fix GenesisElectronDist.twiss() miscalculation

.gitignore

@@ -4,3 +4,25 @@
 *.swp
 .project
 .pydevproject
+.vscode/
+*.log
+**.ipynb_checkpoints/
+.venv
+build/
+dist/
+ocelot.egg-info/
+.DS_Store
+arcline_traj.png
+arcline_traj_0.png
+dev_tests/5_CSR.py
+dev_tests/__init__.py
+docs/_build/
+docs/_sources
+# ignore tmp files that are created when execuding pytests
+tmp_*
+test.ast
+test.fmt1
+test.npz
+unit_tests/ebeam_test/linac_orb_correct/ref_results/test.p
+unit_tests/ebeam_test/section_track/data/
+filed_map.txt

AUTHORS

@@ -1,23 +1,35 @@
-Ilya Agapov ilya.agapov@desy.de
-architecture, releases
-optimizer, x-ray optics
+Sergey Tomin sergey.tomin@desy.de
+architecture, releases,
+cpbd modules, optics functions, CSR,
+tracking module, orbit correction module,
+optimizer, SR module, LH, tutorials
 
-Sergey Tomin sergey.tomin@xfel.eu
-cpbd modules, optics functions, CSR
-tracking module, orbit correction module
-optimizer, SR module
-releases
+Ilya Agapov ilya.agapov@desy.de
+architecture, optimizer, x-ray optics,
+genesis2 adaptor
 
 Igor Zagorodnov 
 cpbd module, space charge, wakefields
 
 Martin Dohlus
-space charge, CSR, wakefields
+space charge, CSR, wakefields, LH
 
 Gianluca Geloni
-genesis adaptor
+genesis2 adaptor
+
+Svitozar Serkez svitozar.serkez@xfel.eu
+genesis2 & genesis4 adaptors,
+coherent radiation class,
+SASE estimator & imitator,
+Stokes parameters class.
 
-Svitozar Serkez
-genesis adaptor
+Mykola Veremchuk, Andrei Trebushinin
+Stokes parameters calculation & visualization,
+coherent radiation class, unit tests, examples
 
+Michael Boese michael.boese@desy.de
+architecture, cpbd
 
+Christoph Lechner
+adaptors for "GENESIS 1.3", v4 and v2; functions for plotting of simulation results;
+control of MPI simulation jobs

CHANGELOG.md

@@ -0,0 +1,71 @@
+# Changelog
+
+All notable changes to OCELOT will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+~and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).~ (Not yet, maybe it won't.  Versioning is based on year.month.day.
+
+## [Unreleased]
+
+### Changed
+
+- The `CSR` class now gives an explicit `logging` `error` when failing in `arcline` and
+  a more useful explanation.  This error often occurs because the user has mixed CSR for
+  vertical bends with horizontal bends.
+- `Navigator.add_physics_process` should now be a lot faster by doing fewer unnecessary deepcopies.
+
+### Added
+
+- New properties on `ParticleArrray`, `beta` and `gamma`, providing the relativistic
+  properties of each particle.
+- New method `sort` on `ParticleArray` for possibly sorting in place with respect to one
+  of the properties or functions (e.g. `beta`, `x`, `p0c`, etc.) returning the indices
+  that sort the `ParticleArray`.
+- Implementation of `__len__` for `ParticleArray` which simply returns the number of
+  particles it contains.  Identical in function to `size`.
+- `get_envelope` now also calculates the normalised emittances `emit_xn` and `emit_yn`,
+  not just the geometric ones, as was previously the case.
+- Added `overwrite_progress` kwarg to `cpbd.track.track` function which allows
+  tracking progress to optionally be written on new lines rather than
+  overwritten repeatedly using carriage returns. This is particularly useful
+  when logging the output of a running ocelot simulation to avoid extremely long
+  lines and unreadable log files.
+- Inactive processes in `Navigator` instances are now stored in the
+  `inactive_proccses` attribute. This way processes attached to a `Navigator`
+  remain accessible in that for the lifetime of the Navigator.
+- New `ParameterScanner` class in `cpbd.track` for scanning arbitrary parameters
+  in parallel (either using multiprocessing mpi4py). For example one might scan
+  different compression schemes. Results are compiled into a single hdf5 file.
+- insert_markers_by_predicate now has optional arbitrary name suffixes for the markers
+- Twiss.from_series allows for Twiss instances to be made from pd.Series (or a dictionary for example).
+- ParticleArray slicing: `parray[10:100]` returns a ParticleArray instance with slices rparticles and q_array.
+- `remove_coupler_kick` convenience method for Cavity class
+- Integrated quad strengths for `k1` and `k2` convenience getters/setters (`k1l` and `k2l).
+- Added new method `Navigator.add_physics_processes` for adding multiple physics processes at the same time.  This will be a lot fastwe when lots of physics processes are to be added.
+- `Navigator.jump_to` method allowing a `Navigator` instance to jump
+  to arbitrary points in z along the magnetic lattice.  Useful as it
+  does not require modifying the underling beamling to achieve
+  equivalent behaviour.
+- new `__repr__` methods for some common physics processes: `CSR`, `SmoothBeam`, `SpaceCharge` and `WakeTable`.
+- modified the 'MagneticLattice.transfer_maps()' method. When using the 'output_at_each_step=True' flag,
+  the method returns (Bs, Rs, Ts, S), where 'S' is a list of coordinates after each transfer map.
+- New `WakeTable3` and `Wake3` class for third order Taylor expansion of wakefield tracking.
+- New wake table for the wakefields of parallel plate structure based on analytical results, `WakeTableParallelPlate_origin`, `WakeTableParallelPlate`, 
+  `WakeTableParallelPlate3_origin`, `WakeTableParallelPlate3`. The waketables with `origin` use point charge wake at the vicinity of the drive particle, which is the upper limit for wake. 
+  The other two waketables contain exponential decay term. The waketables with `3` provide third order Taylor expansion and should be used with `Wake3`.
+
+
+
+### Fixed
+
+- fixed bugs in matching function if Drift length is in list of variables. 
+
+### Removed
+
+- None yet.
+
+### Deprecated
+
+- None yet.
+
+[unreleased]: https://github.com/ocelot-collab/ocelot/compare/dev_2021..HEAD

Pipfile

@@ -0,0 +1,17 @@
+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+autopep8 = "*"
+
+[packages]
+ocelot = {path = "."}
+numba = "==0.50.0"
+numexpr = "==2.6.1"
+pyfftw = "==0.12.0"
+pytest = "*"
+
+[requires]
+python_version = "3.8"