Resources for Materials Science and Engineering

by Gerhard Klimeck, Alejandro Strachan, Benjamin P Haley

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Version 36
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''This is a draft accumulation of the electronic structure and molecular dynamics codes hosted on nanoHUB. When complete, this page will link to both the tools and the supplemental material.''
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[[Image(MaterialsModels.jpg, 800, class=align-center)]]
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==Tools==
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[[Resource(strainbands)]]
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powered by:
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Electronic structure calculations performed by PWscf and Quantum-Espresso v3.2.2. Maximally-localised Wannier functions calculated by Wannier90 v1.0.2
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[[Resource(dftqe)]]
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[[Resource(abinit)]]
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[[Resource(qclab)]] powered by GAMESS
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== Ab initio electronic structure simulation tools ==
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[[Resource(nmst_dft)]] powered by Seaquest
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=== [[Resource(abinit)]] ===
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[[Image(benzene_wavefunction.png, 120, class=align-right)]]
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[[Image(benzene_edensity.png, 120, class=align-right)]]
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[[Image(benzene_structure.png, 120, class=align-right)]]
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[[Image(abinit_si_BandStructure.jpg, 120, class=align-right)]]
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[[Image(abinit_si_ElectronDensityfordataset1.jpg, 120, class=align-right)]]
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:ABINIT is a package whose main program allows to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory, using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulation using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. In addition to the main ABINIT code, different utility programs are provided.
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:[/resources/6874 First Time User Guide for ABINIT on nanoHUB.org]
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:[http:///www.abinit.org/ Official ABINIT site]
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:[http:///www.abinit.org/documentation/helpfiles/for-v5.7/users/new_user_guide.html ABINIT New User Guide]
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[[Resource(matsimtk)]] powered by Strachan Group MD
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[[Div(start, class=clear)]][[Div(end)]]
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==Supplemental Material==
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[/topics/MD Molecular dynamics simulations of materials] is a topics page on MD which summarizes some of the MD tools.
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=== [[Resource(siesta)]] ===
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[[Image(Siesta_DensityofStatesPDOSsi.png, 90, class=align-right)]]
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[[Image(siesta_Bandstructure.jpg, 120, class=align-right)]]
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: Siesta is a fast electronic structure program that uses a local basis. It can produce band structures and minimum energy geometries, and can perform first principles molecular dynamics calculations.
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:[http:///www.icmab.es/siesta/ siesta Website]
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[[Div(start, class=clear)]][[Div(end)]]
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=== [[Resource(nmst_dft)]] ===
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[[Image(SeqQuest1.png, 150, class=align-right)]]
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:powered by {{{SeqQuest}}}
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:This tool provides access to the density functional theory code {{{SeqQuest}}} via nanoHUB.org. {{{SeqQuest}}} is being developed at Sandia National Laboratories by Dr. Peter A. Schultz of the Multiscale Dynamic Materials Modeling Department and collaborators. Using {{{SeqQuest}}} the tool enables users to calculate the total energy, atomic forces and stress for molecules, wires, slabs and bulk systems.
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:[http://dft.sandia.gov/Quest/ seqQuest webpage]
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[[Div(start, class=clear)]][[Div(end)]]
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=== [[Resource(qclab)]] ===
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[[Image(QClab_fructose_ishot-70.jpg, 100, class=align-right)]]
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[[Image(QClab_CNT_70_ishot-70.jpg, 100, class=align-right)]]
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[[Image(CQlab_CNT_55_ishot-70.jpg, 100, class=align-right)]]
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:powered by GAMESS
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:QC-Lab - Quantum Chemistry Lab. It provides Ab Initio and DFT molecular and electronic structure calculations of small molecules.
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:[http:///www.msg.ameslab.gov/GAMESS/GAMESS.html GAMESS Website]
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[[Div(start, class=clear)]][[Div(end)]]
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=== [[Resource(strainbands)]] ===
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[[Image(strainbands3.png, 100, class=align-right)]]
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[[Image(strainbands_si_BandstructurePlot.jpg, 100, class=align-right)]]
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[[Image(strainbands_si_DOS.jpg, 100, class=align-right)]]
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:powered by: Electronic structure calculations performed by [[http://www.pwscf.org/ PWscf and Quantum-Espresso v3.2.2]]. Maximally-localized Wannier functions calculated by [[http://www.wannier.org/ Wannier90 v1.0.2]].
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:This tool can be used to explore the influence of strain on first-principles bandstructures of semiconductors.
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[[Div(start, class=clear)]][[Div(end)]]
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=== [[Resource(dftqe)]] ===
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[[Image(quantum_espresso_Si_BandStructure.jpg, 120, class=align-right)]]
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[[Image(quantum_espresso_Si_PhononDispersionCurve.jpg, 120, class=align-right)]]
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:This tool enables nanoHUB users to run quantum ESPRESSO, a powerful electronic structure code. Users can perform total energy calculations, energy minimization to predict structures, obtain the Kohn-Sham band structure of periodic systems as well as phonons.
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[[Div(start, class=clear)]][[Div(end)]]
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=== [[Resource(qwalk)]] ===
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[[Image(qwalk_ishot-70.jpg, 120, class=align-right)]]
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[[Image(qwalk_ishot-71.jpg, 120, class=align-right)]]
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: Quantum Monte Carlo methods solve the Schrodinger equation for many electrons to high accuracy--exactly in some cases. In most implementations, it also has favorable scaling with system size, approximately the same as mean-field theories like density functional theory, although with a larger prefactor. This allows us to obtain accurate ground and excited state energies for realistic chemical systems. Quantities such as binding energies, reaction barriers, and band gaps are accurately simulated using QMC methods.
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:[http://www.qwalk.org/ qwalk Website]
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[[Div(start, class=clear)]][[Div(end)]]
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== Molecular dynamics simulations Tools==
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=== [[Resource(matsimtk)]] ===
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[[Image(MD_Slide5.jpg, 120, class=align-right)]]
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[[Image(MD_Slide4.jpg, 120, class=align-right)]]
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[[Image(MD_Slide3.jpg, 120, class=align-right)]]
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: powered by Strachan Group MD
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:The nanoMATERIALS simulation toolkit enables users to perform molecular dynamics simulations of materials using a variety of force fields as well as electronic structure calculations.
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:[/topics/LearningModulePlasticityMD Learning Module: Atomic Picture of Plastic Deformation in Metals]
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[[Div(start, class=clear)]][[Div(end)]]
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=== LAMMPS for Carbon Nanostructures in [[Resource(ucb_compnano)]] ===
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[[Image(MD_LAMMPS_C_ishot-70.jpg, 90, class=align-right)]]
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[[Image(MD_LAMMPS_in_ishot-71.jpg, 122, class=align-right)]]
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: powered by LAMMPS
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:This tool is part of [[Resource(ucb_compnano)]] which serves [[Resource(3944)]]
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:[http://lammps.sandia.gov/ LAMMPS Website]
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[[Div(start, class=clear)]][[Div(end)]]
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=== Lennard-Jones Potential with LAMMPS in [[Resource(ucb_compnano)]] ===
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[[Image(MD_LAMMPS_LJ_struc_ishot-71.jpg, 90, class=align-right)]]
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[[Image(MD_LAMMS_LJ_in_ishot-70.jpg, 122, class=align-right)]]
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: powered by LAMMPS
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:This tool is part of [[Resource(ucb_compnano)]] which serves [[Resource(3944)]]
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:[http://lammps.sandia.gov/ LAMMPS Website]
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[[Div(start, class=clear)]][[Div(end)]]
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== Educational Material ==
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[/topics/LearningModulePlasticityMD Atomic Picture of Plastic Deformation in Metals] is a Learning Module with Introductory Lectures, Tutorials and a Online-simulation Lab Assignment to the atomic-level processes responsible for plastic deformation in metals. Students will perform and analyze online molecular dynamics simulations and study.'''Audience''': undegraduate and graduate students as well as instructors interested in mechanical response of materials.
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[/topics/LearningModuleSiliconBandstructureDFT Bonding and Bandstructure in Silicon] is a Learning Module with Introductory Lectures, Tutorials and a Online-simulation Lab Assignment to explore how electronic bands form in Silicon and other materials. Students will perform online density functional theory calculations and explore the band structure and bonding of various materials. '''Audience''': undegraduate and graduate students as well as instructors interested in electronic properties of materials.
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[/topics/MD Molecular dynamics simulations of materials] is a topics page that summarizes educational resources and tools for molecular dynamics simulations.'''Audience''': researchers interested in atomistic materials modeling and simulation.