This package contains the code for performing data assimilated MD
simulation [1] or using reinforcement learning to fit experimental
data [2]. The added code is mainly contained in src/DIFFRACTION
directory. Go to release for detailed usage examples.
[1] Y. Z., R. S., and S. T., Journal of Non-Crystalline Solids,
vol. 600, p. 122028, 2023.
[2] Y. Z., The Journal of Chemical Physics, vol. 155, no. 23,
p. 234501, 2021.
---------------------
Data assimilation:
- Use `xndaf' pair style, usually combined with hybrid/overlay.
- `omp' and `gpu' versions are also available
- Coefficients should be set by
pair_coeff * * sqex_file atom_types neutron_bs nbin_r r_max \
nbin_q qmax force_cutoff_r factorx factorn update_interval \
output_interval sq_out_file gr_out_file
Last 3 variables are mainly for debugging purposes.
The older version does not take the force_cutoff_r argument (set
to r_max automatically).
- Experimental file sqex_file should have for following format:
q sq_x weight_x k_x m_x sq_neutron weight_neutron k_n m_n
q must be compatible with nbin_q and qmax in pair_coeff:
q[i] = (i + .05) * qmax / nbin_q
Here, the structure factor sq is related to the intensity iq by
iq = k * sq + m.
- The penalty function is added to total energy, but the resulting
pressure is not. Therefore, never use NPT thermostat with xndaf.
---------------------
Reinforcement learning:
- Use `fmirl' pair style, may combine with hybrid/overlay.
- Coefficients
pair_coeff * * data_file init_file force_cutoff base \
learning_rate momentum update_interval output_interval \
fe_out gr_out
if base==1, g(r)-1 is used to compute features instead of g(r).
- Format for binary `data_file':
nfea, r_max, nbin_r, n_type, u0_0_0...u0_[npair-1]_[nbin_r-1], \
uf__...uf__, f0__...f0__, ff__...ff__,fea_true_...,l2__
Total potential is then
u_{ij} = u0_{ij} + \sum_k^{nfea} uk_{ij}.
f0 and ff is the corresponding force divided by r.
fea_true is the true features:
Fk = \sum_{ij} uf_{ij}(r_{ij}).
`init_file' is a binary file containing initial weights.
**********************************************************************
======================================================================
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