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# $Id$
Copyright 2006-2007 Nanorex, Inc. See LICENSE file for details.
This is Nanorex's modified version of the CoNTub source code written
by S. Melchor and J. Dobado at the Universidad de Granada in Spain.
Citations of this work should be formatted as follows:
"CoNTub: an algorithm for connecting two arbitrary carbon
nanotubes." S. Melchor; J.A. Dobado. Journal of Chemical Information
and Computer Sciences, 44, 1639-1646 (2004)
Nanorex's modifications include translation from Java to C++,
performance improvement in bond inference, changing the output file
format from pdb to mmp, and revising the stderr messages and exit code.
There are three executables. You can build them by typing "make" in this
directory. This should work on Windows (DOS or cygwin), Mac, or Linux.
Where arguments below are specified as floats, they are C/C++ double
precision floats. Integers are 32-bit signed, though in all cases
only a smaller range of values is actually valid. When the arguments
are not valid, the code prints an error message to stderr and exits
with a nonzero exitcode.
--------------------------------------------
I. Single-wall nanotubes
The SW executable (SW.exe on Windows) generates single-wall nanotubes.
It takes the following command line arguments. All six are mandatory.
SW <n> <m> <L> <T> <I> <filename>
n is an integer, the n number for chirality.
m is an integer, the m number for chirality.
L is a float, the tube's length in angstroms.
T is termination: 0 for no termination
1 for termination with hydrogen
7 for termination with nitrogen
I is an integer, the index used for the molecule name in the
model tree.
filename is the name for the output file.
--------------------------------------------
II. Multi-wall nanotubes
The MW executable (MW.exe on Windows) generates multi-wall nanotubes.
It takes the following command line arguments. All eight are
mandatory.
MW <n> <m> <L> <N> <S> <T> <I> <filename>
n is an integer, the n number for chirality.
m is an integer, the m number for chirality.
L is a float, the tube's length in angstroms.
N is an integer, the number of shells or walls.
S is the separation between shells in angstroms.
T is termination: 0 for no termination
1 for termination with hydrogen
7 for termination with nitrogen
I is an integer, the index used for the molecule name in the
model tree.
filename is the name for the output file.
--------------------------------------------
III. Heterojunctions
The HJ executable (HJ.exe on Windows) generates nanotube
heterojunctions. It takes the following command line arguments. All
nine are mandatory.
HJ <n1> <m1> <L1> <n2> <m2> <L2> <T> <I> <filename>
n1 is an integer, the n number for chirality at one end.
m1 is an integer, the m number for chirality at one end.
L1 is a float, the tube's length in angstroms at one end.
n2 is an integer, the n number for chirality at the other end.
m2 is an integer, the m number for chirality at the other end.
L2 is a float, the tube's length in angstroms at the other end.
T is termination: 0 for no termination
1 for termination with hydrogen
7 for termination with nitrogen
I is an integer, the index used for the molecule name in the
model tree.
filename is the name for the output file.
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