EyeMopacVib

DESCRIPTION

This module reads a Mopac output force file and generates the vibration of the selected eigenvalue. Each step in the vibration is a Chemistry Pyramid. The connectivity of the resting molecule is determined by a vdw radius test and does not change during the vibration. In order for the module to determine the correct number of eigenvalues, the Mopac input file should contain both the keywords FORCE and LARGE. Mopac versions 5, 6 and 93 are supported.

INPUTS

WIDGETS

Port: Filename
Type: Text
Filename of Mopac output force file.

Port: Element
Type: Text
Filename of reference chemical data. This file includes the following properties for all atoms : atom number, covalent radius, Van Der Waals radius, maximum number of bonds.

Port: Cycles
Type: Dial
The selected cycles of vibrations.

Port: Increments
Type: Dial
Number of increments between resting molecule and displacement.

Port: Eigenvalue
Type: Dial
The selected eigenvalue to be analyzed.

Port: Coordinate Analysis
Type: Option Menu
Menu Item: Normal
Menu Item: Mass-weighted
Menu Item: Eigenvectors
The selected vibration mode.

Port: Multiplier
Type: Dial
Enhances or dampens the displacement.

OUTPUTS

Port: Molecule
Type: Pyramid
Constraints: n-layer.
optional-baseLat.
n-D compression.
n-compression type.
The output is a Chemical-based pyramid. This pyramid has 2 layers of lattices. The base layer (0) contains the bond order and 2 atom numbers that comprise the bond. The next layer (1), contains the connectivity information, atom data, and the cartesian coordinates. Eact atom has 4 data variables: ID, element number vdw radius, and colour number.

PROBLEMS