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rLAMMPS lammps
README_FIRST.TXT
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###########################################################
# Interaction of a carbon nanotube with a pair of "mystery
# molecules" (extracted from the cnat-cnt.data/in files).
###########################################################
# Author: Aysun Itai and Andrew Jewett
This example uses "ltemplify.py" to create molecule templates out
of two different molecules in a pre-existing LAMMPS IN/DATA file.
Then I show how to use "moltemplate.sh" to make copies of these
molecules and to move and rotate them (creating new LAMMPS IN/DATA files).
Disclaimer:
The molecules in this example are not physically realistic.
The purpose of this example is to demonstrate ltemplify usage.
REQUIRED INPUT FILES
cnad-cnt.data cnad-cnt.in system.lt
cnad-cnt.data
This is a LAMMPS data file containing the coordinates and the topology
for a system combining the two molecules together. ltemplify will extract
molecules from this file, one at a time.
cnad-cnt.in
This file contains force-field parameters and old run settings for the system.
(We ignore the run settings in this file.) The force-field parameters in
the "cnad-cnt.in" file are only necessary because we are going to build
a completely new set of simulation input files. (We are not only going to
rotate them and duplicate the molecules.) ltemplify.py will extract the
force field parameters from this file. This approach allows us to combine
these molecules with other types of molecules later on.)
system.lt
The "system.lt" contains the instructions what we will do with these molecules
after ltemplify.py has converted them into .LT format. In this example
it contains instructions for rotating and copying the two molecules,
(It also defines the periodic boundary conditions.)
OUTPUT FILES
cnad.lt
cnt.lt
These files are referenced in system.lt.
Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt")
creates new LAMMPS data and input files:
system.data, system.in, system.in.init, system.in.settings
(These files are referenced in run.in.nvt.)
You can run a simulation from the files created by moltemplate using
lmp_linux -i run.in.nvt
NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY
ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED.
(This was done to protect the original source of the files.)
The goal of this example is only to demonstrate how to use
"ltemplify.py" to convert lammps input and data files into
LT format and back again.)
-----------
Instructions:
Run the commands (follow the instructions) in these files:
step 1)
README_step1_run_ltemplify.sh
and then
step 2)
README_step2_run_moltemplate.sh
step 3) OPTIONAL
To run a short LAMMPS simulation, you can use the "in.nvt" file, for example:
$LAMMPS_BINARY -i run.in.nvt
where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps
(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...).
-----------
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