LAMMPS is a classical molecular dynamics code, and an acronym for
Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS has potentials for solid-state materials (metals,
semiconductors) and soft matter (biomolecules, polymers) and
coarse-grained or mesoscopic systems. It can be used to model atoms
or, more generically, as a parallel particle simulator at the atomic,
meso, or continuum scale.
LAMMPS runs on single processors or in parallel using message-passing
techniques and a spatial-decomposition of the simulation domain. Many
of its models have versions that provide accelerated performance on
CPUs, GPUs, and Intel Xeon Phis. The code is designed to be easy to
modify or extend with new functionality.
LAMMPS is distributed as an open source code under
the terms of the GPL. The current version can be downloaded
here. Links are also included to older F90/F77
versions. Periodic releases are also available on
(see the Pictures and
Movies pages for more examples of LAMMPS
Blood flow in capillaries
This is work by Kirill Lykov (kirill.lykov at usi.ch), Xuejin Li et al
at the USI, Switzerland and Brown University, USA to develop new Open
Boundary Condition (OBC) methods for particle-based methods suitable
to simulate flow of deformable bodies in complex computational domains
with several inlets and outlets.
The image (left) and movie (right) show the application of the OBCs to
red blood cell flow in a straight pipe, bifurcation, and a part of a
capillary network. The program Blender was used for the rendering.
This paper has further details.
Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow
Simulations: Application to Arterial Bifurcations and Trees, K.
Lykov, X. Li, H. Lei, I. V. Pivkin, G. E. Karniadakis, PLoS
Computational Biology 11(8): e1004410