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lammps/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt
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# This file contains a unit cell for building graphene and nanotubes
#
#
# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any
# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg")
# Surfaces constructed with this unit cell can be flat or curved into tubes.
# The distance between nearest-neighbor carbon atoms (ie the length of a
# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms.
#
# d = length of each hexagon's side = 1.42 Angstroms
# L = length of each hexagon = 2*d = 2.84 Angstroms
# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms
# w = width of hexagon rows = 1.5*d = 2.13 Angstroms
#
# Consequently, the Lattice-cell vectors for singe-layer graphene are:
# (2.4595121467478, 0, 0) (aligned with X axis)
# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d)
# So, to build a sheet of graphite, you could use:
# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
# [10].move(1.2297560733739,2.13,0)
Graphene {
2AtomCellAlignX
{
# atomID molID atomType charge x y z
write("Data Atoms") {
$atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0
$atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0
}
}
# Now define properties of the Carbon graphene atom
write_once("In Init") {
pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
}
write_once("Data Masses") {
@atom:C 12.0
}
write_once("In Settings") {
# i j epsilon sigma
pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407
# These Lennard-Jones parameters come from
# R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus,
# Chem Phys Lett, 348:187 (2001)
# Define a group consisting of only carbon atoms in graphene molecules
group Cgraphene type @atom:C
}
# Notice that the two atoms in the unit-cell above lie in the XY plane.
# (Their z-coordinate is zero). It's also useful to have a version of
# this object which lies in the XZ plan. So we define this below:
2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0)
} # Graphene
# ------------ Graphite -----------
#
# Note: For graphite: sheets stacked in the Z direction are separated by a
# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction
# by a distance of d (1.42 Angstroms). To add additional graphene layers
# you could use:
# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
# [10].move(1.2297560733739,2.13,0)
# sheet2[*][*].move(0, 1.42, 3.35)
# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0)
# [10].move(1.2297560733739,2.13,0)
# sheet3[*][*].move(0, -1.42, 6.70)
# etc...
# However, to build a thick sheet of graphite, it would
# be more efficient to use a 4-atom unit cell:
#
#Graphene {
# GraphiteCell {
# # atomID molID atomType charge x y z
# write("Data Atoms") {
# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0
# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0
# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35
# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35
# }
# } # GraphiteCell
#}
#
# Then you could create a thick sheet of graphite this way:
#
# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0)
# [10].move(1.2297560733739,2.13,0)
# [5].move(0,0,6.70)
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