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Molcas grid viewer (grid_it) (Read 7297 times)
Gerrit-Jan Linker
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Molcas grid viewer (grid_it)
16.08.09 at 16:46:47
 
Molcas grid viewer (grid_it)
 
To view orbitals with the grid viewer you need to first calculate the grid. To do this just add the following input to your input file
&GRID_IT &End
End of Input

 
A grid file will be produced. You need to start molcas with the gv option to view the grid:
molcas gv project.grid
 
You can view differences between grid files by using the following command:
molcas gv -a -1.0 a.grid another.grid
(ps: -1.0 is the coefficient with which the second grid is added)
 
Press F3 to view all orbitals. Each orbital can be rotated individually by left clicking and dragging with the mouse.
 
Right clicking with the mouse shows the menu.
 
The orbitals are ordered in energy (highest to lowest). In the menu, in the edit orbitals menu, you can see which orbitals are listed, the orbital energies and occupation numbers.
 
There may be multiple grid files labeled project.a.grid, project.b.grid. Each contains a specific set of orbitals.
 
See also:
Grid Viewer
http://www.oraxcel.com/cgi-bin/yabb2/YaBB.pl?num=1209031939/0#0
 
Reference:
http://molcas.org/documentation/manual/node100.html
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« Last Edit: 16.06.14 at 07:02:44 by Gerrit-Jan Linker »  

Gerrit-Jan Linker
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Gerrit-Jan Linker
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Molcas grid viewer to view xyz files
Reply #1 - 10.10.09 at 23:04:52
 
Molcas grid viewer to view xyz files
 
You can use the molcas grid viewer to view ball stick diagrams of molecules. Use the following command line:
molcas gv myfile.xyz
 
In the xyz file put a atom on each line followed by the x, y and z coordinate, just separated by spaces.
Start the xyz file with on the first line the number of atoms you have defined and on the second line a comment.  
On the second line you can also give the units. If your coordinates are in Angstrom you do not need to do anything. If they are in bohr just add the following to the second line: [bohr]
 
Example of an .xyz file where the units are in both:

5
testing [bohr]
C 1.602866 5.583573 9.583556
C 0.069731 5.216022 11.580808
C 4.935208 7.477457 6.662229
C -2.147863 5.620234 15.864250
C 7.440796 8.478634 3.2503123

 
Actually these XYZ files can be modified and saved again. To modify a bond or angle, select the atoms to mark the bond, angle or dihedral, press F4 and enter a new value. Press space to clear the selection.
Right click and use the menu to save your file.
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« Last Edit: 15.12.10 at 21:08:33 by Gerrit-Jan Linker »  

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grid_it: Grid size
Reply #2 - 16.09.10 at 19:15:33
 
grid_it: Grid size
 
The grid size can be specified using the keyword npoints with on the next line the number of points in the x,y and z direction, e.g.:
 
NPOINTS
50 50 50
 
You can also set the SPARSE or DENSE options for the grid density.
 
The keyword TOTAL can be used to specify the total density.
 
Grid_it manual:
http://www.teokem.lu.se/molcas/documentation/manual/node59.html
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Gerrit-Jan Linker
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grid_it: accidentally using the start orbitals
Reply #3 - 25.11.10 at 10:23:48
 
grid_it: accidentally using the start orbitals
 
Beware that grid_it uses the file INPORB to read the input orbitals. I am experiencing the problem in molcas 7.4. that after a RASSCF calculation the INPORB file still contain input orbitals and not the RASSCF optimized orbitals.  
 
It seems necessary therefore to copy the obtained RasOrb file to INPORB and only then using grid_it to calculate the grid. Another possibility is to remove the INPORB file prior to calling GRID_IT:
>rm INPORB
 
Note that is is possible to set a title for the INPORB. That may also help to verify optimised orbitals were used.
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« Last Edit: 15.05.11 at 19:35:33 by Gerrit-Jan Linker »  

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grid_it: Selecting orbitals to plot
Reply #4 - 05.12.10 at 21:04:05
 
grid_it: Selecting orbitals to plot
 
By default grid_it selects a set of MO's around the HOMO to plot. A specification of orbitals can also be given. The Orbital keyword should be used followed by the number of orbitals to plot on the next line. For each orbital a new line should be given with the symmetry and the orbital number.
 
 &GRID_IT &END
Orbital
2
1 333
1 334
End of Input
 
Note that the input needs to be give in ascending order of orbital number. When a descending order is given a memory error results.
 
Alternatively the select keyword can be used. In the input below orbitals 334 to 341 of symmetry 1 are plotted:
 
 &GRID_IT &END
select
1:334-341
End of Input
 
The keyword TOTAL can be used to specify the total density.  
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« Last Edit: 21.11.13 at 10:02:38 by Gerrit-Jan Linker »  

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