Real-space grids are a powerful alternative for the simulation of electronic systems. One of the main advantages of the approach is the flexibility and simplicity of working directly in real space where the different fields are discretized on a grid, combined with competitive numerical performance and great potential for parallelization. These properties constitute a great advantage at the time of implementing and testing new physical models. Based on our experience with the Octopus code, in this article we discuss how the real-space approach has allowed for the recent development of new ideas for the simulation of electronic systems. Among these applications are approaches to calculate response properties, modeling of photoemission, optimal control of quantum systems, simulation of plasmonic systems, and the exact solution of the Schrödinger equation for low-dimensionality systems.
Octopus is a general-purpose density-functional theory (DFT) code, with a particular emphasis on the time-dependent version of DFT (TDDFT). In this article we present the ongoing efforts for the parallelisation of octopus. We focus on the real-time variant of TDDFT, where the time-dependent Kohn-Sham equations are directly propagated in time. This approach has a great potential for execution in massively parallel systems such as modern supercomputers with thousands of processors and graphics processing units (GPUs).For harvesting the potential of conventional supercomputers, the main strategy is a multilevel parallelisation scheme that combines the inherent scalability of real-time TDDFT with a real-space grid domain-partitioning approach. A scalable Poisson solver is critical for the efficiency of this scheme. For GPUs, we show how using blocks of Kohn-Sham states * email@example.com 60 provides the required level of data-parallelism and that this strategy is also applicable for code-optimisation on standard processors. Our results show that real-time TDDFT, as implemented in octopus, can be the method of choice to study the excited states of large molecular systems in modern parallel architectures.
In this note, we explain how asymptotically globally AdS spacetimes can be given an alternate dual description as entangled states of a pair of hyperbolic space CFTs, which are associated with complementary Rindler
We present a computer package designed to generate and test norm-conserving pseudo-potentials within Density Functional Theory. The generated pseudo-potentials can be either non-relativistic, scalar relativistic or fully relativistic and can explicitly include semi-core states. A wide range of exchange-correlation functionals is included. Restrictions: Relativistic spin-polarized calculations are not possible. The set of exchange-correlation functionals implemented in the code does not include orbital-dependent functionals. Unusual features: The program creates pseudo-potential files suitable for the most widely used ab-initio packages and, besides the standard non-relativistic Hamann and Troullier-Martins potentials, it can generate pseudo-potentials using the relativistic and semi-core extensions to the Troullier-Martins scheme. APE also has a very sophisticated and user-friendly input system. Running time: The example given in this paper (Si) takes 10 s to run on a Pentium IV machine clocked at 2 GHz.
A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive because it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here, we use action spectroscopy to compare the absorption by the firefly oxyluciferin lumophore isolated in vacuo and complexed with a single water molecule. While the process relevant to bioluminescence within the luciferase cavity is light emission, the absorption data presented here provide a unique insight into how the electronic states of oxyluciferin are altered by microenvironmental perturbations. For the bare ion we observe broad absorption with a maximum at 548 ± 10 nm, and addition of a water molecule is found to blue-shift the absorption by approximately 50 nm (0.23 eV). Test calculations at various levels of theory uniformly predict a blue-shift in absorption caused by a single water molecule, but are only qualitatively in agreement with experiment highlighting limitations in what can be expected from methods commonly used in studies on oxyluciferin. Combined molecular dynamics simulations and time-dependent density functional theory calculations closely reproduce the broad experimental peaks and also indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. Predicting the effects of microenvironmental interactions on the electronic structure of the oxyluciferin anion with high accuracy is a nontrivial task for theory, and our experimental results therefore serve as important benchmarks for future calculations.
scite is a Brooklyn-based startup that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.