Hello everyone,
I have a graphene sheet with 252 carbon atoms and 12% -OH groups (30 sites: 30 oxygen+30 hydrogen). I am stretching them along zigzag direction. I want to group the C atoms and (O+H) atoms separately using the region command. But as the -OH groups are protruding from the graphene sheet, I am confused about how to group them into different regions with mass attributes. I currently have these dimensions for C and O-H atoms:
For C atoms: For O and H atoms:
-3.05 17.85 xlo xhi 3.23 7.12
-12.80 15.60 ylo yhi -13.63 15.72
36.16 36.18 zlo zhi 34.67 36.28
#------------ define groups ------------------xxx
lattice sc 6.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region sheet block -3.05 17.85 -12.80 15.60 34.163 34.185
region R1region block -INF INF -INF INF -INF INF units box
My question is, not all O-H groups are homogeneously distributed. For example, Some C atoms are attached to a -OH groups but the neighbouring C atoms are not. So, I can’t use the coordinates of O and H atoms to define the region. Can anyone help me with this?
Regards,
Baig
As Axel said, assuming the C,O,H atoms have different
types (as defined in your input data file), then you can
create groups based on the type of the atoms, not
their coords/region. That will be much simpler for
what you are asking.
Steve
Thank you Axel and Steve for replying.
I changed the group ID in fix NVT so that graphene atoms don’t move. This is what I did:
#------------ define groups ------------------xxx
group graphene type 1
group oxygen type 2
group ho type 3
group hydroxyl type 2 3
group mobile subtract all graphene
Applying axial and shear strain by fix deform
fix 8 mobile nvt temp {temp} {temp} 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
But as I am applying strain along ZZ direction, the graphene sheet kept on stretching without fracture upto 0.5 strain (because I am running 50000 steps) which is unrealistic because pristine graphene breaks around 0.28 strain. And the stress also goes upto 192 GPa (because of the steps). If I had run longer steps I would have gotten much higher stress and strain. So, something is definitely not right. But, when I am doing fix all, the results seem reasonable but the graphene sheet travels through space which I don’t like. Do you think it’s reasonable that the sheet is moving?
Regards,
Baig
Thank you Axel and Steve for replying.
I changed the group ID in fix NVT so that graphene atoms don't move. This is
what I did:
#------------ define groups ------------------xxx
group graphene type 1
group oxygen type 2
group ho type 3
group hydroxyl type 2 3
group mobile subtract all graphene
# Applying axial and shear strain by fix deform
fix 8 mobile nvt temp \{temp\} {temp} 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
But as I am applying strain along ZZ direction, the graphene sheet kept on
stretching without fracture upto 0.5 strain (because I am running 50000
steps) which is unrealistic because pristine graphene breaks around 0.28
strain. And the stress also goes upto 192 GPa (because of the steps). If I
had run longer steps I would have gotten much higher stress and strain. So,
something is definitely not right. But, when I am doing fix all, the results
seem reasonable but the graphene sheet travels through space which I don't
like. Do you think it's reasonable that the sheet is moving?
LAMMPS is doing what you are asking it to do and follows the physics
of your model. it doesn't care whether you like it or not.
since you seems to be using well tested component, chances are that
the problem is with your design of your model.
axel.