def _test_patch_ghost_on_refined_level_case(self, has_patch_ghost,
**kwargs):
import pyphare.pharein as ph
from pybindlibs import cpp
from pyphare.simulator.simulator import startMPI
startMPI()
out = "phare_outputs"
test_id = self.ddt_test_id()
for dim in [1]:
for interp in [1, 2, 3]:
b0 = [[10 for i in range(dim)], [19 for i in range(dim)]]
refinement_boxes = {"L0": {"B0": b0}}
local_out = f"{out}/dim{dim}_interp{interp}_mpi_n_{cpp.mpi_size()}_id{test_id}/{str(has_patch_ghost)}"
kwargs["diag_outputs"] = local_out
datahier = self.getHierarchy(interp, refinement_boxes,
"particles_patch_ghost", **kwargs)
self.assertTrue(
any([
diagInfo.quantity.endswith("patchGhost")
for diagInfo in ph.global_vars.sim.diagnostics
]))
key = "protons_particles"
self.assertTrue((1 in datahier.levels()) == has_patch_ghost)
def _test_patch_ghost_on_refined_level_case(self, dim, has_patch_ghost,
**kwargs):
import pyphare.pharein as ph
from pyphare.simulator.simulator import startMPI
startMPI()
out = "phare_outputs"
test_id = self.ddt_test_id()
refinement_boxes = {"L0": [nDBox(dim, 10, 19)]}
kwargs["interp_order"] = kwargs.get("interp_order", 1)
local_out = f"{out}/dim{dim}_interp{kwargs['interp_order']}_mpi_n_{cpp.mpi_size()}_id{test_id}/{str(has_patch_ghost)}"
kwargs["diag_outputs"] = local_out
datahier = self.getHierarchy(refinement_boxes=refinement_boxes,
qty="particles_patch_ghost",
ndim=dim,
**kwargs)
self.assertTrue(
any([
diagInfo.quantity.endswith("patchGhost")
for diagInfo in ph.global_vars.sim.diagnostics
]))
self.assertTrue((1 in datahier.levels()) == has_patch_ghost)
def main():
import random
startMPI()
rando = random.randint(0, 1e10)
Simulator(config(L0_diags, {"seed": rando})).run().reset()
refinement_boxes={"L0": {"B0": [( 7, 40), ( 20, 60)]}}
sim = config(L0L1_diags, {"seed": rando}, refinement_boxes)
Simulator(sim, post_advance=post_advance).run()
def main():
import random
startMPI()
rando = random.randint(0, 1e10)
refinement_boxes = {"L0": {"B0": [(10, 10), (14, 14)]}}
Simulator(config(L0_diags, {"seed": rando}),
post_advance=post_advance_0).run().reset()
sim = config(L0L1_diags, {"seed": rando}, refinement_boxes)
Simulator(sim, post_advance=post_advance_1).run()
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 setUp(self):
from pyphare.simulator.simulator import startMPI
startMPI()
from pyphare.pharein import Simulation
from pyphare.pharein import MaxwellianFluidModel
from pyphare.pharein import ElectromagDiagnostics, FluidDiagnostics, ParticleDiagnostics
from pyphare.pharein import ElectronModel
from pyphare.simulator.simulator import Simulator, startMPI
from pyphare.pharein import global_vars as gv
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
mpl.use('Agg')
from pyphare.cpp import cpp_lib
cpp = cpp_lib()
startMPI()
if cpp.mpi_rank() == 0:
# log per mpi proc
import os
from pathlib import Path
os.environ["PHARE_LOG"] = "RANK_FILES"
Path(".log").mkdir(exist_ok=True)
diag_outputs = "phare_outputs/test/harris/2d"
from datetime import datetime
def config():
Simulation(
smallest_patch_size=15,
def __init__(self, *args, **kwargs):
super(DiagnosticsTest, self).__init__(*args, **kwargs)
startMPI()
self.simulator = None
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):
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)
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"] * 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) #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 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 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
