# Internal Coordinates

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 Spring Member Profile Send PM
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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 Profile Send PM
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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 6-31g* 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: ``` Z-matrix (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

 Spring Member Profile Send PM
 Just Got Here Threads 1 Posts 2
 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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