helix.create_helix

helix.create_helix(file_lattice='', output_name='helix.data', output_name_cast='helix_cast.data', mass_map={}, cap_missing=2)

create_syst(rota,D,pitch,width,thickness,int_thick,clean_structure=True,periodic=True,circling=True,do_rota_transf=False,file_lattice=”beta_quartz.data”,do_angles=False)

This functions creates the whole system using the dimensions stated. It creates two files : by default quartz_dupl.data and quartz_int.data which contains the data of the surface and the data of the cast respectively.

Parameters:

• rota (float) – the amount of turns made by the helix

• diameter (float) – the diameter of the circle containing the helix.

• pitch (float) – the pitch, or the period of the helix

• width (float) – the width of the helix

• thickness (float) – the thickness of the helix

• clean_structure (bool, optional) – To clean or not the structure by adding H2O. By default True

• periodic (bool, optional) – do the creation of a periodic system after the transformation

• circling (bool, optional) – Circle the basis of the cuboid. This should be used to create helices as is gives much better curvatures. By default True

• do_rota_transf (bool, optional,) – Use the rota transformation instead of the helix one. This should not be used as it gives much worse structure. By default False

• file_lattice (float, optional,) – the file containing the lattice that will be duplicated

• do_angles (bool, optional) – write the angles SiOH

Returns:

• Helix (helix) – helix object that contains the information of the system

• Two files are also created (quartz_dupl.data and quartz_int.data by default)