Category:Nanoscale

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(Merged Visualization Code list to Visualization in earlier section.)
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== LAMMPS ==
 
== LAMMPS ==
This section includes brief tutorials for learning to use LAMMPS.
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* [[Precompiled_LAMMPS_Versions_at_CAVS | How do I run parallel LAMMPS on LINUX?]]
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* [[PBS_script | How do I run LAMMPS on a cluster with and without PBS scripting?]]
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* [[Precompiled_LAMMPS_Versions_at_CAVS | What are the precompiled LAMMPS versions at HPC & CAVS?]]
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Here are some brief tutorials for learning to use LAMMPS.
 
* [[LAMMPS tutorials]]
 
* [[LAMMPS tutorials]]
 
** [[LAMMPS_Help | How to calculate cohesive energy and lattice parameter for aluminum: Part 1]]
 
** [[LAMMPS_Help | How to calculate cohesive energy and lattice parameter for aluminum: Part 1]]
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See the [[MPC| MEAM Parameter Calibration - MPC Wiki page]].
 
See the [[MPC| MEAM Parameter Calibration - MPC Wiki page]].
 
== Miscellaneous ==
 
 
* [[Precompiled_LAMMPS_Versions_at_CAVS | How do I run parallel LAMMPS on LINUX?]]
 
* [[PBS_script | How do I run LAMMPS on a cluster with and without PBS scripting?]]
 
* [[Precompiled_LAMMPS_Versions_at_CAVS | What are the precompiled LAMMPS versions at HPC & CAVS?]]
 
  
 
== Preprocessing & Postprocessing Codes ==
 
== Preprocessing & Postprocessing Codes ==

Revision as of 13:30, 14 March 2016

MetalsCeramicsPolymersBiomaterialsGeomaterialsReferences


Contents

Overview

Tensile Loading of an Aluminum Single Crystal. Movie showing deformation of single crystal aluminum loaded in the <100> direction at a strain rate of 1010 s-1 and a temperature of 300 K.

The nanoscale material models are molecular dynamics codes and tools used to ascertain properties at the atomistic scale. These simulations generally use interatomic potentials, or force fields, developed using properties obtained from both electronic scale) calculations and experiments, and feed these results into higher scale models, such as dislocation dynamics at the microscale, or continuum models at the macroscale. To date, much of the research at the atomistic scale has focused on informing continuum models for multiscale modeling of metal and polymer material systems. This particular site contains production and research codes that have been developed both at CAVS and outside for performing and analyzing atomistic simulation results. The production codes have user's manuals and a theoretical manual and have been used in practice to solve complex atomistic problems at the nanoscale. The codes that are research codes have not enjoyed the wealth of application and might not have a user's manual or a theoretical manual. We caution the user that there is some risk in using the research version of the codes. Another resource for computational chemistry can be found at computational chemistry.

Tutorials

If you are just beginning with atomistic codes, we recommend that you familiarize yourself with LAMMPS, MATLAB (pre- and post-processing) and some of the visualization codes.

LAMMPS

Here are some brief tutorials for learning to use LAMMPS.

MATLAB

This section includes a brief tutorial for using MATLAB.

Visualization

This section shows links to visualization packages used at the atomistic scale. Of these, AtomEye, Ensight, OVITO, and VMD are most frequently used at CAVS. AtomEye, OVITO, and VMD are open source codes.

MEAM Parameter Calibration

MEAM Parameter Calibration (MPC) is a graphical MATLAB application for:

  1. interactive editing of MEAM library and parameter files,
  2. running LAMMPS with an input file containing the commands 'pair_style meam' and 'pair_coeff * * LIBRARY_FILE ELEMENTS PARAMETER_FILE ATOM_TYPES', and
  3. automatic calibration of user-specified MEAM parameters.

See the MEAM Parameter Calibration - MPC Wiki page.

Preprocessing & Postprocessing Codes

This section includes codes used for preprocessing and postprocessing atomistic results. This section can also include scripts used to generate initial structures for inclusion in molecular dynamics simulations. Additionally, this subsection will include examples of xyz coordinate files that can be used in conjunction with the LAMMPS read_data command to upload.

K-12 Projects

This project(s) is designed to help introduce high school students to STEM-related 'relevant' research in physics and materials science and engineering.

Material Models

Molecular Dynamics Codes

This section includes links to molecular dynamics codes. LAMMPS[1] (Large-scale Atomic/Molecular Massively Parallel Simulator) is commonly used for many molecular dynamics simulations related to metal and polymer systems at CAVS. LAMMPS' Fortran predecessor WARP can also be used for parallel molecular dynamics simulations. Last, DYNAMO is commonly used for MEAM (modified embedded atom method)[2] interatomic potential generation.

Interatomic Potentials available online

For more information on interatomic potential generation using electronic structure information, use the following links.


Atomistic Research

This section includes interatomic potential information for atomistic simulations. Embedded atom method[3] potentials can be found at the NIST Interatomic Potential website. A number of modified embedded atom method[2] potentials have been developed here at CAVS for lightweight metals and steel research. Some published and ongoing interatomic potential work at CAVS includes

Metals

Aluminum

Copper

Magnesium

Iron

Tungsten

Calcium

Ceramics

Polymers

Polyethylene

Coarse Grain Simulations
Polymer Atomistic Research. Movie showing deformation of an amorphous polyethylene structure with 20 chains of 1000 monomers length. The strain rate is 1010 s-1 and the temperature is 100 K[12][13].

An example of tensile deformation in amorphous polyethylene using a united atom method potential.

All Atom Simulations

Reactive molecular dynamics simulation of hydrocarbon-based polymers, such as polyethylene and polypropylene, is now possible using the recently parameterized modified embedded-atom method (MEAM) potential for hydrocarbons (C/H system).[14] For more information about the potential, please visit the following link:

Biomaterials

ICME Overview of Mechanical Properties of the Lipid Bilayer during Traumatic Brain Injury

Geomaterials

Python Based Testing of Atomistic Potentials

References

  1. S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics," J. Comp. Phys., 117, 1-19 (1995).
  2. 2.0 2.1 Baskes, M.I. (1992). Modified embedded-atom potentials for cubic materials and impurities. Phys. Rev. B, 46, 2727 (http://link.aps.org/doi/10.1103/PhysRevB.46.2727).
  3. Murray S. Daw, Stephen M. Foiles, Michael I. Baskes,(1993) The embedded-atom method: a review of theory and applications, Materials Science Reports, Volume 9, Issues 7-8, Pages 251-310. (http://dx.doi.org/10.1016/0920-2307(93)90001-U).
  4. 4.0 4.1 4.2 Tschopp, M. A., & McDowell, D.L. (2007). Structures and energies of Sigma3 asymmetric tilt grain boundaries in Cu and Al. Philosophical Magazine, 87, 3147-3173 (http://dx.doi.org/10.1080/14786430701455321).
  5. 5.0 5.1 5.2 Tschopp, M. A., & McDowell, D.L. (2007). Asymmetric tilt grain boundary structure and energy in copper and aluminum. Philosophical Magazine, 87, 3871-3892 (http://dx.doi.org/10.1016/j.commatsci.2010.02.003).
  6. Spearot, D.E., Tschopp, M.A., Jacob, K.I., McDowell, D.L., "Tensile strength of <100> and <110> tilt bicrystal copper interfaces," Acta Materialia 55 (2007) p. 705-714 (http://dx.doi.org/10.1016/j.actamat.2006.08.060).
  7. Tschopp, M.A., Spearot, D.E., McDowell, D.L., "Atomistic simulations of homogeneous dislocation nucleation in single crystal copper," Modelling and Simulation in Materials Science and Engineering 15 (2007) 693-709 (http://dx.doi.org/10.1088/0965-0393/15/7/001).
  8. 8.0 8.1 8.2 Tschopp, M.A., McDowell, D.L., "Influence of single crystal orientation on homogeneous dislocation nucleation under uniaxial loading," Journal of Mechanics and Physics of Solids 56 (2008) 1806-1830. (http://dx.doi.org/10.1016/j.jmps.2007.11.012).
  9. K. Solanki, M.F. Horstemeyer, M. I. Baskes, and H. Feng, Multiscale study of dynamic void collapse in single crystals, Mechanics of Materials Volume 37, Issues 2-3, February-March 2005, Pages 317-330 dx.doi.org/10.1016/j.mechmat.2003.08.014
  10. Tang, T., Kim, S., & Horstemeyer, M. (2010). Fatigue Crack Growth in Magnesium Single Crystals under Cyclic Loading: Molecular Dynamics Simulation. Computational Materials Science, 48, 426., 48, 426-439 (http://dx.doi.org/10.1080/14786430701255895).
  11. Barrett, C.D., El Kadiri, H., Tschopp, M.A. (2011). Breakdown of the Schmid Law in Homogenous and Heterogenous Nucleation Events of Slip and Twinning in Magnesium. Journal of Mechanics and Physics of Solids, in review.
  12. 12.0 12.1 Hossain, D., Tschopp, M.A., Ward, D.K., Bouvard, J.L., Wang, P., Horstemeyer, M.F., "Molecular dynamics simulations of deformation mechanisms of amorphous polyethylene," Polymer, 51 (2010) 6071-6083.
  13. 13.0 13.1 Tschopp, M.A., Ward, D.K., Bouvard, J.L., Horstemeyer, M.F., "Atomic Scale Deformation Mechanisms of Amorphous Polyethylene under Tensile Loading," TMS 2011 Conference Proceedings, accepted.
  14. S Nouranian, MA Tschopp, SR Gwaltney, MI Baskes, and MF Horstemeyer, An Interatomic Potential for Saturated Hydrocarbons Based on the Modified Embedded-Atom Method, Physical Chemistry Chemical Physics 16 (13) (2014):6233-6249.

Subcategories

This category has the following 3 subcategories, out of 3 total.

Pages in category "Nanoscale"

The following 75 pages are in this category, out of 75 total.

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