This a major release with several important features and bug fixes
- Enable use of ridge regression alpha for parameter selection via the
- Add ternary parameter selection. Works by default, just add data.
- Set memory limit to zero to avoid dask killing workers near the dask memory limits.
- Remove ideal mixing from plotting models so that
plot_parametersgives the correct entropy values.
- Add recipes documentation <https://github.com/PhasesResearchLab/ESPEI/blob/master/docs/recipes.rst> that contains some Python code for common utility operations.
- Add documentation for running custom distributed schedulers in ESPEI
This is a update including breaking changes to the input files and several minor improvements.
- Update input file schema and Python API to be more consistent so that the
tracealways refers to the collection of chains and
chainrefers to individual chains. Additionally removed some redundancy in the parameters nested under the
save_intervalin the input file and Python API. See Writing Input documentation for all of the updates.
- The default save interval is now 1, which is more reasonable for most MCMC systems with significant numbers of phase equilibria.
- Bug fixes for plotting and some better plotting defaults for plotting input data
- Dataset parsing and cleaning improvements.
- Documentation improvements (see the PDF!)
This is a major bugfix release for MCMC multi-phase fitting runs for single phase data.
- Fixed a major issue where single phase thermochemical data was always compared to Gibbs energy, giving incorrect errors in MCMC runs.
- Single phase errors in ESPEI incorrectly compared values with ideal mixing contributions to data, which is excess only.
- Fixed a bug where single phase thermochemical data with that are dependent on composition and pressure and/or temperature were not fit correctly.
- Added utilities for analyzing ESPEI results and add them to the Cu-Mg example docs.
This is a minor bugfix release.
- Parameter generation for phases with vacancies would produce incorrect parameters because the vacancy site fractions were not being correctly removed from the contributions due to their treatement as
- Parameter selection now uses the corrected AIC, which further prevents overparameterization where there is sparse training data.
- Activity and single phase thermochemical data can now be included in MCMC fitting runs. Including single phase data can help anchor metastable phases to DFT data when they are not on the stable phase diagram. See the Gathering input data documentation for information on how to input activity data.
- Dataset checking has been improved. Now there are checks to make sure sublattice interactions are properly sorted and mole fractions sum to less than 1.0 in ZPF data.
- Support for fitting phases with arbitrary pycalphad Models in MCMC, including (charged and neutral) species and ionic liquids. There are several consequences of this:
- ESPEI requires support on
- ESPEI now uses pycalphad
Modelobjects directly. Using the JIT compiled Models has shown up to a 50% performance improvement in MCMC runs.
- Using JIT compiled
Modelobjects required the use of
cloudpickleeverywhere. Due to challenges in overriding
picklefor upstream packages, we now rely solely on
daskfor scheduler tasks, including
dask-mpi. Note that users must turn off
- ESPEI requires support on
- [Developers] Each method for calculating error in MCMC has been moved into a module for that method in an
error_functionssubpackage. One top level function from each module should be imported into the
mcmc.pyand used in
lnprob. Developers should then just customize
- [Developers] Significant internal docs improvements: all non-trival functions have complete docstrings.
- Enable plotting of isothermal sections with data using
- Tielines are now plotted in
dataplotfor isothermal sections and T-x phase diagrams
- Add a useful
ravel_conditionsmethod to unpack conditions from datasets
- MCMC is now deterministic by default (can be toggled off with the
- Added support for having no scheduler (running with no parallelism) with the
mcmc.scheduleroption set to
None. This may be useful for debugging.
- Logging improvements
- Extraneous warnings that may be confusing for users and dirty the log are silenced.
- A warning is added for when there are no datasets found.
- Fixed a bug where logging was silenced with the dask scheduler
optimal_parametersutility function as a helper to get optimal parameter sets for analysis
- Several improvements to plotting
- Users can now plot phase diagram data alone with
dataplot, useful for checking datasets visually. This changes the API for
dataplotto no longer infer the conditions from an equilibrium
Dataset(from pycalphad). That functionality is preserved in
- Experimental data points are now plotted with unique symbols depending on the reference key in the dataset. This is for both phase diagram and single phase parameter plots.
- Options to control plotting parameters (e.g. symbol size) and take user supplied Axes and Figures in the plotting functions. The symbol size is now smaller by default.
- Users can now plot phase diagram data alone with
- Documentation improvements for API and separation of theory from the Cu-Mg example
- Fixes a bug where elements with single character names would not find the correct reference state (which are typically named GHSERCC for the example of C).
- [Developer] All MCMC code is moved from the
paramselectmodule to the
mcmcmodule to separate these tasks
- [Developer] Support for arbitrary user reference states (so long as the reference state is in the
refdatamodule and follows the same format as SGTE91)
- Propogate the new entry point to setup.py
- Fix for module name/function conflict in entry point
- ESPEI is much easier to run interactively in Python and in Jupyter Notebooks
- Reference data is now included in ESPEI instead of in pycalphad
- Several reference data fixes including support for single character elements (‘V’, ‘B’, ‘C’, …)
- Support for using multiprocessing to parallelize MCMC runs, used by default (@olivia-higgins)
- Improved documentation for installing and developing ESPEI
- Add input-schema.yaml file to installer
- Add LICENSE to manifest
- ESPEI input is now described by a file. This change is breaking. Old command line arguments are not supported. See Writing input files for a full description of all the inputs.
- New input options are supported, including modifying the number of chains and standard deviation from the mean
- ESPEI is now available on conda-forge
- TinyDB 2 support is dropped in favor of TinyDB 3 for conda-forge deployment
- Allow for restarting previous mcmc calculations with a trace file
- Add Cu-Mg example to documentation
Fixes to the 0.2 release plotting interface
multiplotis renamed from
multi_plot, as in docs.
- Fixed an issue where phases in datasets, but not in equilibrium were not plotted by dataplot and raised an error.
multiplotinterface for convienent plotting of phase diagrams + data.
dataplotfunction underlies key data plotting features and can be used with
eqplot. See their API docs for examples. Will break existing code using multiplot.
MPI support for local/HPC runs. Only single node runs are explictly supported currently. Use
--scheduler='MPIPool'command line option. Requires
Default debug reporting of acceptance ratios
Option (and default) to output the log probability array matching the trace. Use
--probfileoption to control.
Optimal parameters are now chosen based on lowest error in chain.
Bug fixes including
- py2/3 compatibiltiy
- unicode datasets
- handling of singular matrix errors from pycalphad’s
- reporting of failed conditions
- Significant error checking of JSON inputs.
- Add new
--check-datasetsoption to check the datasets at path. It should be run before you run ESPEI fittings. All errors must be resolved before you run.
- Move the espei script module from
- Better docs building with mocking
- Google docstrings are now NumPy docstrings
- Documentation improvements for usage and API docs
- Fail fast on JSON errors
- Fix bad version pinning in setup.py
- Explicitly support Python 2.7
- Fix dask incompatibilty due to new API usage
- Fix a bug that caused logging to raise if bokeh isn’t installed
ESPEI is now a package! New features include
- Fork https://github.com/richardotis/pycalphad-fitting
- Use emcee for MCMC fitting rather than pymc
- Support single-phase only fitting
- More control options for running ESPEI from the command line
- Better support for incremental saving of the chain
- Control over output with logging over printing
- Significant code cleanup
- Better usage documentation