10 - Write density in gOpenMol cube format

This option allows one to save a density in a so-called Cube format that can be then read in by gOpenMol to do nice pictures of isodensity surfaces. For extra convenience, the density can only be saved that fits inside a box. The latter may run across the cells. In addition, atomic positions inside the same or bigger box can also be saved (in the xyz format), so that gOpenMol would be able to show atoms alongside the density surfaces.

The menu that opens is this:

............MENU for gOpenMol writer .................

......... Change these parameters if necessary:.......

1. The box center is at: ( 0.00000, 0.00000, 0.00000)

    Directions of the box sides are fixed along:

         1 < 1.00000, 0.00000, 0.00000 >

         2 < 0.00000, 1.00000, 0.00000 >

         3 < 0.00000, 0.00000, 1.00000 >

2. Lengths of the box sides (in A) are: 1.00000 1.00000 1.00000

   >>>> the starting point (corner) of the box is at -0.50 -0.50 -0.50

3. Box extension for xyz-file: [ 0.00000 0.00000 0.00000]

4. The grid in the box in 3 directions: 1 1 1

   >>>> total number of grid points = 1

   >>>> steps along 3 directions are 1.00000 1.00000 1.00000

5. Scan the box and integrate the charge (reference only):

W. Write the cube-format file for gOpenMol

---- G e n e r a l  s e t t i n g s -----

An. Coordinates are specified in: <Angstroms>

Co. Show current atomic positions in fractional/Cartesian

cT. Centre of a triangle of points/atoms

mD. Middle distance between two points/atoms

XY. Atoms in the XYZ box: constrained by the density box

--- L e a v e  t h e   m e n u -------

Q. Return to the previous menu

---> Choose the item and press ENTER:

The box for the density is specified in options 1 and 2, and its possible extension for the atomic positions - in 3 (this option can be disabled by XY). The grid inside the box for the density interpolation is given in 4. Note that the directions of the box faces are fixed along the Cartesian axes.

To check how much electron charge is inside the box, run 5. The actual calculation is performed in W, after which the two files are saved:

• gOpenMol.cube - the Cube file with the density on the grid inside the box
• gOpenMol.xyz - atomic poisitons inside the same or larger box

Under the settings there are usual options An (how coordinates are specified) and Co (show atomic positions). In addition to those, two options cT and mD serve as a mini-calculator that may be sometimes useful to find the best position for the box centre in 1.