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the fixes atom/swap, gcmc, widom, and charge_regulation would call Modify::end_of_step() in order to make certain that all energy contributions to the total energy are properly tallied. However, this is no longer true and it causes lots of unexpected problems, since fixes like fix ave/time, fix store/state, fix print and many more are called at the wrong time during a timestep and possibly multiple times which can lead to very unexpected and incorrect results. fix atc and fix colvars are currently the only fixes that signal that they contribute to the global energy *and* run during Modify::end_of_step(). However, they do not perform any actions related to the global energy in those calls.
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 primary author of the code is Steve Plimpton, who can be emailed at sjplimp@sandia.gov. 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