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−  __NOTOC__
 +  #REDIRECT [[:Category:NanoscaleCategory:Nanoscale]] 
−  {{Menu_Models}}
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−  == Overview ==
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−  [[Image:Al_SC_100_movie2.gifthumb600px [[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.]]  +  
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−  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].
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−   +  
−  == Tutorials ==
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−   +  
−  If you are just beginning with atomistic codes, we recommend that you familiarize yourself with LAMMPS, MATLAB (pre and postprocessing) and some of the visualization codes.
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−   +  
−  === LAMMPS ===
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−  This section includes brief tutorials for learning to use LAMMPS.
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−  * [[LAMMPS tutorials]]
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−  ** [[LAMMPS_Help  How to calculate cohesive energy and lattice parameter for aluminum: Part 1]]
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−  ** [[LAMMPS_Help2  How to calculate cohesive energy and lattice parameter for aluminum: Part 2]]
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−  ** [[Uniaxial_Tension  How to deform a threedimensional periodic simulation cell in uniaxial tension for aluminum]]
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−  ** [[Uniaxial_Compression  How to deform a threedimensional periodic simulation cell in uniaxial compression for aluminum]]
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−  ** [[LAMMPS_Help3  How to generate a Sigma5(310) symmetric tilt grain boundary in aluminum]]
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−  ** [[LAMMPS_Fracture  How to calculate fracture stress of an iron symmetric tilt grain boundary]]
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−  ** [[LAMMPS_Nanowire_Deformation  How to deform a nanowire in LAMMPS]]
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−  ** [[LAMMPS_Polymer  How to construct polymer chains in LAMMPS]]
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−  ** [[LAMMPS_Relaxed_Bilayer  How to construct relaxed bilayer in LAMMPS]]
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−  ** [[LAMMPS_Stacking_Fault_Energy  How to find the generalized stacking fault energy for aluminum]]
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−   +  
−  === MATLAB ===
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−   +  
−  This section includes a brief tutorial for using MATLAB.
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−  * [[MATLAB_Tutorials  MATLAB Tutorials]]
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−  ** [[MATLAB_Basics  How to use MATLAB: The Basics of MATLAB]]
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−  ** [[MATLAB_Basics_2  How to use MATLAB: The Basics of MATLAB 2]]
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−  ** [[MATLAB_Import_Data  How to Import Data from a Textfile]]
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−  ** [[MATLAB_Export_Data  How to Write Data to a Textfile]]
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−  ** [[StressStrain Plot  How to make a stressstrain plot using MATLAB]]
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−  ** [[Journal_Quality_Plotting  How to make a journal quality plot using MATLAB]]
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−  ** [[Errorbars_Plot  Example: How to make a journal quality plot with errorbars]]
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−  ** [[Image_Processing_with_MATLAB_1  How to do basic image processing with MATLAB]]
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−  ** [[DOE_with_MATLAB_1  Design of Experiments with MATLAB: Part 1]]
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−  ** [[DOE_with_MATLAB_2  Design of Experiments with MATLAB: Part 2]]
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−  ** [[DOE_with_MATLAB_3  Design of Experiments with MATLAB: Part 3]]
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−  ** [[DOE_with_MATLAB_4  Design of Experiments with MATLAB: Part 4]]
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−   +  
−  === Visualization ===
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−   +  
−  * Atomeye Basics
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−  ** [[Movie_AtomEye  How to make a movie using AtomEye and ImageJ]]
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−  * OVITO Basics
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−  ** [[Movie_OVITO  How to make a movie using OVITO]]
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−   +  
−  === Miscellaneous ===
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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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−   +  
−  === Preprocessing & Postprocessing Codes ===
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−   +  
−  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.
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−   +  
−  * Initial Structure Generation
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−  ** [[Amorphous_Polymer_Generator  Initial amorphous polymer configurations for LAMMPS]]
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−  * Data Analysis and Plotting
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−  ** [[StressStrain Plot  How to make a stressstrain plot using MATLAB]]
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−  * Visualization
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−  ** [[Movie_AtomEye  How to make a movie using AtomEye and ImageJ]]
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−  ** [[Movie_OVITO  How to make a movie using OVITO]]
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−   +  
−  === K12 Projects ===
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−  This project(s) is designed to help introduce high school students to STEMrelated 'relevant' research in physics and materials science and engineering.
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−  * [[FeCrHe  K12 Project for FeCr and FeHe systems]]
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−  ** [[FormBind  What are formation energies and binding energies?]]
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−   +  
−  == Material Models ==
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−   +  
−  === Molecular Dynamics Codes ===
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−  This section includes links to molecular dynamics codes. LAMMPS<ref>S. Plimpton, "Fast Parallel Algorithms for ShortRange Molecular Dynamics," J. Comp. Phys., 117, 119 (1995). </ref> (Largescale 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 embeddedatom 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.
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−  * [[Code:_LAMMPS  LAMMPS Code]] (see also: [[LAMMPS tutorials]])
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−  * [[Code:_WARPWARP Code]]
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−  * [[Code:_DYNAMODYNAMO Code]]
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−  * [http://www.stfc.ac.uk/cse/default.aspx DLPoly]  Daresbury Laboratory POLY tools MD program
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−  * [http://www.gromacs.org/ Gromacs]  GROningen MAchine for Chemical Simulation
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−  * [http://imd.itap.physik.unistuttgart.de/ IMD]  The ITAP Molecular Dynamics program
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−  * [http://www.ccp5.ac.uk/moldy/moldy.html MOLDY]  MOLecular DYnamics
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−  * [http://www.ks.uiuc.edu/Research/namd/ NAMD]  Not (just) Another Molecular Dynamics program
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−  * [https://simtk.org/home/openmm OpenMM]  OPEN source library for Molecular Modeling simulations
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−  * [http://www.modelingmaterials.org/resources "Modeling Materials" Other Links]
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−  === Interatomic Potentials available online ===
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−  * [http://www.ctcms.nist.gov/potentials/ Interatomic Potentials Repository Project at NIST]
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−  * [http://enpub.fulton.asu.edu/cms/potentials/submain/available.htm EAM Potential Database at Computational Materials Science Group in Arizona State University]
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−  * [http://www.princeton.edu/mae/people/faculty/carter/homepage/research/potentials/ EAM potentials for hydrogen in BCC iron]
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−  * [http://sites.google.com/a/gmu.edu/eampotentialdatabase/ Potentials developed by Howard Sheng of George Mason University]
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−  * [http://cstwww.nrl.navy.mil/ccm6/ap/eam/index.html CCM6 EAM potentials]
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−  * [http://potfit.itap.physik.unistuttgart.de/wiki/Main_Page potfit]  the ITAP forcematching Code
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−  For more information on interatomic potential generation using electronic structure information, use the following links.
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−  * [http://dx.doi.org/10.1016/09202307(93)90001U The embeddedatom method: a review of theory and applications ]
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−  * [http://link.aps.org/doi/10.1103/PhysRevB.46.2727 Modified embeddedatom potentials for cubic materials and impurities]
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−  * [http://link.aps.org/doi/10.1103/PhysRevB.62.8564 Second nearestneighbor modified embeddedatommethod potential]
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−  * [http://dx.doi.org.proxy.library.msstate.edu/10.1016/j.calphad.2010.10.007 The modified embeddedatom method interatomic potentials and recent progress in atomistic simulations]
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−  * [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]
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−  * [http://link.aps.org/doi/10.1103/PhysRevB.63.165106 Parametrization of modified embeddedatommethod potentials for Rh, Pd, Ir, and Pt based on density functional theory calculations, with applications to surface properties]
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−  * [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 ]
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−   +  
−  === Visualization Codes ===
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−   +  
−  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.
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−  * [http://mt.seas.upenn.edu/Archive/Graphics/A/ AtomEye]
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−  * [http://en.wikipedia.org/wiki/Avizo Avizo_(software)]  3d visualization and analysis software.
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−  * [http://avogadro.openmolecules.net/wiki/Main_Page Avogadro] – Advanced molecule editor and visualizer
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−  * [http://en.wikipedia.org/wiki/BOSS BOSS (molecular mechanics)]  MC in [http://en.wikipedia.org/wiki/OPLS OPLS]
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−  * [http://www.ensight.com Ensight]
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−  * [http://esra.sourceforge.net/cgibin/index.cgi esra]  Lightweight molecular modeling and analysis library (Java/Jython/Mathematica).
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−  * [http://www.pirx.com/iMol/ iMol] – Molecular visualizer for Mac OS X
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−  * [http://jmol.sourceforge.net/ JMol] – An opensource Java viewer for chemical structures in 3D
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−  * [http://mw.concord.org/modeler/ Molecular Workbench]  Interactive molecular dynamics simulations on your desktop.
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−  * [http://ovito.org/ OVITO]
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−  * [http://www.ime.unicamp.br/~martinez/packmol Packmol] Package for building starting configurations for MD in an automated fashion.
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−  * [http://sourceforge.net/projects/punto/ Punto] is a freely available visualisation tool for particle simulations.
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−  * [http://en.wikipedia.org/wiki/PyMol PyMol]  Molecular Visualization software written in python.
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−  * [http://www.openrasmol.org/ RasMol]  Molecular Graphics Visualisation Tool
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−  * [http://en.wikipedia.org/wiki/Sirius Sirius visualization software]  Molecular modeling, analysis and visualization of MD trajectories.
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−  * [http://www.ks.uiuc.edu/Research/vmd/ Visual molecular dynamics (VMD)]  MD simulation trajectories can be visualized and analyzed.
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−   +  
−  == Atomistic Research ==
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−  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 embeddedatom method: a review of theory and applications, Materials Science Reports, Volume 9, Issues 78, Pages 251310. (http://dx.doi.org/10.1016/09202307(93)90001U).</ref> potentials can be found at the [http://www.ctcms.nist.gov/potentials/ NIST Interatomic Potential] website. A number of [[Modified Embedded Atom Methodmodified embedded atom method]]<ref name="MEAM">Lee, B.J., Baskes, M.I. (2000). Second nearestneighbor modified embeddedatommethod 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
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−   +  
−  == Metals ==
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−  [[Image:PE_deformation.gifthumb600px[[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.,
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−  "Molecular dynamics simulations of deformation mechanisms of amorphous polyethylene," Polymer, 51 (2010) 60716083.</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>.]]
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−  Aluminum
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−  * [[AlMg  Modified Embedded Atom Method (MEAM) potential for AlMg]]
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−  * [http://arxiv.org/abs/1107.0544 MEAM potential for Al, Si, Mg, Cu, and Fe alloys] (see also: [http://code.google.com/p/aseatomisticpotentialtests/ routines to reproduce the results])
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−  * [[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, 31473173 ([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, 38713892 ([http://dx.doi.org/10.1016/j.commatsci.2010.02.003 http://dx.doi.org/10.1016/j.commatsci.2010.02.003]).</ref>
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−  * [[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. 705714 ([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) 693709 ([http://dx.doi.org/10.1088/09650393/15/7/001 http://dx.doi.org/10.1088/09650393/15/7/001]).</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) 18061830. ([http://dx.doi.org/10.1016/j.jmps.2007.11.012 http://dx.doi.org/10.1016/j.jmps.2007.11.012]).</ref>
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−  * [[Uniaxial_Tension  Uniaxial Tension in Single Crystal Aluminum]]<ref name="Tsc2008a" />
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−  * [[Uniaxial_Compression  Uniaxial Compression in Single Crystal Aluminum]]<ref name="Tsc2008a" />
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−  Copper
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−  * [[GB_Gen  Grain Boundary Generation of Copper]]<ref name="Tsc2007a" /><ref name="Tsc2007b" />
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−  * [[Multiscale Study Dynamic Void Collapse in Single Crystals Multiscale study of dynamic void collapse in single crystals]]<ref name="msdvcsc"/>
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−  Magnesium
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−  * [[AlMg  Modified Embedded Atom Method (MEAM) potential for MgAl]]
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−  * [[Grain boundary generation in Mg  Grain boundary generation in Mg]]<ref name="Tsc2007a" /><ref name="Tsc2007b" />
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−  * [[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, 426439 ([http://dx.doi.org/10.1080/14786430701255895 http://dx.doi.org/10.1080/14786430701255895]).</ref>
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−  * [[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>
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−  Iron
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−  * [[FeV  Modified Embedded Atom Method (MEAM) potential for FeV]]
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−  * [[FeC  Modified Embedded Atom Method (MEAM) potential for FeC]]
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−  * [[FeHe  Modified Embedded Atom Method (MEAM) potential for FeHe]]
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−  Tungsten
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−  * [[W  Modified Embedded Atom Method (MEAM) potential for W]]
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−  Calcium
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−  * [[Ca  Modified Embedded Atom Method (MEAM) potential for Ca]]
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−  == Ceramics ==
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−  == Polymers ==
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−  An example of tensile deformation in amorphous polyethylene using a united atom method potential.
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−  * [[MD_PE_deformation  Atomistic Deformation of Amorphous Polyethylene]]<ref name="Hos2010" /><ref name="Tsc_2010TMS" />
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−  ** [[Amorphous_Polymer_Generator  Initial amorphous polymer generator used for polyethylene]]
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−  == Biomaterials ==
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−   +  
−  == Geomaterials ==
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−  == ==
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−  [[Media:Bohumir_NIST2011_ASE.pdfThe universal interface for testing atomistic potentials]]
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−  == References ==
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−  <references>
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−  <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
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−  Volume 37, Issues 23, FebruaryMarch 2005, Pages 317330 [http://dx.doi.org/10.1016/j.mechmat.2003.08.014 dx.doi.org/10.1016/j.mechmat.2003.08.014]</ref>
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−  [[Material_Models  Back to Materials Models Home]]
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−   +  
−   +  
−  [[Category: Overview]]
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−  [[Category: Nanoscale]]
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