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 neighboring 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
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.
grouping is done with the group command. using regions is only one
option, and in this case it doesn't make much sense. why don't you
just used the atom type to define your groups?
axel.
Hello Axel,
That is what I did actually. But I want to do NVT time integration with all the atoms except C atoms. This is what I am doing now,
group graphene type 1
group oxygen type 2
group ho type 3
Applying axial and shear strain by fix deform
fix 8 all nvt temp {temp} {temp} 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
In fix 8 I want to have any atoms other than C atoms (graphene type 1) because when I am stretching the sheet is moving. That’s why I was thinking about using region command. But I don’t know how to add oxygen and hydrogen in a different group. Should I use region UNION command?
Regards,
Baig
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.
grouping is done with the group command. using regions is only one
option, and in this case it doesn’t make much sense. why don’t you
just used the atom type to define your groups?
axel.
Hello Axel,
That is what I did actually. But I want to do NVT time integration with all
the atoms except C atoms. This is what I am doing now,
that is a rather strange idea. i don't think the resulting trajectory
will have much physical meaning.
group graphene type 1
group oxygen type 2
group ho type 3
# Applying axial and shear strain by fix deform
fix 8 all nvt temp \{temp\} {temp} 5.0 drag 1
fix 9 all deform 1 x erate ${erate1} units box remap x
In fix 8 I want to have any atoms other than C atoms (graphene type 1)
because when I am stretching the sheet is moving. That's why I was thinking
about using region command. But I don't know how to add oxygen and hydrogen
in a different group. Should I use region UNION command?
just RTFM:
type or id or molecule
args = list of one _or more_ atom types, atom IDs, or molecule IDs
any entry in list can be a sequence formatted as A:B or A:B:C where
A = starting index, B = ending index,
C = increment between indices, 1 if not specified
axel