17,335 research outputs found
Analysis of the Basic Implementation Aspects of Hardware-Accelerated Density Functional Theory Calculations
This paper presents a Field Programmable Gate Array (FPGA) implementation of a calculation module for exponential part of Gaussian Type Orbital (GTO). The module is composed of several specially crafted floating-point modules which are fully pipelined and optimized for high performance. The hardware implementation revealed significant speed-up for the finite sum of the exponential products calculation ranging from 2.5x to 20x in comparison to a general-purpose Central Processing Unit (CPU) version. Calculating values of GTOs is one of computationally critical parts of the Kohn-Sham algorithm. The approach proposed in the paper aims to increase the performance of a part of the quantum chemistry computational system by employing FPGA-based accelerator. Several issues are addressed, such as identification of code fragments which benefit most from hardware acceleration, porting a part of the Kohn-Sham algorithm to FPGA, data precision adjustment and data transfer overhead. The authors' intention was also to make hardware implementation of calculating the orbital function universal and easily attachable to different quantum-chemistry software packages
A spectral scheme for Kohn-Sham density functional theory of clusters
Starting from the observation that one of the most successful methods for
solving the Kohn-Sham equations for periodic systems -- the plane-wave method
-- is a spectral method based on eigenfunction expansion, we formulate a
spectral method designed towards solving the Kohn-Sham equations for clusters.
This allows for efficient calculation of the electronic structure of clusters
(and molecules) with high accuracy and systematic convergence properties
without the need for any artificial periodicity. The basis functions in this
method form a complete orthonormal set and are expressible in terms of
spherical harmonics and spherical Bessel functions. Computation of the occupied
eigenstates of the discretized Kohn-Sham Hamiltonian is carried out using a
combination of preconditioned block eigensolvers and Chebyshev polynomial
filter accelerated subspace iterations. Several algorithmic and computational
aspects of the method, including computation of the electrostatics terms and
parallelization are discussed. We have implemented these methods and algorithms
into an efficient and reliable package called ClusterES (Cluster Electronic
Structure). A variety of benchmark calculations employing local and non-local
pseudopotentials are carried out using our package and the results are compared
to the literature. Convergence properties of the basis set are discussed
through numerical examples. Computations involving large systems that contain
thousands of electrons are demonstrated to highlight the efficacy of our
methodology. The use of our method to study clusters with arbitrary point group
symmetries is briefly discussed.Comment: Manuscript submitted (with revisions) to Journal of Computational
Physic
Roadmap on Electronic Structure Codes in the Exascale Era
Electronic structure calculations have been instrumental in providing many
important insights into a range of physical and chemical properties of various
molecular and solid-state systems. Their importance to various fields,
including materials science, chemical sciences, computational chemistry and
device physics, is underscored by the large fraction of available public
supercomputing resources devoted to these calculations. As we enter the
exascale era, exciting new opportunities to increase simulation numbers, sizes,
and accuracies present themselves. In order to realize these promises, the
community of electronic structure software developers will however first have
to tackle a number of challenges pertaining to the efficient use of new
architectures that will rely heavily on massive parallelism and hardware
accelerators. This roadmap provides a broad overview of the state-of-the-art in
electronic structure calculations and of the various new directions being
pursued by the community. It covers 14 electronic structure codes, presenting
their current status, their development priorities over the next five years,
and their plans towards tackling the challenges and leveraging the
opportunities presented by the advent of exascale computing.Comment: Submitted as a roadmap article to Modelling and Simulation in
Materials Science and Engineering; Address any correspondence to Vikram
Gavini ([email protected]) and Danny Perez ([email protected]
Roadmap on Electronic Structure Codes in the Exascale Era
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing
Roadmap on electronic structure codes in the exascale era
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry, and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing
Quantum ESPRESSO toward the exascale
Quantum ESPRESSO is an open-source distribution of computer codes for quantum-mechanical materials modeling, based on density-functional theory, pseudopotentials, and plane waves, and renowned for its performance on a wide range of hardware architectures, from laptops to massively parallel computers, as well as for the breadth of its applications. In this paper, we present a motivation and brief review of the ongoing effort to port Quantum ESPRESSO onto heterogeneous architectures based on hardware accelerators, which will overcome the energy constraints that are currently hindering the way toward exascale computing
Roadmap on Electronic Structure Codes in the Exascale Era
Electronic structure calculations have been instrumental in providing many important insights into a range of physical and chemical properties of various molecular and solid-state systems. Their importance to various fields, including materials science, chemical sciences, computational chemistry and device physics, is underscored by the large fraction of available public supercomputing resources devoted to these calculations. As we enter the exascale era, exciting new opportunities to increase simulation numbers, sizes, and accuracies present themselves. In order to realize these promises, the community of electronic structure software developers will however first have to tackle a number of challenges pertaining to the efficient use of new architectures that will rely heavily on massive parallelism and hardware accelerators. This roadmap provides a broad overview of the state-of-the-art in electronic structure calculations and of the various new directions being pursued by the community. It covers 14 electronic structure codes, presenting their current status, their development priorities over the next five years, and their plans towards tackling the challenges and leveraging the opportunities presented by the advent of exascale computing
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
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Bond-Order Time Series Analysis for Detecting Reaction Events in Ab Initio Molecular Dynamics Simulations.
Ab initio molecular dynamics is able to predict novel reaction mechanisms by directly observing the individual reaction events that occur in simulation trajectories. In this article, we describe an approach for detecting reaction events from simulation trajectories using a physically motivated model based on time series analysis of ab initio bond orders. We found that applying a threshold to the bond order was insufficient for accurate detection, whereas peak finding on the first time derivative resulted in significantly improved accuracy. The model is trained on a reference set of reaction events representing the ideal result given unlimited computing resources. Our study includes two model systems: a heptanylium carbocation that undergoes hydride shifts and an unsaturated iron carbonyl cluster that features CO ligand migration and bridging behavior. The results indicate a high level of promise for this analysis approach to be used in mechanistic analysis of reactive AIMD simulations more generally
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