3. Executing program

This script run symeess from terminal

To run the program from terminal just use

$ symeess_script

3.1. Shape

This flags requires the “-label reference_polyhedra” flag. The list of flags to run shape in symeess are the following

· -m *Shape measure of input structure with reference polyhedra*
· -s *Calculate the ideal structure for the input structure*
· -t *Print the reference structure of the given label*

Optional flags for shape are

· -c int\ *where int is the postion of the central atom in your structure*
· -o output_name *output name without extension*

Extra flags

· -n int\ *generate the possible ideal structures with int vertices stored in the program*
· -map *calculates the minimal distortion interconversion path between two given polyhedra*
· -path *calculates the path deviation function as well as the generalized coordinate of the studied
structures in a given path*

3.1.1. Examples

If you want to make a simple measure of a tetrahedron molecule and compared to the ideal tetrahedron structure

$ symeess_script -m -label T-4 -input_file input_name

Also you can do the same but for a tetrahedron molecule that have a central atom, i.e. in the first position

$ symeess_script -m -label T-4 -c 1 -input_file input_name

To save it with a specific name

$ symeess_script -m -label T-4 -c 1 -output_name example_name -input_file input_name

To calculate the map between the tetrahedron and the square

$ symeess_script -map -label T-4 SP-4

the output will be in the results folder.

3.2. Symgroup

This flags requires the “-group reference_polyhedra” flag. The list of flags to run shape in symeess are the following

· -symm *Symgroup measure of input structure with reference polyhedra*