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compute_lk command for LAMMPS

The compute_lk command can be used in LAMMPS scripts to compute topological parameters in polymers. The commands enables the computation of Writhe, Average Crossing Number, Linking integral, Periodic Writhe and Periodic Linking Number

Copyright 2021 Eleni Panagiotou and Tom Herschberg

 

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

 

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

 

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

 

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

 

Acknowledging support from NSF CAREER #2047587, NSF DMS #1913180 and NSF #1925603.

Please use the following reference to acknowledge compute_lk:

Herschberg, T. and Panagiotou, E., 2021, A computational package for measuring Topological Entanglement in Polymers, Proteins and Periodic systems (TEPPP)