Merge pull request #52 from picmi-standard/make_data_list_none

In the diagnostics, data_list defaults to None

Author: ax3l

PICMI_Python/diagnostics.py

@@ -15,7 +15,8 @@ class PICMI_FieldDiagnostic(_ClassWithInit):
     Defines the electromagnetic field diagnostics in the simulation frame
       - grid: Grid object for the diagnostic
       - period: Period of time steps that the diagnostic is performed
-      - data_list: List of quantities to write out. Possible values 'rho', 'E', 'B', 'J', 'Ex' etc.
+      - data_list=None: List of quantities to write out. Possible values 'rho', 'E', 'B', 'J', 'Ex' etc.
+                        Defaults to the output list of the implementing code.
       - write_dir='.': Directory where data is to be written
       - step_min=None: Minimum step at which diagnostics could be written (optional)
                        Defaults to step 0.
@@ -31,7 +32,7 @@ class PICMI_FieldDiagnostic(_ClassWithInit):
       - name: Sets the base name for the diagnostic output files (optional)
 
     """
-    def __init__(self, grid, period, data_list,
+    def __init__(self, grid, period, data_list=None,
                  write_dir = None,
                  step_min = None,
                  step_max = None,
@@ -42,7 +43,8 @@ def __init__(self, grid, period, data_list,
                  name = None,
                  **kw):
 
-        assert isinstance(data_list, list), 'FieldDiagnostic: data_list must be a list'
+        if data_list is not None:
+            assert isinstance(data_list, list), 'FieldDiagnostic: data_list must be a list'
 
         self.grid = grid
         self.period = period
@@ -64,7 +66,8 @@ class PICMI_ElectrostaticFieldDiagnostic(_ClassWithInit):
     Defines the electrostatic field diagnostics in the simulation frame
       - grid: Grid object for the diagnostic
       - period: Period of time steps that the diagnostic is performed
-      - data_list: List of quantities to write out. Possible values 'rho', 'E', 'B', 'Ex' etc.
+      - data_list=None: List of quantities to write out. Possible values 'rho', 'E', 'B', 'Ex' etc.
+                        Defaults to the output list of the implementing code.
       - write_dir='.': Directory where data is to be written
       - step_min=None: Minimum step at which diagnostics could be written (optional)
                        Defaults to step 0.
@@ -79,7 +82,7 @@ class PICMI_ElectrostaticFieldDiagnostic(_ClassWithInit):
       - parallelio=None: If set to True, field diagnostics are dumped in parallel (optional)
       - name: Sets the base name for the diagnostic output files (optional)
     """
-    def __init__(self, grid, period, data_list,
+    def __init__(self, grid, period, data_list=None,
                  write_dir = None,
                  step_min = None,
                  step_max = None,
@@ -90,7 +93,8 @@ def __init__(self, grid, period, data_list,
                  name = None,
                  **kw):
 
-        assert isinstance(data_list, list), 'ElectrostaticFieldDiagnostic: data_list must be a list'
+        if data_list is not None:
+            assert isinstance(data_list, list), 'ElectrostaticFieldDiagnostic: data_list must be a list'
 
         self.grid = grid
         self.period = period
@@ -113,7 +117,8 @@ class PICMI_ParticleDiagnostic(_ClassWithInit) :
       - period: Period of time steps that the diagnostic is performed
       - species: Species or list of species to write out
                  Note that the name attribute must be defined for the species.
-      - data_list: The data to be written out. Possible values 'position', 'momentum', 'weighting'.
+      - data_list=None: The data to be written out. Possible values 'position', 'momentum', 'weighting'.
+                        Defaults to the output list of the implementing code.
       - write_dir='.': Directory where data is to be written
       - step_min=None: Minimum step at which diagnostics could be written (optional)
                        Defaults to step 0.
@@ -123,15 +128,16 @@ class PICMI_ParticleDiagnostic(_ClassWithInit) :
       - name: Sets the base name for the diagnostic output files (optional)
     """
 
-    def __init__(self, period, species, data_list,
+    def __init__(self, period, species, data_list=None,
                  write_dir = None,
                  step_min = None,
                  step_max = None,
                  parallelio = None,
                  name = None,
                  **kw):
 
-        assert isinstance(data_list, list), 'ParticleDiagnostic: data_list must be a list'
+        if data_list is not None:
+            assert isinstance(data_list, list), 'ParticleDiagnostic: data_list must be a list'
 
         self.period = period
         self.species = species
@@ -156,21 +162,23 @@ class PICMI_LabFrameFieldDiagnostic(_ClassWithInit):
       - grid: Grid object for the diagnostic
       - num_snapshots: Number of lab frame snapshots to make
       - dt_snapshots: Time between each snapshot in lab frame
-      - data_list: List of quantities to write out. Possible values 'rho', 'E', 'B', 'J', 'Ex' etc.
+      - data_list=None: List of quantities to write out. Possible values 'rho', 'E', 'B', 'J', 'Ex' etc.
+                        Defaults to the output list of the implementing code.
       - z_subsampling=1: A factor which is applied on the resolution of the lab frame reconstruction. (integer)
       - time_start=0.: Time for the first snapshot in lab frame
       - write_dir='.': Directory where data is to be written
       - parallelio=None: If set to True, field diagnostics are dumped in parallel (optional)
       - name: Sets the base name for the diagnostic output files (optional)
     """
-    def __init__(self, grid, num_snapshots, dt_snapshots, data_list,
+    def __init__(self, grid, num_snapshots, dt_snapshots, data_list=None,
                  z_subsampling = 1, time_start = 0.,
                  write_dir = None,
                  parallelio = None,
                  name = None,
                  **kw):
 
-        assert isinstance(data_list, list), 'LabFrameFieldDiagnostic: data_list must be a list'
+        if data_list is not None:
+            assert isinstance(data_list, list), 'LabFrameFieldDiagnostic: data_list must be a list'
 
         self.grid = grid
         self.num_snapshots = num_snapshots
@@ -191,23 +199,25 @@ class PICMI_LabFrameParticleDiagnostic(_ClassWithInit):
       - grid: Grid object for the diagnostic
       - num_snapshots: Number of lab frame snapshots to make
       - dt_snapshots: Time between each snapshot in lab frame
-      - data_list: The data to be written out. Possible values 'position', 'momentum', 'weighting'.
+      - data_list=None: The data to be written out. Possible values 'position', 'momentum', 'weighting'.
+                        Defaults to the output list of the implementing code.
       - time_start=0.: Time for the first snapshot in lab frame
       - species: Species or list of species to write out
                  Note that the name attribute must be defined for the species.
       - write_dir='.': Directory where data is to be written
       - parallelio=None: If set to True, particle diagnostics are dumped in parallel (optional)
       - name: Sets the base name for the diagnostic output files (optional)
     """
-    def __init__(self, grid, num_snapshots, dt_snapshots, data_list,
+    def __init__(self, grid, num_snapshots, dt_snapshots, data_list=None,
                  time_start = 0.,
                  species = None,
                  write_dir = None,
                  parallelio = None,
                  name = None,
                  **kw):
 
-        assert isinstance(data_list, list), 'LabFrameParticleDiagnostic: data_list must be a list'
+        if data_list is not None:
+            assert isinstance(data_list, list), 'LabFrameParticleDiagnostic: data_list must be a list'
 
         self.grid = grid
         self.num_snapshots = num_snapshots