amep - v1.1.0

AMEP 1.1.0 Release Notes

AMEP 1.1.0 supports Python 3.10.0 or higher and requires the following Python libraries:

• h5py (3.7.0 or higher)
• matplotlib (3.6.2 or higher)
• numba (0.56.4 or higher)
• numpy (1.21.6 or higher)
• scipy (1.10.0 or higher)
• scikit-image (0.20.0 or higher)
• tqdm (4.65.0 or higher)
• gsd (3.2.0 or higher)
• chemfiles (0.10.4 or higher)

New features

• added GROMACS reader (KD)
• added HOOMD-blue GSD reader (KD)
• added general distribution function evaluate.Dist (KD)
• added functionality for frame.data to accept lists (KD)
• simplified plot style selection in plot.style (KD)
• unified naming in plot (transition of plot.box to plot.box_boundary) (ME)
• unified functionality and documentation in evaluate (ME)
• major website restructure (KD, KS, LH)
• added information on website for supported data types and more (KD)
• AMEP publication now out (see "How to Cite" at amepproject.de)
• added temperature calculations for multiple definitions in evaluate (LH)
• added plot.draw_arrow (SM, LH)

Bug fixes

• documentation improvements (KD, KS, LH, ME)
• bug in utils.average_func fixed (KD, LH)
• bug in frame.data fixed (KD)
• bugs relating to evaluate.ClusterGrowth fixed (KD)
• bug in utils.detect2peaks related to borders fixed (KD)
• bug in cluster.identify not returning single-particle-"clusters" fixed (KD)
• bug in evaluate.PCFangle fixed (KD, LH)
• bugs relating to cluster.gyration_tensor fixed (KD, LH)
• bug related to mode 'largest' in evaluate.ClusterGrowth fixed (LH)

Contributors

• Lukas Hecht (LH)
• Kay-Robert Dormann (KD)
• Kai Luca Spanheimer (KS)
• Mahdieh Ebrahimi (ME)
• Suvendu Mandal (SM)

- Python
Published by hechtprojects over 1 year ago

amep - v1.0.3

AMEP 1.0.3 Release Notes

AMEP 1.0.3 supports Python 3.10.0 or higher and requires the following Python libraries:

• h5py (3.7.0 or higher)
• matplotlib (3.6.2 or higher)
• numba (0.56.4 or higher)
• numpy (1.21.6 or higher)
• scipy (1.10.0 or higher)
• scikit-image (0.20.0 or higher)
• tqdm (4.65.0 or higher)

Bug fixes:

• documentation improvements (ME, KS, KD, LH)
• bug fix related to trajectory.add_particle_info and trajectory.get_particle_info (KD, KS)
• LammpsReader angular momentum import bug fixed (KD)
• bug in evaluate.Psi6dist related to default value of number of bins fixed (KD)
• bug in evaluate.VelDist related to default value of number of bins fixed (KD)
• faster tests - now based on example data (KS, LH, KD)

Contributors:

• Lukas Hecht (LH)
• Kay-Robert Dormann (KD)
• Kai Luca Spanheimer (KS)
• Mahdieh Ebrahimi (ME)

- Python
Published by kay-ro almost 2 years ago

amep - v1.0.2

AMEP 1.0.2 Release Notes

AMEP 1.0.2 supports Python 3.10.0 or higher and requires the following Python libraries:

• h5py (3.7.0 or higher)
• matplotlib (3.6.2 or higher)
• numba (0.56.4 or higher)
• numpy (1.21.6 or higher)
• scipy (1.10.0 or higher)
• scikit-image (0.20.0 or higher)
• tqdm (4.65.0 or higher)

Bug fixes:

• fps can now be set by the user in amep.plot.animate_trajectory
• bug in amep.evaluate.MSD related to incorrect data availability checks fixed

Contributors:

• Lukas Hecht

- Python
Published by hechtprojects about 2 years ago

amep - v1.0.1

AMEP 1.0.1 Release Notes

AMEP 1.0.1 supports Python 3.10.0 or higher and requires the following Python libraries:

• h5py (3.7.0 or higher)
• matplotlib (3.6.2 or higher)
• numba (0.56.4 or higher)
• numpy (1.21.6 or higher)
• scipy (1.10.0 or higher)
• scikit-image (0.20.0 or higher)
• tqdm (4.65.0 or higher)

Bug fixes:

• bug related to physical times not getting updated when timestep of trajectory object was changed fixed (LH)
• incompatibility with Python 3.12 related to distutils fixed (LH)
• bug in watershed cluster detection related to bubble detection fixed (KS)
• some minor issues in documentation fixed (LH)

Contributors:

• Lukas Hecht (LH)
• Kai Luca Spanheimer (KS)

- Python
Published by hechtprojects over 2 years ago

amep - v1.0.0

AMEP 1.0.0 Release Notes

This is the first public version of AMEP. It fully integrates the analysis of continuum simulation data, fixes various bugs of version 0.5.0, and provides useful new features. It is also the first version that is available from PyPI via pip.

AMEP 1.0.0 supports Python 3.10.0 or higher and requires the following Python libraries:

• h5py (3.7.0 or higher)
• matplotlib (3.6.2 or higher)
• numba (0.56.4 or higher)
• numpy (1.21.6 or higher)
• scipy (1.10.0 or higher)
• scikit-image (0.20.0 or higher)
• tqdm (4.65.0 or higher)

New features:

• gyration tensor and inertia tensor added to amep.continuum.cluster_properties (LH)
• new modes for amep.evaluate.ClusterGrowth (KS)
• amep.plot.draw_box with new text features (KD)
• new cluster detection method for continuum data (KS)
• pbc keyword now consitently available in all evaluate classes (LH)
• property time added to amep.base.BaseField (KS)
• physical time added to continuum data format (KS)
• parallelized calculation of distance matrix (ME, LH)

Bug fixes:

• traj.animate colorbar bug fixed (LH)
• loading trajectories bug when loading process interrupted fixed (LH, KD)
• bug in amep.statistics.distribution for large datasets fixed (ME)
• amep.evaluate.LDdist bug fixed related to keyword forwarding (KD)
• 2d data detection for constant z coordinates (KD)
• unclear error message in particle cluster method fixed (LH)
• incorrect normalization in amep.evaluate.OACF fixed (LH)
• bug in amep.evaluate.ClusterSizeDist related to negative density fields fixed (KS)
• incorrect return in amep.order.local_density fixed (LH)
• amep.plot.add_colorbar now returns the axis object (LH)
• bug in amep.spatialcor.spatialcor fixed related to incorrect calculation for pbc=True (LH)
• incorrect backup behavior in amep.base.BaseEvaluation.save fixed (LH)
• bug in amep.load.traj related to dots in path names fixed (LH, KD)
• bug in amep.order.next_neighbors fixed related to incorrect ids from the voronoi tesselation (KD)
• evaluation HDF5 data format unified (LH)
• cluster methods unified (AM)
• bug related to very slow cluster method fixed (LH)
• not working save method of amep.evaluate.HexOrderCor fixed (LH)
• incorrect directory return of amep.base.check_path fixed (LH)
• bug related to multiple warnings printed when loading continuum data fixed (LH)
• bug in amep.reader.ContinuumReader related to missing keywords nth, start, and stop fixed (LH)
• error for continuum data with reload=True in amep.load.traj fixed (LH)
• bug in amep.base.BaseFrame.data related to wildcard characters fixed (LH, KD)
• incorrect normalization in amep.cluster.sf2d fixed (AM)
• minor bugs in amep.plot.particles fixed (KD)
• bug in amep.order.voronoi_density related to QhullError fixed (KD)
• problem with repeated indices in amep.utils.average_func fixed (LH)
• missing integration limits in `amep.utils.domain_length´ added (LH)
• incorrect calculation of moments in amep.statistics.binder_cumulant fixed (LH, LW)
• bug in amep.pbc.kdtree related to an error occured when particles are exactly at the border of the simulation box fixed (LH)
• new plot styles are now installed when installing AMEP via pip (KS)
• amep.plot.format_axis improved (LH, ME)

Deprecation and removals:

• local_density in module order replaced by the three functions local_number_density, local_mass_density, and local_packing_fraction (LH)
• amep.plot.savefig removed (LH, KD)
• amep.cluster.cluster replaced by amep.cluster.identify (AM)
• amep.cluster.csf2d renamed to amep.cluster.sf2d (LH)
• all functions now take the box boundary as an input instead of the box length (LH)
• amep.continuum.cluster replaced by amep.continuum.identify_clusters and amep.continuum.cluster_properties (AM)

Contributors:

• Lukas Hecht (LH)
• Kay-Robert Dormann (KD)
• Kai Luca Spanheimer (KS)
• Mahdieh Ebrahimi (ME)
• Aritra Mukhopadhyay (AM)
• Lukas Walter (LW)

- Python
Published by hechtprojects over 2 years ago