# Category:Nanoscale

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− | nanoscale | + | __NOTOC__ |

+ | {{Menu_Models}} | ||

+ | |||

+ | |||

+ | == Overview == | ||

+ | [[Image:Al_SC_100_movie2.gif|thumb|600px| [[Uniaxial_Tension | Tensile Loading of an Aluminum Single Crystal]]. Movie showing deformation of single crystal aluminum loaded in the <100> direction at a strain rate of 10<sup>10</sup> s<sup>-1</sup> and a temperature of 300 K.]] | ||

+ | |||

+ | The nanoscale material models are [http://en.wikipedia.org/wiki/Molecular_dynamics molecular dynamics] codes and tools used to ascertain properties at the atomistic scale. These simulations generally use interatomic potentials, or [http://en.wikipedia.org/wiki/Force_field_(chemistry) force fields], developed using properties obtained from both [[MaterialModels:_Electronic_Scale | electronic scale]]) calculations and experiments, and feed these results into higher scale models, such as [http://en.wikipedia.org/wiki/Dislocation_dynamics dislocation dynamics] at the [[MaterialModels:_Microscale | microscale]], or continuum models at the [[MaterialModels:_Microscale | macroscale]]. To date, much of the research at the atomistic scale has focused on informing continuum models for multiscale modeling of [[Metals_Home | metal]] and [[Polymers_Home | 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 [http://cccbdb.nist.gov/ 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]] | ||

+ | ** [[LAMMPS_Help | How to calculate cohesive energy and lattice parameter for aluminum: Part 1]] | ||

+ | ** [[LAMMPS_Help2 | How to calculate cohesive energy and lattice parameter for aluminum: Part 2]] | ||

+ | ** [[Uniaxial_Tension | How to deform a three-dimensional periodic simulation cell in uniaxial tension for aluminum]] | ||

+ | ** [[Uniaxial_Compression | How to deform a three-dimensional periodic simulation cell in uniaxial compression for aluminum]] | ||

+ | ** [[LAMMPS_Help3 | How to generate a Sigma5(310) symmetric tilt grain boundary in aluminum]] | ||

+ | ** [[LAMMPS_Fracture | How to calculate fracture stress of an iron symmetric tilt grain boundary]] | ||

+ | ** [[LAMMPS_Nanowire_Deformation | How to deform a nanowire in LAMMPS]] | ||

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

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

+ | ** [[LAMMPS_Stacking_Fault_Energy | How to find the generalized stacking fault energy for aluminum]] | ||

+ | ** [[LAMMPS_Vacancy_Formation_Energy | How to calculate vacancy formation energy for copper]] | ||

+ | ** [[LAMMPS_Interstitial_Formation_Energy | How to calculate interstitial formation energy for copper]] | ||

+ | |||

+ | === MATLAB === | ||

+ | |||

+ | This section includes a brief tutorial for using MATLAB. | ||

+ | * [[MATLAB_Tutorials | MATLAB Tutorials]] | ||

+ | ** [[MATLAB_Basics | How to use MATLAB: The Basics of MATLAB]] | ||

+ | ** [[MATLAB_Basics_2 | How to use MATLAB: The Basics of MATLAB 2]] | ||

+ | ** [[MATLAB_Import_Data | How to Import Data from a Textfile]] | ||

+ | ** [[MATLAB_Export_Data | How to Write Data to a Textfile]] | ||

+ | ** [[Stress-Strain Plot | How to make a stress-strain plot using MATLAB]] | ||

+ | ** [[Journal_Quality_Plotting | How to make a journal quality plot using MATLAB]] | ||

+ | ** [[Errorbars_Plot | Example: How to make a journal quality plot with errorbars]] | ||

+ | ** [[Image_Processing_with_MATLAB_1 | How to do basic image processing with MATLAB]] | ||

+ | ** [[DOE_with_MATLAB_1 | Design of Experiments with MATLAB: Part 1]] | ||

+ | ** [[DOE_with_MATLAB_2 | Design of Experiments with MATLAB: Part 2]] | ||

+ | ** [[DOE_with_MATLAB_3 | Design of Experiments with MATLAB: Part 3]] | ||

+ | ** [[DOE_with_MATLAB_4 | Design of Experiments with MATLAB: Part 4]] | ||

+ | |||

+ | === Visualization === | ||

+ | |||

+ | * Atomeye Basics | ||

+ | ** [[Movie_AtomEye | How to make a movie using AtomEye and ImageJ]] | ||

+ | * OVITO Basics | ||

+ | ** [[Movie_OVITO | How to make a movie using OVITO]] | ||

+ | |||

+ | === MEAM Parameter Calibration === | ||

+ | |||

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

+ | |||

+ | # interactive editing of MEAM library and parameter files, | ||

+ | # running LAMMPS with an input file containing the commands 'pair_style meam' and 'pair_coeff * * LIBRARY_FILE ELEMENTS PARAMETER_FILE ATOM_TYPES', and | ||

+ | # automatic calibration of user-specified MEAM parameters. | ||

+ | |||

+ | 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 === | ||

+ | |||

+ | 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 | ||

+ | ** [[Amorphous_Polymer_Generator | Initial amorphous polymer configurations for LAMMPS]] | ||

+ | * Data Analysis and Plotting | ||

+ | ** [[Stress-Strain Plot | How to make a stress-strain plot using MATLAB]] | ||

+ | * Visualization | ||

+ | ** [[Movie_AtomEye | How to make a movie using AtomEye and ImageJ]] | ||

+ | ** [[Movie_OVITO | How to make a movie using OVITO]] | ||

+ | |||

+ | === 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. | ||

+ | * [[FeCrHe | K-12 Project for Fe-Cr and Fe-He systems]] | ||

+ | ** [[FormBind | What are formation energies and binding energies?]] | ||

+ | |||

+ | == Material Models == | ||

+ | |||

+ | === Molecular Dynamics Codes === | ||

+ | |||

+ | This section includes links to molecular dynamics codes. LAMMPS<ref>S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics," J. Comp. Phys., 117, 1-19 (1995). </ref> (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)<ref name="MEAM">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).</ref> interatomic potential generation. | ||

+ | |||

+ | * [[Code:_LAMMPS | LAMMPS Code]] (see also: [[LAMMPS tutorials]]) | ||

+ | * [[Code:_WARP|WARP Code]] | ||

+ | * [[Code:_DYNAMO|DYNAMO Code]] | ||

+ | * [http://www.stfc.ac.uk/cse/default.aspx DLPoly] - Daresbury Laboratory POLY tools MD program | ||

+ | * [http://www.gromacs.org/ Gromacs] - GROningen MAchine for Chemical Simulation | ||

+ | * [http://imd.itap.physik.uni-stuttgart.de/ IMD] - The ITAP Molecular Dynamics program | ||

+ | * [http://www.ccp5.ac.uk/moldy/moldy.html MOLDY] - MOLecular DYnamics | ||

+ | * [http://www.ks.uiuc.edu/Research/namd/ NAMD] - Not (just) Another Molecular Dynamics program | ||

+ | * [https://simtk.org/home/openmm OpenMM] - OPEN source library for Molecular Modeling simulations | ||

+ | * [http://www.modelingmaterials.org/resources "Modeling Materials" Other Links] | ||

+ | |||

+ | === Interatomic Potentials available online === | ||

+ | |||

+ | * [http://www.ctcms.nist.gov/potentials/ Interatomic Potentials Repository Project at NIST] | ||

+ | * [http://enpub.fulton.asu.edu/cms/potentials/submain/available.htm EAM Potential Database at Computational Materials Science Group in Arizona State University] | ||

+ | * [http://www.princeton.edu/mae/people/faculty/carter/homepage/research/potentials/ EAM potentials for hydrogen in BCC iron] | ||

+ | * [http://sites.google.com/a/gmu.edu/eam-potential-database/ Potentials developed by Howard Sheng of George Mason University] | ||

+ | * [http://cst-www.nrl.navy.mil/ccm6/ap/eam/index.html CCM6 EAM potentials] | ||

+ | * [http://potfit.itap.physik.uni-stuttgart.de/wiki/Main_Page potfit] - the ITAP force-matching Code | ||

+ | |||

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

+ | * [http://dx.doi.org/10.1016/0920-2307(93)90001-U The embedded-atom method: a review of theory and applications ] | ||

+ | * [http://link.aps.org/doi/10.1103/PhysRevB.46.2727 Modified embedded-atom potentials for cubic materials and impurities] | ||

+ | * [http://link.aps.org/doi/10.1103/PhysRevB.62.8564 Second nearest-neighbor modified embedded-atom-method potential] | ||

+ | * [http://dx.doi.org.proxy.library.msstate.edu/10.1016/j.calphad.2010.10.007 The modified embedded-atom method interatomic potentials and recent progress in atomistic simulations] | ||

+ | * [http://dx.doi.org/10.1016/j.physrep.2007.09.004 Interatomic potentials of the binary transition metal systems and some applications in materials physics] | ||

+ | * [http://link.aps.org/doi/10.1103/PhysRevB.63.165106 Parametrization of modified embedded-atom-method potentials for Rh, Pd, Ir, and Pt based on density functional theory calculations, with applications to surface properties] | ||

+ | * [http://www.springerlink.com/content/q73683q272716m78 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. | ||

+ | |||

+ | * [http://mt.seas.upenn.edu/Archive/Graphics/A/ AtomEye] | ||

+ | * [http://en.wikipedia.org/wiki/Avizo Avizo_(software)] - 3d visualization and analysis software. | ||

+ | * [http://avogadro.openmolecules.net/wiki/Main_Page Avogadro] – Advanced molecule editor and visualizer | ||

+ | * [http://en.wikipedia.org/wiki/BOSS BOSS (molecular mechanics)] - MC in [http://en.wikipedia.org/wiki/OPLS OPLS] | ||

+ | * [http://www.ensight.com Ensight] | ||

+ | * [http://esra.sourceforge.net/cgi-bin/index.cgi esra] - Lightweight molecular modeling and analysis library (Java/Jython/Mathematica). | ||

+ | * [http://www.pirx.com/iMol/ iMol] – Molecular visualizer for Mac OS X | ||

+ | * [http://jmol.sourceforge.net/ JMol] – An open-source Java viewer for chemical structures in 3D | ||

+ | * [http://mw.concord.org/modeler/ Molecular Workbench] - Interactive molecular dynamics simulations on your desktop. | ||

+ | * [http://ovito.org/ OVITO] | ||

+ | * [http://www.ime.unicamp.br/~martinez/packmol Packmol] Package for building starting configurations for MD in an automated fashion. | ||

+ | * [http://sourceforge.net/projects/punto/ Punto] is a freely available visualisation tool for particle simulations. | ||

+ | * [http://en.wikipedia.org/wiki/PyMol PyMol] - Molecular Visualization software written in python. | ||

+ | * [http://www.openrasmol.org/ RasMol] - Molecular Graphics Visualisation Tool | ||

+ | * [http://en.wikipedia.org/wiki/Sirius Sirius visualization software] - Molecular modeling, analysis and visualization of MD trajectories. | ||

+ | * [http://www.ks.uiuc.edu/Research/vmd/ 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<ref name="EAM"> 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).</ref> potentials can be found at the [http://www.ctcms.nist.gov/potentials/ NIST Interatomic Potential] website. A number of [[Modified Embedded Atom Method|modified embedded atom method]]<ref name="MEAM">Lee, B.J., Baskes, M.I. (2000). Second nearest-neighbor modified embedded-atom-method potential. Phys. Rev. B, 62, 8564–8567 ([http://link.aps.org/doi/10.1103/PhysRevB.62.8564 http://link.aps.org/doi/10.1103/PhysRevB.62.8564]).</ref> potentials have been developed here at CAVS for lightweight metals and steel research. Some published and ongoing interatomic potential work at CAVS includes | ||

+ | |||

+ | == Metals == | ||

+ | |||

+ | [[Image:PE_deformation.gif|thumb|600px|[[MD_PE_deformation | Polymer Atomistic Research]]. Movie showing deformation of an amorphous polyethylene structure with 20 chains of 1000 monomers length. The strain rate is 10<sup>10</sup> s<sup>-1</sup> and the temperature is 100 K<ref name="Hos2010">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.</ref><ref name="Tsc_2010TMS">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.</ref>.]] | ||

+ | |||

+ | Aluminum | ||

+ | * [[Al-Mg | Modified Embedded Atom Method (MEAM) potential for Al-Mg]] | ||

+ | * [http://arxiv.org/abs/1107.0544 MEAM potential for Al, Si, Mg, Cu, and Fe alloys] (see also: [http://code.google.com/p/ase-atomistic-potential-tests/ routines to reproduce the results]) | ||

+ | * [[GB_Gen | Grain Boundary Generation of Aluminum]]<ref name="Tsc2007a">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 http://dx.doi.org/10.1080/14786430701455321]).</ref><ref name="Tsc2007b">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 http://dx.doi.org/10.1016/j.commatsci.2010.02.003]).</ref> | ||

+ | * [[Aluminum_Dislocation_Nucleation | Dislocation Nucleation in Single Crystal Aluminum]]<ref>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 http://dx.doi.org/10.1016/j.actamat.2006.08.060]).</ref><ref>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 http://dx.doi.org/10.1088/0965-0393/15/7/001]).</ref><ref name="Tsc2008a">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 http://dx.doi.org/10.1016/j.jmps.2007.11.012]).</ref> | ||

+ | * [[Uniaxial_Tension | Uniaxial Tension in Single Crystal Aluminum]]<ref name="Tsc2008a" /> | ||

+ | * [[Uniaxial_Compression | Uniaxial Compression in Single Crystal Aluminum]]<ref name="Tsc2008a" /> | ||

+ | |||

+ | Copper | ||

+ | * [[GB_Gen | Grain Boundary Generation of Copper]]<ref name="Tsc2007a" /><ref name="Tsc2007b" /> | ||

+ | * [[Multiscale Study Dynamic Void Collapse in Single Crystals| Multiscale study of dynamic void collapse in single crystals]]<ref name="msdvcsc"/> | ||

+ | |||

+ | Magnesium | ||

+ | * [[Al-Mg | Modified Embedded Atom Method (MEAM) potential for Mg-Al]] | ||

+ | * [[Grain boundary generation in Mg | Grain boundary generation in Mg]]<ref name="Tsc2007a" /><ref name="Tsc2007b" /> | ||

+ | * [[MD_Fatigue_Crack_Growth | Fatigue Crack Growth Simulation]]<ref>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 http://dx.doi.org/10.1080/14786430701255895]).</ref> | ||

+ | * [[Single Crystal Tensile Deformation | Uniaxial Tension MD]]<ref>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.</ref> | ||

+ | |||

+ | Iron | ||

+ | * [[Fe-V | Modified Embedded Atom Method (MEAM) potential for Fe-V]] | ||

+ | * [[Fe-C | Modified Embedded Atom Method (MEAM) potential for Fe-C]] | ||

+ | * [[FeHe | Modified Embedded Atom Method (MEAM) potential for Fe-He]] | ||

+ | |||

+ | Tungsten | ||

+ | * [[W | Modified Embedded Atom Method (MEAM) potential for W]] | ||

+ | |||

+ | Calcium | ||

+ | * [[Ca | Modified Embedded Atom Method (MEAM) potential for Ca]] | ||

+ | |||

+ | == Ceramics == | ||

+ | |||

+ | == Polymers == | ||

+ | |||

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

+ | |||

+ | * [[MD_PE_deformation | Atomistic Deformation of Amorphous Polyethylene]]<ref name="Hos2010" /><ref name="Tsc_2010TMS" /> | ||

+ | ** [[Amorphous_Polymer_Generator | Initial amorphous polymer generator used for polyethylene]] | ||

+ | |||

+ | 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).<ref name="NTG2014" /> For more information about the potential, please visit the following link: | ||

+ | |||

+ | * [[Modified_Embedded_Atom_Method_(MEAM)_potential_for_hydrocarbon_(C/H) | Modified Embedded Atom Method (MEAM) potential for hydrocarbons (C/H)]] | ||

+ | |||

+ | == Biomaterials == | ||

+ | [[Contribution 8|ICME Overview of Mechanical Properties of the Lipid Bilayer during Traumatic Brain Injury]] | ||

+ | |||

+ | == Geomaterials == | ||

+ | == Python Based Testing of Atomistic Potentials== | ||

+ | * [[Media:Bohumir_NIST2011_ASE.pdf|The universal interface for testing atomistic potentials]] | ||

+ | |||

+ | * [[Media:Bohumir_CCP2011_LAMMPS_ASE.pdf|Routines for basic tests of atomistic potentials with universal interface]] | ||

+ | |||

+ | == References == | ||

+ | |||

+ | <references> | ||

+ | <ref name="msdvcsc">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 [http://dx.doi.org/10.1016/j.mechmat.2003.08.014 dx.doi.org/10.1016/j.mechmat.2003.08.014]</ref> | ||

+ | |||

+ | <ref name="NTG2014">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.</ref> | ||

+ | |||

+ | [[Material_Models | Back to Materials Models Home]] | ||

+ | |||

+ | |||

+ | |||

+ | |||

+ | |||

+ | |||

+ | [[Category: Overview]] | ||

+ | [[Category: Nanoscale]] | ||

+ | |||

[[Category:Multiscale Simulations]] | [[Category:Multiscale Simulations]] |

## Revision as of 15:35, 28 July 2014

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
- How to find the generalized stacking fault energy for aluminum
- How to calculate vacancy formation energy for copper
- How to calculate interstitial formation energy for copper

### 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

### MEAM Parameter Calibration

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

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

See the MEAM Parameter Calibration - MPC Wiki page.

### 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]}

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

- ↑ 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.
- ↑ 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.