Change search
ReferencesLink to record
Permanent link

Direct link
Extended Lagrangian Born-Oppenheimer molecular dynamics with dissipation
KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
Show others and affiliations
2009 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, no 21, 214109- p.Article in journal (Refereed) Published
Abstract [en]

Stability and dissipation in the propagation of the electronic degrees of freedom in time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [Niklasson , Phys. Rev. Lett. 97, 123001 (2006); Phys. Rev. Lett. 100, 123004 (2008)] are analyzed. Because of the time-reversible propagation the dynamics of the extended electronic degrees of freedom is lossless with no dissipation of numerical errors. For long simulation times under "noisy" conditions, numerical errors may therefore accumulate to large fluctuations. We solve this problem by including a dissipative external electronic force that removes noise while keeping the energy stable. The approach corresponds to a Langevin-like dynamics for the electronic degrees of freedom with internal numerical error fluctuations and external, approximately energy conserving, dissipative forces. By tuning the dissipation to balance the numerical fluctuations the external perturbation can be kept to a minimum.

Place, publisher, year, edition, pages
2009. Vol. 130, no 21, 214109- p.
Keyword [en]
ab initio calculations, fluctuations, molecular dynamics method
National Category
Materials Engineering
URN: urn:nbn:se:kth:diva-26991DOI: 10.1063/1.3148075ISI: 000266674400010ScopusID: 2-s2.0-67249126946OAI: diva2:373823
QC 20101201Available from: 2010-12-01 Created: 2010-12-01 Last updated: 2012-03-23Bibliographically approved
In thesis
1. Quantum transport and geometric integration for molecular systems
Open this publication in new window or tab >>Quantum transport and geometric integration for molecular systems
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Molecular electronics is envisioned as a possible next step in device miniaturization. It is usually taken to mean the design and manufacturing of electronic devices and applications where organic molecules work as the fundamental functioning unit. It involves the measurement and manipulation of electronic response and transport in molecules attached to conducting leads. Organic molecules have the advantages over conventional solid state electronics of inherent small sizes, endless chemical diversity and ambient temperature low cost manufacturing.

In this thesis we investigate the switching and conducting properties of photoswitching dithienylethene derivatives. Such molecules change their conformation in solution when acted upon by light. Photochromic molecules are attractive candidates for use in molecular electronics because of the switching between different states with different conducting properties. The possibility of optically controlling the conductance of the molecule attached to conducting leads may lead to new device implementations.

The switching reaction is investigated with potential energy calculations for different values of the reaction coordinate between the closed and the open isomer. The electronic and atomic structure calculations are performed with Density Functional Theory (DFT). The potential energy barrier separating the open and closed isomer is investigated, as well as the nature of the excited states involved in the switching.

The conducting properties of the molecule inserted between gold, silver and nickel leads is calculated within the Non Equilibrium Green Function theory (NEGF). The molecule is found to be a good conductor in both conformations, with the low-bias current for the closed one being about 20 times larger than that of the open in the case of gold contacts, and over 30 times larger in the case of silver contacts. For the Ni leads the current for the closed isomer is almost 40 times larger than that of the open. Importantly, the current-voltage characteristics away from the linear response is largely determined by molecular orbital re-hybridization in an electric field, in close analogy to what happens for Mn12 molecules. However in the case of dithienylethene attached to Au and Ag such a mechanism is effective also in conditions of strong electronic coupling to the electrodes.

In reality these molecules are in constant motion, and the dynamical properties has to be considered. In this thesis such a line of work is initiated. In order to facilitate efficient and stable dynamical simulations of molecular systems the extended Lagrangian formulation of Born-Oppenheimer molecular dynamics have been implemented in two different codes. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence.

In the density functional theory code FreeON, different symplectic integrators up to the 6th order have been adapted and optimized. It is shown how the accuracy can be significantly improved compared to a conventional Verlet integration at the same level of computational cost, in particular for the case of very high accuracy requirements. Geometric integration schemes, including a weak dissipation to remove numerical noise, are developed and implemented in the self-consistent tight-binding code LATTE. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. The modification of the integration breakes symplecticity and introduces a global energy drift. The systematic driftin energy and the broken symplecticity can be kept arbitrarily small without significant perturbations of the molecular trajectories.

Place, publisher, year, edition, pages
Stockholm: KTH, 2010. x, 89 p.
density functional theory, ab initio, first principles, electron transport, photoswitching, molecular dynamics, geometric integration
National Category
Condensed Matter Physics Other Physics Topics
urn:nbn:se:kth:diva-26780 (URN)978-91-7415-810-6 (ISBN)
Public defence
2010-12-20, F3, Lindstedtsvägen 26, KTH, Stockholm, 10:00 (English)
Swedish Research Council, H 6397
QC 20101202Available from: 2010-12-02 Created: 2010-11-26 Last updated: 2012-01-11Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textScopus

Search in DiVA

By author/editor
Niklasson, Anders M. N.Odell, Anders
By organisation
Applied Material Physics
In the same journal
Journal of Chemical Physics
Materials Engineering

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 111 hits
ReferencesLink to record
Permanent link

Direct link