c = open('/compile.py','w')

c = open('/home/guest/someproj/compile.py','w')

c = open('compile.py','w')

 
import os
import shutil

beginh=0 
beginm=0 
begink=0 
beginrep=0

hr=5 # h 
mr=5 # death increment due to foraging
kr=5 # perturbation max and min range difference
seeds=10 #random seed

#it is handy to create string variables with the names of your files, so that you only need to change them in one place in the script

cpp_name = 'JStalin.cpp'
directory_name = 'JStalin'
myprogram = 'JStalin'

for h in range(beginh, beginh+hr):
    if h == 0:
       d = 200
    if h == 1:
       d = 400
    if h == 2:
       d = 600
    if h == 3:
       d = 800
    if h == 4:
       d = 1000
    for m in range(beginm, beginm+mr):
        if m == 0:
           df = 0
        if m == 1:
           df = 0.04
        if m == 2:
           df = 0.08
        if m == 3:
           df = 0.12
        if m == 4:
           df = 0.16
        for k in range(begink, begink+kr):
            if k == 0:
                fp = 2
            if k == 1:
                fp = 4
            if k == 2:
                fp = 6
            if k == 3:
                fp = 8
            if k == 4:
                fp = 10
            for s in range(beginrep, beginrep+seeds):
	    	dirName = directory_name+'_h_'+ str(d) + '_df_' + str(df) + '_fp_' + str(fp) + '_s_' + str(s+1) 
		#if directory is not there yet, create it    
                os.mkdir(dirName)

		#copy necessary files    
		shutil.copyfile('random.h',dirName+'/random.h')
		shutil.copyfile('SocialColony.h',dirName+'/SocialColony.h')
		shutil.copyfile('SocialPopulation.h',dirName+'/SocialPopulation.h')
		shutil.copyfile('Individual.h',dirName+'/Individual.h')
		shutil.copyfile(cpp_name, dirName + '/' + cpp_name)   

		#change to the subdirectory
                os.chdir(dirName)

		#compile within subdirectory, creating the executable within subdirectory 
		os.popen('g++ -g ' + cpp_name + ' -o ' + myprogram)
		#change back to higher directory 
		os.chdir('../')
		#make job description files (handy if they have a keyword that distinguishes them, like 'job')
		job_name='job_' + myprogram +'_h_'+ str(d) + '_df_' + str(df) + '_fp_' + str(fp) + '_s_' + str(s+1) 
		f=open(job_name,'w')
		f.write('#PBS -N'+' job_' + myprogram +'_h_'+ str(d) + '_df_' + str(df) + '_fp_' + str(fp) + '_s_' + str(s+1)+'\n')
		f.write('#PBS -l walltime=100:00:00\n')
		f.write('#PBS -l ncpus=2\n')
		f.write('#PBS -j oe\n')
		f.write('cd aFoodPerturbation'+ dirName+ '\n')
		f.write('./' + myprogram + ' ' + str(d) + ' '+ str(df) + ' ' + str(fp) + ' ' + str(s+1) + '\n')
							
		f.close