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PyGBe Change Log

Current development

0.3.1

Added

  • Suggestions from JOSS reviewers.
  • Dockerfile for alternative installation.

Changed

  • README with latest version of packages tested.
    • Support for CUDA 8.0 using gcc 5.4.0 and, PyCUDA 2017.1.1.

Fixed

  • Problem with format of files needed to run performance check.
  • Broken link in documentation.
  • Small bug: overwriting a variable doesn't allow casting type.

Removed

0.3

Added

  • Ported PyGBe to Python 3 (!!!). This breaks Python 2 support, but who cares.
  • Better regression tests (faster, anyway) using pytest
  • Localized Surface Plasmon Resonance application.
  • lspr main function to run this applications separately.
  • lspr application's examples to the examples folder.
  • Regression and convergence tests for the examples added.
  • Update documentation with new application to github pages

Changed

  • Old regression test suite renamed to convergence_tests
  • All surface related functions are now methods of the surface class
  • All field related functions are now methods of the field class
  • Use scipy.constants instead of hardcoded values
  • Docstrings use proper references now (looks better on Sphinx)
  • GMRES function to accept complex numbers. Changed based on gmres_mgs from PyAMG, where modified Gram-Schmidt is used to orthogonalize the Krylov Space and Givens Rotations are used to provide the residual norm each iteration
  • If complex dielectric, the matvec calls the tree code separately with the Real part and Imaginary part of the solution and multiplies by complex constant afterwards. This prevents to modify the treecode to accept complex numbers.
  • Add to RHS functions the corresponding terms to solve lspr problems.

Fixed

  • Py3 syntax for generator iteration
  • Switched from blas.rotg to lapack.lartg since that apparently works correctly

Removed

  • All commented out code
  • Unused imports and unused variables removed.

0.2.1

Added

  • All documentation is available on github pages
  • Support for Cuda 7.5
  • One liner for setting up Py2.7 environment (sans PyCUDA)
  • Use Doctr to automatically generate documentation using Travis

Changed

  • config and param files are now globbed for so they can have a name different than the folder which contains them.
  • Updated license with new contributors
  • Layout of sphinx documentation toolbars (home button added, more verbose layout)

Fixed

  • Uncaught exception when pygbe doesn't run correctly
  • Wrong error type in regression test master script
  • Performance runs work on non-X backends
  • Uncaught out-of-memory exceptions in regression tests

Removed

0.2

Added

  • setup.py installer
  • argparse ArgumentParser to handle command line arguments (all optional)
    • -c to specify config file
    • -p to specify param file
    • -o to specify output folder
    • -g to specify geometry folder
  • Docstrings to all functions
  • Checks for NVCC version and to warn if user doesn't have NVCC on PATH
  • Sphinx documentation
  • In addition to text output, numerical results are stored to a pickled dictionary for easy access

Changed

  • Repo structure altered to match Python packaging guidelines.
  • Modularized code and removed all relative imports
  • All import * (excepting files in scripts/) have been removed and changed to explicit imports
  • Problems are now grouped-by-folder. A given problem will have the format:
lys 
  ˫ lys.param
  ˫ lys.config
  ˫ built_parse.pqr
  ˫ geometry/Lys1.face
  ˫ geometry/Lys1.vert
  ˫ output/

* Support running in current directory by passing '.' as path
  • Refactored regression tests, added simple caching to avoid test repeats
  • Move many, many functions around so that individual .py filenames are more descriptive and accurate

Removed

  • Makefiles (functionality replaced by setup.py)
  • pygbe_matrix and scripts folder -- to be relocated to a more appropriate repo somewhere