Currently AddData.py checks that mapping file and simulation have the same amount of atoms. If not, they script is stopped but an option to bypass is given. This is good, but it does not give any further information where the problem might be. In practice, I have been ending up to bypass the problem and then running analysis codes to get better idea where the problem is, and then returning back to AddData after locating and fixing the problem. This is not ideal.
I think that the solution would be to write a better sanity check function to AddData.py that would not only check the number of atoms, but also if the names match and report which atoms cause the problem.
Currently AddData.py checks that mapping file and simulation have the same amount of atoms. If not, they script is stopped but an option to bypass is given. This is good, but it does not give any further information where the problem might be. In practice, I have been ending up to bypass the problem and then running analysis codes to get better idea where the problem is, and then returning back to AddData after locating and fixing the problem. This is not ideal.
I think that the solution would be to write a better sanity check function to AddData.py that would not only check the number of atoms, but also if the names match and report which atoms cause the problem.