def __init__(self, hdf5_file, iPlot=1):
'''
Constructor
'''
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
if iPlot > 0 and iPlot < self.grid.nt:
self.iPlot = iPlot
else:
self.iPlot = self.grid.nt
self.potential = Potential(self.grid, self.hdf5)
self.hamiltonian = Hamiltonian(self.grid, hdf5=self.hdf5)
self.distribution = DistributionFunction(self.grid, hdf5=self.hdf5)
self.potential.read_from_hdf5(iPlot)
self.distribution.read_from_hdf5(iPlot)
self.hamiltonian.read_from_hdf5(iPlot)
self.plot = PlotBGK(self.grid,
self.distribution,
self.hamiltonian,
self.potential,
iTime=iPlot,
write=True)
class timetraces(object):
'''
Plots timetraces of the errors of the total particle number, momentum, energy, entropy,
the L1, L2, L3, L4, L6, L8 norms as well as the distribution function at the final timestep.
The script is invoked with
``python diag_timetraces.py -f <findex> -l <lindex> -v <vmax> -i <hdf5_file>``
-f <findex> is the index of the first timestep to plot (*default*: 0)
-l <lindex> is the index of the last timestep to plot (*default*: nt)
-v <vmax> limits the v range to plot in the contour plot of the distribution function
-i <hdf5_file> specifies the data file to read
'''
def __init__(self, hdf5_file, first=-1, last=-1, vMax=0.):
'''
Constructor
'''
self.first = first
self.last = last
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
self.potential = Potential(self.grid, self.hdf5)
self.hamiltonian = Hamiltonian(self.grid, hdf5=self.hdf5)
self.distribution = DistributionFunction(self.grid, hdf5=self.hdf5)
self.potential.read_from_hdf5(0)
self.distribution.read_from_hdf5(0)
self.hamiltonian.read_from_hdf5(0)
self.plot = PlotTimetraces(self.grid, self.distribution,
self.hamiltonian, self.potential, first,
last, vMax)
def __del__(self):
if self.hdf5 != None:
self.hdf5.close()
def run(self, ptime):
if ptime != 0:
for itime in range(1, self.last + 1):
print("it = %5i" % (itime))
self.potential.read_from_hdf5(itime)
self.distribution.read_from_hdf5(itime)
self.hamiltonian.read_from_hdf5(itime)
self.plot.add_timepoint()
if itime == ptime:
self.plot.update()
break
self.plot.save_plots()
self.plot.update(final=True)
def __init__(self, hdf5_file, nPlot=1, iStart=0):
'''
Constructor
'''
self.iStart = iStart
self.nPlot = nPlot
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
self.potential = Potential(self.grid, self.hdf5)
self.hamiltonian = Hamiltonian(self.grid, hdf5=self.hdf5)
self.distribution = DistributionFunction(self.grid, hdf5=self.hdf5)
self.potential.read_from_hdf5(iStart)
self.distribution.read_from_hdf5(iStart)
self.hamiltonian.read_from_hdf5(iStart)
self.plot = PlotNoether(self.grid, self.distribution, self.hamiltonian,
self.potential, self.grid.nt, iStart, nPlot)
def __init__(self, hdf5_file, first=-1, last=-1, vMax=0.):
'''
Constructor
'''
self.first = first
self.last = last
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
self.potential = Potential(self.grid, self.hdf5)
self.hamiltonian = Hamiltonian(self.grid, hdf5=self.hdf5)
self.distribution = DistributionFunction(self.grid, hdf5=self.hdf5)
self.potential.read_from_hdf5(0)
self.distribution.read_from_hdf5(0)
self.hamiltonian.read_from_hdf5(0)
self.plot = PlotTimetraces(self.grid, self.distribution,
self.hamiltonian, self.potential, first,
last, vMax)
class movie(object):
'''
Creates a movie from HDF5 showing the distribution function
and timetraces of the errors in the particle number, energy,
entropy and L2 norm.
'''
def __init__(self, hdf5_file, iPlot=1):
'''
Constructor
'''
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
if iPlot > 0 and iPlot < self.grid.nt:
self.iPlot = iPlot
else:
self.iPlot = self.grid.nt
self.potential = Potential(self.grid, self.hdf5)
self.hamiltonian = Hamiltonian(self.grid, hdf5=self.hdf5)
self.distribution = DistributionFunction(self.grid, hdf5=self.hdf5)
self.potential.read_from_hdf5(iPlot)
self.distribution.read_from_hdf5(iPlot)
self.hamiltonian.read_from_hdf5(iPlot)
self.plot = PlotBGK(self.grid,
self.distribution,
self.hamiltonian,
self.potential,
iTime=iPlot,
write=True)
def __del__(self):
if self.hdf5 != None:
self.hdf5.close()
def __init__(self, hdf5_file, nPlot=1, nmax=0):
'''
Constructor
'''
self.nPlot = nPlot
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
self.potential = Potential(self.grid, self.hdf5)
self.energy = np.zeros(self.grid.nt+1)
for itime in range(0, self.grid.nt+1):
self.potential.read_from_hdf5(itime)
self.energy[itime] = np.sqrt(self.potential.charge * self.potential.E)
tMax = []
EMax = []
# find maxima
for it in range(0, self.grid.nt+1):
itm = (it-1+self.grid.nt+1) % (self.grid.nt+1)
itp = (it+1+self.grid.nt+1) % (self.grid.nt+1)
if self.energy[it] > self.energy[itm] and self.energy[it] > self.energy[itp]:
tMax.append(self.grid.t[it])
EMax.append(self.energy[it])
# fit maxima
if nmax == 0:
nmax = len(tMax)
else:
nmax += 1
fit = np.polyfit(tMax[1:nmax], np.log(EMax[1:nmax]), 1)
fit_fn = np.poly1d(fit)
print("")
print("Fit Parameter (m,b):", fit)
print("")
# set up figure/window size
self.figure1 = plt.figure(num=None, figsize=(16,9))
plt.subplots_adjust(left=0.1, right=0.95, bottom=0.09, top=0.94, wspace=0.1, hspace=0.2)
# plot
plt.semilogy(self.grid.t, self.energy)
plt.plot(tMax, EMax, 'ro')
plt.plot(self.grid.t, np.exp(fit_fn(self.grid.t)), '--k')
# plt.title("Damping of the Electrostatic Field", fontsize=24)
plt.xlabel("$t$", labelpad=15, fontsize=22)
plt.ylabel("$\parallel E (x,t) \parallel_{2}$", fontsize=22)
plt.tight_layout()
plt.draw()
if hdf5_file.rfind('/') >= 0:
filename = hdf5_file[hdf5_file.rfind('/'):]
else:
filename = hdf5_file
filename = filename.replace('.hdf5', '_')
filename += 'potential'
plt.savefig(filename + '.png', dpi=300)
plt.savefig(filename + '.pdf')
class replay(object):
'''
Interactive replay plotting the distribution function, the Hamiltonian,
density, potential and timetraces of kinetic and potential energy
as well as the errors in the particle number, energy, entropy and L2 norm.
'''
def __init__(self, hdf5_file, nPlot=1, iStart=0, vMax=0.0):
'''
Constructor
'''
self.iStart = iStart
self.nPlot = nPlot
self.hdf5 = h5py.File(hdf5_file, 'r')
self.grid = Grid().load_from_hdf5(self.hdf5)
self.potential = Potential(self.grid, self.hdf5)
self.hamiltonian = Hamiltonian(self.grid, hdf5=self.hdf5)
self.distribution = DistributionFunction(self.grid, hdf5=self.hdf5)
self.potential.read_from_hdf5(iStart)
self.distribution.read_from_hdf5(iStart)
self.hamiltonian.read_from_hdf5(iStart)
self.plot = PlotReplay(self.grid, self.distribution, self.hamiltonian,
self.potential, self.grid.nt, iStart, nPlot,
vMax)
# self.plot.save_plots()
def __del__(self):
if self.hdf5 != None:
self.hdf5.close()
def init(self, iStart=0):
self.update(iStart)
def update(self, itime, final=False):
self.potential.read_from_hdf5(itime)
self.distribution.read_from_hdf5(itime)
self.hamiltonian.read_from_hdf5(itime)
print("it = %5i" % (itime))
if itime > 0:
# Ekin = self.hamiltonian.Ekin
# Ekin0 = self.hamiltonian.Ekin0
# Epot = self.hamiltonian.Epot - self.potential.E
# Epot0 = self.hamiltonian.Epot0 - self.potential.E0
# Epot_f = self.hamiltonian.Epot / 2.
# Epot0_f = self.hamiltonian.Epot0 / 2.
# Epot_p = self.potential.E
# Epot0_p = self.potential.E0
#
# dEkin = Ekin - Ekin0
# dEpot = Epot - Epot0
# dEpot_f = Epot_f - Epot0_f
# dEpot_p = Epot_p - Epot0_p
#
# E = Ekin + Epot
# E0 = Ekin0 + Epot0
# E_f = Ekin + Epot_f
# E0_f = Ekin0 + Epot0_f
# E_p = Ekin + Epot_p
# E0_p = Ekin0 + Epot0_p
#
# E_err = (E - E0 ) / E0
# E_err_f = (E_f - E0_f) / E0_f
# E_err_p = (E_p - E0_p) / E0_p
#
# print
# print(" dEpot/dEkin = %24.16E, dEpot(f)/dEkin = %24.16E, dEpot(phi)/dEkin = %24.16E" % (dEpot/dEkin, dEpot_f/dEkin, dEpot_p/dEkin))
# print(" E_pot = %24.16E, E_pot(f) = %24.16E, E_pot(phi) = %24.16E" % (Epot, Epot_f, Epot_p))
# print(" E_err = %24.16E, E_err(f) = %24.16E, E_err(phi) = %24.16E" % (E_err, E_err_f, E_err_p))
self.plot.add_timepoint()
return self.plot.update(final=final)
def run(self):
for itime in range(self.iStart + 1, self.grid.nt + 1):
self.update(itime, final=(itime == self.grid.nt))