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NcGen.py
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import numpy as np
import netCDF4 as nc
import os
import XsecConvert as XC
# Converts .xsec files into .npy files, and then creates a .nc
# for use in corr-k and SOCRATES/ATMO
def NcCreate(filename,mass,homedir,absdir,datadir,xsecfolder,npyfolder,npoints_P=40,npoints_T=20):
files_all=os.listdir(xsecfolder)
files=[]
count=0
for file_ in files_all:
fname, ext=os.path.splitext(file_)
if file_.endswith('.xsec'):
fnamenpy=fname+'.npy'
count+=1
if not os.path.isfile(npyfolder+fnamenpy):
print(count,'Converting {0} to .npy format.'.format(file_))
XC.Convert(xsecfolder,file_,mass,savedir=npyfolder)
# File format is wavenumber (cm-1) and absorption coeff (m^2/kg)
print('Getting list of .npy files')
files_npy=os.listdir(npyfolder)
temp_list=[]
pressure_list=[]
abscoeff_list=[]
fname_list=[]
count=0
for file_ in files_npy:
count+=1
print(count, 'Loading ',file_)
fname,ext=os.path.splitext(file_)
fname=fname.split('_')
temp=float(fname[2])
pressure=float(fname[3])
temp_list.append(temp)
pressure_list.append(pressure)
fname_list.append(file_)
#abscoeff_list.append(absc)
temp_list=np.array(temp_list)
pressure_list=np.array(pressure_list)
fname_list=np.array(fname_list)
abscoeff_list=np.array(abscoeff_list)
idx_P=np.argsort(pressure_list)
temp_list=temp_list[idx_P]
pressure_list=pressure_list[idx_P]
#abscoeff_list=abscoeff_list[idx_P]
fname_list=fname_list[idx_P]
temp_ss=[]
pressure_ss=[]
fname_ss=[]
filenp=np.load(npyfolder+fname_list[0])
nu, absc = filenp[0]*100,filenp[1] # m^{-1}, m^2/kg
proper_nu_length=len(nu)
del filenp
del nu
del absc
for pressure in np.unique(pressure_list):
# List of pressure indices
idx=np.where(pressure_list == pressure)
#print(idx)
temp_slice=temp_list[idx]
if (npoints_T - len(temp_slice)) > 1:
print('{0:.3e} Bar is missing {1} points, skipping.'.format(pressure,40-len(temp_slice)))
continue
elif (npoints_T - len(temp_slice)) ==1:
print('{0:.3e} Bar is missing {1} point, skipping.'.format(pressure,40-len(temp_slice)))
continue
#print('{0:.3e} Bar has all {1} points, adding to the .nc.'.format(pressure,len(temp_slice)))
fname_slice=fname_list[idx]
idx_t=np.argsort(temp_slice)
temp_slice=temp_slice[idx_t]
fname_slice=fname_slice[idx_t]
#print(pressure,len(temp_slice),len(abs_slice),len(abs_slice[0]))
for i in range(len(temp_slice)):
pressure_ss.append(pressure)
temp_ss.append(temp_slice[i])
fname_ss.append(fname_slice[i])
pressure_ss=np.array(pressure_ss)
temp_ss=np.array(temp_ss)
fname_ss=np.array(fname_ss)
#Okay, so they're all in .npy format for easy access, now what?
# Let's make a .nc file for them!
fnc=nc.Dataset(absdir+filename,'w')
scalar_dim=fnc.createDimension('scalar',1)
nu_dim=fnc.createDimension('nu',proper_nu_length)
pt_pair_dim=fnc.createDimension('pt_pair',len(temp_ss))
nu_var=fnc.createVariable('nu','f8',('nu',))
kabs=fnc.createVariable('kabs','f4',('pt_pair','nu',))
t_calc= fnc.createVariable('t_calc','f8',('pt_pair',))
p_calc= fnc.createVariable('p_calc','f8',('pt_pair',))
filenp=np.load(npyfolder+fname_ss[0])
nu, absc = filenp[0]*100,filenp[1] # m^{-1}, m^2/kg
del filenp
nu_var[:]=nu
nu_var.step=abs(nu[1]-nu[0])
print(nu_var.step)
#nu_var.step=0.1
#nu_var.step=10.0 # Equivalent to 0.1 in cm-1
# Number of PT points
PTnum=npoints_P*npoints_T
print('Loading .npy files and placing into .nc file.')
for i in range(0,len(pressure_ss)):
print(i,PTnum,fname_ss[i])
filenp=np.load(npyfolder+fname_ss[i])
nu, absc = filenp[0]*100,filenp[1] # m^{-1}, m^2/kg
t_calc[i]=temp_ss[i]
p_calc[i]=pressure_ss[i]*1e5 # Bar to Pa
#for j in range(1,len(abs_ss[i])):
# kabs[i,j]=abs_ss[i][j]
#print(i,pressure_ss[i])
kabs[i,:] = absc
fnc.close()
print('File written to: {0}'.format(absdir+filename))
return None
################ End of Functions
################ Beginning of work area
import shutil
homedir='/home/dc-ridg1/data/Exocross/'
absdir='/home/dc-ridg1/AbsCoeffs/'
datadir='/data/dp015/dc-ridg1/NewSpecies/AbsCoeffs/AlO/'
AlCount=[26,27,27,27]
OCount=[16,16,17,18]
# https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl
# in Da
masses=[41.981807, # 26Al-16O
42.976454, # 27Al-16O
43.980671, # 27Al-17O
44.980700] # 27Al-18O
Da_kg=1.660539e-27
masses=(np.array(masses))*Da_kg
for i in range(0,len(masses)):
Al=AlCount[i]
O=OCount[i]
xsecfolder=homedir+'Results/AlO_ATP/{0}Al-{1}O/'.format(Al,O)
npyfolder=homedir+'npys/AlO_ATP/{0}Al-{1}O/'.format(Al,O)
filename='abs_coeff_{0}Al-{1}O_ATP_pt800.nc'.format(Al,O)
NcCreate(filename,masses[i],homedir,absdir,datadir,xsecfolder,npyfolder,npoints_P=40,npoints_T=20)
shutil.copy(absdir+filename,datadir+filename)