change ions.density in ions.chargeDensity... doesnt work !

pyphare/pyphare/pharein/diagnostics.py

@@ -222,6 +222,7 @@ def population_in_model(population):
 class FluidDiagnostics_(Diagnostics):
     fluid_quantities = [
         "density",
+        "charge_density",
         "mass_density",
         "flux",
         "bulkVelocity",
@@ -290,7 +291,7 @@ def __init__(self, **kwargs):
             if for_total_ions(**kwargs):
                 needed_quantities = ["mass_density", "bulkVelocity", "momentum_tensor"]
             else:
-                needed_quantities = ["density", "flux", "momentum_tensor"]
+                needed_quantities = ["charge_density", "flux", "momentum_tensor"]
 
             for quantity in needed_quantities:
                 kwargs["quantity"] = quantity

pyphare/pyphare/pharesee/plotting.py

@@ -274,7 +274,7 @@ def finest_field_plot(run_path, qty, **kwargs):
             time = times[0]
         interpolator, finest_coords = r.GetVi(time, merged=True, interp=interp)[qty]
     elif qty == "rho":
-        file = os.path.join(run_path, "ions_density.h5")
+        file = os.path.join(run_path, "ions_charge_density.h5")
         if time is None:
             times = get_times_from_h5(file)
             time = times[0]

pyphare/pyphare/pharesee/run/run.py

@@ -27,7 +27,7 @@
     "EM_B": "B",
     "EM_E": "E",
     "ions_bulkVelocity": "Vi",
-    "ions_density": "Ni",
+    "ions_charge_density": "Ni",
     "particle_count": "nppc",
 }
 
@@ -116,7 +116,7 @@ def GetMassDensity(self, time, merged=False, interp="nearest", **kwargs):
         return ScalarField(self._get(hier, time, merged, interp))
 
     def GetNi(self, time, merged=False, interp="nearest", **kwargs):
-        hier = self._get_hierarchy(time, "ions_density.h5", **kwargs)
+        hier = self._get_hierarchy(time, "ions_charge_density.h5", **kwargs)
         return ScalarField(self._get(hier, time, merged, interp))
 
     def GetN(self, time, pop_name, merged=False, interp="nearest", **kwargs):
@@ -153,7 +153,7 @@ def GetPi(self, time, merged=False, interp="nearest", **kwargs):
         return self._get(Pi, time, merged, interp)  # should later be a TensorField
 
     def GetPe(self, time, merged=False, interp="nearest", all_primal=True):
-        hier = self._get_hierarchy(time, "ions_density.h5")
+        hier = self._get_hierarchy(time, "ions_charge_density.h5")
 
         Te = hier.sim.electrons.closure.Te
 

pyphare/pyphare_tests/test_pharesee/test_hierarchy.py

@@ -145,7 +145,7 @@ def vthz(x, y):
             for quantity in ["E", "B"]:
                 ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-            for quantity in ["density", "bulkVelocity"]:
+            for quantity in ["charge_density", "bulkVelocity"]:
                 ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
             return sim

src/amr/messengers/hybrid_hybrid_messenger_strategy.hpp

@@ -539,7 +539,7 @@ namespace amr
 
                 auto& J  = hybridModel.state.J;
                 auto& Vi = hybridModel.state.ions.velocity();
-                auto& Ni = hybridModel.state.ions.density();
+                auto& Ni = hybridModel.state.ions.chargeDensity();
 
                 Jold_.copyData(J);
                 ViOld_.copyData(Vi);

src/diagnostic/detail/types/fluid.hpp

@@ -146,7 +146,7 @@ void FluidDiagnosticWriter<H5Writer>::createFiles(DiagnosticProperties& diagnost
     for (auto const& pop : this->h5Writer_.modelView().getIons())
     {
         std::string tree{"/ions/pop/" + pop.name() + "/"};
-        checkCreateFileFor_(diagnostic, fileData_, tree, "density", "flux", "momentum_tensor");
+        checkCreateFileFor_(diagnostic, fileData_, tree, "charge_density", "flux", "momentum_tensor");
     }
 
     std::string tree{"/ions/"};
@@ -206,8 +206,8 @@ void FluidDiagnosticWriter<H5Writer>::getDataSetInfo(DiagnosticProperties& diagn
     }
 
     std::string tree{"/ions/"};
-    if (isActiveDiag(diagnostic, tree, "density"))
-        infoDS(ions.density(), "density", patchAttributes[lvlPatchID]["ion"]);
+    if (isActiveDiag(diagnostic, tree, "charge_density"))
+        infoDS(ions.chargeDensity(), "charge_density", patchAttributes[lvlPatchID]["ion"]);
     if (isActiveDiag(diagnostic, tree, "mass_density"))
         infoDS(ions.massDensity(), "mass_density", patchAttributes[lvlPatchID]["ion"]);
     if (isActiveDiag(diagnostic, tree, "bulkVelocity"))
@@ -275,8 +275,8 @@ void FluidDiagnosticWriter<H5Writer>::initDataSets(
         }
 
         std::string tree{"/ions/"};
-        if (isActiveDiag(diagnostic, tree, "density"))
-            initDS(path, attr["ion"], "density", null);
+        if (isActiveDiag(diagnostic, tree, "charge_density"))
+            initDS(path, attr["ion"], "charge_density", null);
         if (isActiveDiag(diagnostic, tree, "mass_density"))
             initDS(path, attr["ion"], "mass_density", null);
         if (isActiveDiag(diagnostic, tree, "bulkVelocity"))
@@ -315,8 +315,8 @@ void FluidDiagnosticWriter<H5Writer>::write(DiagnosticProperties& diagnostic)
     }
 
     std::string tree{"/ions/"};
-    if (isActiveDiag(diagnostic, tree, "density"))
-        writeDS(path + "density", ions.density());
+    if (isActiveDiag(diagnostic, tree, "charge_density"))
+        writeDS(path + "charge_density", ions.chargeDensity());
     if (isActiveDiag(diagnostic, tree, "mass_density"))
         writeDS(path + "mass_density", ions.massDensity());
     if (isActiveDiag(diagnostic, tree, "bulkVelocity"))
@@ -344,7 +344,7 @@ void FluidDiagnosticWriter<H5Writer>::writeAttributes(
     for (auto& pop : h5Writer.modelView().getIons())
     {
         std::string tree = "/ions/pop/" + pop.name() + "/";
-        checkWrite(tree, "density", pop);
+        checkWrite(tree, "charge_density", pop);
         checkWrite(tree, "flux", pop);
         checkWrite(tree, "momentum_tensor", pop);
     }

src/phare/phare_init.py

@@ -101,7 +101,7 @@ def vthz(x):
     ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
 
-for quantity in ["density", "bulkVelocity"]:
+for quantity in ["charge_density", "bulkVelocity"]:
     ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
 pops = [

src/phare/phare_init_small.py

@@ -104,7 +104,7 @@ def vthz(x):
     ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
 
-for quantity in ["density", "bulkVelocity"]:
+for quantity in ["charge_density", "bulkVelocity"]:
     ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
 pops = [

src/python3/patch_level.hpp

@@ -37,7 +37,7 @@ class PatchLevel
         auto& ions = model_.state.ions;
 
         auto visit = [&](GridLayout& grid, std::string patchID, std::size_t /*iLevel*/) {
-            setPatchDataFromField(patchDatas.emplace_back(), ions.density(), grid, patchID);
+            setPatchDataFromField(patchDatas.emplace_back(), ions.chargeDensity(), grid, patchID);
         };
 
         PHARE::amr::visitLevel<GridLayout>(*hierarchy_.getPatchLevel(lvl_),

tests/core/data/electrons/test_electrons.cpp

@@ -368,7 +368,7 @@ TYPED_TEST(ElectronsTest, ThatElectronsDensityEqualIonDensity)
     electrons.update(layout);
 
     auto& Ne = electrons.density();
-    auto& Ni = ions.density();
+    auto& Ni = ions.chargeDensity();
 
     if constexpr (dim == 1)
     {

tests/core/data/ions/test_ions.cpp

@@ -154,7 +154,7 @@ TEST_F(theIons, areSettableUponConstruction)
 #ifndef NDEBUG // no throw in release mode! JUST SEGFAULTS! :D
 TEST_F(theIons, throwIfAccessingDensityWhileNotUsable)
 {
-    EXPECT_ANY_THROW(auto& n = ions.density()(0));
+    EXPECT_ANY_THROW(auto& n = ions.chargeDensity()(0));
 }
 #endif
 

tests/diagnostic/__init__.py

@@ -28,7 +28,7 @@ def dump_all_diags(pops=[], flush_every=100, timestamps=None):
     #     write_timestamps=timestamps
     # )
 
-    for quantity in ["density", "bulkVelocity", "pressure_tensor"]:
+    for quantity in ["charge_density", "bulkVelocity", "pressure_tensor"]:
         ph.FluidDiagnostics(
             quantity=quantity,
             write_timestamps=timestamps,

tests/diagnostic/test_diagnostics.hpp

@@ -125,7 +125,7 @@ void validateFluidDump(Simulator& sim, Hi5Diagnostic& hi5)
             checkF(layout, path, "/ions/pop/" + pop.name(), "/density"s, pop.chargeDensity());
             checkVF(layout, path, "/ions/pop/" + pop.name(), "/flux"s, pop.flux());
         }
-        checkF(layout, path, "/ions"s, "/density"s, ions.density());
+        checkF(layout, path, "/ions"s, "/charge_density"s, ions.chargeDensity());
 
         std::string tree{"/ions"}, var{"/bulkVelocity"};
         auto hifile = hi5.writer.makeFile(hi5.writer.fileString(tree + var), hi5.flags_);
@@ -236,7 +236,7 @@ void validateAttributes(Simulator& sim, Hi5Diagnostic& hi5)
     auto nbrPop = dict["simulation"]["ions"]["nbrPopulations"].template to<std::size_t>();
     EXPECT_EQ(nbrPop, expectedPopNbr);
 
-    std::vector<std::string> h5FileTypes{"/EM_B", "/EM_E", "/ions/density", "/ions/bulkVelocity"};
+    std::vector<std::string> h5FileTypes{"/EM_B", "/EM_E", "/ions/charge_density", "/ions/bulkVelocity"};
 
     for (std::size_t i = 0; i < nbrPop; ++i)
     {

tests/diagnostic/test_diagnostics.ipp

@@ -14,7 +14,7 @@ void fluid_test(Simulator&& sim, std::string out_dir)
 
     { // Scoped to destruct after dump
         Hi5Diagnostic<Hierarchy, HybridModel> hi5{hierarchy, hybridModel, out_dir, NEW_HI5_FILE};
-        hi5.dMan.addDiagDict(hi5.fluid("/ions/density"))
+        hi5.dMan.addDiagDict(hi5.fluid("/ions/charge_density"))
             .addDiagDict(hi5.fluid("/ions/bulkVelocity"))
             .addDiagDict(hi5.fluid("/ions/momentum_tensor"))
             .addDiagDict(hi5.fluid("/ions/pop/alpha/density"))

tests/functional/alfven_wave/alfven_wave1d.py

@@ -96,7 +96,7 @@ def vthz(x):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     return sim

tests/functional/dispersion/dispersion.py

@@ -171,7 +171,7 @@ def vthz(x):
             quantity=quantity, write_timestamps=timestamps, flush_every=0
         )
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(
             quantity=quantity, write_timestamps=timestamps, flush_every=0
         )

tests/functional/harris/harris_2d_lb.py

@@ -133,11 +133,11 @@ def vthxyz(x, y):
 
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     ph.FluidDiagnostics(
-        quantity="density", write_timestamps=timestamps, population_name="protons"
+        quantity="charge_density", write_timestamps=timestamps, population_name="protons"
     )
     ph.InfoDiagnostics(quantity="particle_count")
 

tests/functional/shock/shock.py

@@ -107,7 +107,7 @@ def vthz(x):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     return sim

tests/functional/td/td1d.py

@@ -100,7 +100,7 @@ def vthz(x):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(
             quantity=quantity,
             write_timestamps=timestamps,

tests/functional/tdtagged/td1dtagged.py

@@ -117,7 +117,7 @@ def config(**options):
 
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     for pop in sim.model.populations:

tests/functional/translation/translat1d.py

@@ -87,7 +87,7 @@ def vthz(x):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     return sim
@@ -182,7 +182,7 @@ def vthz(x):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     return sim

tests/simulator/refinement/test_2d_10_core.py

@@ -101,7 +101,7 @@ def vthz(x, y):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     return sim

tests/simulator/refinement/test_2d_2_core.py

@@ -101,7 +101,7 @@ def vthz(x, y):
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     return sim

tests/simulator/test_advance.py

@@ -152,7 +152,7 @@ def vthz(*xyz):
         for quantity in ["E", "B"]:
             ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
-        for quantity in ["density", "bulkVelocity"]:
+        for quantity in ["charge_density", "bulkVelocity"]:
             FluidDiagnostics(
                 quantity=quantity,
                 write_timestamps=timestamps,
@@ -222,7 +222,7 @@ def vthz(*xyz):
                 h5_filename=diag_outputs + "/EM_B.h5", hier=eb_hier
             )
             mom_hier = hierarchy_from(
-                h5_filename=diag_outputs + "/ions_density.h5", hier=eb_hier
+                h5_filename=diag_outputs + "/ions_charge_density.h5", hier=eb_hier
             )
             mom_hier = hierarchy_from(
                 h5_filename=diag_outputs + "/ions_bulkVelocity.h5", hier=mom_hier
@@ -231,7 +231,7 @@ def vthz(*xyz):
 
         if qty == "moments" or qty == "fields":
             mom_hier = hierarchy_from(
-                h5_filename=diag_outputs + "/ions_density.h5", hier=eb_hier
+                h5_filename=diag_outputs + "/ions_charge_density.h5", hier=eb_hier
             )
             mom_hier = hierarchy_from(
                 h5_filename=diag_outputs + "/ions_bulkVelocity.h5", hier=mom_hier

tests/simulator/test_initialization.py

@@ -170,7 +170,7 @@ def vthz(*xyz):
                 quantity=quantity, write_timestamps=np.zeros(time_step_nbr)
             )
 
-        for quantity in ["density", "bulkVelocity"]:
+        for quantity in ["charge_density", "bulkVelocity"]:
             FluidDiagnostics(
                 quantity=quantity, write_timestamps=np.zeros(time_step_nbr)
             )
@@ -232,7 +232,7 @@ def vthz(*xyz):
             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_charge_density.h5")
             mom_hier = hierarchy_from(
                 h5_filename=diag_outputs + "/ions_bulkVelocity.h5", hier=mom_hier
             )

tests/simulator/test_run.py

@@ -146,7 +146,7 @@ def vthz(x, y):
 
     for quantity in ["E", "B"]:
         ph.ElectromagDiagnostics(quantity=quantity, write_timestamps=timestamps)
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["charge_density", "bulkVelocity"]:
         ph.FluidDiagnostics(quantity=quantity, write_timestamps=timestamps)
 
     pop = "protons"