More details on obtaining the molecular coordinates in the local axis system

On running NEIGHCRYS, the atomic coordinates in the crystallographic axis system in the input .res file are converted to orthogonal coordinates with the origin at the centre of mass and the axes as defined in the molecular definition file, dmacrys.mols. In our example, the resulting fort.21 has the following section towards the end.

Local axis set for molecule: 1
x=> -0.742140 -0.007149 0.670207
y=> 0.016054 0.999467 0.028439
z=> -0.670053 0.031865 -0.741629

Atom positions in local axis system for molecule 1

basis No. Species x y z (Angstroms) Mass

1 C_F1_1____ -1.464668 0.014782 0.001573 12.010700
5 C_F1_2____ -0.736236 -1.183753 0.001573 12.010700
9 C_F1_3____ 0.616610 -1.189502 -0.049122 12.010700
13 C_F1_4____ 1.294184 0.014782 0.001573 12.010700
17 C_F1_5____ 0.645310 1.187066 0.055042 12.010700
21 C_F1_6____ -0.740184 1.174088 0.038737 12.010700
25 C_F1_7____ -2.960790 -0.018204 -0.030948 12.010700
29 F_F1_1____ 2.653749 0.005131 -0.009648 18.998403
33 H_F1_1____ -1.267869 -2.126345 0.043688 1.007940
37 H_F1_2____ 1.159528 -2.123091 -0.130000 1.007940
41 H_F1_3____ 1.190824 2.121134 0.108152 1.007940
45 H_F1_4____ -1.269580 2.118703 0.056894 1.007940
49 H_F1_5____ -3.290223 -0.589366 -0.890097 1.007940
53 H_F1_6____ -3.342225 0.992971 -0.101091 1.007940
57 H_F1_7____ -3.331774 -0.481880 0.874736 1.007940

basis No. Species x y z (AU) Mass

1 C_F1_1____ -2.767823 0.027934 0.002972 12.010700
5 C_F1_2____ -1.391285 -2.236969 0.002972 12.010700
9 C_F1_3____ 1.165225 -2.247835 -0.092827 12.010700
13 C_F1_4____ 2.445654 0.027934 0.002972 12.010700
17 C_F1_5____ 1.219460 2.243230 0.104013 12.010700
21 C_F1_6____ -1.398746 2.218705 0.073201 12.010700
25 C_F1_7____ -5.595084 -0.034401 -0.058483 12.010700
29 F_F1_1____ 5.014862 0.009696 -0.018231 18.998403
33 H_F1_1____ -2.395927 -4.018212 0.082559 1.007940
37 H_F1_2____ 2.191190 -4.012063 -0.245665 1.007940
41 H_F1_3____ 2.250332 4.008363 0.204377 1.007940
45 H_F1_4____ -2.399159 4.003771 0.107514 1.007940
49 H_F1_5____ -6.217623 -1.113740 -1.682040 1.007940
53 H_F1_6____ -6.315893 1.876445 -0.191035 1.007940
57 H_F1_7____ -6.296143 -0.910621 1.653013 1.007940

The atom positions (in Angstroms) are what is required for the following run of your ab initio programme.