1. SPRING
TWO MASSES – CREATING XYZ FILE
AND ANIMATION

2. XYZ file format

3. XYZ file format - animation

4. SPRING
OPEN NEW SCRIPT!

5. SPRING - initial values
clc
clear
L=1;
k=1;
m=1;
T=10;
dt=0.1;
n=T/dt;

6. SPRING - initial values
x1(1)=-0.5;
x2(1)=L+1;
t(1)=0;

7. SPRING - animation
f=mopen("harmonic.xyz", "w"); //creating file "harmonic.xyz" for writing
mfprintf(f,"2\n"); // 2 for the number of atoms and "\n" for the new line
mfprintf(f,"\n");
mfprintf(f,"C %8.3f %8.3f %8.3f\n",x1(1),0,0);
mfprintf(f,"C %8.3f %8.3f %8.3f\n",x2(1),0,0);
// C is the symbol of atom, 8 represents the size of the text box with number, 3 - number of decimal digits, x2(1) represents x coordinate, y and z

8. SPRING - loop for i=1:n dl=(x2(i)-x1(i)-L); dv1=k*dl/m*dt; dv2=-dv1;
v1(i+1)=v1(i)+dv1;
v2(i+1)=v2(i)+dv2;
x1(i+1)=x1(i)+v1(i+1)*dt;
x2(i+1)=x2(i)+v2(i+1)*dt;
t(i+1)=t(i)+dt;
mfprintf(f,"2\n");
mfprintf(f,"\n");
mfprintf(f,"C %8.3f %8.3f %8.3f\n",x1(i+1),0,0);
mfprintf(f,"C %8.3f %8.3f %8.3f\n",x2(i+1),0,0);
end
plot(t,x1,t,x2)
mclose(f) // closing the file

9. TO EXECUTE

10. SPRING - results

11. SPRING - animation
Open VMD. Go to File|New Molecule…

12. SPRING - animation In the Molecule File Browser click Browse…
Look for file: harmonic.xyz in the
Documents and open it. Click Load.

13. SPRING - animation
Then go to Graphics|
Representations…

14. SPRING - animation Go to Drawing method and choose CPK.
Open VMD OpenGL Display Window
and enjoy the result.