First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metallorganic systems. Our results show that accurate Density-Functional Theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.Comment: 29 pages, 4 Postscript figures, revtex

DC Conductance of Molecular Wires

Inspired by the work of Kamenev and Kohn, we present a general discussion of the two-terminal dc conductance of molecular devices within the framework of Time Dependent Current-Density Functional Theory. We derive a formally exact expression for the adiabatic conductance and we discuss the dynamical corrections. For junctions made of long molecular chains that can be either metallic or insulating, we derive the exact asymptotic behavior of the adiabatic conductance as a function of the chain's length. Our results follow from the analytic structure of the bands of a periodic molecular chain and a compact expression for the Green's functions. In the case of an insulating chain, not only do we obtain the exponentially decaying factors, but also the corresponding amplitudes, which depend very sensitively on the electronic properties of the contacts. We illustrate the theory by a numerical study of a simple insulating structure connected to two metallic jellium leads.Comment: 15 pgs and 9 figure

First principles study of adsorbed Cu_n (n=1-4) microclusters on MgO(100): structural and electronic properties

We present a density functional study of the structural and electronic properties of small Cu_n (n=1,4) aggregates on defect-free MgO(100). The calculations employ a slab geometry with periodic boundary conditions, supercells with up to 76 atoms, and include full relaxation of the surface layer and of all adsorbed atoms. The preferred adsorption site for a single Cu adatom is on top of an oxygen atom. The adsorption energy and Cu-O distance are E_S-A = 0.99 eV and d_S-A = 2.04 Angstroems using the Perdew-Wang gradient corrected exchange correlation functional. The saddle point for surface diffusion is at the "hollow" site, with a diffusion barrier of around 0.45 eV. For the adsorbed copper dimer, two geometries, one parallel and one perpendicular to the surface, are very close in energy. For the adsorbed Cu_3, a linear configuration is preferred to the triangular geometry. As for the tetramer, the most stable adsorbed geometry for Cu_4 is a rhombus. The adsorption energy per Cu atom decreases with increasing the size of the cluster, while the Cu-Cu cohesive energy increases, rapidly becoming more important than the adsorption energy.Comment: Major revision, Latex(2e) document, 23 pages, 11 figures, accepted for publication in J. of Chem. Phys., paper available at http://irrmawww.epfl.ch/vm/vm_wor

Electronic Properties of Molecules and Surfaces with a Self\uad-Consistent Interatomic van der Waals Density Functional.

How strong is the effect of van der Waals (vdW) interactions on the electronic properties of molecules and extended systems? To answer this question, we derived a fully self-consistent implementation of the density-dependent interatomic vdW functional of Tkatchenko and Scheffler [Phys. Rev. Lett. 102, 073005 (2009)]. Not surprisingly, vdW self-consistency leads to tiny modifications of the structure, stability, and electronic properties of molecular dimers and crystals. However, unexpectedly large effects were found in the binding energies, distances, and electrostatic moments of highly polarizable alkali-metal dimers. Most importantly, vdW interactions induced complex and sizable electronic charge redistribution in the vicinity of metallic surfaces and at organic-metal interfaces. As a result, a substantial influence on the computed work functions was found, revealing a nontrivial connection between electrostatics and long-range electron correlation effects

A Branching Time Model of CSP

I present a branching time model of CSP that is finer than all other models of CSP proposed thus far. It is obtained by taking a semantic equivalence from the linear time - branching time spectrum, namely divergence-preserving coupled similarity, and showing that it is a congruence for the operators of CSP. This equivalence belongs to the bisimulation family of semantic equivalences, in the sense that on transition systems without internal actions it coincides with strong bisimilarity. Nevertheless, enough of the equational laws of CSP remain to obtain a complete axiomatisation for closed, recursion-free terms.Comment: Dedicated to Bill Roscoe, on the occasion of his 60th birthda

Acceleration Schemes for Ab-Initio Molecular Dynamics and Electronic Structure Calculations

We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest descent algorithms while retaining their numerical cost per time step. Our damped dynamics has efficiency comparable to that of conjugate gradient methods in typical electronic minimization problems. Then, we analyse the factors that limit the size of the integration time step in approaches based on plane-wave expansions. The maximum allowed time step is dictated by the highest frequency components of the fictitious electronic dynamics. These can result either from the large wavevector components of the kinetic energy or from the small wavevector components of the Coulomb potential giving rise to the so called {\it charge sloshing} problem. We show how to eliminate large wavevector instabilities by adopting a preconditioning scheme that is implemented here for the first-time in the context of Car-Parrinello ab-initio molecular dynamics simulations of the ionic motion. We also show how to solve the charge-sloshing problem when this is present. We substantiate our theoretical analysis with numerical tests on a number of different silicon and carbon systems having both insulating and metallic character.Comment: RevTex, 9 figures available upon request, to appear in Phys. Rev.