Merge pull request #276 from skuschel/dev

last merge should have merged into master instead of dev

CHANGELOG.md

@@ -5,6 +5,19 @@ current master
 --------------
 
 
+**Highlights**
+
+* Add support to read the `Smilei` PIC (https://smileipic.github.io/Smilei/) data format in both cartesian and azimuthal geometry. Postpic uses a build in azimuthal mode expansion very similar to the one used for fbpic.
+* To read smilei data, postpic only relies on the hdf5 package and not smilei's happi module for data access. Paricle ID's (ParticleTracking as described by smilei) can be read directly from the hdf5. Happi requires to sort the IDs and write a new hdf5, which can be twice as big as the original dumps. Using postpic's access this step will be skipped and thus access is much faster (but by default with unordered particle IDs as in any other code).
+
+
+**Incompatible adjustments to previous version**
+
+
+
+**Other improvements and new features**
+
+
 v0.5
 ----
 

pip-requirements.txt

@@ -4,6 +4,7 @@ pycodestyle
 nose2
 Cython>=0.18
 numpy>=1.8
+setuptools
 
 # required for building the docs
 recommonmark

postpic/datareader/__init__.py

@@ -188,6 +188,10 @@ def chooseCode(code):
  from .vsimhdf5 import Hdf5reader, VSimReader
  setdumpreadercls(Hdf5reader)
  setsimreadercls(VSimReader)
+ elif code.lower() in ['smilei']:
+ from .smileih5 import SmileiReader, SmileiSeries
+ setdumpreadercls(SmileiReader)
+ setsimreadercls(SmileiSeries)
  elif code.lower() in ['dummy']:
  from .dummy import Dummyreader, Dummysim
  setdumpreadercls(Dummyreader)

postpic/datareader/openPMDh5.py

@@ -46,16 +46,23 @@ class OpenPMDreader(Dumpreader_ifc):
  Args:
  h5file : String
  A String containing the relative Path to the .h5 file.
+
+ Kwargs:
+ iteration: Integer
+ An integer indicating the iteration to be loaded. Default is None, leading
+ to the first iteration found in the h5file.
  '''
 
- def __init__(self, h5file, **kwargs):
+ def __init__(self, h5file, iteration=None, **kwargs):
  super(OpenPMDreader, self).__init__(h5file, **kwargs)
  import os.path
  import h5py
  if not os.path.isfile(h5file):
  raise IOError('File "' + str(h5file) + '" doesnt exist.')
  self._h5 = h5py.File(h5file, 'r')
- self._iteration = int(list(self._h5['data'].keys())[0])
+ self._iteration = iteration
+ if self._iteration is None:
+ self._iteration = int(list(self._h5['data'].keys())[0])
  self._data = self._h5['/data/{:d}/'.format(self._iteration)]
  self.attrs = self._data.attrs