JobSubmit-Clean.py

import os
import numpy as np
import InpWrite as InpW
import time
import subprocess

# Counts the number of active jobs
def JobCount(user='dc-ridg1'):
    var = os.popen('qstat -u {0} > test_count.txt ; grep -rnc "./test_count.txt" -e "{0}"'.format(user)).read()
    #os.popen('rm test_count.txt')
    return int(var)

# Generates a list of PT points
def PTGen(numP,numT,Ps,Ts):
    P=np.logspace(np.log10(Ps[0]),np.log10(Ps[1]),num=numP)  # in Bar
    T=np.logspace(np.log10(Ts[0]),np.log10(Ts[1]),num=numT)  # in Kelvin
    PT_idx=[]
    PTPairs=[[],[]]
    count=0
    for pressure in P:
        for temp in T:
            PT_idx.append(count)
            count+=1
            PTPairs[0].append(pressure)
            PTPairs[1].append(temp)
    return PT_idx,PTPairs

def ptRead(filename):
    f=open(filename,'r')
    lines=f.readlines()
    f.close()
    count=0
    pressure=[]
    temperature=[]
    for line in lines:
        line=line.rstrip()
        line=line.split(' ')
        for i in range(0,len(line)):
            p=float(line[0].replace("D","E"))
            
            pressure.append(np.float64(line[0]))
            temperature.append(np.float64(line[i]))

# Submits jobs (assuming DiRaC)
def QSubmit(input_file,species,idx):
    line=['qsub submit_job.pbs -v param_file={0} -N AbsCoeff_{1}_{2}'.format(input_file,species,idx)]
    os.popen(line[0])
    return None


# Creates a list of .inp files for use with Exocross
def InpCreate(species, PTidx,PTPairs,npoints,range_,broadeners,offset=25,note=''):
    # Create .inp files
    for i in range(len(PTPairs[0])):
        pressure= PTPairs[0][i]
        temperature = PTPairs[1][i]
        print(PTidx[i],PTPairs[0][i],PTPairs[1][i])
        InpW.InpWrite(species,temperature,pressure,npoints,range_,peturbers=broadeners,offset=offset,note=note)
    return None


# Submits jobs to the queue
def JobSubmit(species,PTPairs,range_,maxJobs=100,forceRecreation=False,note=''):
    for i in range(len(PTPairs[0])):
        pressure= PTPairs[0][i]
        temperature = PTPairs[1][i]
    
        filenameInp='{0}_{1}_{2:8.7e}_{3:8.7e}_{4}_{5}{6}.inp'.format(species.molecule,species.source,temperature,pressure,range_[0],range_[1],note)
        filenameXsec='{0}_{1}_{2:8.7e}_{3:8.7e}_{4}_{5}{6}.xsec'.format(species.molecule,species.source,temperature,pressure,range_[0],range_[1],note)
        numJobs=JobCount()
        # Only submits job if file doesn't exist or recreation asked
        # Just for TiO
        xsecfolder=os.getcwd()+'/{0}/'.format(species.molecule)
        if not os.path.isfile(xsecfolder+filenameXsec) or forceRecreation:
            #print(filenameInp,species.molecule,i)
            QSubmit(filenameInp,species.molecule,i)
            time.sleep(5)
            numJobs=JobCount()
            if numJobs == 1:
                print('The {0:6.3e} Bar {1:6.3e} Kelvin Job has been submitted! {2} Job is currently submitted.'.format(pressure,temperature,numJobs))
            else:
                print('The {0:6.3e} Bar {1:6.3e} Kelvin Job has been submitted! {2} Jobs are currently submitted.'.format(pressure,temperature,numJobs))

        #Holds loop while waiting for jobs to finish
        while (numJobs >= maxJobs):
            print('Waiting for jobs to finish...',end='\r')
            time.sleep(100)
            numJobs=JobCount()
            if numJobs < maxJobs:
                print('')

    print('All jobs have been submitted for {0}!'.format(species.molecule))
    return None


###### End of Functions, work area is below
)
species=InpW.Species()
folder_trans=''
species.UpdateVars(mass=,
                   molecule='',
                   source='',
                   states='',
                   pffile ='')
species.UpdateTransitions(folder_trans)

# Empty broadener without file
broadener1=InpW.Peturber()
broadener1.UpdateVars(species=,
                       gamma=,
                       n=,
                       t0=,
                       p0=,
                       ratio =,
                       #file=,
                       #model=
                       )
broadener1.StringCreate()

# Range (cm-1)

offset=0.05
range_=[0.0005,]
npoints= # 0.1 m-1 spacing

wavenumber=np.linspace(range_[0],range_[1],num=npoints)
print('The spacing is ',np.diff(wavenumber)[0]*100, 'm-1, is this correct?',flush=True)
import time
time.sleep(5)
#broadeners=[broadener1.String]
note=''

# Number of Pressure, Temperature points
num_P=40
num_T=20

# Pressure Limits (Bar)
Pmin=1e-11
Pmax=1e3

# 1 Bar = 10^5 Pa
# 1 Pa = 10^-5 Bar
# Matches Davids PT800 file
Pmin = 7.8804628e-05*1e-5 
Pmax = 1e3 # 10^8 Pa


# Temperature Limits (K)
Tmin=70
Tmax=6000


# Matches Davids PT800 file
Tmin=70
Tmax=3000 

P=[Pmin,Pmax]
T=[Tmin,Tmax]

offset=1e-06
PT_idx,PTPairs=PTGen(num_P,num_T,P,T)

# Create input .inp files
InpCreate(species, PT_idx,PTPairs,npoints,range_,broadeners,offset=offset,note=note)
# Loop for submitting jobs
forceRec=False
JobSubmit(species,PTPairs,range_,maxJobs=300,forceRecreation=forceRec,note=note)