Changelog#

v0.7.2 (2023/01/09)#

Philip Loche, Henrik Jaeger

  • Remove superfluous group wise wrapping (!225)

  • Clarify unclear definition in Dieletric modules that could lead to wrong results (!228)

  • Fixed windows string manipulation in test CI (!227)

  • Added coverage posting on GitLab (!226)

  • Corrected wrong comparison in correlation analysis and added tests

  • Fixed link to changelog in pyproject.toml

  • Migrated versioneer to pyproject.toml

  • Added Support for Python 3.11

v0.7.1 (2023/01/01)#

Henrik Jaeger

  • Fix upload to PyPi. This release is identical to v0.7.

v0.7 (2022/12/27)#

Philip Loche, Simon Gravelle, Marc Sauter, Henrik Jaeger, Kira Fischer, Alexander Schlaich, Philipp Staerk

  • Added MacOS pipeline, fixed wheels (!218)

  • Fix CHANGELOG testing (!220)

  • Added dielectric how-to (!208)

  • Raise an error if unwrap=False and refgroup != None in dielectric modules (!215).

  • Fix velocity profiles (!211)

  • Added the Theory to the Dielectric docs (!201)

  • Add a logger info for citations (!205)

  • Rename Diporder to DiporderPlanar (!202)

  • Change default behavior of DielectricPlanar: assume slab geometry by default (removing the xy flag and instead introduce is_3d for 3d-periodic systems) (!202)

  • Rename profile_mean to profile (!202)

  • Major improvements on the documentation (!202)

  • Add a check if the CHANGELOG.rst has been updated (!198)

  • Fix behaviour of refgroup (!192)

  • Resolve +1 is summed for epsilon for each atom group (#101, !193)

  • Flatten file structure of analysis modules (#46, !196)

  • Consistent mass unit in docs

  • Porting examples to sphinx-gallery (!190)

  • Add jitter parameter to AnalysisBase (!183)

  • Test output messages (!191)

  • Fixed typo in DielectricPlanar docs (!194)

  • Add Sphere modules (!175)

  • Add ProfileBase class (!180)

  • Slight restructure of the documenation (!189)

  • Fix py311 windows

  • Update build requirements for py310 and py311

  • Merged setup.cfg into pyproject.toml (!187)

  • Use versioneer for version info (!150)

  • Update project urls (!185)

  • Added repository link in the documentation (!184)

  • Added windows CI/CD pipeline (!182)

  • Update package discovery methods in setup.cfg

  • Refactor CI script (!181)

  • Fix DielectricCylinder (!165)

  • Unified n_bins logging (#93, !179)

  • Add MAICoS UML Class Diagramm (!178)

  • Changed density calculation using range in np.histogram (!77)

  • Update branching model in the documentation (!177)

  • remove ./ from index.rst

  • Improve documentation (!174)

  • Added reference for SAXS calculations (!176)

  • Update type of bin_pos in docs

  • Added VelocityCylinder module

  • Change behavior of sort_atomgroup (#88, !152)

  • get_compound: option for returning indices of topology attributes

  • Added Tutorial for non-spatial analysis module (!170)

  • Check atomgroups if they contain any atoms (!172)

  • New core attributes: bin_edges, bin_area, bin_volume, bin_pos & bin_width (!167)

  • Use frame dict in structure.py (!169)

  • Fix box dimensions for cylindrical boundaries (!168)

  • rmax for cylindrical systems now uses correct dimensions

  • Transport module documentation update (!164)

  • Rename frame dict (!166)

  • Implement SphereBase and ProfileSphereBase (!162)

  • Relative path for data (!163)

  • Create Linux wheels (!160)

  • Fix Diporder tests (!161)

  • norm=number: Declare bins with no atoms as nan (!157)

  • Simplify weight functions (!158)

v0.6.1 (2022/09/26)#

Henrik Jaeger

  • Fix the output of the ChemicalPotentialPlanar module (!173)

v0.6 (2022/09/01)#

Philip Loche, Simon Gravelle, Srihas Velpuri, Henrik Jaeger, Alexander Schlaich, Maximilian Becker, Kira Fischer

  • Write total epsilon as defined in paper (!155)

  • Introduce generic header (!149)

  • Fix error estimate in EpsilonPlanar (!153)

  • Fix sym option in EpsilonPlanar (!148)

  • Use standard error of the mean instead of variance for error estimate (!147)

  • Make all tests that write file use temporary file directory (!151)

  • Rewrite Velocity module using ProfilePlanarBase (!142)

  • Add RDFPlanar (!133)

  • Refactor EpsilonPlanar (!139)

  • Add a correlation time estimator (!137)

  • Add frame dict to AnalysisBase (!138)

  • Generalize comgroup attribute to all dimensions (!132)

  • Output headers do not require residue names anymore (!134)

  • Remove Debyer class (!130)

  • Generalize concfreq attribute in AnalysisBase (!122)

  • Fix broken binning in EpsilonPlanar (!125)

  • Removed repairMolecules (!119)

  • Added grouping and bin_method option (!117)

  • Bump minimum MDAnalysis version to 2.2.0 (!117)

  • Bump minimum Python version to 3.8 (!117)

  • Use base units exclusively (!115)

  • Higher tolerance for non-neutral systems (1E-4 instead of 1E-5)

  • charge``neutral decorator uses ``check_compound now

  • Add option to symmetrize profiles using ProfilePlanarBase (!116)

  • Fix comgroup parameter working only in the z direction (!116)

  • Remove center option from ProfileBase (!116)

  • Introduces new ProfilePlanarBase (!111)

  • Split new DensityPlanar into ChemicalPotentialPlanar, DensityPlanar, TemperaturePlanar (!111)

  • Convert more print statements into logger calls (!111)

  • Fix wrong Diporder normalization + tests (!111)

  • Add zmin and zmax to DensityPlanar and Diporder (!109)

  • Fix EpsilonPlanar (!108)

  • More tests for DensityPlanar, DensityCylinder, KineticEnergy and DipoleAngle (!104)

  • Remove EpsilonBulk (!107)

  • Add Code of Conduct (!97)

  • Fix lint errors (!95)

v0.5.1 (2022/02/21)#

Henrik Jaeger

  • Fix pypi installation (!98)

v0.5 (2022/02/17)#

Philip Loche, Srihas Velpuri, Simon Gravelle

  • Convert Tutorials into notebooks (!93)

  • New docs design (!93)

  • Build gitlab docs only on master branch (!94, #62)

  • Removed oxygen binning from diporder (!85)

  • Improved CI including tests for building and linting

  • Create a consistent value of zmax in every frame (!79)

  • Corrected README for pypi (!83)

  • Use Results class for attributes and improved docs (!81)

  • Bump minimum Python version to 3.7 (!80)

  • Remove spaghetti code in __main__.py and introduce mdacli as cli server library. (!80)

  • Remove SingleGroupAnalysisBase and MultiGroupAnalysisBase classes in favour of a unified AnalysisBase class (!80)

  • Change planar_base decorator to a PlanarBase class (!80)

  • Rename modules to be consistent with PEP8 (density_planar -> DensityPlanar) (!80)

  • Use Numpy’s docstyle for doc formatting (!80)

  • Use Python’s powerful logger library instead of bare print (!80)

  • Use Python 3.6 string formatting (!80)

  • Remove _calculate_results methods. This method is covered by the _conclude method. (!80)

  • Make results saving a public function (save) (!80)

  • Added docstring Decorator for PlanarDocstring and verbose option (!80)

  • Use MDAnalysis’s’ center_of_mass function for center of mass shifting (!80)

v0.4.1 (2021/12/17)#

Philip Loche

  • Fixed double counting of the box length in diporder (#58, !76)

v0.4 (2021/12/13)#

Philip Loche, Simon Gravelle, Philipp Staerk, Henrik Jaeger, Srihas Velpuri, Maximilian Becker

  • Restructure docs and build docs for develop and release version

  • Include README files into sphinx doc

  • Add tutorial for density_cylinder module

  • Add planar_base decorator unifying the syntax for planar analysis modules as denisty_planar, epsilon_planar and diporder (!48)

  • Corrected time_series module and created a test for it

  • Added support for Python 3.9

  • Created sphinx documentation

  • Raise error if end is to small (#40)

  • Add sorting of atom groups into molecules, enabling import of LAMMPS data

  • Corrected plot format selection in dielectric_spectrum (!66)

  • Fixed box dimension not set properly (!64)

  • Add docs for timeseries modulees (!72)

  • Fixed diporder does not compute the right quantities (#55, !75)

  • Added support of calculating the chemical potentials for multiple atomgroups.

  • Changed the codes behaviour of calculating the chemical potential if atomgroups contain multiple residues.

v0.3 (2020/03/03)#

Philip Loche, Amanuel Wolde-Kidan

  • Fixed errors occurring from changes in MDAnalysis

  • Increased minimal requirements

  • Use new ProgressBar from MDAnalysis

  • Increased total_charge to account for numerical inaccuracy

v0.2 (2020/04/03)#

Philip Loche

  • Added custom module

  • Less noisy DeprecationWarning

  • Fixed wrong center of mass velocity in velocity module

  • Fixed documentation in diporder for P0

  • Fixed debug if error in parsing

  • Added checks for charge neutrality in dielectric analysis

  • Added test files for an air-water trajectory and the diporder module

  • Performance tweaks and tests for sfactor

  • Check for molecular information in modules

v0.1 (2019/10/30)#

Philip Loche

  • first release out of the lab