Beyond Classical Physics by Mark A. Cunningham

Author:Mark A. Cunningham
Language: eng
Format: epub, pdf
Publisher: Springer International Publishing, Cham

As we begin our studies into the nature of the chemical bond, we will make use of numerical simulation as a means of developing an understanding of the fundamental properties of chemical systems. To the extent that the simulations accurately reflect the actual properties of the systems, this affords us the opportunity to conduct studies that would be difficult otherwise.5 As with other venues in physics, it is crucial to tie these calculations to experimental data to understand any systematic problems.

Using simulations, we can arrange to move the atoms in the simulation in any particular fashion that we desire and conduct constrained optimizations to study the energy dependence associated with different geometries. A particular complexity arises from the sheer size of the parameter space; there are many degrees of freedom in any collection of atoms but simulation enables us to vary them one at a time. The mechanism within NWChem for constrained optimizations relies on the Z-matrix. The geometry defined by the Z-matrix is illustrated in figure 7.4.

Figure 7.4An alternative way to specify atom positions is the Z-matrix. The Z-matrix defines the atom distances, angles between three adjacent atoms (θ 1, θ 2) and dihedral angles (ϕ) defined as the angle between the two planes formed by four atoms.

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