I want to calculate CH-pi, H bonds, and other kinds of interactions separately in a crystal structure using QTAIM analysis. Is there any guide for doing this? what parameter should be considered?
There are plenty of papers dealing with interaction energy at bcp (bond critical point) and other properties. In this former there are some papers like:
Article Electron Density Characteristics in Bond Critical Point (QTA...
Article Relationships between Interaction Energy and Electron Densit...
For performing QTAIM analysis, I could suggest you using Multiwfn which is a truly powerful software and completely free. For this purpose you would need either a *.fchk file, *.wfn or a *.wfx file. These latter are easily accessible via Gaussian 16 software among others (There are modules and keywords to use to have these kind of files in Gamess and ORCA and certainly others free softwares).
Concerning interaction energy, you may be interested in EDA-NOCV (Energy Decomposition Analysis - Natural Orbitals for Chemical Valence) method implemented in ORCA (free). I personnaly use SAPT (Symmetry Adapted Perturbation Theory) analysis for calculating interaction energy, which is implemented in Psi4 program (free also). It exists also NEDA (Natural Energy Decomposition Analysis) but it relies on NBO (Natural Bond Orbital) software which is not free and last version doesn't allow to perform this kind of calculation with ORCA (it works with Gamess). I think energy decomposition analysis (EDA) as I briefly gave you would be of better interest for your purpose than AIM.
There are papers that might be interesting for you:
If I remember, Multiwfn is able to perform EDA if you provide wavefunctions from your total molecule and the ones from the two fragments for which you want to calculate interaction energy. It must be in the option "100 Others functions" when Multiwfn is on and then option 8 "Generate Gaussian input file with...". The manual online may correct me and give you the procedure to follow perfectly.
Nevertheless, this EDA method suffers from the problem of BSSE (Basis-set superposition error). This latter is absent when using SAPT and option in Psi4 could allow you to access charge transfer (if you are interested in) besides dispersion energy, electrostatic energy, exchange (Pauli repulsion) energy and induction energy. For this former, especially with your system with CH--π bond that might involve it, you should perform two calculations at HF level and MP2 level and do a difference between the two obtained energy to access this dispersion energy. You could also do a HF of DFT calculation and then use dispersion method (D3 for example) to evaluate this dispersion energy comparing to the one without. In both cases, you will have to perform 'many' calculations whereas, it should be more adequate to perform only one SAPT calculation.