## Geomoltools: A set of software modules to easily manipulate molecular geometries

*Geomoltools* is a set of eight pre- and post-treatment Fortran codes that can be used to easily manipulate molecular geometries, allowing to minimize the average energy obtained for a range of internuclear distances for the dimers of each element, and decrease the computational cost of a DFT calculation.

The set of codes are:

- mol2xyz: converts a .mol file into an ordered .xyz file
- pastemol: joins two .xyz files
- movemol: translates and aligns the molecule with some predefined axes
- stackmol: generates (manually or randomly) different stacking arrangements between two molecules
- geodiff: compares the internal coordinates of two molecules
- xyz2zmt_s: converts the cartesian coordinates contained in a .xyz file into Z-matrix (2 possible formats)
- zmt2xyz_s: converts a Z-matrix (from 2 possible formats) into cartesian coordinates
- ucubcellgen: calculates the vectors of a unit cell given some atomic coordinates.

**Modules source codes can be ****found here. For a detailed explanation of the main programs, please have a look to this file. **A complete tutorial on how to use the different codes from the package *Geomoltools* in order to manipulate (rotate, translate, join, pack, convert, etc.) molecular geometries, can be found at this address.

### Motivation and exploitation

These modules have been used to study the stacking arrangements of acceptor:donor molecules for organic photovolatics polymers by high-throughput computation with the SIESTA code. This set of codes are available under the GNU General Public License (GPL) version 2.