal_interval = 1
! FOR DEBUGGING
!RSP_report_undercorrections = .true.
!report_hydro_solver_progress = .true. ! set true to see info about newton iterations
!report_ierr = .true. ! if true, produce terminal output when have some internal error
!stop_for_bad_nums = .true.
!trace_evolve = .true.
! hydro debugging
!hydro_check_everything = .true.
!hydro_inspectB_flag = .true.
!hydro_sizequ_flag = .true.
! for making logs, uncomment hydro_dump_call_number plus the following
! to make residual logs, uncomment hydro_sizequ_flag
! to make correction logs, uncomment hydro_inspectB_flag
! to make jacobian logs, uncomment hydro_numerical_jacobian, hydro_save_numjac_plot_data
! to do dfridr test, uncomment hydro_get_a_numerical_partial, hydro_test_partials_k,
! hydro_numerical_jacobian, hydro_save_numjac_plot_data, hydro_dump_iter_number
!hydro_get_a_numerical_partial = 1d-7
!hydro_test_partials_k = 190
!hydro_numerical_jacobian = .true.
!hydro_save_numjac_plot_data = .true.
!hydro_dump_call_number = 1
!hydro_dump_iter_number = 6
!hydro_epsder_struct = 1d-6
!hydro_epsder_chem = 1d-6
!hydro_save_photo = .true. ! Saves a photo when hydro_call_number = hydro_dump_call_number -1
!fill_arrays_with_NaNs = .true.
!report_why_dt_limits = .true.
!report_all_dt_limits = .true.
!report_hydro_dt_info = .true.
!report_dX_nuc_drop_dt_limits = .true.
!report_bad_negative_xa = .true.
!show_mesh_changes = .true.
!mesh_dump_call_number = 95
!trace_newton_bcyclic_solve_input = .true. ! input is "B" j k iter B(j,k)
!trace_newton_bcyclic_solve_output = .true. ! output is "X" j k iter X(j,k)
!trace_newton_bcyclic_matrix_input = .true.
!trace_newton_bcyclic_matrix_output = .true.
!trace_newton_bcyclic_steplo = 1 ! 1st model number to trace
!trace_newton_bcyclic_stephi = 1 ! last model number to trace
!trace_newton_bcyclic_iterlo = 2 ! 1st newton iter to trace
!trace_newton_bcyclic_iterhi = 2 ! last newton iter to trace
!trace_newton_bcyclic_nzlo = 1 ! 1st cell to trace
!trace_newton_bcyclic_nzhi = 10000 ! last cell to trace; if < 0, then use nz as nzhi
!trace_newton_bcyclic_jlo = 1 ! 1st var to trace
!trace_newton_bcyclic_jhi = 100 ! last var to trace; if < 0, then use nvar as jhi
!trace_k = 0
/ ! end of controls namelist
&pgstar
!pause = .true.
pgstar_interval = 6
Grid2_win_flag = .true.
Grid2_title = '4.165 M\d\(2281)\u Z=0.007 Classical Cepheid'
History_Panels1_xaxis_name='star_age_day'
History_Panels1_max_width = 365 ! only used if > 0. causes xmin to move with xmax.
! Grid2_file_flag = .true.
file_digits = 7
Grid2_file_dir = 'png'
Grid2_file_prefix = 'grid'
Grid2_file_interval = 5 ! output when mod(model_number,Grid2_file_interval)==0
!Profile_Panels1_show_grid = .true.
Profile_Panels1_xaxis_name = 'logtau'
Profile_Panels1_xaxis_reversed = .true.
Profile_Panels1_xmin = -101D0
Profile_Panels1_xmax = -101D0
Profile_Panels1_dymin(4) = 0.02
Profile_Panels1_yaxis_name(2) = 'avg_charge_He'
/ ! end of pgstar namelist
Yet, when I try to run the shell script in bash, inlist_rsp_RR_Lyrae remains unchanged. Instead, this occurs:
Configuring inlist to save settings before full-amplitude pulsations...
Changing model parameters...
sed: no input files
/home/nick/mesa-r11701/star/test_suite/rsp_RR_Lyrae_grid/inlist_rsp_RR_Lyrae: line 1: long-period: command not found
/home/nick/mesa-r11701/star/test_suite/rsp_RR_Lyrae_grid/inlist_rsp_RR_Lyrae: line 3: original: command not found
/home/nick/mesa-r11701/star/test_suite/rsp_RR_Lyrae_grid/inlist_rsp_RR_Lyrae: line 5: syntax error near unexpected token `&'
/home/nick/mesa-r11701/star/test_suite/rsp_RR_Lyrae_grid/inlist_rsp_RR_Lyrae: line 5: `&star_job'
Compiling MESA...
As you can see, it is mistaking the first few lines of comments in inlist_rsp_RR_Lyrae as commands. Is there something I am missing here?

Answer 1

The problem is
sed -i \
...
-e "s/^\([[:blank:]]*photo_directory\).*/\1 = 'photos\/photos_${fields[0]}'/i" \
#-e "s/^\([[:blank:]]*RSP_alfa\).*/\1 = ${fields[6]}/i" \
"$mesa_inlist"
Here the comment before $mesa_inlist also comments out the \ at the end of the line. Therefore the command ends at that comment and sed -i complains that there is no file given. Afterwards bash tries to execute "$mesa_inlist" (that is inlist_rsp_RR_Lyrae) as a command, which fails.
To fix the problem, simply remove the comment line.
Bye the way: With this function you can drastically improve the readability of your script.
sedi() {
mapfile -t args < <(printf -- '-e\ns/^\([[:blank:]]*%s\).*/\\1 = %s/i\n' "$#")
sed -i "${args[#]}" "$mesa_inlist"
}
Now you can replace ...
sed -i \
-e "s/^\([[:blank:]]*photo_interval\).*/\1 = 1000/i" \
-e "s/^\([[:blank:]]*profile_interval\).*/\1 = 1/i" \
-e "s/^\([[:blank:]]*history_interval\).*/\1 = 1/i" \
-e "s/^\([[:blank:]]*terminal_interval\).*/\1 = 4000/i" \
-e "s/^\([[:blank:]]*max_num_profile_models\).*/\1 = -1/i" \
-e "s/^\([[:blank:]]*RSP_max_num_periods\).*/\1 = $max_num_periods_2/i" \
"$mesa_inlist"
... by ...
sedi \
photo_interval 1000 \
profile_interval 1 \
history_interval 1 \
terminal_interval 4000 \
max_num_profile_models -1 \
RSP_max_num_periods "$max_num_periods_2"
... and so on for the other sed commands.