### 323 results

Contributors: E. V. Kahl, J. C. Berengut

Date: 2019-01-14

... We present the AMBiT software package for general atomic structure calculations. This software implements particle–hole configuration interaction with many-body perturbation theory (CI+MBPT) for fully relativistic calculations of atomic energy levels, electric- and magnetic-multipole transition matrix elements, g-factors and isotope shifts. New numerical methods and modern high-performance computing techniques employed by this software allow for the calculation of open-shell systems with many valence-electrons (N greater than or equal to 5) to a high degree of accuracy and in a highly computationally efficient manner.

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Contributors: F. Coradeschi, T. Cridge

Date: 2019-01-14

... In this note, we introduce the new tool reSolve, a Monte Carlo differential cross-section and parton-level event generator whose main purpose is to add transverse momentum resummation to a general class of inclusive processes at hadron colliders, namely all those which do not involve hadrons or jets in the measured final state. This documentation refers to the first main version release, which will form the basis for continued developments, consequently it only implements the key features of those we plan to ultimately include. This article acts as a manual for the program; describing in detail its use, structure, validation and results; whilst also highlighting key aspects of the resummation formalism applied. It details the two classes of processes so far included; these are diphoton production and Drell–Yan production. A main concept behind the development of the tool is that it is a hands-on white box for the user: significant effort has been made to give the program a modular structure, making the various parts which comprise it independent of each other as much as possible and ensuring they are transparently documented, customisable and, in principle, replaceable with something that may better serve the user’s needs. reSolve is a new C++ program, based on an evolution of the private Fortran code 2gres, it is also influenced by the DYRes Fortran code. This initial version calculates the low transverse momentum contribution to the fully differential cross-section for two main categories of processes; the inclusive production of two photons, and inclusive Drell–Yan production. In all cases resummation up to Next-to-Next-to-Leading Logarithm (NNLL) is included. We aim to extend the program to several more processes in the near future. The program is publicly available on Github.

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Contributors: Piotr T. Różański, Michał Zieliński

Date: 2019-01-14

... Atomistic modeling of nanostructures such as quantum dots or nanowires often involves numbers of atoms reaching and even exceeding well beyond 1 million. Such a large quantity of atoms presents a very complex computational challenge especially at a stage of many-body calculation where numerous Coulomb matrix elements need to be calculated. Here we present a practical solution to this problem by performing calculations in the momentum space and utilizing fast Fourier transform combined with a memory-efficient way to compute the convolution that overcomes the problem of spurious interactions with quasi-charges from other super-cells. Finally, calculation of multiple integrals is optimized by reducing the problem to finding a minimum vertex cover of a graph. All these algorithms are implemented and presented here in a self-contained and highly parallelized computer program named Coulombo. Coulombo demonstrates quasi-linear scaling of computational time of Coulomb matrix elements with respect to the number of points in the computational box and, at the same time, significantly reduced memory demand. The proposed solution can have potential applications not only in the realm of nano-physics, but could be applied to other mesoscopic simulations or large-scale quantum chemistry problems.

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Contributors: Alexander Mirzoev, Lars Nordenskiöld, Alexander Lyubartsev

Date: 2018-12-20

... Molecular simulations of many phenomena related to biomolecular systems, soft matter and nanomaterials require consideration of length scales above 10 nm and time scales longer than 1 μs, which necessitates the use of coarse-grained (low resolution) models, where each site of the model represents a group of atoms, and where the solvent is often omitted. Our software package MagiC is designed to perform systematic structure-based coarse-graining of molecular models, in which the effective pairwise potentials between coarse-grained sites of low-resolution molecular models are constructed to reproduce structural distribution functions obtained from modeling of systems in a high resolution (atomistic) description. The software takes as input atomistic trajectories generated by an external molecular dynamics package, and produce as an output interaction potentials for coarse-grained models which can be directly used in a coarse-grained simulations package. Here we present a major update (v.3) of the software with substantially improved functionality, compatibility with several major atomistic and coarse-grained simulations packages (GROMACS, LAMMPS, GALAMOST), analysis suite with graphical possibilities, diagnostics, documentation. We describe briefly the coarse-graining methodology, the structure of the software, describe users actions, and illustrate the whole process with two complex examples: cholesterol containing lipid bilayers and condensation of DNA caused by multivalent ions.

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Contributors: Patrick Avery, Cormac Toher, Stefano Curtarolo, Eva Zurek

Date: 2018-12-20

... Version 12 of XtalOpt, an evolutionary algorithm for crystal structure prediction, is now available for download from the CPC program library or the XtalOpt website, http://xtalopt.github.io. The new version includes: a method for calculating hardness using a machine learning algorithm within AFLOW-ML (Automatic FLOW for Materials Discovery — Machine Learning), the ability to predict hard materials, a generic optimizer (which allows the user to employ many optimizers that were previously not supported), and the ability to generate simulated XRD (X-ray diffraction) patterns.

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Contributors: Tian Qin, Qi Zhang, Renata M. Wentzcovitch, Koichiro Umemoto

Date: 2018-12-13

... In this work, we present a Python package, qha, which can calculate the equation of state and various thermodynamic properties of both single- and multi-configuration crystalline materials within a user-specified pressure and temperature range in the framework of the quasi-harmonic approximation (QHA). Two examples, one for single-configuration calculation and the other for multi-configuration calculation, are also distributed along with source code. Apart from its versatility, qha has been tested to be both accurate and computationally efficient.

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Contributors: Klaus Reuter, Jürgen Köfinger

Date: 2018-12-13

... We report on the design, implementation, optimization, and performance of the CADISHI software package, which calculates histograms of pair-distances of ensembles of particles on CPUs and GPUs. These histograms represent 2-point spatial correlation functions and are routinely calculated from simulations of soft and condensed matter, where they are referred to as radial distribution functions, and in the analysis of the spatial distributions of galaxies and galaxy clusters. Although conceptually simple, the calculation of radial distribution functions via distance binning requires the evaluation of O(N^2) particle-pair distances where N is the number of particles under consideration. CADISHI provides fast parallel implementations of the distance histogram algorithm for the CPU and the GPU, written in templated C++ and CUDA. Orthorhombic and general triclinic periodic boxes are supported, in addition to the non-periodic case. The CPU kernels feature cache-blocking, vectorization and thread-parallelization to obtain high performance. The GPU kernels are tuned to exploit the memory and processor features of current GPUs, demonstrating histogramming rates of up to a factor 40 higher than on a high-end multi-core CPU. To enable high-throughput analyses of molecular dynamics trajectories, the compute kernels are driven by the Python-based CADISHI engine. It implements a producer–consumer data processing pattern and thereby enables the complete utilization of all the CPU and GPU resources available on a specific computer, independent of special libraries such as MPI, covering commodity systems up to high-end HPC nodes. Data input and output are performed efficiently via HDF5. In addition, our CPU and GPU kernels can be compiled into a standard C library and used with any application, independent from the CADISHI engine or Python. The CADISHI software is freely available under the MIT license.

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Contributors: Rubén Jesús García-Hernández, Dieter Kranzlmüller

Date: 2018-12-13

... We describe a suite of open source virtual reality programs which can be used to visualize the results of chemical simulations of various types (including access to NOMAD, the largest database of materials science compounds). The programs target virtual reality environments at different price points (M€ CAVE-like systems, commercial products such as the ~500€ HTC Vive, ~100€ Samsung GearVR, to ~10€ Google Cardboards) in order to let final users select the device which best suits their needs. We provide a coherent interface, with graceful degradation of features for less capable devices. Tests with final users in the domains of materials science, theoretical chemistry, biochemistry and biological sciences show that the program can be used to solve certain problems much more easily and intuitively than with previous tools. Users in other fields (fluid dynamics, or climate research) were also interested in adopting the system. Applications to teaching, dissemination, outreach and marketing have also been successful. The system is currently implanted in several universities and enterprises. Additionally, outreach materials in the form of stereoscopic (panoramic) videos can be easily prepared from the viewer’s output or the visualization pipeline. We describe the design and implementation of the system, and mention some caveats about using standard graphic optimization techniques in virtual reality environments.

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Contributors: Hongxia Zheng, Xinning Yu, Wanli Lu, Jack Ng, Zhifang Lin

Date: 2018-12-13

... A MATLAB function GCforce is presented for the calculation of gradient and scattering parts of optical force (OF). The decomposition of OF into the gradient and scattering parts, or, equivalently, the conservative and nonconservative components, is of great importance to the physical understanding of optical micromanipulation. In this paper, we propose a formulation to decompose the OF acting on a spherical particle immersed in an arbitrary monochromatic optical field, based on the generalized Lorenz-Mie theory and the Cartesian multipole expansion approach. The expressions for the gradient and scattering forces are given explicitly in terms of the partial wave expansion coefficients of the optical field shining on the particle and the Mie coefficients of the particle. A MATLAB function GCforce.m is also presented for the calculation. The explicit and rigorous decomposition of the OF into conservative and nonconservative forces shed light on the understanding of light-matter interaction as well as contribute significantly to the designing of optical fields to achieve various optical micromanipulation.

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Contributors: De-Chang Dai, Cigdem Issever, Eram Rizvi, Glenn Starkman, Dejan Stojkovic, Jeff Tseng

Date: 2018-12-13

... This is the users manual of the black-hole event generator BlackMax (Dai et al., 2008), which simulates the experimental signatures of microscopic and Planckian black-hole production and evolution at proton–proton, proton–antiproton and electron–positron colliders in the context of brane world models with low-scale quantum gravity. The generator is based on phenomenologically realistic models free of serious problems that plague low-scale gravity. It includes all of the black-hole gray-body factors known to date and incorporates the effects of black-hole rotation, splitting between the fermions, non-zero brane tension and black-hole recoil due to Hawking radiation (although not all simultaneously). The main code can be downloaded from Dai et al. (0000).

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