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gbms_gk_Cabpj_input.py
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Mon, Feb 24, 10:22

gbms_gk_Cabpj_input.py
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#!/usr/bin/env python
# generates GK collision matrices for different kperp
import os
import sys
import numpy as np
import h5py as h5
# directories
cwd = os.getcwd()
scandir_name = 'gk.sugama'
scandir_path = os.path.join( cwd, scandir_name)
# Define kperp scan (should be changed manually...)
#coordkperp =
coordkperp = np.loadtxt(os.path.join( scandir_path, 'kperp.log.txt'))
# Define size of matrices (all matrices are assumed to have the same size)
Pmaxi = 20
Jmaxi = 6
Pmaxe = 20
Jmaxe = 6
# Create ouput file in the current directory
output_name = 'gk.sugama.h5'
outh5 = h5.File(os.path.join( cwd, 'gk.sugama.h5'), 'w')
outh5.create_dataset('/dims_i', data = [Pmaxi, Jmaxi])
outh5.create_dataset('/dims_e', data = [Pmaxe, Jmaxe])
outh5.create_dataset('/coordkperp', data = coordkperp)
outh5.create_dataset('/Nkperp', data= np.alen(coordkperp))
# gather
for ikperp, kperp in enumerate(coordkperp):
# scanfiles_<num> directory
job_directory= os.path.join(scandir_path, "scanfiles_"+"{0:05d}".format(ikperp))
print('Read ' + job_directory + ' ...')
# files path
eicolls_file = os.path.join( job_directory, 'ei.h5' )
iecolls_file = os.path.join( job_directory, 'ie.h5')
selfcolls_file = os.path.join( job_directory, 'self.h5')
# Open the h5 files in read mode
eih5 = h5.File(eicolls_file, 'r')
ieh5 = h5.File(iecolls_file, 'r')
selfh5 = h5.File(selfcolls_file, 'r')
# Flush Cabpj
# ei
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Ceipj/CeipjF/", data = eih5['/Ceipj/CeipjF'])
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Ceipj/CeipjT/", data = eih5['/Ceipj/CeipjT'])
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Ceipj/fort.f90", data = eih5['/files/fort.f90'])
# ie
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Ciepj/CiepjF/", data = ieh5['/Ciepj/CiepjF'])
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Ciepj/CiepjT/", data = ieh5['/Ciepj/CiepjT'])
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Ciepj/fort.f90", data = ieh5['/files/fort.f90'])
# ee
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Caapj/Ceepj", data = selfh5['/Caapj/Ciipj'])
# ii
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Caapj/Ciipj", data = selfh5['/Caapj/Ciipj'])
outh5.create_dataset( "{0:05d}".format(ikperp) + "/Caapj/fort.f90", data = selfh5['/files/fort.f90'])
eih5.close()
ieh5.close()
selfh5.close()
# close file
outh5.close()

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