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* oxDNA potential file reading and real units This allows for pair and bond coefficients to be read from an appropriately formatted potential file, and also allows for the use of 'real' units within oxDNA1. The correct backend coefficients for pair and bonded interactions are set when the atom vector is initialised through the "ConstantsOxdna" class, based on the units specified within the input file. * Extract seqav/seqdep and temp from potential files Also includes miscellaneous string consistency changes and removes unnecessary parameter from reader.next_line instances. * oxDNA2 potential file reading and real units This extends previous changes to oxDNA2 specific potentials, being FENE, excluded volume, coaxial stacking and Debye-Hückel. Units now default to LJ values rather than 0. * oxDNA potential files * LJ <-> real units conversion tool Converts standard oxDNA data and input file to real units, with inverse flag available for real -> LJ. * oxRNA2 potential file reading and real units For RNA, d_cs_x is treated as d_cs within ConstantsOxdna in order to reduce code duplication and complexity. * Reparameterise real units * Generalise PotentialFileReader logs * Extract stk xi and kappa from potential files This allows users to edit these values from the input script, as is documented, rather than them being within the potential files. * Real unit and potential file documentation This adds examples for real unit parameters and specific potential file documentation for each bond and pair style.
This is the LAMMPS software package. LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. ---------------------------------------------------------------------- LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL) version 2. The code is maintained by the LAMMPS development team who can be emailed at developers@lammps.org. The LAMMPS WWW Site at www.lammps.org has more information about the code and its uses. The LAMMPS distribution includes the following files and directories: README this file LICENSE the GNU General Public License (GPL) bench benchmark problems cmake CMake build files doc documentation examples simple test problems fortran Fortran wrapper for LAMMPS lib additional provided or external libraries potentials interatomic potential files python Python wrappers for LAMMPS src source files tools pre- and post-processing tools Point your browser at any of these files to get started: https://docs.lammps.org/Manual.html LAMMPS manual https://docs.lammps.org/Intro.html hi-level introduction https://docs.lammps.org/Build.html how to build LAMMPS https://docs.lammps.org/Run_head.html how to run LAMMPS https://docs.lammps.org/Commands_all.html Table of available commands https://docs.lammps.org/Library.html LAMMPS library interfaces https://docs.lammps.org/Modify.html how to modify and extend LAMMPS https://docs.lammps.org/Developer.html LAMMPS developer info You can also create these doc pages locally: % cd doc % make html # creates HTML pages in doc/html % make pdf # creates Manual.pdf