Merge pull request #9 from PyCOMPLETE/develop

PyHEADTAIL v1.3.0

New features:
- RFBucket Hamiltonian supports other potentials and fields (like space charge)
- Multiturn wakefields
- higher-order chromaticities (arbitrary order)
- dispersion supported
- unit tests
- beam optics (optics functions like the beta function as inferred from the beam solely via statistical methods)
- full phase advance for each segment (in addition to previous smoothed phase advance)
- new SliceSet interface with statistics saved at creation for the slices and slice profile / derivative profile, also beam properties are taken over
- Bassetti Erskine space charge
- performance optimisation

Author: aoeftiger

.gitignore

@@ -13,4 +13,5 @@ scripts/
 *.h5
 *.h5part
 .ipynb_checkpoints
+.DS_Store
 *.__afs*

README.md

@@ -1,4 +1,4 @@
 PyHEADTAIL
 ==========
 
-CERN PyHEADTAIL simulation code for simulation of multi-particle beam dynamics and collective effects
+CERN PyHEADTAIL numerical n-body simulation code for simulating macro-particle beam dynamics with collective effects

_version.py

@@ -1,2 +1,8 @@
-__version__ = "1.2.0"
-
+import os, subprocess
+worktree = os.path.dirname(os.path.abspath(__file__))
+gitdir = worktree + '/.git/'
+__version__ = subprocess.check_output(
+    'git --git-dir=' + gitdir + ' --work-tree=' +
+    worktree + ' describe --long --dirty --abbrev=10 --tags', shell=True)
+__version__ = __version__.rstrip() # remove trailing \n
+__version__ = __version__[1:] # remove leading v

aperture/aperture.pyx

@@ -43,10 +43,16 @@ class Aperture(Element):
         change its (longitudinal) state. '''
         alive = self.tag_lost_particles(beam)
 
-        if not np.all(alive):
-            # Move lost particles to the end of the beam.u arrays.
-            n_alive = relocate_lost_particles(beam, alive)
 
+        if not np.all(alive):
+            # check whether all particles are lost, it's not safe to call
+            # relocate_all_particles in this case
+            if not np.any(alive):
+                self.warns('ALL particles were lost')
+                n_alive = 0
+            else :
+                # Move lost particles to the end of the beam.u arrays.
+                n_alive = relocate_lost_particles(beam, alive)
             # Update beam.u arrays, i.e. remove lost particles.
             beam.macroparticlenumber = n_alive
             beam.x = beam.x[:n_alive]
@@ -191,6 +197,10 @@ def relocate_lost_particles(beam, int[::1] alive):
     z, ...). Returns the number of alive particles n_alive_post after
     considering the losses.
 
+    Precondition:
+    - At least one particle must be tagged as alive, otherwise bad things
+      might happen...
+
     Description of the algorithm:
     (1) Starting from the end of the numpy array 'alive', find the index
         of the last particle in the array which is still alive. Store its