Large-scale DFT simulations with a linear-scaling DFT code CONQUEST on K-computer

We present the implementation of a hybrid continuum-atomistic model for including the effects of surrounding electrolyte in large-scale density functional theory (DFT) calculations within the ONETEP linear-scaling DFT code, which allows the simulation of large complex systems such as electrochemical interfaces. The model represents the electrolyte ions as a scalar field and the solvent as a polarisable dielectric continuum, both surrounding the quantum solute. The overall energy expression is a grand canonical functional incorporating the electron kinetic and exchange correlation energies, the total electrostatic energy, entropy and chemical potentials of surrounding electrolyte, osmotic pressure, and the effects of cavitation, dispersion and repulsion. The DFT calculation is performed fully self-consistently in the electrolyte model, allowing the quantum mechanical system and the surrounding continuum environment to interact and mutually polarize. A bespoke parallel Poisson-Boltzmann solver library, DL_MG, deals with the electrostatic problem, solving a generalized Poisson-Boltzmann equation. Our model supports open boundary conditions, which allows the treatment of molecules, entire biomolecules or larger nanoparticle assemblies in electrolyte. We have also implemented the model for periodic boundary conditions, allowing the treatment of extended systems such as electrode surfaces in contact with electrolyte. A key feature of the model is the use of solute-size and solvation-shell-aware accessibility functions that prevent the unphysical accumulation of electrolyte charge near the quantum solute boundary. The model has a small number of parameters: here we demonstrate their calibration against experimental mean activity coefficients. We also present an exemplar simulation of a 1634-atom model of the interface between a graphite anode and LiPF<sub>6</sub> electrolyte in ethylene carbonate solvent. We compare the cases where Li atoms are intercalated at opposite edges of the graphite slab and in solution, demonstrating a potential application of the model in simulations of fundamental processes in Li-ion batteries.

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Linear-scaling density functional simulations of the effect of crystallographic structure on the electronic and optical properties of fullerene solvates

Physical Chemistry Chemical Physics ◽

10.1039/c6cp08165g ◽

2017 ◽

Vol 19 (7) ◽

pp. 5617-5628 ◽

Cited By ~ 7

Author(s):

Hong-Tao Xue ◽

Gabriele Boschetto ◽

Michal Krompiec ◽

Graham E. Morse ◽

Fu-Ling Tang ◽

...

Keyword(s):

Optical Properties ◽

Optical Absorption ◽

Dft Calculations ◽

Density Functional ◽

Large Scale ◽

Crystallographic Structure ◽

Linear Scaling ◽

Optical Absorption Spectra ◽

Novel Structure ◽

Structural And Electronic Properties

Large-scale DFT calculations of fullerene solvates including one novel structure probe, the structural and electronic properties and optical absorption spectra.

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Linear-scaling three-dimensional fragment method for large-scale electronic structure calculations

Physical Review B ◽

10.1103/physrevb.77.165113 ◽

2008 ◽

Vol 77 (16) ◽

Cited By ~ 51

Author(s):

Lin-Wang Wang ◽

Zhengji Zhao ◽

Juan Meza

Keyword(s):

Electronic Structure ◽

Large Scale ◽

Three Dimensional ◽

Electronic Structure Calculations ◽

Linear Scaling ◽

Fragment Method ◽

Structure Calculations

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Inertia–Gravity Waves Emitted from Balanced Flow: Observations, Properties, and Consequences

Journal of the Atmospheric Sciences ◽

10.1175/2008jas2480.1 ◽

2008 ◽

Vol 65 (11) ◽

pp. 3543-3556 ◽

Cited By ~ 55

Author(s):

Paul D. Williams ◽

Thomas W. N. Haine ◽

Peter L. Read

Keyword(s):

Gravity Waves ◽

Large Scale ◽

Significant Contribution ◽

Rotation Period ◽

Mesoscale Eddies ◽

Energy Budgets ◽

Linear Scaling ◽

Deep Interior ◽

Balanced Flow ◽

Inertia Gravity Waves

Abstract This paper describes laboratory observations of inertia–gravity waves emitted from balanced fluid flow. In a rotating two-layer annulus experiment, the wavelength of the inertia–gravity waves is very close to the deformation radius. Their amplitude varies linearly with Rossby number in the range 0.05–0.14, at constant Burger number (or rotational Froude number). This linear scaling challenges the notion, suggested by several dynamical theories, that inertia–gravity waves generated by balanced motion will be exponentially small. It is estimated that the balanced flow leaks roughly 1% of its energy each rotation period into the inertia–gravity waves at the peak of their generation. The findings of this study imply an inevitable emission of inertia–gravity waves at Rossby numbers similar to those of the large-scale atmospheric and oceanic flow. Extrapolation of the results suggests that inertia–gravity waves might make a significant contribution to the energy budgets of the atmosphere and ocean. In particular, emission of inertia–gravity waves from mesoscale eddies may be an important source of energy for deep interior mixing in the ocean.

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Linear Scaling 3D Fragment Method for Large-Scale ElectronicStructure Calculations

10.2172/918121 ◽

2006 ◽

Author(s):

Lin-Wang Wang ◽

Zhengji Zhao ◽

Juan Meza

Keyword(s):

Large Scale ◽

Linear Scaling ◽

Fragment Method

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Parallel Implementation of Large-Scale Linear Scaling Density Functional Theory Calculations With Numerical Atomic Orbitals in HONPAS

Frontiers in Chemistry ◽

10.3389/fchem.2020.589910 ◽

2020 ◽

Vol 8 ◽

Author(s):

Zhaolong Luo ◽

Xinming Qin ◽

Lingyun Wan ◽

Wei Hu ◽

Jinlong Yang

Keyword(s):

Density Matrix ◽

Dft Calculations ◽

Density Functional ◽

Large Scale ◽

Parallel Implementation ◽

Sparse Matrix ◽

Matrix Multiplication ◽

Linear Scaling ◽

Functional Theory ◽

Atomic Orbitals

Linear-scaling density functional theory (DFT) is an efficient method to describe the electronic structures of molecules, semiconductors, and insulators to avoid the high cubic-scaling cost in conventional DFT calculations. Here, we present a parallel implementation of linear-scaling density matrix trace correcting (TC) purification algorithm to solve the Kohn–Sham (KS) equations with the numerical atomic orbitals in the HONPAS package. Such a linear-scaling density matrix purification algorithm is based on the Kohn's nearsightedness principle, resulting in a sparse Hamiltonian matrix with localized basis sets in the DFT calculations. Therefore, sparse matrix multiplication is the most time-consuming step in the density matrix purification algorithm for linear-scaling DFT calculations. We propose to use the MPI_Allgather function for parallel programming to deal with the sparse matrix multiplication within the compressed sparse row (CSR) format, which can scale up to hundreds of processing cores on modern heterogeneous supercomputers. We demonstrate the computational accuracy and efficiency of this parallel density matrix purification algorithm by performing large-scale DFT calculations on boron nitrogen nanotubes containing tens of thousands of atoms.

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Statistics of Heat Transfer in Two-Dimensional Turbulent Rayleigh-Bénard Convection at Various Prandtl Number

Entropy ◽

10.3390/e20080582 ◽

2018 ◽

Vol 20 (8) ◽

pp. 582 ◽

Cited By ~ 2

Author(s):

Hui Yang ◽

Yikun Wei ◽

Zuchao Zhu ◽

Huashu Dou ◽

Yuehong Qian

Keyword(s):

Heat Transfer ◽

Structure Function ◽

Dissipation Rate ◽

Large Scale ◽

Thermal Dissipation ◽

Small Scale ◽

Linear Scaling ◽

Two Dimensional ◽

Large Scale Circulation ◽

Rayleigh Benard

Statistics of heat transfer in two-dimensional (2D) turbulent Rayleigh-Bénard (RB) convection for Pr=6,20,100 and 106 are investigated using the lattice Boltzmann method (LBM). Our results reveal that the large scale circulation is gradually broken up into small scale structures plumes with the increase of Pr, the large scale circulation disappears with increasing Pr, and a great deal of smaller thermal plumes vertically rise and fall from the bottom to top walls. It is further indicated that vertical motion of various plumes gradually plays main role with increasing Pr. In addition, our analysis also shows that the thermal dissipation is distributed mainly in the position of high temperature gradient, the thermal dissipation rate εθ already increasingly plays a dominant position in the thermal transport, εu can have no effect with increase of Pr. The kinematic viscosity dissipation rate and the thermal dissipation rate gradually decrease with increasing Pr. The energy spectrum significantly decreases with the increase of Pr. A scope of linear scaling arises in the second order velocity structure functions, the temperature structure function and mixed structure function(temperature-velocity). The value of linear scaling and the 2nd-order velocity decrease with increasing Pr, which is qualitatively consistent with the theoretical predictions.

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