overlaps during tests

.gitignore

@@ -24,4 +24,4 @@ perf.*
 PHARE_REPORT.zip
 .cache
 .gdbinit
-.phlop
+.phlop

tests/simulator/refinement/CMakeLists.txt

@@ -17,5 +17,6 @@ if(HighFive)
   endif(testMPI)
 
   phare_python3_exec(9 simple_2d_refinement test_2d_2_core.py  ${CMAKE_CURRENT_BINARY_DIR})
+  phare_python3_exec(9  test_2d_overlaps test_2d_overlaps.py  ${CMAKE_CURRENT_BINARY_DIR})
 
 endif()

tests/simulator/refinement/test_2d_overlaps.py

@@ -0,0 +1,188 @@
+#!/usr/bin/env python3
+
+import numpy as np
+import matplotlib as mpl
+from pathlib import Path
+
+import pyphare.pharein as ph
+from pyphare.cpp import cpp_lib
+from pyphare.simulator.simulator import Simulator, startMPI
+
+from tests.simulator import SimulatorTest
+from tests.simulator.test_advance import AdvanceTestBase
+from tests.diagnostic import dump_all_diags
+
+mpl.use("Agg")
+
+cpp = cpp_lib()
+
+
+cells = (40, 80)
+time_step = 0.005
+final_time = 1
+timestamps = np.arange(0, final_time + time_step, time_step)
+diag_dir = "phare_outputs/test/refinenment/2d/overlaps"
+test = AdvanceTestBase(rethrow=True)
+
+
+def config():
+    L = 0.5
+
+    sim = ph.Simulation(
+        time_step=time_step,
+        final_time=final_time,
+        largest_patch_size=10,
+        cells=cells,
+        dl=(0.40, 0.40),
+        refinement="tagging",
+        max_nbr_levels=2,
+        hyper_resistivity=0.002,
+        resistivity=0.001,
+        diag_options={
+            "format": "phareh5",
+            "options": {"dir": diag_dir, "mode": "overwrite"},
+        },
+        strict=False,
+    )
+
+    def density(x, y):
+        Ly = sim.simulation_domain()[1]
+        return (
+            0.4
+            + 1.0 / np.cosh((y - Ly * 0.3) / L) ** 2
+            + 1.0 / np.cosh((y - Ly * 0.7) / L) ** 2
+        )
+
+    def S(y, y0, l):
+        return 0.5 * (1.0 + np.tanh((y - y0) / l))
+
+    def by(x, y):
+        Lx = sim.simulation_domain()[0]
+        Ly = sim.simulation_domain()[1]
+        sigma = 1.0
+        dB = 0.1
+
+        x0 = x - 0.5 * Lx
+        y1 = y - 0.3 * Ly
+        y2 = y - 0.7 * Ly
+
+        dBy1 = 2 * dB * x0 * np.exp(-(x0**2 + y1**2) / (sigma) ** 2)
+        dBy2 = -2 * dB * x0 * np.exp(-(x0**2 + y2**2) / (sigma) ** 2)
+
+        return 0.0  # dBy1 + dBy2
+
+    def bx(x, y):
+        Lx = sim.simulation_domain()[0]
+        Ly = sim.simulation_domain()[1]
+        sigma = 1.0
+        dB = 0.1
+
+        x0 = x - 0.5 * Lx
+        y1 = y - 0.3 * Ly
+        y2 = y - 0.7 * Ly
+
+        dBx1 = -2 * dB * y1 * np.exp(-(x0**2 + y1**2) / (sigma) ** 2)
+        dBx2 = 2 * dB * y2 * np.exp(-(x0**2 + y2**2) / (sigma) ** 2)
+
+        v1 = -1
+        v2 = 1.0
+        return v1 + (v2 - v1) * (S(y, Ly * 0.3, L) - S(y, Ly * 0.7, L))  # + dBx1 + dBx2
+
+    def bz(x, y):
+        return 0.0
+
+    def b2(x, y):
+        return bx(x, y) ** 2 + by(x, y) ** 2 + bz(x, y) ** 2
+
+    def T(x, y):
+        K = 0.7
+        temp = 1.0 / density(x, y) * (K - b2(x, y) * 0.5)
+        assert np.all(temp > 0)
+        return temp
+
+    def vx(x, y):
+        return 0.0
+
+    def vy(x, y):
+        return 0.0
+
+    def vz(x, y):
+        return 0.0
+
+    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": 20,
+    }
+
+    model = ph.MaxwellianFluidModel(
+        bx=bx,
+        by=by,
+        bz=bz,
+        protons={"charge": 1, "density": density, **vvv, "init": {"seed": 12334}},
+    )
+    ph.ElectronModel(closure="isothermal", Te=0.0)
+
+    dump_all_diags(model.populations, flush_every=1)
+
+    return sim
+
+
+def get_time(path, time=None, datahier=None):
+    if time is not None:
+        time = "{:.10f}".format(time)
+    from pyphare.pharesee.hierarchy import hierarchy_from
+
+    datahier = hierarchy_from(h5_filename=path + "/EM_E.h5", times=time, hier=datahier)
+    datahier = hierarchy_from(h5_filename=path + "/EM_B.h5", times=time, hier=datahier)
+
+    return datahier
+
+
+def get_hier(path):
+    return get_time(path)
+
+
+class HarrisTest(SimulatorTest):
+    def __init__(self, *args, **kwargs):
+        super(HarrisTest, self).__init__(*args, **kwargs)
+        self.simulator = None
+        self.plot_dir = Path(f"{diag_dir}_plots") / str(cpp.mpi_size())
+        self.plot_dir.mkdir(parents=True, exist_ok=True)
+
+    def tearDown(self):
+        super(HarrisTest, self).tearDown()
+        if self.simulator is not None:
+            self.simulator.reset()
+        self.simulator = None
+        ph.global_vars.sim = None
+
+    def test_run(self):
+        sim = Simulator(config(), post_advance=self.post_advance)
+        sim.initialize()
+        self.post_advance(0)
+        sim.run().reset()
+        return self
+
+    def post_advance(self, new_time):
+        if cpp.mpi_rank() == 0:
+            L0L1_datahier = get_hier(diag_dir)
+            test.base_test_overlaped_fields_are_equal(L0L1_datahier, new_time)
+
+
+if __name__ == "__main__":
+    startMPI()
+    HarrisTest().test_run().tearDown()