def clean_up_diags_dirs(self):
from pyphare.cpp import cpp_lib
cpp_lib().mpi_barrier() # synchronize first
if cpp_lib().mpi_rank() > 0:
return # only delete h5 files for rank 0
if self.success:
import os
import shutil
for diag_dir in self.diag_dirs:
if os.path.exists(diag_dir):
shutil.rmtree(diag_dir)
def initialize(self):
if self.cpp_sim is not None:
raise ValueError(
"Simulator already initialized: requires reset to re-initialize"
)
try:
from pyphare.cpp import cpp_lib
from pyphare.pharein import populateDict
startMPI()
populateDict()
self.cpp_hier = cpp_lib().make_hierarchy()
self.cpp_sim = make_cpp_simulator(
self.simulation.ndim, self.simulation.interp_order,
self.simulation.refined_particle_nbr, self.cpp_hier)
self.cpp_sim.initialize()
self._auto_dump() # first dump might be before first advance
return self
except:
import sys
print('Exception caught in "Simulator.initialize()": {}'.format(
sys.exc_info()[0]))
raise ValueError(
"Error in Simulator.initialize(), see previous error")
def __init__(self, simulator):
from .. import pharein as ph
from pyphare.cpp import cpp_lib
self.dim = ph.global_vars.sim.ndim
self.interp = ph.global_vars.sim.interp_order
self.refined_particle_nbr = ph.global_vars.sim.refined_particle_nbr
self.cpp = getattr(cpp_lib(), f"DataWrangler_{self.dim}_{self.interp}_{self.refined_particle_nbr}")\
(simulator.cpp_sim, simulator.cpp_hier)
def main():
from pyphare.cpp import cpp_lib
cpp = cpp_lib()
from pyphare.pharesee.run import Run
from pyphare.pharesee.hierarchy import flat_finest_field
config()
Simulator(gv.sim).run()
if cpp.mpi_rank() == 0:
vphi, t, phi, a, k = phase_speed(".", 0.01, 1000)
r = Run(".")
t = get_times_from_h5("EM_B.h5")
fig, ax = plt.subplots(figsize=(9, 5), nrows=1)
B = r.GetB(t[int(len(t) / 2)])
by, xby = flat_finest_field(B, "By")
ax.plot(xby, by, label="t = 500", alpha=0.6)
sorted_patches = sorted(B.patch_levels[1].patches,
key=lambda p: p.box.lower[0])
x0 = sorted_patches[0].patch_datas["By"].x[0]
x1 = sorted_patches[-1].patch_datas["By"].x[-1]
B = r.GetB(t[-1])
by, xby = flat_finest_field(B, "By")
ax.plot(xby, by, label="t = 1000", alpha=0.6)
ax.plot(xby,
wave(xby, 0.01, 2 * np.pi / 1000., 2 * np.pi / 1000 * 500),
color="k",
ls="--",
label="T=500 (theory)")
B = r.GetB(t[0])
by, xby = flat_finest_field(B, "By")
ax.plot(xby, by, label="t = 0", color="k")
ax.set_xlabel("x")
ax.set_ylabel(r"$B_y$")
ax.legend(ncol=4, loc="upper center")
ax.set_ylim((-0.012, 0.013))
ax.set_title(r"$V_\phi = {:6.4f}$".format(vphi.mean()))
ax.axvspan(x0, x1, alpha=0.2)
fig.tight_layout()
fig.savefig("alfven_wave.png", dpi=200)
assert np.mean(np.abs(vphi - 1) < 5e-2)
def _log_to_file(self):
"""
send C++ std::cout logs to files with env var PHARE_LOG
Support keys:
RANK_FILES - logfile per rank
DATETIME_FILES - logfile with starting datetime timestamp per rank
NONE - no logging files, display to cout
"""
import os
if "PHARE_LOG" not in os.environ:
os.environ["PHARE_LOG"] = "RANK_FILES"
from pyphare.cpp import cpp_lib
if os.environ["PHARE_LOG"] != "NONE" and cpp_lib().mpi_rank() == 0:
from pathlib import Path
Path(".log").mkdir(exist_ok=True)
def run(self):
from pyphare.cpp import cpp_lib
self._check_init()
perf = []
end_time = self.cpp_sim.endTime()
t = 0.
while t < end_time:
tick = timem.time()
self.advance()
tock = timem.time()
ticktock = tock - tick
perf.append(ticktock)
t = self.cpp_sim.currentTime()
if cpp_lib().mpi_rank() == 0:
print("t = {:8.5f} - {:6.5f}sec - total {:7.4}sec".format(
t, ticktock, np.sum(perf)))
print("mean advance time = {}".format(np.mean(perf)))
print("total advance time = {}".format(np.sum(perf)))
return self.reset()
def _throw(self, e):
import sys
from pyphare.cpp import cpp_lib
if cpp_lib().mpi_rank() == 0:
print(e)
sys.exit(1)
def startMPI():
if "samrai" not in life_cycles:
from pyphare.cpp import cpp_lib
life_cycles["samrai"] = cpp_lib().SamraiLifeCycle()
def make_cpp_simulator(dim, interp, nbrRefinedPart, hier):
from pyphare.cpp import cpp_lib
make_sim = f"make_simulator_{dim}_{interp}_{nbrRefinedPart}"
return getattr(cpp_lib(), make_sim)(hier)
#!/usr/bin/env python3
from pyphare.cpp import cpp_lib
cpp = cpp_lib()
from tests.diagnostic import dump_all_diags
from tests.simulator import populate_simulation
from pyphare.pharein import ElectronModel
from pyphare.pharein import ElectromagDiagnostics, FluidDiagnostics, ParticleDiagnostics
from pyphare.simulator.simulator import Simulator, startMPI
from pyphare.pharesee.hierarchy import hierarchy_from, h5_filename_from, h5_time_grp_key
import pyphare.pharein as ph
import unittest
import os
import h5py
import numpy as np
from ddt import ddt, data
from pyphare.core.box import Box, Box1D
from tests.simulator.config import project_root
def setup_model(ppc):
def density(x):
return 1.
def by(x):
return 0.
def bz(x):
return 0.
import numpy as np
from pyphare.cpp import cpp_lib # must be first
cpp_lib("pybindlibs.cpp_sim_2_1_4")
import pyphare.pharein as ph
seed = 133333333337
cells, dl = 100, .2
patch_sizes = [50,100]
diag_outputs="tools/bench/real/harris/outputs"
def density(x, y):
L = ph.global_vars.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 by(x, y):
sim = ph.global_vars.sim
Lx = sim.simulation_domain()[0]
Ly = sim.simulation_domain()[1]
w1, w2 = 0.2, 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 S(y, y0, l): return 0.5*(1. + np.tanh((y-y0)/l))
def bx(x, y):
def __call__(self, *xyz):
from pyphare.cpp import cpp_lib
# convert numpy array to C++ SubSpan
# couples vector init functions to C++
return cpp_lib().makePyArrayWrapper(super().__call__(*xyz))
def try_cpp_dep_vers():
try:
from pyphare.cpp import cpp_lib
return cpp_lib().phare_deps()
except ImportError:
return {}
