automate_radmc3d.py

import os
import sys
import numpy as np 
import scipy as sp



line_list = ['CO_J10',
'NeII_12mu',
'NeIII_3869A',
'NeV_3426A',
'NII_122mu',
'OI_145mu',
'OI_63mu',
'OIII_88mu',
'SII_6716A',
'SIII_18mu',
'CII_158mu',
'H2_S1',
'NeIII_15mu',
'NeV_14mu',
'NeVI_7mu',
'NII_6548A',
'OI_6300A',
'OIII_5007A',
'OIV_25mu',
'SII_6731A']


for line in line_list:
    #line_name = input('Please provide the linename with wavelength (eg, CII_158mu etc):\n')

    line_name = line
    print('Line name = ', line_name)
    underscore_index = line_name.rindex('_')
    species = line_name[:underscore_index]
    
    
    print('Species = ', species)
    
    print('We are now in directory:')
    os.system('pwd')
    os.system('mkdir '+line_name)
    
    os.chdir(line_name)
    
    print('We are now in directory:')
    os.system('pwd')
    
    
    #data_dir = input('Please provide the RIC output directory WITH the last \'/\':\n')
    #data_dir = '\''+ data_dir + '\''
    data_dir = '/mnt/home/nroy/galaxy-mock-obs-pipeline/rt-pipeline-tools/run/subtract_com_velocity/A4_33000_snum151/3kpc/'
    
    common_files_dir = '/mnt/home/nroy/galaxy-mock-obs-pipeline/radmc3d-2.0/run/CommonFilesForAllLines/'
    line_data_directory = '/mnt/home/nroy/galaxy-mock-obs-pipeline/rt-pipeline-tools/common_data_files/'
    
    source_file = ['amr_grid.inp', 
            'cell_volume_kpc3.dat',
            'dust_density.binp',
            'dustkappa_graphite.inp',
            'dustkappa_silicate.inp',
            'dustopac.inp',
            'dust_temperature_zero.dat',
            'gas_nHtot_'+ species +'.binp',
            'gas_temperature_'+ species +'.binp',
            'gas_velocity_'+ species +'.binp',
            species +'/lines.inp',
            'microturbulence.binp',
            species +'/molecule_'+ species +'.inp',
            'numberdens_'+ species +'.binp',
            'numberdens_elec.binp',
            'numberdens_HI.binp',
            'numberdens_HII.binp',
            'numberdens_oH2.binp',
            'numberdens_pH2.binp',
            'stellarsrc_density.binp',
            'stellarsrc_templates.inp',
            'wavelength_micron.inp']
    
    destination_file = ['amr_grid.inp', 
            'cell_volume_kpc3.dat', 
            'dust_density.binp', 
            'dustkappa_graphite.inp',
            'dustkappa_silicate.inp',
            'dustopac.inp',
            'dust_temperature_zero.dat',
            'gas_nHtot.binp',
            'gas_temperature.binp',
            'gas_velocity.binp',
            'lines.inp',
            'microturbulence.binp',
            'molecule_'+species+'.inp',
            'numberdens_'+species+'.binp',
            'numberdens_elec.binp',
            'numberdens_HI.binp',
            'numberdens_HII.binp',
            'numberdens_oH2.binp',
            'numberdens_pH2.binp',
            'stellarsrc_density.binp',
            'stellarsrc_templates.inp',
            'wavelength_micron.inp']
    
    for i in range(np.size(source_file)):
    
        if ( (destination_file[i] == 'dustkappa_graphite.inp') or 
                (destination_file[i] == 'dustkappa_silicate.inp') or 
                (destination_file[i] == 'dustopac.inp') or 
                (destination_file[i] == 'lines.inp') or 
                (destination_file[i] == 'wavelength_micron.inp') ):
            command = 'ln -s ' + line_data_directory + source_file[i] + ' ' + destination_file[i]
        elif ( destination_file[i] == 'molecule_'+species+'.inp' ):
            command = 'ln -s ' + line_data_directory + '/'+ source_file[i] + ' ' + destination_file[i]
        else:
            command = 'ln -s '+ data_dir  + source_file[i] + ' ' + destination_file[i]
     
        os.system(command)
    
    os.system('cp '+common_files_dir+'* .')
    print('\n\nNecessary files symbolically linked to the {} folder...\n\n'.format(line_name))
    
    #Changing the line_label paramter in the run.param file 
    fin = open(common_files_dir+'run.param','rt')
    fout = open('run.param','wt')
    for line in fin:
        fout.write(line.replace('line_label                  CII_158mu', 'line_label                  '+line_name)) 
    fout.close()
    fin.close()
    
    
    
    #Changing the job name in the job.sh file to avoid confusion
    job_in = open(common_files_dir+'job.sh','rt')
    job_out = open('job.sh','wt')
    
    for line in job_in:
        job_out.write(line.replace('#SBATCH --job-name=\"TEST\"', '#SBATCH --job-name='+'\"'+line_name+'\"'))
    job_in.close()
    job_out.close()


    os.system('sbatch job.sh')
    print('Job submitted for {}'.format(line_name))

    os.chdir('..')