Examples: Default openPMD Backend

We default to ADIOS2 output when available for
performance in the I/O of our `BeamMonitor` element.

For CI and correctness tests, because sometimes it is easier/faster
to install from packages (e.g., Debian), we hard-code the HDF5
openPMD backend, to avoid that the test behaves differently if
ADIOS2 is present (switches to bp) or not (switches to h5).

Now, we can actually let the code switch automatically because
with openPMD 0.16+, we have a generic pattern `.%E` in analsy
scripts to read the written files and match the first openPMD
backend that works (by file name extension). That way, we can now
simplify our examples by not adding the extra lines to control
the openPMD backend anymore.

Author: ax3l

docs/source/dataanalysis/dataanalysis.rst

@@ -52,7 +52,7 @@ Example to print the integrated orbit path length ``s`` at each beam monitor pos
 
    import openpmd_api as io
 
-   series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+   series = io.Series("diags/openPMD/monitor.%E", io.Access.read_only)
 
    for k_i, i in series.iterations.items():
        beam = i.particles["beam"]

examples/achromatic_spectrometer/analysis_spectrometer.py

@@ -35,7 +35,7 @@ def get_moments(beam):
 
 
 # initial/final beam
-series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+series = io.Series("diags/openPMD/monitor.%E", io.Access.read_only)
 last_step = list(series.iterations)[-1]
 initial = series.iterations[1].particles["beam"].to_df()
 final = series.iterations[last_step].particles["beam"].to_df()

examples/achromatic_spectrometer/input_spectrometer.in

@@ -25,7 +25,6 @@ lattice.elements = monitor bend1 plasma_lens drift1 monitor
 lattice.nslice = 25
 
 monitor.type = beam_monitor
-monitor.backend = h5
 
 bend1.type = sbend_exact
 bend1.ds = 1.0

examples/achromatic_spectrometer/run_spectrometer.py

@@ -43,7 +43,7 @@
 sim.add_particles(bunch_charge_C, distr, npart)
 
 # add beam diagnostics
-monitor = elements.BeamMonitor("monitor", backend="h5")
+monitor = elements.BeamMonitor("monitor")
 
 # design the accelerator lattice
 ns = 25  # number of slices per ds in the element

examples/alignment/analysis_alignment.py

@@ -37,7 +37,7 @@ def get_moments(beam):
 
 
 # initial/final beam
-series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+series = io.Series("diags/openPMD/monitor.%E", io.Access.read_only)
 last_step = list(series.iterations)[-1]
 initial = series.iterations[1].particles["beam"].to_df()
 final = series.iterations[last_step].particles["beam"].to_df()

examples/alignment/input_alignment.in

@@ -25,7 +25,6 @@ lattice.elements = monitor quad_err monitor
 lattice.nslice = 1
 
 monitor.type = beam_monitor
-monitor.backend = h5
 
 quad_err.type = quad
 quad_err.ds = 1.0

examples/alignment/run_alignment.py

@@ -43,7 +43,7 @@
 sim.add_particles(bunch_charge_C, distr, npart)
 
 # add beam diagnostics
-monitor = elements.BeamMonitor("monitor", backend="h5")
+monitor = elements.BeamMonitor("monitor")
 
 # design the accelerator lattice)
 ns = 1  # number of slices per ds in the element

examples/aperture/analysis_absorber.py

@@ -34,12 +34,12 @@ def get_moments(beam):
 
 
 # initial/final beam
-series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+series = io.Series("diags/openPMD/monitor.%E", io.Access.read_only)
 last_step = list(series.iterations)[-1]
 initial = series.iterations[1].particles["beam"].to_df()
 final = series.iterations[last_step].particles["beam"].to_df()
 
-series_lost = io.Series("diags/openPMD/particles_lost.h5", io.Access.read_only)
+series_lost = io.Series("diags/openPMD/particles_lost.%E", io.Access.read_only)
 particles_lost = series_lost.iterations[0].particles["beam"].to_df()
 
 # compare number of particles

examples/aperture/analysis_aperture.py

@@ -34,12 +34,12 @@ def get_moments(beam):
 
 
 # initial/final beam
-series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+series = io.Series("diags/openPMD/monitor.%E", io.Access.read_only)
 last_step = list(series.iterations)[-1]
 initial = series.iterations[1].particles["beam"].to_df()
 final = series.iterations[last_step].particles["beam"].to_df()
 
-series_lost = io.Series("diags/openPMD/particles_lost.h5", io.Access.read_only)
+series_lost = io.Series("diags/openPMD/particles_lost.%E", io.Access.read_only)
 particles_lost = series_lost.iterations[0].particles["beam"].to_df()
 
 # compare number of particles

examples/aperture/analysis_aperture_periodic.py

@@ -34,12 +34,12 @@ def get_moments(beam):
 
 
 # initial/final beam
-series = io.Series("diags/openPMD/monitor.h5", io.Access.read_only)
+series = io.Series("diags/openPMD/monitor.%E", io.Access.read_only)
 last_step = list(series.iterations)[-1]
 initial = series.iterations[1].particles["beam"].to_df()
 final = series.iterations[last_step].particles["beam"].to_df()
 
-series_lost = io.Series("diags/openPMD/particles_lost.h5", io.Access.read_only)
+series_lost = io.Series("diags/openPMD/particles_lost.%E", io.Access.read_only)
 particles_lost = series_lost.iterations[0].particles["beam"].to_df()
 
 # compare number of particles