# Nanoscale

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** [[LAMMPS_Polymer | How to construct polymer chains in LAMMPS]] | ** [[LAMMPS_Polymer | How to construct polymer chains in LAMMPS]] | ||

** [[LAMMPS_Relaxed_Bi-layer | How to construct relaxed bi-layer in LAMMPS]] | ** [[LAMMPS_Relaxed_Bi-layer | How to construct relaxed bi-layer in LAMMPS]] | ||

+ | ** [[LAMMPS_Relaxed_Bi-layer | Test bi-layer in LAMMPS]] | ||

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=== MATLAB === | === MATLAB === | ||

## Revision as of 11:13, 27 July 2012

Metals • Ceramics • Polymers • Biomaterials • Geomaterials • References

## Overview

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

This section includes brief tutorials for learning to use LAMMPS.

- LAMMPS tutorials
- How to calculate cohesive energy and lattice parameter for aluminum: Part 1
- How to calculate cohesive energy and lattice parameter for aluminum: Part 2
- How to deform a three-dimensional periodic simulation cell in uniaxial tension for aluminum
- How to deform a three-dimensional periodic simulation cell in uniaxial compression for aluminum
- How to generate a Sigma5(310) symmetric tilt grain boundary in aluminum
- How to calculate fracture stress of an iron symmetric tilt grain boundary
- How to deform a nanowire in LAMMPS
- How to construct polymer chains in LAMMPS
- How to construct relaxed bi-layer in LAMMPS
- Test bi-layer in LAMMPS

### MATLAB

This section includes a brief tutorial for using MATLAB.

- MATLAB Tutorials
- How to use MATLAB: The Basics of MATLAB
- How to use MATLAB: The Basics of MATLAB 2
- How to Import Data from a Textfile
- How to Write Data to a Textfile
- How to make a stress-strain plot using MATLAB
- How to make a journal quality plot using MATLAB
- Example: How to make a journal quality plot with errorbars
- How to do basic image processing with MATLAB
- Design of Experiments with MATLAB: Part 1
- Design of Experiments with MATLAB: Part 2
- Design of Experiments with MATLAB: Part 3
- Design of Experiments with MATLAB: Part 4

### Visualization

- Atomeye Basics
- OVITO Basics

### Miscellaneous

- How do I run parallel LAMMPS on LINUX?
- How do I run LAMMPS on a cluster with and without PBS scripting?
- What are the precompiled LAMMPS versions at HPC & CAVS?

### 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.

- Initial Structure Generation
- Data Analysis and Plotting
- Visualization

### 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.

- LAMMPS Code (see also: LAMMPS tutorials)
- WARP Code
- DYNAMO Code
- DLPoly - Daresbury Laboratory POLY tools MD program
- Gromacs - GROningen MAchine for Chemical Simulation
- IMD - The ITAP Molecular Dynamics program
- MOLDY - MOLecular DYnamics
- NAMD - Not (just) Another Molecular Dynamics program
- OpenMM - OPEN source library for Molecular Modeling simulations
- "Modeling Materials" Other Links

### Interatomic Potentials available online

- Interatomic Potentials Repository Project at NIST
- EAM Potential Database at Computational Materials Science Group in Arizona State University
- EAM potentials for hydrogen in BCC iron
- Potentials developed by Howard Sheng of George Mason University
- CCM6 EAM potentials
- potfit - the ITAP force-matching Code

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

- The embedded-atom method: a review of theory and applications
- Modified embedded-atom potentials for cubic materials and impurities
- Second nearest-neighbor modified embedded-atom-method potential
- The modified embedded-atom method interatomic potentials and recent progress in atomistic simulations
- Interatomic potentials of the binary transition metal systems and some applications in materials physics
- Parametrization of modified embedded-atom-method potentials for Rh, Pd, Ir, and Pt based on density functional theory calculations, with applications to surface properties
- Density functional theory (DFT)-based modified embedded atom method potentials: Bridging the gap between nanoscale theoretical simulations and DFT calculations

### Visualization Codes

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.

- AtomEye
- Avizo_(software) - 3d visualization and analysis software.
- Avogadro – Advanced molecule editor and visualizer
- BOSS (molecular mechanics) - MC in OPLS
- Ensight
- esra - Lightweight molecular modeling and analysis library (Java/Jython/Mathematica).
- iMol – Molecular visualizer for Mac OS X
- JMol – An open-source Java viewer for chemical structures in 3D
- Molecular Workbench - Interactive molecular dynamics simulations on your desktop.
- OVITO
- Packmol Package for building starting configurations for MD in an automated fashion.
- Punto is a freely available visualisation tool for particle simulations.
- PyMol - Molecular Visualization software written in python.
- RasMol - Molecular Graphics Visualisation Tool
- Sirius visualization software - Molecular modeling, analysis and visualization of MD trajectories.
- Visual molecular dynamics (VMD) - MD simulation trajectories can be visualized and analyzed.

## 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

- Modified Embedded Atom Method (MEAM) potential for Al-Mg
- MEAM potential for Al, Si, Mg, Cu, and Fe alloys (see also: routines to reproduce the results)
- Grain Boundary Generation of Aluminum
^{[6]}^{[7]} - Dislocation Nucleation in Single Crystal Aluminum
^{[8]}^{[9]}^{[10]} - Uniaxial Tension in Single Crystal Aluminum
^{[10]} - Uniaxial Compression in Single Crystal Aluminum
^{[10]}

Copper

- Grain Boundary Generation of Copper
^{[6]}^{[7]} - Multiscale study of dynamic void collapse in single crystals
^{[11]}

Magnesium

- Modified Embedded Atom Method (MEAM) potential for Mg-Al
- Grain boundary generation in Mg
^{[6]}^{[7]} - Fatigue Crack Growth Simulation
^{[12]} - Uniaxial Tension MD
^{[13]}

Iron

- Modified Embedded Atom Method (MEAM) potential for Fe-V
- Modified Embedded Atom Method (MEAM) potential for Fe-C
- Modified Embedded Atom Method (MEAM) potential for Fe-He

Tungsten

Calcium

## Ceramics

## Polymers

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

- Atomistic Deformation of Amorphous Polyethylene
^{[4]}^{[5]}

## Biomaterials

## Geomaterials

## References

- ↑ S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics," J. Comp. Phys., 117, 1-19 (1995).
- ↑
^{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). - ↑ 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).
- ↑
^{4.0}^{4.1}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. - ↑
^{5.0}^{5.1}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. - ↑
^{6.0}^{6.1}^{6.2}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). - ↑
^{7.0}^{7.1}^{7.2}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). - ↑ 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).
- ↑ 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).
- ↑
^{10.0}^{10.1}^{10.2}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). - ↑ 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
- ↑ 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).
- ↑ 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.