Paul J. Atzberger

Documentation: Tutorials and Examples | GitHub: mango-selm | Installation Instructions

Quick Start

To install for Python use

>> pip install selm-lammps

To test the package installed run

>> python -c "from selm_lammps.tests import t1; t1.test()"

This includes pre-compiled binaries for (Debian 9+ / Ubuntu x86_64 and Centos 7+ / Python 3.6+).

Examples (clone github):

>> git clone https://github.com/atzberg/mango-selm.git

See the git-hub page for models and scripts at [link].

Examples: Jupyter notebooks, python scripts, and models can be found at github/mango-selm.

Other ways to install the package For running prototype models and simulations on a desktop, such as Windows and MacOS, we recommend using Docker container. For example, install Docker Desktop or docker for linux and then load a standard ubuntu container by using in the terminal "docker run -it ubuntu:20.04 /bin/bash". You then use "apt update; apt install python3-pip", and can then pip install and run the simulation package as above. Note use command "python3" in place of "python" when calling scripts.

The source package and additional binaries are available on the download page.

For more information on other ways to install or compile the package, please see the document page.

Git-Hub Page: github: mango-selm

Related Talks

Tutorial: How to Setup Models and Simulations using Jupyter Notebooks and Python.
Interactive Session, USER-SELM
Fluid-Structure Interaction Modeling and Simulation
Slides: [PDF]

Download Mango-Selm Package

Additional videos are available on the Atzberger YouTube Channel.

• LAMMPS Documentation (on-line at the LAMMPS website)
• JavaDocs for the Mango-Selm Graphical Interface

References:

1. Fluctuating Hydrodynamics Methods for Dynamic Coarse-Grained Implicit-Solvent Simulations in LAMMPS, Y. Wang, J. K. Sigurdsson, and P.J. Atzberger, SIAM J. Sci. Comp., 38(5), S62–S77, (2016) [preprint] [full paper]
2. Stochastic Reductions for Inertial Fluid-Structure Interactions Subject to Thermal Fluctuations, G. Tabak and P.J. Atzberger, SIAM J. Appl. Math., 75(4), 1884–1914, (2015) [full paper]
3. Fluctuating Hydrodynamic Methods for Fluid-Structure Interactions in Confined Channel Geometries, Y. Wang, H. Lei, P. Atzberger, Applied Mathematics and Mechanics (Springer), January, Volume 39, Issue 1, pp 125–152, (2018) [full paper].
4. Spatially Adaptive Stochastic Methods for Fluid-Structure Interactions Subject to Thermal Fluctuations in Domains with Complex Geometries, P. Plunkett, J. Hu, C. Siefert, P.J. Atzberger, Journal of Computational Physics, Vol. 277, 15 Nov. 2014, pg. 121--137, (2014) [full paper]
5. Dynamic Implicit-Solvent Coarse-Grained Models of Lipid Bilayer Membranes : Fluctuating Hydrodynamics Thermostat, Y. Wang, J. K. Sigurdsson, E. Brandt, and P.J. Atzberger, Phys. Rev. E 88, 023301, (2013) [full paper]
6. Incorporating Shear into Stochastic Eulerian Lagrangian Methods for Rheological Studies of Complex Fluids and Soft Materials, P.J. Atzberger, Physica D, Vol. 265, pg. 57–70, (2013). [full paper]
   
   
7. Stochastic Eulerian Lagrangian Methods for Fluid Structure Interactions with Thermal Fluctuations, P.J. Atzberger, J. of Comp. Phys., 230, pp. 2821--2837, (2011). [full paper]
   
   
8. A Stochastic Immersed Boundary Method for Fluid-Structure Dynamics at Microscopic Length Scales, P.J. Atzberger, P.R. Kramer, and C.S. Peskin, J. Comp. Phys., Vol. 224, Iss. 2, (2007). [full paper]
   
   

Additional Information:

• Download Latest Release
• Documentation
• github-mango-selm
• http://atzberger.org/