Hi everyone
I want to make the broken molecules whole at boundary by lammps. But lammps seems do not have such key words. So I used dump tool with owrap() keywords in pizza.py to do it. I have got unscaled atom coordinates(x,y,z) from lammps. I start pizza.py on my computer, and then I type following command
d=dump(“coro-x.lammpstrj”) #coro-x.lammpstrj is name of dump file from lammps
d.owrap(’'id")
d.write(“trj”)
I got new trj file processed by the owrap() keywords without any error message.
However, the molecules are still broken at boundaries when I load trj file in ovito to visualize it. My questions are
(1)Can I get the broken molecules whole at boundary by lammps directly?
(2)If (1) is impossible?Can owrap() keyword in pizza.py make broken molecules whole at boundary ? If it can do that, is there something wrong with my processes?
(3)If owrap() keyword cannot do it, is there other tool in pizza.py can do that?
Sincerely
Fan Li
Hi everyone
I want to make the broken molecules whole at boundary by lammps. But lammps
seems do not have such key words. So I used dump tool with owrap() keywords
in pizza.py to do it. I have got unscaled atom coordinates(x,y,z) from
what you want is different from what the dump.owrap() method does.
lammps. I start pizza.py on my computer, and then I type following command
d=dump("coro-x.lammpstrj") #coro-x.lammpstrj is name of dump file from
lammps
d.owrap(''id")
d.write("trj")
I got new trj file processed by the owrap() keywords without any error
message.
However, the molecules are still broken at boundaries when I load trj file
in ovito to visualize it. My questions are
i don't know ovito, but VMD.
(1)Can I get the broken molecules whole at boundary by lammps directly?
molecules can be visualized as whole, if you output unwrapped
coordinates (or wrapped coordinates *and* image flags). that requires
that your molecules were not wrapped in your original restart/data
file (LAMMPS prints a warning when this happens).
however, this will scatter the molecules across multiple periodic
images. there is no mechanism in LAMMPS to keep molecules whole *and*
wrap them as whole molecules. in VMD, this can be done after the fact
with the pbctools plugin, which allows wrapping by "fragment".
(2)If (1) is impossible?Can owrap() keyword in pizza.py make broken
molecules whole at boundary ? If it can do that, is there something wrong
with my processes?
dump.owrap() does not do what you think it does.
(3)If owrap() keyword cannot do it, is there other tool in pizza.py can do
that?
i don't know. again, the pbctools plugin for VMD has a join function
that can do what you are looking for.
axel.