Coordinate system

About: Coordinate system is a research topic. Over the lifetime, 22675 publications have been published within this topic receiving 269822 citations. The topic is also known as: system of coordinates.

Using redundant internal coordinates to optimize equilibrium geometries and transition states

Abstract: A redundant internal coordinate system for optimizing molecular geometries is constructed from all bonds, all valence angles between bonded atoms, and all dihedral angles between bonded atoms. Redundancies are removed by using the generalized inverse of the G matrix; constraints can be added by using an appropriate projector. For minimizations, redundant internal coordinates provide substantial improvements in optimization efficiency over Cartesian and nonredundant internal coordinates, especially for flexible and polycyclic systems. Transition structure searches are also improved when redundant coordinates are used and when the initial steps are guided by the quadratic synchronous transit approach. © 1996 by John Wiley & Sons, Inc.

Animating rotation with quaternion curves

Abstract: Solid bodies roll and tumble through space. In computer animation, so do cameras. The rotations of these objects are best described using a four coordinate system, quaternions, as is shown in this paper. Of all quaternions, those on the unit sphere are most suitable for animation, but the question of how to construct curves on spheres has not been much explored. This paper gives one answer by presenting a new kind of spline curve, created on a sphere, suitable for smoothly in-betweening (i.e. interpolating) sequences of arbitrary rotations. Both theory and experiment show that the motion generated is smooth and natural, without quirks found in earlier methods.

General methods for geometry and wave function optimization

Abstract: A combination of variable-metric second-order update schemes and the DIIS method for both geometry and Hartree-Fock wave function optimization is described. A recursive procedure for updating large Hessians is presented. The performances of geometry optimizations with respect to the choice of the coordinate system (symmetry-adapted, internal, and Cartesian coordinates), the initial nuclear Hessian, and the optimization procedure have been investigated by a series of benchmark molecules. Formulas for the generation of initial nuclear Hessians are given

Deformable templates using large deformation kinematics

Abstract: A general automatic approach is presented for accommodating local shape variation when mapping a two-dimensional (2-D) or three-dimensional (3-D) template image into alignment with a topologically similar target image. Local shape variability is accommodated by applying a vector-field transformation to the underlying material coordinate system of the template while constraining the transformation to be smooth (globally positive definite Jacobian). Smoothness is guaranteed without specifically penalizing large-magnitude deformations of small subvolumes by constraining the transformation on the basis of a Stokesian limit of the fluid-dynamical Navier-Stokes equations. This differs fundamentally from quadratic penalty methods, such as those based on linearized elasticity or thin-plate splines, in that stress restraining the motion relaxes over time allowing large-magnitude deformations. Kinematic nonlinearities are inherently necessary to maintain continuity of structures during large-magnitude deformations, and are included in all results. After initial global registration, final mappings are obtained by numerically solving a set of nonlinear partial differential equations associated with the constrained optimization problem. Automatic regridding is performed by propagating templates as the nonlinear transformations evaluated on a finite lattice become singular. Application of the method to intersubject registration of neuroanatomical structures illustrates the ability to account for local anatomical variability.

STRUCTURE TIDY– a computer program to standardize crystal structure data

Abstract: A computer program has been written for the purpose of standardizing crystal structure data according to rules formulated by Parthe & Gelato [Acta Cryst. (1984). A40, 169–183]. From input consisting of space-group symbol, unit-cell parameters and positional coordinates of the atoms, a reordered and renumbered list of standardized atom coordinates is obtained. The space group is now in the standard setting and the cell is reduced if applicable. The origin and the orientation of the coordinate system have been chosen in such a way as to minimize the standardization parameter Γ. A second standardization parameter, based on the position of the centre of gravity of the atoms in the asymmetric unit, is introduced. The Wyckoff sequence, obtained from the standardized structure data, can be used to recognize structures which are isopointal. An example of the application of STRUCTURE TIDY is given.