def withTagging(**kwargs):
Simulation(smallest_patch_size=20,
largest_patch_size=20,
time_step_nbr=2000,
final_time=20.,
boundary_types="periodic",
cells=200,
dl=1.0,
refinement="tagging",
max_nbr_levels=3,
diag_options={
"format": "phareh5",
"options": {
"dir": kwargs["diagdir"],
"mode": "overwrite"
}
})
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
**vvv
})
ElectronModel(closure="isothermal", Te=0.12)
sim = ph.global_vars.sim
timestamps = all_timestamps(sim)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def config():
# most unstable mode at k=0.19, that is lambda = 33
# hence the length of the box is 33, and the fourier mode will be 1
Simulation(
smallest_patch_size=20,
largest_patch_size=60,
final_time=50,
time_step=0.0005,
boundary_types="periodic",
cells=165,
dl=0.2,
hyper_resistivity = 0.01,
refinement_boxes={"L0": {"B0": [( 50, ), (110, )]},
"L1": {"B0": [(140, ), (180, )]} },
diag_options={"format": "phareh5",
"options": {"dir": "ion_ion_beam1d", "mode": "overwrite"}}
)
def densityMain(x):
return 1.
def densityBeam(x):
return .01
def bx(x):
return 1.
def by(x):
return 0.
def bz(x):
return 0.
def vB(x):
return 5.
def v0(x):
return 0.
def vth(x):
return np.sqrt(0.1)
vMain = {
"vbulkx": v0, "vbulky": v0, "vbulkz": v0,
"vthx": vth, "vthy": vth, "vthz": vth
}
vBulk = {
"vbulkx": vB, "vbulky": v0, "vbulkz": v0,
"vthx": vth, "vthy": vth, "vthz": vth
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
main={"charge": 1, "density": densityMain, **vMain},
beam={"charge": 1, "density": densityBeam, **vBulk}
)
ElectronModel(closure="isothermal", Te=0.0)
sim = ph.global_vars.sim
timestamps = np.arange(0, sim.final_time, 1.)
for quantity in ["B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
vvv = {
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz
}
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
**vvv, "init": {
"seed": 1337
}
})
ElectronModel(closure="isothermal", Te=0.12)
sim = ph.global_vars.sim
timestamps = np.arange(0, sim.final_time + sim.time_step, 10 * sim.time_step)
for quantity in ["E", "B"]:
ph.ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
def config():
""" Configure the simulation
This function defines the Simulation object,
user initialization model and diagnostics.
"""
Simulation(
smallest_patch_size=20,
largest_patch_size=20,
time_step_nbr=
6000, # number of time steps (not specified if time_step and final_time provided)
final_time=
30, # simulation final time (not specified if time_step and time_step_nbr provided)
boundary_types=
"periodic", # boundary condition, string or tuple, length == len(cell) == len(dl)
cells=2500, # integer or tuple length == dimension
dl=0.2, # mesh size of the root level, float or tuple
#max_nbr_levels=1, # (default=1) max nbr of levels in the AMR hierarchy
nesting_buffer=0,
refinement_boxes={"L0": {
"B0": [(125, ), (750, )]
}},
diag_options={
"format": "phareh5",
"options": {
"dir": "shock_20dx_dx02_refined",
"mode": "overwrite"
}
})
def density(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()[0]
v1 = 1
v2 = 1.
return v1 + (v2 - v1) * (S(x, L * 0.2, 1) - S(x, L * 0.8, 1))
def S(x, x0, l):
return 0.5 * (1 + np.tanh((x - x0) / l))
def bx(x):
return 0.
def by(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()[0]
v1 = 0.125
v2 = 4.0
return v1 + (v2 - v1) * (S(x, L * 0.2, 1) - S(x, L * 0.8, 1))
def bz(x):
return 0.
def T(x):
return 0.1
def vx(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()[0]
v1 = 0.
v2 = 0.
return v1 + (v2 - v1) * (S(x, L * 0.25, 1) - S(x, L * 0.75, 1))
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return T(x)
def vthy(x):
return T(x)
def vthz(x):
return T(x)
vvv = {
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz
}
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
**vvv
})
ElectronModel(closure="isothermal", Te=0.12)
sim = ph.global_vars.sim
timestamps = np.arange(0, sim.final_time + sim.time_step, sim.time_step)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def config():
""" Configure the simulation
This function defines the Simulation object,
user initialization model and diagnostics.
"""
Simulation(
smallest_patch_size=20,
largest_patch_size=20,
time_step_nbr=
2000, # number of time steps (not specified if time_step and final_time provided)
final_time=
20., # simulation final time (not specified if time_step and time_step_nbr provided)
boundary_types=
"periodic", # boundary condition, string or tuple, length == len(cell) == len(dl)
cells=500, # integer or tuple length == dimension
dl=1., # mesh size of the root level, float or tuple
refinement_boxes={
"L0": {
"B0": [(80, ), (180, )]
},
"L1": {
"B0": [(200, ), (300, )]
}
},
diag_options={
"format": "phareh5",
"options": {
"dir": "td_noflow",
"mode": "overwrite"
}
})
def density(x):
return 1.
def S(x, x0, l):
return 0.5 * (1 + np.tanh((x - x0) / l))
def bx(x):
return 0.
def by(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()[0]
v1 = -1
v2 = 1.
return v1 + (v2 - v1) * (S(x, L * 0.25, 1) - S(x, L * 0.75, 1))
def bz(x):
return 0.5
def b2(x):
return bx(x)**2 + by(x)**2 + bz(x)**2
def T(x):
K = 1
return 1 / density(x) * (K - b2(x) * 0.5)
def vx(x):
return 0.
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return T(x)
def vthy(x):
return T(x)
def vthz(x):
return T(x)
vvv = {
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz
}
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
**vvv
})
ElectronModel(closure="isothermal", Te=0.12)
sim = ph.global_vars.sim
dt_dump = 0.1
n_dump = int(sim.final_time / dt_dump) + 1
timestamps = np.linspace(0, sim.final_time, n_dump)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def config():
""" Configure the simulation
This function defines the Simulation object,
user initialization model and diagnostics.
"""
Simulation(
smallest_patch_size=10,
largest_patch_size=20,
time_step_nbr=2000, # number of time steps (not specified if time_step and final_time provided)
final_time=20, # simulation final time (not specified if time_step and time_step_nbr provided)
boundary_types="periodic", # boundary condition, string or tuple, length == len(cell) == len(dl)
cells=400, # integer or tuple length == dimension
dl=0.5, # mesh size of the root level, float or tuple
max_nbr_levels=3, # (default=1) max nbr of levels in the AMR hierarchy
nesting_buffer=2,
refinement = "tagging",
diag_options={"format": "phareh5", "options": {"dir": "refine_dx05_lvl3","mode":"overwrite"}}
)
def density(x):
return 1.
def S(x,x0,l):
return 0.5*(1+np.tanh((x-x0)/l))
def bx(x):
return 0.
def by(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()[0]
v1=-1
v2=1.
return v1 + (v2-v1)*(S(x,L*0.25,1) -S(x, L*0.75, 1))
def bz(x):
return 0.5
def b2(x):
return bx(x)**2 + by(x)**2 + bz(x)**2
def T(x):
K = 1
return 1/density(x)*(K - b2(x)*0.5)
def vx(x):
return 1.
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return T(x)
def vthy(x):
return T(x)
def vthz(x):
return T(x)
vvv = {
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
protons={"charge": 1, "density": density, **vvv}
)
ElectronModel(closure="isothermal", Te=0.12)
timestamps = all_timestamps(gv.sim)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def prescribedModes():
# in this configuration there user prescribed
# wavelength, at which more energy is thus expected
# than in modes naturally present in the simulation noise
Simulation(
smallest_patch_size=20,
largest_patch_size=20,
# the following time step number
# and final time mean that the
# smallest frequency will be 2/100
# and the largest 2/dt = 2e3
time_step_nbr=100000,
final_time=100.,
boundary_types="periodic",
# smallest wavelength will be 2*0.2=0.4
# and largest 50
cells=500,
dl=0.2,
diag_options={"format": "phareh5", "options": {"dir": "dispersion",
"mode":"overwrite"}}
)
def density(x):
return 1.
def by(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1*np.cos(2*np.pi*x/L[0])
def bz(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return -0.1*np.sin(2*np.pi*x/L[0])
def bx(x):
return 1.
def vx(x):
return 0.
def vy(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1*np.cos(2*np.pi*x/L[0])
def vz(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1*np.sin(2*np.pi*x/L[0])
def vthx(x):
return 0.01
def vthy(x):
return 0.01
def vthz(x):
return 0.01
vvv = {
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
protons={"charge": 1, "density": density, **vvv}
)
ElectronModel(closure="isothermal", Te=0.)
sim = ph.global_vars.sim
timestamps = np.arange(0, sim.final_time +sim.time_step, sim.time_step)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def uniform(vth, dl, cells, nbr_steps):
Simulation(
smallest_patch_size=20,
largest_patch_size=20,
time_step_nbr=nbr_steps,
final_time=50.,
boundary_types="periodic",
cells=cells,
dl=dl,
diag_options={"format": "phareh5",
"options": {"dir": "vth{}dx{}".format(vth,dl),
"mode":"overwrite"}}
)
def density(x):
return 1.
def by(x):
return 0.
def bz(x):
return 0.
def bx(x):
return 1.
def vx(x):
return 0.
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return vth
def vthy(x):
return vth
def vthz(x):
return vth
vvv = {
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
protons={"charge": 1, "density": density, **vvv}
)
ElectronModel(closure="isothermal", Te=0.)
sim = ph.global_vars.sim
timestamps = np.arange(0, sim.final_time, 50*sim.time_step)
for quantity in ["B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for name in ["domain", "levelGhost", "patchGhost"]:
ParticleDiagnostics(quantity=name,
compute_timestamps=timestamps,
write_timestamps=timestamps,
population_name="protons")
def config_uni(**kwargs):
""" Configure the simulation
This function defines the Simulation object,
user initialization model and diagnostics.
"""
Simulation(
smallest_patch_size=20,
largest_patch_size=20,
time_step_nbr=2000, # number of time steps (not specified if time_step and final_time provided)
final_time=20., # simulation final time (not specified if time_step and time_step_nbr provided)
boundary_types="periodic", # boundary condition, string or tuple, length == len(cell) == len(dl)
cells=500, # integer or tuple length == dimension
dl=1.0, # mesh size of the root level, float or tuple
refinement_boxes={"L0": {"B0": [(100, ), (200, )]},
"L1":{"B0":[(300,),(350,)]}},
diag_options={"format": "phareh5", "options": {"dir": kwargs["diagdir"],"mode":"overwrite"}}
)
def density(x):
return 1.
def bx(x):
return 0.
def by(x):
return 1.
def bz(x):
return 0.5
def vx(x):
return kwargs["vx"]
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return 0.1
def vthy(x):
return 0.1
def vthz(x):
return 0.1
vvv = {
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
protons={"charge": 1, "density": density, **vvv}
)
ElectronModel(closure="isothermal", Te=0.12)
timestamps = all_timestamps(gv.sim)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def getHierarchy(self,
interp_order,
refinement_boxes,
qty,
diag_outputs,
nbr_part_per_cell=100,
density=_density,
extra_diag_options={},
beam=False,
time_step_nbr=1,
smallest_patch_size=None,
largest_patch_size=10,
cells=120,
dl=0.1,
ndim=1):
diag_outputs = f"phare_outputs/init/{diag_outputs}"
from pyphare.pharein import global_vars
global_vars.sim = None
if smallest_patch_size is None:
from pyphare.pharein.simulation import check_patch_size
_, smallest_patch_size = check_patch_size(
ndim, interp_order=interp_order, cells=cells)
extra_diag_options["mode"] = "overwrite"
extra_diag_options["dir"] = diag_outputs
self.register_diag_dir_for_cleanup(diag_outputs)
Simulation(
smallest_patch_size=smallest_patch_size,
largest_patch_size=largest_patch_size,
time_step_nbr=time_step_nbr,
final_time=30.,
boundary_types=["periodic"] * ndim,
cells=[cells] * ndim,
dl=[dl] * ndim,
interp_order=interp_order,
refinement_boxes=refinement_boxes,
diag_options={
"format": "phareh5",
"options": extra_diag_options
},
strict=True,
)
def beam_density(*xyz):
return np.zeros_like(xyz[0]) + 0.3
def bx(*xyz):
return 1.
def by(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def bz(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.sin(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vx(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vy(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vz(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.sin(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vth(*xyz):
return 0.01 + np.zeros_like(xyz[0])
def vthx(*xyz):
return vth(*xyz)
def vthy(*xyz):
return vth(*xyz)
def vthz(*xyz):
return vth(*xyz)
if beam:
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": {
"seed": 1337
}
},
beam={
"charge": 1,
"density": beam_density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": {
"seed": 1337
}
})
else:
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": {
"seed": 1337
}
})
ElectronModel(closure="isothermal", Te=0.12)
for quantity in ["E", "B"]:
ElectromagDiagnostics(quantity=quantity,
write_timestamps=np.zeros(time_step_nbr),
compute_timestamps=np.zeros(time_step_nbr))
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=np.zeros(time_step_nbr),
compute_timestamps=np.zeros(time_step_nbr))
poplist = ["protons", "beam"] if beam else ["protons"]
for pop in poplist:
for quantity in ["density", "flux"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=np.zeros(time_step_nbr),
compute_timestamps=np.zeros(time_step_nbr),
population_name=pop)
for quantity in ['domain', 'levelGhost', 'patchGhost']:
ParticleDiagnostics(quantity=quantity,
compute_timestamps=np.zeros(time_step_nbr),
write_timestamps=np.zeros(time_step_nbr),
population_name=pop)
Simulator(global_vars.sim).initialize().reset()
eb_hier = None
if qty in ["e", "eb"]:
eb_hier = hierarchy_from(h5_filename=diag_outputs + "/EM_E.h5",
hier=eb_hier)
if qty in ["b", "eb"]:
eb_hier = hierarchy_from(h5_filename=diag_outputs + "/EM_B.h5",
hier=eb_hier)
if qty in ["e", "b", "eb"]:
return eb_hier
is_particle_type = qty == "particles" or qty == "particles_patch_ghost"
if is_particle_type:
particle_hier = None
if qty == "particles":
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_domain.h5")
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_levelGhost.h5",
hier=particle_hier)
if is_particle_type:
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_patchGhost.h5",
hier=particle_hier)
if qty == "particles":
merge_particles(particle_hier)
if is_particle_type:
return particle_hier
if qty == "moments":
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_density.h5")
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_bulkVelocity.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_density.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_flux.h5",
hier=mom_hier)
if beam:
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_beam_density.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_beam_flux.h5",
hier=mom_hier)
return mom_hier
def getHierarchy(self,
interp_order,
refinement_boxes,
qty,
diag_outputs,
nbr_part_per_cell=100,
density=_density,
smallest_patch_size=None,
largest_patch_size=20,
cells=120,
time_step=0.001,
model_init={},
dl=0.2,
extra_diag_options={},
time_step_nbr=1,
timestamps=None,
ndim=1,
block_merging_particles=False):
diag_outputs = f"phare_outputs/advance/{diag_outputs}"
from pyphare.pharein import global_vars
global_vars.sim = None
if smallest_patch_size is None:
from pyphare.pharein.simulation import check_patch_size
_, smallest_patch_size = check_patch_size(
ndim, interp_order=interp_order, cells=cells)
extra_diag_options["mode"] = "overwrite"
extra_diag_options["dir"] = diag_outputs
self.register_diag_dir_for_cleanup(diag_outputs)
Simulation(
smallest_patch_size=smallest_patch_size,
largest_patch_size=largest_patch_size,
time_step_nbr=time_step_nbr,
time_step=time_step,
boundary_types=["periodic"] * ndim,
cells=np_array_ify(cells, ndim),
dl=np_array_ify(dl, ndim),
interp_order=interp_order,
refinement_boxes=refinement_boxes,
diag_options={
"format": "phareh5",
"options": extra_diag_options
},
strict=True,
)
def S(x, x0, l):
return 0.5 * (1 + np.tanh((x - x0) / l))
def bx(*xyz):
return 1.
def by(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def bz(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vx(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vy(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vz(*xyz):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
_ = lambda i: 0.1 * np.cos(2 * np.pi * xyz[i] / L[i])
return np.asarray([_(i) for i, v in enumerate(xyz)]).prod(axis=0)
def vth(*xyz):
return 0.01 + np.zeros_like(xyz[0])
def vthx(*xyz):
return vth(*xyz)
def vthy(*xyz):
return vth(*xyz)
def vthz(*xyz):
return vth(*xyz)
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": model_init,
})
ElectronModel(closure="isothermal", Te=0.12)
if timestamps is None:
timestamps = all_timestamps(global_vars.sim)
for quantity in ["E", "B"]:
ElectromagDiagnostics(quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps)
poplist = ["protons"]
for pop in poplist:
for quantity in ["density", "flux"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
population_name=pop)
for quantity in ['domain', 'levelGhost', 'patchGhost']:
ParticleDiagnostics(quantity=quantity,
compute_timestamps=timestamps,
write_timestamps=timestamps,
population_name=pop)
Simulator(global_vars.sim).run()
eb_hier = None
if qty in ["e", "eb", "fields"]:
eb_hier = hierarchy_from(h5_filename=diag_outputs + "/EM_E.h5",
hier=eb_hier)
if qty in ["b", "eb", "fields"]:
eb_hier = hierarchy_from(h5_filename=diag_outputs + "/EM_B.h5",
hier=eb_hier)
if qty in ["e", "b", "eb"]:
return eb_hier
is_particle_type = qty == "particles" or qty == "particles_patch_ghost"
if is_particle_type:
particle_hier = None
if qty == "particles":
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_domain.h5")
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_levelGhost.h5",
hier=particle_hier)
if is_particle_type:
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_patchGhost.h5",
hier=particle_hier)
if not block_merging_particles and qty == "particles":
merge_particles(particle_hier)
if is_particle_type:
return particle_hier
if qty == "moments" or qty == "fields":
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_density.h5",
hier=eb_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_bulkVelocity.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_density.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_flux.h5",
hier=mom_hier)
return mom_hier
def setup(**kwargs):
from pyphare.pharein import Simulation, MaxwellianFluidModel
from pyphare.pharein import ElectronModel, ElectromagDiagnostics, FluidDiagnostics
import matplotlib as mpl
mpl.use("Agg")
def getFn(key):
return kwargs.get(key, globals()["_" + key])
density = getFn("density")
bx, by, bz = getFn("bx"), getFn("by"), getFn("bz")
vx, vy, vz = getFn("vx"), getFn("vy"), getFn("vz")
vthx, vthy, vthz = getFn("vthx"), getFn("vthy"), getFn("vthz")
ndim = kwargs.get("ndim", 1)
interp = kwargs.get("ndim", 1)
smallest_patch_size = kwargs.get("smallest_patch_size", 20)
largest_patch_size = kwargs.get("largest_patch_size", 20)
time_step_nbr = kwargs.get("time_step_nbr", 100)
final_time = kwargs.get("final_time", 0.1)
cells = [kwargs.get("cells", 100)] * ndim
dl = [kwargs.get("dl", 0.2)] * ndim
Te = kwargs.get("Te", 0.12)
charge = kwargs.get("charge", 1)
ppc = kwargs.get("ppc", 10)
boundary_types = [kwargs.get("boundary_types", "periodic")] * ndim
diag_dir = kwargs.get("diag_dir", ".")
Simulation(
interp_order=interp,
smallest_patch_size=smallest_patch_size,
largest_patch_size=largest_patch_size,
time_step_nbr=time_step_nbr,
final_time=final_time,
boundary_types=boundary_types,
cells=cells,
dl=dl,
diag_options={
"format": "phareh5",
"options": {
"dir": diag_dir,
"mode": "overwrite"
},
},
)
MaxwellianFluidModel(
bx=bx,
by=by,
bz=bz,
protons={
"charge": charge,
"density": density,
"nbr_part_per_cell": ppc,
**{
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
},
},
)
ElectronModel(closure="isothermal", Te=Te)
def fromNoise():
# in this configuration there are no prescribed waves
# and only eigen modes existing in the simulation noise
# will be visible
Simulation(
smallest_patch_size=20,
largest_patch_size=20,
# the following time step number
# and final time mean that the
# smallest frequency will be 2/100
# and the largest 2/dt = 2e3
time_step_nbr=100000,
final_time=100.,
boundary_types="periodic",
# smallest wavelength will be 2*0.2=0.4
# and largest 50
cells=500,
dl=0.2,
diag_options={"format": "phareh5",
"options": {"dir": "dispersion",
"mode":"overwrite"}}
)
def density(x):
return 1.
def by(x):
return 0.
def bz(x):
return 0.
def bx(x):
return 1.
def vx(x):
return 0.
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return 0.01
def vthy(x):
return 0.01
def vthz(x):
return 0.01
vvv = {
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
protons={"charge": 1, "density": density, **vvv}
)
ElectronModel(closure="isothermal", Te=0.)
sim = ph.global_vars.sim
timestamps = np.arange(0, sim.final_time +sim.time_step, sim.time_step)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def config():
# configure the simulation
Simulation(
smallest_patch_size=50,
largest_patch_size=50,
time_step_nbr=
100000, # number of time steps (not specified if time_step and final_time provided)
final_time=
1000, # simulation final time (not specified if time_step and time_step_nbr provided)
boundary_types=
"periodic", # boundary condition, string or tuple, length == len(cell) == len(dl)
cells=1000, # integer or tuple length == dimension
dl=1, # mesh size of the root level, float or tuple
hyper_resistivity=0.001,
refinement_boxes={"L0": {
"B0": [(450, ), (550, )]
}},
diag_options={
"format": "phareh5",
"options": {
"dir": ".",
"mode": "overwrite"
}
})
def density(x):
return 1.
def by(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.01 * np.cos(2 * np.pi * x / L[0])
def bz(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.01 * np.sin(2 * np.pi * x / L[0])
def bx(x):
return 1.
def vx(x):
return 0.
def vy(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.01 * np.cos(2 * np.pi * x / L[0])
def vz(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.01 * np.sin(2 * np.pi * x / L[0])
def vthx(x):
return 0.01
def vthy(x):
return 0.01
def vthz(x):
return 0.01
vvv = {
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz
}
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
**vvv
})
ElectronModel(closure="isothermal", Te=0.0)
timestamps = all_timestamps(gv.sim)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def config(diag_outputs, model_init={}, refinement_boxes=None):
ph.global_vars.sim = None
Simulation(
smallest_patch_size=10,
largest_patch_size=20,
time_step_nbr= 1,
final_time= 0.001,
#boundary_types="periodic",
cells=(50, 100),
dl=(0.40, 0.40),
#refinement="tagging",
#max_nbr_levels = 3,
refinement_boxes=refinement_boxes,
hyper_resistivity=0.0050,
resistivity=0.001,
diag_options={"format": "phareh5",
"options": {"dir": diag_outputs,
"mode":"overwrite", "fine_dump_lvl_max": 10}}
)
def density(x, y):
from pyphare.pharein.global_vars import sim
Lx = sim.simulation_domain()[0]
return 1.
def bx(x, y):
return 0.1
def by(x, y):
from pyphare.pharein.global_vars import sim
Lx = sim.simulation_domain()[0]
Ly = sim.simulation_domain()[1]
return 0.2
def bz(x, y):
return 1.
def T(x, y):
return 1.
def vx(x, y):
return 1.0
def vy(x, y):
return 0.
def vz(x, y):
return 0.
def vthx(x, y):
return np.sqrt(T(x, y))
def vthy(x, y):
return np.sqrt(T(x, y))
def vthz(x, y):
return np.sqrt(T(x, y))
vvv = {
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz,
"nbr_part_per_cell":100,
"init": model_init,
}
MaxwellianFluidModel(
bx=bx, by=by, bz=bz,
protons={"charge": 1, "density": density, **vvv}
)
ElectronModel(closure="isothermal", Te=0.0)
sim = ph.global_vars.sim
dt = 1*sim.time_step
nt = sim.final_time/dt+1
timestamps = dt * np.arange(nt)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
return sim
import numpy as np
Te = 0.12
def n(x):
return 1.
def bx(x):
xmax = getSimulation().simulation_domain()[0]
return np.cos(2*np.pi/xmax * x)
MaxwellianFluidModel(bx=bx,
protons={"density":n},
background={})
ElectronModel(closure="isothermal",Te = Te)
ElectromagDiagnostics(
diag_type="E", # available : ("E", "B")
write_every=10,
compute_every=5,
start_teration=0,
last_iteration=990,
path = 'ElectromagDiagnostics1' # where output files will be written, [default: name]
)
def config():
Simulation(
smallest_patch_size=15,
largest_patch_size=25,
time_step_nbr=1000,
time_step=0.001,
# boundary_types="periodic",
cells=(100, 100),
dl=(0.2, 0.2),
refinement_boxes={},
hyper_resistivity=0.001,
resistivity=0.001,
diag_options={
"format": "phareh5",
"options": {
"dir": diag_outputs,
"mode": "overwrite"
}
},
strict=True,
)
def density(x, y):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()[1]
return 0.2 + 1. / np.cosh((y - L * 0.3) / 0.5)**2 + 1. / np.cosh(
(y - L * 0.7) / 0.5)**2
def S(y, y0, l):
return 0.5 * (1. + np.tanh((y - y0) / l))
def by(x, y):
from pyphare.pharein.global_vars import sim
Lx = sim.simulation_domain()[0]
Ly = sim.simulation_domain()[1]
w1 = 0.2
w2 = 1.0
x0 = (x - 0.5 * Lx)
y1 = (y - 0.3 * Ly)
y2 = (y - 0.7 * Ly)
w3 = np.exp(-(x0 * x0 + y1 * y1) / (w2 * w2))
w4 = np.exp(-(x0 * x0 + y2 * y2) / (w2 * w2))
w5 = 2.0 * w1 / w2
return (w5 * x0 * w3) + (-w5 * x0 * w4)
def bx(x, y):
from pyphare.pharein.global_vars import sim
Lx = sim.simulation_domain()[0]
Ly = sim.simulation_domain()[1]
w1 = 0.2
w2 = 1.0
x0 = (x - 0.5 * Lx)
y1 = (y - 0.3 * Ly)
y2 = (y - 0.7 * Ly)
w3 = np.exp(-(x0 * x0 + y1 * y1) / (w2 * w2))
w4 = np.exp(-(x0 * x0 + y2 * y2) / (w2 * w2))
w5 = 2.0 * w1 / w2
v1 = -1
v2 = 1.
return v1 + (v2 - v1) * (S(y, Ly * 0.3, 0.5) - S(y, Ly * 0.7, 0.5)) + (
-w5 * y1 * w3) + (+w5 * y2 * w4)
def bz(x, y):
return 0.
def b2(x, y):
return bx(x, y)**2 + by(x, y)**2 + bz(x, y)**2
def T(x, y):
K = 1
temp = 1. / density(x, y) * (K - b2(x, y) * 0.5)
assert np.all(temp > 0)
return temp
def vx(x, y):
return 0.
def vy(x, y):
return 0.
def vz(x, y):
return 0.
def vthx(x, y):
return np.sqrt(T(x, y))
def vthy(x, y):
return np.sqrt(T(x, y))
def vthz(x, y):
return np.sqrt(T(x, y))
vvv = {
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": 100
}
MaxwellianFluidModel(
bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
**vvv, "init": {
"seed": 12334
}
},
)
ElectronModel(closure="isothermal", Te=0.0)
sim = ph.global_vars.sim
dt = 10 * sim.time_step
nt = sim.final_time / dt + 1
timestamps = (dt * np.arange(nt))
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
)
def getHierarchy(self,
interp_order,
refinement_boxes,
qty,
nbr_part_per_cell=100,
diag_outputs="phare_outputs",
density=lambda x: 0.3 + 1. / np.cosh((x - 6) / 4.)**2,
beam=False,
smallest_patch_size=10,
largest_patch_size=10,
cells=120,
dl=0.1):
from pyphare.pharein import global_vars
global_vars.sim = None
startMPI()
Simulation(smallest_patch_size=smallest_patch_size,
largest_patch_size=largest_patch_size,
time_step_nbr=30000,
final_time=30.,
boundary_types="periodic",
cells=cells,
dl=dl,
interp_order=interp_order,
refinement_boxes=refinement_boxes,
diag_options={
"format": "phareh5",
"options": {
"dir": diag_outputs,
"mode": "overwrite"
}
})
def beam_density(x):
return np.zeros_like(x) + 0.3
def by(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1 * np.cos(2 * np.pi * x / L[0])
def bz(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1 * np.sin(2 * np.pi * x / L[0])
def bx(x):
return 1.
def vx(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1 * np.cos(2 * np.pi * x / L[0]) + 0.2
def vy(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1 * np.cos(2 * np.pi * x / L[0])
def vz(x):
from pyphare.pharein.global_vars import sim
L = sim.simulation_domain()
return 0.1 * np.sin(2 * np.pi * x / L[0])
def vthx(x):
return 0.01 + np.zeros_like(x)
def vthy(x):
return 0.01 + np.zeros_like(x)
def vthz(x):
return 0.01 + np.zeros_like(x)
if beam:
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": {
"seed": 1337
}
},
beam={
"charge": 1,
"density": beam_density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": {
"seed": 1337
}
})
else:
MaxwellianFluidModel(bx=bx,
by=by,
bz=bz,
protons={
"charge": 1,
"density": density,
"vbulkx": vx,
"vbulky": vy,
"vbulkz": vz,
"vthx": vthx,
"vthy": vthy,
"vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": {
"seed": 1337
}
})
ElectronModel(closure="isothermal", Te=0.12)
for quantity in ["E", "B"]:
ElectromagDiagnostics(quantity=quantity,
write_timestamps=np.zeros(1),
compute_timestamps=np.zeros(1))
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=np.zeros(1),
compute_timestamps=np.zeros(1))
poplist = ["protons", "beam"] if beam else ["protons"]
for pop in poplist:
for quantity in ["density", "flux"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=np.zeros(1),
compute_timestamps=np.zeros(1),
population_name=pop)
for quantity in ['domain', 'levelGhost', 'patchGhost']:
ParticleDiagnostics(quantity=quantity,
compute_timestamps=np.zeros(1),
write_timestamps=np.zeros(1),
population_name=pop)
simulator = Simulator(global_vars.sim)
simulator.initialize()
if qty == "b":
b_hier = hierarchy_from(h5_filename=diag_outputs + "/EM_B.h5")
return b_hier
is_particle_type = qty == "particles" or qty == "particles_patch_ghost"
if is_particle_type:
particle_hier = None
if qty == "particles":
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_domain.h5")
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_levelGhost.h5",
hier=particle_hier)
if is_particle_type:
particle_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_patchGhost.h5",
hier=particle_hier)
if qty == "particles":
merge_particles(particle_hier)
if is_particle_type:
return particle_hier
if qty == "moments":
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_density.h5")
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_bulkVelocity.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_density.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_protons_flux.h5",
hier=mom_hier)
if beam:
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_beam_density.h5",
hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs +
"/ions_pop_beam_flux.h5",
hier=mom_hier)
return mom_hier
def getHierarchy(self, interp_order, refinement_boxes, qty, nbr_part_per_cell=100,
diag_outputs="phare_outputs",
smallest_patch_size=5, largest_patch_size=20,
cells=120, time_step=0.001, model_init={},
dl=0.1, extra_diag_options={}, time_step_nbr=1, timestamps=None):
from pyphare.pharein import global_vars
global_vars.sim = None
startMPI()
extra_diag_options["mode"] = "overwrite"
extra_diag_options["dir"] = diag_outputs
Simulation(
smallest_patch_size=smallest_patch_size,
largest_patch_size=largest_patch_size,
time_step_nbr=time_step_nbr,
time_step=time_step,
boundary_types="periodic",
cells=cells,
dl=dl,
interp_order=interp_order,
refinement_boxes=refinement_boxes,
diag_options={"format": "phareh5",
"options": extra_diag_options}
)
def density(x):
return 1.
def S(x,x0,l):
return 0.5*(1+np.tanh((x-x0)/l))
def bx(x):
return 1.
def by(x):
L = global_vars.sim.simulation_domain()[0]
v1=-1
v2=1.
return v1 + (v2-v1)*(S(x,L*0.25,1) -S(x, L*0.75, 1))
def bz(x):
return 0.5
def b2(x):
return bx(x)**2 + by(x)**2 + bz(x)**2
def T(x):
K = 1
return 1/density(x)*(K - b2(x)*0.5)
def vx(x):
return 0.
def vy(x):
return 0.
def vz(x):
return 0.
def vthx(x):
return T(x)
def vthy(x):
return T(x)
def vthz(x):
return T(x)
MaxwellianFluidModel(bx=bx, by=by, bz=bz,
protons={"charge": 1,
"density": density,
"vbulkx": vx, "vbulky": vy, "vbulkz": vz,
"vthx": vthx, "vthy": vthy, "vthz": vthz,
"nbr_part_per_cell": nbr_part_per_cell,
"init": model_init})
ElectronModel(closure="isothermal", Te=0.12)
if timestamps is None:
timestamps = np.arange(0, global_vars.sim.final_time + global_vars.sim.time_step, global_vars.sim.time_step)
for quantity in ["E", "B"]:
ElectromagDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps
)
for quantity in ["density", "bulkVelocity"]:
FluidDiagnostics(
quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps
)
poplist = ["protons"]
for pop in poplist:
for quantity in ["density", "flux"]:
FluidDiagnostics(quantity=quantity,
write_timestamps=timestamps,
compute_timestamps=timestamps,
population_name=pop)
for quantity in ['domain', 'levelGhost', 'patchGhost']:
ParticleDiagnostics(quantity=quantity,
compute_timestamps=timestamps,
write_timestamps=timestamps,
population_name=pop)
Simulator(global_vars.sim).initialize().run()
eb_hier = None
if qty in ["e", "eb"]:
eb_hier = hierarchy_from(h5_filename=diag_outputs+"/EM_E.h5", hier=eb_hier)
if qty in ["b", "eb"]:
eb_hier = hierarchy_from(h5_filename=diag_outputs+"/EM_B.h5", hier=eb_hier)
if qty in ["e", "b", "eb"]:
return eb_hier
is_particle_type = qty == "particles" or qty == "particles_patch_ghost"
if is_particle_type:
particle_hier = None
if qty == "particles":
particle_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_pop_protons_domain.h5")
particle_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_pop_protons_levelGhost.h5", hier=particle_hier)
if is_particle_type:
particle_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_pop_protons_patchGhost.h5", hier=particle_hier)
if qty == "particles":
merge_particles(particle_hier)
if is_particle_type:
return particle_hier
if qty == "moments":
mom_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_density.h5")
mom_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_bulkVelocity.h5", hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_pop_protons_density.h5", hier=mom_hier)
mom_hier = hierarchy_from(h5_filename=diag_outputs+"/ions_pop_protons_flux.h5", hier=mom_hier)
return mom_hier
