Tutorial:Centering geometry

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Before running an Octopus calculation of a molecule, it is always a good idea to run the oct-center-geom utility, which will translate the center of mass to the origin, and align the molecule, by default so its main axis is along the x-axis. Doing this is often helpful for visualization purposes, and making clear the symmetry of the system, and also it will help to construct the simulation box efficiently in the code. The current implementation in Octopus constructs a parallelepiped containing the simulation box and the origin, and it will be much larger than necessary if the system is not centered and aligned. For periodic systems, these considerations are not relevant (at least in the periodic directions).

We need only a very simple input file, specifying the units and the coordinates.

inp

XYZCoordinates = "tAB.xyz"

We will use this coordinates file, for the molecule trans-azobenzene, which has the interesting property of being able to switch between trans and cis isomers by absorption of light.

tAB.xyz

24

C   -0.520939   -1.29036    -2.47763
C   -0.580306    0.055376   -2.10547
C    0.530312    0.670804   -1.51903
C    1.71302    -0.064392   -1.30151
C    1.76264    -1.41322    -1.67813
C    0.649275   -2.02387    -2.26419
H   -1.38157    -1.76465    -2.93131
H   -1.48735     0.622185   -2.27142
H    2.66553    -1.98883    -1.51628
H    0.693958   -3.06606    -2.55287
H    0.467127    1.71395    -1.23683
N    2.85908     0.52877    -0.708609
N    2.86708     1.72545    -0.355435
C    4.01307     2.3187      0.237467
C    3.96326     3.66755     0.614027
C    5.0765      4.27839     1.20009
C    6.2468      3.54504     1.41361
C    6.30637     2.19928     1.04153
C    5.19586     1.58368     0.455065
H    5.25919     0.540517    0.17292
H    3.06029     4.24301     0.4521
H    5.03165     5.32058     1.48872
H    7.10734     4.01949     1.86731
H    7.21349     1.63261     1.20754

oct-center-geom is a serial utility, and it will be found in the bin directory after installation of Octopus.

When you run the utility, you should obtain a new coordinates file adjusted.xyz for use in your calculations with Octopus. The output is not especially interesting (except for perhaps the symmetries and moment of inertia tensor). Visualize the original and new coordinates files with xcrysden or your favorite visualization program (e.g. Jmol, Avogadro, VMD, Vesta, etc.), and see what transformations the utility performed. You can see more options about how to align the system at AxisType and MainAxis.


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