moving startTimer/stopTimer outside loop over particles and - avoiding string
 comparison inside loops over particles

src/Classic/Structure/LossDataSink.cpp

- openH5(mode): passed mode argument was not used, H5_O_RDONLY was
  hard-coded in case of H5hut 2 (fixes issue #29)
- save(): read number of steps after opening file in append mode

Closes #29

See merge request !7

- openH5(mode): passed mode argument was not used, H5_O_RDONLY was
  hard-coded in case of H5hut 2 (fixes issue #29)
- save(): read number of steps after opening file in append mode

ParallelTTracker. Particle-Matter interaction doesn't work either at the moment.

I hope that I didn't create too much of a mess when merging!

fixes #21: add OPAL include directories at the beginning

See merge request !4

modified:   ippl/test/AMR/testTracker.cpp

modified:   ippl/test/AMR/AmrPartBunch.h
modified:   ippl/test/AMR/CMakeLists.txt
new file:   ippl/test/AMR/testTracker.cpp

In case of a multi-bunch simulation with

MBMODE=FORCE (in OPAL input file)

the npart_mb, q_mb, p_mb, m_mb and r_mb are not set. Leading to a segfault.
I did as provisional fix in ParallelCyclotronTracker::Tracker_Generic()
(A 10 bunch simulation worked without errors).

modified:   src/Algorithms/ParallelCyclotronTracker.cpp

allow 0 in dump frequency (frequ is maxint) and supress h5 writes of number of partcles are 1 and 2 in OPAL_cycl

modified:   ippl/test/AMR/AmrPartBunch.cpp
modified:   ippl/test/AMR/AmrPartBunch.h

modified:   ippl/test/AMR/AmrPartBunch.cpp
modified:   ippl/test/AMR/AmrPartBunch.h

modified:   ippl/test/AMR/AmrPartBunch.cpp
modified:   ippl/test/AMR/AmrPartBunch.h

modified:   ippl/test/AMR/AmrOpal.cpp
modified:   ippl/test/AMR/AmrOpal.h
modified:   ippl/test/AMR/helper_functions.h
modified:   ippl/test/AMR/testGaussian.cpp

modified:   ippl/test/AMR/testUniform.cpp