Bulletin of the American Physical Society
APS March Meeting 2018
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session C34: Petascale Science and Beyond: Applications and Opportunities for Materials, Chemical, and Bio Physics IIIFocus

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Sponsoring Units: DCOMP DBIO DCP DCMP Chair: Jack Deslippe, Lawrence Berkeley National Laboratory Room: LACC 409A 
Monday, March 5, 2018 2:30PM  3:06PM 
C34.00001: Largescale first principles calculations with leadership class HPC using manybody perturbation theory Invited Speaker: Marco Govoni Predictive modeling of excited state properties typically employs Green's function based manybody perturbation theory (MBPT) methods. Preexascale machines offer the opportunity to expand the science domain of such methods to systems of unprecedented size, accounting for the realistic complexity of e.g. nanostructured, interfaced, disordered, and defective materials. In this talk we discuss how methodological advances coded in WEST [www.westcode.org] provide an efficient formulation of electronelectron, electronphonon and electronhole interactions, that is applied to systems with thousands of electrons. We will discuss the advantages of the algorithms used in WEST over standard techniques, its parallel performance on leadership class HPC machines, and provide results for the calculation of spectroscopic features of liquids and defective solids. We will discuss the inclusion of electronphonon coupling effects to simulate photoelectron spectra and carrier lifetimes of carbonbased nanoparticles. Finally, we will present the new functionalities enabled by the concurrent use of WEST and the Qbox code [qboxcode.org], with focus on the interoperability paradigm that the coupling advocates. Work in collaboration with: A. Gaiduk, G. Galli, M. Gerosa, F. Gygi, I. Hamada, C. Knight, H. Ma, R. McAvoy, N.L. Nguyen, H. Yang, H. Seo, H. Zheng. 
Monday, March 5, 2018 3:06PM  3:18PM 
C34.00002: Massively Parallel RealTime TDDFT Simulations of Electronic Excitations in DNA by Energetic Protons Dillon Yost, Yosuke Kanai In electronic stopping processes, electronic excitations are produced by fastmoving ions. This phenomenon is at the heart of DNA damage via ion irradiation, which is central to ion beam cancer therapy. A molecularlevel understanding of this process is necessary to advance medical technology. Unfortunately, experimental studies remain scarce due to their requirement for extensive use of synchrotron facilities. Quantummechanical simulations on supercomputers offer an alternative route for investigating this problem. We will discuss results acquired from our highly scalable implementation of realtime timedependent density functional theory (RTTDDFT) simulations (1,2) on current generation HPC systems, as well as nextgeneration manyintegratedcore architectures. This cuttingedge application of RTTDDFT simulations has unveiled details of energy transfer, electronic excitations, and charge fluctuations in DNA under ion irradiation that would be unattainable without petascale simulations. 
Monday, March 5, 2018 3:18PM  3:30PM 
C34.00003: Petascale simulation of electron currents in nanoscale interconnects LinWang Wang The ondie interconnect has become the dominate heat generating source in a modern chip. As the transistor size gets even smaller, or the device architecture changes to 3D stacking, the interconnect problem will only become worse. Petascale high performance computing is used to study the current flow in such a nanoscale interconnect. Ab initio simulation is used to construct the Schrodinger’s equation for a system with tens of thousands of copper atoms based on linear scaling density functional theory. The electron scattering states are calculated using a linear combination of perturbation induced “system” states. The direct viewing of the intensity of such scattering states (current) will show some insights for where the heat is generated. Future calculation of electronphonon coupling will allow the calculation of heat generation. The challenges of the simulations will be discussed, as well as the computational issues in such large scale simulation. 
Monday, March 5, 2018 3:30PM  3:42PM 
C34.00004: Improved Molecular Dynamics Calculations using HighOrder Forces in Real Space Density Functional Theory Joshua Neitzel, Charles Lena, James Chelikowsky We present an improved method for calculation of nonlocal contributions to interatomic forces resulting from the real space density functional theory Hamiltonian. Our method utilizes a high order Gaussian integration scheme. We demonstrate the efficacy of our method through molecular dynamics simulations of polyatomic molecules. We show that our method reduces energy drift for each molecule. Additionally, our method improves convergence of dynamic variables including center of mass drift and vibrational frequency. 
Monday, March 5, 2018 3:42PM  3:54PM 
C34.00005: Scaling the Force Calculations of the Real Space Pseudopotential DFT solver PARSEC on Haswell and KNL systems Kevin Gott, Charles Lena, KaiHsin Liou, James Chelikowsky, Jack Deslippe The ability to compute atomic forces through quantum contributions rather than through simple pairwise potentials is one of the most compelling reasons materials scientists use KohnSham pseudopotential density functional theory (DFT). PARSEC is an actively developed real space pseudopotential DFT solver that uses Fortran MPI+OpenMP parallelization. PARSEC provides atomic forces by selfconsistently solving for the electronic structure and then summing local and nonlocal contributions. Through experimentation with PARSEC, we present why increasingly bulk synchronous processing and vectorization of the contributions is not enough to fully utilize current HPC hardware. We address this limitation through a demonstration of multithreaded communication approaches for local and nonlocal force computations on Intel Knights Landing supercomputers that yield feasible calculation times for systems of over 20,000 atoms. 
Monday, March 5, 2018 3:54PM  4:06PM 
C34.00006: A parallel eigensolver: Using spectrum slicing method to solve the KohnSham problem for large systems KaiHsin Liou, Charles Lena, James Chelikowsky, Yousef Saad Solving the Kohn–Sham equation within density functional theory (DFT) finds extensive use in solving for the electronic structure of a variety of condensed materials, including complex biomolecules, nanostructures and interfacial systems. PARSEC, a realspace pseudopotential DFT code developed by our group, routinely solves the electronic structure problem for localized and extended systems of thousands of atoms using Chebyshev polynomial subspace filtering; however, many systems of interest contain tens of thousands of atoms, where the computational demands of orthonormalization can overwhelm current machines. In an effort to address this numerical constraint, we add an additional level of parallelism to our eigensolver by focusing on spectrum slicing. Spectrum slicing assigns energy windows to eigenpairs and treats each window as an independent task, which may be assigned to groups of processing units. We will demonstrate the advantages of this approach for a large (over 20,000 atoms) silicon nanocrystal with and without defects. 
Monday, March 5, 2018 4:06PM  4:18PM 
C34.00007: Towards Abinit on ExaScale supercomputers : the challenge for electronic structure physicists. Jordan Bieder, Marc Torrent, Yohan Chatelain In Abinit, physical properties are computed from the stateofthe art first principles methods. 
Monday, March 5, 2018 4:18PM  4:30PM 
C34.00008: Unified Access To KohnSham DFT Solvers for Different Scales and HPC: The ELSI Project William Huhn, Alberto Garcia, Luigi Genovese, Ville Havu, Mathias Jacquelin, Weile Jia, Murat Keceli, Raul Laasner, Yingzhou Li, Lin Lin, Jianfeng Lu, Stephan Mohr, Nkwe Monama, Happy Sithole, Alvaro VazquezMayagoitia, Chao Yang, Haizhao Yang, Victor Yu, Volker Blum One major bottleneck in KohnSham DFT is the solution of the KohnSham eigenvalue equation to obtain the density matrix, which limits achievable system size. In this talk, we present updates to the ELectronic Structure Infrastructure (ELSI), an opensource effort that facilitates access to efficient KohnSham solvers via a unified, codeindependent interface for different system size scales, system types, and HPC architectures. Features that will be presented include support for several solver libraries (ELPA, libOMM, PEXSI, SIPs, CheSS) and a flexible, massivelyparallel densitymatrixbased restart method. Comparative benchmarks up to ten thousands of atoms on leading HPC resources will be shown. Special attention will be paid to the performance and scaling benchmark set created for this work, which is designed to be applicable to other aspects of electronic structure theory. These benchmarks will be the foundation of a decision layer to automatically select the optimal solver for a given problem based on the performance profile of the underlying HPC architecture. 
Monday, March 5, 2018 4:30PM  4:42PM 
C34.00009: RMG – An Open Source Electronic Structure Code for MultiPetaflops Calculations Emil Briggs, Wenchang Lu, Miroslav Hodak, Jerry Bernholc Density functional theory provides an accurate but computationally demanding framework for studying the properties of a broad range of problems. RMG is an open source package that solves the KohnSham equations that arise from the DFT formalism using realspace grids, multigrid preconditioning, and subspace diagonalization. RMG is well suited for petascale level calculations and makes efficient use of GPU accelerators on platforms that support them. It is cross platform and runs on Linux, Windows and MacIntosh systems as well as clusters and supercomputers. Applications range from semiconductors to biological systems. RMG provides support for a variety of exchange correlation functionals including Van der Waals interactions via vdWdf. The base code uses delocalized orbitals but a localized orbital variant is also available. It is used for quantum transport calculations via the nonequilibrium Green’s function formalism, by which selfconsistent calculations for over 10,000 atoms have been performed. 
Monday, March 5, 2018 4:42PM  4:54PM 
C34.00010: Fullpotential fully relativistic LSMS Method Xianglin Liu, Markus Eisenbach, Yang Wang, G. Malcolm Stocks The locally selfconsistent multiple scattering (LSMS) method is an electronic structure calculation method based on the multiple scattering theory (MST) and density functional theory (DFT). As an O(N) approach, the LSMS method makes use of the "nearsightedness" principle, and consider the multiplescattering process only within the "local interaction zone" (LIZ), therefore is highly parallelizable and very efficient to treat large systems. Traditionally, the LSMS method adopts the muffintin approximation, and has been successfully used to treat alloy systems with tens of thousands of atoms. For a more general application of the LSMS method, such as treating directional covalent bonding, 2D structures, or evaluating the interatomic forces, it is desirable to implement the full potential scheme instead of the muffintin approximation. Moreover, due the crucial role of spinorbit coupling in many technological applications, it is important to extend the LSMS method to a relativistic scheme. In this talk, we will demonstrate our implementation of the LSMS method that solves the fullpotential Dirac equation directly, show example calculations, and discuss the results. 
Monday, March 5, 2018 4:54PM  5:06PM 
C34.00011: Opportunities for Simulating Large Systems using Accurate and Efficient Density Functional Theory Calculations Laura Ratcliff, Stephan Mohr, Michel Masella, Luigi Genovese Thanks to a combination of the availability of petascale supercomputers and algorithmic developments such as linear scaling density functional theory, in recent years it has become possible to perform quantum mechanical (QM) simulations for systems containing several thousand atoms. This not only opens up new possibilities for treating large and complex systems using QM, but also enables the direct comparison with nonQM methods such as force fields or coarse graining methods, at the (large) length scales at which they are typically applied. To this end, it is desirable to have a means of reducing the effective complexity of a QM simulation, i.e. to reduce the number of degrees of freedom without a significant loss of accuracy or the introduction of any bias. For such a complexity reduction, it is necessary to identify other analysis schemes for understanding and interpreting the behaviour of a QM system, for example by partitioning a large system into objects, or fragments, of a smaller size. In this talk we will discuss the opportunities for large scale QM simulations, and introduce a quantitative method for assessing the partitioning of a system into fragments, presenting examples of how such a partitioning might be exploited. 
Monday, March 5, 2018 5:06PM  5:18PM 
C34.00012: Proper alignment of Fermi Level in a Trianionic Molecule Deryou Kao, Shawn DomagalGoldman Descriptions of anionic molecules, within approximations to densityfunctional theory, has been problematic due to selfinteraction error which pushes the eigenvalues to higher energy and creates nonsystematic errors in Fermi levels. A new approach for improving the PerdewZunger selfinteraction[A], referred to as the FermiLöwdin orbitalbased selfinteraction correction (FLOSIC), is introduced to treat a trianionic system. The Fermi–Löwdin orbitals are localized but due to the fact they are constructed directly from the spindensity matrices, they lead to a set of orbitals that have the property that each and every orbital is explicitly invariant to unitary transformations which leads to a unitarily invariant and sizeextensive expression for the energy. The improvement of alignment of Fermi level in the system is demonstrated and related isotope fractionation is reported. Zeropoint splittings will also be presented and the impact of selfinteraction correction will be discussed. 
Monday, March 5, 2018 5:18PM  5:30PM 
C34.00013: Rigorous definition of builtin potentials at interfaces DukHyun Choe, Damien West, Shengbai Zhang The builtin potential is the interfacial potential difference due to electric dipole at the interface of two dissimilar materials. It is of central importance to the understanding of many phenomena in interface/surface science because it determines the band alignment between the materials. Despite more than 50 years of investigation, however, its exact sign and magnitude have generally been generally recognized as an illdefined quantity. In this work, we provide a universal definition of the builtin potential. We find that the builtin potential is explicitly determined by the bulk (i.e., innate) properties of the constituent materials when the system is in electronic equilibrium, while it is subject to the properties of the interface only in the absence of equilibrium. Our theory enables a unified description of a variety of important properties in all types of interfaces, ranging from work functions and Schottky barriers in electronic devices to electrode potentials and redox potentials in electrochemical cells. 
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