I want to read .xyz file which looks like....
3 !no. of particles
1.0000 ! time step
a 2.345 2.458 0.564 ! ID x y z for 1st particle
a 5.455 2.486 5.456 ! ID x y z for 2nd particle
a 6.545 4.566 2.665 ! ID x y z for 3rd particle
3 !no.of particles (same as before)
2.000 ! next time step
a 4.345 3.458 4.564 ! ID x y z for 1st particle
a 4.455 3.486 4.456 ! ID x y z for 2nd particle
a 8.545 3.566 4.665 ! ID x y z for 3rd particle
...... continue..... for 1000 time step
I want to calculate distance of each particle from others at each time step. How to read this file?
program size
implicit none
integer i,j,k
integer,parameter :: n=400,t=714
integer dn(n),n1
real*8 px(n,t),py(n,t),dt,pz
character(75) nam
open (unit=50,file='vmd.xyz',status='old',action='read')
do k=1,t
do i=1,n
read(50,*) n1
read(50,*) dt
read(50,*) nam,px(i,k),py(i,k),pz
end do
end do
close(50)
end program
Now that you posted a code, it is much easier to help you.
You always read 400 coordinates, whatever the number of particles.
You repeat 400 times the reading of the number of particles and of the timestep. Only the line read(50,*) nam,px(i,k),py(i,k),pz should be in the loop. Try
program size
implicit none
integer i,j,k
integer,parameter :: n=400,t=2
integer dn(n),n1
real*8 px(n,t),py(n,t),dt,pz
character(75) nam
open (unit=50,file='vmd.xyz',status='old',action='read')
do k=1,t
read(50,*) n1
read(50,*) dt
do i=1,n1
read(50,*) nam,px(i,k),py(i,k),pz
end do
end do
close(50)
end program
This method for analyzing MD data (read all in memory then proceed) can be very memory intensive and useful only for short/small simulations.
You can try existing libraries: