Robust model benchmarking and bias-imbalance in data-driven materials science: a case study on MODNet

As the number of novel data-driven approaches to material science continues to grow, it is crucial to perform consistent quality, reliability and applicability assessments of model performance. In this paper, we benchmark the Materials Optimal Descriptor Network (MODNet) method and architecture against the recently released MatBench v0.1, a curated test suite of materials datasets. MODNet is shown to outperform current leaders on 6 of the 13 tasks, whilst closely matching the current leaders on a further 2 tasks; MODNet performs particularly well when the number of samples is below 10,000. Attention is paid to two topics of concern when benchmarking models. First, we encourage the reporting of a more diverse set of metrics as it leads to a more comprehensive and holistic comparison of model performance. Second, an equally important task is the uncertainty assessment of a model towards a target domain. Significant variations in validation errors can be observed, depending on the imbalance and bias in the training set (i.e., similarity between training and application space). By using an ensemble MODNet model, confidence intervals can be built and the uncertainty on individual predictions can be quantified. Imbalance and bias issues are often overlooked, and yet are important for successful real-world applications of machine learning in materials science and condensed matter

Accuracy of generalized gradient approximation functionals for density functional perturbation theory calculations

We assess the validity of various exchange-correlation functionals for computing the structural, vibrational, dielectric, and thermodynamical properties of materials in the framework of density-functional perturbation theory (DFPT). We consider five generalized-gradient approximation (GGA) functionals (PBE, PBEsol, WC, AM05, and HTBS) as well as the local density approximation (LDA) functional. We investigate a wide variety of materials including a semiconductor (silicon), a metal (copper), and various insulators (SiO$_2$ $\alpha$-quartz and stishovite, ZrSiO$_4$ zircon, and MgO periclase). For the structural properties, we find that PBEsol and WC are the closest to the experiments and AM05 performs only slightly worse. All three functionals actually improve over LDA and PBE in contrast with HTBS, which is shown to fail dramatically for $\alpha$-quartz. For the vibrational and thermodynamical properties, LDA performs surprisingly very good. In the majority of the test cases, it outperforms PBE significantly and also the WC, PBEsol and AM05 functionals though by a smaller margin (and to the detriment of structural parameters). On the other hand, HTBS performs also poorly for vibrational quantities. For the dielectric properties, none of the functionals can be put forward. They all (i) fail to reproduce the electronic dielectric constant due to the well-known band gap problem and (ii) tend to overestimate the oscillator strengths (and hence the static dielectric constant)

Structural, electronic, vibrational and dielectric properties of LaBGeO5_5 from first principles

Structural, electronic, vibrational and dielectric properties of LaBGeO$_5$ with the stillwellite structure are determined based on \textit{ab initio} density functional theory. The theoretically relaxed structure is found to agree well with the existing experimental data with a deviation of less than $0.2\%$. Both the density of states and the electronic band structure are calculated, showing five distinct groups of valence bands. Furthermore, the Born effective charge, the dielectric permittivity tensors, and the vibrational frequencies at the center of the Brillouin zone are all obtained. Compared to existing model calculations, the vibrational frequencies are found in much better agreement with the published experimental infrared and Raman data, with absolute and relative rms values of 6.04 cm$^{-1}$, and $1.81\%$, respectively. Consequently, numerical values for both the parallel and perpendicular components of the permittivity tensor are established as 3.55 and 3.71 (10.34 and 12.28), respectively, for the high-(low-)frequency limit

Ab initio study of the volume dependence of dynamical and thermodynamical properties of silicon

Motivated by the negative thermal expansion observed for silicon between 20 K and 120 K, we present first an ab initio study of the volume dependence of interatomic force constants, phonon frequencies of TA(X) and TA(L) modes, and of the associated mode Gruneisen parameters. The influence of successive nearest neighbors shells is analysed. Analytical formulas, taking into account interactions up to second nearest neighbors, are developped for phonon frequencies of TA(X) and TA(L) modes and the corresponding mode Gruneisen parameters. We also analyze the volume and pressure dependence of various thermodynamic properties (specific heat, bulk modulus, thermal expansion), and point out the effect of the negative mode Gruneisen parameters of the acoustic branches on these properties. Finally, we present the evolution of the mean square atomic displacement and of the atomic temperature factor with the temperature for different volumes, for which the anomalous effects are even greater.Comment: 24 pages, Revtex 3.0, 11 figures, accepted for publication in Phys. Rev.

Development and tests of a new prototype detector for the XAFS beamline at Elettra Synchrotron in Trieste

The XAFS beamline at Elettra Synchrotron in Trieste combines X-ray absorption spectroscopy and X-ray diffraction to provide chemically specific structural information of materials. It operates in the energy range 2.4-27 keV by using a silicon double reflection Bragg monochromator. The fluorescence measurement is performed in place of the absorption spectroscopy when the sample transparency is too low for transmission measurements or the element to study is too diluted in the sample. We report on the development and on the preliminary tests of a new prototype detector based on Silicon Drift Detectors technology and the SIRIO ultra low noise front-end ASIC. The new system will be able to reduce drastically the time needed to perform fluorescence measurements, while keeping a short dead time and maintaining an adequate energy resolution to perform spectroscopy. The custom-made silicon sensor and the electronics are designed specifically for the beamline requirements.Comment: Proceeding of the 6YRM 12th-14th Oct 2015 - L'Aquila (Italy). Accepted for publication on Journal of Physics: Conference Serie

ASPETTI DELLA PRODUZIONE DEI PICCOLI RUMINANTI CON IMPATTO SULLA SALUTE UMANA

Negli ultimi anni l’attenzione del consumatore si è sempre più orientata verso le caratteristiche nutrizionali degli alimenti. Queste proprietà sono di grande importanza anche per quanto riguarda le produzioni dei piccoli ruminanti. Il presente lavoro ha lo scopo di riassumere i principali risultati emersi dal progetto di ricerca “Aspetti della produzione dei piccoli ruminanti con particolare impatto sulla salute umana”. Sono stati analizzati mediante i metodi descritti in letteratura: 1) i polimorfismi genetici dei biopeptidi del latte dei piccoli ruminanti; 2) le attività di alcuni enzimi della membrana del globulo di grasso e la frazione lipidica del latte ovino; 3) la qualità nutrizionale del latte e del formaggio ovino in relazione all’intensità di pascolamento; 4) le componenti bioattive di siero e scotta residui alla produzione dei formaggi ovi-caprini; 5) la resistenza genetica alle encefalopatie spongiformi trasmissibili e l’efficienza economica e biologica in razze ovine. I risultati ottenuti evidenziano, da svariati punti di vista, numerose potenzialità legate alle produzioni dei piccoli ruminanti e alle loro ricadute sulla salute umana

Electronic structure and the minimum conductance of a graphene layer on SiO2 from density-functional methods.

The effect of the SiO$_2$ substrate on a graphene film is investigated using realistic but computationally convenient energy-optimized models of the substrate supporting a layer of graphene. The electronic bands are calculated using density-functional methods for several model substrates. This provides an estimate of the substrate-charge effects on the behaviour of the bands near $E_F$, as well as a variation of the equilibrium distance of the graphene sheet. A model of a wavy graphene layer is examined as a possible candidate for understanding the nature of the minimally conducting states in graphene.Comment: 6 pages, 5 figure

Raman spectra and structural analysis in ZrOxNy thin films

Raman spectroscopy has been used as a local probe to characterize the structural evolution of magnetron-sputtered decorative zirconium oxynitride ZrOxNy films which result from an increase of reactive gas flow in the deposition The lines shapes, the frequency position and widths of the Raman bands show a systematic change as a function of the reactive gas flow (a mixture of both oxygen and nitrogen). The as-deposited zirconium nitride film presents a Raman spectrum with the typical broadened bands, due to the disorder induced by N vacancies. The recorded Raman spectrum of the zirconium oxide film is typical of the monoclinic phase of ZrO2, which is shown also by X-ray diffraction. Raman spectra of zirconium oxynitride thin films present changes, which are found to be closely related with the oxygen content in films and the subsequent structural changes.FCT institution by the project nº POCTI/CTM/38086/2001 co-financed by European community fund FEDEREuropean Union through the NMP3-CT-2003 505948 project "HARDECOAT

Numerical atomic orbitals for linear scaling

The performance of basis sets made of numerical atomic orbitals is explored in density-functional calculations of solids and molecules. With the aim of optimizing basis quality while maintaining strict localization of the orbitals, as needed for linear-scaling calculations, several schemes have been tried. The best performance is obtained for the basis sets generated according to a new scheme presented here, a flexibilization of previous proposals. The basis sets are tested versus converged plane-wave calculations on a significant variety of systems, including covalent, ionic and metallic. Satisfactory convergence (deviations significantly smaller than the accuracy of the underlying theory) is obtained for reasonably small basis sizes, with a clear improvement over previous schemes. The transferability of the obtained basis sets is tested in several cases and it is found to be satisfactory as well.Comment: 9 pages with 2 encapsulated postscript figures, submitted to Phys. Rev.