#!/bin/bash
# this script makes directories for all the one-parameter runs and 
# soft links the source code and executable and copies over 
# the namelist.input for CM1

cd /raid00/annareli/cm1_output/OLYMPEX_20151113_ideal/mp_param_runs/one-time/runs/one-param_morePRs 

# Create each directory first
var1=1
while [ $var1 -le 60 ]
do

cd  /raid00/annareli/cm1_output/OLYMPEX_20151113_ideal/mp_param_runs/one-time/runs/one-param_morePRs

   mkdir 1p-run_PRs_$var1
   cd 1p-run_PRs_$var1
    ln -sf /home/annareli/MODEL/cm1r17_2Xdom_shift_hh1km_WR+SDEP+morePRs/include ./include
    ln -sf /home/annareli/MODEL/cm1r17_2Xdom_shift_hh1km_WR+SDEP+morePRs/src ./src
   
   mkdir run 
   cd run 
    ln -sf /home/annareli/MODEL/cm1r17_2Xdom_shift_hh1km_WR+SDEP+morePRs/run/LANDUSE.TBL ./LANDUSE.TBL
    ln -sf /home/annareli/MODEL/cm1r17_2Xdom_shift_hh1km_WR+SDEP+morePRs/run/cm1.exe ./cm1.exe
    cp /raid00/annareli/cm1_output/OLYMPEX_20151113_ideal/mp_param_runs/one-time/paramlist/one-param_withPRs/namelist.input .     
    cp /raid00/annareli/cm1_output/OLYMPEX_20151113_ideal/mp_param_runs/one-time/paramlist/one-param_withPRs/paramlist.input_$var1 .
    mv paramlist.input_$var1 paramlist.input
   
    /usr/local/openmpi/bin/mpirun -np 14 ./cm1.exe >& cm1.print.out 
 
echo $var1

let var1=$var1+1
done