molecular code in matlab

This is code for molucular dynamics, but I am not sure why this code couldn't run. Error message is as belows:

error in untitled (line 4)

sum_Vsq(it) = sum_Vsq(it)+ vhx(k,it)*vhx(k,it)+vhy(k,it)*vhy(k,it);

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nonIdealTerm = 0;
sum_PE=0;    
for k=1:nP
    sum_Vsq(it) = sum_Vsq(it)+ vhx(k,it)*vhx(k,it)+vhy(k,it)*vhy(k,it);
    for k1=1:nP
        if (k1 ~= k)
            dx1=hx(k,it)-hx(k1,it); 
            dy1=hy(k,it)-hy(k1,it);
            
            % check for boundary conditions 
            if(bC == 0)
                if(dx1>sL/2) 
                    dx1=dx1-sL; 
                end 
                if(dx1<-sL/2) 
                    dx1=dx1+sL; 
                end 
                if(dy1>sL/2) 
                    dy1=dy1-sL; 
                end 
                if(dy1<-sL/2) 
                    dy1=dy1+sL; 
                end 
            end
            r1=sqrt(dx1^2+dy1^2); 
            sum_PE=sum_PE +  4*(1/r1^12-1/r1^6); 
            
            % Lennard-Jones model
            f1=24*(2/r1^13-1/r1^7); 
            fx1=f1*dx1/r1;
            fy1=f1*dy1/r1; 
            nonIdealTerm = nonIdealTerm + fx1*dx1 + fy1*dy1;
        end
    end
end

KE(it)=0.5* sum_Vsq(it);
PE(it)= 0.5*sum_PE;
TE(it) = KE(it) + PE(it);
T(it) = sum_Vsq(it)/( 2*(nP-1));
p(it) = nP*T(it)/(sL*sL);
pNonIdeal(it) = p(it) + (1/(2*sL*sL))*nonIdealTerm;
nonIdealTerm = 0
sum_PE=0;    
for k=1:nP
    sum_Vsq(it) = sum_Vsq(it)+ vhx(k,it)*vhx(k,it)+vhy(k,it)*vhy(k,it);
    for k1=1:nP
        if (k1 ~= k)
            dx1=hx(k,it)-hx(k1,it); 
            dy1=hy(k,it)-hy(k1,it);
            
            % check for boundary conditions 
            if(bC == 0)
                if(dx1>sL/2) 
                    dx1=dx1-sL; 
                end 
                if(dx1<-sL/2) 
                    dx1=dx1+sL; 
                end 
                if(dy1>sL/2) 
                    dy1=dy1-sL; 
                end 
                if(dy1<-sL/2) 
                    dy1=dy1+sL; 
                end 
            end
            r1=sqrt(dx1^2+dy1^2); 
            sum_PE=sum_PE +  4*(1/r1^12-1/r1^6); 
            
            % Lennard-Jones model
            f1=24*(2/r1^13-1/r1^7); 
            fx1=f1*dx1/r1;
            fy1=f1*dy1/r1; 
            nonIdealTerm = nonIdealTerm + fx1*dx1 + fy1*dy1;
        end
    end
end

KE(it)=0.5* sum_Vsq(it);
PE(it)= 0.5*sum_PE;
TE(it) = KE(it) + PE(it);
T(it) = sum_Vsq(it)/( 2*(nP-1));
p(it) = nP*T(it)/(sL*sL);
pNonIdeal(it) = p(it) + (1/(2*sL*sL))*nonIdealTerm;

Answer 1

[Walter Roberson]

There are a lot of undefined variables there.

There are two possibilities:

1. There might be another script that you have to execute that defines the variables; OR
2. This code might originally have been part of a function, but the function line might have been removed. The code might be intended to be invoked as a function passing in values of the missing variables.