Bicyclohexane.world

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[CONSTANTS]

% We define a reference frame attache to each C atom with the  
% X axis along one of the C-C bonds and with the X-Y plane in
% the planed defined by the two bonds coincident in the C.
 
% All distances are in Amstrongs and all angles are in radiants

% H-C bond length
HCb:=1.09

% H-C distance for C the neighbouring C of the C to which H
% is connected
HCb2:=2.151077

% C-C bond length
CCb:=1.526

% C-C-C squared distnace
CCC2:=6.212008043466126

% Bond bending angle
BBa:=1.911135530933790887
% BBa:=pi/2

% The firts CC bond is aligned with the X axis and has lenght CCb
% The second is in the XY plane at position:
CC2x:=CCb*cos(BBa)
CC2y:=CCb*sin(BBa)

% x-y-z position of one of the H w.r.t. a frame attached to the C
% The second H is symmetrically placed (w.r.t. the X-Y plane).
% This H is at (Hx,Hy,Hz) that is at the intersection of three circunferences
%   Hx^2+Hy^2+Hz^2=HCb^2
%   (Hx-CCb)^2+Hy^2+Hz^2=HCb2^2
%   (Hx-CC2x)^2+(Hy-CC2y)^2+Hz^2=HCb2^2
%
Hx:=(HCb^2-HCb2^2+CCb^2)/(2*CCb)
Hy:=((Hx-CC2x)^2-(Hx-CCb)^2+CC2y^2)/(2*CC2y)
Hz:=sqrt(Hx^2+Hy^2)

% x-y-z position of the Carbon atom in the "other" ring for atoms 4 and 5
% This is like the H position but taking into account the correct C-C bond lenght
%   Cx^2+Cy^2+Cz^2=CCb^2
%   (Cx-CCb)^2+Cy^2+Cz^2=CCC2
%   (Cx-CC2x)^2+(Cy-CC2y)^2+Cz^2=CCC2
%
Cx:=(2*CCb^2-CCC2)/(2*CCb)
Cy:=((Cx-CC2x)^2-(Cx-CCb)^2+CC2y^2)/(2*CC2y)
Cz:=sqrt(CCb^2-Cx^2-Cy^2)

% Radious of the spheres representing atoms (75% Van der Waals radii)
rC:=1.7*0.25
rH:=1.2*0.25

% Radii of the cylinders representing bonds
rCC:=0.15
rCH:=0.15

% Colors for the atoms (Carbon/Hydrogen)
Cr:=0.2
Cg:=0.6
Cb:=0.6

Hr:=1
Hg:=1
Hb:=1

[LINKS]

C1 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

C2 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

C3 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

C4 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCC (0,0,0) (Cx/2,Cy/2,-Cz/2) color (Cr,Cg,Cb) decoration

C5 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCC (0,0,0) (Cx/2,Cy/2,-Cz/2) color (Cr,Cg,Cb) decoration

C6 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)


C7 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

C8 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

C9 : sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

C10: sphere rC (0,0,0) color (Cr,Cg,Cb)
     cylinder rCC (0,0,0) (CCb/2,0,0) color (Cr,Cg,Cb) decoration
     cylinder rCC (0,0,0) (CC2x/2,CC2y/2,0) color (Cr,Cg,Cb) decoration
     cylinder rCH (0,0,0) (Hx/2,Hy/2,Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,Hz/2) (Hx,Hy,Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,Hz) color (Hr,Hg,Hb)
     cylinder rCH (0,0,0) (Hx/2,Hy/2,-Hz/2) color (Cr,Cg,Cb) decoration
     cylinder rCH (Hx/2,Hy/2,-Hz/2) (Hx,Hy,-Hz) color (Hr,Hg,Hb) decoration
     sphere rH (Hx,Hy,-Hz) color (Hr,Hg,Hb)

[JOINTS]

% We define the revolute joints trying to use as much zeros as possible
% in the two first points of the two axes in local coordinates. This produces
% simpler equation sets.
revolute: C1 (CCb,0,0) (0,0,0) 
          C2 (0,0,0) (CC2x,CC2y,0)  

revolute: C2 (CCb,0,0) (0,0,0) 
          C3 (0,0,0) (CC2x,CC2y,0)  

revolute: C3 (CCb,0,0) (0,0,0) 
          C4 (0,0,0) (CC2x,CC2y,0) 

revolute: C4 (CCb,0,0) (0,0,0) 
          C5 (0,0,0) (CC2x,CC2y,0) 

revolute: C5 (CCb,0,0) (0,0,0) 
          C6 (0,0,0) (CC2x,CC2y,0) 

revolute: C6 (CCb,0,0) (0,0,0) 
          C1 (0,0,0) (CC2x,CC2y,0)     

revolute: C4 (Cx,Cy,-Cz) (0,0,0) 
          C7 (0,0,0) (CC2x,CC2y,0) 

revolute: C7 (CCb,0,0) (0,0,0) 
          C8 (0,0,0) (CC2x,CC2y,0) 

revolute: C8 (CCb,0,0) (0,0,0) 
          C9 (0,0,0) (CC2x,CC2y,0) 

revolute: C9 (CCb,0,0) (0,0,0) 
          C10 (0,0,0) (CC2x,CC2y,0) 

revolute: C10 (CCb,0,0) (0,0,0) 
          C5 (0,0,0) (Cx,Cy,-Cz)

[COLLISIONS]

CHECK : ALL