MiMiCPy guesses (or takes from a user provided list) the element symbols if not present in the topology. This is fine for the CPMD script. But, the topology used in the final MiMiC run should also have the element symbols added to the first atomtypes section in the .top file. There should be an option in the mimicpy command line tools (like repair_top or something) to do this automatically and output the right atomtypes section (or the whole topology if we get to it).
This will involve making a top writer in addition to the reader. And we should recycle the code for guessing atom symbols in top reader.
MiMiCPy guesses (or takes from a user provided list) the element symbols if not present in the topology. This is fine for the CPMD script. But, the topology used in the final MiMiC run should also have the element symbols added to the first atomtypes section in the .top file. There should be an option in the mimicpy command line tools (like repair_top or something) to do this automatically and output the right atomtypes section (or the whole topology if we get to it).
This will involve making a top writer in addition to the reader. And we should recycle the code for guessing atom symbols in top reader.