Adaptive Localization Regions for O(N) Density Functional Theory

A linear scaling approach for general and accurate pseudopotential Density Functional Theory calculations is presented. It is based on a Finite Difference discretization. Effective O(N) scaling is achieved by confining the orbitals in spherical localization regions. To improve accuracy and flexibility while computing the smallest possible number of orbitals, we propose an algorithm to adapt localization regions during computation. Numerical results for a polyacethylene chain and a magnesium oxide ring are presented

Estimating wild boar ( Sus scrofa ) abundance and density using capture-resights in Canton of Geneva, Switzerland

We estimated wild boar abundance and density using capture-resight methods in the western part of the Canton of Geneva (Switzerland) in the early summer from 2004 to 2006. Ear-tag numbers and transmitter frequencies enabled us to identify individuals during each of the counting sessions. We used resights generated by self-triggered camera traps as recaptures. Program Noremark provided Minta-Mangel and Bowden's estimators to assess the size of the marked population. The minimum numbers of wild boars belonging to the unmarked population (juveniles and/or piglets) were added to the respective estimates to assess total population size. Over the 3years, both estimators showed a stable population with a slight diminishing tendency. We used mean home range size determined by telemetry to assess the sampled areas and densities. Mean wild boar population densities calculated were 10.6individuals/km2 ± 0.8 standard deviation (SD) and 10.0ind/km2 ± 0.6 SD with both estimators, respectively, and are among the highest reported from Western Europe. Because of the low proportion of marked animals and, to a lesser extent, of technical failures, our estimates showed poor precision, although they displayed similar population trends compared to the culling bag statistics. Reported densities were consistent with the ecological conditions of the study are

O(N) complexity algorithms for First-Principles Electronic Structure Calculations

The fundamental equation governing a non-relativistic quantum system of N particles is the time-dependant Schroedinger Equation [Schroedinger, 1926]. In 1965, Kohn and Sham proposed to replace this original many-body problem by an auxiliary independent-particles problem that can be solved more easily (Density Functional Theory). Solving this simplified problem requires to find the subspace of dimension N spanned by the N eigenfunctions {Psi}{sub i} corresponding to the N lowest eigenvalues {var_epsilon}{sub i} of a non-linear Hamiltonian operator {cflx H} determined from first-principles. From the solution of the Kohn-Sham equations, forces acting on atoms can be derived to optimize geometries and simulate finite temperature phenomenon by molecular dynamics. This technique is used at LLNL to determine the Equation of State of various materials, and to study biomolecules and nanomaterials

Linear scaling first-principles molecular dynamics with plane waves accuracy

We propose a real-space finite differences approach for accurate and unbiased O(N) Density Functional Theory molecular dynamics simulations based on a localized orbitals representation of the electronic structure. The discretization error can be reduced systematically by adapting the mesh spacing, while the orbitals truncation error decreases exponentially with the radius of the localization regions. For regions large enough, energy conservation in microcanonical simulations is demonstrated for liquid water. We propose an explanation for the energy drift observed for smaller regions

First principles study of the aggregation of oligo and polythiophene cations in solution

The stacking of positively charged (or doped) terthiophene oligomers and quaterthiophene polymers in solution is investigated applying a recently developed unified electrostatic and cavitation model for first-principles calculations in a continuum solvent. The thermodynamic and structural patterns of the dimerization are explored in different solvents, and the distinctive roles of polarity and surface tension are characterized and analyzed. Interestingly, we discover a saturation in the stabilization effect of the dielectric screening that takes place at rather small values of {epsilon}{sub 0}. Moreover, we address the interactions in trimers of terthiophene cations, with the aim of generalizing the results obtained for the dimers to the case of higher order stacks and nanoaggregates

Finite Elements approach for Density Functional Theory calculations on locally refined meshes

We present a quadratic Finite Elements approach to discretize the Kohn-Sham equations on structured non-uniform meshes. A multigrid FAC preconditioner is proposed to iteratively solve the equations by an accelerated steepest descent scheme. The method was implemented using SAMRAI, a parallel software infrastructure for general AMR applications. Examples of applications to small nanoclusters calculations are presented

Finite Element approach for Density Functional Theory calculations on locally refined meshes

We present a quadratic Finite Element approach to discretize the Kohn-Sham equations on structured non-uniform meshes. A multigrid FAC preconditioner is proposed to iteratively solve the equations by an accelerated steepest descent scheme. The method was implemented using SAMRAI, a parallel software infrastructure for general AMR applications. Examples of applications to small nanoclusters calculations are presented

A novel multigrid method for electronic structure calculations

A general real-space multigrid algorithm for the self-consistent solution of the Kohn-Sham equations appearing in the state-of-the-art electronic-structure calculations is described. The most important part of the method is the multigrid solver for the Schroedinger equation. Our choice is the Rayleigh quotient multigrid method (RQMG), which applies directly to the minimization of the Rayleigh quotient on the finest level. Very coarse correction grids can be used, because there is no need to be able to represent the states on the coarse levels. The RQMG method is generalized for the simultaneous solution of all the states of the system using a penalty functional to keep the states orthogonal. The performance of the scheme is demonstrated by applying it in a few molecular and solid-state systems described by non-local norm-conserving pseudopotentials.Comment: 9 pages, 3 figure

Cats, connectivity and conservation: incorporating datasets and integrating scales for wildlife management

Understanding resource selection and quantifying habitat connectivity are fundamental to conservation planning for both land-use and species management plans. However, datasets available to management authorities for resource selection and connectivity analyses are often highly limited and fragmentary. As a result, measuring connectivity is challenging, and often poorly integrated within conservation planning and wildlife management. To exacerbate the challenge, scale-dependent resource use makes inference across scales problematic, resource use is often modelled in areas where the species is not present, and connectivity is typically measured using a source-to-sink approach, erroneously assuming animals possess predefined destinations. Here, we used a large carnivore, the leopard Panthera pardus, to characterise resource use and landscape connectivity across a vast, biodiverse region of southern Africa. Using a range of datasets to counter data deficiencies inherent in carnivore management, we overcame methodological limitations by employing occupancy modelling and resource selection functions across three orders of selection, and estimated landscape-scale habitat connectivity – independent of a priori source and sink locations – using circuit theory. We evaluated whether occupancy modelling on its own was capable of accurately informing habitat connectivity, and identified conservation priorities necessary for applied management. We detected markedly different scale-dependent relationships across all selection orders. Our multi-data, multi-scale approach accurately predicted resource use across multiple scales and demonstrates how management authorities can more suitably utilise fragmentary datasets. We further developed an unbiased landscape-scale depiction of habitat connectivity, and identified key linkages in need of targeted management. We did not find support for the use of occupancy modelling as a proxy for landscape-scale habitat connectivity and further caution its use within a management context. Synthesis and applications. Maintaining habitat connectivity remains a fundamental component of wildlife management and conservation, yet data to inform these biological and ecological processes are often scarce. We present a robust approach that incorporates multi-scale fragmentary datasets (e.g. mortality data, permit data, sightings data), routinely collected by management authorities, to inform wildlife management and land-use planning. We recommend that management authorities employ a multi-data, multi-scale connectivity approach—as we present here—to identify management units at risk of low connectivity