Changelog

Changelog#

2.4.0#

  • expanded documentation on exporting networks (#805) and physical constants (#793)

  • some doc test fixes (#806, #807, #809)

  • expanded unit testing (#802)

  • update pylint disabled features (#794)

  • dropped support for python 3.9 (#787)

  • we now compute the Q value for rates from masses instead of binding energies if it is not available (#797)

  • updated the nuclear properties to all be based on Nubase 2020, with the mass excesses being the primary quantity used and binding energies now derived from the mass excesses. (#788, #792, #796)

  • added a get_all_nuclei() method that returns every nucleus for which we have a mass (#798)

  • removed unused scripts in the nucdata module (#789)

  • fixed the labels for trace nuclei in a Composition pie chart (#781)

2.3.0#

  • added a warning if we use the ReacLib n decay rate (#778)

  • doc updates, including an example of dealing with duplicate rates (#777), new theme (#775), axis label fixes (#774), some examples of nuclear astrophysics concepts (#762, #766)

  • fix the limits for TabularRate plots (#779)

  • created a new alternate_rates module and added the de Boer et al. 2017 C12(a,g)O16 rate (#769)

  • the minimum version of python supported is now 3.8 (#768)

  • some test fixes (#755, #757, #760, #763)

  • C++ autodiff changes / cleanups (#752, #759)

  • AmrexAstroCxxNetwork now create a ydot_weak function that evaluates the weak rate contributions to compute dYe/dt (#739)

2.2.1#

  • numpy 2.0 support added (#748)

  • new logo! (#744, #746)

  • pynucastro can now be installed by conda (#741, #743)

  • minor test fixes (#729, #735, #740, #745)

  • doc fixes (#737)

  • pylint fixes (#733)

  • Composition now allows for direct key-value indexing (#731), and has a new set_random() method (#728)

  • The screen5 screening routine has been added (#730)

  • C++ partition function interpolation is now cached (#726)

2.2.0#

  • Switch to using math.fsum() instead of sum() for better python 3.12 compatibility (#720)

  • Some modernization of the AMReX-Astro C++ code output (#709, #714, #717)

  • Documentation improvements, including references and contributing instructions, and NSE table (#669, #679, #695, #697, #706, #707)

  • Clean-up up some plot interfaces to always take rho, T, comp in that order (#693)

  • Performance improvements (#680, #685, #692)

  • A new constants module was added to provide fundamental constants (#688)

  • A new NumpyNetwork was added for use with the rate reduction algorithm (#684)

  • Neutrino cooling routines based on Itoh et al. 1996 were added (#628)

  • A new method for generating an NSE table was added (#676)

  • A new NSENetwork class was added for dealing with NSE (#675)

  • Moved some screening utilities out of RateCollection (#666)

  • A PythonNetwork now write out a function to compute the energy release (#640)

2.1.1#

  • RateCollection.evaluate_energy_generation() can now return the neutrino losses from weak rates separately. (#665)

  • AmrexAstroCxxNetwork now capitalizes the species names to be consistent with other AMReX-Astro Microphysics networks (#652)

  • The pynucastro project configuration was updated and reorganized to pyproject.toml (#657, #660, #661)

  • Library.get_rate_by_name no longer returns None if one of the input rate names is not found (#659)

  • A C++ indexing error at the boundary of a weak rate table was fixed. (#654)

  • The C++ AmrexAstroCxxNetwork for evaluating weak rate neutrino losses was cleaned up to fix a bounds error (#655)

  • We now explicitly check in the C++ code if a weak rate table if found and contains data (#654)

  • a RateCollection now enforces that there are no duplicate rates. A find_duplicate_links() method has been added to Library to allow one to construct a Library without duplicates and then create a RateCollection or other network from that. (#651)

  • Some documentation updates (#643, #650)

  • The positron rates in the Langanke weak rate tables have been merged with the corresponding electron rates and the n <-> p rate was added (#648)

  • The Composition.bin_as() method now takes a list of nuclei to exclude from being binned into (#642)

  • RateCollection.evaluate_ydots() now can take a filter to only evaluate a subset of the rates. (#641)

2.1.0#

  • add eval_zbar() to Composition (#632)

  • fix get_rate_by_name to work with “pp” reactions (#632)

  • created a method to reduce a Composition from one set of nuclei to another based on the nuclei masses and charge number (#625)

  • switch AmrexAstroCxxNetwork to do bilinear interpolation in terms of log(T) and log(rhoY) (#592, #611)

  • tabular rates in python now do linear interpolation (#602)

  • added an example of creating a custom rate (#615)

  • Rate now calls _set_q() to set the Q value if it is not passed in (#617)

  • added a TableInterpolator that works both for interactive python and PythonNetwork (#612, 610, 609)

  • added a RateCollection method to find duplicate links (#601)

  • python networks with tabular rates now copy the table files (#605)

  • added a get_nuclei_in_range method to return a range of nuclei (#593)

  • we now do a binary search in the C++ partition function interpolation (#581)

  • added a simple C++ network (SimpleCxxNetwork) (#591, #585)

  • added the weak rates from Langanke 2001 (#536)

  • cleaned up partition functions in C++ (#578, 573, 569, 565)

  • converted the Suzuki tabular rates to be in terms of log (#550)

  • fixed a bounds issue in C++ table interpolation (#566)

  • eliminated a variable length array in the C++ table interpolation (#567)

  • added rate indices to the C++ networks (#563)

  • added a network reduction algorithm (#529, #528, #527, #526, #525, #523)

  • added a molar fraction method to Composition (#546)

  • added examples of interfacing with Julia (#539)

  • added a code of conduct (#504)

  • added gamma heating to tabular weak rates (#502)

2.0.3#

  • add functions to numerically evaluate the Jacobian (#467)

  • Fix C++ compilation with partition functions and approximate rates and derived rates (#407, #494)

  • The Explorer class now takes all of the options as RateCollection.plot() (#496)

  • Rates edges can be highlighted via a user-defined function in the RateCollection plot (#486)

  • All of the plot routines in RateCollection now return a matplotlib Figure object (#490)

  • add get_rate_by_nuclei and add_rate to Library() (#484)

  • RateCollection.remove_rates() can now act on a single rate and a new method, add_rates(), will add a rate directly to the collection.

  • Fixed printing of TabularLibrary (#479)

  • Documentation updates (#473)

  • added get_rate_by_name to RateCollection (#468)

  • added tabular rates to PythonNetwork (#451)

  • fixed NSE state for network without protons (#463)

2.0.2#

  • Fix the installation of the C++ templates via setup.py (#460)

2.0.1#

  • Fix some setup.py metadata for PyPI (#453)

  • Change how tabular rate tables are stored and read (#450)

  • Support historical ReacLib format (#449)

2.0.0#

  • Added a method to get a rate by short name: A(x,y)B (#438)

  • Added the option to show rate links hidden by ydot < ydot_cutoff_value (#436)

  • Added a TabularLibrary (#429)

  • Moved validate into RateCollection (#433)

  • renamed StarKillerCxxNetwork to AmrexAstroCxxNetwork (#426)

  • Fixed formatting of tabular rate strings (#421)

  • Fixed normalization of colorbar in grid_plot (#424)

  • Added the ability to plot neutrino loss for tabular rates (#422)

  • Added support for partition functions in C++ networks (#404)

  • NSE solver now can return chemical potentials (#415)

  • Add spins to NSE calculatons (#405)

  • Separate the Coulomb calculation from the NSE screening, make it switchable (#398, #380)

  • Fixed StarKillerCxxNetwork output directory (#400)

  • Added Potekhin screening (#385)

  • Added screening to python networks (#383)

  • Numba accelerated screening (#373)

  • Fixed C++ approximate rate screening (#384)

  • Added RateCollection remove_rates() (#368), and allow remove_rates to operate on dictionary keys (#375)

  • Added NSE solver (#339, #364, #377)

  • added find_unimportant_rates method (#367, #369, #374)

  • added spins to partition functions (#371)

  • Split rate up into several classes, including ReacLibRate (#362) and TabularRate (#360)

  • added partition function support to python networks (#358)

  • fixed definition of inverse rate for symmetric screening (#363)

  • Moved Nucleus into nucdata (#346)

  • Added screening to RateCollection (#344)

  • Added approximate rate support to C++ (#333)

  • C++ networks now hardcode the coefficients in a function to compute the rates instead of storing a metadata table that is read at runtime (#329)

1.7.0#

  • the Rate class now knows how to make its function string in python and C++ (#328)

  • C++ networks now have a std::vector&lt;std::string&gt; of rate names (#326)

  • support for Fortran networks was removed (#324)

  • numerous optimizations (#263, #264, #321, #331)

  • a DerivedRate class was added (#272)

  • approximate rate support was added to python networks (#316, #315, #313, #271)

  • energy generation was added to python networks (#301)

  • support for inert nuclei was added (#307)

  • the ability to disable rates in C++ networks was added (#304, #290)

  • methods for finding reverse rates were added (#303)

  • a method to find neutrino loss energy from tabulated rates was added (#302)

  • the ability to run without Numba was added (#300)

  • weak rate table units in the header were fixed (#297)

  • python nuclei variable indices now begin with ‘j’ (#296)

  • python implementations of screening were added (#281)

  • the network chart plot was added (#202)

  • a rate filter for the network plot was added (#187)

  • the Explorer class was expanded to have more options (#251)

  • the rate plot now returns a matplotlib Figure object (#231)

  • added the ability to modify rate products (#252)

  • allow for the edges between nodes to be curved (#257)

  • add a RatePair object that groups forward and reverse rates (#212)

  • updated the ReacLib rate library (#248)

  • added nuclear spin tables (#238)

  • added partition function tables (#241, #204)

  • a Nucleus now knows its binding energy (#220)

  • many improvements to C++ output (#246, #214, #185, #183)

  • added a diff method to a Library (#194)

  • fixed rate sorting so it is more deterministic (#216)

  • added forward() and backward() methods to Library (#207)

  • added a default ReacLibLibrary function (#206)

  • added a validate() method for a library to find potentially important missing rates (#188, #172)

  • added a method to get the number of rates in a library (#173)

  • add a method to remove a rate from a library (#199)

  • libraries are now sorted when printed, with more information shown (#195, #168)

  • added a symmetric screening option (#178)

  • a “rotated” plot type for the network structure was added (#161)

  • versioning is now managed by setuptools_scm (#158)

1.6.0#

  • added support for C++ StarKiller / AMReX Microphysics networks (#152, #151, #149)

  • centralized sympy code generation and removed common subexpression support from network generation (#145)

  • added an example on integrating a python network

1.5.0#

  • Added gridplot function for plotting nuclides on a grid and coloring the cells by X, Y, Xdot, Ydot or activity

  • Created a notebook and a script for generating rp-process networks. The script allows an arbitrary endpoint to be specified.

  • Added a filter_function option to RateFilter and to the plotting functions that allows for filtering rates or nuclei using a user-defined Boolean map.

  • Fixed a write_network crash if the RateCollection contains multiple rates with the same name.

  • Deleted unused BLAS and VODE files previously used for the standalone Fortran outputs. These have been deprecated in favor of the StarKiller Microphysics network output as of v1.3.0.

  • fixed screening for the 3-alpha rate

1.4.1#

  • Improvements for locating rate files in directories also containing python scripts or Jupyter notebooks

  • Fixed a warning when using Numba

  • Updates to the StarKiller Microphysics format for compile time variables

  • Enhancements for the RateCollection Explorer to use NetworkX 2.5

  • Updated the requirements

1.4.0#

  • Added general support for tabulated weak rates from Suzuki, et al. 2016

  • Added a simple pp network example

  • Updated StarKiller Microphysics output to track latest changes in Microphysics network API

  • Added a core developers policy in the Readme

1.3.0#

  • Replace double precision reals in StarKiller networks with custom real type _rt

  • Incorporate modifications to thermal neutrino Jacobian contributions from Microphysics (#210) in StarKiller networks

  • Simplify rate evaluation code in StarKiller networks

  • Deprecated standalone Fortran output with VODE integration.

  • BaseFortranNetwork is now an abstract class to require users to either use StarKillerNetwork or provide templates

1.2.0#

  • Fix tabular rate bug where electron chemical potential contributions were not included

  • Update documentation and code comments

  • Add Numba support for Python networks

  • Enable sparse Jacobian (CSR) for StarKiller networks

  • Incorporate CUDA Fortran port for StarKiller networks including tabulated rates

  • Optimize rate screening evaluation for StarKiller networks

  • Fix bug to include the electron fraction and correct density dependence for Reaclib electron capture rates

  • Allow a nuclide to be both reactant and product

  • Updates an error message for multiple degenerate rates

  • Add example code generating a 160-isotope network

  • Fix table compilation issue for StarKiller networks

  • Moved energy generation subroutine into RHS module for StarKiller networks

1.1.1#

  • pynucastro published on JOSS is archived to Zenodo

1.1.0#

  • JOSS reviewer changes merged and pynucastro accepted to JOSS