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para_e2_decomp_1d.py
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#
# extracting forward and backward components of e2. suitable for 1D data
#
# FST, (c) 2019 Regents of The University of California
#
import sys
sys.path.append('/Users/franktsung/Documents/codes/python-tsung/')
sys.path.append('/Volumes/Lacie-5TB/codes/pyVisOS/')
import osh5io
import osh5def
import osh5vis
import osh5utils
from h5_utilities import *
import matplotlib.pyplot as plt
import sys
import getopt
import glob
import numpy as np
from mpi4py import MPI
def print_help():
print('python para_e2_decomp.py [options] <InputDir> <OutputDir>')
print('InputDir - Location of the MS folder')
print('OutputDir - Location of the output folder, makes 2 files for e2+ and e2-')
print('options:')
print(' -n: plasma density (needed to calculate epsilon)')
print(' --avg: look into the -savg directory')
print(' --env: look into the -senv directory')
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
argc = len(sys.argv)
try:
opts, args = getopt.gnu_getopt(sys.argv[1:], "hxyn:", ['avg', 'env'])
except getopt.GetoptError:
print_help()
sys.exit(2)
if len(args) < 2:
print_help()
sys.exit(2)
dirName = args[0]
outDir = args[1]
dir_ext = ''
density = 0.1
for opt, arg in opts:
if opt == '-h':
print_help()
sys.exit()
elif opt == '--avg':
dir_ext = '-savg'
elif opt == '--env':
dir_ext = '-senv'
elif opt == '-n':
density = float(arg)
else:
print(print_help())
sys.exit(2)
index_of_refraction = np.sqrt(1-density)
v_phase = 1/index_of_refraction
print( repr(index_of_refraction)+' , '+repr(v_phase) )
e2 = sorted(glob.glob(dirName + '/FLD/e2' + dir_ext + '/*.h5'))
e3 = sorted(glob.glob(dirName + '/FLD/e3' + dir_ext + '/*.h5'))
b2 = sorted(glob.glob(dirName + '/FLD/b2' + dir_ext + '/*.h5'))
b3 = sorted(glob.glob(dirName + '/FLD/b3' + dir_ext + '/*.h5'))
total_time = len(e2)
my_share = total_time // size
i_begin = rank * my_share
if rank < (size - 1):
i_end = (rank + 1) * my_share
else:
i_end = total_time
part = total_time / size
#
# read the second file to get the time-step
#
h5_filename = e2[1]
h5_data = osh5io.read_h5(h5_filename)
array_dims = h5_data.shape
nx = array_dims[0]
# ny = array_dims[1]
time_step = h5_data.run_attrs['TIME'][0]
# h5_output = hdf_data()
# h5_output.shape = [total_time, nx]
print('nx=' + repr(nx))
# print('ny=' + repr(ny))
print('time_step=' + repr(time_step))
print('total_time=' + repr(total_time))
e2_plus_output = np.zeros((total_time, nx))
e2_minus_output = np.zeros((total_time, nx))
total = np.zeros((total_time,nx))
#total = 0
total2 = 0
# if rank == 0:
# total = np.zeros((total_time, nx))
xaxis=h5_data.axes[1]
taxis=osh5def.DataAxis(0, time_step * (total_time -1), total_time,
attrs={'NAME':'t', 'LONG_NAME':'time', 'UNITS':'1 / \omega_p'})
data_attrs_eplus = { 'UNITS': osh5def.OSUnits('m_e^2 c \omega_p/e'), 'NAME': 'e+', 'LONG_NAME': 'e2_+' }
data_attrs_eminus = { 'UNITS': osh5def.OSUnits('m_e^2 c \omega_p/e'), 'NAME': 'e-', 'LONG_NAME': 'e2_-' }
run_attrs = {'XMAX' : np.array( [ time_step * (total_time-1),xaxis.max] ) ,
'XMIN' : np.array( [0, xaxis.min, 0] ) }
i_count = 0
file_number = 0
for file_number in range(i_begin, i_end):
e2_filename = e2[file_number]
e3_filename = e3[file_number]
b2_filename = b2[file_number]
b3_filename = b3[file_number]
if (i_count % 10 == 0 and rank == 0):
print(e2_filename)
i_count = i_count+1
e2_data = osh5io.read_h5(e2_filename)
# e3_data = osh5io.read_h5(e3_filename)
# b2_data = osh5io.read_h5(b2_filename)
b3_data = osh5io.read_h5(b3_filename)
e2_plus = (e2_data + v_phase * b3_data)/2.0
e2_minus = (e2_data - v_phase * b3_data)/2.0
# print(s1_data.shape)
e2_plus_output[file_number, 1:ny] = e2_plus[1:ny]
e2_minus_output[file_number, 1:ny] = e2_minus[1:ny]
# temp = np.sum(s1_data, axis=0) / nx
# sum up the results to node 0 and output, 2 datasets, one for +
# component abd one for the - component
# first let's do the + root
comm.Reduce(e2_plus_output, total, op=MPI.SUM, root=0)
if rank == 0:
b=osh5def.H5Data(total, timestamp='x', data_attrs=data_attrs_eplus,
run_attrs=run_attrs, axes=[taxis,xaxis])
outFilename=outDir+'/'+'e2-plus.h5'
osh5io.write_h5(b,filename=outFilename)
# now let's do the - component
comm.Reduce(e2_minus_output, total, op=MPI.SUM, root=0)
if rank == 0:
b=osh5def.H5Data(total, timestamp='x', data_attrs=data_attrs_eminus,
run_attrs=run_attrs, axes=[taxis,xaxis])
outFilename=outDir+'/'+'e2-minus.h5'
osh5io.write_h5(b,filename=outFilename)
# write_hdf(h5_output, outFilename)
print('Before barrier'+repr(rank))
comm.barrier()
# comm.Reduce(income, total, op=MPI.SUM, root=0)
# if rank == 0:
# h5_output.data = total
# newName = outFilename.rsplit('.', 1)[0] + '-x-n' + str(n_avg) + '.h5'
# write_hdf(h5_output, newName)
# comm.barrier()
# comm.Reduce(h5_output2.data, total2, op=MPI.SUM, root=0)
# if rank == 0:
# h5_output2.data = total2
# write_hdf(h5_output2, outFilename)
# comm.barrier()
# comm.Reduce(income2, total2, op=MPI.SUM, root=0)
# if rank == 0:
# h5_output2.data = total2
# newName = outFilename.rsplit('.', 1)[0] + '-y-n' + str(n_avg) + '.h5'
# write_hdf(h5_output2, newName)