(* Kimball model and energy derived from experimental molecule data source, ES end january 2013 *)

t=1.889726*{{-0.022,-2.325,16.178},{1.155,-2.805,15.751},{1.153,-3.952,15.067},{-0.024,-4.560,14.784},{-1.202,-3.947,15.062},{-1.202,-2.800,15.746},{-0.022,-1.141,16.742},{-0.025,-5.683,14.049},{-2.355,-4.376,14.519},{1.149,-6.211,13.640},{-1.201,-6.207,13.635},{-2.359,-5.533,13.841},{-3.506,-5.952,13.276},{2.308,-5.543,13.849},{2.306,-4.385,14.528},{-3.517,-7.122,12.611},{-4.666,-7.544,12.053},{-2.367,-7.816,12.426},{-1.199,-7.330,12.894},{-0.026,-7.914,12.551},{1.146,-7.335,12.899},{2.314,-7.825,12.434},{3.465,-7.136,12.624},{3.456,-5.967,13.289},{-4.680,-8.717,11.396},{-3.530,-9.401,11.180},{-5.833,-9.145,10.857},{-2.365,-8.929,11.664},{-1.198,-9.518,11.315},{-0.028,-9.002,11.750},{1.142,-9.523,11.320},{2.310,-8.938,11.673},{3.474,-9.415,11.193},{4.626,-8.735,11.412},{4.615,-7.562,12.071},{5.779,-9.167,10.876},{2.171,-0.739,16.185},{2.993,0.233,15.756},{4.085,-0.124,15.076},{4.303,-1.433,14.796},{3.354,-2.361,15.073},{2.262,-2.006,15.754},{1.043,-0.370,16.743},{5.373,-1.781,14.063},{3.407,-3.589,14.531},{6.238,-0.828,13.655},{5.509,-3.059,13.652},{4.510,-3.951,13.856},{4.556,-5.172,13.292},{5.958,0.481,13.860},{4.854,0.837,14.536},{5.667,-5.545,12.632},{5.714,-6.768,12.075},{6.684,-4.667,12.447},{6.580,-3.406,12.914},{7.499,-2.473,12.573},{7.309,-1.178,12.918},{8.137,-0.220,12.454},{7.835,1.087,12.641},{6.717,1.441,13.299},{6.828,-7.145,11.419},{7.836,-6.264,11.207},{6.880,-8.373,10.881},{7.746,-5.010,11.691},{8.668,-4.084,11.345},{8.536,-2.811,11.777},{9.395,-1.860,11.349},{9.197,-0.568,11.697},{10.011,0.391,11.218},{9.718,1.698,11.433},{8.596,2.049,12.087},{10.487,2.660,10.900},{1.337,1.837,16.181},{0.668,2.917,15.749},{1.346,3.842,15.066},{2.658,3.645,14.789},{3.248,2.458,15.071},{2.572,1.531,15.754},{0.638,0.880,16.742},{3.320,4.552,14.055},{4.435,2.129,14.534},{2.682,5.668,13.644},{4.580,4.288,13.649},{5.121,3.063,13.857},{6.299,2.731,13.298},{1.350,5.807,13.846},{0.669,4.869,14.523},{6.998,3.672,12.639},{8.179,3.339,12.087},{6.477,4.909,12.452},{5.244,5.199,12.913},{4.639,6.361,12.569},{3.348,6.578,12.908},{2.693,7.661,12.443},{1.355,7.777,12.626},{0.673,6.824,13.283},{8.883,4.282,11.435},{8.357,5.513,11.221},{10.070,3.953,10.901},{7.134,5.814,11.699},{6.537,6.977,11.353},{5.284,7.244,11.778},{4.646,8.354,11.349},{3.354,8.564,11.692},{2.694,9.635,11.212},{1.360,9.757,11.422},{0.678,8.798,12.072},{0.683,10.787,10.888},{-2.212,-0.730,16.178},{-2.305,-1.998,15.746},{-3.397,-2.348,15.062},{-4.342,-1.417,14.782},{-4.122,-0.109,15.063},{-3.030,0.244,15.747},{-1.085,-0.367,16.740},{-5.410,-1.760,14.046},{-4.887,0.855,14.522},{-5.550,-3.038,13.633},{-6.273,-0.805,13.636},{-5.990,0.503,13.844},{-6.744,1.466,13.281},{-4.553,-3.934,13.839},{-3.453,-3.576,14.519},{-7.861,1.117,12.617},{-8.617,2.080,12.062},{-8.165,-0.190,12.429},{-7.342,-1.151,12.894},{-7.534,-2.445,12.547},{-6.620,-3.380,12.891},{-6.725,-4.641,12.423},{-5.712,-5.522,12.611},{-4.601,-5.154,13.275},{-9.738,1.733,11.403},{-10.033,0.429,11.185},{-10.502,2.697,10.867},{-9.224,-0.534,11.667},{-9.422,-1.825,11.315},{-8.569,-2.778,11.746},{-8.703,-4.050,11.312},{-7.785,-4.980,11.661},{-7.878,-6.233,11.177},{-6.875,-7.117,11.394},{-5.761,-6.745,12.054},{-6.930,-8.346,10.856},{-1.371,1.842,16.179},{-2.606,1.540,15.748},{-3.277,2.470,15.064},{-2.682,3.655,14.784},{-1.371,3.848,15.063},{-0.698,2.919,15.748},{-0.677,0.883,16.741},{-3.340,4.564,14.048},{-0.689,4.871,14.521},{-4.600,4.305,13.638},{-2.698,5.678,13.637},{-1.365,5.812,13.843},{-0.683,6.827,13.282},{-5.146,3.083,13.845},{-4.464,2.145,14.523},{-1.361,7.782,12.621},{-0.679,8.801,12.069},{-2.699,7.670,12.434},{-3.359,6.589,12.898},{-4.650,6.377,12.556},{-5.258,5.219,12.900},{-6.492,4.932,12.434},{-7.017,3.697,12.621},{-6.323,2.754,13.282},{-1.358,9.762,11.416},{-2.690,9.642,11.201},{-0.676,10.789,10.886},{-3.355,8.574,11.679},{-4.647,8.368,11.332},{-5.289,7.261,11.761},{-6.542,7.000,11.331},{-7.143,5.838,11.678},{-8.365,5.542,11.196},{-8.895,4.314,11.408},{-8.197,3.369,12.064},{-10.082,3.988,10.870},{4.462,12.015,8.457},{3.274,12.353,8.991},{5.145,10.990,8.992},{6.322,10.634,8.445},{7.017,9.620,8.991},{8.197,9.269,8.447},{8.896,8.258,8.995},{10.083,7.924,8.462},{2.678,11.570,9.923},{3.337,10.504,10.405},{1.366,11.733,10.220},{4.599,10.254,9.991},{5.256,9.183,10.472},{6.490,8.897,10.009},{7.141,7.812,10.476},{8.364,7.514,9.995},{8.988,6.391,10.412},{10.205,6.091,9.930},{10.768,6.896,8.997},{10.761,4.891,10.229},{-10.077,7.958,8.428},{-10.766,6.933,8.962},{-8.891,8.288,8.964},{-8.187,9.296,8.418},{-7.007,9.640,8.964},{-6.308,10.653,8.421},{-5.131,11.003,8.972},{-4.443,12.027,8.440},{-10.207,6.126,9.898},{-8.991,6.422,10.383},{-10.767,4.928,10.195},{-8.362,7.541,9.966},{-7.140,7.834,10.450},{-6.485,8.917,9.984},{-5.251,9.199,10.453},{-4.589,10.267,9.972},{-3.329,10.513,10.391},{-2.666,11.576,9.912},{-3.257,12.362,8.978},{-1.354,11.736,10.213},{-10.693,-7.112,8.400},{-9.934,-8.083,8.937},{-10.640,-5.881,8.936},{-11.380,-4.901,8.386},{-11.345,-3.672,8.932},{-12.091,-2.696,8.386},{-12.064,-1.468,8.938},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n=Length[t]

u=Table["C",{i,1,n}]

u1=Table[If[u[[i]]=="C",0.2555,If[u[[i]]=="H",0.15,If[u[[i]]=="N",0.24,If[u[[i]]=="O",0.178,If[u[[i]]=="Cl",0.5]]]]],{i,1,n}];
u2=Table[If[u[[i]]=="C",0.2555,If[u[[i]]=="H",0.6,If[u[[i]]=="N",0.22522,If[u[[i]]=="O",0.178,If[u[[i]]=="Cl",0.5]]]]],{i,1,n}];

cn=Table[If[u[[i]]=="C",6.0,If[u[[i]]=="H",1.0,If[u[[i]]=="N",7.0,If[u[[i]]=="O",8.0,If[u[[i]]=="Cl",17.0,If[us[[i,1]]=="B",5.0]]]]]],{i,1,n}];

M=n*12.0107

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

(*lp=ListPlot[v, Axes->False];*)

(*Plot1=Table[Graphics[{Circle[{v[[i,1]]/0.5292,v[[i,2]]/0.5292},If[i<5,0.18,0.26]]}],{i,1,13}];*)
Plot1=Table[Graphics3D[{Lighter[Brown],Sphere[{t[[i,1]],t[[i,2]],t[[i,3]]},u1[[i]]]}],{i,1,n}];

Plot2=Table[Graphics3D[Text[i,{t[[i,1]]-0.5,t[[i,2]],t[[i,3]]} ,{1,0}]],{i,1,n}];
(*Show[Plot2,{AspectRatio->Automatic,Axes -> False,Frame -> Automatic,PlotRange -> {{0,14},{-6,6}}}];*)

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

x=Table[t[[i,1]],{i,1,n}];   xs=Sum[x[[i]],{i,1,n}]/n
y=Table[t[[i,2]],{i,1,n}];   ys=Sum[y[[i]],{i,1,n}]/n
z=Table[t[[i,3]],{i,1,n}];    zs=Sum[z[[i]],{i,1,n}]/n

(* Distance matrix Bohr *)

(*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[[1]]*)

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];*)

u2=u1;

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[j<n+1,0.5*Lij[[i,j]],Lij[[i,j]]],0]," "],{i,1,n},{j,1,n}]; 
Qij=Lij;
(*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[2.25/u2[[i]]^2,{i,1,n}]

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]

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,nb}];
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,nb}];   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,nb}];
Plot7=Table[Graphics3D[{Opacity[0.6],Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]}],{i,1,nb}];

rpo=1.7;
px=Table[d=Sqrt[x[[i]]^2+y[[i]]^2+z[[i]]^2];x[[i]]*(d+rpo)/d,{i,1,n}];
py=Table[d=Sqrt[x[[i]]^2+y[[i]]^2+z[[i]]^2];y[[i]]*(d+rpo)/d,{i,1,n}];
pz=Table[d=Sqrt[x[[i]]^2+y[[i]]^2+z[[i]]^2];z[[i]]*(d+rpo)/d,{i,1,n}];
Plot8=Table[Graphics3D[{Opacity[0.3],Lighter[Cyan],Sphere[{px[[i]],py[[i]],pz[[i]]},rpo]}],{i,1,n}];
rpi=1.2;
qx=Table[d=Sqrt[x[[i]]^2+y[[i]]^2+z[[i]]^2];x[[i]]*(d-rpi)/d,{i,1,n}];
qy=Table[d=Sqrt[x[[i]]^2+y[[i]]^2+z[[i]]^2];y[[i]]*(d-rpi)/d,{i,1,n}];
qz=Table[d=Sqrt[x[[i]]^2+y[[i]]^2+z[[i]]^2];z[[i]]*(d-rpi)/d,{i,1,n}];
Plot8a=Table[Graphics3D[{Opacity[0.4],Lighter[Yellow],Sphere[{qx[[i]],qy[[i]],qz[[i]]},rpi]}],{i,1,n}];

Plot9= Table[Graphics3D[{Darker[Red,1.0],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]]]]}},0.2]}],{i,1,nb}];

Show[Plot1,(*Plot7,*)Plot8,Plot8a,Plot9,{AspectRatio->Automatic,Boxed->False, SphericalRegion->True}]

Show[Plot1,Plot7,(*Plot8,Plot8a,*)Plot9,{AspectRatio->Automatic,Boxed->False, SphericalRegion->True}]

Plot8=Table[Graphics3D[{Opacity[0.2],Lighter[Cyan],Sphere[{px[[i]],py[[i]],pz[[i]]},rpo]}],{i,1,n}];
Plot8a=Table[Graphics3D[{Opacity[0.2],Lighter[Yellow],Sphere[{qx[[i]],qy[[i]],qz[[i]]},rpi]}],{i,1,n}];
Show[Plot1,Plot7,Plot8,Plot8a,Plot9,{AspectRatio->Automatic,Boxed->False, SphericalRegion->True}]

Show[Plot1(*,Plot2*),Plot9,{AspectRatio->Automatic,SphericalRegion->True}]

tc=Table[{x[[i]],y[[i]],z[[i]]},{i,1,n}];   (* core clouds *)
tpo=Table[{px[[i]],py[[i]],pz[[i]]},{i,1,n}]; (* pi clouds above *)
tpu=Table[{qx[[i]],qy[[i]],qz[[i]]},{i,1,n}]; (* pi clouds below *) 
twc=Table[{wx[[i]],wy[[i]],wz[[i]]},{i,1,nb}];  (* Bond clouds between cores *)
(*twh=Table[{wxh[[i]],wyh[[i]],wzh[[i]]},{i,1,bh}];*) (* H-bonding clouds *)
tw=Join[tc,twc,tpo,tpu];
bt=Length[tw]
(*MatrixForm[tw]*)
(* coordinates of clouds *)
(* cloud-cloud distances *)
dw=Table[Sqrt[(tw[[i,1]]-tw[[j,1]])^2+(tw[[i,2]]-tw[[j,2]])^2+(tw[[i,3]]-tw[[j,3]])^2],{i,1,bt},{j,1,bt}];
(*MatrixForm[dw]*)

(* nucleus-nucleus distances *)
dc=Table[Sqrt[(t[[i,1]]-t[[j,1]])^2+(t[[i,2]]-t[[j,2]])^2+(t[[i,3]]-t[[j,3]])^2],{i,1,n},{j,1,n}];
(*MatrixForm[dc]*)

tv1=Table[{x[[i]],y[[i]],z[[i]]},{i,1,n}];
tv2=Table[{0,0,0},{i,1,nb}];
(*tv3= Table[{x[[i]],y[[i]],z[[i]]},{i,bc+1,n}];*)
tv4 =Table[{0,0,0},{i,1,n}]; 
tv5 =Table[{0,0,0},{i,1,n}]; 
tv  = Join[tv1,tv2,(*tv3,*)tv4,tv5];
(*MatrixForm[tv]*)

ow=Join[Table[-2.0,{i,1,n+nb}],Table[-0.5,{i,1,2*n}]];

cnv=Join[Table[cn[[i]],{i,1,n}],(*Table[0.0,{i,1,cw}],*)Table[0.0,{i,1,nb}],Table[0.0,{i,1,2*n}]];

dcw=Table[sq=Sqrt[(tw[[i,1]]-tv[[j,1]])^2+(tw[[i,2]]-tv[[j,2]])^2+(tw[[i,3]]-tv[[j,3]])^2];If[sq> 0.1,1/sq,0],{i,1,bt},{j,1,bt}];
dcw=Table[If[i== j,dcw[[i,j]]=0.0,dcw[[i,j]]],{i,1,bt},{j,1,bt}];
(*MatrixForm[dcw]  *)
(* nucleus-cloud distances *)

Vee=0.0; Vnn=0.0;

(* all clouds repulsion *)
For[i=1,i<bt,i++,
For[j=i+1,j<bt+1,j++,
Vee=Vee+ow[[i]]*ow[[j]]/dw[[i,j]]]];
(* half cloud with other common halfcloud: subtract WW *)
For [i=nb+1,i<nb+n+1,i++,Vee=Vee-ow[[i]]*ow[[i+n]]/dw[[i,i+n]]];
Vee

sc=0.308;   (* core clouds *)
For[i=1 ,i<n+1,i++,Vee=Vee+3*sc/u2[[i]]]
sw=0.3;  (* bonding clouds *)
For[i=1 ,i<nb+1,i++,Vee=Vee+3*sw/a[[i,3]]]
Vee

(* all nuclei with all clouds, except i = j *)
Vne=cnv.(ow.dcw)
(*Vne=Apply[Plus,cnv.dcw]*)

(* core nuclei in their cloud centers *)

For[i=1,i<n+1,i++,Vne=Vne-3*cn[[i]]/u2[[i]]]
Vne

(* protons in their bonding cloud, distance u2[[a[[i,1]]]] to cloud center *)
(*For[i=cw+1,i<nb+1,i++,Vne=Vne-(3-(u2[[a[[i,1]]]]/a[[i,3]])^2)/a[[i,3]]]
Vne*)

(* nucleus-nucleus *)
For[i=1,i<n,i++,
For[j=i+1,j<n+1,j++,Vnn=Vnn+cn[[i]]*cn[[j]]/dc[[i,j]]]]
Vnn

Vee
Vnn
Vne
Tpi = 1.64*n*0.5*1.125*(1/rpo+1/rpi) (* pi kin e added *)
Vtot=Vne+Vee+Vnn
Ttot=Tsigma+Tpi
-Vtot/Ttot
Etot=Ttot+Vtot