The extensional package for the UEF package in LAMMPS. This package is useful for Langevin dynamics and dissipative particle dynamics to apply uniform extensional flows.
Authored by:
Takahiro Murashima
Tohoku University, Japan
Initial commit: Feb 22, 2018
Last updated: Mar 16, 2024
Support provided via issues and/or email.
This package is compiled within LAMMPS and depends on the original UEF package. Download and install LAMMPS and the UEF package according to the following sites.
(Note) The UEF package has been included in LAMMPS several years ago. You DO NOT need to get the UEF package from Rutledge Group's site.
wget https://download.lammps.org/tars/lammps-23Jun2022.tar.gz
tar zxvf lammps-23Jun2022.tar.gz
git clone https://github.com/t-murash/LAMMPS-UEFEX
cp -r LAMMPS-UEFEX/UEFEX lammps-*/src/.
mv lammps-*/src/UEFEX/domain.cpp lammps-*/src/.
Edit the following files to include UEFEX
.
lammps-*/cmake/CMakeLists.txt
lammps-*/cmake/presets/all_off.cmake
lammps-*/cmake/presets/all_on.cmake
The easiest way is, find UEF
in the above files and place UEFEX
below UEF
.
Namely, edit the following part
TALLY
UEF
VORONOI
to
TALLY
UEF
UEFEX
VORONOI
Then, build using cmake
with -DPKG_UEFEX=yes
cd lammps-*
mkdir build
cd build
cmake ../cmake -DBUILD_MPI=yes -DLAMMPS_SIZES=bigbig -DPKG_MOLECULE=yes -DPKG_UEF=yes -DPKG_UEFEX=yes
make
wget https://download.lammps.org/tars/lammps-23Jun2022.tar.gz
tar xvf lammps-23Jun2022.tar.gz
cd lammps-*/src/
make yes-molecule
make yes-uef
(yes-molecule
is necessary for examples.)
Then, get this package and install.
git clone https://github.com/t-murash/LAMMPS-UEFEX.git
cp -r LAMMPS-UEFEX/UEFEX lammps-*/src/.
cd lammps-*/src/
make yes-uefex
Finally, compile LAMMPS.
cd lammps-*/src/
make mpi mode=static
You can find 2021-Sep-29
, 2020-Oct-29
, and 2020-Mar-3
directories in LAMMPS-UEFEX/UEFEX/old
.
2021-Sep-29
contains source files compatible with 29Sep2021
of LAMMPS.
2020-Oct-29
contains source files compatible with 29Oct2020
of LAMMPS.
The source files in 2020-Mar-3
are compatible with 3Mar20
of LAMMPS and the more previous versions of LAMMPS.
Copy the source files to the lammps-*/src/UEFEX
directory according to your versions.
Then, make or cmake in the same way as described above.
(Note) These old versions are not up-to-date.
You can find several example files in LAMMPS-UEFEX/examples
.
mpirun ./lmp_mpi -in in.example
or
mpirun ./lmp -in in.example
Users of this package are encouraged to cite the following articles in scientific publications:
-
D. A. Nicholson, G. C. Rutledge, "Molecular simulation of flow-enhanced nucleation in n-eicosane melts under steady shear and uniaxial extension", J. Chem Phys. (2016) 145 (24) 244903, https://doi.org/10.1063/1.4972894.
-
T. Murashima, K. Hagita, T. Kawakatsu, "Elongational Viscosity of Weakly Entangled Polymer Melt via Coarse-Grained Molecular Dynamics Simulation", Nihon Reoroji Gakkaishi (J. Soc. Rheol. Jpn.) (2018) 46 (5) 207-220, https://doi.org/10.1678/rheology.46.207.