UEFEX

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.

Installation

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.

• LAMMPS
• RutledgeGroupMIT/UEF

(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.

Build LAMMPS with cmake

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

Build LAMMPS with 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

For old version users (29Sep2021, 29Oct20, 3Mar20)

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.

Usage

You can find several example files in LAMMPS-UEFEX/examples.

mpirun ./lmp_mpi -in in.example

or

mpirun ./lmp -in in.example

Citing the UEFEX package

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.