import sys
import os
import argparse
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.', default=None)
args = parser.parse_args()
print "z,v/c";
with open(args.list_of_directories) as f:
for line in f:
line = line.rstrip()
output =[]
folder_metadata = parse_folder_for_metadata(line)
output.append(folder_metadata["total_electrons"])
cosy_output = CosyOutput()
cosy_output.injectScreenFile(os.path.join(line,"2-Cosy/screen.txt"))
row_numbers = cosy_output.returnRowNumbersWithKeyValuePair("time",120e-12,comparison = 'gt')
if row_numbers == []:
continue
output.append(str(100 * int(cosy_output.returnTableValue("number macroparticles",row_numbers[0]))))
output.append(folder_metadata["applied_field"])
print ",".join(output)
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"]))
#print p_mean
mean_phase_volume.addParticle(mean_phase_volume.mass,x=x_mean,p=p_mean)
sum_covariance_matrix.cov_matrix = sum_covariance_matrix.cov_matrix/len(mean_phase_volume)
#sum_covariance_matrix.printCovarianceMatrix()
det_cov_matrix = sum_covariance_matrix.getSubDeterminant()
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")
ex = simulation_output.calcEmittance("x") / args.number_of_electrons_per_macroparticle
ez = simulation_output.calcEmittance("z") / args.number_of_electrons_per_macroparticle
if ex == 0 or ez == 0:
continue
parser.add_argument('-r','--run_template', dest="run_template", type=str, help='The template with the qsub script.',default="/mnt/home/zerbe/src/tem_simulations/2-Cosy/run_120ps.template")
parser.add_argument('-f','--positive_hole_files_dir', dest="pos_dir", type=str, help='The directory where the files are stored describing the positive hole geometry.',default="/mnt/home/zerbe/src/tem_simulations/2-Cosy/Files")
parser.add_argument('-b','--bin_file', dest="bin_file", type=str, help='The path to the cosy binary.',default="/mnt/home/zerbe/src/tem_simulations/2-Cosy/cosy.bin")
args = parser.parse_args()
parameter_set_list = ParameterSetList()
parameter_set_list.injectParametersFromCsv(args.filepath)
for parameter_set in parameter_set_list.list:
parameter_set.createMainOutputPath(args.working_dir)
parameter_set.createStepnamePath("Cosy")
#Idenfity step number to begin from.
screen_file = os.path.join(parameter_set.returnStepnamePath("Cosy"),"screen.txt")
cosy_output = CosyOutput()
cosy_output.injectScreenFile(screen_file)
last_step = cosy_output.returnTableValue("step number")
parameter_set.step_to_continue_from = int((floor(float(last_step)/float(10))-1)*10)
#Create output dir
continue_dir = os.path.join(parameter_set.returnStepnamePath("Cosy"),"continue_from_" + str(parameter_set.step_to_continue_from))
if not os.path.exists(continue_dir) or not os.path.isdir(continue_dir):
os.mkdir(continue_dir)
#Grab the correct step's files for new initial conditions file.
parameter_set.initial_conditions_file = os.path.join(continue_dir,"InitCondition_from_" + str(parameter_set.step_to_continue_from) + ".txt")
make_continuing_initial_condition_file(parameter_set.returnStepnamePath("Cosy"),parameter_set.step_to_continue_from, parameter_set.initial_conditions_file)
#Edit existing PE-setup.txt file.
relevant_row_numbers = cosy_output.returnRowNumbersWithKeyValuePair("step number",str(parameter_set.step_to_continue_from))
parameter_set.time_to_continue_from = cosy_output.returnTableValue("time",row_number=relevant_row_numbers[0])
parameter_set.total_particles_generated = cosy_output.returnTableValue("number macroparticles",row_number=relevant_row_numbers[0])
