I crushed my nanoparticles with mortar and pestles before XRD analysis. Can this process loose crystalline nature? If so, please suggest some good technique for deagglomeration?
If you are working with the material close to Cu2S, the loss of crystallinity is not dangerous. These materials have very high diffusion mobility of copper, allowing correct defects in the crystal structure at high speed. If you are working with materials rich in sulfur, they are fragile and are easily dispersed.
Usually, grinding incorporates stresses into the material, which in-turn causes broadening of XRD peaks (ones having 2 theta greater than 45 degree). you can relax the stresses by low temperature inert thermal treatments.
You can use deaggregate those nanopartcle by using an ultrasonic probe. By sending ultrasonic waves to the aggregate, usually the aggregates dissolve and become smaller.