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Changelog.rst

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CHANGELOG

Changes from 0.2 to 0.3

New in 0.3.4

  • New classes DetectorGeometry and DetectorPanel as interfaces to 2D pixel area detectors.
  • Use of physical units in Diffractors, DiffractofParameters, and DetectorGeometry.
  • Compatible with new pysingfel interface.
  • Fixed FindHDF cmake utility (Thanks to Andrea Dotti).
  • Small improvements in Analysis classes.

New in 0.3.3

New features

  • EstherExperiment: A workflow for radiation-hydrodynamics simulations
  • Added CrystFEL to external libraries (building simex_platform will download, build, and install CrystFEL as well). Controllable via the DCrystFELPhotonDiffractor flag to cmake.

Bug fixes

  • Various small bug fixes related to Esther interfaces, enabled minimal working example with the EstherPhotonMatterInteractor.

Tests

  • Disabled lengthy tests on the CI server.

New in 0.3.2

Documentation

  • Tutorial for PlasmaXRTSCalculator (in the wiki).
  • Tutorial for CrystFELPhotonDiffracto (in the wiki).

Bug fix

  • Fixed a bug in WPG leading to segfault if wavefront mesh not quadratic shape (nx != ny).
  • Various bug fixes in PlasmaXRTSCalculator and CrystFELPhotonDiffractor which were discovered while writing the tutorial.

New in 0.3.1

New features

  • FEFFPhotonMatterInteractor: Calculator for the opensource part of FEFF8.5 allowing calculation
of EXAFS spectra for a given sample specification.

Documentation

  • Including more utility functions and new calculators (added since version 0.2) to the reference manual.

Bug fixes and enhancements

  • Fixed missing documentation in 0.3.0

New in 0.3.0

New features

  • CrystFELPhotonDiffractor for serial crystallography simulation (backengine: CrystFEL.pattern_sim http://www.desy.de/~twhite/crystfel/). Beam parameters can be extracted from wavefront data.
  • PhotonBeamParameters to parametrize photon beams.
  • XCSITPhotonDetector and XCSITPhotonDetectorParameters for 2D pixel detector simulation. Requires Geant4 and XCSIT being installed, these are not part of the external libraries shipped with simex_platform (partly due to licensing issues). Disabled in the build system by default.
  • PlasmaXRTSCalculator reads propagated wavefront data to synthesize scattering spectrum with instrumental broadening.
  • XFELPhotonAnalysis for diagnostics of wavefront data stored in native FAST/WPG wavefront format. OpenPMD currently not supported. bin/prop_diagnostics.py added as CLI.
  • DiffractionAnalysis for diagnostics of diffraction data. CLI: bin/diffr_diagnostics.py
  • Added option for no rotation in SingFELPhotonDiffractor.
  • ComptonScatteringCalculator for Compton scattering from plasmas.
  • Support for sample structures in xyz format.
  • GenesisPhotonSource to describe FELs using Genesis and conversion utilities to convert genesis output to wpg readable format, as well as PIC openPMD data to genesis readable format.
  • Conversion from PIC openPMD to simplex FEL code input.
  • Adding ocelot electron beam simulation framework and FEL code to external libraries.
  • Various tools to steer Esther radiation-hydrodynamics simulations and experiment design.
  • Converter for Shadow3 raytracing beams into OpenPMD particle-mesh data. To be used as python script in Oasys.

Bug fixes and enhancements

  • Removed random rotation in XMDYNDemoPhotonMatterInteractor since done in SingFELPhotonDiffractor
  • Improve MPI parallelization in EMCOrientation
  • Make use of units more consistent in PlasmaXRTSCalculator
  • Replaced singfel by pysingfel (reimplementation in python, less dependencies on fat libraries like boost, armadillo).
  • Exposing most Calculators, Parameters, Utilities, and Analysis objects in SimEx top level module. (>>> from SimEx import SingFELPhotonDiffractor).
  • Azimuthal integration of diffraction patterns uses pyFAI.
  • Fixing pdb parser to parse large (>100000 atoms) pdbs.
  • WPG uses threaded version (openmp) of SRW.
  • Ability to process time-independent wavefront data (one slice in frequency space).
  • PhotonDiffractors write one single hdf5 file which links to individual patterns.
  • Using xraydb (github/scikit-beam/xraydb) for x-ray material properties and atomic levels.
  • Automated collection of system variables to setup MPI parameters for parallel backengine execution.
  • Various bugs in XMDYNDemoPhotonMatterInteractor
  • EMCOrientation: Parallel improvements to create backengine input data photons.dat
  • Fixing EMC for new diffr data format.
  • Adding parameters cpus_per_task and forced_mpi_command and default handling.
  • Adding parallel backengines for high performance backengine execution.

Documentation

  • SimEx single-particle imaging tutorial moved to wiki (github.com/eucall-software/simex_platform/wiki
  • New tutorial for usage of Esther rad-hydro simulations
  • Demonstration of new diagnostics tools for wavefront and diffraction data.

Build system and deployment

  • Various improvements in docker image generation and usage.
  • Added pyqt to dockerfiles
  • Added --bind-to none to mpi command
  • Updated Docker files