update python diags

pyphare/pyphare/pharesee/hierarchy.py

@@ -168,14 +168,14 @@ def __init__(self, layout, field_name, data, **kwargs):
 
         self.dataset = data
 
-
     def meshgrid(self, select=None):
         def grid():
             if self.ndim == 1:
                 return [self.x]
             if self.ndim == 2:
                 return np.meshgrid(self.x, self.y, indexing="ij")
             return np.meshgrid(self.x, self.y, self.z, indexing="ij")
+
         mesh = grid()
         if select is not None:
             return tuple(g[select] for g in mesh)
@@ -1496,6 +1496,12 @@ def isFieldQty(qty):
         "flux_x",
         "flux_y",
         "flux_z",
+        "momentumTensor_xx",
+        "momentumTensor_xy",
+        "momentumTensor_xz",
+        "momentumTensor_yy",
+        "momentumTensor_yz",
+        "momentumTensor_zz",
     )
 
 

src/core/data/tensorfield/tensorfield.hpp

@@ -16,15 +16,15 @@ namespace PHARE::core
 {
 
 
-template<typename NdArrayImpl, typename PhysicalQuantity, std::size_t rank = 1>
+template<typename NdArrayImpl, typename PhysicalQuantity, std::size_t rank_ = 1>
 class TensorField
 {
 private:
     constexpr static std::size_t dimFromRank()
     {
-        if constexpr (rank == 1) // Vector field
+        if constexpr (rank_ == 1) // Vector field
             return 3;
-        else if constexpr (rank == 2) // symmetric 3x3 tensor field
+        else if constexpr (rank_ == 2) // symmetric 3x3 tensor field
             return 6;
     }
 
@@ -37,6 +37,7 @@ class TensorField
 
     using value_type                       = typename NdArrayImpl::type;
     static constexpr std::size_t dimension = NdArrayImpl::dimension;
+    static constexpr std::size_t rank      = rank_;
     using tensor_t                         = typename PhysicalQuantity::template TensorType<rank>;
 
     TensorField(std::string const& name, tensor_t physQty)

src/core/data/vecfield/vecfield_component.hpp

@@ -43,7 +43,8 @@ namespace core
     inline std::unordered_map<std::string, Component> const Components::vecComponentMap{
         {"x", Component::X}, {"y", Component::Y}, {"z", Component::Z}};
     inline std::unordered_map<std::string, Component> const Components::tensComponentMap{
-        {"x", Component::X}, {"y", Component::Y}, {"z", Component::Z}};
+        {"xx", Component::XX}, {"xy", Component::XY}, {"xz", Component::XZ},
+        {"yy", Component::YY}, {"yz", Component::YZ}, {"zz", Component::ZZ}};
 
 } // namespace core
 } // namespace PHARE

src/diagnostic/detail/h5writer.hpp

@@ -139,12 +139,13 @@ class H5Writer
 
 
 
-    template<typename VecField>
-    static void writeVecFieldAsDataset(HighFiveFile& h5, std::string path, VecField& vecField)
+    template<typename TensorField>
+    static void writeTensorFieldAsDataset(HighFiveFile& h5, std::string path,
+                                          TensorField& tensorField)
     {
-        for (auto& [id, type] : core::Components::componentMap())
+        for (auto& [id, type] : core::Components::componentMap<TensorField::rank>())
             h5.write_data_set_flat<dimension>(path + "_" + id,
-                                              &(*vecField.getComponent(type).begin()));
+                                              &(*tensorField.getComponent(type).begin()));
     }
 
     auto& modelView() { return modelView_; }

src/diagnostic/detail/types/electromag.hpp

@@ -151,9 +151,9 @@ void ElectromagDiagnosticWriter<H5Writer>::write(DiagnosticProperties& diagnosti
 
     for (auto* vecField : h5Writer.modelView().getElectromagFields())
         if (diagnostic.quantity == "/" + vecField->name())
-            h5Writer.writeVecFieldAsDataset(*fileData_.at(diagnostic.quantity),
-                                            h5Writer.patchPath() + "/" + vecField->name(),
-                                            *vecField);
+            h5Writer.writeTensorFieldAsDataset(*fileData_.at(diagnostic.quantity),
+                                               h5Writer.patchPath() + "/" + vecField->name(),
+                                               *vecField);
 }
 
 

src/diagnostic/detail/types/fluid.hpp

@@ -247,6 +247,10 @@ void FluidDiagnosticWriter<H5Writer>::initDataSets(
         for (auto& [id, type] : core::Components::componentMap())
             initDS(path, attr, key + "_" + id, null);
     };
+    auto initTF = [&](auto& path, auto& attr, std::string key, auto null) {
+        for (auto& [id, type] : core::Components::componentMap<2>())
+            initDS(path, attr, key + "_" + id, null);
+    };
 
     auto initPatch = [&](auto& lvl, auto& attr, std::string patchID = "") {
         bool null        = patchID.empty();
@@ -261,17 +265,17 @@ void FluidDiagnosticWriter<H5Writer>::initDataSets(
                 initDS(path, attr[popId], "density", null);
             if (isActiveDiag(diagnostic, tree, "flux"))
                 initVF(path, attr[popId], "flux", null);
-            // if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
-            //     initTF(path, attr[popId], "momentum_tensor", null);
+            if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
+                initTF(path, attr[popId], "momentum_tensor", null);
         }
 
         std::string tree{"/ions/"};
         if (isActiveDiag(diagnostic, tree, "density"))
             initDS(path, attr["ion"], "density", null);
         if (isActiveDiag(diagnostic, tree, "bulkVelocity"))
             initVF(path, attr["ion"], "bulkVelocity", null);
-        // if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
-        //     initTF(path, attr["ion"], "momentum_tensor", null);
+        if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
+            initTF(path, attr["ion"], "momentum_tensor", null);
     };
 
     initDataSets_(patchIDs, patchAttributes, maxLevel, initPatch);
@@ -288,8 +292,8 @@ void FluidDiagnosticWriter<H5Writer>::write(DiagnosticProperties& diagnostic)
     auto writeDS = [&](auto path, auto& field) {
         h5file.template write_data_set_flat<GridLayout::dimension>(path, &(*field.begin()));
     };
-    auto writeVF
-        = [&](auto path, auto& vecF) { h5Writer.writeVecFieldAsDataset(h5file, path, vecF); };
+    auto writeTF
+        = [&](auto path, auto& vecF) { h5Writer.writeTensorFieldAsDataset(h5file, path, vecF); };
 
     std::string path = h5Writer.patchPath() + "/";
     for (auto& pop : ions)
@@ -298,19 +302,19 @@ void FluidDiagnosticWriter<H5Writer>::write(DiagnosticProperties& diagnostic)
         if (isActiveDiag(diagnostic, tree, "density"))
             writeDS(path + "density", pop.density());
         if (isActiveDiag(diagnostic, tree, "flux"))
-            writeVF(path + "flux", pop.flux());
-        // if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
-        //     writeTF(path + "momentum_tensor", momentum_tensor_[pop.name()]);
+            writeTF(path + "flux", pop.flux());
+        if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
+            writeTF(path + "momentum_tensor", pop.momentumTensor());
     }
 
     std::string tree{"/ions/"};
     auto& density = ions.density();
     if (isActiveDiag(diagnostic, tree, "density"))
         writeDS(path + "density", density);
     if (isActiveDiag(diagnostic, tree, "bulkVelocity"))
-        writeVF(path + "bulkVelocity", ions.velocity());
-    // if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
-    //     writeTF(path + "momentum_tensor", momentum_tensor_["ion"]);
+        writeTF(path + "bulkVelocity", ions.velocity());
+    if (isActiveDiag(diagnostic, tree, "momentum_tensor"))
+        writeTF(path + "momentum_tensor", ions.momentumTensor());
 }
 
 

tests/diagnostic/__init__.py

@@ -1,12 +1,13 @@
-
-
 def timestamps_with_step(sim, dump_step):
     import numpy as np
+
     nbr_dump_step = sim.final_time / dump_step
     return dump_step * np.arange(nbr_dump_step)
 
+
 def all_timestamps(sim):
     import numpy as np
+
     nbr_dump_step = int(sim.final_time / sim.time_step) + 1
     return sim.time_step * np.arange(nbr_dump_step)
 
@@ -25,7 +26,7 @@ def dump_all_diags(pops=[], flush_every=100, timestamps=None):
         compute_timestamps=timestamps,
     )
 
-    for quantity in ["density", "bulkVelocity"]:
+    for quantity in ["density", "bulkVelocity", "pressure_tensor"]:
         ph.FluidDiagnostics(
             quantity=quantity,
             write_timestamps=timestamps,
@@ -35,21 +36,21 @@ def dump_all_diags(pops=[], flush_every=100, timestamps=None):
 
     for pop in pops:
         for quantity in ["density", "flux"]:
-          ph.FluidDiagnostics(
-              quantity=quantity,
-              write_timestamps=timestamps,
-              compute_timestamps=timestamps,
-              flush_every=flush_every,
-              population_name=pop
-          )
-
-        for quantity in ['domain', 'levelGhost', 'patchGhost']:
+            ph.FluidDiagnostics(
+                quantity=quantity,
+                write_timestamps=timestamps,
+                compute_timestamps=timestamps,
+                flush_every=flush_every,
+                population_name=pop,
+            )
+
+        for quantity in ["domain", "levelGhost", "patchGhost"]:
             ph.ParticleDiagnostics(
                 quantity=quantity,
                 compute_timestamps=timestamps,
                 write_timestamps=timestamps,
                 flush_every=flush_every,
-                population_name=pop
+                population_name=pop,
             )
 
     for quantity in ["E", "B"]:

tests/simulator/test_diagnostic_timestamps.py

@@ -124,7 +124,7 @@ def test_dump_diags_timestamps(self):
         def make_time(stamp):
             return "{:.10f}".format(stamp)
 
-        for diagInfo in ph.global_vars.sim.diagnostics:
+        for diagname, diagInfo in ph.global_vars.sim.diagnostics.items():
             h5_filename = os.path.join(out, h5_filename_from(diagInfo))
             self.assertTrue(os.path.exists(h5_filename))
 
@@ -166,7 +166,7 @@ def test_hierarchy_timestamp_cadence(self, refinement_boxes):
 
                 Simulator(simulation).run()
 
-                for diagInfo in simulation.diagnostics:
+                for diagname, diagInfo in simulation.diagnostics.items():
                     h5_filename = os.path.join(diag_outputs, h5_filename_from(diagInfo))
                     self.assertTrue(os.path.exists(h5_filename))
 

tests/simulator/test_diagnostics.py

@@ -182,13 +182,13 @@ def _test_dump_diags(self, dim, **simInput):
                 any(
                     [
                         diagInfo.quantity.endswith("domain")
-                        for diagInfo in ph.global_vars.sim.diagnostics
+                        for diagname, diagInfo in ph.global_vars.sim.diagnostics.items()
                     ]
                 )
             )
 
             particle_files = 0
-            for diagInfo in ph.global_vars.sim.diagnostics:
+            for diagname, diagInfo in ph.global_vars.sim.diagnostics.items():
                 h5_filepath = os.path.join(local_out, h5_filename_from(diagInfo))
                 self.assertTrue(os.path.exists(h5_filepath))
 

tests/simulator/test_initialization.py

@@ -713,7 +713,7 @@ def _test_patch_ghost_on_refined_level_case(self, dim, has_patch_ghost, **kwargs
             any(
                 [
                     diagInfo.quantity.endswith("patchGhost")
-                    for diagInfo in ph.global_vars.sim.diagnostics
+                    for diagname, diagInfo in ph.global_vars.sim.diagnostics.items()
                 ]
             )
         )

tests/simulator/test_tagging.py

@@ -172,14 +172,14 @@ def _test_dump_diags(self, dim, **simInput):
                 any(
                     [
                         diagInfo.quantity.endswith("tags")
-                        for diagInfo in ph.global_vars.sim.diagnostics
+                        for diagname, diagInfo in ph.global_vars.sim.diagnostics.items()
                     ]
                 )
             )
 
             checks = 0
             found = 0
-            for diagInfo in ph.global_vars.sim.diagnostics:
+            for diagname, diagInfo in ph.global_vars.sim.diagnostics.items():
                 h5_filepath = os.path.join(local_out, h5_filename_from(diagInfo))
                 self.assertTrue(os.path.exists(h5_filepath))