3,602 research outputs found
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 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 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
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