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5:18:03 AM PDT  Thu, Aug 30th 2012 

Hello every body,
I am a new NWChem user, I need to find the internal coordinates for a polymer , Could you tell me how to start?
Thank you




Huub Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop


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9:38:48 AM PDT  Thu, Aug 30th 2012 

Hi Spring,
A simple approach to getting this information is to use the autoz capabilities in NWChem. In this approach you simply provide the cartesian coordinates of the atoms in the input and NWChem tries to work out a sensible set of internal coordinates and prints them on standard output.
Whether this approach is sensible depends on what you want to do with the information. Just as an example for benzene you write an input like:
geometry autoz units angstrom print
C 0.98348719 0.98348719 0.00000000
C 1.34346849 0.35998130 0.00000000
C 0.35998130 1.34346849 0.00000000
C 0.98348719 0.98348719 0.00000000
C 1.34346849 0.35998130 0.00000000
C 0.35998130 1.34346849 0.00000000
H 1.74853940 1.74853940 0.00000000
H 2.38854924 0.64000984 0.00000000
H 0.64000984 2.38854924 0.00000000
H 1.74853940 1.74853940 0.00000000
H 2.38854924 0.64000984 0.00000000
H 0.64000984 2.38854924 0.00000000
end
basis "ao basis" spherical
* library 631g*
end
task scf
For getting the internal coordinates any basis set will do, and of course you don't need to complete the SCF calculation either. In the output you will then find a section as follows:
Zmatrix (autoz)

Units are Angstrom for bonds and degrees for angles
Type Name I J K L M Value
       
1 Stretch 1 5 1.39086
2 Stretch 1 6 1.39086
3 Stretch 1 7 1.08195
4 Stretch 2 4 1.39086
...
13 Bend 1 5 3 120.00000
14 Bend 1 5 11 120.00000
15 Bend 1 6 2 120.00000
...
31 Torsion 1 5 3 4 0.00000
32 Torsion 1 5 3 9 180.00000
33 Torsion 1 6 2 4 0.00000
34 Torsion 1 6 2 8 180.00000
where "stretch" refers to bond lengths, "bend" refers to bond angles, and "torsion" refers to dihedral angles. The integer numbers following these terms refer to the atoms involved as specified in the geometry block. Finally the floating point number is the value of the bond length, bond angle, or dihedral angle.
This would be one way of doing it. This way has disadvantages if you, e.g. want to construct a zmatrix to provide in an input. To answer those kinds of questions I need to know a little more on how you want to use the internal coordinates.
Best wishes, Huub




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1:41:30 PM PDT  Thu, Aug 30th 2012 

Thank u so much for taking time to answer me.
I have another question if u don't mind , how to calculate the charges using dft?



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