The grid-based fast multipole method--a massively parallel numerical scheme for calculating two-electron interaction energies.

نویسندگان

  • Elias A Toivanen
  • Sergio A Losilla
  • Dage Sundholm
چکیده

Algorithms and working expressions for a grid-based fast multipole method (GB-FMM) have been developed and implemented. The computational domain is divided into cubic subdomains, organized in a hierarchical tree. The contribution to the electrostatic interaction energies from pairs of neighboring subdomains is computed using numerical integration, whereas the contributions from further apart subdomains are obtained using multipole expansions. The multipole moments of the subdomains are obtained by numerical integration. Linear scaling is achieved by translating and summing the multipoles according to the tree structure, such that each subdomain interacts with a number of subdomains that are almost independent of the size of the system. To compute electrostatic interaction energies of neighboring subdomains, we employ an algorithm which performs efficiently on general purpose graphics processing units (GPGPU). Calculations using one CPU for the FMM part and 20 GPGPUs consisting of tens of thousands of execution threads for the numerical integration algorithm show the scalability and parallel performance of the scheme. For calculations on systems consisting of Gaussian functions (α = 1) distributed as fullerenes from C20 to C720, the total computation time and relative accuracy (ppb) are independent of the system size.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

A parallel fast multipole method for elliptic difference equations

A new fast multipole formulation for solving elliptic difference equations on unbounded domains and its parallel implementation are presented. These difference equations can arise directly in the description of physical systems, e.g. crystal structures, or indirectly through the discretization of PDEs. In the analog to solving continuous inhomogeneous differential equations using Green’s functi...

متن کامل

Development of an Implicit Numerical Model for Calculation of Sub and Super Critical Flows

A two dimensional numerical model of shallow water equations was developed tocalculate sub and super-critical open channel flows. Utilizing an implicit scheme the steady stateequations were discretized based on control volume method. Collocated grid arrangement was appliedwith a SIMPLEC like algorithm for depth-velocity coupling. Power law scheme was used fordiscretization of convection and dif...

متن کامل

"New-version-fast-multipole-method" accelerated electrostatic calculations in biomolecular systems

In this paper, we present an efficient and accurate numerical algorithm for calculating the electrostatic interactions in biomolecular systems. In our scheme, a boundary integral equation (BIE) approach is applied to discretize the linearized Poisson–Boltzmann (PB) equation. The resulting integral formulas are well conditioned for single molecule cases as well as for systems with more than one ...

متن کامل

Development of an Implicit Numerical Model for Calculation of SUB-and Super-Critical Flows

A two dimensional numerical model of shallow water equations was developed to calculate sub and super-critical open channel flows. Utilizing an implicit scheme the steady state equations were discretized based on a control volume method. Collocated grid arrangement was applied with a SIMPLEC like algorithm for depth-velocity coupling. A power law scheme was used for discretization of convection...

متن کامل

RECFMM: Recursive Parallelization of the Adaptive Fast Multipole Method for Coulomb and Screened Coulomb Interactions

We present RECFMM, a program representation and implementation of a recursive scheme for parallelizing the adaptive fast multipole method (FMM) on sharedmemory computers. It achieves remarkable high performance while maintaining mathematical clarity and flexibility. The parallelization scheme signifies the recursion feature that is intrinsic to the FMM but was not well exploited. The program mo...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Physical chemistry chemical physics : PCCP

دوره 17 47  شماره 

صفحات  -

تاریخ انتشار 2015