Solution: How to compare 'atomic' densities in different parts of the molecule.

Posted by Valera Veryazov on February 18, 2011 at 16:19:05:

Problem: we want to compare 'local' density on atom A and A' in the molecule.
Grid_it can compute density for the molecule, but it is not obvious - how to visualize the difference between two atoms.

Solution:
keyword GORI (Grid ORIgin) allows to set up coordinates for lower left corner of a cube, and 3 vectors.
Assuming that atom A has coordinates 0 0 0, and A' has coordinates 3.5 0 0
we make construct the following input:

&GATEWAY
..
>>copy $CurrDir/$Project.ScfOrb INPORB
&GRID_IT
GORI
-2 -2 -2 // the starting point for grid
4 0 0 // vectors
0 4 0
0 0 4
Npoint
20 20 20 // quality of grid
total // compute total density
Orange
10 20 // to avoid calculations for orbitals

In this case atom A is in the center of cube.
now repeat the calculation, changing the corner to 1.5 -2 -2 (so, atom A' is in the center).

and finally, use molcas gv -a -1.0 A.grid Aprime.grid
to visualize the density difference..

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Comments:
: Problem: we want to compare 'local' density on atom A and A' in the molecule. : Grid_it can compute density for the molecule, but it is not obvious - how to visualize the difference between two atoms. : Solution: : keyword GORI (Grid ORIgin) allows to set up coordinates for lower left corner of a cube, and 3 vectors. : Assuming that atom A has coordinates 0 0 0, and A' has coordinates 3.5 0 0 : we make construct the following input: : &GATEWAY : .. : >>copy $CurrDir/$Project.ScfOrb INPORB : &GRID_IT : GORI : -2 -2 -2 // the starting point for grid : 4 0 0 // vectors : 0 4 0 : 0 0 4 : Npoint : 20 20 20 // quality of grid : total // compute total density : Orange : 10 20 // to avoid calculations for orbitals : In this case atom A is in the center of cube. : now repeat the calculation, changing the corner to 1.5 -2 -2 (so, atom A' is in the center). : and finally, use molcas gv -a -1.0 A.grid Aprime.grid : to visualize the density difference..

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