add pressure tensor diagnostics

generalize vecfield to tensorfield
add momentum tensor to ion and ion populations
add pressure tensor to quantities proposed by Run
add mass density diag and refac compute_hier_from
get Patch convenience debug tool

pyphare/pyphare/core/gridlayout.py

@@ -31,6 +31,18 @@
         "Vthx": "primal",
         "Vthy": "primal",
         "Vthz": "primal",
+        "Mxx": "primal",
+        "Mxy": "primal",
+        "Mxz": "primal",
+        "Myy": "primal",
+        "Myz": "primal",
+        "Mzz": "primal",
+        "Pxx": "primal",
+        "Pxy": "primal",
+        "Pxz": "primal",
+        "Pyy": "primal",
+        "Pyz": "primal",
+        "Pzz": "primal",
         "tags": "dual",
     },
     "y": {
@@ -54,6 +66,18 @@
         "Vthx": "primal",
         "Vthy": "primal",
         "Vthz": "primal",
+        "Mxx": "primal",
+        "Mxy": "primal",
+        "Mxz": "primal",
+        "Myy": "primal",
+        "Myz": "primal",
+        "Mzz": "primal",
+        "Pxx": "primal",
+        "Pxy": "primal",
+        "Pxz": "primal",
+        "Pyy": "primal",
+        "Pyz": "primal",
+        "Pzz": "primal",
         "tags": "dual",
     },
     "z": {
@@ -77,6 +101,18 @@
         "Vthx": "primal",
         "Vthy": "primal",
         "Vthz": "primal",
+        "Mxx": "primal",
+        "Mxy": "primal",
+        "Mxz": "primal",
+        "Myy": "primal",
+        "Myz": "primal",
+        "Mzz": "primal",
+        "Pxx": "primal",
+        "Pxy": "primal",
+        "Pxz": "primal",
+        "Pyy": "primal",
+        "Pyz": "primal",
+        "Pzz": "primal",
         "tags": "dual",
     },
 }

pyphare/pyphare/pharein/__init__.py

@@ -253,7 +253,7 @@ def as_paths(rb):
 
     #### adding diagnostics
     diag_path = "simulation/diagnostics/"
-    for diag in simulation.diagnostics:
+    for _, diag in simulation.diagnostics.items():
         type_path = diag_path + diag.type + "/"
         name_path = type_path + diag.name
         add_string(name_path + "/" + "type", diag.type)

pyphare/pyphare/pharein/diagnostics.py

@@ -47,7 +47,6 @@ def wrapper(diagnostics_object, name, **kwargs):
 
 import numpy as np
 
-
 # ------------------------------------------------------------------------------
 def validate_timestamps(clazz, key, **kwargs):
     sim = global_vars.sim
@@ -127,18 +126,30 @@ def __init__(self, name, **kwargs):
                 f"{self.__class__.__name__,}.flush_every cannot be negative"
             )
 
-        if any(
-            [
-                self.quantity == diagnostic.quantity
-                for diagnostic in global_vars.sim.diagnostics
-            ]
-        ):
-            raise RuntimeError(
-                f"Error: Diagnostic ({kwargs['quantity']}) already registered"
-            )
-
         self.__extent = None
-        global_vars.sim.add_diagnostics(self)
+
+        # if a diag already is registered we just contactenate the timestamps
+        addIt = True
+        registered_diags = global_vars.sim.diagnostics
+        for diagname, diag in registered_diags.items():
+            if self.quantity == diag.quantity:
+                print(
+                    f"{diag.name} already registered {self.quantity}, merging timestamps"
+                )
+                my_times = self.write_timestamps
+                existing_times = diag.write_timestamps
+                new_times = np.concatenate((my_times, existing_times))
+                new_times.sort()
+                mask = np.ones(len(new_times), dtype=bool)
+                mask[1:] = (
+                    np.diff(new_times) > 1e-10
+                )  # assumed smaller than any realistic dt
+                global_vars.sim.diagnostics[diagname].write_timestamps = new_times[mask]
+                addIt = False
+                break  # there can be only one
+
+        if addIt:
+            global_vars.sim.add_diagnostics(self)
 
     def extent(self):
         return self.__extent
@@ -162,6 +173,7 @@ 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
@@ -188,14 +200,21 @@ def population_in_model(population):
     return population in [p for p in global_vars.sim.model.populations]
 
 
-class FluidDiagnostics(Diagnostics):
-    fluid_quantities = ["density", "flux", "bulkVelocity"]
+class FluidDiagnostics_(Diagnostics):
+
+    fluid_quantities = [
+        "density",
+        "mass_density",
+        "flux",
+        "bulkVelocity",
+        "momentum_tensor",
+    ]
     type = "fluid"
 
     def __init__(self, **kwargs):
-        super(FluidDiagnostics, self).__init__(
-            FluidDiagnostics.type
-            + str(global_vars.sim.count_diagnostics(FluidDiagnostics.type)),
+        super(FluidDiagnostics_, self).__init__(
+            FluidDiagnostics_.type
+            + str(global_vars.sim.count_diagnostics(FluidDiagnostics_.type)),
             **kwargs,
         )
 
@@ -206,15 +225,17 @@ def _setSubTypeAttributes(self, **kwargs):
         elif "population_name" in kwargs:
             self.population_name = kwargs["population_name"]
 
-        if kwargs["quantity"] not in FluidDiagnostics.fluid_quantities:
+        if kwargs["quantity"] not in FluidDiagnostics_.fluid_quantities:
             error_msg = "Error: '{}' not a valid fluid diagnostics : " + ", ".join(
-                FluidDiagnostics.fluid_quantities
+                FluidDiagnostics_.fluid_quantities
             )
             raise ValueError(error_msg.format(kwargs["quantity"]))
         elif kwargs["quantity"] == "flux" and kwargs["population_name"] == "ions":
             raise ValueError(
                 "'flux' is only available for specific populations, try 'bulkVelocity"
             )
+        elif kwargs["quantity"] == "pressure_tensor":
+            raise ValueError("'pressure_tensor' is not available yet")
         else:
             self.quantity = kwargs["quantity"]
 
@@ -232,7 +253,7 @@ def _setSubTypeAttributes(self, **kwargs):
     def to_dict(self):
         return {
             "name": self.name,
-            "type": FluidDiagnostics.type,
+            "type": FluidDiagnostics_.type,
             "quantity": self.quantity,
             "write_timestamps": self.write_timestamps,
             "compute_timestamps": self.compute_timestamps,
@@ -241,6 +262,25 @@ def to_dict(self):
         }
 
 
+def for_total_ions(**kwargs):
+    return "population_name" not in kwargs
+
+
+class FluidDiagnostics:
+    def __init__(self, **kwargs):
+        if kwargs["quantity"] == "pressure_tensor":
+            if for_total_ions(**kwargs):
+                needed_quantities = ["mass_density", "bulkVelocity", "momentum_tensor"]
+            else:
+                needed_quantities = ["density", "flux", "momentum_tensor"]
+
+            for quantity in needed_quantities:
+                kwargs["quantity"] = quantity
+                FluidDiagnostics_(**kwargs)
+        else:
+            FluidDiagnostics_(**kwargs)
+
+
 # ------------------------------------------------------------------------------
 
 
@@ -262,6 +302,12 @@ def _setSubTypeAttributes(self, **kwargs):
             )
             raise ValueError(error_msg.format(kwargs["quantity"]))
 
+        if kwargs["quantity"] not in ParticleDiagnostics.particle_quantities:
+            error_msg = "Error: '{}' not a valid particle diagnostics : " + ", ".join(
+                ParticleDiagnostics.particle_quantities
+            )
+            raise ValueError(error_msg.format(kwargs["quantity"]))
+
         self.quantity = kwargs["quantity"]
 
         self.space_box(**kwargs)
@@ -281,6 +327,7 @@ 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"
@@ -305,6 +352,7 @@ def to_dict(self):
 
 
 class MetaDiagnostics(Diagnostics):
+
     meta_quantities = ["tags"]
     type = "info"
 

pyphare/pyphare/pharein/simulation.py

@@ -810,7 +810,7 @@ def __init__(self, **kwargs):
 
         self.ndim = compute_dimension(self.cells)
 
-        self.diagnostics = []
+        self.diagnostics = {}
         self.model = None
         self.electrons = None
 
@@ -869,7 +869,7 @@ def __setstate__(self, state):
     # ------------------------------------------------------------------------------
 
     def add_diagnostics(self, diag):
-        if diag.name in [diagnostic.name for diagnostic in self.diagnostics]:
+        if diag.name in self.diagnostics:
             raise ValueError(
                 "Error: diagnostics {} already registered".format(diag.name)
             )
@@ -880,7 +880,7 @@ def add_diagnostics(self, diag):
         ):
             raise RuntimeError("Error: invalid diagnostics spatial extent")
 
-        self.diagnostics.append(diag)
+        self.diagnostics[diag.name] = diag
 
     # ------------------------------------------------------------------------------
 
@@ -893,7 +893,13 @@ def is_restartable_compared_to(self, sim):
     # ------------------------------------------------------------------------------
 
     def count_diagnostics(self, type_name):
-        return len([diag for diag in self.diagnostics if diag.type == type_name])
+        return len(
+            [
+                diag
+                for diagname, diag in self.diagnostics.items()
+                if diag.type == type_name
+            ]
+        )
 
     # ------------------------------------------------------------------------------