Manual:External utilities:oct-center-geom

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1 NAME
2 SYNOPSIS
3 DESCRIPTION
4 AUTHOR
5 REPORTING BUGS
6 COPYRIGHT
7 SEE ALSO

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NAME

oct-center-geom - Centers a molecule's geometry

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SYNOPSIS

oct-center-geom

[oct-center-geom does not read the standard input: all standard input will be simply ignored. An input file named inp must be present in the running directory. Also, oct-center-geom accepts no command-line arguments, since there is not a standard way to do this with Fortran 90.]

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DESCRIPTION

This program is one of the Octopus utilities.

It reads the xyz file pointed by the XYZCoordinates variable in the inp file, and constructs one output xyz file, that will be called adjusted.xyz file, that describes the same system but in which the atomic coordinates are centered.

TO DO MERGE THIS

This utility centers and aligns the coordinates of the molecule. It reads the file specified in the input file (either by the Coordinates block, or by the XYZCoordinates or PDBCoordinates variables), and outputs the adjusted coordinates to the file adjusted.xyz.

To control the orientation of the centered molecule there are two parameters: MainAxis and AxisType.

Do not forget then to change your input file to use this file instead of your old geometry (by changing XYZCoordinates='adjusted.xyz').

Be careful with units, this utility honours the Units, UnitsInput and UnitsOutput variables, so the adjusted.xyz file will be in the specified output units.

The man pages of Octopus and of the auxiliary Octopus sub-programs (oct-something) are not intended to contain the documentation of the programs, but only their basic description. For where to find more documentation, see the SEE ALSO section below.

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