Thanks for your suggestion Ihab Eddine Djellas , but in my view,i know SageMath is a free and open source software for performing mathematical calculations.
Is there any methods to draw crystal structures with this software?
You can use GeoGebra too. GeoGebra is also FREE software, multi-platform, and translated on many languages. I am aware it is not the best tool, but smth like that on above figure ^^ can be done in GeoGebra for sure, and it is nothing hard to do...
Thanks a lot Anton Vrdoljak for your suggestion. I downloaded the GeoGebra,although there is no equation or formula for solid crystals to put in this software.
For instance, there is a site that illustrates all the graphs related to the solid structure by the lattice parameter,fractional coordinates and material details.
To Malikeh Rostamzadeh : your site seems very good! Regarding GeoGebra, I already wrote that is not the best tool for this issue, but such graphs can be done there. GeoGebra is having 3D window, where we can place dots or even spheres with some constant radius. All elements can be in colors... Lines (bonds) is easy to draw and to color too...