File Formats

.xyz files

atomaccess expects the XMOL standard for .xyz files, and will exit with an error message if this standard is not followed.

A .xyz file should be formatted as follows

.xyz file format supported by atom_access

 NUMBER OF ATOMS AS INTEGER
 COMMENT LINE (CAN BE EMPTY)
 ATOMLABEL1 XCOORD YCOORD ZCOORD
 ATOMLABEL2 XCOORD YCOORD ZCOORD
 ATOMLABEL3 XCOORD YCOORD ZCOORD
 ...

Where the atom label consists only of letters, and all coordinates are in Angstrom.

For example, here is the contents of a valid .xyz file for benzene

benzene.xyz

 12
 Benzene
 H      1.2194     -0.1652      2.1600
 C      0.6825     -0.0924      1.2087
 C     -0.7075     -0.0352      1.1973
 H     -1.2644     -0.0630      2.1393
 C     -1.3898      0.0572     -0.0114
 H     -2.4836      0.1021     -0.0204
 C     -0.6824      0.0925     -1.2088
 H     -1.2194      0.1652     -2.1599
 C      0.7075      0.0352     -1.1973
 H      1.2641      0.0628     -2.1395
 C      1.3899     -0.0572      0.0114
 H      2.4836     -0.1022      0.0205