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,
)
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]
)
FluidDiagnostics(
diag_type="density", # choose in (rho_s, flux_s)
write_every=10, # write on disk every x iterations
compute_every=5, # compute diagnostics every x iterations ( x <= write_every)
start_iteration=0, # iteration at which diag is enabled
last_iteration=990, # iteration at which diag is turned off
population_name="protons" # name of the population for which the diagnostics is made
#,path = 'FluidDiagnostics1' # where output files will be written, [default: name]
)
FluidDiagnostics(
diag_type="bulkVelocity",
write_every=10,
compute_every=5,
start_iteration=0,
last_iteration=990,
population_name="background"
)
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():
""" 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 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
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 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,
)
