header.append("det_cov_matrix")
header.append("log_emittance")
print ",".join(header)
step = 100 #Only calculate once all particles are present.
in_loop = True
while in_loop is True:
output = []
sum_covariance_matrix = MyEditableCovarianceMatrix()
mean_phase_volume=Phase6DVolume(mass=mass_of_macroparticle)
with open(args.list_of_directories) as f:
initialized = False
for directory in f:
directory = directory.rstrip()
if not initialized:
cosy_output = CosyOutput()
cosy_output.injectFile(os.path.join(directory,"screen.txt"))
row_numbers = cosy_output.getRowNumbersWithKeyValuePair("step number",step,comparison = 'eq')
if row_numbers == []:
in_loop = False
break
time = float(cosy_output.returnTableValue("time",row_numbers[0]))
output.append(time)
initialized = True
phase_volume = Phase6DVolume()
for filename in os.listdir(directory):
if filename.startswith(str(step)+"-x-") and filename.endswith(".txt"):
phase_volume.injectFile(os.path.join(directory,filename),mass=mass_of_macroparticle)
sum_covariance_matrix.cov_matrix += phase_volume.getCovarianceMatrix().cov_matrix
x_mean = Cartesian3DVector(x=scaling_factor_for_x_mean*phase_volume.getMean(["x"]),y=scaling_factor_for_x_mean*phase_volume.getMean(["y"]),z=scaling_factor_for_x_mean*phase_volume.getMean(["z"]))
#print x_mean
p_mean = Cartesian3DVector(x=scaling_factor_for_p_mean*phase_volume.getMean(["px"]),y=scaling_factor_for_p_mean*phase_volume.getMean(["py"]),z=phase_volume.getMean(["pz"]))
type=int,
help="The number of electrons per macroparticle for the simulation. This defaults to 100 unless specified.",
default=100,
)
args = parser.parse_args()
mass_of_electron = constants.physical_constants["electron mass energy equivalent in MeV"][0]
mass_of_macroparticle = args.number_of_electrons_per_macroparticle * mass_of_electron
print "Ne,ex,ez,Fa"
with open(args.list_of_directories) as f:
for line in f:
line = line.rstrip()
output = []
folder_metadata = parse_folder_for_metadata(line)
cosy_output = CosyOutput()
cosy_output.injectFile(os.path.join(line, "2-Cosy/screen.txt"))
row_numbers = cosy_output.getRowNumbersWithKeyValuePair("time", 120e-12, comparison="gt")
if row_numbers == []:
continue
step = int(cosy_output.returnTableValue("step number", row_numbers[0]))
number_of_macroparticles = int(cosy_output.returnTableValue("number macroparticles", row_numbers[0]))
number_of_electrons = number_of_macroparticles * args.number_of_electrons_per_macroparticle
files = []
for filename in os.listdir(os.path.join(line, "2-Cosy")):
if filename.startswith(str(step) + "-x"):
files.append(os.path.join(line, "2-Cosy/" + filename))
simulation_output = SimulationOutput()
for path in files:
simulation_output.injectFile(path)
simulation_output.convertCoordinatesToBetterUnits(mass_of_macroparticle)
simulation_output = simulation_output.boostCoordinates("z")
import sys
import os
import argparse
from scipy import constants
import numpy
from folder_convention import parse_folder_for_metadata
from cosy_output import CosyOutput
parser = argparse.ArgumentParser(description='Write the two columns for the velocity data: z,v/c')
parser.add_argument('screen_file', type=str, help='The path screen.txt are stored.')
parser.add_argument('-m','--number_of_electron_per_macroparticle', dest="number_of_electrons_per_macroparticle", type=int, help='The number of electrons per macroparticle for the simulation. This defaults to 100 unless specified.', default=100)
args = parser.parse_args()
print "z,std_z";
mass_of_electron = constants.physical_constants["electron mass energy equivalent in MeV"][0]
mass_of_macroparticle = args.number_of_electrons_per_macroparticle*mass_of_electron
z_conv = 10**3;
std_z_conv = 10**6;
cosy_output = CosyOutput()
cosy_output.injectFile(args.screen_file)
#cosy_output.addGammaField(mass_of_macroparticle)
for row in cosy_output.rows:
output = []
lorentz_gamma = numpy.sqrt(1 + (row.getCellWithFieldname("p_z").getValue()/mass_of_macroparticle)**2)
output.append(str(row.getCellWithFieldname("z").getValue()*z_conv))
output.append(str(row.getCellWithFieldname("std_z").getValue()*std_z_conv/lorentz_gamma))
print ",".join(output)
