My problem is about calculation of rdf for a group of center of mass of user-defined atom groups. i.e.
Each atom-group provides one COM, and I need the rdf of these COMs. This can be related to
more generalized cases, such as the rdf of dummy atoms associated with a group of atoms in some way.
To my knowledge about lammps, rdf fix allows to calculate rdf based on atom groups. But I can’t see
an easy way to use dummy atom with this fix. One possible solution is to put some particles/atoms into
the system and decouple them from the REAL particles and the thermostat. Then update the positions of these dummy
particles manually while the position of real atoms being changed. Finally apply fix rdf to these dummy
However, there are some things uncertain to me.
Should I manually handle the PBC for these dummy particles? E.g. the real atoms associating with
a dummy particle can be wrapped into another side of the simulation box when they flee away , should I have to
ensure all dummy atoms also be wrapped into the simulation box by hand? Does this handled correctly by
fix rdf when I use dummy particles?
Is there a better way to achieve this without using ‘real’ dummy particles? E.g. I see we can easily obtain
COM by the group function xcm(ID) of variable or com fix. How can I use these available variables with
‘fix rdf’ directly(without really putting particles into the system)? It will be very convenient and powerful if
lammps supports using a group of variables as parameter for some ‘computes’ and ‘fixes’ in addition to group-ID.
(something like ‘fix ID var-group-ID rdf…’) Or allows to define some variables in memory as a normal ‘atom-group’.
This will save a lot of energy on designing and constructing some tricky model systems, since people can really
‘design’ a new model system on the fly based on some computed data.
I have to say I’m not quite familiar with lammps yet. So the questions or suggestion may be stupid. Please
leave me some advice or solution if you can. Thanks in advance!