6,948 research outputs found
Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials
Quantum ESPRESSO is an integrated suite of computer codes for
electronic-structure calculations and materials modeling, based on
density-functional theory, plane waves, and pseudopotentials (norm-conserving,
ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn
Source Package for Research in Electronic Structure, Simulation, and
Optimization". It is freely available to researchers around the world under the
terms of the GNU General Public License. Quantum ESPRESSO builds upon
newly-restructured electronic-structure codes that have been developed and
tested by some of the original authors of novel electronic-structure algorithms
and applied in the last twenty years by some of the leading materials modeling
groups worldwide. Innovation and efficiency are still its main focus, with
special attention paid to massively-parallel architectures, and a great effort
being devoted to user friendliness. Quantum ESPRESSO is evolving towards a
distribution of independent and inter-operable codes in the spirit of an
open-source project, where researchers active in the field of
electronic-structure calculations are encouraged to participate in the project
by contributing their own codes or by implementing their own ideas into
existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte
Fast, Scalable, and Interactive Software for Landau-de Gennes Numerical Modeling of Nematic Topological Defects
Numerical modeling of nematic liquid crystals using the tensorial Landau-de
Gennes (LdG) theory provides detailed insights into the structure and
energetics of the enormous variety of possible topological defect
configurations that may arise when the liquid crystal is in contact with
colloidal inclusions or structured boundaries. However, these methods can be
computationally expensive, making it challenging to predict (meta)stable
configurations involving several colloidal particles, and they are often
restricted to system sizes well below the experimental scale. Here we present
an open-source software package that exploits the embarrassingly parallel
structure of the lattice discretization of the LdG approach. Our
implementation, combining CUDA/C++ and OpenMPI, allows users to accelerate
simulations using both CPU and GPU resources in either single- or multiple-core
configurations. We make use of an efficient minimization algorithm, the Fast
Inertial Relaxation Engine (FIRE) method, that is well-suited to large-scale
parallelization, requiring little additional memory or computational cost while
offering performance competitive with other commonly used methods. In
multi-core operation we are able to scale simulations up to supra-micron length
scales of experimental relevance, and in single-core operation the simulation
package includes a user-friendly GUI environment for rapid prototyping of
interfacial features and the multifarious defect states they can promote. To
demonstrate this software package, we examine in detail the competition between
curvilinear disclinations and point-like hedgehog defects as size scale,
material properties, and geometric features are varied. We also study the
effects of an interface patterned with an array of topological point-defects.Comment: 16 pages, 6 figures, 1 youtube link. The full catastroph
SlicerAstro: a 3-D interactive visual analytics tool for HI data
SKA precursors are capable of detecting hundreds of galaxies in HI in a
single 12 hours pointing. In deeper surveys one will probe more easily faint HI
structures, typically located in the vicinity of galaxies, such as tails,
filaments, and extraplanar gas. The importance of interactive visualization has
proven to be fundamental for the exploration of such data as it helps users to
receive immediate feedback when manipulating the data. We have developed
SlicerAstro, a 3-D interactive viewer with new analysis capabilities, based on
traditional 2-D input/output hardware. These capabilities enhance the data
inspection, allowing faster analysis of complex sources than with traditional
tools. SlicerAstro is an open-source extension of 3DSlicer, a multi-platform
open source software package for visualization and medical image processing.
We demonstrate the capabilities of the current stable binary release of
SlicerAstro, which offers the following features: i) handling of FITS files and
astronomical coordinate systems; ii) coupled 2-D/3-D visualization; iii)
interactive filtering; iv) interactive 3-D masking; v) and interactive 3-D
modeling. In addition, SlicerAstro has been designed with a strong, stable and
modular C++ core, and its classes are also accessible via Python scripting,
allowing great flexibility for user-customized visualization and analysis
tasks.Comment: 18 pages, 11 figures, Accepted by Astronomy and Computing.
SlicerAstro link: https://github.com/Punzo/SlicerAstro/wiki#get-slicerastr
Multi-Architecture Monte-Carlo (MC) Simulation of Soft Coarse-Grained Polymeric Materials: SOft coarse grained Monte-carlo Acceleration (SOMA)
Multi-component polymer systems are important for the development of new
materials because of their ability to phase-separate or self-assemble into
nano-structures. The Single-Chain-in-Mean-Field (SCMF) algorithm in conjunction
with a soft, coarse-grained polymer model is an established technique to
investigate these soft-matter systems. Here we present an im- plementation of
this method: SOft coarse grained Monte-carlo Accelera- tion (SOMA). It is
suitable to simulate large system sizes with up to billions of particles, yet
versatile enough to study properties of different kinds of molecular
architectures and interactions. We achieve efficiency of the simulations
commissioning accelerators like GPUs on both workstations as well as
supercomputers. The implementa- tion remains flexible and maintainable because
of the implementation of the scientific programming language enhanced by
OpenACC pragmas for the accelerators. We present implementation details and
features of the program package, investigate the scalability of our
implementation SOMA, and discuss two applications, which cover system sizes
that are difficult to reach with other, common particle-based simulation
methods
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