VNL files

[gump]

Hi,everybody,with the  value and corresponding atom's coordinate, how to create the files so as to view at VNL or other tools?
such as:
# Index  Element  x (Ang)  y (Ang)  z (Ang)   Population
      0       C      6.10     5.00     5.54            1.23333
      1       C      8.94     5.00     5.54            1.12
      2       C     10.36     5.00     5.54            0.89
      3       C     13.21     5.00     5.54            1.2
      .............
Thanks a lot.

[zh]

If it is a molecule,  you may create a XYZ file format.  The 'xyz' format  consists of:
<number of atoms>
comment line
atom_symbol-1  x-coord1 y-coord1 z-coord1
atom_symbol-2  x-coord2 y-coord1 z-coord2
...
atom_symbol-n  x-coordn y-coordn z-coordn

The details can be found here: http://openbabel.org/wiki/XYZ_(format)
 
An example for methane molecule:

5
methane molecule (comment)
C     0.000000     0.000000     0.000000
H     0.000000     0.000000     1.089000
H     1.026719     0.000000    -0.363000
H    -0.513360    -0.889165    -0.363000
H    -0.513360     0.889165    -0.363000

The coordinates of all atoms must be given by cartesian coordinates (in Ångströms) . After preparing the XYZ file format for your molecule, you may import it into VNL by the "Result Browser" module and then visualize it by the "Nanoscope" module.

If it is a bulk system, you should also know the lattice parameters and lattice type. The crystal structure of a bulk can be created and visualized by the "Bulk Builder" module of VNL.

[gump]

Hi,Zh,thanks for your reply.according to your answer, I just can plot the molecular's structure. However, my question is how to view the calculation result with the atom's coordinate.Maybe Mathlab can be used, but I prefer to show all the atom with corresponding caculation vale at the schematic at the same time, just as use VNL to see the ElectronDensity.

[zh]

Please make your question more clear.  What are you calculated results? Are they the Mulliken charges of atoms? If the calculation results you have mentioned are the Mulliken population,  the problem is that it is hard to visualize the Mulliken charge of each  atom in the manner of contour or iso-surface plot of electron density.  Definitely, the distance between two nearest neighboring atoms is  much larger than the one between two points in the contour or iso-surface plot of electron density.  Then it is obvious that the visualization of Mulliken charge of atoms in the contour or iso-surface plot will be very awful. It is also meaningless.  You may try the following better way:
i) Use VNL to visualize the structure of the system you have calculated;
ii) Export  the graph for your structure from VNL, e.g.,  screen capture or the functional "Camera---->Export View" in the VNL.
iii) Copy this graph to MS powerpoint and manually add text with the Mulliken charge to each atom.
If there are too many atoms in your structure or in the 3rd step mentioned above, it is indeed terrible.

Since you think Matlab could visualize your calculation results, please try it by yourself.

[gump]

Zh,Thanks a lot.