icet - A Python library for constructing and sampling alloy cluster expansions

Alloy cluster expansions (CEs) provide an accurate and computationally efficient mapping of the potential energy surface of multi-component systems that enables comprehensive sampling of the many-dimensional configuration space. Here, we introduce \textsc{icet}, a flexible, extensible, and computationally efficient software package for the construction and sampling of CEs. \textsc{icet} is largely written in Python for easy integration in comprehensive workflows, including first-principles calculations for the generation of reference data and machine learning libraries for training and validation. The package enables training using a variety of linear regression algorithms with and without regularization, Bayesian regression, feature selection, and cross-validation. It also provides complementary functionality for structure enumeration and mapping as well as data management and analysis. Potential applications are illustrated by two examples, including the computation of the phase diagram of a prototypical metallic alloy and the analysis of chemical ordering in an inorganic semiconductor.Comment: 10 page

Does N-2(-) exist? A coupled-cluster study

Potential energy curves of the ground-state N2 molecule and its doublet N−2 anion are calculated at the coupled-cluster level with single and double excitations and with noniterative triples [CCSD(T)] as well as with the multireference averaged-quadratic coupled-cluster (MR-AQCC) method. The N−2 anion is shown to be temporary and decays to its neutral parent plus a free electron at bond lengths shorter than ≈1.4 and larger than ≈2.5 Å. Thus, the N−2 anion exists within the 1.4⩽R(N–N)⩽2.5 Å range at the Born–Oppenheimer approximation

Guidelines for collaborative development of sustainable data treatment software

Software development for data reduction and analysis at large research facilities is increasingly professionalized, and internationallycoordinated. To foster software quality and sustainability, and to facilitate collaboration, representatives from software groups of Europeanneutron and muon facilities have agreed on a set of guidelines for development practices, infrastructure, and functional and non-functionalproduct properties. These guidelines have been derived from actual practices in software projects from the EU funded consortium ‘Scienceand Innovation with Neutrons in Europe in 2020’ (SINE2020), and have been enriched through extensive literature review. Besides guiding thework of the professional software engineers in our computing groups, we hope to influence scientists who are willing to contribute their owndata treatment software to our community. Moreover, this work may also provide inspiration to scientific software development beyond theneutron and muon field

Amino-Acid Adsorption in MFI-Type Zeolites Enabled by the pH-Dependent Ability to Displace Water

Downstream processing of biochemical products strongly depends on the interaction between biomolecules and material surfaces that can be influenced greatly by the pH level. In this study, the influence of the pH value on the adsorption of the amino acids glycine, alanine, and lysine in MFI-type zeolite was investigated using density functional theory (DFT) and microcalorimetric experiments. Different pH values were modeled by varying the amino acids protonation states. The investigated protonation states exhibit two different adsorption motifs in the pores, with the neutral α-C-amino group motifs being significantly less stable than the protonated ones. In the case of neutral glycine and alanine, the adsorption energy is insufficient to overcome the adsorption of the four water molecules usually present in the pores. This result explains the pH-dependent adsorption behavior that has also been observed experimentally and provides an avenue for designing efficient adsorption processes

sasview: SasView 4.0 Beta 1

Beta Release This release is a beta, meaning it is intended as a relatively stable test release prior to the final 4.0 production release. There are many improvements over the last production release (3.1.2) as detailed in the previous alpha release notes. The main improvement is the restructuring of the models interface meaning that user supplied models are written in the same way as core models and can be added without rebuilding SasView. User models can also take advantage of polydispersity and GPU acceleration in the same way as core models. Bug Reporting Please support the project by reporting bugs that you find to [email protected] All the known bugs/feature requests can be found at: http://trac.sasview.org/report/3 Regular developer builds are also available from https://jenkins.esss.dk/sasview/ if you wish to test the very latest (most likely unstable) versions of SasView. New Features This beta release adds support for the magnetic and multilevel models of 3.1.2 along with a host of bug fixes found in the alpha. Model package changes and improvements All 3.1.2 models now available in new interface Old custom models should now still work '''NOTE:''' These will be deprecated in a future version. Old custom models should be converted to the new model format which is now the same as the built in models and offers much better support. Custom model editor now creates new style models Custom model editor supports better error checking Documentation improvements Continued general cleanup Other improvements/additions Support for new canSAS 2D data files added Plot axes range can now be set manually as well as by zooming Plot annotations can now be moved around after being placed on plot. The active optimizer is now listed on the top of the fit panel. Linear fits now update qmin and max when the x scale limits are changed. Also the plot range no longer resets after a fit. Bug fixes Fixes bug #511 Errors in linearized fits and clean up of interface including Kratky representation Fixes bug #186 Data operation Tool now executes when something is entered in the text box and does not wait for the user to hit enter Fixes bug #459 plot context menu bug Fixes bug #559 copy to clipboard in graph menu broken Fixes bug #466 cannot remove a linear fit from graph Numerous bugs introduced in the alph

SasView version 4.0

<p>The main purpose of this major version release is a significant restructuring of the way models work to address one of the biggest issues identified by the community: the difficulty of adding complex custom models. With this release all models are essentially treated the same within the computational framework. The "built-in" models have been separated out into an independent sasmodels package. Custom models continue to be discovered by placing them in the user plugin directory. All models consist of 1 or optionally 2 files: a model.py file containing much of the details (name, parameters, etc) and either the methods for computing intensity or links to an optional model.c which contains the computational code. All models, whether from sasmodels package or in the plugins directory are treated the same by the SasView application.</p> <p>Other things of note in this release:</p> <ul> <li>Support for openCL means that running on macs will automatically use GPUs or multiple CPU if they exist. This is true for most windows machines as well, but in some cases the user will need to download and install the openCL drivers for their computer. </li> <li>All model documentation has been reviewed and updated</li> <li>A number of other minor bugs and improvement</li> </ul> <p>New Features</p> <p>Model package changes and improvements</p> <ul> <li>All 3.1.2 models now available in new interface <ul> <li>NB: RPA model is currently not available, but will be made available again later in the next point release.</li> </ul> </li> <li>Most old custom models should now still work <ul> <li>NOTE These will be deprecated in a future version. Old custom models should be converted to the new model format which is now the same as the built in models and offers much better support.</li> </ul> </li> <li>Custom model editor now creates new style models</li> <li>Custom model editor supports better error checking</li> </ul> <p>Documentation improvements</p> <ul> <li>Continued general cleanup</li> <li>Documentation of how to write new style models</li> <li>All model docs checked for correctness and consistency with code</li> </ul> <p>Other improvements/additions</p> <ul> <li>Support for new canSAS 2D data files added</li> <li>Plot axes range can now be set manually as well as by zooming</li> <li>Plot annotations can now be moved around after being placed on plot.</li> <li>The active optimizer is now listed on the top of the fit panel.</li> <li>Linear fits now update qmin and max when the x scale limits are changed. Also the plot range no longer resets after a fit.</li> <li>Magnetic models now supported in builtin models and custom models using C</li> <li>Multilevel models (with the exception of RPA) now supported</li> </ul> <p>Bug Fixes</p> <ul> <li>Fixes bug #604 Pringle model questions</li> <li>Fixes bug #472 Reparameterize Teubner-Strey</li> <li>Fixes bug #530 Numerical instabilities in Teubner Strey model</li> <li>Fixes bug #658 ASCII reader very broken</li> <li>Fixes bug #511 Errors in linearized fits and clean up of interface including Kratky representation</li> <li>Fixes bug #186 Data operation Tool now executes when something is entered in the text box and does not wait for the user to hit enter</li> <li>Fixes bug #459 plot context menu bug</li> <li>Fixes bug #559 copy to clipboard in graph menu broken</li> <li>Fixes bug #466 cannot remove a linear fit from graph</li> <li>Numerous bugs introduced in the alpha</li> <li>Fixes bug #636 qmin error erroneuously thrown to console before successfully fitting for select models</li> <li>Fixes #633 P(r) crashing on Sasview when entering 0.0 for Dmax</li> <li>Fixes #642 canSAS 1D xml file take forever to load</li> <li>Fixes #644 Loading saved fit or project opens multiple plot and fit windows and can throw error messages to the console</li> <li>Fixes #635 n_layers = 0 causes errors to be thrown at least on windows</li> <li>Fixes #658 Generic ASCII reader broken (should not be fixed to properly read most ASCII columnar data)</li> <li>Fixes #651 Documentation on how to write new style models added</li> <li>Fixes #654 Problem saving projects (should now work again as it used to).</li> </ul