A KIM-compliant potfit for fitting sloppy interatomic potentials : application to the EDIP model for silicon

Fitted interatomic potentials are widely used in atomistic simulations thanks to their ability to compute the energy and forces on atoms quickly. However, the simulation results crucially depend on the quality of the potential being used. Force matching is a method aimed at constructing reliable and transferable interatomic potentials by matching the forces computed by the potential as closely as possible, with those obtained from first principles calculations. The potfit program is an implementation of the force-matching method that optimizes the potential parameters using a global minimization algorithm followed by a local minimization polish. We extended potfit in two ways. First, we adapted the code to be compliant with the KIM Application Programming Interface (API) standard (part of the Knowledgebase of Interatomic Models Project). This makes it possible to use potfit to fit many KIM potential models, not just those prebuilt into the potfit code. Second, we incorporated the geodesic Levenberg–Marquardt (LM) minimization algorithm into potfit as a new local minimization algorithm. The extended potfit was tested by generating a training set using the KIM Environment-Dependent Interatomic Potential (EDIP) model for silicon and using potfit to recover the potential parameters from different initial guesses. The results show that EDIP is a “sloppy model” in the sense that its predictions are insensitive to some of its parameters, which makes fitting more difficult. We find that the geodesic LM algorithm is particularly efficient for this case. The extended potfit code is the first step in developing a KIM-based fitting framework for interatomic potentials for bulk and two-dimensional materials. The code is available for download via https://www.potfit.net

Magnetic properties of Gd_xY_{1-x}Fe_2Zn_{20}: dilute, large, S\textbf {S} moments in a nearly ferromagnetic Fermi liquid

Single crystals of the dilute, rare earth bearing, pseudo-ternary series, Gd_xY_{1-x}Fe_2Zn_{20} were grown out of Zn-rich solution. Measurements of magnetization, resistivity and heat capacity on Gd_xY_{1-x}Fe_2Zn_{20} samples reveal ferromagnetic order of Gd^{3+} local moments across virtually the whole series ($x \geq 0.02$). The magnetic properties of this series, including the ferromagnetic ordering, the reduced saturated moments at base temperature, the deviation of the susceptibilities from Curie-Weiss law and the anomalies in the resistivity, are understood within the frame work of dilute, $\textbf {S}$ moments (Gd^{3+}) embedded in a nearly ferromagnetic Fermi liquid (YFe_2Zn_{20}). The s-d model is employed to further explain the variation of $T_{\mathrm{C}}$ with x as well as the temperature dependences of of the susceptibilities

Surface energy and stability of stress-driven discommensurate surface structures

A method is presented to obtain {\it ab initio} upper and lower bounds to surface energies of stress-driven discommensurate surface structures, possibly non-periodic or exhibiting very large unit cells. The instability of the stressed, commensurate parent of the discommensurate structure sets an upper bound to its surface energy; a lower bound is defined by the surface energy of an ideally commensurate but laterally strained hypothetical surface system. The surface energies of the phases of the Si(111):Ga and Ge(111):Ga systems and the energies of the discommensurations are determined within $\pm 0.2$ eV.Comment: 4 pages RevTeX. 2 Figures not included. Ask for a hard copy (through regular mail) to [email protected]

Population Monte Carlo algorithms

We give a cross-disciplinary survey on ``population'' Monte Carlo algorithms. In these algorithms, a set of ``walkers'' or ``particles'' is used as a representation of a high-dimensional vector. The computation is carried out by a random walk and split/deletion of these objects. The algorithms are developed in various fields in physics and statistical sciences and called by lots of different terms -- ``quantum Monte Carlo'', ``transfer-matrix Monte Carlo'', ``Monte Carlo filter (particle filter)'',``sequential Monte Carlo'' and ``PERM'' etc. Here we discuss them in a coherent framework. We also touch on related algorithms -- genetic algorithms and annealed importance sampling.Comment: Title is changed (Population-based Monte Carlo -> Population Monte Carlo). A number of small but important corrections and additions. References are also added. Original Version is read at 2000 Workshop on Information-Based Induction Sciences (July 17-18, 2000, Syuzenji, Shizuoka, Japan). No figure

A strong decline of the endangered Apollo butterfly over 20 years in the archipelago of southern Finland

Insect groups are declining worldwide; Lepidoptera are among the taxa most affected in terrestrial ecosystems. The main drivers of these declines are a diverse set of factors relating to environmental change including habitat loss, pollution, and climate change. In 2019 and 2020, we surveyed 118 and 90 islands, respectively, in southern Finland's archipelago for occupancy of Parnassius apollo larvae and counted the abundance of their host plant Hylotelephium telephium. Compared with historical data (1997-2003), the occupancy of Apollo butterfly larvae has decreased remarkably from about 75% to about 20% of islands and abundance declined as well. However, the abundance of their host plant has not changed. Occupancy models showed that the present occupancy probability is not affected by host plant numbers, and shows substantial colonization-extinction dynamics making the population vulnerable to stochastic extinction.Implications for insect conservation Our results show that this Apollo butterfly population is declining, and conservation actions are needed.</p

First-Principles Studies of Hydrogenated Si(111)--7×\times7

The relaxed geometries and electronic properties of the hydrogenated phases of the Si(111)-7$\times$7 surface are studied using first-principles molecular dynamics. A monohydride phase, with one H per dangling bond adsorbed on the bare surface is found to be energetically favorable. Another phase where 43 hydrogens saturate the dangling bonds created by the removal of the adatoms from the clean surface is found to be nearly equivalent energetically. Experimental STM and differential reflectance characteristics of the hydrogenated surfaces agree well with the calculated features.Comment: REVTEX manuscript with 3 postscript figures, all included in uu file. Also available at http://www.phy.ohiou.edu/~ulloa/ulloa.htm

Local Isoelectronic Reactivity of Solid Surfaces

The quantity w^N(r) = ( 1/ k^2 T_el)[partial n(r, T_el) / partial T_el]_(v(r),N) is introduced as a convenient measure of the local isoelectronic reactivity of surfaces. It characterizes the local polarizability of the surface and it can be calculated easily. The quantity w^N(r) supplements the charge transfer reactivity measured e.g. by the local softness to which it is closely related. We demonstrate the applicability and virtues of the function w^N(r) for the example of hydrogen dissociation and adsorption on Pd(100).Comment: RevTeX, 13 pages, 3 figures, to appear in Phys. Rev. Let

Critical-sized cartilage defects in the equine carpus

Aim: The horse joint, due to its similarity with the human joint, is the ultimate model for translational articular cartilage repair studies. This study was designed to determine the critical size of cartilage defects in the equine carpus and serve as a benchmark for the evaluation of new cartilage treatment options. Material and Methods: Circular full-thickness cartilage defects with a diameter of 2, 4, and 8 mm were created in the left middle carpal joint and similar osteochondral (3.5 mm in depth) defects in the right middle carpal joint of 5 horses. Spontaneously formed repair tissue was examined macroscopically, with MR and mu CT imaging, polarized light microscopy, standard histology, and immunohistochemistry at 12 months. Results: Filling of 2 mm chondral defects was good (77.8 +/- 8.5%), but proteoglycan depletion was evident in Safranin-O staining and gadolinium-enhanced MRI (T-1Gd). Larger chondral defects showed poor filling (50.6 +/- 2.7% in 4 mm and 31.9 +/- 7.3% in 8 mm defects). Lesion filling in 2, 4, and 8 mm osteochondral defects was 82.3 +/- 3.0%, 68.0 +/- 4.6% and 70.8 +/- 15.4%, respectively. Type II collagen staining was seen in 9/15 osteochondral defects but only in 1/15 chondral defects. Subchondral bone pathologies were evident in 14/15 osteochondral samples but only in 5/15 chondral samples. Although osteochondral lesions showed better neotissue quality than chondral lesions, the overall repair was deemed unsatisfactory because of the subchondral bone pathologies. Conclusion: We recommend classifying 4 mm as critical osteochondral lesion size and 2 mm as critical chondral lesion size for cartilage repair research in the equine carpal joint model.Peer reviewe

Integrating evolution into ecological modelling: accommodating phenotypic changes in agent based models.

PMCID: PMC3733718This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Evolutionary change is a characteristic of living organisms and forms one of the ways in which species adapt to changed conditions. However, most ecological models do not incorporate this ubiquitous phenomenon. We have developed a model that takes a 'phenotypic gambit' approach and focuses on changes in the frequency of phenotypes (which differ in timing of breeding and fecundity) within a population, using, as an example, seasonal breeding. Fitness per phenotype calculated as the individual's contribution to population growth on an annual basis coincide with the population dynamics per phenotype. Simplified model variants were explored to examine whether the complexity included in the model is justified. Outputs from the spatially implicit model underestimated the number of individuals across all phenotypes. When no phenotype transitions are included (i.e. offspring always inherit their parent's phenotype) numbers of all individuals are always underestimated. We conclude that by using a phenotypic gambit approach evolutionary dynamics can be incorporated into individual based models, and that all that is required is an understanding of the probability of offspring inheriting the parental phenotype

Invasive species control with apex predators: increasing presence of wolves is associated with reduced occurrence of the alien raccoon dog

The role of an alien predator in the community depends on its interaction with native predators. The absence of apex predators may facilitate outbreaks of invasive mesopredators, but the effect of apex predators may vary between species and environments. We analysed the occurrence of a common invasive mesopredator in Europe, the raccoon dog (Nyctereutes procyonoides), and native mesopredators, the red fox and the Eurasian badger, in camera-trap data from Finland. The observations in cameras were analysed in relation to the presence of apex predators in the landscape (grey wolf and Eurasian lynx), human density, and habitat. We observed negative effect of increasing presence of wolves and lynxes on the occurrence of raccoon dogs. This effect appeared clear compared to the effects of habitat and human density. The effect of lynxes on raccoon dogs was clearer in areas with short growth season. For the occurrence of badgers, the presence of wolves had a weak negative effect and the presence of lynxes had a positive effect. For the occurrence of red foxes, wolves had a positive effect when agricultural fields were sparse in the landscape and lynxes had no effect. We also observed that the invasive raccoon dog currently appears to be the most common mesopredator within the study area. We conclude that the effect of apex predators on mesopredators depends on the environment and, in our case, was more suppressive on the alien mesopredator than on the native mesopredators. Thus, apex predators can play an important role in controlling invasive mesopredators