Jacoby

Another reason why mass-scaled coordinates are useful is that they simplify the transfomiation to the Jacobi coordinates that are associated with the products AB + C. If we define. S as the distance from C to the centre of mass of AB, and s as the AB distance, mass scaling is accomplished via... 

We have expressed P in tenns of Jacobi coordinates as this is the coordmate system in which the vibrations and translations are separable. The separation does not occur in hyperspherical coordinates except at p = oq, so it is necessary to interrelate coordinate systems to complete the calculations. There are several approaches for doing this. One way is to project the hyperspherical solution onto Jacobi s before perfonning the asymptotic analysis, i.e. 

The classical action, or solution of the Flamilton-Jacobi equation V S (/ ) = k (/ ), for relative motion under... 

The vector potential is derived in hyperspherical coordinates following the procedure in [54], where the connections between Jacobi and the hyperspherical coordinates have been considered as below (see [67])... 

It would be convenient for obtaining the expressions of the gradient of the hyperangle Jacobi coordinates to inboduce the physical region of the conical intersection in the following manner ... 

The gradient of v l with respect to Jacobi coordinates (the vector potential) considering the physical region of the conical intersection, is obtained by using Eqs. (C.6-C.8) and after some simplification ( ) we get,... 

Section VI shows the power of the modulus-phase formalism and is included in this chapter partly for methodological purposes. In this formalism, the equations of continuity and the Hamilton-Jacobi equations can be naturally derived in both the nonrelativistic and the relativistic (Dirac) theories of the electron. It is shown that in the four-component (spinor) theory of electrons, the two exha components in the spinor wave function will have only a minor effect on the topological phase, provided certain conditions are met (nearly nonrelativistic velocities and external fields that are not excessively large). 

The aim of this section is to show how the modulus-phase formulation, which is the keytone of our chapter, leads very directly to the equation of continuity and to the Hamilton-Jacobi equation. These equations have formed the basic building blocks in Bohm s formulation of non-relativistic quantum mechanics [318]. We begin with the nonrelativistic case, for which the simplicity of the derivation has... 

Again, the summation convention is used, unless we state otherwise. As will appear below, the same strategy can be used upon tbe Dirac Lagrangean density to obtain the continuity equation and Hamilton-Jacobi equation in the modulus-phase representation. 

Variationally deriving with respect to a leads to the Hamilton-Jacobi equation... 

The result of interest in the expressions shown in Eqs. (160) and (162) is that, although one has obtained expressions that include corrections to the nonrelativistic case, given in Eqs. (141) and (142), still both the continuity equations and the Hamilton-Jacobi equations involve each spinor component separately. To the present approximation, there is no mixing between the components. 

The terms before the square brackets give the nonrelativistic part of the Hamilton-Jacobi equation and the continuity equation shown in Eqs. (142) and (141), while the term with the squaie brackets contribute relativistic corrections. All terms from are of the nonmixing type between components. There are further relativistic terms, to which we now turn. 

In Eq. (168), the first, magnetic-field term admixes different components of the spinors both in the continuity equation and in the Hamilton-Jacobi equation. However, with the z axis chosen as the direction of H, the magnetic-field temi does not contain phases and does not mix component amplitudes. Therefore, there is no contribution from this term in the continuity equations and no amplitude mixing in the Hamilton-Jacobi equations. The second, electric-field term is nondiagonal between the large and small spinor components, which fact reduces its magnitude by a further small factor of 0 particle velocityjc). This term is therefore of the same small order 0(l/c ), as those terms in the second line in Eqs. (164) and (166) that refer to the upper components. 

This part of our chapter has shown that the use of the two variables, moduli and phases, leads in a direct way to the derivation of the continuity and Hamilton-Jacobi equations for both scalar and spinor wave functions. For the latter case, we show that the differential equations for each spinor component are (in the nearly nomelativistic limit) approximately decoupled. Because of this decoupling (mutual independence) it appears that the reciprocal relations between phases and moduli derived in Section III hold to a good approximation for each spinor component separately, too. For velocities and electromagnetic field strengths that ate nomrally below the relativistic scale, the Berry phase obtained from the Schrddinger equation (for scalar fields) will not be altered by consideration of the Dirac equation. 

Consider a polyatomic system consisting of N nuclei (where > 3) and elecbons. In the absence of any external fields, we can rigorously separate the motion of the center of mass G of the whole system as its potential energy function V is independent of the position vector of G (rg) in a laboratory-fixed frame with origin O. This separation introduces, besides rg, the Jacobi vectors R = (R , , R , .. , Rxk -1) = (fi I "21 I fvji) fot nuclei and electrons,... 

In Eqs. (5) and (6), M is the total mass of the nuclei and is the mass of one electron. By using Eq. (2), the system s internal kinetic energy operator is given in terms of the mass-scaled Jacobi vectors by... 

Figure 1. Jacobi vectors for a three-nuclei, four-electron system. The nuclei are Pi, P2, P3, and the electrons are ei, 02, 63, 64,...

Consider a triatomic system with the three nuclei labeled A, Ap, and Ay. Let the arrangement channel -1- A A be called the X arrangement channel, where Xvk is a cyclic permutation of apy. Let Rx,r be the Jacobi vectors associated with this arrangement channel, where r is the vector from A to and the vector from the center of mass of AyA to A . Let R i, rx be the corresponding mass-scaled Jacobi coordinates defined by... 

Figure 1, Coordinates used for describing the dynamics of a) H -I- H2 (6) NOCl, (c) butatriene, (a), (b) Are Jacobi coordinates, where and are the dissociative and vibrational coordinates, respectively, (c) Shows the two most important normal mode coordinates, Qs and Q a, which are the torsional and central C—C bond stretch, respectively.

Schlitter et al., 1993] Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. Targeted molecular dynamics simulation of conformational change - application to the t <- r transition in insulin. Molecular Simulation. 10 (1993) 291-308... 

Caustics The above formulae can only be valid as long as Eq. (9) describes a unique map in position space. Indeed, the underlying Hamilton-Jacobi theory is only valid for the time interval [0,T] if at all instances t [0, T] the map (QOi4o) —> Q t, qo,qo) is one-to-one, [6, 19, 1], i.e., as long as trajectories with different initial data do not cross each other in position space (cf. Fig. 1). Consequently, the detection of any caustics in a numerical simulation is only possible if we propagate a trajectory bundle with different initial values. Thus, in pure QCMD, Eq. (11), caustics cannot be detected. 

Using Jacobi coordinates and reduced masses, the Hydrogen-Chlorine interaction is modeled quantum mechanically whereas the Ar-HCl interaction classically. The potentials used, initial data and additional computational parameters are listed in detail in [16]. 

Fig. 2. Collinear ArHCl-systera with the Jacobi-coordinates used.

The Jacobi method is probably the simplest diagonalization method that is well adapted to computers. It is limited to real symmetric matrices, but that is the only kind we will get by the formula for generating simple Huckel molecular orbital method (HMO) matrices just described. A rotation matrix is defined, for example. 

Thus the Jacobi procedure, by making many rotations of the elements of the operand matrix, ultimately arrives at the operator matrix that diagonalizes it. Mathematically, we can imagine one operator matr ix that would have diagonalized the operand matr ix R, all in one step... 

Having filled in all the elements of the F matr ix, we use an iterative diagonaliza-tion procedure to obtain the eigenvalues by the Jacobi method (Chapter 6) or its equivalent. Initially, the requisite electron densities are not known. They must be given arbitrary values at the start, usually taken from a Huckel calculation. Electron densities are improved as the iterations proceed. Note that the entire diagonalization is carried out many times in a typical problem, and that many iterative matrix multiplications are carried out in each diagonalization. Jensen (1999) refers to an iterative procedure that contains an iterative procedure within it as a macroiteration. The term is descriptive and we shall use it from time to time. 

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