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Recent Releases of kinisi

kinisi - kinisi-2.0.0

What's Changed

  • scippify Jump_diffusion broken by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/74
  • Change to using time interval as the coord name by @arm61 in https://github.com/kinisi-dev/kinisi/pull/75
  • 'Scipp'ification of the MDAnlysis parser by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/77
  • Some small fixes and changes by @arm61 in https://github.com/kinisi-dev/kinisi/pull/78
  • scipified the COM function getmolecules by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/85
  • Scippified Predict posterior by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/87
  • Added improved method for Centre of mass calculation by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/89
  • Scipp-ification of notebooks in documentation by @arm61 in https://github.com/kinisi-dev/kinisi/pull/86
  • Rebase from master by @arm61 in https://github.com/kinisi-dev/kinisi/pull/101
  • A solution to #97 by @arm61 in https://github.com/kinisi-dev/kinisi/pull/106
  • Fixed nan issue with correct_drift by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/104
  • New version number for scipp by @arm61 in https://github.com/kinisi-dev/kinisi/pull/110
  • Adds tests for displacement.py by @arm61 in https://github.com/kinisi-dev/kinisi/pull/107
  • Improvments to CI by @BaerCMI in https://github.com/kinisi-dev/kinisi/pull/115
  • CI error fix by @BaerCMI in https://github.com/kinisi-dev/kinisi/pull/117
  • Simplification of the parsers by @arm61 in https://github.com/kinisi-dev/kinisi/pull/116
  • Add the Samples class by @arm61 in https://github.com/kinisi-dev/kinisi/pull/120
  • Fix dependencies by @arm61 in https://github.com/kinisi-dev/kinisi/pull/125
  • Update parser.py by @jd15489 in https://github.com/kinisi-dev/kinisi/pull/128
  • Added new centre of mass and scippified, add property to access coords by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/126
  • Lint displacements and tests by @arm61 in https://github.com/kinisi-dev/kinisi/pull/122
  • Small fix by @arm61 in https://github.com/kinisi-dev/kinisi/pull/134
  • Added test for calc_com by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/131
  • Remove some random test docs pages by @arm61 in https://github.com/kinisi-dev/kinisi/pull/124
  • fixed struccoordslatt, reduced distance unit pass by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/138
  • msd_da -> da, etc by @arm61 in https://github.com/kinisi-dev/kinisi/pull/139
  • Add ASEParser by @jd15489 in https://github.com/kinisi-dev/kinisi/pull/137
  • Test diffusion by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/140
  • Scippification of the Arrhenius modelling by @arm61 in https://github.com/kinisi-dev/kinisi/pull/133
  • fixed msd issues, fixed path issue by @Harry-Rich in https://github.com/kinisi-dev/kinisi/pull/144
  • Remove old files by @arm61 in https://github.com/kinisi-dev/kinisi/pull/145
  • Scippification of the documentation by @BaerCMI in https://github.com/kinisi-dev/kinisi/pull/135
  • Save and loading of HDF5 files by @osoulas in https://github.com/kinisi-dev/kinisi/pull/109
  • Triclinic unwrapping by @jd15489 in https://github.com/kinisi-dev/kinisi/pull/129
  • Update papers.md by @arm61 in https://github.com/kinisi-dev/kinisi/pull/149
  • Fixing post sprint bugs by @arm61 in https://github.com/kinisi-dev/kinisi/pull/148
  • Fixed bugs by @arm61 in https://github.com/kinisi-dev/kinisi/pull/152
  • Coverage via a github action by @arm61 in https://github.com/kinisi-dev/kinisi/pull/154
  • Update papers.md by @arm61 in https://github.com/kinisi-dev/kinisi/pull/158
  • Remove generate_indices and change unwrapping FAQ. by @jd15489 in https://github.com/kinisi-dev/kinisi/pull/159
  • Docs and duecredit by @arm61 in https://github.com/kinisi-dev/kinisi/pull/155
  • scippification and therefore kinisi-2.0.0 by @arm61 in https://github.com/kinisi-dev/kinisi/pull/111

New Contributors

  • @BaerCMI made their first contribution in https://github.com/kinisi-dev/kinisi/pull/115
  • @osoulas made their first contribution in https://github.com/kinisi-dev/kinisi/pull/109

Full Changelog: https://github.com/kinisi-dev/kinisi/compare/1.1.1...2.0.0

Scientific Software - Peer-reviewed - Python
Published by arm61 5 months ago

kinisi - kinisi-1.1.1

What's Changed

  • Move np.product to np.prod by @arm61 in https://github.com/bjmorgan/kinisi/pull/70
  • Typo in the documentation by @arm61 in https://github.com/bjmorgan/kinisi/pull/71
  • Updated mcmc docs by @Harry-Rich in https://github.com/bjmorgan/kinisi/pull/73
  • Update vasp_d.ipynb docs by @Harry-Rich in https://github.com/bjmorgan/kinisi/pull/79
  • Raise a warning and fix to documentation with respect to units by @arm61 in https://github.com/bjmorgan/kinisi/pull/83

Full Changelog: https://github.com/bjmorgan/kinisi/compare/1.1.0...1.1.1

Scientific Software - Peer-reviewed - Python
Published by arm61 about 1 year ago

kinisi - kinisi-1.1.0

What's Changed

  • Replace the getmatrix function. by @jd15489 in https://github.com/bjmorgan/kinisi/pull/62
  • Change to using matrix conditioning by @arm61 in https://github.com/bjmorgan/kinisi/pull/60
  • Support for NPT unwrapping by @jd15489 in https://github.com/bjmorgan/kinisi/pull/64
  • Add MSD test to aid future development by @jd15489 in https://github.com/bjmorgan/kinisi/pull/67
  • Update timestep to time interval where appropriate by @arm61 in https://github.com/bjmorgan/kinisi/pull/68

Full Changelog: https://github.com/bjmorgan/kinisi/compare/1.0.0...1.1.0

Scientific Software - Peer-reviewed - Python
Published by arm61 over 1 year ago

kinisi - kinisi-1.0.1

This is a bug-fix release. The bug is related to triclinic cells and produced an underestimate of the mean-squared displacement and, therefore, the diffusion coefficient.

Full Changelog: https://github.com/bjmorgan/kinisi/compare/1.0.0...1.0.1

Scientific Software - Peer-reviewed - Python
Published by arm61 over 1 year ago

kinisi - kinisi-1.0.0

What's Changed

  • Int now valid for get_indices by @arm61 in https://github.com/bjmorgan/kinisi/pull/38
  • Move to cov_nearest by @arm61 in https://github.com/bjmorgan/kinisi/pull/48
  • Add support for variance estimation using the block averaging approach. by @arm61 in https://github.com/bjmorgan/kinisi/pull/49
  • Unwrapping FAQ by @arm61 in https://github.com/bjmorgan/kinisi/pull/50
  • Change abbreviations in paper.md by @zhubonan in https://github.com/bjmorgan/kinisi/pull/51
  • Correct typos in paper.md by @jd15489 in https://github.com/bjmorgan/kinisi/pull/53
  • Faster implementation of the get_disp function by @jd15489 in https://github.com/bjmorgan/kinisi/pull/54
  • Adds centre of geometry and centre of mass functionality by @arm61 in https://github.com/bjmorgan/kinisi/pull/47
  • Cog remove history by @arm61 in https://github.com/bjmorgan/kinisi/pull/56
  • Fix off-by-one error for framework indices by @jd15489 in https://github.com/bjmorgan/kinisi/pull/59

New Contributors

  • @zhubonan made their first contribution in https://github.com/bjmorgan/kinisi/pull/51
  • @jd15489 made their first contribution in https://github.com/bjmorgan/kinisi/pull/53

Full Changelog: https://github.com/bjmorgan/kinisi/compare/0.7.2...1.0.0

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 2 years ago

kinisi - kinisi-0.7.2

Changes

  • @arm61 Revert the posterior predictive use for the extrapolation, as it is not possible given there is no known uncertainty in the extrapolated value.

Scientific Software - Peer-reviewed - Python
Published by arm61 about 2 years ago

kinisi - kinisi-0.7.1

Changes

  • @arm61 Support for the posterior predictive of the MSD distribution.
  • @arm61 Start using uravu version 1.3.0 which supports the posterior predictive of the Relationship object. This is used to extrapolate the diffusion at a given temperature for the StandardArrhenius and SuperArrhenius objects.

Scientific Software - Peer-reviewed - Python
Published by arm61 about 2 years ago

kinisi - kinisi-0.7.0

Changes

  • @arm61 - An argument has been added to the diffusion method. It is now necessary to pass the first time interval (in kinisi units of picoseconds) that should be used in the diffusion analysis. This should be greater than the start of the diffusive regime.
  • @alexsquires - Support for ASE objects has been added.
  • @alexsquires - Improvements to the saving and loading .hdf file functionality.
  • @arm61 - Documentation improvements.

Scientific Software - Peer-reviewed - Python
Published by arm61 over 2 years ago

kinisi - kinisi-0.6.5

Changes

  • Bug fixes

Scientific Software - Peer-reviewed - Python
Published by arm61 over 2 years ago

kinisi - kinisi-0.6.4

Changes

  • Bug fixes

Scientific Software - Peer-reviewed - Python
Published by arm61 over 2 years ago

kinisi - kinisi-0.6.3

Changes

  • The scaled variance is now used to estimate the variance of the mean-squared displacement. Bootstrapping can still be used to find the distribution of the MSD with the bootstrap=True flag

Scientific Software - Peer-reviewed - Python
Published by arm61 over 2 years ago

kinisi - kinisi-0.6.2

Changes

  • Large improvements to documentation
  • Moving to using the pyproject.toml
  • Changing 'non-overlapping' to 'multi-origin'

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 3 years ago

kinisi - kinisi-0.6.1

Changes

  • Remove rogue print statement in Bootstrap method
  • Improvements to documentation

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 3 years ago

kinisi - kinisi-0.6.0

Changes

  • Reverting to using all samples but with the minimum number of non-overlapping samples.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 3 years ago

kinisi - kinisi-0.5.1

Changes

  • Fix bug in n_steps keyword argument.
  • Set default number of steps to 100, based on the observation that (within reason) there was little dependence of the variance of the diffusion coefficient on the number of steps.
  • Enable minimum and maximum dt values in the parser.
  • Enable the use of logarithmic steps in dt.
  • Some minor refactoring.
  • Improvements to estimation of size of disp_3d object.
  • Improvements to documentation.

Scientific Software - Peer-reviewed - Python
Published by arm61 about 3 years ago

kinisi - kinisi-0.5.0

Changes

  • Resolves the correctness bug introduces in 0.4.0 where the identification of non-overlapping samples was incorrect.
  • Using hand rolled log-likelihood calculation, do to problems with the scipy.stats.multivariate_normal.pdf() method arising from changes in https://github.com/scipy/scipy/pull/5288.

Scientific Software - Peer-reviewed - Python
Published by arm61 about 3 years ago

kinisi - kinisi-0.4.0

Changes

  • Previously, we had been using overlapping samples of displacements (i.e. the blue and orange observations in the figure below). However, this puts us on thin statistical ice and we were using a “fudge factor” to account for this (which in turn leads to a slightly overestimated variance in diffusion coefficient. We have changed this to only use non-overlapping samples (i.e. the blue and green observations in the figure below). This is more statistically sound and gives a more accurate estimate of the variance in the diffusion coefficient. (https://github.com/bjmorgan/kinisi/commit/03a6edc86e9975f1e9ace93396df5ed5ac06396b)
  • Removal of the parser keyword arguments min_obs and ndelta_t these were artefacts of the old overlapping sampling approach and therefore have been removed. (https://github.com/bjmorgan/kinisi/commit/03a6edc86e9975f1e9ace93396df5ed5ac06396b)
  • Now by default, the number of Δt points will reflect that in the simulation (previously there was a reduced sampling approach that has been removed). (https://github.com/bjmorgan/kinisi/commit/03a6edc86e9975f1e9ace93396df5ed5ac06396b)
  • Thinning and the ability to add a random_state to the Markov chain Monte Carlo process have been introduced (see the keyword arguments for the diffusion params, thin and random_state). (https://github.com/bjmorgan/kinisi/commit/03a6edc86e9975f1e9ace93396df5ed5ac06396b)

Scientific Software - Peer-reviewed - Python
Published by arm61 about 3 years ago

kinisi - kinisi-0.3.11

Changes

  • Improvements to documentation (233c211)
  • Add support for ions from pymatgen files (daa6e94 and 01a079a)
  • Raise error if there are no species of the defined type (16ad8a8)
  • Covariance matrix now only produced for max_ngp and greater (c17fef5)
  • Fix off by one bug (8c5a313)
  • Update to use the latest version of uravu (e8ac5e0)

Scientific Software - Peer-reviewed - Python
Published by arm61 over 3 years ago

kinisi - kinisi-0.3.10

Changes

  • Addition of save and load functionality for the Analyzer class objects
  • Fix to bug that means that the diffusion coefficient would be incorrect for non-xyz systems

Scientific Software - Peer-reviewed - Python
Published by arm61 over 3 years ago

kinisi - kinisi-0.3.9

Changes

  • Improvement in stability for covariance matrix estimation
  • Addition of memory limit feature to control memory exposure
  • Enabling investigation of diffusion in particular dimensions or planes

Scientific Software - Peer-reviewed - Python
Published by arm61 over 3 years ago

kinisi - kinisi-0.3.8

Changes

  • Fix small bug in PymatgenParser for sub-sampled trajectories
  • Improvements to the documentation

Scientific Software - Peer-reviewed - Python
Published by arm61 over 3 years ago

kinisi - kinisi-0.3.7

Changes

  • Bug fix in the diffusion resampling, previously the p_value parameter was never updated leading to normal test only being applied once. This has been resolved with this release.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.6

Changes

  • Return to using the SciPy multivariate normal distribution.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.5

Changes

  • Remove the condition number control from the matrix module

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.4a

See kinisi-0.3.4. This release is to trigger the PyPI distribution release.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.4

Changes

  • Improve stability of likelihood sampling by using hand rolled likelihood function.
  • Reverted the removal the rtol parameter from the bootstrap method.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.3

Changes

  • Improve stability of covariance matrix
  • Remove the rtol parameter from the bootstrap method.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.2

Changes

  • Reverted to using likelihood sampling, which with the fixes to the covariance matrix gives the same results as the bootstrap approach.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.1

Changes

  • SciPy 1.7.0 is now required on installation

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.3.0

Changes

  • The variance is now determined from using generalised least squares on a number of random samples from the Gaussian process, this has the benefit of being more accurate and efficient.
  • As a result of the above there is no longer a "Sampling Likelihood" tqdm bar.
  • There is now a rtol kwarg for the bootstap_GLS method, this controls the rtol in the call to the scipy.linalg.pinvh that is used to stabilise the large matrices.
  • All documentation has been adapted to reflect this methodological change.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.2.2

Changes

  • Add the ability to use multiple identical simulations from an MDAnalysis.Universe class object.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.2.1

Changes

  • Add the flatchain property to the Analyzer classes, this returns the samples from the MCMC sampling of the diffusion parameter and intercept.
  • Include the use of the new flatchain property in the documentation.
  • Pin to the latest (1.2.5) version of uravu, which includes the flatchain property for Relationship class objects.
  • Use the flatchain property from uravu in the Arrhenius tutorial.

Scientific Software - Peer-reviewed - Python
Published by arm61 almost 4 years ago

kinisi - kinisi-0.2.0

Changes

  • Significant improvements to documentation, including a detailed description of the methodology used by kinisi, a tutorial showing the use of the Arrhenius functionality and the addition of a covariance matrix derivation document.
  • Running and testing on python 3.10 (via CI and support in setup.py).
  • A transition in the API to follow a more pymatgen style, where Analyzer objects are accessed by calling a from_* method based on the inputs.
  • Addition of a logo file to the repository.

Scientific Software - Peer-reviewed - Python
Published by arm61 about 4 years ago

kinisi - kinsi-0.1.1

Changes

  • Previously, the sampling of the diffusion coefficient allowed for negative values, this was determined to be unphysical. Therefore, a Bayesian prior of a Heaviside step function at 0 has been assigned to the gradient/diffusion coefficient to stop this.
  • It was noted that for very large number of atoms/timesteps (which are typically handled using MDAnalysis), there could be a memory overflow. This is due to the creation of a list of numpy arrays, for which the largest could be in the gigabyte range. item_size * atoms * timesteps * dimensions * to Gb 8 * 20000 * 10000 * 3 * 1e-9 = 4.8 #Gb Therefore, in addition to being able to sub_sample_traj, it is also possible to sub_sample_atoms (current this is only supported of MDAnalysis objects), which performed the same function as sub_sample_traj but on the atoms instead of timesteps.
  • The code is now fully typed and formatted to follow PEP8 formatted guidelines (with the exception of a 120 max line length).

Scientific Software - Peer-reviewed - Python
Published by arm61 about 4 years ago

kinisi - kinisi-0.1.0

First Release

Scientific Software - Peer-reviewed - Python
Published by arm61 over 4 years ago