Yes. Although you could also add things like CH4 to the atom-mass table.
and then confuse it with oxygen???
or CH2 with nitrogen?
> proper masses, but that is also difficult. there are slightly
> different conventions on what is the proper mass for a hydrogen,
In my code I assign a symbol that has the closest mass to the given
mass, so slightly different mass is not a problem.
> carbon etc. and how do you handle united atoms or other systems.
> also some people would prefer to have some arbitrary text label.
There are visualization programs that can understand atom symbols, and
that's why I like to have symbols in the file. If you use arbitrary
text labels, I suppose they won't be of any help to a visualization
au contraire, there are a lot of reasons to differentiate
between different atoms of the same element. e.g. atoms in
different regions or in different compounds.
> for (bio)molecular systems, i usually prepare a .psf file with
> the information that i want to assign to atoms (and i can
> have atom name and type) and then use the .dcd + .psf combination
> in analysis and visualization.
OK, no doubt .xyz is not the best format for everything.
exactly. it is more like the lowest common denominator.
>> If you think it can be useful, I'll try to add it as a feature of dump command.
> well, it is not up to me to decide what goes into the code or not.
I'm glad that you wrote what you think about my proposal although I'm
not sure what are you conclusions.
my conclusion is that rather than trying to improve output in
a file format that has many known deficiencies, i'd rather try
make the programs that don't read the native lammps format better.
e.g., i just had an off-list discussion and received some code fragments
that will in combination with some additional changes help making
the native text mode LAMMPS support in VMD much better. this way
more information is preserved and passed on.
xyz is not a perfect format, and the symbol guessing, as I wrote,
won't work in all cases.
Perhaps I didn't write it explicitely, but since it sometimes wouldn't
work, I meant it as an optional feature, perhaps triggered by
additional argument to dump command.
that is what i understood. i just wanted to point out that if you
add a change like this, it should be as generic as possible, and
i know from my work on the VMD plugins, that mass based guessing
is a matter of last resort and fails quite often.