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Updated README for USER-DIELECTRIC

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Trung Nguyen
2021-06-04 22:41:25 -05:00
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* Description
The USER-DIELECTRIC package provides several solvers for computing surface induced charges
at the interface between two media with different dielectric constants:
The USER-DIELECTRIC package provides several solvers for computing surface induced charges:
* the boundary element method using the GMRES solver (fix polarize/bem/gmres),
* the induced charge computation (ICC*) (fix polarize/bem/icc), and
* the direct optimization of an energy functional derived from the variational approach (fix polarize/functional).
* the boundary element solver using the GMRES algorithm (fix polarize/bem/gmres),
* the boundary element solver using the successive overelaxation algorithm (fix polarize/bem/icc),
* the direct optimization of an energy functional (fix polarize/functional).
The interfaces can be immobile (for example, graphene layers in contact with water),
or mobile (for example, dielectric colloids in a solvent).
See the header of the source files for more details on the references of the methods.
Example input scripts are given at examples/USER/dielectric.
The USER-DIELECTRIC package was created by Trung Nguyen while at Northwestern,
with contribution from Honghao Li (FixQeqDielectric) while at Northwestern.
The USER-DIELECTRIC package was created by Trung Nguyen while at Northwestern.
Questions can be addressed to Trung Nguyen (ndactrung@gmail.com).
* Citation
Please cite the following paper if you use the code for your publications
Trung Dac Nguyen, Honghao Li, Debarshee Bagchi, Francisco J. Solis, Monica Olvera de la Cruz,
"Incorporating surface polarization effects into large-scale coarse-grained Molecular Dynamics simulation",
Computer Physics Communications 241, 80--91 (2019); DOI: 10.1016/j.cpc.2019.03.006.
T. D. Nguyen, H. Li, D. Bagchi, F. J. Solis, M. Olvera de la Cruz,
"Incorporating surface polarization effects into large-scale coarse-grained
Molecular Dynamics simulation", Computer Physics Communications 241, 80--91 (2019).
* Installation
* Examples
1. Clone the git repo: git clone https://bitbucket.org/ndtrung/lammps.git
2. Check out the dielectric branch: git checkout dielectric
3. Build: go to src/, and run
make yes-molecule
make yes-kspace
make yes-user-dielectric
a. If you don't have GSL libraries (libgsl.a and libgslcblas.a) installed in your machine,
remove fix_qeq_dielectric.cpp and fix_qeq_dielectric.h. Then build with
make mpi -j8
b. If you do have GSL headers and libraries installed, assuming that they are in /path/to/gsl/install,
copy MAKE/Makefile.mpi to MAKE/Makefile.mpi_gsl, and add to the variables CCFLAGS and LINKFLAGS
in MAKE/Makefile.mpi_gsl:
GSL_PATH = /path/to/gsl/install
...
CCFLAGS = -O2 -march=native -funroll-loops -ffast-math -fopenmp -I$(GSL_PATH)/include
...
LINKFLAGS = -O2 -fopenmp -L$(GSL_PATH)/lib
LIB = -lgsl -lgslcblas
Finally, build with
make mpi_gsl -j8
* Test
Go to examples/USER/dielectric, and run
Example input scripts and data files can be found under examples/USER/dielectric:
mpirun -np 8 ../../../src/lmp_mpi -in in.confined
or with the modified Makefile.mpi_gsl:
mpirun -np 8 ../../../src/lmp_mpi_gsl -in in.confined