Inviwo - A Visualization System with Usage Abstraction Levels.

The complexity of today's visualization applications demands specific visualization systems tailored for the development of these applications. Frequently, such systems utilize levels of abstraction to improve the application development process, for instance by providing a data flow network editor. Unfortunately, these abstractions result in several issues, which need to be circumvented through an abstraction-centered system design. Often, a high level of abstraction hides low level details, which makes it difficult to directly access the underlying computing platform, which would be important to achieve an optimal performance. Therefore, we propose a layer structure developed for modern and sustainable visualization systems allowing developers to interact with all contained abstraction levels. We refer to this interaction capabilities as usage abstraction levels, since we target application developers with various levels of experience. We formulate the requirements for such a system, derive the desired architecture, and present how the concepts have been exemplary realized within the Inviwo visualization system. Furthermore, we address several specific challenges that arise during the realization of such a layered architecture, such as communication between different computing platforms, performance centered encapsulation, as well as layer-independent development by supporting cross layer documentation and debugging capabilities.

Extended Lagrangian free energy molecular dynamics.

Extended free energy Lagrangians are proposed for first principles molecular dynamics simulations at finite electronic temperatures for plane-wave pseudopotential and local orbital density matrix-based calculations. Thanks to the extended Lagrangian description, the electronic degrees of freedom can be integrated by stable geometric schemes that conserve the free energy. For the local orbital representations both the nuclear and electronic forces have simple and numerically efficient expressions that are well suited for reduced complexity calculations. A rapidly converging recursive Fermi operator expansion method that does not require the calculation of eigenvalues and eigenfunctions for the construction of the fractionally occupied density matrix is discussed. An efficient expression for the Pulay force that is valid also for density matrices with fractional occupation occurring at finite electronic temperatures is also demonstrated.

Extended Lagrangian Born-Oppenheimer molecular dynamics with dissipation.

Stability and dissipation in the propagation of the electronic degrees of freedom in time-reversible extended Lagrangian Born-Oppenheimer molecular dynamics [Niklasson et al., 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.