At real situation, it can happen, that a crystal can have defects, for instance, some of them are point defects — Schottky, Frenkel defects, line defects — dislocations, planar defects — grain boundaries, twin boundaries. So is there a free software that can help to model a crystal structure with defects to get afterwards crystal nodes coordinates to prepare input file for a calculation, for example, in the Quantum Espresso? Or maybe is there some free Python scripts to model these things with or without visualization?
For point defects like a Schottky pair, you can get the defect formation energies from DFT calculations at 0 K or from AIMD calculations at finite temperatures. For these, you can use codes like VASP or Quantum ESPRESSO. The uncertainty in these calculations is typically in the range of a few tenths of eV.
VASP or Quantum ESPRESSO inputs/outputs are visualized using VESTA or XCrySDen.
If you have a really good interatomic potential, e.g., a modified embedded-atom method (MEAM) potential, or an angular-dependent potential (ADP), you can also get point defect formation energies from MD simulations employing codes like LAMMPS. The uncertainty in these calculations is typically in the range of 1-3 eV. Bigger uncertainty just means your potential is not suitable for this kind of calculation.
For 1-D defects (e.g., dislocations) and 2-D defects (e.g., grain boundaries), LAMMPS is typically used to get the linear/interfacial energies of these defects.
LAMMPS inputs/outputs are visualized using OVITO or VMD. For OVITO, you may need to use some modifications (e.g., Atomic Strain and then Color Coding) to be able to see 1-D and 2-D defects.
For 3-D defects, typically people resort to phase-field modeling, using codes like MOOSE. These calculations usually take many inputs from experiments and DFT/MD calculations.
MOOSE outputs are visualized using PraraView or MOOSE's built-in software Peacock.
Except for VASP, all these tools are free. OVITO has a free version and a Pro version.