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Molecular Dynamics and Atomic Scale Simulation Tools
This page contains the following MD simulation tools
This tool allows users who are experienced with LAMMPS to upload a command script and data file for any system and run LAMMPS either as a serial calculation or a parallel run on a HPC system. Users can upload command scripts with pair_style kim, and the tool will automatically download and load Models from the OpenKIM repository.
This tool models supersonic crack propagation in a 2D triangular lattice with pair interaction potentials between atoms.
This tool is for those who would like to explore fundamental properties of materials such as dislocations, crack propagation, nanowire tensile testing, melting and the martensite transformation through atomistic Molecular Dynamics simulations. All simulations in this explorer are powered by the LAMMPS simulation code. The tool is set up for default operation with sets of preselected inputs for those who are new to MD simulation. Enabling the advanced functions allows users to define simulation parameters for their specific needs.
This set of tools will allow you to:
- visualize how dislocations either glide or nucleate in a crystal based on the applied stress direction relative to the Burgers vector, slip plane, and dislocation line.
- visualize how a nanowire deforms under uni-axial tensile loading, observe the process of yielding and necking, and simulate values of key engineering parameters such as the Young's modulus and yield stress. Visualize a defect in a Nickel(FCC) or Tantalum(BCC) that under uniaxial tension grows into a crack that will cause brittle fracture. Stress-strain curve, yield stress and yield strain are generated, and advanced options allow study of the brittle to ductile transition in BCC metals.
- visualize melting at the atomic level, and generate a radial distribution function. The effect of pressure on melting temperature can be studied.
- visualize a fast quench of two Ni-Al alloys, and identify the martensite transformation.
How to download simulation files for local use
Powered by Strachan Group MD
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.
Hands-on tutorial that will get you started with the nanomaterials simulation toolkit.
This learning module describes how this simulation tool can be used to teach concepts about plastic deformation to sophomore-level MSE students.
This tool allows the user to simulate the effects of applying tensile stress at each end of a Copper nanowire.
This tool will enable the users to calculate two heat transport properties: thermal conductivity and phonon relaxation time. The first one is to run thermal conductivity simulations on various Si/Ge structures by non-equilibrium MD with LAMMPS package. Pure Si/Ge bulks, pure Si/Ge square nanowires, or supperlattice Si/Ge nanolaminates and nanowires with different periodicity can be selected from the prebuilt structures. Also, users can create Si/Ge supperlattice structures with different sizes and the number of priods by their own. In addition to thermal conductivity, energies, temperature profiles, and atomic trajectories during the simulation will also be output. The second one is to run phonon relaxation time simulations on different bulk materials (e.g. Si and Ar) by spectral energy density analysis. Users can choose different temperature for their own needs. The phonon dispersion relation, relaxation time and mean free path with wave vector in 100 direction will be outputted.
The Nano Heatflow tool allows users to explore the time evolution of kinetic and potential energy among the vibrational modes of a carbon nanotube over the course of a molecular dynamics (MD) simulation. It is possible to observe the cascade of vibrational energy through the modes of the system as a non-equilibrium population of phonons is dissipated towards thermal equilibrium, and thus gives insight into the intrinsic sources of damping and dissipation within nanoscale objects.
MiniMol is a minimal molecular dynamics and statics program provided with the book “Modeling Materials: Continuum, Atomistic and Multiscale Techniques” by Ellad B. Tadmor and Ronald E. Miller, Cambridge University Press, 2011.
LAMMPS for Carbon Nanostructures in MIT Atomic-Scale Modeling Toolkit
This tool is part of MIT Atomic-Scale Modeling Toolkit which serves Overview of Computational Nanoscience: a UC Berkeley Course. Powered by LAMMPS.
Powered by LAMMPS.
This tool is part of MIT Atomic-Scale Modeling Toolkit which serves Overview of Computational Nanoscience: a UC Berkeley Course
These tools allow students to focus on the atomic-scale physics and chemistry underlying four separate energy conversion and storage materials: thermoelectrics, solar fuels, solar photovoltaics, and hydrogen storage. Within each of these four different tools, the user can compute properties that are directly relevant to the key fundamental conversion and storage mechanisms.
This talk describes an atomistic molecular dynamics laboratory on 'soft materials' that was used in a junior-level course in materials science and engineering that had over 70 participants. In this course, both molecular and continuum methods were studied and applied to relevant materials problems. The objective of the laboratory was to perform state-of-the-art molecular dynamics in series and parallel, using the Polymatic and nuSIMM computational simulation tools on nanoHUB to study polymeric materials, which are amorphous and lack long-range order or periodicity in their structure. Using these tools, students were able to set up simulations to build and visualize these materials structures and analyze the results. They developed an understanding of which method(s) can be used to solve for some important materials problems.
The assignment was designed for undergraduate students who had little or no experience with running molecular dynamics simulations. It assumed no prior knowledge of either polymatic or nuSIMM. The use of online resources (tutorials) and in person training (hands-on sessions) were demonstrated to be effective tools of engagement.
This tool provides a chain builder, with options to specify monomers, monomer arrangements (tacticity), torsion angles between monomers, system parameters such as density and temperature, as well as some prebuilt epoxy structures from current research interests. The resulting structure (constructed or prebuilt) can be used as input to LAMMPS to run molecular dynamics (MD) simulations. Many MD options are available.
Crystal Viewer 2.3.4 Classic Version
Crystal Viewer is a great introductory simulation tool that allows users to create unit cells of common materials as well as carbon nanostructures that include graphene, carbon nanotubes with varying chirality, and bucky balls.
Crystal Viewer 3.0.2 All-New Version!
Crystal Viewer 3.0 is a new tool starting from scratch that is based on the old version 2.3.4 but aims to include better visualization and new features. It visualizes 14 Bravais lattices, Miller planes, and crystal structures of specific materials needed for many courses in materials science, electronics and solid state chemistry. Users can also create and view materials not included in the database. The main purpose of this educational tool is to provide insight about the crystalline structure of various materials.
This tool generates realistic random-network models of a-Si with periodic boundary conditions.