RMT3D: Reference Map Technique 3D

RMT3D simulates 3D incompressible fluid-structure interaction with solids that undergoes large deformation. An incompressible neo-Hookean material model is used.

Authors: Yuexia Luna Lin, Nicholoas J. Derr, Chris H. Rycroft

John A. Paulson School of Engineering and Applied Sciences, Harvard University

Software/library requirements:

• GNUMake
• GNUGCC compiler
• PGMG library
• Perl (For image processing only)
• Povray 3.7 (For image processing only)

Get started:

1. Download or git clone RMT3D repository.
2. Download or git clone PGMG repository. For convenience, put PGMG/ and RMT3D/ on the same file system level.
3. Create a config.mk file to configure which compiler to use and basic compiler and linker flags. Sample config.mk files are provided for Mac and Linux in the make_configs/ folder.
4. Change into Execs/ folder and open Make.defs. Modify the line PGMG_DIR = to point to the path to PGMG/ repo. For example,

    PGMG_DIR = /Users/gitcodes/PGMG/ 

   Notice that the library name is libmg3d.
5. After these changes, typing make in the commandline in Execs/ directory will build an MPI-enable application, with executable run_sim.
6. To run the application, a config file (must have file extension .cfg) for the simulation must be provided as command line argument. To run it in serially,

    ./run_sim mySim.cfg 

   To run it with N processes,

    mpirun -np N run_sim mySim.cfg 

7. Sample simulation config files can be found in sim_configs/ directory. Examples include

• a full fluid test case with manufactured solution
• a full solid test case with solid shear wave
• a lid-driven cavity flow (full fluid)
• a lid-driven cavity flow with a sphere
• a pre-stretched sphere relaxing in fluid

9. If POV-Ray is installed and the necessary output files (contours and tracers) are available, the perl script pov-movie.pl can be used to render the output files into 3D snapshots. For detailed usage, see the output of

    perl pov-movie.pl -h 

More complete documentation is under development. In the meantime, for any questions, feel free to contact the authors of this repository.

Acknowledgement

This work has been partially supported by the Applied Mathematics Program of the U.S. DOE Office of Science Advanced Scientific Computing Research under contract number DE-AC02-05CH11231, the Department of Energy Computational Science Graduate Fellowship, the Department of Defense NDSEG Fellowship, and the Harvard NSF-Simons Center Quantitative Biology Initiative student fellowship, supported by the National Science Foundation grant DMS-1764269.

References

Yuexia Luna Lin, Nicholas J. Derr, and Chris H. Rycroft, Eulerian simulation of complex suspensions and biolocomotion in three dimensions, arXiv:2104.00095 [physics.flu-dyn].

Chris H. Rycroft et al., Reference map technique for incompressible fluid-structure interaction, Journal of Fluid Mechanics, 898, A9 (2020). doi:10.1017/jfm.2020.353