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