Quaternionic

These various techniques were recently applied to molecular simulations [11, 20]. Both of these articles used the rotation matrix formulation, together with either the explicit reduction-based integrator or the SHAKE method to preserve orthogonality directly. In numerical experiments with realistic model problems, both of these symplectic schemes were shown to exhibit vastly superior long term stability and accuracy (measured in terms of energy error) compared to quaternionic schemes. 

The quaternions obey coupled differential equations involving the angular velocities tJi, tbody frame (i.e. tJi represents the angular velocity about the first axis of inertia, etc.). These differential equations take the form... 

A Hamiltonian version of the quaternionic description is also possible by viewing the quaternions as a set of generalized coordinates, introducing those variables into the rigid body Lagrangian (1), and finally determining the canonical momenta through the formula... 

Thus we find that the choice of quaternion variables introduces barriers to efficient symplectic-reversible discretization, typically forcing us to use some off-the-shelf explicit numerical integrator for general systems such as a Runge-Kutta or predictor-corrector method. 

Observe that, in principle, it is possible to introduce quaternions in the solution of the free rotational part of a Hamiltonian splitting, although there is no compelling reason to do so, since the rotation matrix is usually a more natural coordinatization in which to describe interbody force laws. 

These experiments confirm observations in the recent articles [20] and [11] symplectic methods easily outperform more traditional quaternionic integration methods in long term rigid body simulations. 

First of all, one needs to choose the local coordinate frame of a molecule and position it in space. Figure 2a shows the global coordinate frame xyz and the local frame x y z bound with the molecule. The origin of the local frame coincides with the first atom. Its three Cartesian coordinates are included in the whole set and are varied directly by integrators and minimizers, like any other independent variable. The angular orientation of the local frame is determined by a quaternion. The principles of application of quaternions in mechanics are beyond this book they are explained in detail in well-known standard texts... 

Theobald, D. L. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallogr. 2005, A61, 478 80. 

The unit vector n may be taken to lie on the surface of a sphere and the angles a may be chosen from a set Q of angles. For instance, for a given a, the set of rotations may be taken to be = a, —a. This rule satisfies detailed balance. Also, a may be chosen uniformly from the set Q = a 0 < a < 71. Other rotation rules can be constructed. The rotation operation can also be carried out using quaternions [13]. The collision rule is illustrated in Fig. 1 for two particles. From this figure it is clear that multiparticle collisions change both the directions and magnitudes of the velocities of the particles. 

The group Sp(n) consists of n x n matrices with quaternion entries such that the inverse is the conjugate transpose... 

The generation of invariants in the Lorentz transformation of four-vectors has been interpreted to mean that the transformation is equivalent to a rotation. The most general rotation of a four-vector, defined as the quaternion q = w + ix + jy + kz is given by [39]... 

The book contains very little original material, but reviews a fair amount of forgotten results that point to new lines of enquiry. Concepts such as quaternions, Bessel functions, Lie groups, Hamilton-Jacobi theory, solitons, Rydberg atoms, spherical waves and others, not commonly emphasized in chemical discussion, acquire new importance. To prepare the ground, the... 

The second term on the right-hand side of the equation gives for point nuclei directly the one-electron spin-orhit operator (2) of the Breit-Pauli Hamiltonian and can he eliminated to give a spin-free equation that becomes equivalent to the Schrddinger equation in the non-relativistic limit. In a quaternion formulation of the Dirac equation the elimination becomes particularly simple. The algebra of the quaternion units is that of the Pauli spin matrices... 

In the quaternion modified Dirac equation the spin-free equation is thereby obtained simply by deleting the quaternion imaginary parts. For further details, the reader is referred to Ref. [13]. 

Table 4. The isotropic indirect spin-spin coupling constant of calculated at various levels of theory. LL refers to the Levy-Leblond Hamiltonian, std refers to a full relativistic calculation using restricted (RKB) or unrestricted (UKB) kinetic balance, spf refers to calculations based on a spin-free relativistic Hamiltonian. Columns F, G and whether quaternion imaginary parts are deleted (0) or not (1) from the regular Fock matrix F prior to one-index transformation, from the two-electron Fock matrix G...

From the above discussion it becomes clear that in order to eliminate the spin-orbit interaction in four-component relativistic calculations of magnetic properties one must delete the quaternion imaginary parts from the regular Fock matrix and not from other quantities appearing in the response function (35). It is also possible to delete all spin interactions from magnetic properties, but this requires the use of the Sternheim approximation [57,73], that is calculating the diamagnetic contribution as an expectation value. 

We then turn to the question of how to eliminate the spin-orbit interaction in four-component relativistic calculations. This allows the assessment of spin-orbit effects on molecular properties within the framework of a single theory. In a previous publication [13], we have shown how the spin-orbit interaction can be eliminated in four-component relativistic calculations of spectroscopic properties by deleting the quaternion imaginary parts of matrix representations of the quaternion modified Dirac equation. We show in this chapter how the application of the same procedure to second-order electric properties takes out spin-forbidden transitions in the spectrum of the mercury atom. Second-order magnetic properties require more care since the straightforward application of the above procedure will extinguish all spin interactions. After careful analysis on how to proceed we... 

The hyper-Kahler structure is a quaternionic version of the Kahler structure. However, there is no good definition of the integrability (i.e. the existence of local charts) for the almost hyper-complex structure. Hence we generalize the second equivalent dehnition explained in above. 

The hermitian metric and the quaternion module structure on M descends to Mp. In particular, M " is a hyper-Kahler manifold. There is a natural action on M " of a Lie group Ur(F) = rifcU(Ffc). This action preserves the hyper-Kahler structure. The corresponding hyper-Kahler moment map is p o o where i is the inclusion M " C M, /r is the hyper-Kahler moment map for U(F)-action on M, and p is the orthogonal projection to 0 u Vk) in u(F). We denote this hyper-Kahler moment map also by p = (/ri, /T2, / s)- This increases the flexibility of the choice of parameters. Take = (Co> Cn > Cn) ( = 1) 2, 3) such that (I is a scalar matrix in u(14)- Then we can consider a hyper-Kahler quotient... 

Salomon, Y. and Avnir, D. (1999) Continuous symmetry measures Finding the closest C2-symmetric object or closest reflection-symmetric object using unit quaternions. J. Comput. Chem. 20, 772-780. 

Fig. 1. Computer simulations of four selective excitation pulses. (Top) Pulse shapes. From left to right 90° rectangular pulse, 270° Gaussian truncated at 2.5%, Quaternion cascade Q, and E-BURP-1. The vertical axis shows the relative rf amplitudes, whereas the horizontal axis shows the time. (Middle) Trajectories of Cartesian operators in the rotating frame...

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