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CHANGELOG.md

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Change Log

All notable changes to AMEP will be documented in this file. AMEP adheres to semantic versioning.

AMEP 1.0.3 (22 Oct 2024)

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)

AMEP 1.0.2 (22 Mai 2024)

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

AMEP 1.0.1 (22 Apr 2024)

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)

AMEP 1.0.0 (21 Mar 2024)

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 can be installed via conda and pip.

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)

AMEP 0.5.0 (26 Oct 2023)

This version includes many new features and fixes important bugs of version 0.4.0. Additionally, the usability has been improved and the syntax has been simplified. This version also has various visualization features and improved storage methods for evaluation results. Furthermore, the parallelization of methods has been made robust and has been successfully tested on different HPC hardware.

New features:

  • progress bar (LH)
  • cluster algorithm for particles of different sizes (LH)
  • Gaussian kernel density estimation (LH)
  • method to plot the simulation box (LH)
  • loading continuum data (KS)
  • analyzing continuum data with evaluate objects (LH, AM)
  • domain length function (KS)
  • weighted running mean (KS, KD)
  • segmented mean (KS, KD)
  • cluster detection for continuum fields (AM, KS)
  • Voronoi tesselation (KD, SM)
  • cluster properties: center of mass, radius of gyration, end-to-end distance, inertia tensor, linear extension (AM)
  • save evaluate results in HDF5 file (LH)
  • HDF5-based database for evaluation results (LH)
  • plot particles with correct size (ME, AM)
  • nearest neighbors and k nearest neighbors (LH)
  • general bond order parameter (AM)
  • general time correlation function (ME)
  • video creation (ME, KD, KS)
  • 2d histogram (ME)
  • general fit class (KS, AM, MC)
  • AMEP plot styles (ME, LH)
  • local density calculation from Voronoi diagrams (KD)
  • number of next neighbors from Voronoi diagrams (KD)
  • plot fields (AM)

Bug fixes:

  • amep.plot.format_axis improved (LH)
  • hexagonal order parameter calculation improved (SM)
  • small bugs in amep.plot.add_inset fixed (LH)
  • bug in amep.load.traj fixed related to wrong error message for reload=False (LH)
  • amep.utils.time_average renamed to amep.utils.average_func and returns correct number of outputs (MC)
  • wrong values of the structure factor for q=0 are now excluded from the result (MC)
  • bug related to accuracy value in amep.spatialcor.sf2d fixed (LH)
  • bug in amep.base.BaseFrame.data fixed (MC)
  • small bugs in evaluate module fixed (LH)
  • kdtree bug with coords at box border fixed (LH)
  • amep.pbc.pbc_points twod keyword simplified (LH)
  • storing h5amep files in different directory (LW, LH)
  • bug related to cancelling parallelized methods (LH)
  • parallelization improved (LH)
  • amep.base.BaseFrame.data bug related to fnmatch (wildcard characters ignored) fixed (LH)
  • metadata handling in trajectory files improved and simplified (LH)
  • bug fixed in amep.base.BaseReader related to temporary h5amep files that are not deleted (KD)
  • amep.base.BaseFrame "get_" removed for better usability (LH)
  • Gaussian fit function improved (MC, KS, AM)
  • bug in amep.thermo.kintemp fixed (ME, KD)
  • amep.spatialcor.pcf_angle problems if other_coords contains only one particle fixed (KS, MC)
  • evaluate objects now also have times as property (MC)
  • getting data from evaluate objects improved (MC, LH)
  • local density calculation now possible for particles of different size (LH)

Contributors:

  • Lukas Hecht (LH)
  • Kay-Robert Dormann (KD)
  • Kai Luca Spanheimer (KS)
  • Aritra Mukhopadhyay (AM)
  • Suvendu Mandal (SM)
  • Malte Coordts (MC)
  • Mahdieh Ebrahimi (ME)
  • Lukas Walter (LW)

AMEP 0.4.0 (22 Feb 2023)

This version fixes many important bugs of version 2.0.0 and now allows to efficiently use the new HDF5-based data format. The loading of the data has been improved significantly and is robust against data loss. With this version, it is also possible to install AMEP via pip.

New features:

  • pip support added (KS)
  • possibility to add insets to a plot implemented (KS)
  • axiscolor option added to format_axis (KS)
  • .h5amep files now also store AMEP version for backwards compatibility (LH)
  • non-LaTeX mode for plots implemented (KD)
  • get_data method improved; allows individual keys and wildcard characters now (LH)
  • energy functions added for energy calculations (KD)
  • sort particles by id during loading (KD)
  • general evaluation function added (KD)
  • frame.get_torque implemented (LH)

Bug fixes:

  • bug in adding scripts to trajectory objects fixed (LH)
  • time_average improved (KD)
  • bug in spatial_cor fixed (LH)
  • bug in reader objects related to uncomplete dump files fixed (LH)
  • bug in MSD fixed - now checks if required data available (LH)
  • data loading backend improved (KD, LH)

Contributors:

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

AMEP 0.3.0 (09 Nov 2022)

This is the new AMEP version which includes full HDF5 support and uses HDF5 files in the backend.

New features:

  • new backend with full HDF5 support
  • velocity autocorrelation function added
  • orientational autocorrelation function added

Bug fixes:

  • improved calculation of structure factors

Deprecation and removals:

  • loading of previous .pkl trajectory file format not supported anymore

Contributors:

  • Lukas Hecht

AMEP 0.2.0 (21 Oct 2022)

New features:

  • fast mode for 2d structure factor implemented
  • replace_frame added to BaseTrajectory
  • cluster-resolved kinetic temperature added
  • real fft and spectrum added
  • axis line width and tick width added to amep.plot.format_axis
  • cluster-resolved msd added
  • linear_mappable added
  • radius of gyration added
  • get_ids() added to BaseFrame
  • in_circle added
  • cluster-resolved calculation of the number of next neighbors added
  • ClusterFraction added

Bug fixes:

  • small bug fixed in pbc.pbc_points
  • bug in traj.get_forces() fixed
  • bug in loading LAMMPS data fixed
  • saving results of evaluate objects now possible with user-defined file name

Contributors:

  • Lukas Hecht

AMEP 0.1.1 (27 Jun 2022)

This version includes small bug fixes and improvements.

Contributors:

  • Lukas Hecht

AMEP 0.1.0 (30 Mar 2022)

This is the first complete AMEP version ready to be shared with our group members.

Contributors

  • Lukas Hecht