Accuracy control in ultra-large-scale electronic structure calculation

Numerical aspects are investigated in ultra-large-scale electronic structure calculation. Accuracy control methods in process (molecular-dynamics) calculation are focused. Flexible control methods are proposed so as to control variational freedoms, automatically at each time step, within the framework of generalized Wannier state theory. The method is demonstrated in silicon cleavage simulation with 10^2-10^5 atoms. The idea is of general importance among process calculations and is also used in Krylov subspace theory, another large-scale-calculation theory.Comment: 8 pages, 3 figures. To appear in J.Phys. Condens. Matter. A preprint PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm

A hierarchical research by large-scale and ab initio electronic structure theories -- Si and Ge cleavage and stepped (111)-2x1 surfaces --

The ab initio calculation with the density functional theory and plane-wave bases is carried out for stepped Si(111)-2x1 surfaces that were predicted in a cleavage simulation by the large-scale (order-N) electronic structure theory (T. Hoshi, Y. Iguchi and T. Fujiwara, Phys. Rev. B72 (2005) 075323). The present ab initio calculation confirms the predicted stepped structure and its bias-dependent STM image. Moreover, two (meta)stable step-edge structures are found and compared. The investigation is carried out also for Ge(111)-2x1 surfaces, so as to construct a common understanding among elements. The present study demonstrates the general importance of the hierarchical research between large-scale and ab initio electronic structure theories.Comment: 5 pages, 4 figures, to appear in Physica

Large-scale electronic-structure theory and nanoscale defects formed in cleavage process of silicon

Several methods are constructed for large-scale electronic structure calculations. Test calculations are carried out with up to 10^7 atoms. As an application, cleavage process of silicon is investigated by molecular dynamics simulation with 10-nm-scale systems. As well as the elementary formation process of the (111)-(2 x 1) surface, we obtain nanoscale defects, that is, step formation and bending of cleavage path into favorite (experimentally observed) planes. These results are consistent to experiments. Moreover, the simulation result predicts an explicit step structure on the cleaved surface, which shows a bias-dependent STM image.Comment: 4 page 4 figures. A PDF file with better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses

Million-atom molecular dynamics simulation by order-N electronic structure theory and parallel computation

Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for silicon nanocrystals of more than millions atoms with the transferable tight-binding Hamiltonian. The efficiency of parallelism is perfect, 98.8 %, and the method is the most suitable to parallel computation. The elapse time for a system of $2\times 10^6$ atoms is 3.0 minutes by a computer system of 64 processors of SGI Origin 3800. The calculated results are in good agreement with the results of the exact diagonalization, with an error of 2 % for the lattice constant and errors less than 10 % for elastic constants.Comment: 5 pages, 3 figure

Large-scale electronic structure theory for simulating nanostructure process

Fundamental theories and practical methods for large-scale electronic structure calculations are given, in which the computational cost is proportional to the system size. Accuracy controlling methods for microscopic freedoms are focused on two practical solver methods, Krylov-subspace method and generalized-Wannier-state method. A general theory called the 'multi-solver' scheme is also formulated, as a hybrid between different solver methods. Practical examples are carried out in several insulating and metallic systems with 10^3-10^5 atoms. All the theories provide general guiding principles of constructing an optimal calculation for simulating nanostructure processes, since a nanostructured system consists of several competitive regions, such as bulk and surface regions, and the simulation is designed to reproduce the competition with an optimal computational cost.Comment: 19 pages, 6 figures. To appear in J. Phys. Cond. Matt. A preprint PDF file in better graphics is available at http://fujimac.t.u-tokyo.ac.jp/lses/index_e.htm

Large scale simulation of quantum-mechanical molecular dynamics for nano-polycrystalline diamond

Quantum-mechanical molecular-dynamics simulations are carried out to explore possible precursor states of nano-polycrystalline diamond, a novel ultra-hard material produced directly from graphite. Large-scale simulation with 10^5 atoms is realized by using the ' order-N' simulation code 'ELSES' (http://www.elses.jp). The simulation starts with a diamond structure that contains initial structural defects and results in a mixture of graphite(sp^2)-like and diamond(sp^3)-like regions as nano-meter-scale domains. We speculate that the domains are metastable and are possible candidates of the precursor structures.Comment: 4 pages 2 figures. A PDF file in better graphics is available at http://www.elses.jp

An order-N electronic structure theory with generalized eigenvalue equations and its application to a ten-million-atom system

A linear-algebraic theory called 'multiple Arnoldi method' is presented and realizes large-scale (order-N) electronic structure calculation with generalized eigen-value equations. A set of linear equations, in the form of (zS-H) x = b, are solved simultaneously with multiple Krylov subspaces. The method is implemented in a simulation package ELSES (http://www.elses.jp) with tight-binding-form Hamiltonians. A finite-temperature molecular dynamics simulation is carried out for metallic and insulating materials. A calculation with $10^7$ atoms was realized by a workstation. The parallel efficiency is shown upto 1,024 CPU cores.Comment: 9 pages, 3 figures. To appear in J. Phys.: Condens. Matte

Krylov Subspace Method for Molecular Dynamics Simulation based on Large-Scale Electronic Structure Theory

For large scale electronic structure calculation, the Krylov subspace method is introduced to calculate the one-body density matrix instead of the eigenstates of given Hamiltonian. This method provides an efficient way to extract the essential character of the Hamiltonian within a limited number of basis set. Its validation is confirmed by the convergence property of the density matrix within the subspace. The following quantities are calculated; energy, force, density of states, and energy spectrum. Molecular dynamics simulation of Si(001) surface reconstruction is examined as an example, and the results reproduce the mechanism of asymmetric surface dimer.Comment: 7 pages, 3 figures; corrected typos; to be published in Journal of the Phys. Soc. of Japa

Neurohormonal modulation of the Limulus heart: amine actions on neuromuscular transmission and cardiac muscle

The responses of Limulus cardiac neuromuscular junctions and cardiac muscle cells to four endogenous amines were determined in order to identify the cellular targets underlying amine modulation of heartbeat amplitude. The amines increased the amplitude of the Limulus heartbeat, with dopamine (DA) being more potent than octopamine, epinephrine or norepinephrine. The effect of DA on heartbeat amplitude was not blocked by phentolamine. DA enhanced the contractility of deganglionated heart muscle, with time course and dose-dependence similar to its effect on the intact heart. The amines also enhanced neuromuscular transmission, with time course and dose-dependence similar to their effects upon the intact heart. The amplitude of unitary excitatory junction potentials (EJPs) and frequency of miniature excitatory junction potentials (mEJPs) were increased by DA, while mEJP amplitude was unchanged. Thus DA, and probably the other amines, had a presynaptic effect. Combined actions upon cardiac muscle and cardiac neuromuscular transmission account for the ability of these amines to increase the amplitude of the Limulus heartbeat