arXiv subjects

John E. Pask

Publications and source records attributed to John E. Pask.

34 records · Page 2Linked to original sources

arXiv2020

SPARC: Simulation Package for Ab-initio Real-space Calculations

We present SPARC: Simulation Package for Ab-initio Real-space Calculations. SPARC can perform Kohn-Sham density functional theory calculations for isolated systems such as molecules as well as extended systems such as crystals and surfaces, in both static and dynamic settings. It is straightforward to install/use and highly competitive with state-of-the-art planewave codes, demonstrating comparable performance on a small number of processors and increasing advantages as the number of processors grows. Notably, SPARC brings solution times down to a few seconds for systems with $\mathcal{O}(100-500)$ atoms on large-scale parallel computers, outperforming planewave counterparts by an order of magnitude and more.

physics.comp-ph↗

arXiv2019

Equation of state of warm-dense boron nitride combining computation, modeling, and experiment

The equation of state (EOS) of materials at warm dense conditions poses significant challenges to both theory and experiment. We report a combined computational, modeling, and experimental investigation leveraging new theoretical and experimental capabilities to investigate warm-dense boron nitride (BN). The simulation methodologies include path integral Monte Carlo (PIMC), several density functional theory (DFT) molecular dynamics methods [plane-wave pseudopotential, Fermi operator expansion (FOE), and spectral quadrature (SQ)], activity expansion (ACTEX), and all-electron Green's function Korringa-Kohn-Rostoker (MECCA), and compute the pressure and internal energy of BN over a broad range of densities ($ρ$) and temperatures ($T$). Our experiments were conducted at the Omega laser facility and measured the Hugoniot of BN to unprecedented pressures (12--30 Mbar). The EOSs computed using different methods cross validate one another, and the experimental Hugoniot are in good agreement with our theoretical predictions. We assess that the largest discrepancies between theoretical predictions are $<$4% in pressure and $<$3% in energy and occur at $10^6$ K. We find remarkable consistency between the EOS from DFT calculations performed on different platforms and using different exchange-correlation functionals and those from PIMC using free-particle nodes. This provides strong evidence for the accuracy of both PIMC and DFT in the warm-dense regime. Moreover, SQ and FOE data have significantly smaller error bars than PIMC, and so represent significant advances for efficient computation at high $T$. We also construct tabular EOS models and clarify the ionic and electronic structure of BN over a broad $T-ρ$ range and quantify their roles in the EOS. The tabular models may be utilized for future simulations of laser-driven experiments that include BN as a candidate ablator material.

physics.chem-ph↗

arXiv2018

Discrete discontinuous basis projection method for large-scale electronic structure calculations

We present an approach to accelerate real-space electronic structure methods several fold, without loss of accuracy, by reducing the dimension of the discrete eigenproblem that must be solved. To accomplish this, we construct an efficient, systematically improvable, discontinuous basis spanning the occupied subspace and project the real-space Hamiltonian onto the span. In calculations on a range of systems, we find that accurate energies and forces are obtained with 8--25 basis functions per atom, reducing the dimension of the associated real-space eigenproblems by 1--3 orders of magnitude.

physics.comp-ph↗

arXiv2018

Alternating Anderson-Richardson method: An efficient alternative to preconditioned Krylov methods for large, sparse linear systems

We present the Alternating Anderson-Richardson (AAR) method: an efficient and scalable alternative to preconditioned Krylov solvers for the solution of large, sparse linear systems on high performance computing platforms. Specifically, we generalize the recently proposed Alternating Anderson-Jacobi (AAJ) method (Pratapa et al., J. Comput. Phys. (2016), 306, 43--54) to include preconditioning, discuss efficient parallel implementation, and provide serial MATLAB and parallel C/C++ implementations. In serial applications to nonsymmetric systems, we find that AAR is comparably robust to GMRES, using the same preconditioning, while often outperforming it in time to solution; and find AAR to be more robust than Bi-CGSTAB for the problems considered. In parallel applications to the Helmholtz and Poisson equations, we find that AAR shows superior strong and weak scaling to GMRES, Bi-CGSTAB, and Conjugate Gradient (CG) methods, using the same preconditioning, with consistently shorter times to solution at larger processor counts. Finally, in massively parallel applications to the Poisson equation, on up to 110,592 processors, we find that AAR shows superior strong and weak scaling to CG, with shorter minimum time to solution. We thus find that AAR offers a robust and efficient alternative to current state-of-the-art solvers, with increasing advantages as the number of processors grows.

math.NA↗

arXiv2018

Orbital-enriched Flat-top Partition of Unity Method for the Schrödinger Eigenproblem

Quantum mechanical calculations require the repeated solution of a Schrödinger equation for the wavefunctions of the system. Recent work has shown that enriched finite element methods significantly reduce the degrees of freedom required to obtain accurate solutions. However, time to solution has been adversely affected by the need to solve a generalized eigenvalue problem and the ill-conditioning of associated systems matrices. In this work, we address both issues by proposing a stable and efficient orbital-enriched partition-of-unity method to solve the Schrödinger boundary-value problem in a parallelepiped unit cell subject to Bloch-periodic boundary conditions. In our proposed PUM, the three-dimensional domain is covered by overlapping patches, with a compactly-supported, non-negative weight function, that is identically equal to unity over some finite subset of its support associated with each patch. This so-called flat-top property provides a pathway to devise a stable approximation over the whole domain. On each patch, we use $p$-th degree orthogonal polynomials that ensure $p$-th order completeness, and in addition include eigenfunctions of the radial solution of the Schrödinger equation. Furthermore, we adopt a variational lumping approach to construct a block-diagonal overlap matrix that yields a standard eigenvalue problem and demonstrate accuracy, stability and efficiency of the method.

physics.comp-ph↗

arXiv2018

Two-level Chebyshev filter based complementary subspace method: pushing the envelope of large-scale electronic structure calculations

We describe a novel iterative strategy for Kohn-Sham density functional theory calculations aimed at large systems (> 1000 electrons), applicable to metals and insulators alike. In lieu of explicit diagonalization of the Kohn-Sham Hamiltonian on every self-consistent field (SCF) iteration, we employ a two-level Chebyshev polynomial filter based complementary subspace strategy to: 1) compute a set of vectors that span the occupied subspace of the Hamiltonian; 2) reduce subspace diagonalization to just partially occupied states; and 3) obtain those states in an efficient, scalable manner via an inner Chebyshev-filter iteration. By reducing the necessary computation to just partially occupied states, and obtaining these through an inner Chebyshev iteration, our approach reduces the cost of large metallic calculations significantly, while eliminating subspace diagonalization for insulating systems altogether. We describe the implementation of the method within the framework of the Discontinuous Galerkin (DG) electronic structure method and show that this results in a computational scheme that can effectively tackle bulk and nano systems containing tens of thousands of electrons, with chemical accuracy, within a few minutes or less of wall clock time per SCF iteration on large-scale computing platforms. We anticipate that our method will be instrumental in pushing the envelope of large-scale ab initio molecular dynamics. As a demonstration of this, we simulate a bulk silicon system containing 8,000 atoms at finite temperature, and obtain an average SCF step wall time of 51 seconds on 34,560 processors; thus allowing us to carry out 1.0 ps of ab initio molecular dynamics in approximately 28 hours (of wall time).

physics.comp-ph↗

arXiv2017

SQDFT: Spectral Quadrature method for large-scale parallel $\mathcal{O}(N)$ Kohn-Sham calculations at high temperature

We present SQDFT: a large-scale parallel implementation of the Spectral Quadrature (SQ) method for $\mathcal{O}(N)$ Kohn-Sham Density Functional Theory (DFT) calculations at high temperature. Specifically, we develop an efficient and scalable finite-difference implementation of the infinite-cell Clenshaw-Curtis SQ approach, in which results for the infinite crystal are obtained by expressing quantities of interest as bilinear forms or sums of bilinear forms, that are then approximated by spatially localized Clenshaw-Curtis quadrature rules. We demonstrate the accuracy of SQDFT by showing systematic convergence of energies and atomic forces with respect to SQ parameters to reference diagonalization results, and convergence with discretization to established planewave results, for both metallic and insulating systems. We further demonstrate that SQDFT achieves excellent strong and weak parallel scaling on computer systems consisting of tens of thousands of processors, with near perfect $\mathcal{O}(N)$ scaling with system size and wall times as low as a few seconds per self-consistent field iteration. Finally, we verify the accuracy of SQDFT in large-scale quantum molecular dynamics simulations of aluminum at high temperature.

physics.comp-ph↗

arXiv2016

Partition of unity finite element method for quantum mechanical materials calculations

The current state of the art for large-scale quantum-mechanical simulations is the planewave (PW) pseudopotential method, as implemented in codes such as VASP, ABINIT, and many others. However, since the PW method uses a global Fourier basis, with strictly uniform resolution at all points in space, it suffers from substantial inefficiencies in calculations involving atoms with localized states, such as first-row and transition-metal atoms, and requires significant nonlocal communications, which limit parallel efficiency. Real-space methods such as finite-differences and finite-elements have partially addressed both resolution and parallel-communications issues but have been plagued by one key disadvantage relative to PW: excessive number of degrees of freedom needed to achieve the required accuracies. We present a real-space partition of unity finite element (PUFE) method to solve the Kohn-Sham equations of density functional theory. In the PUFE method, we build the known atomic physics into the solution process using partition-of-unity enrichment techniques in finite element analysis. The method developed herein is completely general, applicable to metals and insulators alike, and particularly efficient for deep, localized potentials, as occur in calculations at extreme conditions of pressure and temperature. Full self-consistent Kohn-Sham calculations are presented for LiH, involving light atoms, and CeAl, involving heavy atoms with large numbers of atomic-orbital enrichments. We find that the new PUFE approach attains the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the PW method. We compute the equation of state of LiH and show that the computed lattice constant and bulk modulus are in excellent agreement with reference PW results, while requiring an order of magnitude fewer degrees of freedom to obtain.

physics.comp-ph↗

arXiv2016

Chebyshev polynomial filtered subspace iteration in the Discontinuous Galerkin method for large-scale electronic structure calculations

The Discontinuous Galerkin (DG) electronic structure method employs an adaptive local basis (ALB) set to solve the Kohn-Sham equations of density functional theory (DFT) in a discontinuous Galerkin framework. The adaptive local basis is generated on-the-fly to capture the local material physics, and can systematically attain chemical accuracy with only a few tens of degrees of freedom per atom. A central issue for large-scale calculations, however, is the computation of the electron density (and subsequently, ground state properties) from the discretized Hamiltonian in an efficient and scalable manner. We show in this work how Chebyshev polynomial filtered subspace iteration (CheFSI) can be used to address this issue and push the envelope in large-scale materials simulations in a discontinuous Galerkin framework. We describe how the subspace filtering steps can be performed in an efficient and scalable manner using a two-dimensional parallelization scheme, thanks to the orthogonality of the DG basis set and block-sparse structure of the DG Hamiltonian matrix. The on-the-fly nature of the ALBs requires additional care in carrying out the subspace iterations. We demonstrate the parallel scalability of the DG-CheFSI approach in calculations of large-scale two-dimensional graphene sheets and bulk three-dimensional lithium-ion electrolyte systems. Employing 55,296 computational cores, the time per self-consistent field iteration for a sample of the bulk 3D electrolyte containing 8,586 atoms is 90 seconds, and the time for a graphene sheet containing 11,520 atoms is 75 seconds.

physics.comp-ph↗

arXiv2016

Convergence analysis of a locally accelerated preconditioned steepest descent method for Hermitian-definite generalized eigenvalue problems

By extending the classical analysis techniques due to Samokish, Faddeev and Faddeeva, and Longsine and McCormick among others, we prove the convergence of preconditioned steepest descent with implicit deflation (PSD-id) method for solving Hermitian-definite generalized eigenvalue problems. Furthermore, we derive a nonasymptotic estimate of the rate of convergence of the \psdid method. We show that with the proper choice of the shift, the indefinite shift-and-invert preconditioner is a locally accelerated preconditioner, and is asymptotically optimal that leads to superlinear convergence. Numerical examples are presented to verify the theoretical results on the convergence behavior of the \psdid method for solving ill-conditioned Hermitian-definite generalized eigenvalue problems arising from electronic structure calculations. While rigorous and full-scale convergence proofs of preconditioned block steepest descent methods in practical use still largely eludes us, we believe the theoretical results presented in this paper sheds light on an improved understanding of the convergence behavior of these block methods.

math.NA↗

arXiv2016

Periodic Pulay method for robust and efficient convergence acceleration of self-consistent field iterations

Pulay's Direct Inversion in the Iterative Subspace (DIIS) method is one of the most widely used mixing schemes for accelerating the self-consistent solution of electronic structure problems. In this work, we propose a simple generalization of DIIS in which Pulay extrapolation is performed at periodic intervals rather than on every self-consistent field iteration, and linear mixing is performed on all other iterations. We demonstrate through numerical tests on a wide variety of materials systems in the framework of density functional theory that the proposed generalization of Pulay's method significantly improves its robustness and efficiency.

physics.comp-ph↗

arXiv2015

Adaptive local basis set for Kohn-Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracy required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann-Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H$_2$ and liquid Al-Si alloy systems, where we find excellent agreement with independent benchmark results in literature.

physics.comp-ph↗

arXiv2015

A Projected Preconditioned Conjugate Gradient Algorithm for Computing Many Extreme Eigenpairs of a Hermitian Matrix

We present an iterative algorithm for computing an invariant subspace associated with the algebraically smallest eigenvalues of a large sparse or structured Hermitian matrix A. We are interested in the case in which the dimension of the invariant subspace is large (e.g., over several hundreds or thousands) even though it may still be small relative to the dimension of A. These problems arise from, for example, density functional theory based electronic structure calculations for complex materials. The key feature of our algorithm is that it performs fewer Rayleigh--Ritz calculations compared to existing algorithms such as the locally optimal precondition conjugate gradient or the Davidson algorithm. It is a block algorithm, hence can take advantage of efficient BLAS3 operations and be implemented with multiple levels of concurrency. We discuss a number of practical issues that must be addressed in order to implement the algorithm efficiently on a high performance computer.

math.NA↗

arXiv2015

Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First Principles and Classical Reactive Molecular Dynamics

Lithium-ion battery performance is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact both solvation and diffusivity of Li ions. We use first principles molecular dynamics to examine the solvation and diffusion of Li ions in the bulk organic solvents ethylene carbonate (EC), ethyl methyl carbonate (EMC), and a mixture of EC/EMC. We find that Li ions are solvated by either carbonyl or ether oxygen atoms of the solvents and sometimes by the PF$_6^-$ anion. Li$^+$ prefers a tetrahedrally-coordinated first solvation shell regardless of which species are involved, with the specific preferred solvation structure dependent on the organic solvent. In addition, we calculate Li diffusion coefficients in each electrolyte, finding slightly larger diffusivities in the linear carbonate EMC compared to the cyclic carbonate EC. The magnitude of the diffusion coefficient correlates with the strength of Li$^+$ solvation. Corresponding analysis for the PF$_6^-$ anion shows greater diffusivity associated with a weakly-bound, poorly defined first solvation shell. These results may be used to aid in the design of new electrolytes to improve Li-ion battery performance.

cond-mat.mtrl-sci↗

arXiv2013

Hybrid preconditioning for iterative diagonalization of ill-conditioned generalized eigenvalue problems in electronic structure calculations

The iterative diagonalization of a sequence of large ill-conditioned generalized eigenvalue problems is a computational bottleneck in quantum mechanical methods employing a nonorthogonal basis for {\em ab initio} electronic structure calculations. We propose a hybrid preconditioning scheme to effectively combine global and locally accelerated preconditioners for rapid iterative diagonalization of such eigenvalue problems. In partition-of-unity finite-element (PUFE) pseudopotential density-functional calculations, employing a nonorthogonal basis, we show that the hybrid preconditioned block steepest descent method is a cost-effective eigensolver, outperforming current state-of-the-art global preconditioning schemes, and comparably efficient for the ill-conditioned generalized eigenvalue problems produced by PUFE as the locally optimal block preconditioned conjugate-gradient method for the well-conditioned standard eigenvalue problems produced by planewave methods.

cond-mat.mtrl-sci↗

arXiv2013

dftatom: A robust and general Schrödinger and Dirac solver for atomic structure calculations

A robust and general solver for the radial Schrödinger, Dirac, and Kohn--Sham equations is presented. The formulation admits general potentials and meshes: uniform, exponential, or other defined by nodal distribution and derivative functions. For a given mesh type, convergence can be controlled systematically by increasing the number of grid points. Radial integrations are carried out using a combination of asymptotic forms, Runge-Kutta, and implicit Adams methods. Eigenfunctions are determined by a combination of bisection and perturbation methods for robustness and speed. An outward Poisson integration is employed to increase accuracy in the core region, allowing absolute accuracies of $10^{-8}$ Hartree to be attained for total energies of heavy atoms such as uranium. Detailed convergence studies are presented and computational parameters are provided to achieve accuracies commonly required in practice. Comparisons to analytic and current-benchmark density-functional results for atomic number $Z$ = 1--92 are presented, verifying and providing a refinement to current benchmarks. An efficient, modular Fortran 95 implementation, \ttt{dftatom}, is provided as open source, including examples, tests, and wrappers for interface to other languages; wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

physics.atom-ph↗