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Asked: 2026-06-17T11:24:54+00:00

Trying to create an array from an xyz data file. The data file is

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Trying to create an array from an xyz data file. The data file is arranged so that x,y,z of each atom is on a new line and I want the array to reflect this.
Then to use this array to find find the distance from each atom in the list with all the others.

To do this the array has been copied such that atom1 & atom2 should be identical to the input file.

length is simply the number of atoms in the list.
The write statement: WRITE(20,'(3F12.9)’) atom1 actually gives the matrix wanted but when I try to find individual elements they’re all wrong!

Any help would be really appreciated!
Thanks guys.

DOUBLE PRECISION, DIMENSION(:,:), ALLOCATABLE ::atom1,atom2'
ALLOCATE(atom1(length,3),atom2(length,3))       
READ(10,*)  ((atom1(i,j), i=1,length), j=1,3)       
atom2=atom1                 
distn=0
distc=0                         

DO n=1,length
        x1=atom1(n,1)
        y1=atom1(n,2)               !1st atom
        z1=atom1(n,3)
        DO m=1,length
          x2=atom2(m,1)
          y2=atom2(m,2)         !2nd atom
          z2=atom2(m,3)`
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1 Answer

  1. Editorial Team

    Your READ statement reads all the x coordinates for all atoms from however many records, then all the y coordinates, then all the z coordinates. That’s inconsistent with your description of the input file. You have the nesting of the io-implied-do’s in the READ statement around the wrong way – it should be ((atom1(i,j),j=1,3),i=1,length).

    Similarly, as per the comment, your diagnostic write mislead you – you were outputting all x ordinates, followed by all y ordinates, etc. Array element order of a whole array reference varies the first (leftmost) dimension fastest (colloquially known as column major order).

    (There are various pitfalls associated with list directed formatting that mean I wouldn’t recommend it for production code (or perhaps for input specifically written with the knowledge of and defence against those pitfalls). One of those pitfalls is that the READ under list directed formatting will pull in as many records as it requires to satisfy the input list. You may have detected the problem earlier if you were using an explicit format that nominated the number of fields per record.)

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