National Nanotechnology Infrastructure Network

National Nanotechnology Infrastructure Network

Serving Nanoscale Science, Engineering & Technology

Computation at Michigan


The NNIN computation site at Michigan is located in the Electrical Engineering and Computer Engineering (EECS) Building at the University of Michigan.

Micro/Nano devices have revolutionized modern communications, sensors, and signal processing systems. To date, their exploitation in industrial and military capabilities has been impeded by the lack of understanding of the fundamental multi-physics/multi-scale phenomena that govern such systems functionality. Modeling and simulation of MEMS/NEMS provide interpretive and predictive framework for understanding complexity of interactions between various physical domains and size scales, failure mechanisms, and sensitivity to operational variations.

In order to address this requirement, our site provides consulting, computation and software support to researchers and engineers who tackle fundamental science and engineering problems at the micro/nanoscale that can provide orders of magnitude performance improvement over current MEMS/NEMS technologies.

NNIN computation resources at Michigan are open to researchers and engineers from academia, industry and national laboratories for the following:

  • Simulation tools that unite different size and time scales, capturing the entire workings of a design, from its nanoscale layout to its macroscale features.
  • Software packages in multi-physics couplings (mechanical-thermal-electrical- magnetic- optical etc.), complex flow phenomena involving single phase and particle-laden (i.e., beads, cells, and macromolecules) flows driven by pressure, electric, and magnetic fields, and by surface tension.
  • Computation support in code development related to understanding of experimentally observed, fundamental principles and processes governing MEMS/NEMS performance for applications such as micro/nanofluidics, bioengineering, optics, magnetics, imaging, energy, thermal systems, and carbon nanotubes. Also, support of code development related to the lifetime performance and functionality and prevent failure of NEMS/MEMS (ranging from billionths of a second to several months).
  • Simulation expertise, modeling support and consulting for multi-physics/multi-scale nanosystems and working with users to modify existing codes and constructing new approaches.
  • Software packages which can be used in the fabrication cycle, for design optimization, uncertainty quantification and characterization of micro/nano devices.

Dr. Behrouz Shiari is the computation expert for the NNIN/C at Michigan. Dr. Shiari is not only proficient in most software packages; he can also assist in the development of new simulation tools for clients' specific needs.

Hardware available

The “Michigan Nano Computational Cluster” (MNC2) consists of 14 nodes. Each compute node contains a hexa-core Intel Xeon X5660 processor running at 2.66 GHz, 24 GB of memory. MNC2 contains 168 processing cores linked with Gigabit ethernet, 12 TB of disk space.

Simulation Tools Available

MNC2 currently hosts simulation tools for micro/nanoscale systems including codes for first principles calculation, photonic devices, molecular dynamics, multiphysics, and multiscale.

Multiscale Approaches

  • QC - The Quasicontinuum (QC) method is a mixed continuum (FE) and atomistic (MD) approach for simulating the mechanical response of polycrystalline materials at zero temperature.
  • OCTA - OCTA is an integrated simulation system for soft materials developed by the joint project of industry and academia funded by Ministry of Economy, Trade and Industry (METI), Japan. The objective of the project is to bridge microstructural (or molecular) characteristics of soft materials with their material characteristics by simulation and modeling.
  • CADD - Coupled atomistic (MD) /continuum (FE) /discrete dislocation (DD) at finite temperature.
  • LibMultiScale: The LibMultiScale Library has been designed by INRIA, France. It is a tool developed to study the multiscale methods currently employed on material simulations. It distincts the base code components (CM and MD) from the coupling components.

Molecular Dynamics

  • LAMMPS - general purpose molecular dynamics simulator that has the option to use leonard jones potentials, embedded atom potentials, and potentials for biomolecules and proteins.  This parallel code can easily handle systems with thousands of atoms.  The ability to incorporate the effect of temperature provides an important complement to density functional techniques.
  • DL_POLY - DL_POLY is a parallel molecular dynamics simulation package developed at Daresbury Laboratory.

Continuum Approaches

Finite Element Analysis/Nonlinear Finite Element

  • CalculiX: Finite element solver for linear/nonlinear field problems.
  • Impact: Explicit nonlinear finite element code.
  • OOFEM: Linear/Nonlinear finite elements for solids and some fluid and transport problems. Developed at the Czech Technical University at Prague.
  • Tahoe: Nonlinear Finite Element and Mesh Free software from Sandia.
  • Warp3D: Nonlinear finite elements for solid mechanics from the University of Illinois at Urbana-Champagne.
  • FEBio: Package is specifically designed to address problems in computational biomechanics.

Linear Finite Elements

  • Elmer: A multiphysics finite element software developed in Finland. 
  • FEMPACK finite element routines: Suite of Matlab routines for PDEs.
  • OOF:Tool for the linear finite element analysis of complex scanned microstructures.

Pre- and Post-Processors

  • Gmsh: A three-dimensional mesh generator with some CAD and post-processing features.
  • Triangle:A two-dimensional triangular element mesh generator.

Meshfree Methods

  • Element-free Galerkin Matlab routines: Matlab routines for 1D and 2D Element-free Galerkin (EFG) simulations from John Dolbow.
  • Uintah: Parallel C++ code for Material Point Method calculations from University of Utah. MIT License.

CFD and Coupled Codes

  • CoolFluid : CFD code.
  • FeatFlow : Solver library and user interface for incompressible Navier-Stokes in 2D and 3D from the University of Dortmund.
  • GETDP: CFD code.
  • HEDRA: CFD code
  • LibMesh: Finite element library that's primarily been used for CFD applications.
  • Uintah: Parallel C++ code for couple fluid-structure interaction simulations. Uses an Implicit Compressible Eulerian (ICE) CFD code for the fluid and the Material Point Method for the solid. From University of Utah.  MIT License.  Available for free upon request. Limited user documentation.