DeaLAMMPS

Heterogeneous Multiscale Method implementation featuring Deal.II (FE) and LAMMPS (MD). Enables simulations coupling semi-concurrently the evolution of an atomistic and a continuum system. The evolution of the continuum system drives the mechanical evolution of the periodic homogeneous atomistic replicas.

More details about this algorithm can be found in the following publication:

Maxime Vassaux, Robin Richardson and Peter Coveney. The heterogeneous multiscale method applied to inelastic polymer mechanics. Philosophical Transactions A, 377(2142), doi:10.1098/rsta.2018.0150.

Dependencies:

At the moment, there are strict dependencies on the versions of various packages required by this softare stack. The bootstrap/platform infrastructure below has been tested on a number of clusters/supercomputers (running linux) and is therefore recommended.

• gcc 6.3.0
• cmake 3.5.2
• gnu make 4.1 or greater, preferably 4.2.1

v8.4.1 of Deal.II is the only supported one. Deal.II need to be compiled with the dependencies required to run the tutorial step-18, that is the following dependencies: MPI, PETSc, METIS, BOOST, HDF5, LAPACK, MUPARSER, NETCDF, ZLIB, HDF5, and UMFPACK. Complete instructions can be found here. An important aspect is that the MPI support for DealII and its dependencies must be built with MPICH (will not work with OpenMPI!)

The recommended versions of a few libraries are given below

• Boost libraries 1.60.0
• Petsc & slepc 3.6.4 with 64-bit int support

LAMMPS versions 17Nov16 through 7Aug19 have been tested.

LAMMPS need to be compiled as a shared library with MPI support, along with the RIGID and USER-REAXC packages:

Here is an example make invocation for the 16Nov16 version

cd /path/to/lammps-17Nov16/src
make yes-RIGID
make yes-USER-REAXC
make mode=shlib mpi

Continuum mechanics equilibrium equations are solved on the basis of a linear elastic material. Non-linear stress/strain beahvior is captured running MD simulations of a sample of material subject to the continuum strain when needed.

The number of MD simulations can be drastically reduced through a graph reduction method with thresholding of "similarity" of one microstate's material history (strain vs time) with another - currently using L2 norm.

Compile and run:

After installing separately LAMMPS and Deal.II, and building your MD input lammps data file.

cd /path/to/DeaLAMMPS
cp CMakeLists/example_machine.CMakeLists.txt CMakeLists.txt
mkdir build

cmake ../
./dealammps inputs_hmm.json

Additionally, a FE mesh can be imported from a GMSH file, and most of the parameters of the simulation can be found in dealammps.cc

Publications:

Vassaux, M., Richardson, R. A., & Coveney, P. V. (2019). The heterogeneous multiscale method applied to inelastic polymer mechanics. Philosophical Transactions of the Royal Society A, 377(2142), 20180150.

Vassaux, M., Sinclair, R. C., Richardson, R. A., Suter, J. L., & Coveney, P. V. (2019). The Role of Graphene in Enhancing the Material Properties of Thermosetting Polymers. Advanced Theory and Simulations, 2(5), 1800168.

Vassaux, M., Sinclair, R. C., Richardson, R. A., Suter, J. L., & Coveney, P. V. (2019). Towards high fidelity materials property prediction from multiscale modelling and simulation", Advanced Theory and Simulations. Accepted for publication.