[CPMD-list] Pair correlation function

[Younes Ansari]

I have a trajectory file like: 

5 ----->no. of atoms 

1 ------>no. of iteration 

x1 y1 z1 

x2 y2 z2 

x3 y3 z3 

.. 

.. 

5 

2 

x1 y1 z1 

. 

. 

. 

and I want to know if you can help me write a program in Matlab. 

I have writen a program in matlab but I think there are many mistakes in it. 

would you please send me how schematicly do it.

" in this section the program gets I=no. of terations you want to calculate g(r)"';
'"                                  the time step of cpmd"';
'"                                  g=the final distance to calculate g(r)     "';
'"                                  B=the box lenght witch is mostly similar to g'";
'"                                  z=the no. of atoms                           '";
'"                                  delta=the dr                                 '";
I=input('Please input the number of Iterations: ');
timestep=input('please insert the time step of CPMD Iterations: ');
g=input('Please insert the distance: ');
B=input('Inser! t box lenght: ');
z=input('insert no. of atms: ');
delta=input('insert delta: ');
'"in this section, the program gets some parameters such as: "';
'"                t,z1,n are some parameters to get the data from EXEL that you have changed TRAJEC.xyz to an exel format and import it to Matlab program"';
'"                 j,p are counters for the final normalization of g(r) '";
'"                 e is counting the no. of lines of deteminal G(by e(lines) & 1 (columns) ,v the same as G '";
t=1;
z1=2;
n=3;
y=0;
j=1;
e=g/.2;
G=zeros(e,1);
v=zeros(e,1);
d=1;
new=0;
p=0;
'" in this section the program starts to read the first r which is 0--->g and changes by 0.2 '";
'" every time the program c! alculates r the lin=lin+1 that used to normalize g(r) '";
for r=0:0.2:g
    disp('r= ');r  
    mint=0;
    min=0;
    lin=0;
    H=0;
    '" q : in here we start to calculate the first iteration of the input file which is a 22 atom Cesium '"
    '" l is a counter to read 22 lines of the input file '"
    '" k= the first 22 line- x,y,z for the first atom and after the k is ended l=2 to calcu.. the second atom and so on to 22th atom'"
    for q=1:I
        for l=1:z
            disp('r= ');r
            for k=1:z-1
                z1=z1+1;
                if z1==n
                z1=z1+1;
                end
                y=y+1;
                '"in here the distance of each coordinate from others is calculated.'"
                R(y)=((((TRAJEC((n),1)-TRAJEC((z1),1))^2)+((TRAJEC((n),2)-TRAJEC((z1),2))^2)+((TRAJEC((n),3)-TRAJEC((z1),3))^2))^(0.5));
                '"o=the histogram to calculate'"
                o=(R(y)/delta)+0.5;
                '"fix is the same as (int) in Fortran '" 
                X = fix(o);
                mint(y)=X;
                '" in this section the program checks if the would be a R between r-delta to r+delta and if it is mint will be added to the min "';
                if y>1
                    lin=lin+1;
                    if R(y)<(r+delta) & R(y)>(r-delta)
                    min=(mint(y)+H);
                    end
                end
                '"in here mint(y) is sent to H and next time if the condition=ok the mint=mint(y)+mint(y-1)"';
                mint(y)=H;
            end
            '"in here n and z1 ar! e some parameters to chand the lines of the input file to read"'
            n=n+1;
            z1=t+1;
        end
           '" changing the lines of input file foe the next iteration'"
           t=t+z+2;
           z1=t+2;
           n=t+2;
   end
   '"calculation of the slice and the volume'" ;
   slice=((4/3)*3.141595*(((r+delta)^3)-(r^3)));
    V=(((B^3)/z)*6.02E-2);
    j=j+1; 
    v(j,1)=r;
    p=p+1;
    '"in this section g(r) will be calculated and if the first peak is appeared the mi! n of g(r) changes from zero to 1'";
    if mint>0
        new=1;
    end
    if new>=1
        G(j,1)=1+((min*V)/(slice*z*2.4*lin*p));
        else
        G(j,1)=((min*V)/(slice*z*2.4));
   end
    n=3;
    z1=2;
    t=1;
 end    





		
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