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z_tersoff_GA_Si3_2_ONLYpeNOforce_NoGLOBALvariable.m
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z_tersoff_GA_Si3_2_ONLYpeNOforce_NoGLOBALvariable.m
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% function [Vij,DEDmov] = tersoff_GA_Si3(coord,total,numMov,numPeriph,numBound,numSurface,movAtom,periphAtom,boundAtom,surfaceAtom);
% function [Vij,DEDmov] = tersoff_GA_Si3_2(A,B,lmda1,lamda2,lamda3,alpha,beta,eta,c,d,h,dat)%GA
function [Vij] = tersoff_GA_Si3_2_ONLYpeNOforce_NoGLOBALvariable(variables,dat,config)%GA
% global x y z;
% global A B lamda1 lamda2 lamda3 alpha beta eta c d h R D rCutoff;
% global countStore;% ****THIS MODIFICATION IS MADE WHILE STORING THE CONFIGURATIONS
% global coordStore;% ****THIS MODIFICATION IS MADE WHILE STORING THE CONFIGURATIONS
% global countFFT;
% global rijFFT;
% global countSurface;
% global coordSurface;
A=variables(1); B=variables(2); lamda1=variables(3); lamda2=variables(4); lamda3=variables(5); alpha=variables(6); beta=variables(7); eta=variables(8);
c=variables(9); d=variables(10); h=variables(11);
% A=1.8308e3;
% B=4.7118e2;
% lamda1=2.4799;
% lamda2=1.7322;
% lamda3=1.7322;
% alpha=0;
% beta=1.0999e-6;
% eta=7.8734e-1;
% c=1.0039e5;
% d=1.6218e1;
% h=-5.9826e-1;
% A=2846.53791410021;
% B=332.112304577964;
% lamda1=2.98165901883066;
% lamda2=1.42762362654664;
% lamda3=1.34312076622734;
% alpha=0;
% beta=0.00065961668112477;
% eta=0.214823171353063;
% c=133907.435600856;
% d=22.8707825146121;
% h=-0.700632490870871;
% A=3583.193659;
% B=410.2105509;
% lamda1=2.940194934;
% lamda2=1.539244681;
% lamda3=1.539244681;
% alpha=0;
% beta=9.38E-05;
% eta=0.663110379;
% c=106865.0717;
% d=18.55683974;
% h=-0.820575637;
% A=1.8308e3;
% B=4.7116e2;
% lamda1=2.4799;
% lamda2=1.7322;
% lamda3=1.7322;
% alpha=0;
% beta=1.099901e-6;
% eta=7.8734e-1;
% c=1.00391e5;
% d=1.6219e1;
% h=-5.9824e-1;
% A=2093.79801764599;
% B=676.777761593833;
% lamda1=2.73410014276209;
% lamda2=1.89146813149318;
% lamda3=2.38761159247034;
% alpha=0;
% beta=9.39935771935504e-006;
% eta=0.379764473760383;
% c=102125.324574127;
% d=16.5205130687821;
% h=-0.000900398912451326;
% A= 1.77e3;
% B= 4.7e2;
% lamda1= 2.472;
% lamda2= 1.721;
% lamda3= 1.721;
% alpha= 0;
% beta= 9.99e-7;
% eta= 7.2e-1;
% c= 1.11e5;
% d= 1.69e1;
% h= -6.44e-1;
R=2.85;
D=0.15;
rCutoff=3.0;
clust = 5;%GA
% dat= xlsread('siCartesian_DFT_B3LYP_FORCE_TRY.xls');%GA
temp=size(dat);%GA
total=temp(1);%GA
Vij=0;
% Vij=zeros(1,total);%GA
% xALL=zeros(total,clust);%GA
% yALL=zeros(total,clust);%GA
% zALL=zeros(total,clust);%GA
% xALL(:,3) = dat(:,3); xALL(:,4) = dat(:,5); xALL(:,5) = dat(:,8);%GA
% yALL(:,4) = dat(:,6); yALL(:,5) = dat(:,9);%GA
% zALL(:,2) = dat(:,2); zALL(:,3) = dat(:,4); zALL(:,4) = dat(:,7); zALL(:,5) = dat(:,10);%GA
% x=coord(:,1);
% y=coord(:,2);
% z=coord(:,3);
list = zeros(total,clust);%GA
list(:,1) = clust-1;%GA
list(:,2) = 2;%GA
list(:,3) = 3;%GA
list(:,4) = 4;%GA
list(:,5) = 5;%GA
% list=bondList(coord,numMov,total,rCutoff,movAtom);
% [list,listSurface] = bondList_surface(coord,numMov,numSurface,total,rCutoff,movAtom,surfaceAtom);
% countStore = 0; % ****THIS MODIFICATION IS MADE WHILE STORING THE CONFIGURATIONS
config=1;
numMov = clust;%GA
% for config = 1:total %GA%WAS WRITTEN FOR GA MAY BE USEFUL IF only Tersoff file IS RUN STANDALONE
% x= xALL(config,:); y= yALL(config,:); z= zALL(config,:);%GA
x= [0 0 dat(3) dat(5) dat(8)];
y= [0 0 0 dat(6) dat(9)];
z= [0 dat(2) dat(4) dat(7) dat(10)];
for i=1:numMov
% iMov=movAtom(i);
iMov = i;%GA
% if(list(iMov,1) ~=1 & list(iMov,1) ~=2 & list(iMov,1) ~=4)
% iMov
% end
% for j=2:list(iMov,1)+1
% jBond=list(iMov,j);
for j=1:list(config,1)+1
jBond = j;
if(jBond == iMov)
continue;
end
rij= sqrt( (x(iMov)-x(jBond)).^2 + (y(iMov)-y(jBond)).^2 + (z(iMov)-z(jBond)).^2 );
[fR] = fr(rij, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
[fA] = fa(rij, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
% [fC,Dfcij] = fc(rij,iMov,jBond);
zetaij=0;
% Dzetak= zeros(total,3);
%START 3-body parameters calculation
% for k=2:list(iMov,1)+1
% k3Body=list(iMov,k);
for k=1:list(config,1)+1
k3Body = k;
if((k3Body == iMov) | (k3Body == jBond))
continue
end
rik= sqrt( (x(iMov)-x(k3Body)).^2 + (y(iMov)-y(k3Body)).^2 + (z(iMov)-z(k3Body)).^2 );
rjk= sqrt( (x(jBond)-x(k3Body)).^2 + (y(jBond)-y(k3Body)).^2 + (z(jBond)-z(k3Body)).^2 );
[zetaij] = zeta(k3Body,rij,rik,rjk,zetaij, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
end
[bij] = b(iMov,jBond,zetaij,list, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
[fC] = fc(rij, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
Vij = Vij + fC*(fR + bij * fA);
% Vij(config) = Vij(config) + fC*(fR + bij * fA);
end %end for jBond
end %end for iMov
config;
% end %end for config
Vij = Vij/2;
% Vij(config) = Vij(config)/2;%WAS WRITTEN FOR GA
%**************************************************************************
function [fR] = fr(r, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D)
% global x y z;
% global A B lamda1 lamda2 lamda3 alpha beta n c d h R D;
fR = A.*exp(-1.*lamda1.*r);
% DrijDxi= (x(iMov)-x(jBond))./r;
% DrijDyi= (y(iMov)-y(jBond))./r;
% DrijDzi= (z(iMov)-z(jBond))./r;
%-------------------------------------------------------
function [fA] = fa(r, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D)
% global A B lamda1 lamda2 lamda3 alpha beta n c d h R D;
fA = -1.*B.*exp(-1.*lamda2.*r);
%-------------------------------------------------------
function [fC] = fc(r, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D)
% global A B lamda1 lamda2 lamda3 alpha beta n c d h R D;
if (r < (R-D))
fC = 1;
% end
elseif (r >= (R-D) & r <= (R+D))
% fC(j,k,i)=0.5-0.5.*sin(pi./2.*(r(j,k,i)-R)./D);
fC = 0.5+0.5.*cos(pi.*(r-(R-D))./(2.*D));
% end
elseif (r > (R+D))
fC=0;
end
%--------------------------------------------------------------------------
function [g_ijk] = g(rij,rik,rjk, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D)
% global A B lamda1 lamda2 lamda3 alpha beta n c d h R D;
cosTh = (rij^2 + rik^2 - rjk^2)/(2 * rij * rik);
th=acos(cosTh);
sinTh = sin(th);
g_ijk = 1+ c^2/d^2 - c^2/(d^2+(h-cosTh)^2);
%-------------------------------------------------------------------
function [zetaij] = zeta(k3Body,rij,rik,rjk,zetaij, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D)
% global A B lamda1 lamda2 lamda3 alpha beta n c d h R D;
[fC] = fc(rik, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
[g_ijk] = g(rij,rik,rjk, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D);
zetaij = zetaij + fC*g_ijk;
%--------------------------------------------------------------------------
function [bij] = b(iMov,jBond,zetaij,list, A,B,lamda1,lamda2,lamda3,alpha,beta,eta,c,d,h,R,D)
% global A B lamda1 lamda2 lamda3 alpha beta eta c d h R D;
bij=(1+ (beta^eta * zetaij^eta))^(-1/(2*eta));
if(zetaij == 0)
zetaij = 1.0e-10; % to avoid infinity if zeta is 0 then in the calculation of derivative of the bij index of beta becomes -ve, therefore it becomes infinity
end