I would like to deposit 3 types of atoms (Al, Ga, N) on an AlN substrate. At the end of the simulation I find the number of atoms deposited less than the exact value(3478 in the simulation but the number of deposit atoms 4000)
Not without seeing your input script and the deposit commands you used.
this my input file
deposit.in (2.2 KB)
The documentation of fix deposit discusses in great detail how and when atoms are deposited. If the total number of atoms deposited is less than requested, there should be a warning in the output. This usually means that you are depositing atoms too quickly or allow them to be deposited too close to each other or have too small a region where atoms can be deposited or that region is too close to the area that you are depositing atoms to. There are many possibilities for making bad choices here, but they are usually easy to debug through visualization and careful testing of your simulation input.
In addition, your input file contains the
thermo_modify lost ignore keyword. If you want to keep all atoms in your system, you must not use it. It may well be that the requested number of atoms was deposited, but then some atoms - for whatever reason were lost (by leaving the system through the non-periodic boundary or by moving far too fast).