Dear All:
I am trying to simulate a system consisting of fullerene
molecules
on heterogeneous silicon surface having defects using lammps. The
surface contains two types of silicon atoms, on the top of which
there are some fullerene molecules. The surface atoms are supposed
to keep
frozen during simulation and fullerene molecules are treated as
rigid body.
For the sake of simplicity, I have taken a
homogeneous silicon surface containing only one type of silicon
atoms and few fullerene molecules on the top.
units real
atom_style atomic
boundary p p p
read_data [data.si](http://data.si)
pair_style tersoff
pair_coeff * * SiC.tersoff Si C
velocity all create 300.0 352839
timestep 1.0
group clump1 id <> 1 3276
group c60 id <> 3277 4236
fix 1 clump1 recenter INIT INIT INIT units box
fix 2 c60 rigid molecule
#fix 2 c60 nve
#fix 2 c60 nvt 300.0 300.0 100.0
thermo 100
dump 1 all xyz 50 dump.c60
run 2000
#data file Si and C60
4236 atoms
2 atom types
-31.7 31.7 xlo xhi
-57.2 57.2 ylo yhi
-75.0 75.0 zlo zhi
Masses
1 28.0000
2 12.0000
Atoms
atom-type x y z
1 1 -31.1849995 31.1850204 3.0400000
----- --- ----- ---- ---
3276 1 ---- ---- ----
----- --- ---- ---- ----
3277 2 --- --- --
---- --- --- --- ---
4236 2 --- -- --
then it is showing error: Must use a molecular atom style with fix
rigid
molecule,
then I moved to "fix 2 c60 rigid single", then I found that all the
fullerene molecules are moving as a single body and silicon surface
remain as
stationary. After that I changed atom_style to "atom_style
molecular" along
with
the data file-
group c60 id <> 3277 4236
fix 1 clump1 recenter INIT INIT INIT units box
fix 2 c60 rigid molecule
and data file having format as given below
4236 atoms
2 atom types
-31.7 31.7 xlo xhi
-57.2 57.2 ylo yhi
-75.0 75.0 zlo zhi
Masses
1 28.0000
2 12.0000
Atoms
molecule-tag atom-type x y z
1 1 1 -31.1849995 31.1850204
3.0400000
----- --- ----- ---- ---
3276 1 ---- ---- ----
If you want to use fix rigid molecule, then the clumps
of atoms you want to be rigid (fullerenes) have to
have a moleclue ID in the data file. Hence you need
to use atom_style molecular or another one that
includes moleclue IDs. Atom_style molecular does
not define charges, so I don't follow your comment on q.
If you assign molecule IDs correctly, then each fullerene
will be your rigid body. I.e. different mol IDs for
the atoms of each fullerene.
Steve