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lammps/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
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nanotube.lt
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import "graphene.lt"
# ------------------ nanotube ---------------
# Now use this to build a simple ("zigzag") nanotube where the long-axis of each
# hexagon is aligned with the tube axis (along the Z direction). If the
# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of
# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon
# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms
# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms.
nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0) # 5.45 = R
[14].rot(25.7142857,0,0,1) #25.7=360/14
[12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14
#2.13= d*1.5
# Note: The length is 12 hexegons, the circumference is
# 14 hexegons (~=25.56 and 34.43 Angstroms, respectively).
# Move all of the unit-cells in the nanotube between the two graphene sheets.
nanotube[*][*].move(0, 0, 33.42)
# ---------- BUILDING CHIRAL NANOTUBES USING EXTERNAL SOFTWARE -------------
#
# The approach shown here works well for "zig-zag" nanotubes.
# Nanotubes with other chiralities are more difficult to make this way
# (because the tube axis is no longer perpendicular to graphene basis vectors).
# For those nanotubes, I recommend using an external program to generate
# a LAMMPS data file for the nanotube. If you want to combine the tube
# with other molecules created by moltemplate, you can then import it into
# moltemplate as a molecule object using the "ltemplify.py" utility. Details:
#
# --- VMD plugins (by Axel Kohlmeyer and Robert R. Johnson) ---
#
# The nanotube-builder for VMD can generate nanotubes (with smooth tips)
# for any chirality. These tubes also have explicit bonds between carbons:
# http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
#
# The resulting nanotube can be converted to a data file using topotools:
# https://sites.google.com/site/akohlmey/software/topotools
# To do that, select the "Extensions"->"Tk Console" menu and enter
#
# topo writelammpsdata nanotube.data full
#
# --- ltemplify.py ---
#
# That data file can be converted to moltemplate format (an .LT file)
# using the "ltemplify.py" utility.
#
# The first step is to create a short input script containing the atom_style
# command (ltemplify.py will read this script. Presumably atom_style is "full").
#
# echo "atom_style full" > nanotube.in
#
# Then run ltemplify to convert nanotube.data into a moltemplate file:
# ltemplify.py -name Nanotube nanotube.in nanotube.data > nanotube.lt
#
# You will need to edit the "nanotuble.lt" file to replace all of the
# "@atom:type1" atoms types file to match the carbon atom types in the other lt
# files (ie "@atom:../C"). If you don't plan on defining bonded interactions
# between carbon atoms, then be sure to remove the write("Data Bonds") section
# of the "nanotube.lt" file (if it is present).
#
# Finally make sure the "system.lt" contains these lines:
#
# import "nanotube.lt"
# nanotube = new Nanotube.move(?,?,?)
#
# (Replace ?,?,? with the location where you want the nanotube to go.
# You can also rotate it using .rot(angle,axisx,axisy,axiz).)
#
# ... and then run moltemplate the normal way
#
# Let me know if you run into trouble with this approach,
# and I will make note of that in this file.
#
# --- links ---
# Note: there are numerous programs for specifying the coordinates
# of the atoms in a nanotube, some of which are below.
# http://www.nanotube.msu.edu/tubeASP/
# http://turin.nss.udel.edu/research/tubegenonline.html
# http://www.ugr.es/~gmdm/java/contub/contub.html
# (You can load coordinates into moltemplate using the "-xyz" or "-pdb"
# arguments. However currently (2013-12-01), the file must contain coordinates
# for all of the atoms in your sytem, not just the nanotube.)
# -------------------------------------------------------------------------
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