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cosolver/python_scripts/gkcoulomb_ii.py
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gkcoulomb_ii.py
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#!/usr/bin/env python
# This scripts compute the GK Coulomb collision operator from the COSOlver output files
# Performs the summation over the last indices, i.e. (p,j,m,n,np) -> (p,j)
# Writes the results matrices
import numpy as np
import os
import sys
import h5py as h5
# Define directories
cwd = os.getcwd()
cwd = '/misc/bjfrei/cosolver_marconi/gk.coulomb.TEM.kperp.1.18.m.4.NFLR.8.ee'
print('Create GK Coulomb from ' + cwd)
# Define h5 files
selfcolls_file = os.path.join( cwd, 'self.h5')
# Defines new h5 files
selfcolls_file_out = os.path.join( cwd, 'self.pj.h5')
############################################################
# Self collisions
print('Self collisions....')
# Open file
selfh5 = h5.File(selfcolls_file, 'r')
selfh5_out = h5.File(selfcolls_file_out, 'w')
# Ion-ion
# get dimension
Pmaxi = selfh5['/Caapj/Ciipjpjnn'].attrs['Pmaxi']
Jmaxi = selfh5['/Caapj/Ciipjpjnn'].attrs['Jmaxi']
def numb(pp,jj):
lbari = (Jmaxi +1)*pp + jj +1
return lbari
# Get 4 dim rows
rows_4dim= selfh5['/Caapj/rows_i']
# Get Cippj
Cpj_4dim=selfh5['/Caapj/Ciipjpjnn']
#Cpj_4dim
Cpj = np.zeros((numb(Pmaxi,Jmaxi), numb(Pmaxi,Jmaxi)))
for irow in np.arange(1, numb(Pmaxi,Jmaxi)+1,1):
idx_of_row, = np.where(rows_4dim[0,:] == irow)
Cpj_ = Cpj_4dim[:, idx_of_row]
Cpj[irow-1,:] = np.sum(Cpj_,axis = 1, initial = 0)
# Create output
Cpj_dst = selfh5_out.create_dataset("/Caapj/Ciipj", data = Cpj)
Cpj_dst.attrs['Pmaxi'] = Pmaxi
Cpj_dst.attrs['Jmaxi'] = Jmaxi
Cpj_dst.attrs['kperp'] = selfh5['/Caapj/Ceepjpjnn'].attrs['kperp']
selfh5_out.create_dataset("/files/fort.90", data = selfh5['/files/fort.90'])
# close file
selfh5_out.close()
selfh5.close()
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