H. Metin Aktulga

H. Metin Aktulga
Michigan State University | MSU · Department of Computer Science and Engineering

PhD

About

78
Publications
12,998
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
4,152
Citations
Citations since 2017
40 Research Items
3621 Citations
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
201720182019202020212022202302004006008001,0001,2001,400
Additional affiliations
August 2014 - present
Michigan State University
Position
  • Professor (Assistant)
September 2010 - present
Lawrence Berkeley National Laboratory
Position
  • PostDoc Position
June 2005 - July 2010
Purdue University
Position
  • Research Assistant
Education
August 2004 - December 2009
Purdue University
Field of study
  • Computer Science
August 2004 - August 2010
Purdue University
Field of study
  • Computer Science
September 2000 - May 2004
Bilkent University
Field of study
  • Computer Science

Publications

Publications (78)
Article
Evaluation of pair potentials is critical in a number of areas of physics. The classical $N$ -body problem has its root in evaluating the Laplace potential, and has spawned tree-algorithms, the fast multipole method (FMM), as well as kernel independent approaches. Over the years, FMM for Laplace potential has had a profound impact on a number of...
Preprint
Full-text available
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra operations. General performance improv...
Preprint
Full-text available
Many integral equations used to analyze scattering, such as the standard combined field integral equation (CFIE), are not well-conditioned for a wide range of frequencies and multi-scale geometries. There has been significant effort to alleviate this problem. A more recent one is using a set of decoupled potential integral equations (DPIE). These e...
Article
The reactive force field (ReaxFF) model bridges the gap between traditional classical models and quantum mechanical (QM) models by incorporating dynamic bonding and polarizability. To achieve realistic simulations using ReaxFF, model parameters must be optimized against high fidelity training data which typically come from QM calculations. Existing...
Article
Recently, integral equation formulations that use potentials as opposed to fields as unknown quantities have been developed for scattering from dielectric objects. It has been shown that these formulations can be construed so that they are well-conditioned across a broad frequency spectrum, a result that has been theoretically proven for spherical...
Article
A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can fluctuate to respond to the e...
Preprint
Full-text available
A novel locally polarizable multisite model based on the original cation dummy atom (CDA) model is described for molecular dynamics simulations of ions in condensed phases. Polarization effects are introduced by the electronegativity equalization model (EEM) method where charges on the metal ion and its dummy atoms can respond to the environment. T...
Preprint
Full-text available
Molecular dynamics (MD) simulations facilitate the study of physical and chemical processes of interest. Traditional classical MD models lack reactivity to explore several important phenomena; while quantum mechanical (QM) models can be used for this purpose, they come with steep computational costs. The reactive force field (ReaxFF) model bridges...
Preprint
Full-text available
Molecular dynamics (MD) simulations facilitate the study of physical and chemical processes of interest. Traditional classical MD models lack reactivity to explore several important phenomena; while quantum mechanical (QM) models can be used for this purpose, they come with steep computational costs. The reactive force field (ReaxFF) model bridges...
Article
The growing interest in the effects of external electric fields on reactive processes requires predictive methods that can reach longer length and time scales than quantum mechanical simulations. Recently, many studies have included electric fields in ReaxFF, a widely used reactive molecular dynamics method. In the case of modeling an external elec...
Article
Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesoscale to continuum. Reasons for its popularity are that it provides a wide variety of particle interaction models for different mat...
Preprint
Full-text available
Molecular dynamics (MD) simulations ease the study of the chemistry of interest. While classical models that governs the interaction of the atoms lack reactivity, the quantum mechanics based methods increase the computational cost drastically. ReaxFF fills the gap between these two ends of the spectrum by allowing bond breaking and dynamic charges....
Preprint
Molecular dynamics (MD) simulations ease the study of the chemistry of interest. While classical models that governs the interaction of the atoms lack reactivity, the quantum mechanics based methods increase the computational cost drastically. ReaxFF fills the gap between these two ends of the spectrum by allowing bond breaking and dynamic charges....
Article
Reactive force fields provide an affordable model for simulating chemical reactions at a fraction of the cost of quantum mechanical approaches. However, classically accounting for chemical reactivity often comes at the expense of accuracy and transferability, while computational cost is still large relative to nonreactive force fields. In this Pers...
Preprint
div> We report a new multi-GPU capable ab initio Hartree-Fock/density functional theory implementation integrated into the open source QUantum Interaction Computational Kernel (QUICK) program. Details on the load balancing algorithms for electron repulsion integrals and exchange correlation quadrature across multiple GPUs are described. Benchmarki...
Article
Full-text available
Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models...
Article
Studies using molecular dynamics (MD) have long struggled to simulate the failure modes of materials, predicting unrealistically high ductility and failing to capture brittle fracture. The primary cause of this shortcoming is an inadequate description of bond breaking. While reactive force fields such as ReaxFF show improvements compared to traditi...
Preprint
Full-text available
Evaluation of pair potentials is critical in a number of areas of physics. The classicalN-body problem has its root in evaluating the Laplace potential, and has spawned tree-algorithms, the fast multipole method (FMM), as well as kernel independent approaches. Over the years, FMM for Laplace potential has had a profound impact on a number of discip...
Chapter
Achieving high performance and performance portability for large-scale scientific applications is a major challenge on heterogeneous computing systems such as many-core CPUs and accelerators like GPUs. In this work, we implement a widely used block eigensolver, Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG), using two popular dire...
Article
Pair potentials or kernels, ψ(|r|), play a critical role in a number of areas; these include biophysics, electrical engineering, fluid dynamics, diffusion physics, solid state physics, and many more. The need to evaluate these potentials rapidly for N particles gives rise to the classical N-body problem. In this paper, we present scalable parallel...
Preprint
Full-text available
Drip-line nuclei have very different properties from those of the valley of stability, as they are weakly bound and resonant. Therefore, the models devised for stable nuclei can no longer be applied therein. Hence, a new theoretical tool, the Gamow Shell Model (GSM), has been developed to study the many-body states occurring at the limits of the nu...
Article
Background: Nuclear pasta, emerging due to the competition between the long-range Coulomb force and the short-range strong force, is believed to be present in astrophysical scenarios, such as neutron stars and core-collapse supernovae. Its structure can have a high impact, e.g., on neutrino transport or the tidal deformability of neutron stars.
Article
Drip-line nuclei have very different properties from those of the valley of stability, as they are weakly bound and resonant. Therefore, the models devised for stable nuclei can no longer be applied therein. Hence, a new theoretical tool, the Gamow Shell Model (GSM), has been developed to study the many-body states occurring at the limits of the nu...
Conference Paper
Reactive molecular dynamics (MD) simulations are important for high-fidelity simulations of large systems with chemical reactions. Iterative linear solvers used to dynamically determine atom polarizations in reactive MD models and redundancies related to bond order calculations constitute significant bottlenecks in terms of time-to-solution and the...
Preprint
Background: Nuclear pasta, emerging due to the competition between the long-range Coulomb force and the short-range strong force, is believed to be present in astrophysical scenarios, such as neutron stars and core-collapse supernovae. Its structure can have a high impact e.g. on neutrino transport or the tidal deformability of neutron stars. Purpo...
Chapter
We consider the problem of detecting a unique experimental signature in time-series data recorded in nuclear physics experiments aimed at understanding the shape of atomic nuclei. The current method involves fitting each sample in the dataset to a given parameterized model function. However, this procedure is computationally expensive due to the na...
Article
Electromagnetic scattering from electrically large objects with multiscale features is an increasingly important problem in computational electromagnetics. A conventional approach is to use an integral equation-based solver that is then augmented with an accelerator, a popular choice being a parallel multilevel fast multipole algorithm (MLFMA). One...
Conference Paper
The fast multipole method (FMM) provides a fast and accurate method of solving large N-body problems with application in a broad range of physics problems. While there exists a large body of work for efficient implementation of the Laplace variant of the FMM algorithm, an optimized implementation of the Helmholtz variant of FMM which is used to stu...
Article
Full-text available
Nuclear structure and reaction theory is undergoing a major renaissance with advances in many-body methods, strong interactions with greatly improved links to Quantum Chromodynamics (QCD), the advent of high performance computing, and improved computational algorithms. Predictive power, with well-quantified uncertainty, is emerging from non-perturb...
Article
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this paper, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for multi-core architectu...
Article
As on-node parallelism increases and the performance gap between the processor and the memory system widens, achieving high performance in large-scale scientific applications requires an architecture-aware design of algorithms and solvers. We focus on the eigenvalue problem arising in nuclear Configuration Interaction (CI) calculations, where a few...
Article
Full-text available
In nuclear astro-physics, the quantum simulation of large inhomogenous dense systems as present in the crusts of neutron stars presents big challenges. The feasible number of particles in a simulation box with periodic boundary conditions is strongly limited due to the immense computational cost of the quantum methods. In this paper, we describe th...
Article
We describe a number of recently developed techniques for improving the performance of large-scale nuclear configuration interaction calculations on high performance parallel computers. We show the benefit of using a preconditioned block iterative method to replace the Lanczos algorithm that has traditionally been used to perform this type of compu...
Conference Paper
The fast multipole method (FMM) has slowly become ubiquitous in its use to ameliorate both CPU and memory costs for integral equation (IE) solvers. This is reflected in a number of papers on this topic. However, a long-standing problem is effective parallelization of FMM based IE solvers. While techniques exist that have shown reasonable scalabilit...
Article
Full-text available
The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider th...
Article
We present a parallel implementation of the ReaxFF force field on massively parallel heterogeneous architectures, called PuReMD-Hybrid. PuReMD, on which this work is based, along with its integration into LAMMPS, is currently used by a large number of research groups worldwide. Accelerating this important community codebase that implements a comple...
Article
Full-text available
There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant results within the ab initio No Core Shell Model (NCSM) closely tied to three major factors enabling this pro...
Article
Sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core arch...
Article
Reactive force fields make low-cost simulations of chemical reactions possible. However, optimizing them for a given chemical system is difficult and time-consuming. We present a high-performance implementation of global force-field parameter optimization, which delivers parameter sets of the same quality with much less effort and in far less time...
Article
In datacenters, non-volatile memory storages are experiencing a fast adoption rate due to the high bandwidth and low latency advantages that they provide over the traditional disk-based storage systems in the management and analysis of large datasets. The drastic changes in system architecture will require rethinking systems software as well. Speci...
Article
We describe an efficient and scalable symmetric iterative eigensolver developed for distributed memory multi-core platforms. We achieve over 80% parallel efficiency by major reductions in communication overheads for the sparse matrix-vector multiplication and basis orthogonalization tasks. We show that the scalability of the solver is significantly...
Article
We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RD...
Article
We discuss the possibility of using multiple shift-invert Lanczos and contour integral based spectral projection method to compute a relatively large number of eigenvalues of a large sparse and symmetric matrix on distributed memory parallel computers. The key to achieving high parallel efficiency in this type of computation is to divide the spectr...
Conference Paper
Full-text available
Obtaining highly accurate predictions on the properties of light atomic nuclei using the configuration interaction (CI) approach requires computing a few extremal Eigen pairs of the many-body nuclear Hamiltonian matrix. In the Many-body Fermion Dynamics for nuclei (MFDn) code, a block Eigen solver is used for this purpose. Due to the large size of...
Article
Drawing parallels to the rise of general purpose graphical processing units (GPGPUs) as accelerators for specific high-performance computing (HPC) workloads, there is a rise in the use of non-volatile memory (NVM) as accelerators for I/O-intensive scientific applications. However, existing works have explored use of NVM within dedicated I/O nodes,...
Conference Paper
Full-text available
Drawing parallels to the rise of general purpose graphical processing units (GPGPUs) as accelerators for specific high-performance computing (HPC) workloads, there is a rise in the use of non-volatile memory (NVM) as accelerators for I/O-intensive scientific applications. However, existing works have explored use of NVM within dedicated I/O nodes,...
Article
Full-text available
The atomic nucleus is a self-bound system of strongly interacting nucleons. In No-Core Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions (Configurations), and the many-body Schrödinger equation becomes a large sparse matrix problem. The challenge is to reach numerical...
Article
Full-text available
In ab-initio Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions and the many-body Schrodinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using fin...
Conference Paper
Full-text available
The emergence of high performance computing (HPC) platforms equipped with solid state drives (SSD) presents an opportunity to dramatically increase the efficiency of out-of-core numerical linear algebra computations. In this paper, we explore the advantages and challenges associated with performing sparse matrix vector multiplications (SpMV) on a s...
Conference Paper
Full-text available
Obtaining highly accurate predictions on properties of light atomic nuclei using the Configuration Interaction (CI)approach requires computing few extremal eigenpairs of a large many-body nuclear Hamiltonian matrix, Ĥ. A forefront challenge in CI calculations is the massive size of Ĥ and its eigenvectors. The emergence of clusters equipped with non...
Conference Paper
Obtaining highly accurate predictions for properties of light atomic nuclei using the Configuration Interaction (CI) approach requires computing the lowest eigenvalues and associated eigenvectors of a large many-body nuclear Hamiltonian matrix, $\hat{H}$. Since $\hat{H}$ is a large sparse matrix, a parallel iterative eigensolver designed for multi-...
Article
Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems – ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a static bond s...
Article
Full-text available
Modeling atomic and molecular systems requires computation-intensive quantum mechanical methods such as, but not limited to, density functional theory [R. A. Friesner, Proc. Natl. Acad. Sci. USA, 102 (2005), pp. 6648-6653]. These methods have been successful in predicting various properties of chemical systems at atomistic scales. Due to the inhere...
Article
Full-text available
At the heart of many scientific applications is the solution of algebraic systems, such as linear systems of equations, eigenvalue problems, and optimization problems, to name a few. TOPS, which stands for Towards Optimal Petascale Simulations, is a SciDAC applied math center focused on the development of solvers for tackling these algebraic system...
Conference Paper
Obtaining highly accurate predictions on properties of light atomic nuclei using the Configuration Interaction (CI) method requires computing the lowest eigenvalues and associated eigenvectors of a large many-body nuclear Hamiltonian, H. One particular approach, the J-scheme, requires the projection of the H matrix into an invariant subspace. Since...
Conference Paper
One of the emerging computational approaches in nuclear physics is the configuration interaction (CI) method for solving the many-body nuclear Hamiltonian in a sufficiently large single-particle basis space to obtain exact answers - either directly or by extrapolation. One particular goal is to compute a number of lowest eigen-values and eigenvecto...
Article
Full-text available
We report our study of a silica-water interface using reactive molecular dynamics. This first-of-its-kind simulation achieves length and time scales required to investigate the detailed chemistry of the system. Our molecular dynamics approach is based on the ReaxFF force field of van Duin et al. [J. Phys. Chem. A 107, 3803 (2003)]. The specific Rea...
Article
Full-text available
We use molecular dynamics (MD) with the reactive interatomic potential ReaxFF to characterize the local strains of epitaxial Si/Ge/Si nanoscale bars as a function of their width and height. While the longitudinal strain (along the bars length) is independent of geometry, surface relaxation leads to transverse strain relaxation in the Ge section. Th...
Article
Full-text available
Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that...
Conference Paper
Full-text available
We demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is...
Article
Abstract Molecular dynamics modeling has provided a powerful tool for simulating and understanding diverse systems - ranging from materials processes to biophysical phenomena. Parallel formulations of these methods have been shown to be among the most scalable scientific computing applications. Many instances of this class of methods rely on a stat...