(* Kimball model and energy derived from experimental molecule data source, ES end january 2013 *)
Clear[Plot9];
ChemicalData["Coronene","MoleculePlot"]

t=0.01889726*ChemicalData["Coronene","AtomPositions"]; 
MatrixForm[t]

bt=ChemicalData["Coronene","BondTally"]

{{{{"C","C"},2},7},{{{"C","C"},1},9},{{{"C","H"},1},10}}

{{{{"C","C"},1},3},{{{"C","H"},1},10}}
bc=0;

u=ChemicalData["Coronene","VertexTypes"]

n=Length[u]

For[i=1, i<n+1,i++,If[u[[i]]≠"H", bc=bc+1]];
bc
bh=n-bc

DeleteFile[ "C:\\Kimb_Mathem\\tmp3"];
For[i=1,i<n+1,i++,
{u[[i]],Extract[t,{i}]}>>> "C:\\Kimb_Mathem\\tmp3"]
u1=Table[If[u[[i]]=="C",0.2556,If[u[[i]]=="H",0.1,If[u[[i]]=="N",0.213,If[u[[i]]=="O",0,178]]]],{i,1,n}]
u2=Table[If[u[[i]]=="C",0.2556,If[u[[i]]=="H",0.564,If[u[[i]]=="N",0.213,If[u[[i]]=="O",0,178]]]],{i,1,n}]

ChemicalData["Coronene","MolecularFormulaString"]

M=ChemicalData["Coronene","MolecularWeight"]

m=Table[If[u[[i]]=="C",12.0107,If[u[[i]]=="H",1.00794]],{i,1,n}];
coords=(m.t)/M

(* t=t-coords; *)

(*v=0.01889726*ChemicalData["Coronene","VertexCoordinates"];*)

Plot2=Table[Graphics3D[Text[i,{t[[i,1]]-0.5,t[[i,2]],t[[i,3]]} ,{1,0}]],{i,1,n}];
Plot1=Table[Graphics3D[{If[u[[i]]=="H",Lighter[White],If[u[[i]]=="N",Lighter[Blue],If[u[[i]]=="O",Lighter[Red],Lighter[Green]]]],Sphere[{t[[i,1]],t[[i,2]],t[[i,3]]},u1[[i]]]}],{i,1,n}];

Show[Plot1,Plot2,{AspectRatio->Automatic, Axes->Automatic}]

ChemicalData["Coronene","CHStructureDiagram"]

x=Table[t[[i,1]]-coords[[1]],{i,1,n}]; 
y=Table[t[[i,2]]-coords[[2]],{i,1,n}];
z=Table[t[[i,3]]-coords[[3]],{i,1,n}];
t=Table[{x[[i]],y[[i]],z[[i]]},{i,1,n}];
coords=(m.t)/M

c1=t[[7]]
c2=t[[12]]
a1=t[[16]]
a2=t[[19]]
b1=t[[18]]
b2=t[[21]]
d1=0.5*(a1+a2)
d2=0.5*(b1+b2)
0.5*(d1+d2)
0.5*(c1+c2)

(* Distance matrix Bohr *)
Dij=Table[If[i≥j,If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,sq,0]," "],{i,1,n},{j,1,n}];
(*Dij=Table[If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,sq," "],{i,1,n},{j,1,n}];*)
(*MatrixForm[Dij]*)

(*Eij=Table[If[i≥j,If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,0.529177*sq,0]," "],{i,1,n},{j,1,n}];
MatrixForm[Eij];*)

Fij=Dij-u2;
(*MatrixForm[Fij];*)
Gij=Table[If[i≥j,If[Fij[[i,j]]>0,Fij[[i,j]],0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Gij]*)

Hij=Transpose[Gij];
(*MatrixForm[Hij];*)

Kij=Hij-u2;
(*MatrixForm[Kij];*)
Lij=Table[If[i≤j,If[Kij[[i,j]]>0,Kij[[i,j]],0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Lij]*)

Lij=Table[If[i≤j,If[Lij[[i,j]]>0,If[u[[j]]≠"H",0.5*Lij[[i,j]],Lij[[i,j]]],0]," "],{i,1,n},{j,1,n}]; 
(*MatrixForm[Lij];*)

Nij=Table[If[i≤j,If[Lij[[i,j]]>0,2.25/Lij[[i,j]]^2,0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Nij];*)

(* Total kinetic energy in Eh, = |Etot| *)
Tsigma=Sum[If[i≤j,Nij[[i,j]],0],{i,1,n},{j,1,n}]+Sum[If[u[[i]]≠"H",2.25/u2[[i]]^2,0],{i,1,n}]

Qij=Lij;
Mij=Prepend[Qij,u];
Oij=Transpose[Mij];
Pij=Prepend[Oij,Prepend[u," "]];

(*MatrixForm[Pij]*)

(* sigma bond cloud radii *)

(*For[i=2,i<n+2,i++,
For[j=2,j≤i,j++,
If[Pij[[i,j]]>0,Print[u[[i-1]],i-1," ",u[[j-1]],j-1,"  ",Extract[Pij,{i,j}]]]]];*)

DeleteFile[ "C:\\Kimb_Mathem\\tmp4"];
For[i=2,i<n+2,i++,
For[j=2,j≤i,j++,
If[Pij[[i,j]]>0,{i-1,j-1,Extract[Pij,{i,j}]}>>> "C:\\Kimb_Mathem\\tmp4"]]]

a=ReadList["C:\\Kimb_Mathem\\tmp4"]
nb=Length[a]

cw=nb-bh

wx=Table[(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(x[[a[[i,2]]]]-x[[a[[i,1]]]])+x[[a[[i,1]]]],{i,1,cw}];     wy=Table[(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(y[[a[[i,2]]]]-y[[a[[i,1]]]])+y[[a[[i,1]]]],{i,1,cw}];      wz=Table[(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(z[[a[[i,2]]]]-z[[a[[i,1]]]])+z[[a[[i,1]]]],{i,1,cw}];
Plot7=Table[Graphics3D[{Darker[Gray],{Opacity[0.6],Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]}}],{i,1,cw}];

wx=Table[(a[[i,3]]-0.14+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(x[[a[[i,1]]]]-x[[a[[i,2]]]])+x[[a[[i,2]]]],{i,cw+1,nb}];
wy=Table[(a[[i,3]]-0.14+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(y[[a[[i,1]]]]-y[[a[[i,2]]]])+y[[a[[i,2]]]],{i,cw+1,nb}];
wz=Table[(a[[i,3]]-0.14+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(z[[a[[i,1]]]]-z[[a[[i,2]]]])+z[[a[[i,2]]]],{i,cw+1,nb}];
Plot8=Table[Graphics3D[{Opacity[0.4],Lighter[White],Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]}],{i,1,bh}];

(*PLot9= Table[Graphics3D[{Cylinder[{{x[[a[[i,1]]]],y[[a[[i,1]]]],z[[a[[i,1]]]]},{x[[a[[i,2]]]],y[[a[[i,2]]]],z[[a[[i,2]]]]}},0.1]}],{i,1,nb}];*)
Plot9= Table[Graphics3D[{(*Darker[Red,0.8],*)Tube[{{x[[a[[i,1]]]],y[[a[[i,1]]]],z[[a[[i,1]]]]},{x[[a[[i,2]]]],y[[a[[i,2]]]],z[[a[[i,2]]]]}},0.1]}],{i,1,nb}];
(*Plot10= Line[{{*)

Show[Plot1,Plot2,Plot7,Plot8,Plot9,{AspectRatio->Automatic, Axes->True,AxesLabel->{"x","y","z"},SphericalRegion->True(*,Boxed->False*)}]