def __init__(self, *file_names, do_print=False):
Configuration.__init__(self, *file_names)
#--------------------------------------------------
# problem specific initializations
if do_print:
print("Initializing gyration setup...")
#--------------------------------------------------
# particle initialization
#local variables just for easier/cleaner syntax
c = self.cfl
self.larmor = self.gamma * c**2
self.beta = sqrt(1 - 1 / self.gamma**2.)
self.vy = sqrt(self.gamma**2. - 1)
self.vy = self.beta * self.gamma
#plasma reaction & subsequent normalization
self.omp = c / self.c_omp
self.qe = -1
#--------------------------------------------------
# field initialization
self.Nx = 1
self.Ny = 1
self.Nz = 1
self.NxMesh = int(self.larmor * 2.2)
self.NyMesh = int(self.larmor * 2.2)
self.NzMesh = 1
self.dx = 1.0
self.dy = 1.0
self.dz = 1.0
self.x_start = np.floor(self.larmor * 0.1)
print(self.larmor)
print(self.NxMesh)
print(self.x_start)
#---------cold plasma-----------
self.bphi = 90.0 #Bfield z angle (bphi=0 bz, bphi=90 -> x-y plane)
self.btheta = 0.0 #Bfield x-y angle: btheta=0 -> parallel
# set external magnetic field strength
self.binit = 1.0
def parse_input():
parser = argparse.ArgumentParser()
parser.add_argument('-c',
'--conf',
dest='conf_filename',
default=None,
type=str,
help='Name of the configuration file (default: None)')
parser.add_argument(
'-l',
'--lap',
dest='lap',
default=None,
type=int,
help='Specific lap to analyze (default: all that can be found)')
parser.add_argument('-d',
'--dir',
dest='fdir',
default=None,
type=str,
help='Directory to analyze')
parser.add_argument('-v',
'--var',
dest='var',
default=None,
type=str,
help='Variable to analyze')
args = parser.parse_args()
#args = parser.parse_known_args()
if not (args.conf_filename == None):
conf = Configuration(args.conf_filename)
fdir = conf.outdir
if not (args.fdir == None):
fdir = args.fdir
#look for conf file inside dir
if args.conf_filename == None:
print("looking for Conf file inside {}".format(args.fdir))
print("TODO: not implemented")
return conf, fdir, args
plt.rc('axes', labelsize=8)
gs = plt.GridSpec(1, 2)
gs.update(hspace=0.5)
gs.update(wspace=0.07)
axs = []
axs.append(plt.subplot(gs[0]))
axs.append(plt.subplot(gs[1]))
# what to plot
ispcs = 0
vdir = "x"
prefix = 'twostream/out/'
conf = Configuration('config-twostream-relativistic.ini')
#simulation box size
xmin = 0.0
ymin = 0.0
xmax = conf.dx * conf.Nx * conf.NxMesh
ymax = conf.dy * conf.Ny * conf.NyMesh
# create panels from snapshots
laps = range(0, 4001, 1000)
for i, lap in enumerate(laps):
print(lap)
# check if this is top/bottom panel
if i == 0:
top = True
def __init__(self, *file_names, do_print=False):
Configuration.__init__(self, *file_names)
#--------------------------------------------------
# problem specific initializations
if do_print:
print("Initializing shock setup...")
#--------------------------------------------------
# particle initialization
#local variables just for easier/cleaner syntax
me = np.abs(self.me)
mi = np.abs(self.mi)
c = self.cfl
ppc = self.ppc*2.0 #multiply x2 to account for 2 species/pair plasma
# if gammas < 1, we interpret it as beta/c
if self.gamma == 0:
self.gamma = 1.0
self.beta = 0.0
else:
if(self.gamma < 1.):
self.gamma = sqrt(1./(1.-self.gamma**2.))
self.beta = sqrt(1.-1./self.gamma**2.)
#plasma reaction & subsequent normalization
omp=c/self.c_omp
self.qe = -(omp**2.*self.gamma)/((ppc*.5)*(1.+me/mi))
self.qi = -self.qe
me *= abs(self.qi)
mi *= abs(self.qi)
#temperatures
self.delgam_e = self.delgam
self.delgam_i = self.temp_ratio*self.delgam_e
#--------------------------------------------------
# printing
if do_print:
print("init: Positron thermal spread: ", self.delgam_i)
print("init: Electron thermal spread: ", self.delgam_e)
sigmaeff = self.sigma #* temperature corrections
if do_print:
print("init: Alfven (outflow) three-velocity: ",sqrt(sigmaeff/(1.+sigmaeff)))
print("init: Ion beta: ", 2.*self.delgam_i/(self.sigma*(mi/me+1.)/(mi/me)) )
print("init: Electron beta: ",2.*self.delgam_e/(self.sigma*(mi/me+1.)) )
#--------------------------------------------------
# field initialization
#---------cold plasma-----------
# parse external magnetic field strength from sigma_ext
#self.bz_ext = sqrt( (self.gamma-1.0)*.5*ppc*c**2*(mi+me)*self.sigma_ext)
#determine initial magnetic field based on magnetization sigma which
#is magnetic energy density/ kinetic energy density
#this definition works even for nonrelativistic flows.
#self.binit = sqrt((self.gamma)*ppc*.5*c**2.*(mi+me)*self.sigma)
#----------hot plasma----------
corrdelgam_qe = 1.0
corrdelgam_sig = 1.0
delgam_i = self.delgam_i
delgam_e = self.delgam_e
zeta=delgam_i/(0.24 + delgam_i)
gad_i=1./3.*(5 - 1.21937*zeta + 0.18203*zeta**2 - 0.96583*zeta**3 + 2.32513*zeta**4 - 2.39332*zeta**5 + 1.07136*zeta**6)
delgam_e=self.delgam*mi/me*self.temp_ratio
zeta=delgam_e/(0.24 + delgam_e)
gad_e=1./3.*(5 - 1.21937*zeta + 0.18203*zeta**2 - 0.96583*zeta**3 + 2.32513*zeta**4 - 2.39332*zeta**5 + 1.07136*zeta**6)
self.binit=1.*sqrt(ppc*.5*c**2.* \
(mi*(1.+corrdelgam_sig*gad_i/(gad_i-1.)*self.delgam_i)+me*(1.+ \
corrdelgam_sig*gad_e/(gad_e-1.)*self.delgam_e))*self.sigma)
if do_print:
print("init: sigma: ", self.sigma)
print("init: B_guide: ", self.binit)
#possibly moving piston wall
if(self.wallgamma < 1.):
self.wallgamma = sqrt(1./(1.-self.wallgamma**2.))
self.beta = sqrt(1.-1./self.gamma**2.)
#--------------------------------------------------
# radiation drag, if any
if "gammarad" in self.__dict__:
if not(self.gammarad == 0.0):
self.drag_amplitude = 0.1*self.binit/(self.gammarad**2.0)
if do_print:
print("using radiation drag...")
print(" drag amplitude: {} with gamma_rad: {}".format(self.drag_amplitude, self.gammarad))
else:
self.gammarad = 0.0
if "radtemp" in self.__dict__:
if not(self.radtemp == 0.0):
if do_print:
print("using radiation drag with temperature...")
print(" drag temperature: {}".format(self.radtemp))
else:
self.radtemp = 0.0
plt.rc('ytick', labelsize=8)
plt.rc('axes', labelsize=8)
gs = plt.GridSpec(1, 2)
gs.update(hspace=0.5)
gs.update(wspace=0.07)
axs = []
axs.append(plt.subplot(gs[0]))
axs.append(plt.subplot(gs[1]))
# what to plot
ispcs = 0
vdir = "x"
prefix = "../projects/tests/"
conf = Configuration(prefix + 'config-landau.ini')
#simulation box size
xmin = 0.0
ymin = 0.0
xmax = conf.dx * conf.Nx * conf.NxMesh
ymax = conf.dy * conf.Ny * conf.NyMesh
# create panels from snapshots
laps = [0, 1, 2]
for i, lap in enumerate(laps):
# check if this is top/bottom panel
if i == 0:
top = True
else:
import numpy as np
import matplotlib.pyplot as plt
import h5py
import sys, os
import matplotlib.ticker as ticker
from scipy.stats import mstats
from scipy.optimize import curve_fit
from combine_files import combine_files, combine_tiles
from configSetup import Configuration
#--------------------------------------------------
# combine multiple files
fdir = 'weibel/out/'
conf = Configuration('config-weibel.ini')
print("files...")
ex = combine_files(fdir, "field", "ex", conf)
ey = combine_files(fdir, "field", "ey", conf)
ez = combine_files(fdir, "field", "ez", conf)
bx = combine_files(fdir, "field", "bx", conf)
by = combine_files(fdir, "field", "by", conf)
bz = combine_files(fdir, "field", "bz", conf)
rho = combine_files(fdir, "field", "rho", conf)
ekin = combine_files(fdir, "analysis", "edens", conf, isp=0)
#--------------------------------------------------
# read simulation data from file
print "Ex shape:", np.shape(ex)
#Read simulation values
def flatten_spatial(arr):
return arr.reshape(arr.shape[:-3] + (-1, )).T
read_files = True
read_runf = False
#--------------------------------------------------
# read simulation data from file
#fdir = 'twostream/out/'
fdir = 'twostream_kebne/ub2/'
if read_files:
#conf = Configuration('config-twostream-relativistic.ini')
conf = Configuration(fdir + 'config-ts2.ini')
#--------------------------------------------------
print("files...")
ex_sparse = flatten_spatial(combine_files(fdir, "field", "ex", conf))
#ey_sparse = flatten_spatial( combine_files(fdir, "field", "ey", conf) )
#ez_sparse = flatten_spatial( combine_files(fdir, "field", "ez", conf) )
#bx_sparse = flatten_spatial( combine_files(fdir, "field", "bx", conf) )
#by_sparse = flatten_spatial( combine_files(fdir, "field", "by", conf) )
#bz_sparse = flatten_spatial( combine_files(fdir, "field", "bz", conf) )
rh_sparse = flatten_spatial(combine_files(fdir, "field", "rho", conf))
ed_sparse1 = flatten_spatial(
combine_files(fdir, "analysis", "edens", conf, isp=0))
ed_sparse2 = flatten_spatial(
combine_files(fdir, "analysis", "edens", conf, isp=1))
ed_sparse = ed_sparse1 + ed_sparse2
tile = f[dset][fvar][()]
tile = np.reshape(tile, (NzMesh, NyMesh, NxMesh))
for s in range(NzMesh):
for r in range(NyMesh):
for q in range(NxMesh):
arr[ii + q, jj + r, kk + s] = tile[s, r, q]
return arr
##################################################
if __name__ == "__main__":
conf = Configuration('../pic/config-weibel.ini')
fdir = "../pic/weibel/out/"
#fname = "field"
#var = "ex"
fname = "analysis"
var = "mgamma"
#arrs = combine_files(fdir, fname, var, conf)
#arrs = combine_files(fdir, fname, var, conf, func=np.max)
arrs = combine_files(fdir, fname, var, conf, isp=0)
print(arrs)
print(arrs.shape)
print(len(arrs))
# Timer for profiling
timer = Timer(["total", "init", "step", "io"])
timer.start("total")
timer.start("init")
# parse command line arguments
parser = argparse.ArgumentParser(
description='Simple PIC-Maxwell simulations')
parser.add_argument('--conf',
dest='conf_filename',
default=None,
help='Name of the configuration file (default: None)')
args = parser.parse_args()
if args.conf_filename == None:
conf = Configuration('config-landau.ini')
else:
print("Reading configuration setup from ", args.conf_filename)
conf = Configuration(args.conf_filename)
#grid = plasma.Grid(conf.Nx, conf.Ny)
grid = corgi.Grid(conf.Nx, conf.Ny, conf.Nz)
xmin = 0.0
xmax = conf.Nx * conf.NxMesh #XXX scaled length
ymin = 0.0
ymax = conf.Ny * conf.NyMesh
grid.set_grid_lims(xmin, xmax, ymin, ymax)
#init.loadMpiRandomly(grid)
#axs.append( plt.subplot(gs[1]) )
#axs.append( plt.subplot(gs[2]) )
#axs.append( plt.subplot(gs[3]) )
#axs.append( plt.subplot(gs[4]) )
#axs.append( plt.subplot(gs[5]) )
#axs.append( plt.subplot(gs[6]) )
#axs.append( plt.subplot(gs[7]) )
# Timer for profiling
timer = Timer(["total", "init", "step", "io"])
timer.start("total")
timer.start("init")
##################################################
#initialize grid
conf = Configuration('config-landau.ini')
#conf = Configuration('config-twostream.ini')
#conf = Configuration('config-twostream-fast.ini')
#conf = Configuration('config-bump-on-tail.ini')
#conf = Configuration('config-twostream-relativistic.ini')
#conf = Configuration('config-plasmaosc.ini')
#conf = Configuration('config-dispersion.ini')
grid = plasma.Grid(conf.Nx, conf.Ny)
xmin = 0.0
xmax = conf.dx * conf.Nx * conf.NxMesh
ymin = 0.0
ymax = conf.dy * conf.Ny * conf.NyMesh
grid.set_grid_lims(xmin, xmax, ymin, ymax)
# Timer for profiling
timer = Timer()
timer.start("total")
timer.start("init")
timer.do_print = do_print
# parse command line arguments
parser = argparse.ArgumentParser(description='Simple PIC-Maxwell simulations')
parser.add_argument('--conf', dest='conf_filename', default=None,
help='Name of the configuration file (default: None)')
args = parser.parse_args()
if args.conf_filename == None:
conf = Configuration('gyration.ini', do_print=do_print)
else:
if do_print:
print("Reading configuration setup from ", args.conf_filename)
conf = Configuration(args.conf_filename, do_print=do_print)
grid = corgi.Grid(conf.Nx, conf.Ny, conf.Nz)
xmin = 0.0
xmax = conf.Nx*conf.NxMesh #XXX scaled length
ymin = 0.0
ymax = conf.Ny*conf.NyMesh
grid.set_grid_lims(xmin, xmax, ymin, ymax)
#init.loadMpiRandomly(grid)
axs.append( plt.subplot(gs[3]) )
axs.append( plt.subplot(gs[4]) )
axs.append( plt.subplot(gs[5]) )
axs.append( plt.subplot(gs[6]) )
axs.append( plt.subplot(gs[7]) )
# Timer for profiling
timer = Timer(["total", "init", "step", "io"])
timer.start("total")
timer.start("init")
##################################################
#initialize grid
conf = Configuration('config-plasmaosc.ini')
#conf = Configuration('config-dispersion.ini')
grid = plasma.Grid(conf.Nx, conf.Ny)
xmin = 0.0
xmax = conf.dx*conf.Nx*conf.NxMesh
ymin = 0.0
ymax = conf.dy*conf.Ny*conf.NyMesh
grid.set_grid_lims(xmin, xmax, ymin, ymax)
#grid.initMpi()
#loadMpiXStrides(grid)
plt.rc('font', family='serif', size=12)
plt.rc('xtick')
plt.rc('ytick')
gs = plt.GridSpec(4, 1)
gs.update(hspace=0.5)
axs = []
axs.append(plt.subplot(gs[0]))
axs.append(plt.subplot(gs[1]))
axs.append(plt.subplot(gs[2]))
axs.append(plt.subplot(gs[3]))
##################################################
#initialize node
conf = Configuration('config.ini')
node = plasma.Grid(conf.Nx, conf.Ny)
node.setGridLims(conf.xmin, conf.xmax, conf.ymin, conf.ymax)
#node.initMpi()
#loadMpiXStrides(node)
init.loadCells(node, conf)
##################################################
# Path to be created
if node.master:
if not os.path.exists(conf.outdir):
os.makedirs(conf.outdir)