AFIRサンプル

Part designation for random structure generation

Part designation for random structure generation

The terms "part" and "fragment" are used in different meanings in this manual (the term "fragment" means the fragment to which the artificial force is applied by the AFIR function). Parts can be specified in the coordinate section as follows:

C        0.000000    0.000000   -0.542432   1
O        0.000000    0.000000    0.689131   1
C        0.000000    0.449088    0.000000   2
C        1.229479   -0.074689    0.000000   2
O       -1.202903   -0.246241    0.000000   2
H       -0.199138    1.513645    0.000000   2
H        1.411363   -1.146198    0.000000   2
H        2.098519    0.571041    0.000000   2
H       -1.064389   -1.214959    0.000000   2
H        0.000000    0.933503   -1.129226   1
H        0.000000   -0.933503   -1.129226   1

In this example, part-1 is formaldehyde and part-2 is vinyl-alcohol. The part number should start from 1 and should be assigned to different parts. In random geometry generation, all parts are randomly distributed, but atoms without part designation are put at the original position (atoms without part designation are set as part-0). For example, formaldehyde is randomly distributed around vinyl-alcohol with the following input.

C        0.000000    0.000000   -0.542432   1
O        0.000000    0.000000    0.689131   1
C        0.000000    0.449088    0.000000
C        1.229479   -0.074689    0.000000
O       -1.202903   -0.246241    0.000000
H       -0.199138    1.513645    0.000000
H        1.411363   -1.146198    0.000000
H        2.098519    0.571041    0.000000
H       -1.064389   -1.214959    0.000000
H        0.000000    0.933503   -1.129226   1
H        0.000000   -0.933503   -1.129226   1

The part designation has the other effect when it is used together with the NoBondRearrange keyword; the bond connectivity in the given initial structure is checked only within each part. In addition, the part designation is necessary when Opt=Fragment, Opt=Fragment=Independent, Read Part-n, SC=InterOnly, or SC=IntraOnly option is used.

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Updated At:Feb. 13, 2018, 6:17 p.m.

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