[MMTK] Molecule problems?

Jochen Küpper jochen@jochen-kuepper.de
30 Sep 2001 02:17:40 -0400


Dear All,

one more s.s. problem: I am trying to get a benzene molecule set up,
so I add the following database entry:


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# -*- Python -*-

name = 'benzene'
 
H1  = Atom('H')
H2  = Atom('H')
H3  = Atom('H')
H4  = Atom('H')
H5  = Atom('H')
H6  = Atom('H')
C1  = Atom('C')
C2  = Atom('C')
C3  = Atom('C')
C4  = Atom('C')
C5  = Atom('C')
C6  = Atom('C')
 
bonds = [Bond(C1, C2), Bond(C2, C3), Bond(C3, C4), Bond(C4, C5), Bond(C5, C6), Bond(C6, C1),
         Bond(H1, C1), Bond(H2, C2), Bond(H3, C3), Bond(H4, C4), Bond(H5, C5), Bond(H6, C6)]
 
re_HC   =   1.0
re_CC   =   1.39
ae      = 120.0
de      =   0.0
deH     = 180.0

configurations = {
    'default': ZMatrix([[C1],
                        [C2, C1, re_CC*Ang],
                        [C3, C2, re_CC*Ang, C1, ae*deg],
                        [C4, C3, re_CC*Ang, C2, ae*deg, C1, de],
                        [C5, C4, re_CC*Ang, C3, ae*deg, C2, de],
                        [C6, C5, re_CC*Ang, C4, ae*deg, C3, de],
                        [H1, C1, re_HC*Ang, C2, ae*deg, C3, deH],
                        [H2, C2, re_HC*Ang, C3, ae*deg, C4, deH],
                        [H3, C3, re_HC*Ang, C4, ae*deg, C5, deH],
                        [H4, C4, re_HC*Ang, C5, ae*deg, C6, deH],
                        [H5, C5, re_HC*Ang, C6, ae*deg, C1, deH],
                        [H6, C6, re_HC*Ang, C1, ae*deg, C2, deH]
                        ])
    }
-------------------------------------------------------


and run the following script:


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import MMTK

benz = MMTK.Molecule('benzene')
benz.view()
-------------------------------------------------------



All I get is a bowl, not exactly what one would expect... 
Any idea what I am doing wrong?

Greetings,
Jochen
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