Merge pull request #392 from AngelFP/add_r_particles

Simplify names of radial particle components

openpmd_viewer/openpmd_timeseries/data_reader/data_reader.py

@@ -280,7 +280,7 @@ def read_species_data( self, iteration, species, record_comp, extensions):
 
         record_comp: string
             The record component to extract
-            Either 'x', 'y', 'z', 'ux', 'uy', 'uz', or 'w'
+            Either 'x', 'y', 'z', 'r', 'ux', 'uy', 'uz', 'ur', or 'w'
 
         extensions: list of strings
             The extensions that the current OpenPMDTimeSeries complies with

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/params_reader.py

@@ -207,6 +207,10 @@ def simplify_record(record_comps):
         record_comps.remove('position/z')
         record_comps.remove('positionOffset/z')
         record_comps.append('z')
+    if ('position/r' in record_comps) and ('positionOffset/r' in record_comps):
+        record_comps.remove('position/r')
+        record_comps.remove('positionOffset/r')
+        record_comps.append('r')
 
     # Replace the names of the momenta
     if 'momentum/x' in record_comps:
@@ -218,6 +222,9 @@ def simplify_record(record_comps):
     if 'momentum/z' in record_comps:
         record_comps.remove('momentum/z')
         record_comps.append('uz')
+    if 'momentum/r' in record_comps:
+        record_comps.remove('momentum/r')
+        record_comps.append('ur')
 
     # Replace the name for 'weights'
     if 'weighting' in record_comps:

openpmd_viewer/openpmd_timeseries/data_reader/h5py_reader/particle_reader.py

@@ -32,7 +32,7 @@ def read_species_data(filename, iteration, species, record_comp, extensions):
 
     record_comp: string
         The record component to extract
-        Either 'x', 'y', 'z', 'ux', 'uy', 'uz', or 'w'
+        Either 'x', 'y', 'z', 'r', 'ux', 'uy', 'uz', 'ur', or 'w'
 
     extensions: list of strings
         The extensions that the current OpenPMDTimeSeries complies with
@@ -43,9 +43,11 @@ def read_species_data(filename, iteration, species, record_comp, extensions):
     dict_record_comp = {'x': 'position/x',
                         'y': 'position/y',
                         'z': 'position/z',
+                        'r': 'position/r',
                         'ux': 'momentum/x',
                         'uy': 'momentum/y',
                         'uz': 'momentum/z',
+                        'ur': 'momentum/r',
                         'w': 'weighting'}
     if record_comp in dict_record_comp:
         opmd_record_comp = dict_record_comp[record_comp]
@@ -78,11 +80,11 @@ def read_species_data(filename, iteration, species, record_comp, extensions):
             data *= w ** (-weighting_power)
 
     # - Return positions, with an offset
-    if record_comp in ['x', 'y', 'z']:
+    if record_comp in ['x', 'y', 'z', 'r']:
         offset = get_data(species_grp['positionOffset/%s' % record_comp])
         data += offset
     # - Return momentum in normalized units
-    elif record_comp in ['ux', 'uy', 'uz' ]:
+    elif record_comp in ['ux', 'uy', 'uz', 'ur']:
         m = get_data(species_grp['mass'])
         # Normalize only if the particle mass is non-zero
         if np.all( m != 0 ):

openpmd_viewer/openpmd_timeseries/data_reader/io_reader/params_reader.py

@@ -184,6 +184,10 @@ def simplify_record(record_comps):
         record_comps.remove('position/z')
         record_comps.remove('positionOffset/z')
         record_comps.append('z')
+    if ('position/r' in record_comps) and ('positionOffset/r' in record_comps):
+        record_comps.remove('position/r')
+        record_comps.remove('positionOffset/r')
+        record_comps.append('r')
 
     # Replace the names of the momenta
     if 'momentum/x' in record_comps:
@@ -195,6 +199,9 @@ def simplify_record(record_comps):
     if 'momentum/z' in record_comps:
         record_comps.remove('momentum/z')
         record_comps.append('uz')
+    if 'momentum/r' in record_comps:
+        record_comps.remove('momentum/r')
+        record_comps.append('ur')
 
     # Replace the name for 'weights'
     if 'weighting' in record_comps:

openpmd_viewer/openpmd_timeseries/data_reader/io_reader/particle_reader.py

@@ -32,7 +32,7 @@ def read_species_data(series, iteration, species_name, component_name,
 
     component_name: string
         The record component to extract
-        Either 'x', 'y', 'z', 'ux', 'uy', 'uz', or 'w'
+        Either 'x', 'y', 'z', 'r', 'ux', 'uy', 'uz', 'ur', or 'w'
 
     extensions: list of strings
         The extensions that the current OpenPMDTimeSeries complies with
@@ -43,9 +43,11 @@ def read_species_data(series, iteration, species_name, component_name,
     dict_record_comp = {'x': ['position', 'x'],
                         'y': ['position', 'y'],
                         'z': ['position', 'z'],
+                        'r': ['position', 'r'],
                         'ux': ['momentum', 'x'],
                         'uy': ['momentum', 'y'],
                         'uz': ['momentum', 'z'],
+                        'ur': ['momentum', 'r'],
                         'w': ['weighting', None]}
 
     if component_name in dict_record_comp:
@@ -84,11 +86,11 @@ def read_species_data(series, iteration, species_name, component_name,
             data *= w ** (-weighting_power)
 
     # - Return positions, with an offset
-    if component_name in ['x', 'y', 'z']:
+    if component_name in ['x', 'y', 'z', 'r']:
         offset = get_data(series, species['positionOffset'][component_name])
         data += offset
     # - Return momentum in normalized units
-    elif component_name in ['ux', 'uy', 'uz' ]:
+    elif component_name in ['ux', 'uy', 'uz', 'ur']:
         mass_component = next(species['mass'].items())[1]
         m = get_data(series, mass_component)
         # Normalize only if the particle mass is non-zero