Problem with ghost atoms

[mcaroba]

I got an error when running according to the instructions. The error seems to be related to the implicit assumption than the extract_atom() function only returns the real atoms. Lammps also seems to return the ghost atoms (see the Note here: https://docs.lammps.org/Python_module.html#lammps.lammps.extract_atom).

I hacked the panda.py file like so to enable execution of the program, but I don't know if I'm breaking something else by doing this ("migudo is just to remind me where I made changes):

#        atom_ids = self.lmp.numpy.extract_atom("id")
#        x = self.lmp.numpy.extract_atom("x")
        atom_ids = self.lmp.numpy.extract_atom("id")[0:len(self.atom_ids)] # migudo
        x = self.lmp.numpy.extract_atom("x")[0:len(self.atom_ids)] # migudo

This ugly hack seems to let me run the simulation. I'm now try to figure out how to set up the actual physical parameters (barostat, thermostat, and various inputs) to more or less transform the system in the ways I want it to.