- Research Article
3
- 10.1016/s0378-4754(97)00091-8
Non-equilibrium molecular dynamics integrators using Maple
- Jan 01, 1998
- Mathematics and Computers in Simulation
- Debra J Searles + 2 more +2
Non-equilibrium molecular dynamics integrators using Maple
It is known, that i.r. of double point groups can be expressed in terms of Wigner functions. Using the projection method proposed by O. Barut and R. Raczka the appropriate basis of i.r. of double point groups within the harmonic oscillator space have been derived. The appropriate numeric and symbolic algebra programs have been constructed.
Non-equilibrium molecular dynamics integrators using Maple
Non-equilibrium molecular dynamics integrators using Maple
Kinetic Theory of Granular Gases
Granular gases are composed of macroscopic bodies kept in motion by an external energy source such as a violent shaking. The behaviour of such systems is quantitatively different from that of ordinary molecular gases: due to the size of the constituents, external fields have a stronger effect on the dynamics and, more importantly, the kinetic energy of the gas is no longer a conserved quantity. The key role of the inelasticity of collisions has been correctly appreciated for about fifteen years, and the ensuing consequences in terms of phase behaviour or transport properties studied in an increasing and now vast body of literature. The purpose of this book is to help the newcomer to the field in acquiring the essential theoretical tools together with some numerical techniques. As emphasized by the authors—who were among the pioneers in the domain— the content could be covered in a one semester course for advanced undergraduates, or it could be incorporated in a more general course dealing with the statistical mechanics of dissipative systems. The book is self-contained, clear, and avoids mathematical complications. In order to elucidate the main physical ideas, heuristic points of views are sometimes preferred to a more rigorous route that would lead to a longer discussion. The 28 chapters are short; they offer exercises and worked examples, solved at the end of the book. Each part is supplemented with a relevant foreword and a useful summary including take-home messages. The editorial work is of good quality, with very few typographical errors. In spite of the title, kinetic theory stricto sensu is not the crux of the matter covered. The authors discuss the consequences of the molecular chaos assumption both at the individual particle level and in terms of collective behaviour. The first part of the book addresses the mechanics of grain collisions. It is emphasized that considering the coefficient of restitution e —a central quantity governing the inelasticity of inter-grain encounters—as velocity independent is inconsistent with the mechanical point of view. An asymptotic expression for the impact velocity dependence of e is therefore derived for visco-elastic spheres. The important inelastic Boltzmann equation is introduced in part II and the associated velocity distribution characterized for a force-free medium (so-called free cooling regime). Transport processes can then be analyzed in part III at the single particle level, and part IV from a more macroscopic viewpoint. The corresponding Chapman–Enskog-like hydrodynamic approach is worked out in detail, in a clear fashion. Finally, the tendency of granular gases to develop instabilities is illustrated in part V where the hydrodynamic picture plays a pivotal role. This book clearly sets the stage. For the sake of simplicity, the authors have discarded some subtle points, such as the open questions underlying the hydrodynamic description (why include the temperature among the hydrodynamic modes, and what about the separation of space and time scales between kinetic and hydrodynamic excitations?). Such omissions are understandable. To a certain extent however, the scope of the book is centered on previous work by the authors, and I have a few regrets. Special emphasis is put on the (variable e) visco-elastic model, which enhances the technical difficulty of the presentation. On the other hand, the important physical effects including scaling laws, hydrodynamic behaviour and structure formation, can be understood in two steps, from the results derived within the much simpler constant e model, allowing subsequently $\varepsilon$ to depend on the granular temperature. The authors justify their choice with the inconsistency of the constant e route. The improvements brought by the visco-elastic model remain to be assessed, since the rotational degrees of freedom, discarded in the book, play an important role and require due consideration of both tangential and normal restitution coefficients, that are again velocity dependent. This seems to be the price of a consistent approach, which does not lend itself to much insight. In addition, the behaviour of driven systems is not addressed, whereas in the realm of granular media, force-free systems are the exception rather than the rule. The differences between constant e and visco-elastic models is presumably less pronounced in the driven case. Study of driven systems also reveals that the rheology of granular gases is intrinsically non-Newtonian, which is a key feature. Finally, the powerful direct simulation Monte Carlo technique is not described, whereas it is an important tool, particularly relevant for the physics of the Boltzmann equation, and straightforward to implement in its simplest version. N Brilliantov and T Poschel concentrate on the (equally relevant) molecular dynamics method instead. In conclusion, the book fills a gap in the field. The companion webpage from where molecular dynamics and symbolic algebra programs can be downloaded is also useful.
Read moreAnalytical SN solutions in heterogeneous slabs using symbolic algebra computer programs
Analytical SN solutions in heterogeneous slabs using symbolic algebra computer programs
POP, A Broad-Spectrum Programming Language, 1967–2002
Abstract. This paper discusses the POP-2 language and Multipop time-sharing system developed during the second half of the 1960s. POP-2's expressiveness spanned numeric and symbolic programming and supported experiments in logic of programming languages (by Boyer and Moore) and programming language concepts (for example, Michie's memoisation). The paper also discusses how the goals of POP-2 might be achieved in a successor language.
Read moreUse of a symbolic algebra program in NMR
Computer algebra (CA) on microcomputers may be used as a convenient tool to gain greater insight into the use and design of modern NMR pulse sequences and into their relation to the spin parameters. Some applications are demonstrated.
Read moreMaple for APPL
Maple is a computer algebra system and programming language that can be used for numerical computations, solving equations, manipulating symbolic expressions, plotting, and programming, just to name a few of the basics. APPL is, simply, a set of supplementary Maple commands and procedures that augments the existing computer algebra system. In effect, APPL takes the capabilities of Maple and turns it into a computer algebra system for computational probability. This chapter contains guidelines for using Maple, and discusses the Maple commands that are used in APPL programming. After reading this chapter, an APPL user will have the knowledge necessary to modify the APPL code to meet his or her particular needs. We will start with a discussion of basic numeric computation, then advance to defining variables, symbolic computations, functions, data types, solving equations, calculus and graphing. Then we will discuss the programming features of Maple that facilitate building the APPL language: loops, conditions, and procedures.
Read moreHigher-order equation-of-motion coupled-cluster methods.
The equation-of-motion coupled-cluster (EOM-CC) methods truncated after double, triple, or quadruple cluster and linear excitation operators (EOM-CCSD, EOM-CCSDT, and EOM-CCSDTQ) have been derived and implemented into parallel execution programs. They compute excitation energies, excited-state dipole moments, and transition moments of closed- and open-shell systems, taking advantage of spin, spatial (real Abelian), and permutation symmetries simultaneously and fully (within the spin-orbital formalisms). The related Lambda equation solvers for coupled-cluster (CC) methods through and up to connected quadruple excitation (CCSD, CCSDT, and CCSDTQ) have also been developed. These developments have been achieved, by virtue of the algebraic and symbolic manipulation program that automated the formula derivation and implementation altogether. The EOM-CC methods and CC Lambda equations introduce a class of second quantized ansatz with a de-excitation operator (Y), a number of excitation operators (X), and a physical (e.g., the Hamiltonian) operator (A), leading to the tensor contraction expressions that can be performed in the order of ((...((yx)x)...)x)a or ((...((ax)x)...)x)y at the minimal peak operation cost, where x, y, and a are basis-set representations (i.e., tensors) of the respective operators X, Y, and A. Any intermediate tensor resulting from either contraction order is shown to have at most six groups of permutable indices, and this knowledge is used to guide the computer-synthesized programs to fully exploit the permutation symmetry of any tensor to minimize the arithmetic and memory costs.
Read moreA simple approach to solve the time independent Schröedinger equation for 1D systems
A simple algebraic approach based on the well known angular momentum SU(2) algebra is presented to describe 1D systems for arbitrary potentials. The approach is based on the dimension increase of the 1D harmonic oscillator space through the addition of a scalar boson, keeping constant the total number of bosons. In this new space the realization of the coordinate and momentum correspond to components of the angular momentum algebra, which in turn define the coordinate and momentum representation bases. This remarkable result allows the Hamiltonian matrix representationto be expressed in terms of a diagonal matrix characterizing the potential we are considering. The solutions are obtained as an expansion of harmonic oscillator functions by purely algebraic means. As an example of our approach the Morse and asymmetric double Morse potentials are considered.
Read moreAN ALGEBRAIC APPROACH TO CALCULATE FRANCK-CONDON FACTORS
An algebraic approach based on unitary algebras to calculate Franck–Condon factors (FCF’s) is presented. The method is based on the unitary group approach, which consists in adding a scalar boson to the $$\nu $$-D harmonic oscillator space, taking advantage of the transformation brackets connecting the energy, coordinate and momentum representations. In this scheme the solutions are given in terms of an expansion of harmonic oscillator functions. In this way the overlaps are expressed in terms of simple scalar product of the eigenvectors. As a benchmark to illustrate our approach the case of two 1D-Morse potentials is presented. Discussions concerned with both non-Condon contributions and the harmonic limit are included. FCF’s involving the 1D-Morse and asymmetric double Morse potentials are also considered. As an application, the FCF’s involving the S–S stretching in the $$\hbox {S}_2\hbox {O}$$ molecule are described in terms of two Morse potentials.
Read moreCalculation of elementary diagrams using a Metropolis-like simulation method
A method for the evaluation of higher order elementary diagrams is proposed. It utilizes symbolic algebra programming and automatic code generation. The method is used to calculate elementary diagrams for hard spheres up to the fifth. The obtained values are fitted to suitable functions of interparticle distance. The resulting truncated density expansion is compared with recent values of the bridge function calculated directly from the simulated pair distribution function. The method can be straightforwardly extended to hard-body systems and their mixtures.
Read moreDamped second‐order Rayleigh‐Timoshenko beam vibration in space—an exact complex dynamic member stiffness matrix
A uniform linear beam in a uniform linear ambient medium is studied. The beam performs stationary harmonic damped nonsynchronous space vibration in simultaneous tension, torsion, bending and shear in the presence of a large static axial load. Hysteretic and viscous dampings of the beam material and ambient medium are considered. Generalized complex Koloušek functions are derived. A 12 × 12 complex symmetric stiffness matrix is established for a supported beam member excited at its ends by prescribed harmonic translations and rotations which have the same frequency but may be out of phase. This matrix allows for an exact analysis of nonproportionally damped built‐up beam structures, thus avoiding assumed mode shapes and lumped or consistent masses. A general notation is suggested. Numerical examples are given, including applications of the computer program SFVIBAT‐DAMP.
Read moreThe dependence on the mass number of the RMS radius and the oscillator spacing for a hyperon in a nucleus
The dependence on the mass number of the RMS radius and the oscillator spacing for a hyperon in a nucleus
Generalized uncertainty relations and long-time limits for quantum Brownian motion models.
We study the time evolution of the reduced Wigner function for a class of quantum Brownian motion models. We derive two generalized uncertainty relations. The first consists of a sharp lower bound on the uncertainty function, $U = (\Delta p)^2 (\Delta q)^2 $, after evolution for time $t$ in the presence of an environment. The second, a stronger and simpler result, consists of a lower bound at time $t$ on a modified uncertainty function, essentially the area enclosed by the $1-\sigma$ contour of the Wigner function. In both cases the minimizing initial state is a non-minimal Gaussian pure state. These generalized uncertainty relations supply a measure of the comparative size of quantum and thermal fluctuations. We prove two simple inequalites, relating uncertainty to von Neumann entropy, and the von Neumann entropy to linear entropy. We also prove some results on the long-time limit of the Wigner function for arbitrary initial states. For the harmonic oscillator the Wigner function for all initial states becomes a Gaussian at large times (often, but not always, a thermal state). We derive the explicit forms of the long-time limit for the free particle (which does not in general go to a Gaussian), and also for more general potentials in the approximation of high temperature.
Read moreWigner function of a quantum system with polynomial potential
The Moyal equation for the Wigner function was obtained under the assumption that the potential is an analytic function. The polynomial form of the potential is a natural approximation of the analytical potential with any necessary accuracy. The simplest quantum system with a second-order polynomial potential is a quantum harmonic oscillator. In this paper, for a quantum system with a polynomial potential of arbitrary order, explicit expressions are obtained for the matrix elements of the kernel operator in the basis of the eigenfunctions of the harmonic oscillator. Using the explicit representation for the kernel operator matrix elements, we construct the distributions of the Wigner function in the phase space for quantum systems with polynomial potentials. The connection of the modified Vlasov equation with the Moyal equation for the Wigner function is shown. Examples of effective numerical algorithms for finding Wigner functions with high accuracy are given.
Read moreCalculated Molecular Properties of Triangular Tribenzo and Perfluoro-Tribenzo Trimercuronin Macrocycles
Trimeric perfluoro-ortho-phenylene mercury(II) cluster is a prototypical example of a macrocyclic multidentate Lewis acid. In this study we report the electronic structure, the calculated absorption and vibrational spectra via all-electron scalar and spin-orbit relativistic DFT calculations for [Hg(o-C6H4)]3 (1), [Hg(o-C6F4)]3 (2), and the dimeric form of 2, ([Hg(o-C6F4)]3)2 (3). Due to the inclusion of the spin-orbit interaction, double point groups were used (D3h* and D3d*). The calculations suggest small paratropic ring currents at the center of 1 and being smaller for 2 due to the withdrawn properties of the perfluorated ligand. The luminescent properties of the solid state of 2 are well represented by the postulated model of dimer 3, which mimic the solid state, where the proposed mechanism involves a vibronically coupled emission process. The calculated lambda(absorption)max of 3 show an intense peak at 347 nm, which compares well with the reported band at 355 nm; also, the calculated lambda(emission)= 431 nm is close to the experimental value of 440 nm. Moreover, the calculated structural changes of the first excited state (3*) are reflected in the large value of the calculated Stoke shifts of 84 nm, which is in quite good agreement with the value of 85 nm extracted from the experimental data.
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