作者：
Morishita, TKeio Univ
Fac Sci & Technol Dept Phys Kohoku Ku Yokohama Kanagawa 2238522 Japan
A modified and generalized velocity scaling (VS) scheme to integrate equations of motion (EOM) for constant temperature and/or pressure molecular dynamics (MD) simulations in the framework of the leapfrog algorithm is...
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A modified and generalized velocity scaling (VS) scheme to integrate equations of motion (EOM) for constant temperature and/or pressure molecular dynamics (MD) simulations in the framework of the leapfrog algorithm is presented. This modified VS scheme (MVS) enables us to integrate EOM with a velocity dependent force such as a friction term easily maintaining the accuracy of the leapfrog (Verlet) algorithm. The scaling factor in the MVS does not depend on the detailed expression of the friction term. Therefore, it can be incorporated in various constant temperature and/or pressure methods. The accuracy of integrations in the MVS and original VS was compared in a Lennard-Jones fluid. It is confirmed that the MVS holds the Verlet's accuracy, while original VS fails.
The unique properties of two classes of regular-hexagon-shaped benzenoid hydrocarbons are studied. The D-6h point group symmetry of the members of these series have made them natural objects of numerous past studies. ...
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The unique properties of two classes of regular-hexagon-shaped benzenoid hydrocarbons are studied. The D-6h point group symmetry of the members of these series have made them natural objects of numerous past studies. The D-6h total resonant sextet (TRS) one-isomer series among all benzenoid hydrocarbons of the same size has the maximum number of Clar resonant sextets, bay regions, and Kekue resonance structures. (C) 2002 Elsevier Science B.V. All rights reserved.
While reviewing aspects of our topological paradigm and the benchmark role played by the benzenoid polyradicals shaped like equilateral triangles, the topological properties of the reactive polyradicals and their stab...
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While reviewing aspects of our topological paradigm and the benchmark role played by the benzenoid polyradicals shaped like equilateral triangles, the topological properties of the reactive polyradicals and their stable associated leapfrog total-resonant-sextet benzenoids are studied. Copyright (C) 2001 John Wiley Sons, Ltd.
The important concepts of a formula periodic table set, aufbau principle, elementary substructures, excised internal structure/circumscribing algorithm, leapfrog algorithm, and hexagonal-to-pentagonal ring contraction...
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The important concepts of a formula periodic table set, aufbau principle, elementary substructures, excised internal structure/circumscribing algorithm, leapfrog algorithm, and hexagonal-to-pentagonal ring contraction algorithm will be reviewed. These concepts have been instrumental in organizing polyhex/polypent systems from benzenoid hydrocarbons to fullerene carbons. Some recent experimental verification of our prior predictions in this work will be noted.
The important concepts of a formula periodic table set, aufbau principle, elementary substructures, excised internal structure/circumscribing algorithm, leapfrog algorithm, and hexagonal-to-pentagonal ring contraction...
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The important concepts of a formula periodic table set, aufbau principle, elementary substructures, excised internal structure/circumscribing algorithm, leapfrog algorithm, and hexagonal-to-pentagonal ring contraction algorithm will be reviewed. These concepts have been instrumental in organizing polyhex/polypent systems from benzenoid hydrocarbons to fullerene carbons. Some recent experimental verification of our prior predictions in this work will be noted.
The author considers a reparameterized version of the Bayesian ordinal cumulative link regression model as a tool for exploring relationships between covariates and "cutpoint" parameters. The use of this par...
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The author considers a reparameterized version of the Bayesian ordinal cumulative link regression model as a tool for exploring relationships between covariates and "cutpoint" parameters. The use of this parameterization allows one to fit models using the leapfrog hybrid Monte Carlo method, and to bypass latent variable data augmentation and the slow convergence of the cutpoints which it usually entails. The proposed Gibbs sampler is not model specific and can be easily modified to handle different link functions. The approach is illustrated by considering data from a pediatric radiology study.
The "leapfrog" hybrid Monte Carlo algorithm is a simple and effective MCMC method for fitting Bayesian generalized linear models with canonical link. The algorithm leads to large trajectories over the poster...
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The "leapfrog" hybrid Monte Carlo algorithm is a simple and effective MCMC method for fitting Bayesian generalized linear models with canonical link. The algorithm leads to large trajectories over the posterior and a rapidly mixing Markov chain, having superior performance over conventional methods in difficult problems like logistic regression with quasicomplete separation. This method offers a very attractive solution to this common problem, providing a method for identifying datasets that are quasicomplete separated, and for identifying the covariates that are at the root of the problem. The method is also quite successful in fitting generalized linear models in which the link function is extended to include a feedforward neural network. With a large number of hidden units, however, or when the dataset becomes large, the computations required in calculating the gradient in each trajectory can become very demanding. In this case, it is best to mix the algorithm with multivariate random walk Metropolis-Hastings. However, this entails very little additional programming work.
A study is made of four algorithms which integrate the rotational equations of motion for rigid linear molecules. They are leapfrog algorithms in the sense that the quantities saved between time steps are the on-step ...
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A study is made of four algorithms which integrate the rotational equations of motion for rigid linear molecules. They are leapfrog algorithms in the sense that the quantities saved between time steps are the on-step orientation and the mid-step angular velocity. Thermostatted versions of the algorithms as well as conventional energy-conserving versions are described. The algorithms are extensively tested in simulations of liquid nitrogen, the aim being to study the effect of increased time steps on a range of measured properties. The most successful algorithm, based on applying a length constraint to the axis vector, shows remarkable stability and can be used with very large time steps.
A new implicit rotational integrator for the orientation of rigid molecules is introduced, and compared with an existing explicit integrator. Both algorithms are categorised as leapfrogs since the quantities saved bet...
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A new implicit rotational integrator for the orientation of rigid molecules is introduced, and compared with an existing explicit integrator. Both algorithms are categorised as leapfrogs since the quantities saved between time steps are on the on-step orientation and the mid-step angular momentum. Orientations may be expressed in terms of principal axis vectors or, as in the implementations used here, quaternions. Thermostatted versions of the algorithms as well as conventional energy-conserving versions are described. The algorithms are extensively tested in simulations of liquid water, the aim being to study the effect of increased time steps on a range of measured properties. The implicit algorithm is superior to the explicit algorithm, and can be used with time steps up to 3 fs with energy-conserving dynamics. When thermostatted, it may be used with time steps up to at least 6 fs.
The paper presents a molecular dynamics C-language program suitable for mixtures of mono-atomic molecules of different types include in a cuboid box with periodic boundary conditions. The molecules mutually interact w...
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The paper presents a molecular dynamics C-language program suitable for mixtures of mono-atomic molecules of different types include in a cuboid box with periodic boundary conditions. The molecules mutually interact with the short-range Lennard-Jones potential. To solve the Newtonian equations of motion the leapfrog scheme is applied. Neighbours of a particular molecule are searched using the link-cell method. The program has been developed for microcomputers/workstations so that it incorporates the sequential algorithm optimized in respect with CPU-time.
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