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nano-Materials Simulation Toolkit

Molecular Dynamics simulations of nano-materials

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Version 2.0.2 - published on 19 Sep 2014

doi:10.4231/D3416T079 cite this

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Abstract

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.


In order to run a simulation users need need to specify i) the initial atomistic model, ii) an energy expression, and iii) driver options. The graphical user interface of the nanoMATERIALS toolkit assigns a panel to each category of input data as described below.


Input model. Here the user specifies the atomistic model which contains a list of atoms (elements and positions) and the simulation cell geometry. Elements of this panel are:

Initial model: choose from a list of files to specify the initial model. These files determine atomic information (position of atoms, elements, etc.) and the simulation cell geometry. Create supercell enables to use to create a large simulation by replicating the current, periodic cell along its cell vectors. Simulation cell parameters enable the user to modifify the cell parameters. In this process there are two possibilities regarding atomic positions: i) leaving their Cartesian positions fixed, or ii) leaving their fractional (with respect to the cell) coordinates fixed. Translate atoms allows the user to rigidly tranlate all atoms in the model. The last three actions are applied in the order they appear in the GUI.


Energy expression Currently the tool uses defaults potentials based on the material chosen. Embedded atom model potentials for metals and Stillinger-Weber for Si.

Driver specification determines what the program will do with the energy and forces. Three main possibilities are: i) single point calculation (calculate the energy of the current model), ii) energy minimization (relax the model to minimize its energy), and iii) molecular dynamics (where the time evolution of the positions and velocities of all atoms in the model are determined using Newton’s equations of motion.


Options for molecular dynamics simulations are:


Ensemble. The user can choose the thermodynamic state of the system. Possibilities are i) microcanonical ensemble (NVE): constant number of atoms, volume and total energy; ii) canonical ensemble (NVT): constant number of atoms, volume and temperature; and iso-thermal iso-baric (NPT): constant number of atoms, pressure and temperature. Time step determines the step used to numerically integrate the equations of motion. Number of steps determines how many interations will be performed during the MD run Temperature specifies the target temperature for NVT, and NPT runs and the initial “instantaneous temperature” for NVE simulations. Temperature increment. This option allows the continuous heating or cooling of the system. Strain per MD step enables the deformation of the simulation cell. The user specifies the strain (DL/L) that will be applied to the system every time step. Periodic tasks enables to use to determine how often the program will: i) output energys, ii) add a frame to the trajectory file for visualization, and iii) update the neighbors list.

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Molecular dynamics simulations are powered by the Strachan group research code

Credits

This work was partially funded by NSF's Network for Computational Nanotechnology.

Cite this work

Researchers should cite this work as follows:

  • "A general purpose code for molecular dynamics and coarse grain simulations," Alejandro Strachan, unpublished.
  • Alejandro Strachan; Amritanshu Palaria; Ya Zhou; Janam Jhaveri (2014), "nano-Materials Simulation Toolkit," http://nanohub.org/resources/matsimtk. (DOI: 10.4231/D3416T079).

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