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Cell["\<\
(*NH2COH Formamide, with \"orthogonal\" \[Sigma],\[Pi] LPs, 13.01.2013, not \
final optimization: slight overlaps *)\
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Cell["\<\
Clear[ZC,ZN,ZO,sig1,sig2,sig3,sig4,sig5,sig6,sig7,sig8,sig9,k1,k2,k3,k4k5,k6,\
k7,k8,k9,k10,k11,nc,w1,w2,w3,pnh,pch,vee,vne,vnn,
xn,yn,zn,xc,yc,zc,c1,c2,c3,cs1,ss1,cs2,ss2,cs3,ss3,pi,i,j,d,t];
Clear[Cr,Nr,Oa,NH,CH,CO,CN,OL,NM,OC,OO,OM,w1,w2,w3,pch,pnh];
ZC=6.0; ZN=7.0; ZO=8.0; sig1=0.3; sig2=0.3; sig3=0.3; sig4=0.3; sig5=0.3; \
sig6=0.3;
sig7=0.3; sig8=0.3; sig9=0.3;
nc=17; nn=6; pi=0.0;
k1=1.02; k2=1.02; k3=1.02; k4=1.2; k5=1.25; k6=1.3; k7=1.26; k8=1.85; k9=1.1; \
k10=1.1; k11=0.78; k12=0.99;  
bohr=0.529177; rad=57.29578;

(* 17 Variables: Cr,Nr,Or,NH,CH,CN,CO,OL,NM,OC,OO,OM,pnh,pch,w1,w2,w3 *)\
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Cell[BoxData[
 RowBox[{"(*", " ", 
  RowBox[{
   RowBox[{"Cr", "=", "0.26"}], ";", " ", 
   RowBox[{"Nr", "=", "0.22"}], ";", " ", 
   RowBox[{"Oa", "=", "0.186"}], ";", " ", 
   RowBox[{"NH", "=", "1.2"}], ";", " ", 
   RowBox[{"CH", "=", "1.25"}], ";", " ", 
   RowBox[{"CO", "=", "0.928"}], ";", " ", 
   RowBox[{"CN", "=", "1.04"}], ";", " ", 
   RowBox[{"OL", "=", "1.0"}], ";", "\[IndentingNewLine]", 
   RowBox[{"NM", "=", "1.1"}], ";", " ", 
   RowBox[{"OC", "=", "1.4"}], ";", " ", 
   RowBox[{"OM", "=", "1.05"}], ";", " ", 
   RowBox[{"w1", "=", "1.9"}], ";", " ", 
   RowBox[{"w2", "=", "1.0"}], ";", " ", 
   RowBox[{"w3", "=", "1.0"}], ";", " ", 
   RowBox[{"pch", "=", "0.58"}], ";", 
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Cell["\<\
(* C He shell *)
Ekin = 2.25*k1/Cr^2;
vee=3.0*sig1/Cr;
vne=-3.0*ZC/Cr;

(* N He shell *)
Ekin = Ekin+2.25*k2/Nr^2;
vee=vee+3.0*sig2/Nr;
vne=vne-3.0*ZN/Nr;

(* O He shell *)
Ekin = Ekin+2.25*k3/Oa^2;
vee=vee+3.0*sig3/Oa;
vne=vne-3.0*ZO/Oa;\
\>", "Input",
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Cell["\<\
(* bonding and lone pairs *)
Ekin = Ekin + \
2.25*(2*k4/NH^2+k5/CN^2+k6/CO^2+k7/CH^2+k8/NM^2+k9/OL^2+k10/OM^2+k11/OC^2+k12/\
OO^2);

vee=vee+3.0*(2*sig4/NH+sig5/CN+sig6/CO+sig7/CH+sig9/OL);\
\>", "Input",
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Cell["\<\
(*  1  2  3  4  5  6  7  8  9  10 11   12   13   14   15 16 17  *)
(*  C  N  O  Hn Hn Hc B  B  L2 L1 L1   Bp   Bp   Bp   Bp L1 L1  *)
as={C,N,O,H,H,H};    (* atom string *)  
rr={Cr,Nr,Oa,NH,NH,CH,CN,CO,OL,NM,NM,  OC,  OC,  OO,  OO,OM,OM};
oc={-2,-2,-2,-2,-2,-2,-2,-2,-2,-1,-1,-1/2,-1/2,-1/2,-1/2,-1,-1};
ch={ZC,ZN,ZO, 1, 1, 1, 0, 0, 0, 0, 0,   0,   0,   0,   0, 0, 0};
csw1=Cos[w1/2];  ssw1=Sin[w1/2];
csw2=Cos[w2];    ssw2=Sin[w2];
csw3=Cos[w3];    ssw3=Sin[w3];\
\>", "Input",
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Cell["\<\
dcnx=Cr+Nr+2*CN;             dcox=(Cr+Oa+2*CO)*csw2;  dnhx=dcnx+(Nr+NH)*csw1; \
dchx=(Cr+CH)*csw3;           dccnx=Cr+CN; 
pnhx=dcnx+(Nr+NH+pnh)*csw1;  pchx=(Cr+CH+pch)*csw3;
dcoy=(Cr+Oa+2*CO)*ssw2;      dnhy=(Nr+NH)*ssw1;       dchy=(Cr+CH)*ssw3;  
pnhy=(Nr+NH+pnh)*ssw1;       pchy=(Cr+CH+pch)*ssw3;
dccox=(Cr+CO)*csw2;          dccoy=(Cr+CO)*ssw2;      
dolx=(Cr+2*CO+2*Oa+OL)*csw2; doly=(Cr+2*CO+2*Oa+OL)*ssw2;
dom1x=dcox-(Oa+OM)*ssw2;     dom2x=dcox+(Oa+OM)*ssw2;
dom1y=dcoy+(Oa+OM)*csw2;     dom2y=dcoy-(Oa+OM)*csw2;\
\>", "Input",
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Cell["\<\
(* 6 nuclei: coord *)
xn={0,-dcnx,dcox,-pnhx,-pnhx,pchx};
yn={0,0,dcoy,pnhy,-pnhy,-pchy};
zn={0,0,0,0,0,0};\
\>", "Input",
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Cell["\<\
(* 17 clouds: coord *)        
xc={0,-dcnx,dcox,-dnhx,-dnhx,dchx,-dccnx,dccox,dolx,-dcnx,-dcnx,0,0,dcox,dcox,\
dom1x,dom2x};
yc={0,0,dcoy,dnhy,-dnhy,-dchy,0,dccoy,doly,0,0,0,0,dcoy,dcoy,dom1y,dom2y};
zc={0,0,0,0,0,0,0,0,0,NM,-NM,OC,-OC,OO,-OO,0,0};\
\>", "Input",
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Cell["\<\
(* epot terms *)
vne=vne-2*(3-(pnh/NH)^2)/NH;
vne=vne-(3-(pch/CH)^2)/CH;
vnn = 0.0;\
\>", "Input",
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Cell["\<\
(*ww*)
For[i = 1, i < nc, i++,
  For[j = i+1, j < nc+1, j++,
    vee = vee + \
oc[[i]]*oc[[j]]/Sqrt[(xc[[i]]-xc[[j]])^2+(yc[[i]]-yc[[j]])^2+(zc[[i]]-zc[[j]])\
^2]]]\
\>", "Input",
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 CellChangeTimes->{{3.5668390630515456`*^9, 3.566839083924382*^9}, {
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Cell["\<\
(*nn*)
For[i = 1, i < nn, i++,
  For[j = i+1, j < nn+1, j++,
    vnn = vnn + \
ch[[i]]*ch[[j]]/Sqrt[(xn[[i]]-xn[[j]])^2+(yn[[i]]-yn[[j]])^2+(zn[[i]]-zn[[j]])\
^2]]]\
\>", "Input",
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Cell["\<\
(*nw*)
For[i = 1, i < nc+1, i++,
  For[j = 1, j < nn+1, j++,
    If[i \[NotEqual] j,
      vne = vne + \
oc[[i]]*ch[[j]]/Sqrt[(xc[[i]]-xn[[j]])^2+(yc[[i]]-yn[[j]])^2+(zc[[i]]-zn[[j]])\
^2]]]]\
\>", "Input",
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 CellChangeTimes->{{3.5668390630515456`*^9, 3.5668390979332066`*^9}, 
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Cell[CellGroupData[{

Cell["\<\
Epot=vne+vee+vnn;
func=Ekin+Epot;
t = FindMinimum[func,{Cr,0.26},{Nr,0.22},{Oa,0.186},{NH,1.11},{CH,1.12},{CO,0.\
92},{CN,1.03},{OL,0.905},{NM,0.765},{OC,1.36},{OO,1.3},{OM,0.86},{w1,2.15},{\
w2,1.0},{w3,1.12},{pch,0.51},{pnh,0.5},{Method -> \"Newton\"}, {MaxIterations \
-> 800}]\
\>", "Input",
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