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
andrefgroup != 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 introduceis_3d
for 3d-periodic systems) (!202)Rename
profile_mean
toprofile
(!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
moduleChange behavior of
sort_atomgroup
(#88, !152)get_compound
: option for returning indices of topology attributesAdded 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 instructure.py
(!169)Fix box dimensions for cylindrical boundaries (!168)
rmax
for cylindrical systems now uses correct dimensionsTransport module documentation update (!164)
Rename frame dict (!166)
Implement
SphereBase
andProfileSphereBase
(!162)Relative path for data (!163)
Create Linux wheels (!160)
Fix
Diporder
tests (!161)norm=number
: Declare bins with no atoms asnan
(!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 usingProfilePlanarBase
(!142)Add
RDFPlanar
(!133)Refactor
EpsilonPlanar
(!139)Add a correlation time estimator (!137)
Add
frame
dict toAnalysisBase
(!138)Generalize
comgroup
attribute to all dimensions (!132)Output headers do not require residue names anymore (!134)
Remove
Debyer
class (!130)Generalize
concfreq
attribute inAnalysisBase
(!122)Fix broken binning in
EpsilonPlanar
(!125)Removed
repairMolecules
(!119)Added
grouping
andbin_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
nowAdd option to symmetrize profiles using
ProfilePlanarBase
(!116)Fix
comgroup
parameter working only in the z direction (!116)Remove
center
option fromProfileBase
(!116)Introduces new
ProfilePlanarBase
(!111)Split new
DensityPlanar
intoChemicalPotentialPlanar
,DensityPlanar
,TemperaturePlanar
(!111)Convert more
print
statements into logger calls (!111)Fix wrong
Diporder
normalization + tests (!111)Add
zmin
andzmax
to DensityPlanar and Diporder (!109)Fix EpsilonPlanar (!108)
More tests for
DensityPlanar
,DensityCylinder
,KineticEnergy
andDipoleAngle
(!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 introducemdacli
as cli server library. (!80)Remove
SingleGroupAnalysisBase
andMultiGroupAnalysisBase
classes in favour of a unifiedAnalysisBase
class (!80)Change
planar_base
decorator to aPlanarBase
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
andverbose
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 asdenisty_planar
,epsilon_planar
anddiporder
(!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