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cosolver/python_scripts/gbms_collisions_input.py
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gbms_collisions_input.py
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#!/usr/bin/env python
# generates *.h5 files as input for molix
import os
import sys
import h5py as h5
if len(sys.argv) == 2:
cwd = sys.argv[1]
# define file names (default values)
eicolls_filename = 'ei.h5'
iecolls_filename = 'ie.h5'
eecolls_filename = 'self.h5'
iicolls_filename = 'self.h5'
# define output filename
out_filename = 'collisions.h5'
elif len(sys.argv) == 7:
cwd = sys.argv[1]
eicolls_filename = sys.argv[2]
iecolls_filename = sys.argv[3]
eecolls_filename = sys.argv[4]
iicolls_filename = sys.argv[5]
out_filename = sys.argv[6]
else:
print('You need to include a path to the directory, or to write it manualy in this script')
exit(2)
# Define directories
# cwd = os.getcwd()
#cwd = ''
# Where to find the cosolver *.h5 files
#cosolver_dir = os.path.join(cwd, 'self.h5')
#cosolver_dir = cwd
# Define size of matrices (all matrices are assumed to have the same size)
Pmaxi = 16
Jmaxi = 8
Pmaxe = 16
Jmaxe = 8
eicolls_file = os.path.join(cwd, eicolls_filename)
iecolls_file = os.path.join(cwd, iecolls_filename)
eecolls_file = os.path.join( cwd, eecolls_filename)
iicolls_file = os.path.join( cwd, iicolls_filename)
# Define output filename
outputfilename = os.path.join( cwd, out_filename)
# Open the h5 files in read mode
eih5 = h5.File(eicolls_file, 'r')
ieh5 = h5.File(iecolls_file, 'r')
eeh5 = h5.File(eecolls_file, 'r')
iih5 = h5.File(iicolls_file, 'r')
#selfh5 = h5.File(selfcolls_file, 'r')
#selfeeh5 = h5.File( selfeecolls_file, 'r')
# Create ouput file
outh5 = h5.File(outputfilename, 'w')
# Flush ei/ie/ee/ii collisions to output h5 file
dst_CeipjF = outh5.create_dataset("/00000/Ceipj/CeipjF", data = eih5['/Ceipj/CeipjF'])
dst_CeipjF.attrs['Pmaxe'] = Pmaxe
dst_CeipjF.attrs['Jmaxe'] = Jmaxe
dst_CeipjT = outh5.create_dataset("/00000/Ceipj/CeipjT", data = eih5['/Ceipj/CeipjT'])
dst_CeipjT.attrs['Jmaxe'] = Jmaxe
dst_CeipjT.attrs['Pmaxe'] = Pmaxe
outh5.create_dataset("/00000/Ceipj/fort.90", data = eih5['/files/fort.90'])
dst_CiepjF = outh5.create_dataset("/00000/Ciepj/CiepjF", data = ieh5['/Ciepj/CiepjF'])
dst_CiepjF.attrs['Pmaxi'] = Pmaxi
dst_CiepjF.attrs['Jmaxi'] = Jmaxi
dst_CiepjT = outh5.create_dataset("/00000/Ciepj/CiepjT", data = ieh5['/Ciepj/CiepjT'])
dst_CiepjT.attrs['Pmaxi'] = Pmaxi
dst_CiepjT.attrs['Jmaxi'] = Jmaxi
outh5.create_dataset("/00000/Ciepj/fort.90", data = ieh5['/files/fort.90'])
dst_Cii = outh5.create_dataset("/00000/Ciipj", data = iih5['/Caapj/Ciipj'])
dst_Cii.attrs['Pmaxi'] = Pmaxi
dst_Cii.attrs['Jmaxi'] = Jmaxi
outh5.create_dataset("/00000/Cii/fort.90", data = iih5['/files/fort.90'])
dst_Cee= outh5.create_dataset("/00000/Ceepj", data = eeh5['/Caapj/Ceepj'])
#dst_Cee= outh5.create_dataset("/00000/Ceepj", data = selfh5['/Caapj/Ceepj'])
dst_Cee.attrs['Pmaxe'] = Pmaxe
dst_Cee.attrs['Jmaxe'] = Jmaxe
outh5.create_dataset("/00000/Cee/fort.90", data = eeh5['/files/fort.90'])
outh5.create_dataset("/dims_i", data = [Pmaxi, Jmaxi])
outh5.create_dataset("/dims_e", data = [Pmaxe, Jmaxe])
# Set to 0 for DK collision operators
outh5.create_dataset("/coordkperp" , data = [0])
# Close file
outh5.close()
print('Created ' + outputfilename)
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