This module reads a Mopac output file and generates a Chemistry Pyramid of the selected reaction coordinate. It also can generate all reaction coordinates as an animated sequence. The connectivity of each reaction coordinate is determined by a vdw radius test or, if the keyword "BONDS" was included in the input deck, by the bond order information of the output file. Mopac versions 5, 6 and 93 are supported.



Port: Filename
Type: Text
Filename of Mopac output 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: Simulate?
Type: Option Menu
Menu Item: No
Menu Item: Yes
View all reaction coordinates as an animated sequence.

Port: Rxn Coord
Type: Dial
View the selected reaction coordinate when "Simulate" is off.


Port: Molecule
Type: Pyramid
Constraints: n-layer.
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.



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© The Numerical Algorithms Group Ltd, Oxford UK. 1996