### 304 results

Contributors: Iain Bethune, Ralf Banisch, Elena Breitmoser, Antonia B. K. Collis, Gordon Gibb, Gianpaolo Gobbo, Charles Matthews, Graeme J. Ackland, Benedict J. Leimkuhler

Date: 2018-11-09

... We present MIST, the Molecular Integration Simulation Toolkit, a lightweight and efficient software library written in C++ which provides an abstract interface to common molecular dynamics codes, enabling rapid and portable development of new integration schemes for molecular dynamics. The initial release provides plug-in interfaces to NAMD-Lite, GROMACS and Amber, and includes several standard integration schemes, a constraint solver, temperature control using Langevin Dynamics, and two tempering schemes. We describe the architecture and functionality of the library and the C and Fortran APIs which can be used to interface additional MD codes to MIST. We show, for a range of test systems, that MIST introduces negligible overheads for serial, shared-memory parallel, and GPU-accelerated cases, except for Amber where the native integrators run directly on the GPU itself. As a demonstration of the capabilities of MIST, we describe a simulated tempering simulation used to study the free energy landscape of Alanine-12 in both vacuum and detailed solvent conditions.

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Contributors: Ioannis G. Tsoulos, O. T. Kosmas, V. N. Stavrou

Date: 2018-11-09

... Advantageous numerical methods for solving the Dirac equations are derived. They are based on different stochastic optimization techniques, namely the Genetic algorithms, the Particle Swarm Optimization and the Simulated Annealing method, their use of which is favored from intuitive, practical, and theoretical arguments. Towards this end, we optimize appropriate parametric expressions representing the radial Dirac wave functions by employing methods that minimize multi parametric expressions in several physical applications. As a concrete application, we calculate the small (bottom) and large (top) components of the Dirac wave function for a bound muon orbiting around a very heavy (complex) nuclear system (the 208Pb nucleus), but the new approach may effectively be applied in other complex atomic, nuclear and molecular systems.

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Contributors: J. R. King, I. V. Pogorelov, K. M. Amyx, M. Borland, R. Soliday

Date: 2018-11-06

... Elegant is an accelerator physics and particle-beam dynamics code widely used for modeling and design of a variety of high-energy particle accelerators and accelerator-based systems. In this paper we discuss a recently developed version of the code that can take advantage of CUDA-enabled graphics processing units (GPUs) to achieve significantly improved performance for a large class of simulations that are important in practice. The GPU version is largely defined by a framework that simplifies implementations of the fundamental kernel types that are used by Elegant: particle operations, reductions, particle loss, histograms, array convolutions and random number generation. Accelerated performance on the Titan Cray XK-7 supercomputer is approximately 6-10 times better with the GPU than all the CPU cores associated with the same node count. In addition to performance, the maintainability of the GPU-accelerated version of the code was considered a key design objective. Accuracy with respect to the CPU implementation is also a core consideration. Four different methods are used to ensure that the accelerated code faithfully reproduces the CPU results.

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Contributors: Alfred C. K. Farris, Ying Wai Li, Markus Eisenbach

Date: 2018-11-06

... We report a new multicanonical Monte Carlo algorithm to obtain the density of states for physical systems with continuous state variables in statistical mechanics. Our algorithm is able to obtain a closed-form expression for the density of states expressed in a chosen basis set, instead of a numerical array of finite resolution as in previous variants of this class of MC methods such as the multicanonical sampling and Wang-Landau sampling. This is enabled by storing the visited states directly and avoiding the explicit collection of a histogram. This practice also has the advantage of avoiding undesirable artificial errors caused by the discretization and binning of continuous state variables. Our results show that this scheme is capable of obtaining converged results with a much reduced number of Monte Carlo steps, leading to a significant speedup over existing algorithms.

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Contributors: Masashi Noda, Shunsuke A. Sato, Yuta Hirokawa, Mitsuharu Uemoto, Takashi Takeuchi, Shunsuke Yamada, Atsushi Yamada, Yasushi Shinohara, Maiku Yamaguchi, Kenji Iida

Date: 2018-11-01

... SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids based on first-principles time-dependent density functional theory. The core part of the software is the real-time, real-space calculation of the electron dynamics induced in molecules and solids by an external electric field solving the time-dependent Kohn–Sham equation. Using a weak instantaneous perturbing field, linear response properties such as polarizabilities and photoabsorptions in isolated systems and dielectric functions in periodic systems are determined. Using an optical laser pulse, the ultrafast electronic response that may be highly nonlinear in the field strength is investigated in time domain. The propagation of the laser pulse in bulk solids and thin films can also be included in the simulation via coupling the electron dynamics in many microscopic unit cells using Maxwell’s equations describing the time evolution of the electromagnetic fields. The code is efficiently parallelized so that it may describe the electron dynamics in large systems including up to a few thousand atoms. The present paper provides an overview of the capabilities of the software package showing several sample calculations.

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Contributors: Moritz Hütten, Céline Combet, David Maurin

Date: 2018-11-01

... We present the third release of the CLUMPY code for calculating gamma-ray and neutrino signals from annihilations or decays in dark matter structures. This version includes the mean extragalactic signal with several pre-defined options and keywords related to cosmological parameters, mass functions for the dark matter structures, and gamma-ray absorption up to high redshift. For more flexibility and consistency, dark matter masses and concentration are now defined with respect to a user-defined overdensity Delta. We have also made changes for the user’s benefit: distribution and versioning of the code via git, less dependencies and a simplified installation, better handling of options in run command lines, consistent naming of parameters, and a new Sphinx documentation at http://lpsc.in2p3.fr/clumpy/.

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Contributors: Nicola Giuliani

Date: 2018-11-01

... Many applications benefit from an efficient Discrete Fourier Transform (DFT) between arbitrarily spaced points. The Non Uniform Fast Fourier Transform reduces the computational cost of such operation from O(N^2) to O(N logN) exploiting gridding algorithms and a standard Fast Fourier Transform on an equi-spaced grid. The parallelization of the NUFFT of type 3 (between arbitrary points in space and frequency) still poses some challenges: we present a novel and flexible hybrid parallelization in a MPI-multithreaded environment exploiting existing HPC libraries on modern architectures. To ensure the reliability of the developed library, we exploit continuous integration strategies using Travis CI. We present performance analyses to prove the effectiveness of our implementation, possible extensions to the existing library, and an application of NUFFT type 3 to MRI image processing.

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Contributors: N. Sanna, G. Morelli, S. Orlandini, I. Baccarelli

Date: 2018-10-30

... VOLSCAT is a computer program which implements the Single Center Expansion (SCE) method to solve the scattering equation for the elastic collision of electrons/positrons off molecular targets. The scattering potential needed is calculated by on-the-fly calls to the external SCELib library for molecular properties, recently ported to GPU (Graphic Processing Unit) computing environment, and made available by means of an Application Program Interface (SCELib-API) which is also provided with the VOLSCAT package in a beta version. We here announce the new release 2.0 which presents additional features with respect to the previous version aiming at a significant enhancement of its capabilities to deal with larger molecular systems. In VOLSCAT 2.0 we implemented a new method for the calculation of resonances width and position based on the theory of the Time-Delay Matrix (TDM) analysis aimed at improving the spectra resolution when dealing with several overlapping resonances. As implemented in VOLSCAT 2.0 the TDM analysis typically results more efficient as higher is the molecular symmetry thus an extended Breit-Wigner analysis of the computed partial resonances has also been included in the code. Now the end-user can couple both methods of resonance analysis and shed light on their behaviour by dumping cross sections and eigenphases with respect to projectile energy at a level as deep as a single partial wave. Furthermore, the new version of VOLSCAT has been now fully ported on the Message Passing Interface standard and linear algebra operations are now based on CUDA and MAGMA libraries. As such, VOLSCAT 2.0 is able to exploit at best the most recent distributed computing architecture based on hybrid nodes with an efficient method of workload balancing. The result is a high throughput approach to the solution of complex e^-/e^+ -molecule scattering problems finally making feasible the study of larger molecular systems with respect to past versions of the code.

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Contributors: Markus Wallerberger, Andreas Hausoel, Patrik Gunacker, Alexander Kowalski, Nicolaus Parragh, Florian Goth, Karsten Held, Giorgio Sangiovanni

Date: 2018-10-23

... We describe the hybridization-expansion continuous-time quantum Monte Carlo code package “w2dynamics”, developed in Wien and Würzburg. We discuss the main features of this multi-orbital quantum impurity solver for the Anderson impurity model, dynamical mean field theory as well as its coupling to density functional theory. The w2dynamics package allows for calculating one- and two-particle quantities; it includes worm and further novel sampling schemes. Details about its download, installation, functioning and the relevant parameters are provided.

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Contributors: Stanislav Poslavsky

Date: 2018-10-11

... In this paper we briefly discuss Rings — an efficient lightweight library for commutative algebra. Polynomial arithmetic, GCDs, polynomial factorization and Gröbner bases are implemented with the use of modern asymptotically fast algorithms. Rings can be easily interacted or embedded in applications in high-energy physics and other research areas via a simple API with fully typed hierarchy of algebraic structures and algorithms for commutative algebra. The use of the Scala language brings a quite novel powerful, strongly typed functional programming model allowing to write short, expressive, and fast code for applications. At the same time Rings shows one of the best performances among existing software for algebraic calculations.

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