Changelog#

v0.9 (XXXX/XX/XX)#

Philip Loche, Marc Sauter, Kira Fischer, Federico Grasselli, Henrtik Stooß

  • Remove handling of multiple atomgroups in favor of AnalysisCollection (!301)

  • Fix openMP detection during setup (!304)

  • maicos.Saxs additionally provides structure factor. (!303)

  • Remove default arguments from core classes (!302)

  • Add an AnalaysisCollection class to perform multiple analyses on the same trajectory (!298)

  • Remove custom module command line interface (!299)

  • Add example for maicos.core.AnalysisBase and rework own module section in developer docs (!299)

  • Allow running an analysis with a universe without a cell (!297)

  • Test that core.AnalysisBase API and run method is the same as MDAnalysis.analysis.base.AnalysisBase (!297)

  • Add frames and progressbar_kwargs argument to maicos.core.AnalysisBase.run() (!297)

  • Update copyright year (!296)

  • Add new diporder modules: RDFDiporder, DiporderStructureFactor (!296)

  • Add correlation time estimate for SAXS module (!296)

  • Added tests of the analytical error propagation (!292)

  • Remove symbolic links from examples (!295)

v0.8 (2024/02/05)#

Simon Gravelle, Philip Loche, Marc Sauter, Henrik Stooß, Philipp Staerk, Adyant Agrawal, Kira Fischer

  • Skip test for custom modules in case the import is not working (!294)

  • Change to CHANGELOG.rst update check so that it is only executed in MRs (!198)

  • Rename radial distribution function to pair distribution function (!278)

  • Add RDF derivation and explain role of dz. (!278)

  • Implement 1D pair distribution function in RDFCylinder (!276)

  • Sort format and add more atomtypes to atomtypes.dat (!291)

  • Add grouping option to DipoleAngle module (!290)

  • Added Support for Python 3.12 (!289)

  • Remove suffixes -linux, -macos, -windows when building wheels. Platform will be detected automatically. (!288)

  • Use default tox error for non-exsiting enviroment (!285)

  • Parse documentation metadata from pyproject.toml (!287)

  • Convert pathlib.Path into str when using in sys.path.append (#123, !286)

  • Update dev names (!284)

  • Improvements to documentation rendering (#122, !282)

  • Unify Python versions in tox environments i.e. py311-build-macos to build-macos (!283)

  • Remove deprecated pytest tmpdir fixture (!283)

  • Remove deprecated assert_almost_equal in favor of assert_allclose (!283)

  • Move from os.path to pathlib.Path (!283)

  • Added Support for Python 3.11 (!283)

  • Update MacOS images for CI (!281)

  • Removed the obsolete option for the vacuum boundary condition in the DielectricPlanar module and prompt users to use tin-foil boundary conditions instead (!280).

  • Add physical integration test to test that structure factor from Saxs is the same as the Fourier transformed RDF. (!279)

  • Add example and explenation of how to relate the radial distribution function and the structure factor (!279)

  • Add function maicos.lib.math.rdf_structure_factor() for converting a radial distribution function into a structure factor. (!279)

  • Change default biwnwidth (dq) in maicos.Saxs to 0.1. (!279)

  • Move cutils to cmath (!279)

  • Add weight argument to maicos.lib._cmath.compute_structure_factor()

  • Code cleanup of maicos.Saxs (!279)

  • Fixed markup and consistency in correlation function docs (!277)

  • Add info for DielectricPlanar module for ignored combination of vac=True and is_3d=False. (!275)

  • Add description for tox jobs (!275)

  • Cleanup coverage config and move to pyproject.toml (!275)

  • Changed the way number normalization works, introduced sums dict (!274)

  • Fixed typing error in RDF modules (!273)

  • Update docs to reflect changes in mdacli (!271)

  • Add banner to MAICoS output reporting the version (!272)

  • Update UML graphic (!269)

  • Show warnings if set boundaries would result in wrong results (!261)

  • Small corrections to the documentation and type hinting (!268)

  • Add module for calculating radial distribution functions in cylinders (!242)

  • Add modules for calculating cylindrical and spherical dipolar order parameters (!259)

  • Fix reproducibility information in output (!263)

  • Make savetxt work with Pathlib objects (!267)

  • Update versionner to 0.29 (!266)

  • Use dipole_vector methods from MDAnalysis (!265)

  • Bump minimum Python version to 3.9 (!264)

  • Fix dipole calculation in DielectricCylinder (!258)

  • Add example for RDFPlanar (!256)

  • Move geometry transformations to lib.math (!257)

  • Add typehints for examples (!255)

  • Add typehints for modules (!253)

  • Only test minimum and maximum Python version in CI (!252)

  • Add typehints for core classes (!251)

  • Update documentation with parameters, returns and examples for library functions (!248)

  • Update CI to use latest MacOS (!250)

  • Add tables to documentation pages (!249)

  • Fix links to own classes in examples (!247)

  • Update install instructions for users and devs (!246)

  • Show authors on website (!245)

  • Add link to developer documentation in CONTRIBUTING.rst (!244)

  • Remove Python 2.x leftover of specific super() call (!243)

  • Use Gitlab for showing coverage and unit test reports (!241)

  • Use black formatter and 88 chars/line for the code and rst files (!240)

  • Add return values for correlation analysis to all base classes (!235)

  • Added more linting for rst files (!239)

  • Bump minimum version of tqdm to 4.60 (!238)

  • Add prompt toggle to examples (!236)

  • Added description to the ideal chemical potential how-to (!232)

  • Added quotation marks to command in tox.ini to account for spaces in paths (!232)

  • Fixed some typos and made minor modifications to the documentation (!232)

  • Cleanup .gitignore (!233)

  • More consistent molecule wrapping (!230)

  • Added missing AnalysisBase parameters to modules (!231)

  • created dark and light images and logo (!229)

  • Add explicit stacklevel arguments to warnings in the library (!236)

  • Switch to the build module (!234)

v0.7.2 (2023/01/09)#

Philip Loche, Henrik Stooß

  • 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 Stooß

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

v0.7 (2022/12/27)#

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

  • Make sure citation are only printed once (!260)

  • 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 Stooß

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

v0.6 (2022/09/01)#

Philip Loche, Simon Gravelle, Srihas Velpuri, Henrik Stooß, 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 Stooß

  • 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 Stooß, 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