add serialized simulation to diagnostics files

pyphare/pyphare/pharein/__init__.py

@@ -251,9 +251,14 @@ def as_paths(rb):
     addInitFunction(maginit_path + "y_component", fn_wrapper(modelDict["by"]))
     addInitFunction(maginit_path + "z_component", fn_wrapper(modelDict["bz"]))
 
+    serialized_sim = serialize_sim(simulation)
+
     #### adding diagnostics
+
     diag_path = "simulation/diagnostics/"
     for diag in list(simulation.diagnostics.values()):
+        diag.attributes["serialized_simulation"] = serialized_sim
+
         type_path = diag_path + diag.type + "/"
         name_path = type_path + diag.name
         add_string(name_path + "/" + "type", diag.type)
@@ -265,6 +270,7 @@ def as_paths(rb):
         pp.add_array_as_vector(
             name_path + "/" + "compute_timestamps", diag.compute_timestamps
         )
+
         add_size_t(name_path + "/" + "n_attributes", len(diag.attributes))
         for attr_idx, attr_key in enumerate(diag.attributes):
             add_string(name_path + "/" + f"attribute_{attr_idx}_key", attr_key)
@@ -343,7 +349,7 @@ def as_paths(rb):
                 restarts_path + "write_timestamps", restart_options["timestamps"]
             )
 
-        add_string(restarts_path + "serialized_simulation", serialize_sim(simulation))
+        add_string(restarts_path + "serialized_simulation", serialized_sim)
     #### restarts added
 
     #### adding electrons

pyphare/pyphare/pharein/diagnostics.py

@@ -1,3 +1,5 @@
+import numpy as np
+
 from ..core import phare_utilities
 from . import global_vars
 
@@ -45,8 +47,6 @@ def wrapper(diagnostics_object, name, **kwargs):
     return wrapper
 
 
-import numpy as np
-
 # ------------------------------------------------------------------------------
 def validate_timestamps(clazz, key, **kwargs):
     sim = global_vars.sim
@@ -173,7 +173,6 @@ def __init__(self, **kwargs):
         )
 
     def _setSubTypeAttributes(self, **kwargs):
-
         if kwargs["quantity"] not in ElectromagDiagnostics.em_quantities:
             error_msg = "Error: '{}' not a valid electromag diagnostics : " + ", ".join(
                 ElectromagDiagnostics.em_quantities
@@ -201,7 +200,6 @@ def population_in_model(population):
 
 
 class FluidDiagnostics_(Diagnostics):
-
     fluid_quantities = [
         "density",
         "mass_density",
@@ -327,7 +325,6 @@ def _setSubTypeAttributes(self, **kwargs):
         self.quantity = "/ions/pop/" + self.population_name + "/" + self.quantity
 
     def space_box(self, **kwargs):
-
         if "extent" not in kwargs and self.quantity == "space_box":
             raise ValueError(
                 "Error: missing 'extent' parameter required by 'space_box' the ParticleDiagnostics type"
@@ -352,7 +349,6 @@ def to_dict(self):
 
 
 class MetaDiagnostics(Diagnostics):
-
     meta_quantities = ["tags"]
     type = "info"
 

pyphare/pyphare/pharesee/run.py

@@ -111,7 +111,6 @@ def _divB2D(Bx, By, xBx, yBy):
 
 
 def _compute_divB(patchdatas, **kwargs):
-
     reference_pd = patchdatas["Bx"]  # take Bx as a reference, but could be any other
     ndim = reference_pd.box.ndim
 

tests/simulator/test_diagnostics.py

@@ -160,7 +160,7 @@ def _test_dump_diags(self, dim, **simInput):
         simInput["refinement_boxes"] = {"L0": {"B0": b0}}
 
         py_attrs = [f"{dep}_version" for dep in ["samrai", "highfive", "pybind"]]
-        py_attrs += ["git_hash"]
+        py_attrs += ["git_hash", "serialized_simulation"]
 
         for interp in range(1, 4):
             print("test_dump_diags dim/interp:{}/{}".format(dim, interp))
@@ -203,6 +203,13 @@ def _test_dump_diags(self, dim, **simInput):
                 for py_attr in py_attrs:
                     self.assertIn(py_attr, h5_py_attrs)
 
+                assert (
+                    ph.simulation.deserialize(
+                        h5_file["py_attrs"].attrs["serialized_simulation"]
+                    ).electrons.closure.Te
+                    == 0.12
+                )
+
                 hier = hierarchy_from(h5_filename=h5_filepath)
                 if h5_filepath.endswith("domain.h5"):
                     particle_files += 1