Earth and Planetary Sciences

The formal relationship between ultrasoft (US) Vanderbilt-type pseudopotentials and Bl\"ochl's projector augmented wave (PAW) method is derived. It is shown that the total energy functional for US pseudopotentials can be obtained by linearization of two terms in a slightly modified PAW total energy functional. The Hamilton operator, the forces, and the stress tensor are derived for this modified PAW functional. A simple way to implement the PAW method in existing plane-wave codes supporting US pseudopotentials is pointed out. In addition, critical tests are presented to compare the accuracy and efficiency of the PAW and the US pseudopotential method with relaxed core all electron methods. These tests include small molecules $({\mathrm{H}}_{2}{,\mathrm{}\mathrm{H}}_{2}{\mathrm{O},\mathrm{}\

A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and S

We present ab initio quantum-mechanical molecular-dynamics calculations based on the calculation of the electronic ground state and of the Hellmann-Feynman forces in the local-density approximation at each molecular-dynamics step. This is possible using conjugate-gradient techniques for energy minimization, and predicting the wave functions for new ionic positions using subspace alignment. This approach avoids the instabilities inherent in quantum-mechanical molecular-dynamics calculations for metals based on the use of a fictitious Newtonian dynamics for the electronic degrees of freedom. This method gives perfect control of the adiabaticity and allows us to perform simulations over several picoseconds.

A general method, suitable for fast computing machines, for investigating such properties as equations of state for substances consisting of interacting individual molecules is described. The method consists of a modified Monte Carlo integration over configuration space. Results for the two-dimensional rigid-sphere system have been obtained on the Los Alamos MANIAC and are presented here. These results are compared to the free volume equation of state and to a four-term virial coefficient expansion.

Abstract Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, te

Abstract Within the Copernicus Climate Change Service (C3S), ECMWF is producing the ERA5 reanalysis which, once completed, will embody a detailed record of the global atmosphere, land surface and ocean waves from 1950 onwards. This new reanalysis replaces the ERA‐Interim reanalysis (spanning 1979 onwards) which was started in 2006. ERA5 is based on the Integrated Forecasting System (IFS) Cy41r2 which was operational in 2016. ERA5 thus benefits from a decade of developments in model physics, core dynamics and data assimilation. In addition to a significantly enhanced horizontal resolution of 31 km, compared to 80 km for ERA‐Interim, ERA5 has hourly output throughout, and an uncertainty estimate from an ensemble (3‐hourly at half the horizontal resolution). This paper describes the general s

Abstract Summary: MrBayes 3 performs Bayesian phylogenetic analysis combining information from different data partitions or subsets evolving under different stochastic evolutionary models. This allows the user to analyze heterogeneous data sets consisting of different data types—e.g. morphological, nucleotide, and protein—and to explore a wide variety of structured models mixing partition-unique and shared parameters. The program employs MPI to parallelize Metropolis coupling on Macintosh or UNIX clusters. Availability: http://morphbank.ebc.uu.se/mrbayes Contact: fredrik.ronquist@ebc.uu.se * To whom correspondence should be addressed.

The NCEP and NCAR are cooperating in a project (denoted “reanalysis”) to produce a 40-year record of global analyses of atmospheric fields in support of the needs of the research and climate monitoring communities. This effort involves the recovery of land surface, ship, rawinsonde, pibal, aircraft, satellite, and other data; quality controlling and assimilating these data with a data assimilation system that is kept unchanged over the reanalysis period 1957–96. This eliminates perceived climate jumps associated with changes in the data assimilation system. The NCEP/NCAR 40-yr reanalysis uses a frozen state-of-the-art global data assimilation system and a database as complete as possible. The data assimilation and the model used are identical to the global system implemented operationally

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphic

Abstract ERA‐Interim is the latest global atmospheric reanalysis produced by the European Centre for Medium‐Range Weather Forecasts (ECMWF). The ERA‐Interim project was conducted in part to prepare for a new atmospheric reanalysis to replace ERA‐40, which will extend back to the early part of the twentieth century. This article describes the forecast model, data assimilation method, and input datasets used to produce ERA‐Interim, and discusses the performance of the system. Special emphasis is placed on various difficulties encountered in the production of ERA‐40, including the representation of the hydrological cycle, the quality of the stratospheric circulation, and the consistency in time of the reanalysed fields. We provide evidence for substantial improvements in each of these aspects

Summary Trace-element data for mid-ocean ridge basalts (MORBs) and ocean island basalts (OIB) are used to formulate chemical systematics for oceanic basalts. The data suggest that the order of trace-element incompatibility in oceanic basalts is Cs ≈ Rb ≈ (≈ Tl) ≈ Ba(≈ W) > Th > U ≈ Nb = Ta ≈ K > La > Ce ≈ Pb > Pr (≈ Mo) ≈ Sr > P ≈ Nd (> F) > Zr = Hf ≈ Sm > Eu ≈ Sn (≈ Sb) ≈ Ti > Dy ≈ (Li) > Ho = Y > Yb. This rule works in general and suggests that the overall fractionation processes operating during magma generation and evolution are relatively simple, involving no significant change in the environment of formation for MORBs and OIBs. In detail, minor differences in element ratios correlate with the isotopic characteristics of different types of OIB compo

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A new approach to the construction of first-principles pseudopotentials is described. The method allows transferability to be improved systematically while holding the cutoff radius fixed, even for large cutoff radii. Novel features are that the pseudopotential itself becomes charge-state dependent, the usual norm-conservation constraint does not apply, and a generalized eigenproblem is introduced. The potentials have a separable form well suited for plane-wave solid-state calculations, and show promise for application to first-row and transition-metal systems.

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE ADSORPTION OF GASES ON PLANE SURFACES OF GLASS, MICA AND PLATINUM.Irving LangmuirCite this: J. Am. Chem. Soc. 1918, 40, 9, 1361–1403Publication Date (Print):September 1, 1918Publication History Published online1 May 2002Published inissue 1 September 1918https://pubs.acs.org/doi/10.1021/ja02242a004https://doi.org/10.1021/ja02242a004research-articleACS PublicationsRequest reuse permissionsArticle Views24474Altmetric-Citations17033LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreemen

A basic problem in computer vision is to understand the structure of a real world scene given several images of it. Techniques for solving this problem are taken from projective geometry and photogrammetry. Here, the authors cover the geometric principles and their algebraic representation in terms of camera projection matrices, the fundamental matrix and the trifocal tensor. The theory and methods of computation of these entities are discussed with real examples, as is their use in the reconstruction of scenes from multiple images. The new edition features an extended introduction covering the key ideas in the book (which itself has been updated with additional examples and appendices) and significant new results which have appeared since the first edition. Comprehensive background materi

We developed interpolated climate surfaces for global land areas (excluding Antarctica) at a spatial resolution of 30 arc s (often referred to as 1-km spatial resolution). The climate elements considered were monthly precipitation and mean, minimum, and maximum temperature. Input data were gathered from a variety of sources and, where possible, were restricted to records from the 1950–2000 period. We used the thin-plate smoothing spline algorithm implemented in the ANUSPLIN package for interpolation, using latitude, longitude, and elevation as independent variables. We quantified uncertainty arising from the input data and the interpolation by mapping weather station density, elevation bias in the weather stations, and elevation variation within grid cells and through data partitioning and

Finite systems of deterministic ordinary nonlinear differential equations may be designed to represent forced dissipative hydrodynamic flow. Solutions of these equations can be identified with trajectories in phase space. For those systems with bounded solutions, it is found that nonperiodic solutions are ordinarily unstable with respect to small modifications, so that slightly differing initial states can evolve into considerably different states. Systems with bounded solutions are shown to possess bounded numerical solutions. A simple system representing cellular convection is solved numerically. All of the solutions are found to be unstable, and almost all of them are nonperiodic. The feasibility of very-long-range weather prediction is examined in the light of these results.

A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheet-type data entry with univariate and multivariate statistics, curve fitting, timeseries analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for cours

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.